diff --git a/.github/tools/verify_config_has_been_expanded.sh b/.github/tools/verify_config_has_been_expanded.sh deleted file mode 100755 index e43c6964b..000000000 --- a/.github/tools/verify_config_has_been_expanded.sh +++ /dev/null @@ -1,36 +0,0 @@ -#!/usr/bin/env bash - -# This script will fail if original and expanded config are not in sync in a PR. - -# For each underlay, this script expands config. Afterwards, if git reports any -# modified files, this script will fail. - -# Expand configs for all Broad, VUMC underlays. (This repo's SA doesn't have -# permission to read Verily source datasets.) -underlay_root_dirs=$(find service/src/main/resources/config -mindepth 2 -maxdepth 2 -type d | grep -v verily) -for underlay_root_dir in ${underlay_root_dirs} -do - echo "Expanding config for ${underlay_root_dir}" - underlay_absolute_root_dir=$(realpath ${underlay_root_dir}) - underlay_name=$(basename ${underlay_root_dir}) - original_json_file_path=$(echo "${underlay_absolute_root_dir}/original/${underlay_name}.json") - expanded_dir=$(echo "${underlay_absolute_root_dir}/expanded") - ./gradlew indexer:index -Dexec.args="EXPAND_CONFIG ${original_json_file_path} ${expanded_dir}" -done - -# Check for modified files -# https://stackoverflow.com/a/61748401/6447189 -modified_files=$(git status -s -uno service/src/main/resources/config) - -if [[ $(echo ${modified_files} | wc -c) -eq 1 ]] -then - echo "No modified files found" - exit -fi - -git diff --cached . - -echo "Modified files found:" -echo "${modified_files}" -echo "Please expand and add those files to your PR." -exit 1 diff --git a/.github/tools/verify_config_in_sync.sh b/.github/tools/verify_config_in_sync.sh index a0e583dd7..b1951388d 100755 --- a/.github/tools/verify_config_in_sync.sh +++ b/.github/tools/verify_config_in_sync.sh @@ -7,8 +7,8 @@ configs_to_compare_list=" cms_synpuf broad/cms_synpuf verily/cms_synpuf\n -aou_synthetic broad/aou_synthetic verily/aou_synthetic\n -sdd vumc/sdd verily/sdd +sdd vumc/sdd verily/sdd\n +sdd_refresh0323 vumc/sdd_refresh0323 verily/sdd_refresh0323 " # Needed for for loop to split only on newline, not on space @@ -23,8 +23,8 @@ do underlay_2=$(echo ${configs_to_compare} | awk '{print $3}') printf "\nComparing ${underlay_1} to ${underlay_2}\n" - underlay_dir_1=$(echo service/src/main/resources/config/${underlay_1}/original) - underlay_dir_2=$(echo service/src/main/resources/config/${underlay_2}/original) + underlay_dir_1=$(echo service/src/main/resources/config/${underlay_1}) + underlay_dir_2=$(echo service/src/main/resources/config/${underlay_2}) # --ignore-all-space because files sometimes have newline and at of file, and sometimes don't diff_output=$(diff -rq --ignore-all-space --exclude ${underlay_name}.json --exclude sql ${underlay_dir_1} ${underlay_dir_2}) diff --git a/.github/workflows/validate-config.yaml b/.github/workflows/validate-config.yaml index 96af45714..bf5e0d096 100644 --- a/.github/workflows/validate-config.yaml +++ b/.github/workflows/validate-config.yaml @@ -44,8 +44,3 @@ jobs: TEST_PROJECT_SA_KEY: ${{ secrets.TEST_PROJECT_SA_KEY }} - name: Verify configs are in sync, for example vumc/sdd and verily/sdd run: .github/tools/verify_config_in_sync.sh - - name: Verify underlay configs have been expanded - if: always() - run: .github/tools/verify_config_has_been_expanded.sh - env: - GOOGLE_APPLICATION_CREDENTIALS: ../rendered/broad/tanagra_sa.json diff --git a/docs/INDEXING.md b/docs/INDEXING.md index 09d7c528f..e1ccde45c 100644 --- a/docs/INDEXING.md +++ b/docs/INDEXING.md @@ -6,7 +6,7 @@ + [Setup Credentials](#setup-credentials) + [Default Application Credentials](#default-application-credentials) + [gcloud Credentials](#gcloud-credentials) - + [Expand Underlay Config](#expand-underlay-config) + + [Validate Underlay Config](#validate-underlay-config) + [Create Index Dataset](#create-index-dataset) + [Kickoff Jobs](#kickoff-jobs) + [All Jobs](#all-jobs) @@ -63,8 +63,7 @@ Before running the indexing jobs, you need to specify the underlay config files. There are 3 steps to generating the index tables: 1. [Setup](#setup-credentials) credentials with read permissions on the source data, and read-write permissions on the index data. -2. [Expand](#expand-underlay-config) the user-specified underlay config to include information from scanning the -source data. For example, data types and UI hints. +2. [Validate](#validate-underlay-config) the user-specified underlay config. 3. [Create](#create-index-dataset) the index dataset, if it doesn't already exist. 4. [Kickoff](#kickoff-jobs) the jobs. @@ -103,13 +102,14 @@ To use end-user credentials: gcloud auth login ``` -### Expand Underlay Config -Expand the defaults, scan the source data, and generate an expanded underlay config file that includes all this -information. The first argument is a pointer to the user-specified underlay file. -The second argument is a pointer to the directory where Tanagra can write the expanded config files. -Both arguments must be absolute paths. Example: +### Validate Underlay Config +Validate the config files by scanning the source dataset. This not strictly required, but is highly recommended. +In particular, this will check to see if the attribute data types you specified match the underlying source data. +If they don't, or you did not specify a data type, then this command will print out what you should set it to. + +The argument is a pointer to the top-level config file. It must be an absolute path. Example: ``` -./gradlew indexer:index -Dexec.args="EXPAND_CONFIG $HOME/tanagra/service/src/main/resources/config/broad/cms_synpuf/original/cms_synpuf.json $HOME/tanagra/service/src/main/resources/config/broad/cms_synpuf/expanded" +./gradlew indexer:index -Dexec.args="VALIDATE_CONFIG $HOME/tanagra/service/src/main/resources/config/broad/cms_synpuf/cms_synpuf.json" ``` ### Create Index Dataset @@ -128,11 +128,11 @@ Do a dry run of all the indexing jobs. This provides a sanity check that the ind query inputs, are valid. This step is not required, but highly recommended to help catch errors/bugs sooner and without running a bunch of computation first. ``` -./gradlew indexer:index -Dexec.args="INDEX_ALL $HOME/tanagra/service/src/main/resources/config/output/omop.json DRY_RUN" +./gradlew indexer:index -Dexec.args="INDEX_ALL $HOME/tanagra/service/src/main/resources/config/omop/omop.json DRY_RUN" ``` Now actually kick off all the indexing jobs. ``` -./gradlew indexer:index -Dexec.args="INDEX_ALL $HOME/tanagra/service/src/main/resources/config/output/omop.json" +./gradlew indexer:index -Dexec.args="INDEX_ALL $HOME/tanagra/service/src/main/resources/config/omop/omop.json" ``` This can take a long time to complete. If e.g. your computer falls asleep or you need to kill the process on your computer, you can re-run the same command again. You need to check that there are no in-progress Dataflow jobs in the @@ -146,13 +146,13 @@ kicking them off again. You can also kickoff the indexing jobs for a single entity or entity group. This is helpful for testing and debugging. To kick off all the indexing jobs for a particular entity: ``` -./gradlew indexer:index -Dexec.args="INDEX_ENTITY $HOME/tanagra/service/src/main/resources/config/output/omop.json person DRY_RUN" -./gradlew indexer:index -Dexec.args="INDEX_ENTITY $HOME/tanagra/service/src/main/resources/config/output/omop.json person" +./gradlew indexer:index -Dexec.args="INDEX_ENTITY $HOME/tanagra/service/src/main/resources/config/omop/omop.json person DRY_RUN" +./gradlew indexer:index -Dexec.args="INDEX_ENTITY $HOME/tanagra/service/src/main/resources/config/omop/omop.json person" ``` or entity group: ``` -./gradlew indexer:index -Dexec.args="INDEX_ENTITY_GROUP $HOME/tanagra/service/src/main/resources/config/output/omop.json condition_occurrence_person DRY_RUN" -./gradlew indexer:index -Dexec.args="INDEX_ENTITY_GROUP $HOME/tanagra/service/src/main/resources/config/output/omop.json condition_occurrence_person" +./gradlew indexer:index -Dexec.args="INDEX_ENTITY_GROUP $HOME/tanagra/service/src/main/resources/config/omop/omop.json condition_occurrence_person DRY_RUN" +./gradlew indexer:index -Dexec.args="INDEX_ENTITY_GROUP $HOME/tanagra/service/src/main/resources/config/omop/omop.json condition_occurrence_person" ``` All the entities in a group should be indexed before the group. The `INDEX_ALL` command ensures this ordering, but keep this in mind if you're running the jobs for each entity or entity group separately. @@ -163,8 +163,8 @@ this in mind if you're running the jobs for each entity or entity group separat By default, the indexing jobs are run concurrently as much as possible. You can force it to run jobs serially by appending `SERIAL` to the command: ``` -./gradlew indexer:index -Dexec.args="INDEX_ALL $HOME/tanagra/service/src/main/resources/config/output/omop.json DRY_RUN SERIAL" -./gradlew indexer:index -Dexec.args="INDEX_ALL $HOME/tanagra/service/src/main/resources/config/output/omop.json NOT_DRY_RUN SERIAL" +./gradlew indexer:index -Dexec.args="INDEX_ALL $HOME/tanagra/service/src/main/resources/config/omop/omop.json DRY_RUN SERIAL" +./gradlew indexer:index -Dexec.args="INDEX_ALL $HOME/tanagra/service/src/main/resources/config/omop/omop.json NOT_DRY_RUN SERIAL" ``` ### Re-Run Jobs @@ -174,18 +174,18 @@ commands below. Similar to the indexing commands, the clean commands also respec To clean the generated index tables for everything: ``` -./gradlew indexer:index -Dexec.args="CLEAN_ALL $HOME/tanagra/service/src/main/resources/config/output/omop.json DRY_RUN" -./gradlew indexer:index -Dexec.args="CLEAN_ALL $HOME/tanagra/service/src/main/resources/config/output/omop.json" +./gradlew indexer:index -Dexec.args="CLEAN_ALL $HOME/tanagra/service/src/main/resources/config/omop/omop.json DRY_RUN" +./gradlew indexer:index -Dexec.args="CLEAN_ALL $HOME/tanagra/service/src/main/resources/config/omop/omop.json" ``` or a particular entity: ``` -./gradlew indexer:index -Dexec.args="CLEAN_ENTITY $HOME/tanagra/service/src/main/resources/config/output/omop.json person DRY_RUN" -./gradlew indexer:index -Dexec.args="CLEAN_ENTITY $HOME/tanagra/service/src/main/resources/config/output/omop.json person" +./gradlew indexer:index -Dexec.args="CLEAN_ENTITY $HOME/tanagra/service/src/main/resources/config/omop/omop.json person DRY_RUN" +./gradlew indexer:index -Dexec.args="CLEAN_ENTITY $HOME/tanagra/service/src/main/resources/config/omop/omop.json person" ``` or a particular entity group: ``` -./gradlew indexer:index -Dexec.args="CLEAN_ENTITY_GROUP $HOME/tanagra/service/src/main/resources/config/output/omop.json person DRY_RUN" -./gradlew indexer:index -Dexec.args="CLEAN_ENTITY_GROUP $HOME/tanagra/service/src/main/resources/config/output/omop.json person" +./gradlew indexer:index -Dexec.args="CLEAN_ENTITY_GROUP $HOME/tanagra/service/src/main/resources/config/omop/omop.json person DRY_RUN" +./gradlew indexer:index -Dexec.args="CLEAN_ENTITY_GROUP $HOME/tanagra/service/src/main/resources/config/omop/omop.json person" ``` ### Run dataflow locally @@ -216,13 +216,12 @@ You can see the underlay config files defined for this dataset in Note that while the source dataset is public, the index dataset that Tanagra generates is not. ``` -export INPUT_DIR=$HOME/tanagra/service/src/main/resources/config/broad/cms_synpuf/original -export OUTPUT_DIR=$HOME/tanagra/service/src/main/resources/config/broad/cms_synpuf/expanded +export CONFIG_FILE=$HOME/tanagra/service/src/main/resources/config/broad/cms_synpuf/cms_synpuf.json -./gradlew indexer:index -Dexec.args="EXPAND_CONFIG $INPUT_DIR/cms_synpuf.json $OUTPUT_DIR/" +./gradlew indexer:index -Dexec.args="VALIDATE_CONFIG $CONFIG_FILE" bq mk --location=US broad-tanagra-dev:cmssynpuf_index -./gradlew indexer:index -Dexec.args="INDEX_ALL $OUTPUT_DIR/cms_synpuf.json DRY_RUN" -./gradlew indexer:index -Dexec.args="INDEX_ALL $OUTPUT_DIR/cms_synpuf.json" +./gradlew indexer:index -Dexec.args="INDEX_ALL $CONFIG_FILE DRY_RUN" +./gradlew indexer:index -Dexec.args="INDEX_ALL $CONFIG_FILE" ``` diff --git a/indexer/build.gradle b/indexer/build.gradle index 732d43702..fdcd1e17b 100644 --- a/indexer/build.gradle +++ b/indexer/build.gradle @@ -73,7 +73,6 @@ tasks.withType(Test) { } } -// e.g. ./gradlew indexer:index -Dexec.args="input_underlay.json output_dir" task index (type:JavaExec) { main = "bio.terra.tanagra.indexing.Main" classpath = sourceSets.main.runtimeClasspath diff --git a/indexer/src/main/java/bio/terra/tanagra/indexing/BigQueryIndexingJob.java b/indexer/src/main/java/bio/terra/tanagra/indexing/BigQueryIndexingJob.java index e3ad25109..e323d1485 100644 --- a/indexer/src/main/java/bio/terra/tanagra/indexing/BigQueryIndexingJob.java +++ b/indexer/src/main/java/bio/terra/tanagra/indexing/BigQueryIndexingJob.java @@ -99,6 +99,19 @@ protected boolean checkTableExists(TablePointer tablePointer) { .isPresent(); } + protected boolean checkOneRowExists(TablePointer tablePointer) { + // Check if the table has at least one row. + BigQueryDataset dataPointer = getBQDataPointer(tablePointer); + int numRows = + dataPointer + .getBigQueryService() + .getNumRows( + dataPointer.getProjectId(), + dataPointer.getDatasetId(), + tablePointer.getTableName()); + return numRows > 0; + } + protected boolean checkOneNotNullIdRowExists(Entity entity) { // Check if the table has at least 1 id row where id IS NOT NULL FieldPointer idField = diff --git a/indexer/src/main/java/bio/terra/tanagra/indexing/Indexer.java b/indexer/src/main/java/bio/terra/tanagra/indexing/Indexer.java index 85d89355d..23f375c6d 100644 --- a/indexer/src/main/java/bio/terra/tanagra/indexing/Indexer.java +++ b/indexer/src/main/java/bio/terra/tanagra/indexing/Indexer.java @@ -1,24 +1,18 @@ package bio.terra.tanagra.indexing; -import bio.terra.tanagra.indexing.job.BuildNumChildrenAndPaths; -import bio.terra.tanagra.indexing.job.BuildTextSearchStrings; -import bio.terra.tanagra.indexing.job.ComputeDisplayHints; -import bio.terra.tanagra.indexing.job.ComputeRollupCounts; -import bio.terra.tanagra.indexing.job.CreateEntityTable; -import bio.terra.tanagra.indexing.job.DenormalizeEntityInstances; -import bio.terra.tanagra.indexing.job.WriteAncestorDescendantIdPairs; -import bio.terra.tanagra.indexing.job.WriteParentChildIdPairs; -import bio.terra.tanagra.indexing.job.WriteRelationshipIdPairs; +import bio.terra.tanagra.exception.InvalidConfigException; +import bio.terra.tanagra.indexing.job.*; import bio.terra.tanagra.indexing.jobexecutor.JobRunner; import bio.terra.tanagra.indexing.jobexecutor.ParallelRunner; import bio.terra.tanagra.indexing.jobexecutor.SequencedJobSet; import bio.terra.tanagra.indexing.jobexecutor.SerialRunner; +import bio.terra.tanagra.query.Literal; import bio.terra.tanagra.underlay.*; import bio.terra.tanagra.underlay.entitygroup.CriteriaOccurrence; import bio.terra.tanagra.underlay.entitygroup.GroupItems; import com.google.common.annotations.VisibleForTesting; import java.io.IOException; -import java.util.List; +import java.util.*; import java.util.stream.Collectors; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -54,19 +48,55 @@ public static Indexer deserializeUnderlay(String underlayFileName) throws IOExce return new Indexer(Underlay.fromJSON(underlayFileName)); } - /** Scan the source data to validate data pointers, lookup data types, generate UI hints, etc. */ - public void scanSourceData() { - // TODO: Validate existence and access for data/table/field pointers. - underlay - .getEntities() - .values() + public void validateConfig() { + // Check that the attribute data types are all defined and match the expected. + Map> errorsForEntity = new HashMap<>(); + underlay.getEntities().values().stream() + .sorted(Comparator.comparing(Entity::getName)) .forEach( - e -> { - LOGGER.info( - "Looking up attribute data types and generating UI hints for entity: " - + e.getName()); - e.scanSourceData(); + entity -> { + List errors = new ArrayList<>(); + entity.getAttributes().stream() + .sorted(Comparator.comparing(Attribute::getName)) + .forEach( + attribute -> { + LOGGER.info( + "Validating data type for entity {}, attribute {}", + entity.getName(), + attribute.getName()); + Literal.DataType computedDataType = + attribute.getMapping(Underlay.MappingType.SOURCE).computeDataType(); + if (attribute.getDataType() == null + || !attribute.getDataType().equals(computedDataType)) { + String msg = + "attribute: " + + attribute.getName() + + ", expected data type: " + + computedDataType + + ", actual data type: " + + attribute.getDataType(); + errors.add(msg); + LOGGER.info("entity: {}, {}", entity.getName(), msg); + } + }); + if (!errors.isEmpty()) { + errorsForEntity.put(entity.getName(), errors); + } }); + + // Output any error messages. + if (errorsForEntity.isEmpty()) { + LOGGER.info("Validation of attribute data types succeeded"); + } else { + errorsForEntity.keySet().stream() + .sorted() + .forEach( + entityName -> { + LOGGER.warn("Validation of attribute data types for entity {} failed", entityName); + errorsForEntity.get(entityName).stream().forEach(msg -> LOGGER.warn(msg)); + }); + throw new InvalidConfigException("Validation attribute data types had errors"); + } } public JobRunner runJobsForAllEntities( @@ -121,6 +151,7 @@ public SequencedJobSet getJobSetForEntity(Entity entity) { jobSet.startNewStage(); jobSet.addJob(new DenormalizeEntityInstances(entity)); + jobSet.addJob(new ComputeEntityLevelDisplayHints(entity)); if (entity.getTextSearch().isEnabled() || entity.hasHierarchies()) { jobSet.startNewStage(); diff --git a/indexer/src/main/java/bio/terra/tanagra/indexing/Main.java b/indexer/src/main/java/bio/terra/tanagra/indexing/Main.java index 3a324349a..a39312430 100644 --- a/indexer/src/main/java/bio/terra/tanagra/indexing/Main.java +++ b/indexer/src/main/java/bio/terra/tanagra/indexing/Main.java @@ -7,14 +7,13 @@ import bio.terra.tanagra.exception.SystemException; import bio.terra.tanagra.indexing.jobexecutor.JobRunner; import bio.terra.tanagra.utils.FileIO; -import bio.terra.tanagra.utils.FileUtils; import java.nio.file.Path; public final class Main { private Main() {} enum Command { - EXPAND_CONFIG, + VALIDATE_CONFIG, INDEX_ENTITY, INDEX_ENTITY_GROUP, INDEX_ALL, @@ -37,15 +36,8 @@ public static void main(String... args) throws Exception { Indexer.deserializeUnderlay(Path.of(underlayFilePath).getFileName().toString()); switch (cmd) { - case EXPAND_CONFIG: - String outputDirPath = args[2]; - - FileIO.setOutputParentDir(Path.of(outputDirPath)); - FileUtils.createDirectoryIfNonexistent(FileIO.getOutputParentDir()); - - indexer.scanSourceData(); - - indexer.getUnderlay().serializeAndWriteToFile(); + case VALIDATE_CONFIG: + indexer.validateConfig(); break; case INDEX_ENTITY: case CLEAN_ENTITY: diff --git a/indexer/src/main/java/bio/terra/tanagra/indexing/job/ComputeEntityLevelDisplayHints.java b/indexer/src/main/java/bio/terra/tanagra/indexing/job/ComputeEntityLevelDisplayHints.java new file mode 100644 index 000000000..a0b821475 --- /dev/null +++ b/indexer/src/main/java/bio/terra/tanagra/indexing/job/ComputeEntityLevelDisplayHints.java @@ -0,0 +1,150 @@ +package bio.terra.tanagra.indexing.job; + +import bio.terra.tanagra.exception.SystemException; +import bio.terra.tanagra.indexing.BigQueryIndexingJob; +import bio.terra.tanagra.query.TablePointer; +import bio.terra.tanagra.underlay.*; +import bio.terra.tanagra.underlay.datapointer.BigQueryDataset; +import bio.terra.tanagra.underlay.displayhint.EnumVals; +import bio.terra.tanagra.underlay.displayhint.NumericRange; +import bio.terra.tanagra.utils.GoogleBigQuery; +import com.google.cloud.bigquery.Field; +import com.google.cloud.bigquery.LegacySQLTypeName; +import com.google.cloud.bigquery.Schema; +import com.google.cloud.bigquery.TableId; +import java.util.ArrayList; +import java.util.List; +import java.util.concurrent.TimeUnit; +import java.util.stream.Collectors; +import org.json.JSONObject; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +public class ComputeEntityLevelDisplayHints extends BigQueryIndexingJob { + private static final Logger LOGGER = + LoggerFactory.getLogger(ComputeEntityLevelDisplayHints.class); + + public ComputeEntityLevelDisplayHints(Entity entity) { + super(entity); + } + + @Override + public String getName() { + return "COMPUTE ENTITY-LEVEL DISPLAY HINTS (" + getEntity().getName() + ")"; + } + + @Override + public void run(boolean isDryRun) { + // Create an empty table with this schema. + BigQueryDataset outputBQDataset = getBQDataPointer(getEntityIndexTable()); + TableId destinationTable = + TableId.of( + outputBQDataset.getProjectId(), + outputBQDataset.getDatasetId(), + getAuxiliaryTable().getTableName()); + GoogleBigQuery bigQuery = outputBQDataset.getBigQueryService(); + + // Convert the internal representation of the table schema to the BQ object. + List fieldList = + Entity.DISPLAY_HINTS_TABLE_SCHEMA.entrySet().stream() + .map( + entry -> { + String columnName = entry.getKey(); + LegacySQLTypeName columnDataType = + BigQueryDataset.fromSqlDataType(entry.getValue().getKey()); + boolean isRequired = entry.getValue().getValue(); + return Field.newBuilder(columnName, columnDataType) + .setMode(isRequired ? Field.Mode.REQUIRED : Field.Mode.NULLABLE) + .build(); + }) + .collect(Collectors.toList()); + + bigQuery.createTableFromSchema(destinationTable, Schema.of(fieldList), isDryRun); + + // Sleep to make sure the table is found by the time we do the insert. + // TODO: Change this to poll for existence instead. + try { + TimeUnit.SECONDS.sleep(5); + } catch (InterruptedException intEx) { + throw new SystemException( + "Interrupted during sleep after creating entity-level hints table", intEx); + } + + // TODO: Validate queries for computing display hints when the dry run flag is set. + if (isDryRun) { + return; + } + + // Calculate a display hint for each attribute. Build a list of all the hints as JSON records. + List hintRecords = new ArrayList<>(); + getEntity().getAttributes().stream() + .forEach( + attribute -> { + if (getEntity().isIdAttribute(attribute) || attribute.skipCalculateDisplayHint()) { + return; + } + DisplayHint hint = + attribute.getMapping(Underlay.MappingType.SOURCE).computeDisplayHint(); + if (hint == null) { + return; + } + + if (DisplayHint.Type.RANGE.equals(hint.getType())) { + NumericRange range = (NumericRange) hint; + + JSONObject hintRow = new JSONObject(); + hintRow.put("attribute_name", attribute.getName()); + hintRow.put("min", range.getMinVal()); + hintRow.put("max", range.getMaxVal()); + hintRow.put("enum_value", JSONObject.NULL); + hintRow.put("enum_display", JSONObject.NULL); + hintRow.put("enum_count", JSONObject.NULL); + hintRecords.add(hintRow); + LOGGER.info("hint record (numeric range): {}", hintRow); + } else { + ((EnumVals) hint) + .getEnumValsList().stream() + .forEach( + ev -> { + JSONObject hintRow = new JSONObject(); + hintRow.put("attribute_name", attribute.getName()); + hintRow.put("min", JSONObject.NULL); + hintRow.put("max", JSONObject.NULL); + hintRow.put( + "enum_value", ev.getValueDisplay().getValue().getInt64Val()); + hintRow.put("enum_display", ev.getValueDisplay().getDisplay()); + hintRow.put("enum_count", ev.getCount()); + hintRecords.add(hintRow); + LOGGER.info("hint record (enum val): {}", hintRow); + }); + } + }); + + // Do a single batch insert to BQ for all the hint rows. + outputBQDataset + .getBigQueryService() + .insertWithStorageWriteApi( + destinationTable.getProject(), + destinationTable.getDataset(), + destinationTable.getTable(), + hintRecords); + } + + @Override + public void clean(boolean isDryRun) { + LOGGER.info( + "Nothing to clean. CreateEntityLevelDisplayHintsTable will delete the output table, which includes all the rows inserted by this job."); + } + + @Override + public JobStatus checkStatus() { + // Check if the table already exists. + // We can't include a check for a single row here (e.g. checkOneRowExists(getAuxiliaryTable())), + // because there are some cases where an entity has no display hints. + return checkTableExists(getAuxiliaryTable()) ? JobStatus.COMPLETE : JobStatus.NOT_STARTED; + } + + public TablePointer getAuxiliaryTable() { + return getEntity().getMapping(Underlay.MappingType.INDEX).getDisplayHintTablePointer(); + } +} diff --git a/service/local-dev/run_server.sh b/service/local-dev/run_server.sh index ddf09691c..54ec2a313 100755 --- a/service/local-dev/run_server.sh +++ b/service/local-dev/run_server.sh @@ -44,17 +44,17 @@ fi if [[ ${useVerilyUnderlays} ]]; then echo "Using Verily underlays." - export TANAGRA_UNDERLAY_FILES=verily/aou_synthetic/expanded/aou_synthetic.json,verily/cms_synpuf/expanded/cms_synpuf.json,verily/sdd/expanded/sdd.json,verily/sdd_refresh0323/expanded/sdd_refresh0323.json,verily/pilot_synthea_2022q3/expanded/pilot_synthea_2022q3.json + export TANAGRA_UNDERLAY_FILES=verily/aou_synthetic/aou_synthetic.json,verily/cms_synpuf/cms_synpuf.json,verily/sdd/sdd.json,verily/sdd_refresh0323/sdd_refresh0323.json,verily/pilot_synthea_2022q3/pilot_synthea_2022q3.json export TANAGRA_EXPORT_SHARED_GCS_BUCKET_PROJECT_ID=verily-tanagra-dev export TANAGRA_EXPORT_SHARED_GCS_BUCKET_NAMES=verily-tanagra-dev-export-bucket elif [[ ${useAouUnderlays} ]]; then echo "Using AoU test underlays." - export TANAGRA_UNDERLAY_FILES=aou/test/SC2022Q4R6/expanded/SC2022Q4R6.json,aou/test/SR2022Q4R6/expanded/SR2022Q4R6.json + export TANAGRA_UNDERLAY_FILES=aou/test/SC2022Q4R6/SC2022Q4R6.json,aou/test/SR2022Q4R6/SR2022Q4R6.json export TANAGRA_EXPORT_SHARED_GCS_BUCKET_PROJECT_ID=broad-tanagra-dev export TANAGRA_EXPORT_SHARED_GCS_BUCKET_NAMES=broad-tanagra-dev-bq-export else echo "Using Broad underlays." - export TANAGRA_UNDERLAY_FILES=broad/aou_synthetic/expanded/aou_synthetic.json,broad/cms_synpuf/expanded/cms_synpuf.json + export TANAGRA_UNDERLAY_FILES=broad/aou_synthetic/aou_synthetic.json,broad/cms_synpuf/cms_synpuf.json export TANAGRA_EXPORT_SHARED_GCS_BUCKET_PROJECT_ID=broad-tanagra-dev export TANAGRA_EXPORT_SHARED_GCS_BUCKET_NAMES=broad-tanagra-dev-bq-export fi diff --git a/service/src/main/java/bio/terra/tanagra/app/controller/HintsV2ApiController.java b/service/src/main/java/bio/terra/tanagra/app/controller/HintsV2ApiController.java index 8be12c2e6..01afd3c1c 100644 --- a/service/src/main/java/bio/terra/tanagra/app/controller/HintsV2ApiController.java +++ b/service/src/main/java/bio/terra/tanagra/app/controller/HintsV2ApiController.java @@ -13,24 +13,21 @@ import bio.terra.tanagra.generated.model.ApiDisplayHintV2; import bio.terra.tanagra.generated.model.ApiDisplayHintV2DisplayHint; import bio.terra.tanagra.generated.model.ApiHintQueryV2; -import bio.terra.tanagra.query.Literal; -import bio.terra.tanagra.query.QueryRequest; import bio.terra.tanagra.service.AccessControlService; import bio.terra.tanagra.service.FromApiConversionService; import bio.terra.tanagra.service.QuerysService; import bio.terra.tanagra.service.UnderlaysService; import bio.terra.tanagra.service.accesscontrol.Permissions; import bio.terra.tanagra.service.accesscontrol.ResourceId; +import bio.terra.tanagra.service.instances.EntityHintRequest; +import bio.terra.tanagra.service.instances.EntityHintResult; import bio.terra.tanagra.service.utils.ToApiConversionUtils; import bio.terra.tanagra.underlay.Attribute; import bio.terra.tanagra.underlay.DisplayHint; import bio.terra.tanagra.underlay.Entity; -import bio.terra.tanagra.underlay.Underlay; import bio.terra.tanagra.underlay.displayhint.EnumVals; import bio.terra.tanagra.underlay.displayhint.NumericRange; import bio.terra.tanagra.utils.SqlFormatter; -import java.util.HashMap; -import java.util.Map; import java.util.stream.Collectors; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.http.ResponseEntity; @@ -61,49 +58,29 @@ public ResponseEntity queryHints( ResourceId.forUnderlay(underlayName)); Entity entity = underlaysService.getEntity(underlayName, entityName); - if (body == null || body.getRelatedEntity() == null) { - // Return display hints computed across all entity instances (e.g. enum values for - // person.gender). - Map displayHints = new HashMap<>(); - entity.getAttributes().stream() - .forEach( - attr -> { - if (attr.getDisplayHint() != null) { - displayHints.put(attr.getName(), attr.getDisplayHint()); - } - }); - // Currently, these display hints are stored in the underlay config files, so no SQL query is - // necessary to look them up. - return ResponseEntity.ok(toApiObject(entity, displayHints, "")); - } else { + EntityHintRequest.Builder entityHintRequest = new EntityHintRequest.Builder().entity(entity); + if (body != null && body.getRelatedEntity() != null) { // Return display hints for entity instances that are related to an instance of another entity // (e.g. numeric range for measurement_occurrence.value_numeric, computed across // measurement_occurrence instances that are related to measurement=BodyHeight). - Underlay underlay = underlaysService.getUnderlay(underlayName); - Entity relatedEntity = - underlaysService.getEntity(underlayName, body.getRelatedEntity().getName()); - Literal relatedEntityId = - FromApiConversionService.fromApiObject(body.getRelatedEntity().getId()); - QueryRequest queryRequest = - querysService.buildDisplayHintsQuery( - underlay, entity, Underlay.MappingType.INDEX, relatedEntity, relatedEntityId); - Map displayHints = - querysService.runDisplayHintsQuery( - entity.getMapping(Underlay.MappingType.INDEX).getTablePointer().getDataPointer(), - queryRequest); - return ResponseEntity.ok(toApiObject(entity, displayHints, queryRequest.getSql())); - } + entityHintRequest + .relatedEntity( + underlaysService.getEntity(underlayName, body.getRelatedEntity().getName())) + .relatedEntityId(FromApiConversionService.fromApiObject(body.getRelatedEntity().getId())); + } // else {} Return display hints computed across all entity instances (e.g. enum values for + // person.gender). + EntityHintResult entityHintResult = querysService.listEntityHints(entityHintRequest.build()); + return ResponseEntity.ok(toApiObject(entityHintResult)); } - private ApiDisplayHintListV2 toApiObject( - Entity entity, Map displayHints, String sql) { + private ApiDisplayHintListV2 toApiObject(EntityHintResult entityHintResult) { return new ApiDisplayHintListV2() - .sql(SqlFormatter.format(sql)) + .sql(SqlFormatter.format(entityHintResult.getSql())) .displayHints( - displayHints.entrySet().stream() + entityHintResult.getHintMap().entrySet().stream() .map( attrHint -> { - Attribute attr = entity.getAttribute(attrHint.getKey()); + Attribute attr = attrHint.getKey(); DisplayHint hint = attrHint.getValue(); return new ApiDisplayHintV2() .attribute(ToApiConversionUtils.toApiObject(attr)) diff --git a/service/src/main/java/bio/terra/tanagra/service/QuerysService.java b/service/src/main/java/bio/terra/tanagra/service/QuerysService.java index a2a086a22..683da8f75 100644 --- a/service/src/main/java/bio/terra/tanagra/service/QuerysService.java +++ b/service/src/main/java/bio/terra/tanagra/service/QuerysService.java @@ -4,51 +4,20 @@ import static bio.terra.tanagra.underlay.entitygroup.CriteriaOccurrence.MODIFIER_AUX_DATA_ENUM_COUNT_COL; import static bio.terra.tanagra.underlay.entitygroup.CriteriaOccurrence.MODIFIER_AUX_DATA_ENUM_DISPLAY_COL; import static bio.terra.tanagra.underlay.entitygroup.CriteriaOccurrence.MODIFIER_AUX_DATA_ENUM_VAL_COL; -import static bio.terra.tanagra.underlay.entitygroup.CriteriaOccurrence.MODIFIER_AUX_DATA_ID_COL; import static bio.terra.tanagra.underlay.entitygroup.CriteriaOccurrence.MODIFIER_AUX_DATA_MAX_COL; import static bio.terra.tanagra.underlay.entitygroup.CriteriaOccurrence.MODIFIER_AUX_DATA_MIN_COL; -import bio.terra.tanagra.exception.InvalidQueryException; import bio.terra.tanagra.query.*; -import bio.terra.tanagra.query.filtervariable.BinaryFilterVariable; import bio.terra.tanagra.service.instances.*; -import bio.terra.tanagra.underlay.AuxiliaryDataMapping; -import bio.terra.tanagra.underlay.DataPointer; -import bio.terra.tanagra.underlay.DisplayHint; -import bio.terra.tanagra.underlay.Entity; -import bio.terra.tanagra.underlay.EntityGroup; -import bio.terra.tanagra.underlay.Underlay; -import bio.terra.tanagra.underlay.ValueDisplay; +import bio.terra.tanagra.underlay.*; import bio.terra.tanagra.underlay.displayhint.EnumVal; import bio.terra.tanagra.underlay.displayhint.EnumVals; import bio.terra.tanagra.underlay.displayhint.NumericRange; -import bio.terra.tanagra.underlay.entitygroup.CriteriaOccurrence; -import com.google.common.collect.Lists; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.Iterator; -import java.util.List; -import java.util.Map; -import java.util.Optional; -import java.util.OptionalDouble; -import java.util.OptionalLong; -import java.util.stream.Collectors; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.springframework.beans.factory.annotation.Autowired; +import java.util.*; import org.springframework.stereotype.Component; @Component public class QuerysService { - private static final Logger LOGGER = LoggerFactory.getLogger(QuerysService.class); - - private final UnderlaysService underlaysService; - - @Autowired - public QuerysService(UnderlaysService underlaysService) { - this.underlaysService = underlaysService; - } - public EntityQueryResult listEntityInstances(EntityQueryRequest entityQueryRequest) { QueryRequest queryRequest = entityQueryRequest.buildInstancesQuery(); DataPointer indexDataPointer = @@ -94,96 +63,54 @@ public EntityCountResult countEntityInstances(EntityCountRequest entityCountRequ queryRequest.getSql(), instanceCounts, queryResult.getNextPageMarker()); } - public QueryRequest buildDisplayHintsQuery( - Underlay underlay, - Entity entity, - Underlay.MappingType mappingType, - Entity relatedEntity, - Literal relatedEntityId) { - // TODO: Support display hints for any relationship, not just for the CRITERIA_OCCURRENCE entity - // group. - EntityGroup entityGroup = - underlaysService - .getRelationship(underlay.getEntityGroups().values(), entity, relatedEntity) - .getEntityGroup(); - if (!(entityGroup instanceof CriteriaOccurrence)) { - throw new InvalidQueryException( - "Only CRITERIA_OCCURENCE entity groups support display hints queries"); - } - CriteriaOccurrence criteriaOccurrence = (CriteriaOccurrence) entityGroup; - AuxiliaryDataMapping auxDataMapping = - criteriaOccurrence.getModifierAuxiliaryData().getMapping(mappingType); - - TableVariable primaryTableVar = TableVariable.forPrimary(auxDataMapping.getTablePointer()); - List tableVars = Lists.newArrayList(primaryTableVar); - - List selectFieldVars = - auxDataMapping.getFieldPointers().entrySet().stream() - .map( - entry -> entry.getValue().buildVariable(primaryTableVar, tableVars, entry.getKey())) - .collect(Collectors.toList()); - // TODO: Centralize this schema definition used both here and in the indexing job. Also handle - // other enum_value data types. - List columnSchemas = - List.of( - new ColumnSchema(MODIFIER_AUX_DATA_ID_COL, CellValue.SQLDataType.INT64), - new ColumnSchema(MODIFIER_AUX_DATA_ATTR_COL, CellValue.SQLDataType.STRING), - new ColumnSchema(MODIFIER_AUX_DATA_MIN_COL, CellValue.SQLDataType.FLOAT), - new ColumnSchema(MODIFIER_AUX_DATA_MAX_COL, CellValue.SQLDataType.FLOAT), - new ColumnSchema(MODIFIER_AUX_DATA_ENUM_VAL_COL, CellValue.SQLDataType.INT64), - new ColumnSchema(MODIFIER_AUX_DATA_ENUM_DISPLAY_COL, CellValue.SQLDataType.STRING), - new ColumnSchema(MODIFIER_AUX_DATA_ENUM_COUNT_COL, CellValue.SQLDataType.INT64)); - - // Build the WHERE filter variables from the entity filter. - FieldVariable entityIdFieldVar = - selectFieldVars.stream() - .filter(fv -> fv.getAlias().equals(MODIFIER_AUX_DATA_ID_COL)) - .findFirst() - .get(); - BinaryFilterVariable filterVar = - new BinaryFilterVariable( - entityIdFieldVar, BinaryFilterVariable.BinaryOperator.EQUALS, relatedEntityId); - - Query query = - new Query.Builder().select(selectFieldVars).tables(tableVars).where(filterVar).build(); - LOGGER.info("Generated display hint query: {}", query.renderSQL()); - - return new QueryRequest(query.renderSQL(), new ColumnHeaderSchema(columnSchemas)); - } - - public Map runDisplayHintsQuery( - DataPointer dataPointer, QueryRequest queryRequest) { + public EntityHintResult listEntityHints(EntityHintRequest entityHintRequest) { + QueryRequest queryRequest = entityHintRequest.buildHintsQuery(); + DataPointer dataPointer = + entityHintRequest + .getEntity() + .getMapping(entityHintRequest.getMappingType()) + .getTablePointer() + .getDataPointer(); QueryResult queryResult = dataPointer.getQueryExecutor().execute(queryRequest); - Map displayHints = new HashMap<>(); - Map> runningEnumValsMap = new HashMap<>(); + Map displayHints = new HashMap<>(); + Map> runningEnumValsMap = new HashMap<>(); Iterator rowResultsItr = queryResult.getRowResults().iterator(); while (rowResultsItr.hasNext()) { RowResult rowResult = rowResultsItr.next(); + String attrName = rowResult.get(MODIFIER_AUX_DATA_ATTR_COL).getLiteral().orElseThrow().getStringVal(); + Attribute attr = entityHintRequest.getEntity().getAttribute(attrName); OptionalDouble min = rowResult.get(MODIFIER_AUX_DATA_MIN_COL).getDouble(); if (min.isPresent()) { - // This is a numeric range hint. + // This is a numeric range hint, which is contained in a single row. OptionalDouble max = rowResult.get(MODIFIER_AUX_DATA_MAX_COL).getDouble(); - displayHints.put(attrName, new NumericRange(min.getAsDouble(), max.getAsDouble())); + displayHints.put(attr, new NumericRange(min.getAsDouble(), max.getAsDouble())); } else { - // This is an enum values hint. + // This is part of an enum values hint, which is spread across multiple rows -- one per enum + // value. Literal val = rowResult.get(MODIFIER_AUX_DATA_ENUM_VAL_COL).getLiteral().orElseThrow(); Optional display = rowResult.get(MODIFIER_AUX_DATA_ENUM_DISPLAY_COL).getString(); OptionalLong count = rowResult.get(MODIFIER_AUX_DATA_ENUM_COUNT_COL).getLong(); List runningEnumVals = - runningEnumValsMap.containsKey(attrName) - ? runningEnumValsMap.get(attrName) - : new ArrayList<>(); + runningEnumValsMap.containsKey(attr) ? runningEnumValsMap.get(attr) : new ArrayList<>(); runningEnumVals.add(new EnumVal(new ValueDisplay(val, display.get()), count.getAsLong())); - runningEnumValsMap.put(attrName, runningEnumVals); + runningEnumValsMap.put(attr, runningEnumVals); } } runningEnumValsMap.entrySet().stream() - .forEach(entry -> displayHints.put(entry.getKey(), new EnumVals(entry.getValue()))); + .forEach( + entry -> { + // Sort the enum values, so they have a consistent ordering. + List enumVals = entry.getValue(); + enumVals.sort( + Comparator.comparing(ev -> String.valueOf(ev.getValueDisplay().getDisplay()))); + + displayHints.put(entry.getKey(), new EnumVals(enumVals)); + }); - return displayHints; + return new EntityHintResult(queryRequest.getSql(), displayHints); } } diff --git a/service/src/main/java/bio/terra/tanagra/service/UnderlaysService.java b/service/src/main/java/bio/terra/tanagra/service/UnderlaysService.java index f8eeb6878..61a51cc75 100644 --- a/service/src/main/java/bio/terra/tanagra/service/UnderlaysService.java +++ b/service/src/main/java/bio/terra/tanagra/service/UnderlaysService.java @@ -76,7 +76,7 @@ public Entity getEntity(String underlayName, String entityName) { return underlay.getEntity(entityName); } - public Attribute getAttribute(Entity entity, String attributeName) { + public static Attribute getAttribute(Entity entity, String attributeName) { Attribute attribute = entity.getAttribute(attributeName); if (attribute == null) { throw new NotFoundException( @@ -85,7 +85,7 @@ public Attribute getAttribute(Entity entity, String attributeName) { return attribute; } - public Hierarchy getHierarchy(Entity entity, String hierarchyName) { + public static Hierarchy getHierarchy(Entity entity, String hierarchyName) { Hierarchy hierarchy = entity.getHierarchy(hierarchyName); if (hierarchy == null) { throw new NotFoundException("Hierarchy not found: " + hierarchyName); @@ -93,7 +93,7 @@ public Hierarchy getHierarchy(Entity entity, String hierarchyName) { return hierarchy; } - public Relationship getRelationship( + public static Relationship getRelationship( Collection entityGroups, Entity entity, Entity relatedEntity) { for (EntityGroup entityGroup : entityGroups) { Optional relationship = entityGroup.getRelationship(entity, relatedEntity); diff --git a/service/src/main/java/bio/terra/tanagra/service/instances/EntityHintRequest.java b/service/src/main/java/bio/terra/tanagra/service/instances/EntityHintRequest.java new file mode 100644 index 000000000..f3d749794 --- /dev/null +++ b/service/src/main/java/bio/terra/tanagra/service/instances/EntityHintRequest.java @@ -0,0 +1,160 @@ +package bio.terra.tanagra.service.instances; + +import static bio.terra.tanagra.underlay.entitygroup.CriteriaOccurrence.*; + +import bio.terra.tanagra.exception.InvalidQueryException; +import bio.terra.tanagra.query.*; +import bio.terra.tanagra.query.filtervariable.BinaryFilterVariable; +import bio.terra.tanagra.service.UnderlaysService; +import bio.terra.tanagra.underlay.*; +import bio.terra.tanagra.underlay.entitygroup.CriteriaOccurrence; +import com.google.common.collect.Lists; +import java.util.ArrayList; +import java.util.List; +import java.util.stream.Collectors; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +public class EntityHintRequest { + private static final Logger LOGGER = LoggerFactory.getLogger(EntityHintRequest.class); + private final Entity entity; + private final Entity relatedEntity; + private final Literal relatedEntityId; + + private EntityHintRequest(Builder builder) { + this.entity = builder.entity; + this.relatedEntity = builder.relatedEntity; + this.relatedEntityId = builder.relatedEntityId; + } + + public Entity getEntity() { + return entity; + } + + public Underlay.MappingType getMappingType() { + // Hints always hit the index dataset. + return Underlay.MappingType.INDEX; + } + + public Entity getRelatedEntity() { + return relatedEntity; + } + + public Literal getRelatedEntityId() { + return relatedEntityId; + } + + public boolean isEntityLevelHints() { + return relatedEntity == null; + } + + public QueryRequest buildHintsQuery() { + return isEntityLevelHints() ? buildEntityLevelHintsQuery() : buildInstanceLevelHintsQuery(); + } + + private QueryRequest buildEntityLevelHintsQuery() { + TablePointer displayHintsTablePointer = + entity.getMapping(getMappingType()).getDisplayHintTablePointer(); + TableVariable primaryTableVar = TableVariable.forPrimary(displayHintsTablePointer); + List tableVars = Lists.newArrayList(primaryTableVar); + + List selectFieldVars = new ArrayList<>(); + List columnSchemas = new ArrayList<>(); + Entity.DISPLAY_HINTS_TABLE_SCHEMA.entrySet().stream() + .forEach( + entry -> { + String columnName = entry.getKey(); + CellValue.SQLDataType columnDataType = entry.getValue().getKey(); + FieldPointer fieldPointer = + new FieldPointer.Builder() + .tablePointer(displayHintsTablePointer) + .columnName(columnName) + .build(); + selectFieldVars.add(fieldPointer.buildVariable(primaryTableVar, tableVars)); + columnSchemas.add(new ColumnSchema(columnName, columnDataType)); + }); + for (ColumnSchema cs : columnSchemas) { + LOGGER.info("column schema: {}, {}", cs.getColumnName(), cs.getSqlDataType()); + } + + Query query = new Query.Builder().select(selectFieldVars).tables(tableVars).build(); + LOGGER.info("Generated entity-level display hint query: {}", query.renderSQL()); + return new QueryRequest(query.renderSQL(), new ColumnHeaderSchema(columnSchemas)); + } + + private QueryRequest buildInstanceLevelHintsQuery() { + // TODO: Support display hints for any relationship, not just for the CRITERIA_OCCURRENCE entity + // group. + EntityGroup entityGroup = + UnderlaysService.getRelationship( + entity.getUnderlay().getEntityGroups().values(), entity, relatedEntity) + .getEntityGroup(); + if (!(entityGroup instanceof CriteriaOccurrence)) { + throw new InvalidQueryException( + "Only CRITERIA_OCCURENCE entity groups support display hints queries"); + } + CriteriaOccurrence criteriaOccurrence = (CriteriaOccurrence) entityGroup; + AuxiliaryDataMapping auxDataMapping = + criteriaOccurrence.getModifierAuxiliaryData().getMapping(getMappingType()); + + TableVariable primaryTableVar = TableVariable.forPrimary(auxDataMapping.getTablePointer()); + List tableVars = Lists.newArrayList(primaryTableVar); + + List selectFieldVars = + auxDataMapping.getFieldPointers().entrySet().stream() + .map( + entry -> entry.getValue().buildVariable(primaryTableVar, tableVars, entry.getKey())) + .collect(Collectors.toList()); + // TODO: Centralize this schema definition used both here and in the indexing job. Also handle + // other enum_value data types. + List columnSchemas = + List.of( + new ColumnSchema(MODIFIER_AUX_DATA_ID_COL, CellValue.SQLDataType.INT64), + new ColumnSchema(MODIFIER_AUX_DATA_ATTR_COL, CellValue.SQLDataType.STRING), + new ColumnSchema(MODIFIER_AUX_DATA_MIN_COL, CellValue.SQLDataType.FLOAT), + new ColumnSchema(MODIFIER_AUX_DATA_MAX_COL, CellValue.SQLDataType.FLOAT), + new ColumnSchema(MODIFIER_AUX_DATA_ENUM_VAL_COL, CellValue.SQLDataType.INT64), + new ColumnSchema(MODIFIER_AUX_DATA_ENUM_DISPLAY_COL, CellValue.SQLDataType.STRING), + new ColumnSchema(MODIFIER_AUX_DATA_ENUM_COUNT_COL, CellValue.SQLDataType.INT64)); + + // Build the WHERE filter variables from the entity filter. + FieldVariable entityIdFieldVar = + selectFieldVars.stream() + .filter(fv -> fv.getAlias().equals(MODIFIER_AUX_DATA_ID_COL)) + .findFirst() + .get(); + BinaryFilterVariable filterVar = + new BinaryFilterVariable( + entityIdFieldVar, BinaryFilterVariable.BinaryOperator.EQUALS, relatedEntityId); + + Query query = + new Query.Builder().select(selectFieldVars).tables(tableVars).where(filterVar).build(); + LOGGER.info("Generated instance-level display hint query: {}", query.renderSQL()); + return new QueryRequest(query.renderSQL(), new ColumnHeaderSchema(columnSchemas)); + } + + public static class Builder { + private Entity entity; + private Entity relatedEntity; + private Literal relatedEntityId; + + public Builder entity(Entity entity) { + this.entity = entity; + return this; + } + + public Builder relatedEntity(Entity relatedEntity) { + this.relatedEntity = relatedEntity; + return this; + } + + public Builder relatedEntityId(Literal relatedEntityId) { + this.relatedEntityId = relatedEntityId; + return this; + } + + public EntityHintRequest build() { + return new EntityHintRequest(this); + } + } +} diff --git a/service/src/main/java/bio/terra/tanagra/service/instances/EntityHintResult.java b/service/src/main/java/bio/terra/tanagra/service/instances/EntityHintResult.java new file mode 100644 index 000000000..2e069f110 --- /dev/null +++ b/service/src/main/java/bio/terra/tanagra/service/instances/EntityHintResult.java @@ -0,0 +1,24 @@ +package bio.terra.tanagra.service.instances; + +import bio.terra.tanagra.underlay.Attribute; +import bio.terra.tanagra.underlay.DisplayHint; +import java.util.Collections; +import java.util.Map; + +public class EntityHintResult { + private final String sql; + private final Map hintMap; + + public EntityHintResult(String sql, Map hintMap) { + this.sql = sql; + this.hintMap = hintMap; + } + + public String getSql() { + return sql; + } + + public Map getHintMap() { + return Collections.unmodifiableMap(hintMap); + } +} diff --git a/service/src/main/resources/application.yml b/service/src/main/resources/application.yml index fe48ffe22..fb3546824 100644 --- a/service/src/main/resources/application.yml +++ b/service/src/main/resources/application.yml @@ -1,6 +1,6 @@ tanagra: underlay: - files: [ "broad/aou_synthetic/expanded/aou_synthetic.json", "broad/cms_synpuf/expanded/cms_synpuf.json" ] + files: [ "broad/aou_synthetic/aou_synthetic.json", "broad/cms_synpuf/cms_synpuf.json" ] feature: artifact-storage-enabled: true diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/SC2022Q4R6.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/SC2022Q4R6.json similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/SC2022Q4R6.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/SC2022Q4R6.json diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_brand.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_brand.json similarity index 86% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_brand.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_brand.json index 4e845ec61..9a970432c 100644 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_brand.json +++ b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_brand.json @@ -2,10 +2,10 @@ "name": "t_brand", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_condition.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_condition.json similarity index 82% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_condition.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_condition.json index 472bbe841..356ff178b 100644 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_condition.json +++ b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_condition.json @@ -2,11 +2,11 @@ "name": "t_condition", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_condition_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_condition_occurrence.json similarity index 55% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_condition_occurrence.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_condition_occurrence.json index e6cfcd402..12eb43415 100644 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_condition_occurrence.json +++ b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_condition_occurrence.json @@ -2,15 +2,15 @@ "name": "t_condition_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "condition" }, - { "type": "SIMPLE", "name": "start_date" }, - { "type": "SIMPLE", "name": "end_date" }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "condition", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_device.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_device.json similarity index 80% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_device.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_device.json index 76f2ff4fb..49475f07c 100644 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_device.json +++ b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_device.json @@ -2,11 +2,11 @@ "name": "t_device", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_device_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_device_occurrence.json similarity index 58% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_device_occurrence.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_device_occurrence.json index 93062226e..ed2900352 100644 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_device_occurrence.json +++ b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_device_occurrence.json @@ -2,14 +2,14 @@ "name": "t_device_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "device" }, - { "type": "SIMPLE", "name": "start_date" }, - { "type": "SIMPLE", "name": "end_date" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "device", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_ingredient.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_ingredient.json similarity index 84% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_ingredient.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_ingredient.json index 0238dba24..cdc2c9895 100644 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_ingredient.json +++ b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_ingredient.json @@ -2,11 +2,11 @@ "name": "t_ingredient", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_ingredient_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_ingredient_occurrence.json similarity index 51% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_ingredient_occurrence.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_ingredient_occurrence.json index 2668de6d0..cdba8e877 100644 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_ingredient_occurrence.json +++ b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_ingredient_occurrence.json @@ -2,17 +2,17 @@ "name": "t_ingredient_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "ingredient" }, - { "type": "SIMPLE", "name": "start_date" }, - { "type": "SIMPLE", "name": "end_date" }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "refills" }, - { "type": "SIMPLE", "name": "days_supply" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "ingredient", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "refills", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "days_supply", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_measurement.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_measurement.json similarity index 92% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_measurement.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_measurement.json index f53bf7a0c..82b9fb5d1 100644 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_measurement.json +++ b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_measurement.json @@ -2,11 +2,11 @@ "name": "t_measurement", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_measurement_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_measurement_occurrence.json similarity index 63% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_measurement_occurrence.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_measurement_occurrence.json index 9b76a40a2..5fa3a23f7 100644 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_measurement_occurrence.json +++ b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_measurement_occurrence.json @@ -2,16 +2,16 @@ "name": "t_measurement_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "measurement" }, - { "type": "SIMPLE", "name": "date" }, - { "type": "SIMPLE", "name": "value_numeric" }, - { "type": "KEY_AND_DISPLAY", "name": "value_enum" }, - { "type": "KEY_AND_DISPLAY", "name": "unit" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "measurement", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "value_numeric", "dataType": "DOUBLE" }, + { "type": "KEY_AND_DISPLAY", "name": "value_enum", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_observation.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_observation.json similarity index 83% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_observation.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_observation.json index feed01fd9..08e582220 100644 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_observation.json +++ b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_observation.json @@ -2,11 +2,11 @@ "name": "t_observation", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_observation_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_observation_occurrence.json similarity index 62% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_observation_occurrence.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_observation_occurrence.json index 284d0899c..2ba51b674 100644 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_observation_occurrence.json +++ b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_observation_occurrence.json @@ -2,16 +2,16 @@ "name": "t_observation_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "observation" }, - { "type": "SIMPLE", "name": "date" }, - { "type": "SIMPLE", "name": "value_as_string" }, - { "type": "KEY_AND_DISPLAY", "name": "value" }, - { "type": "KEY_AND_DISPLAY", "name": "unit" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "observation", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "value_as_string", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "value", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_person.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_person.json similarity index 75% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_person.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_person.json index 8063a55e7..b280a3cfa 100644 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_person.json +++ b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_person.json @@ -2,13 +2,13 @@ "name": "t_person", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "year_of_birth" }, - { "type": "SIMPLE", "name": "age" }, - { "type": "KEY_AND_DISPLAY", "name": "gender" }, - { "type": "KEY_AND_DISPLAY", "name": "race" }, - { "type": "KEY_AND_DISPLAY", "name": "ethnicity" }, - { "type": "KEY_AND_DISPLAY", "name": "sex_at_birth" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "year_of_birth", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "age", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "gender", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "race", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "ethnicity", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "sex_at_birth", "dataType": "INT64" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_procedure.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_procedure.json similarity index 82% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_procedure.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_procedure.json index cbeca40ca..fd3b0890d 100644 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_procedure.json +++ b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_procedure.json @@ -2,11 +2,11 @@ "name": "t_procedure", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_procedure_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_procedure_occurrence.json similarity index 59% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_procedure_occurrence.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_procedure_occurrence.json index ae09ad795..c1d8921c8 100644 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_procedure_occurrence.json +++ b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_procedure_occurrence.json @@ -2,13 +2,13 @@ "name": "t_procedure_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "procedure" }, - { "type": "SIMPLE", "name": "date" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "procedure", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_visit.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_visit.json similarity index 87% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_visit.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_visit.json index 1670f3b13..925efe4e9 100644 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_visit.json +++ b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_visit.json @@ -2,8 +2,8 @@ "name": "t_visit", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_visit_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_visit_occurrence.json similarity index 61% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_visit_occurrence.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_visit_occurrence.json index c023657a0..d86535110 100644 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_visit_occurrence.json +++ b/service/src/main/resources/config/aou/test/SC2022Q4R6/entity/t_visit_occurrence.json @@ -2,13 +2,13 @@ "name": "t_visit_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "visit" }, - { "type": "SIMPLE", "name": "start_date" }, - { "type": "SIMPLE", "name": "end_date" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entitygroup/t_brand_ingredient.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entitygroup/t_brand_ingredient.json similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entitygroup/t_brand_ingredient.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entitygroup/t_brand_ingredient.json diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entitygroup/t_condition_person_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entitygroup/t_condition_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entitygroup/t_condition_person_occurrence.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entitygroup/t_condition_person_occurrence.json diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entitygroup/t_device_person_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entitygroup/t_device_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entitygroup/t_device_person_occurrence.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entitygroup/t_device_person_occurrence.json diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entitygroup/t_ingredient_person_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entitygroup/t_ingredient_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entitygroup/t_ingredient_person_occurrence.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entitygroup/t_ingredient_person_occurrence.json diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entitygroup/t_measurement_person_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entitygroup/t_measurement_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entitygroup/t_measurement_person_occurrence.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entitygroup/t_measurement_person_occurrence.json diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entitygroup/t_observation_person_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entitygroup/t_observation_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entitygroup/t_observation_person_occurrence.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entitygroup/t_observation_person_occurrence.json diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entitygroup/t_procedure_person_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entitygroup/t_procedure_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entitygroup/t_procedure_person_occurrence.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entitygroup/t_procedure_person_occurrence.json diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entitygroup/t_visit_person_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/entitygroup/t_visit_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entitygroup/t_visit_person_occurrence.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/entitygroup/t_visit_person_occurrence.json diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/SC2022Q4R6.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/SC2022Q4R6.json deleted file mode 100644 index c637635bd..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/SC2022Q4R6.json +++ /dev/null @@ -1,29 +0,0 @@ -{ - "name" : "SC2022Q4R6", - "dataPointers" : [ { - "type" : "BQ_DATASET", - "name" : "index_dataset", - "projectId" : "fc-aou-cdr-synth-test-2", - "datasetId" : "SC2022Q4R6", - "queryProjectId" : "fc-aou-cdr-synth-test-2", - "dataflowServiceAccountEmail" : "tanagra-indexing-runner@all-of-us-ehr-dev.iam.gserviceaccount.com", - "dataflowTempLocation" : "gs://all-of-us-ehr-dev-tanagra-indexing/SC2022Q4R6/tanagra_index_temp", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : true - }, { - "type" : "BQ_DATASET", - "name" : "omop_dataset", - "projectId" : "fc-aou-cdr-synth-test-2", - "datasetId" : "SC2022Q4R6", - "queryProjectId" : "fc-aou-cdr-synth-test-2", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : true - } ], - "entities" : [ "t_device.json", "t_visit_occurrence.json", "t_procedure_occurrence.json", "t_measurement_occurrence.json", "t_measurement.json", "t_condition_occurrence.json", "t_procedure.json", "t_ingredient.json", "t_ingredient_occurrence.json", "t_observation_occurrence.json", "t_brand.json", "t_observation.json", "t_condition.json", "t_device_occurrence.json", "t_person.json", "t_visit.json" ], - "entityGroups" : [ "t_procedure_person_occurrence.json", "t_visit_person_occurrence.json", "t_ingredient_person_occurrence.json", "t_device_person_occurrence.json", "t_condition_person_occurrence.json", "t_measurement_person_occurrence.json", "t_observation_person_occurrence.json", "t_brand_ingredient.json" ], - "primaryEntity" : "t_person", - "uiConfig" : "{ \"dataConfig\": { \"primaryEntity\": { \"displayName\": \"Person\", \"entity\": \"t_person\", \"key\": \"id\", \"classifications\": [ ] }, \"occurrences\": [ { \"id\": \"condition_occurrence\", \"displayName\": \"Condition Occurrences\", \"entity\": \"t_condition_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"condition\", \"attribute\": \"condition\", \"entity\": \"t_condition\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"procedure_occurrence\", \"displayName\": \"Procedure Occurrences\", \"entity\": \"t_procedure_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"procedure\", \"attribute\": \"procedure\", \"entity\": \"t_procedure\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"observation_occurrence\", \"displayName\": \"Observation Occurrence\", \"entity\": \"t_observation_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"observation\", \"attribute\": \"observation\", \"entity\": \"t_observation\", \"entityAttribute\": \"id\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"ingredient_occurrence\", \"displayName\": \"Drug Occurrence\", \"entity\": \"t_ingredient_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"ingredient\", \"attribute\": \"id\", \"entity\": \"t_ingredient\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" }, \"groupings\": [ { \"id\": \"brand\", \"entity\": \"t_brand\", \"defaultSort\": { \"attribute\": \"name\", \"direction\": \"ASC\" }, \"attributes\": [\"name\", \"id\", \"standard_concept\", \"concept_code\"] } ] } ] }, { \"id\": \"measurement_occurrence\", \"displayName\": \"Measurement Occurrence\", \"entity\": \"t_measurement_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"measurement\", \"attribute\": \"measurement\", \"entity\": \"t_measurement\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_item_count\", \"direction\": \"DESC\" } } ] } ] }, \"criteriaConfigs\": [ { \"type\": \"classification\", \"id\": \"tanagra-conditions\", \"title\": \"Condition\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Condition\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"condition_occurrence\", \"classification\": \"condition\", \"modifiers\": [ \"age_at_occurrence\", \"visit_type\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-procedures\", \"title\": \"Procedure\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Procedure\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"procedure_occurrence\", \"classification\": \"procedure\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"] }, { \"type\": \"classification\", \"id\": \"tanagra-observations\", \"title\": \"Observation\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"observation_occurrence\", \"classification\": \"observation\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"] }, { \"type\": \"classification\", \"id\": \"tanagra-drugs\", \"title\": \"Drug\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Drug\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"ingredient_occurrence\", \"classification\": \"ingredient\", \"modifiers\": [ \"age_at_occurrence\", \"visit_type\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-measurement\", \"title\": \"Labs and measurements\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_item_count\", \"width\": 120, \"title\": \"Count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Condition\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"measurement_occurrence\", \"classification\": \"measurement\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"], \"valueConfigs\": [ { \"title\": \"Categorical value\", \"attribute\": \"value_enum\" }, { \"title\": \"Numeric value\", \"attribute\": \"value_numeric\" } ] }, { \"type\": \"attribute\", \"id\": \"tanagra-ethnicity\", \"title\": \"Ethnicity\", \"category\": \"Program data\", \"attribute\": \"ethnicity\" }, { \"type\": \"attribute\", \"id\": \"tanagra-gender\", \"title\": \"Gender identity\", \"category\": \"Program data\", \"attribute\": \"gender\" }, { \"type\": \"attribute\", \"id\": \"tanagra-race\", \"title\": \"Race\", \"category\": \"Program data\", \"attribute\": \"race\" }, { \"type\": \"attribute\", \"id\": \"tanagra-age\", \"title\": \"Age\", \"category\": \"Program data\", \"attribute\": \"age\" } ], \"modifierConfigs\": [ { \"type\": \"unhinted-value\", \"id\": \"start_date_group_by_count\", \"title\": \"Occurrence count\", \"attribute\": \"start_date\", \"groupByCount\": true }, { \"type\": \"unhinted-value\", \"id\": \"date_group_by_count\", \"title\": \"Occurrence count\", \"attribute\": \"date\", \"groupByCount\": true }, { \"type\": \"attribute\", \"id\": \"visit_type\", \"title\": \"Visit type\", \"attribute\": \"visit_type\" }, { \"type\": \"attribute\", \"id\": \"age_at_occurrence\", \"title\": \"Age at occurrence\", \"attribute\": \"age_at_occurrence\" } ], \"demographicChartConfigs\": { \"groupByAttributes\": [\"gender\", \"race\", \"age\"], \"chartConfigs\": [ { \"title\": \"Gender identity\", \"primaryProperties\": [{ \"key\": \"gender\" }] }, { \"title\": \"Gender identity, Current age, Race\", \"primaryProperties\": [ { \"key\": \"gender\" }, { \"key\": \"age\", \"buckets\": [ { \"min\": 18, \"max\": 45, \"displayName\": \"18-44\" }, { \"min\": 45, \"max\": 65, \"displayName\": \"45-64\" }, { \"min\": 65, \"displayName\": \"65+\" } ] } ], \"stackedProperty\": { \"key\": \"race\" } } ] }, \"prepackagedConceptSets\": [ { \"id\": \"_demographics\", \"name\": \"Demographics\", \"occurrence\": \"\" }, { \"id\": \"_analgesics\", \"name\": \"Analgesics\", \"occurrence\": \"ingredient_occurrence\", \"filter\": { \"type\": \"CLASSIFICATION\", \"occurrenceId\": \"ingredient_occurrence\", \"classificationId\": \"ingredient\", \"keys\": [21604253] } } ], \"criteriaSearchConfig\": { \"criteriaTypeWidth\": 120, \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept Name\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up Count\" } ] }, \"cohortReviewConfig\": { \"participantsListColumns\": [ { \"key\": \"id\", \"width\": 100, \"title\": \"Id\" }, { \"key\": \"gender\", \"width\": 100, \"title\": \"Gender\" }, { \"key\": \"race\", \"width\": 100, \"title\": \"Race\" }, { \"key\": \"ethnicity\", \"width\": 100, \"title\": \"Ethnicity\" }, { \"key\": \"age\", \"width\": 60, \"title\": \"Year of Birth\" } ], \"attributes\": [ { \"title\": \"Gender\", \"key\": \"gender\" }, { \"title\": \"Age\", \"key\": \"age\" }, { \"title\": \"Race\", \"key\": \"race\" }, { \"title\": \"Ethnicity\", \"key\": \"ethnicity\" } ], \"pages\": [ { \"type\": \"occurrenceTable\", \"id\": \"condition\", \"title\": \"Conditions\", \"plugin\": { \"occurrence\": \"condition_occurrence\", \"columns\": [ { \"key\": \"condition\", \"width\": \"100%\", \"title\": \"Condition name\" }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\" }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\" } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"procedure\", \"title\": \"Procedures\", \"plugin\": { \"occurrence\": \"procedure_occurrence\", \"columns\": [ { \"key\": \"procedure\", \"width\": \"100%\", \"title\": \"Procedure name\" }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\" } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"observation\", \"title\": \"Observations\", \"plugin\": { \"occurrence\": \"observation_occurrence\", \"columns\": [ { \"key\": \"observation\", \"width\": \"100%\", \"title\": \"Observation name\" }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\" } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"ingredient\", \"title\": \"Drugs\", \"plugin\": { \"occurrence\": \"ingredient_occurrence\", \"columns\": [ { \"key\": \"ingredient\", \"width\": \"100%\", \"title\": \"Drug name\" }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\" }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\" } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"measurements\", \"title\": \"Labs and measurements\", \"plugin\": { \"occurrence\": \"measurement_occurrence\", \"columns\": [ { \"key\": \"measurement\", \"width\": \"100%\", \"title\": \"Lab/measurement name\" }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\" }, { \"key\": \"value_enum\", \"width\": 160, \"title\": \"Categorical value\" }, { \"key\": \"value_numeric\", \"width\": 160, \"title\": \"Numeric value\" }, { \"key\": \"unit\", \"width\": 160, \"title\": \"Unit\" } ] } } ] } } ", - "metadata" : { } -} diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_brand.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_brand.json deleted file mode 100644 index 6cf33dedd..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_brand.json +++ /dev/null @@ -1,190 +0,0 @@ -{ - "name" : "t_brand", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Drug" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Brand Name" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "invalid_reason", - "runtimeCalculated" : false - }, - "operator" : "IS", - "value" : { } - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "RxNorm" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "RxNorm Extension" - } - } ] - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c ) AS textsearch JOIN `all-of-us-ehr-dev.SC2022Q4R6.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND c.concept_class_id = 'Brand Name' AND c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_brand" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_condition.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_condition.json deleted file mode 100644 index e0f53bbe6..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_condition.json +++ /dev/null @@ -1,358 +0,0 @@ -{ - "name" : "t_condition", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 171331 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "PPI" - }, - "display" : "AllOfUs_PPI (Columbia)" - }, - "count" : 74 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CIEL" - }, - "display" : "Columbia International eHealth Laboratory (Columbia University)" - }, - "count" : 38818 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "Healthcare Common Procedure Coding System (CMS)" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HemOnc" - }, - "display" : "HemOnc" - }, - "count" : 240 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICDO3" - }, - "display" : "International Classification of Diseases for Oncology, Third Edition (WHO)" - }, - "count" : 62535 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS)" - }, - "count" : 15760 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "International Classification of Diseases, Tenth Revision, Clinical Modification (NCHS)" - }, - "count" : 90699 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Nebraska Lexicon" - }, - "display" : "Nebraska Lexicon" - }, - "count" : 151336 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OMOP Extension" - }, - "display" : "OMOP Extension (OHDSI)" - }, - "count" : 321 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 180133 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Condition" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c ) AS textsearch JOIN `all-of-us-ehr-dev.SC2022Q4R6.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Condition' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `all-of-us-ehr-dev.SC2022Q4R6.concept_relationship` cr JOIN `all-of-us-ehr-dev.SC2022Q4R6.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `all-of-us-ehr-dev.SC2022Q4R6.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Condition' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED' " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 441840 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_condition" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "t_condition_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "t_condition_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "t_condition" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_condition_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_condition_occurrence.json deleted file mode 100644 index 1b0c6b1cc..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_condition_occurrence.json +++ /dev/null @@ -1,212 +0,0 @@ -{ - "name" : "t_condition_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "condition", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 2.000023411E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020479.0, - "maxVal" : 1.5996259E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201235E7, - "maxVal" : 2.0435757E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "condition_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "condition_end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "condition_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "condition_source_concept_id", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "condition_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "condition_start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_condition_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_condition", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_device.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_device.json deleted file mode 100644 index 71ebd853f..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_device.json +++ /dev/null @@ -1,232 +0,0 @@ -{ - "name" : "t_device", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 218461 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "Current Procedural Terminology version 4 (AMA)" - }, - "count" : 24 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "Healthcare Common Procedure Coding System (CMS)" - }, - "count" : 4634 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10PCS" - }, - "display" : "ICD-10 Procedure Coding System (CMS)" - }, - "count" : 3 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NDC" - }, - "display" : "National Drug Code (FDA and manufacturers)" - }, - "count" : 11233 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 202567 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Device" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c ) AS textsearch JOIN `all-of-us-ehr-dev.SC2022Q4R6.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Device' AND c.standard_concept = 'S' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_device" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_device_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_device_occurrence.json deleted file mode 100644 index 75855f60f..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_device_occurrence.json +++ /dev/null @@ -1,185 +0,0 @@ -{ - "name" : "t_device_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 4.6274116E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020475.0, - "maxVal" : 1.5995732E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "device", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201235E7, - "maxVal" : 2.0435757E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "device_exposure" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "device_exposure_end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "device_source_concept_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "device_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "device_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "device_exposure_start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_device_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_device", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_ingredient.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_ingredient.json deleted file mode 100644 index d87e5d801..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_ingredient.json +++ /dev/null @@ -1,317 +0,0 @@ -{ - "name" : "t_ingredient", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 1983181 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 6509 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm" - }, - "display" : "RxNorm (NLM)" - }, - "count" : 148594 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm Extension" - }, - "display" : "RxNorm Extension (OHDSI)" - }, - "count" : 1834587 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ATC" - }, - "display" : "WHO Anatomic Therapeutic Chemical Classification" - }, - "count" : 6509 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT c.concept_id AS id, c.concept_name AS name, c.vocabulary_id, c.standard_concept, c.concept_code FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c WHERE c.domain_id = 'Drug' AND ( (c.vocabulary_id = 'ATC' AND c.standard_concept = 'C') OR (c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.standard_concept = 'S') ) " - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c ) AS textsearch JOIN `all-of-us-ehr-dev.SC2022Q4R6.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND ((c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.concept_class_id = 'Ingredient' AND c.standard_concept = 'S') OR (c.vocabulary_id = 'RxNorm' AND c.concept_class_id = 'Precise Ingredient') OR (c.vocabulary_id = 'ATC' AND c.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c.standard_concept = 'C')) " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child FROM `all-of-us-ehr-dev.SC2022Q4R6.concept_relationship` cr JOIN `all-of-us-ehr-dev.SC2022Q4R6.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `all-of-us-ehr-dev.SC2022Q4R6.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE c1.concept_id != c2.concept_id AND c1.domain_id = 'Drug' AND c2.domain_id = 'Drug' AND ( /* Populate Ingredients' ancestors', which are ATCs. See https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:atc#:~:text=the%20original%20ATC%20hierarchy%20is%20extended%20by%20Standard%20Drug%20Products%20of%20RxNorm%20and%20RxNorm%20Extension%20vocabularies%2C%20which%20are%20assigned%20to%20be%20descendants%20of%20the%205th%20ATC%20Classes. Eg: ATC 1st (highest ancestor) Subsumes ATC 2nd ATC 5th (direct parent of RxNorm) Maps to RxNorm */ (c1.vocabulary_id IN ('ATC') AND cr.relationship_id IN ('Subsumes', 'Maps to')) OR /* Populate Ingredients and their descendants: Branded Drug, Clinical Drug, etc. Ingredients and their descendants are RxNorm. drug_exposure contains Ingredients or their descendants. Use [1] and [2] to define hierarchy. Eg \"Marketed Product\" is most specific and is bottom of hierarchy. [1] https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:drug_exposure#:~:text=These%20are%20indicated,is%20available%20%E2%80%9CIngredient%E2%80%9D [2] https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:drug#:~:text=are%20not%20implemented.-,Relationships,-As%20usual%2C%20all */ ( c1.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c2.vocabulary_id IN ('RxNorm', 'RxNorm Extension') /* Only keep relationships where c1 is \"parent\" of c2 */ AND cr.relationship_id IN ('Constitutes', 'Contained in' , 'Has form', 'Has quantified form', 'RxNorm ing of', 'RxNorm inverse is a', 'Precise ing of') ) ) " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC 1st" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "C" - } - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 8 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_ingredient" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "t_ingredient_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "t_ingredient_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "t_ingredient" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 8 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_ingredient_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_ingredient_occurrence.json deleted file mode 100644 index 7665ba2e5..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_ingredient_occurrence.json +++ /dev/null @@ -1,256 +0,0 @@ -{ - "name" : "t_ingredient_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ingredient", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "refills", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -9.223372036854776E18, - "maxVal" : 10.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -9.223372036854776E18, - "maxVal" : 2.000007519E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020479.0, - "maxVal" : 1.5996253E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "days_supply", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -9.223372036854776E18, - "maxVal" : 180.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201235E7, - "maxVal" : 2.0435757E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "drug_exposure" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "drug_exposure_end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "drug_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "drug_source_concept_id", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "drug_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "drug_exposure_start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_ingredient_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "ingredient", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ingredient", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_measurement.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_measurement.json deleted file mode 100644 index 35c2e2623..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_measurement.json +++ /dev/null @@ -1,410 +0,0 @@ -{ - "name" : "t_measurement", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 75626 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 41859 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "Logical Observation Identifiers Names and Codes (Regenstrief Institute)" - }, - "count" : 191836 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 29999 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Measurement" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "SNOMED" - } - } ] - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC" - } - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC Hierarchy" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC Component" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Lab Test" - } - } ] - } ] - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c ) AS textsearch JOIN `all-of-us-ehr-dev.SC2022Q4R6.concept` c ON c.concept_id = textsearch.id WHERE ((c.domain_id = 'Measurement' AND c.vocabulary_id = 'SNOMED') OR (c.vocabulary_id = 'LOINC' AND c.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test'))) " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `all-of-us-ehr-dev.SC2022Q4R6.concept_relationship` cr JOIN `all-of-us-ehr-dev.SC2022Q4R6.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `all-of-us-ehr-dev.SC2022Q4R6.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.vocabulary_id = c2.vocabulary_id AND ((c1.vocabulary_id = 'SNOMED' AND c1.domain_id = c2.domain_id AND c1.domain_id = 'Measurement') OR (c1.vocabulary_id = 'LOINC' AND c1.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test') AND c2.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test'))) " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Measurement" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "SNOMED" - } - } ] - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 36206173 - } - } ] - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 11 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_measurement" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "t_measurement_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "t_measurement_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "t_measurement" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 11 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_measurement_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_measurement_occurrence.json deleted file mode 100644 index 8df913266..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_measurement_occurrence.json +++ /dev/null @@ -1,241 +0,0 @@ -{ - "name" : "t_measurement_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -9.223372036854776E18, - "maxVal" : 3.040008559E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020475.0, - "maxVal" : 1.5996262E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_numeric", - "dataType" : "DOUBLE", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value_enum", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "measurement", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201234E7, - "maxVal" : 2.0435758E7 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "measurement" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "measurement_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "measurement_source_concept_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "measurement_id", - "runtimeCalculated" : false - } - }, - "value_numeric" : { - "value" : { - "column" : "value_as_number", - "runtimeCalculated" : false - } - }, - "value_enum" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "measurement" : { - "value" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "measurement_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "measurement_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_measurement_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value_numeric" : { - "value" : { - "column" : "value_numeric", - "runtimeCalculated" : false - } - }, - "value_enum" : { - "value" : { - "column" : "value_enum", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value_enum", - "runtimeCalculated" : false - } - }, - "measurement" : { - "value" : { - "column" : "measurement", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_measurement", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_observation.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_observation.json deleted file mode 100644 index b4a2f0f08..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_observation.json +++ /dev/null @@ -1,340 +0,0 @@ -{ - "name" : "t_observation", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 134800 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "APC" - }, - "display" : "Ambulatory Payment Classification (CMS)" - }, - "count" : 715 - }, { - "enumVal" : { - "value" : { - "stringVal" : "AoU_Custom" - }, - "display" : "AoU_Custom" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "AoU_General" - }, - "display" : "AoU_General" - }, - "count" : 13 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "Current Procedural Terminology version 4 (AMA)" - }, - "count" : 1092 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NAACCR" - }, - "display" : "Data Standards & Data Dictionary Volume II (NAACCR)" - }, - "count" : 96 - }, { - "enumVal" : { - "value" : { - "stringVal" : "DRG" - }, - "display" : "Diagnosis-related group (CMS)" - }, - "count" : 752 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "Healthcare Common Procedure Coding System (CMS)" - }, - "count" : 2667 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICDO3" - }, - "display" : "International Classification of Diseases for Oncology, Third Edition (WHO)" - }, - "count" : 49 - }, { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "Logical Observation Identifiers Names and Codes (Regenstrief Institute)" - }, - "count" : 10831 - }, { - "enumVal" : { - "value" : { - "stringVal" : "MDC" - }, - "display" : "Major Diagnostic Categories (CMS)" - }, - "count" : 26 - }, { - "enumVal" : { - "value" : { - "stringVal" : "PCORNet" - }, - "display" : "National Patient-Centered Clinical Research Network (PCORI)" - }, - "count" : 2 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NUCC" - }, - "display" : "National Uniform Claim Committee Health Care Provider Taxonomy Code Set (NUCC)" - }, - "count" : 4 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Nebraska Lexicon" - }, - "display" : "Nebraska Lexicon" - }, - "count" : 1004 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OMOP Extension" - }, - "display" : "OMOP Extension (OHDSI)" - }, - "count" : 136 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 117406 - }, { - "enumVal" : { - "value" : { - "stringVal" : "UB04 Pri Typ of Adm" - }, - "display" : "UB04 Claim Inpatient Admission Type Code (CMS)" - }, - "count" : 6 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Observation" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "PPI" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "Survey" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c ) AS textsearch JOIN `all-of-us-ehr-dev.SC2022Q4R6.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Observation' AND c.standard_concept = 'S' AND c.vocabulary_id != 'PPI' AND c.concept_class_id != 'Survey' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_observation" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_observation_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_observation_occurrence.json deleted file mode 100644 index 882b93e01..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_observation_occurrence.json +++ /dev/null @@ -1,493 +0,0 @@ -{ - "name" : "t_observation_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 4118133 - }, - "display" : "IU/L" - }, - "count" : 5 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 35289501 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4121007 - }, - "display" : "Seconds" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8799 - }, - "display" : "copies per milliliter" - }, - "count" : 231 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8512 - }, - "display" : "day" - }, - "count" : 2028 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9484 - }, - "display" : "degree" - }, - "count" : 55 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8653 - }, - "display" : "degree Celsius" - }, - "count" : 53 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8529 - }, - "display" : "index" - }, - "count" : 88 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8519 - }, - "display" : "liter" - }, - "count" : 15 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9546 - }, - "display" : "meter" - }, - "count" : 66 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4121396 - }, - "display" : "mg/dL" - }, - "count" : 26047 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8720 - }, - "display" : "microgram per gram" - }, - "count" : 23 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8587 - }, - "display" : "milliliter" - }, - "count" : 87 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8588 - }, - "display" : "millimeter" - }, - "count" : 55 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8876 - }, - "display" : "millimeter mercury column" - }, - "count" : 36 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8753 - }, - "display" : "millimole per liter" - }, - "count" : 22 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8931 - }, - "display" : "million per cubic millimeter" - }, - "count" : 957 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4118323 - }, - "display" : "mmHg" - }, - "count" : 63 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4122417 - }, - "display" : "ng/dL" - }, - "count" : 7 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9372 - }, - "display" : "ounce (apothecary)" - }, - "count" : 25481 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8647 - }, - "display" : "per microliter" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8554 - }, - "display" : "percent" - }, - "count" : 360 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4120725 - }, - "display" : "pg/mL" - }, - "count" : 1235 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8729 - }, - "display" : "picomole per liter" - }, - "count" : 3 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8555 - }, - "display" : "second" - }, - "count" : 7 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8525 - }, - "display" : "titer" - }, - "count" : 534 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4121397 - }, - "display" : "ug/dL" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8510 - }, - "display" : "unit" - }, - "count" : 908557 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8763 - }, - "display" : "unit per milliliter" - }, - "count" : 164 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9234 - }, - "display" : "volume percent" - }, - "count" : 7 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9448 - }, - "display" : "year" - }, - "count" : 129781 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -2.0, - "maxVal" : 2.000023487E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "observation", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_as_string", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020475.0, - "maxVal" : 1.5996262E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201234E7, - "maxVal" : 2.0435758E7 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "observation" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "observation_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "observation_source_concept_id", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "observation_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "observation_id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "observation_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_observation_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_observation", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_person.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_person.json deleted file mode 100644 index e6e651472..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_person.json +++ /dev/null @@ -1,382 +0,0 @@ -{ - "name" : "t_person", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "gender", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 45878463 - }, - "display" : "Female" - }, - "count" : 142307 - }, { - "enumVal" : { - "value" : { - "int64Val" : 45880669 - }, - "display" : "Male" - }, - "count" : 87099 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2000000002 - }, - "display" : "Not man only, not woman only, prefer not to answer, or skipped" - }, - "count" : 5119 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "race", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 2000000001 - }, - "display" : "Another single population" - }, - "count" : 5443 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8515 - }, - "display" : "Asian" - }, - "count" : 7476 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8516 - }, - "display" : "Black or African American" - }, - "count" : 46967 - }, { - "enumVal" : { - "value" : { - "int64Val" : 1177221 - }, - "display" : "I prefer not to answer" - }, - "count" : 1614 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2000000008 - }, - "display" : "More than one population" - }, - "count" : 10727 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 37524 - }, { - "enumVal" : { - "value" : { - "int64Val" : 45882607 - }, - "display" : "None of these" - }, - "count" : 2465 - }, { - "enumVal" : { - "value" : { - "int64Val" : 903096 - }, - "display" : "PMI: Skip" - }, - "count" : 1584 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8527 - }, - "display" : "White" - }, - "count" : 120725 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ethnicity", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 38003563 - }, - "display" : "Hispanic or Latino" - }, - "count" : 44673 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38003564 - }, - "display" : "Not Hispanic or Latino" - }, - "count" : 184189 - }, { - "enumVal" : { - "value" : { - "int64Val" : 903079 - }, - "display" : "PMI: Prefer Not To Answer" - }, - "count" : 1614 - }, { - "enumVal" : { - "value" : { - "int64Val" : 903096 - }, - "display" : "PMI: Skip" - }, - "count" : 1584 - }, { - "enumVal" : { - "value" : { - "int64Val" : 1586148 - }, - "display" : "What Race Ethnicity: Race Ethnicity None Of These" - }, - "count" : 2465 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "sex_at_birth", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 45878463 - }, - "display" : "Female" - }, - "count" : 143479 - }, { - "enumVal" : { - "value" : { - "int64Val" : 45880669 - }, - "display" : "Male" - }, - "count" : 87821 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 257 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2000000009 - }, - "display" : "Not male, not female, prefer not to answer, or skipped" - }, - "count" : 2968 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "age", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 22.0, - "maxVal" : 93.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "year_of_birth", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 1930.0, - "maxVal" : 2001.0 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "person" - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "gender_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "race_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "ethnicity_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "sex_at_birth" : { - "value" : { - "column" : "sex_at_birth_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "sex_at_birth_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "age" : { - "value" : { - "column" : "year_of_birth", - "sqlFunctionWrapper" : "EXTRACT(YEAR FROM CURRENT_DATE()) - ${fieldSql}", - "runtimeCalculated" : true - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_person" - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_gender", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_race", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ethnicity", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "sex_at_birth" : { - "value" : { - "column" : "sex_at_birth", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_sex_at_birth", - "runtimeCalculated" : false - } - }, - "age" : { - "value" : { - "column" : "age", - "sqlFunctionWrapper" : "EXTRACT(YEAR FROM CURRENT_DATE()) - ${fieldSql}", - "runtimeCalculated" : true - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_procedure.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_procedure.json deleted file mode 100644 index d5c2848b8..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_procedure.json +++ /dev/null @@ -1,390 +0,0 @@ -{ - "name" : "t_procedure", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 266323 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 5756 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CIEL" - }, - "display" : "Columbia International eHealth Laboratory (Columbia University)" - }, - "count" : 648 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "Current Procedural Terminology version 4 (AMA)" - }, - "count" : 13409 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NAACCR" - }, - "display" : "Data Standards & Data Dictionary Volume II (NAACCR)" - }, - "count" : 710 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "Healthcare Common Procedure Coding System (CMS)" - }, - "count" : 1289 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HemOnc" - }, - "display" : "HemOnc" - }, - "count" : 99 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10PCS" - }, - "display" : "ICD-10 Procedure Coding System (CMS)" - }, - "count" : 194874 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS)" - }, - "count" : 177 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9Proc" - }, - "display" : "International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 3 (NCHS)" - }, - "count" : 4657 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "International Classification of Diseases, Tenth Revision, Clinical Modification (NCHS)" - }, - "count" : 7 - }, { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "Logical Observation Identifiers Names and Codes (Regenstrief Institute)" - }, - "count" : 9280 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Nebraska Lexicon" - }, - "display" : "Nebraska Lexicon" - }, - "count" : 72683 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OMOP Extension" - }, - "display" : "OMOP Extension (OHDSI)" - }, - "count" : 2 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 86910 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Procedure" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c ) AS textsearch JOIN `all-of-us-ehr-dev.SC2022Q4R6.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Procedure' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `all-of-us-ehr-dev.SC2022Q4R6.concept_relationship` cr JOIN `all-of-us-ehr-dev.SC2022Q4R6.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `all-of-us-ehr-dev.SC2022Q4R6.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Procedure' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED' " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 4322976 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_procedure" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "t_procedure_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "t_procedure_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "t_procedure" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_procedure_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_procedure_occurrence.json deleted file mode 100644 index e2dc63ee7..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_procedure_occurrence.json +++ /dev/null @@ -1,168 +0,0 @@ -{ - "name" : "t_procedure_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 2.000023474E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020476.0, - "maxVal" : 1.5996259E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "procedure", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201235E7, - "maxVal" : 2.0435757E7 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "procedure_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "procedure_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "procedure_source_concept_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "procedure_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "procedure_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_procedure_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_procedure", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_visit.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_visit.json deleted file mode 100644 index b5ea3b01f..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_visit.json +++ /dev/null @@ -1,105 +0,0 @@ -{ - "name" : "t_visit", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Visit" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `all-of-us-ehr-dev.SC2022Q4R6.concept` c ) AS textsearch JOIN `all-of-us-ehr-dev.SC2022Q4R6.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Visit' AND c.standard_concept = 'S' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_visit" - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_visit_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_visit_occurrence.json deleted file mode 100644 index ccf7d7ecd..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entity/t_visit_occurrence.json +++ /dev/null @@ -1,367 +0,0 @@ -{ - "name" : "t_visit_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 5.542608719E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 21039000 - }, - "display" : "10 ML Morphine 0.2 MG/ML Prefilled Syringe Box of 10" - }, - "count" : 21 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21050000 - }, - "display" : "2000 ML benzyl benzoate 250 MG/ML Topical Solution" - }, - "count" : 60 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581478 - }, - "display" : "Ambulance Visit" - }, - "count" : 1746 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38004207 - }, - "display" : "Ambulatory Clinic / Center" - }, - "count" : 80437 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581479 - }, - "display" : "Ambulatory Rehabilitation Visit" - }, - "count" : 179 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21056626 - }, - "display" : "Amiodarone 50 MG/ML Oral Suspension" - }, - "count" : 10 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21090200 - }, - "display" : "Cholecalciferol 50000 UNT Oral Capsule [Aciferol D3] Box of 10 by Rhodes" - }, - "count" : 2 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21090300 - }, - "display" : "Chondroitin Sulfates 400 MG / Glucosamine 500 MG Oral Tablet [Joint-Flex] Box of 60" - }, - "count" : 32 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21036000 - }, - "display" : "Daptomycin 500 MG Injection Box of 1" - }, - "count" : 100 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21090500 - }, - "display" : "Diphenhydramine 25 MG Oral Tablet by Ennogen" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 439748 - }, { - "enumVal" : { - "value" : { - "int64Val" : 262 - }, - "display" : "Emergency Room and Inpatient Visit" - }, - "count" : 25323 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21090400 - }, - "display" : "Ergocalciferol 300000 UNT/ML Prefilled Syringe Box of 10" - }, - "count" : 75 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581476 - }, - "display" : "Home Visit" - }, - "count" : 40500 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 568911 - }, { - "enumVal" : { - "value" : { - "int64Val" : 32036 - }, - "display" : "Laboratory Visit" - }, - "count" : 1850 - }, { - "enumVal" : { - "value" : { - "int64Val" : 12 - }, - "display" : "Modifier" - }, - "count" : 30318 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1340218 - }, { - "enumVal" : { - "value" : { - "int64Val" : 42898160 - }, - "display" : "Non-hospital institution Visit" - }, - "count" : 22 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581477 - }, - "display" : "Office Visit" - }, - "count" : 629739 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814711 - }, - "display" : "Other ambulatory visit" - }, - "count" : 4720 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 9929594 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581458 - }, - "display" : "Pharmacy visit" - }, - "count" : 25279 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21033000 - }, - "display" : "Risperidone 0.5 MG Oral Tablet by Consilient" - }, - "count" : 17 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44818518 - }, - "display" : "Visit derived from EHR record" - }, - "count" : 856887 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201234E7, - "maxVal" : 2.0435758E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "visit_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "visit_end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "visit_source_concept_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "visit_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "visit_start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_visit_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "visit" : { - "value" : { - "column" : "visit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_brand_ingredient.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_brand_ingredient.json deleted file mode 100644 index 1cd93f4df..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_brand_ingredient.json +++ /dev/null @@ -1,101 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "t_brand_ingredient", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "rawSql" : "/* 1. User searches for Brand Tylenol 2. User expands Tylenol to see which ingredients are in Tylenol 3. Ingredient Acetaminophen is shown Acetaminophen has over 300 descendants (eg \"acetaminophen 100 MG/ML Oral Suspension\"). Acetaminophen's concept_class_id is Ingredient; descendants' concept_class_ids are Clinical Drug Comp, Quant Clinical Drug, etc. Most descendants have a relationship with Brand Tylenol in concept_relationship. However, we only want to show Acetaminophen in step 3. So only keep relationships with concept_class_id=Ingredient. */ SELECT cr.* FROM `all-of-us-ehr-dev.SC2022Q4R6.concept_relationship` cr, `all-of-us-ehr-dev.SC2022Q4R6.concept` c2 WHERE cr.concept_id_2 = c2.concept_id AND c2.concept_class_id = 'Ingredient' " - }, - "idPairsIdA" : { - "column" : "concept_id_1", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "concept_id_2", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_t_brand_t_ingredient" - }, - "idPairsIdA" : { - "column" : "id_t_brand", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_brand" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "t_ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_brand_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_brand_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "t_ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_brand", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_brand", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "t_brand", - "itemsEntity" : "t_ingredient" -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_condition_person_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_condition_person_occurrence.json deleted file mode 100644 index b942859a6..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_condition_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "t_condition_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_t_condition_occurrence_t_condition" - }, - "idPairsIdA" : { - "column" : "id_t_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_condition", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_condition", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "t_condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_condition_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_condition_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "t_condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_condition_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_condition_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_condition", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "t_condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "t_condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_condition", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_condition_occurrence_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_condition_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "t_condition", - "occurrenceEntity" : "t_condition_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_device_person_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_device_person_occurrence.json deleted file mode 100644 index 3a6ad63d9..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_device_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "t_device_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_t_device_occurrence_t_device" - }, - "idPairsIdA" : { - "column" : "id_t_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_device", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_device", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_device_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_device_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_device", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_device", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_device_occurrence_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_device_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "t_device", - "occurrenceEntity" : "t_device_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_ingredient_person_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_ingredient_person_occurrence.json deleted file mode 100644 index 39d7e4aab..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_ingredient_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "t_ingredient_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_t_ingredient_occurrence_t_ingredient" - }, - "idPairsIdA" : { - "column" : "id_t_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "t_ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_ingredient_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_ingredient_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "t_ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_ingredient_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_ingredient", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "t_ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "t_ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_ingredient", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_ingredient_occurrence_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "t_ingredient", - "occurrenceEntity" : "t_ingredient_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_measurement_person_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_measurement_person_occurrence.json deleted file mode 100644 index 3533f504d..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_measurement_person_occurrence.json +++ /dev/null @@ -1,287 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "t_measurement_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_t_measurement_occurrence_t_measurement" - }, - "idPairsIdA" : { - "column" : "id_t_measurement_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_measurement", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_measurement_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_measurement", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_measurement", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "t_measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_measurement_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_measurement_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "t_measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_measurement_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_measurement_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_measurement_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_measurement", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "t_measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "t_measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_measurement", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_measurement", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_measurement_occurrence_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_measurement_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_measurement_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_measurement_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_measurement_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { - "modifiers" : { - "tablePointer" : { - "table" : "t_measurement_person_occurrence_modifiers" - }, - "fieldPointers" : { - "min" : { - "column" : "min", - "runtimeCalculated" : false - }, - "enum_count" : { - "column" : "enum_count", - "runtimeCalculated" : false - }, - "max" : { - "column" : "max", - "runtimeCalculated" : false - }, - "enum_display" : { - "column" : "enum_display", - "runtimeCalculated" : false - }, - "enum_value" : { - "column" : "enum_value", - "runtimeCalculated" : false - }, - "attribute_name" : { - "column" : "attribute_name", - "runtimeCalculated" : false - }, - "entity_id" : { - "column" : "entity_id", - "runtimeCalculated" : false - } - } - } - } - }, - "criteriaEntity" : "t_measurement", - "occurrenceEntity" : "t_measurement_occurrence", - "modifierAttributes" : [ "value_numeric", "value_enum" ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_observation_person_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_observation_person_occurrence.json deleted file mode 100644 index 13c5ccc71..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_observation_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "t_observation_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_t_observation_occurrence_t_observation" - }, - "idPairsIdA" : { - "column" : "id_t_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_observation", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_observation", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_observation_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_observation_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_observation", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_observation", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_observation_occurrence_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_observation_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "t_observation", - "occurrenceEntity" : "t_observation_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_procedure_person_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_procedure_person_occurrence.json deleted file mode 100644 index a56cf02b4..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_procedure_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "t_procedure_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_t_procedure_occurrence_t_procedure" - }, - "idPairsIdA" : { - "column" : "id_t_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_procedure", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_procedure", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "t_procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_procedure_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_procedure_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "t_procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_procedure_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_procedure", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "t_procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "t_procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_procedure", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_procedure_occurrence_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "t_procedure", - "occurrenceEntity" : "t_procedure_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_visit_person_occurrence.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_visit_person_occurrence.json deleted file mode 100644 index c3ed53b03..000000000 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/entitygroup/t_visit_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "t_visit_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_t_visit_occurrence_t_visit" - }, - "idPairsIdA" : { - "column" : "id_t_visit_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_visit", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_visit_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_visit", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_visit", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_visit" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_visit_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_visit_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_visit_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_visit", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_visit" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_visit", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_visit", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_visit_occurrence_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_visit_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_visit_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_visit_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_visit_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "t_visit", - "occurrenceEntity" : "t_visit_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_brand_all.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_brand_all.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_brand_all.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_brand_all.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_brand_ingredients.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_brand_ingredients.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_brand_ingredients.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_brand_ingredients.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_brand_textSearch.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_brand_textSearch.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_brand_textSearch.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_brand_textSearch.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_condition_occurrence_all.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_condition_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_condition_occurrence_all.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_condition_occurrence_all.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_condition_parentChild.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_condition_parentChild.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_condition_parentChild.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_condition_parentChild.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_condition_textSearch.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_condition_textSearch.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_condition_textSearch.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_condition_textSearch.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_device_occurrence_all.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_device_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_device_occurrence_all.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_device_occurrence_all.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_device_textSearch.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_device_textSearch.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_device_textSearch.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_device_textSearch.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_ingredient_all.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_ingredient_all.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_ingredient_all.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_ingredient_all.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_ingredient_occurrence_all.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_ingredient_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_ingredient_occurrence_all.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_ingredient_occurrence_all.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_ingredient_parentChild.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_ingredient_parentChild.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_ingredient_parentChild.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_ingredient_parentChild.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_ingredient_textSearch.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_ingredient_textSearch.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_ingredient_textSearch.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_ingredient_textSearch.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_measurement_occurrence_all.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_measurement_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_measurement_occurrence_all.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_measurement_occurrence_all.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_measurement_parentChild.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_measurement_parentChild.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_measurement_parentChild.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_measurement_parentChild.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_measurement_textSearch.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_measurement_textSearch.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_measurement_textSearch.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_measurement_textSearch.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_observation_occurrence_all.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_observation_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_observation_occurrence_all.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_observation_occurrence_all.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_observation_textSearch.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_observation_textSearch.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_observation_textSearch.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_observation_textSearch.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_person.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_person.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_person.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_person.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_procedure_occurrence_all.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_procedure_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_procedure_occurrence_all.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_procedure_occurrence_all.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_procedure_parentChild.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_procedure_parentChild.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_procedure_parentChild.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_procedure_parentChild.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_procedure_textSearch.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_procedure_textSearch.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_procedure_textSearch.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_procedure_textSearch.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_visit_occurrence_all.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_visit_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_visit_occurrence_all.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_visit_occurrence_all.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_visit_textSearch.sql b/service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_visit_textSearch.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/sql/t_visit_textSearch.sql rename to service/src/main/resources/config/aou/test/SC2022Q4R6/sql/t_visit_textSearch.sql diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/ui/top_level.json b/service/src/main/resources/config/aou/test/SC2022Q4R6/ui/top_level.json similarity index 100% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/ui/top_level.json rename to service/src/main/resources/config/aou/test/SC2022Q4R6/ui/top_level.json diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/SR2022Q4R6.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/SR2022Q4R6.json similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/SR2022Q4R6.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/SR2022Q4R6.json diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_brand.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_brand.json similarity index 86% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_brand.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_brand.json index 4e845ec61..9a970432c 100644 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_brand.json +++ b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_brand.json @@ -2,10 +2,10 @@ "name": "t_brand", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_condition.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_condition.json similarity index 82% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_condition.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_condition.json index 472bbe841..356ff178b 100644 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_condition.json +++ b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_condition.json @@ -2,11 +2,11 @@ "name": "t_condition", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_condition_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_condition_occurrence.json similarity index 55% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_condition_occurrence.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_condition_occurrence.json index e6cfcd402..12eb43415 100644 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_condition_occurrence.json +++ b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_condition_occurrence.json @@ -2,15 +2,15 @@ "name": "t_condition_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "condition" }, - { "type": "SIMPLE", "name": "start_date" }, - { "type": "SIMPLE", "name": "end_date" }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "condition", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_device.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_device.json similarity index 80% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_device.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_device.json index 76f2ff4fb..49475f07c 100644 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_device.json +++ b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_device.json @@ -2,11 +2,11 @@ "name": "t_device", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_device_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_device_occurrence.json similarity index 58% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_device_occurrence.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_device_occurrence.json index 93062226e..ed2900352 100644 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_device_occurrence.json +++ b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_device_occurrence.json @@ -2,14 +2,14 @@ "name": "t_device_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "device" }, - { "type": "SIMPLE", "name": "start_date" }, - { "type": "SIMPLE", "name": "end_date" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "device", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_ingredient.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_ingredient.json similarity index 84% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_ingredient.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_ingredient.json index 0238dba24..cdc2c9895 100644 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_ingredient.json +++ b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_ingredient.json @@ -2,11 +2,11 @@ "name": "t_ingredient", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_ingredient_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_ingredient_occurrence.json similarity index 51% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_ingredient_occurrence.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_ingredient_occurrence.json index 2668de6d0..cdba8e877 100644 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_ingredient_occurrence.json +++ b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_ingredient_occurrence.json @@ -2,17 +2,17 @@ "name": "t_ingredient_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "ingredient" }, - { "type": "SIMPLE", "name": "start_date" }, - { "type": "SIMPLE", "name": "end_date" }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "refills" }, - { "type": "SIMPLE", "name": "days_supply" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "ingredient", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "refills", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "days_supply", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_measurement.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_measurement.json similarity index 92% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_measurement.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_measurement.json index f53bf7a0c..82b9fb5d1 100644 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_measurement.json +++ b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_measurement.json @@ -2,11 +2,11 @@ "name": "t_measurement", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_measurement_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_measurement_occurrence.json similarity index 63% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_measurement_occurrence.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_measurement_occurrence.json index 9b76a40a2..5fa3a23f7 100644 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_measurement_occurrence.json +++ b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_measurement_occurrence.json @@ -2,16 +2,16 @@ "name": "t_measurement_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "measurement" }, - { "type": "SIMPLE", "name": "date" }, - { "type": "SIMPLE", "name": "value_numeric" }, - { "type": "KEY_AND_DISPLAY", "name": "value_enum" }, - { "type": "KEY_AND_DISPLAY", "name": "unit" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "measurement", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "value_numeric", "dataType": "DOUBLE" }, + { "type": "KEY_AND_DISPLAY", "name": "value_enum", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_observation.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_observation.json similarity index 83% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_observation.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_observation.json index feed01fd9..08e582220 100644 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_observation.json +++ b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_observation.json @@ -2,11 +2,11 @@ "name": "t_observation", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_observation_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_observation_occurrence.json similarity index 62% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_observation_occurrence.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_observation_occurrence.json index 284d0899c..2ba51b674 100644 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_observation_occurrence.json +++ b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_observation_occurrence.json @@ -2,16 +2,16 @@ "name": "t_observation_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "observation" }, - { "type": "SIMPLE", "name": "date" }, - { "type": "SIMPLE", "name": "value_as_string" }, - { "type": "KEY_AND_DISPLAY", "name": "value" }, - { "type": "KEY_AND_DISPLAY", "name": "unit" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "observation", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "value_as_string", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "value", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_person.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_person.json similarity index 75% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_person.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_person.json index 8063a55e7..b280a3cfa 100644 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_person.json +++ b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_person.json @@ -2,13 +2,13 @@ "name": "t_person", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "year_of_birth" }, - { "type": "SIMPLE", "name": "age" }, - { "type": "KEY_AND_DISPLAY", "name": "gender" }, - { "type": "KEY_AND_DISPLAY", "name": "race" }, - { "type": "KEY_AND_DISPLAY", "name": "ethnicity" }, - { "type": "KEY_AND_DISPLAY", "name": "sex_at_birth" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "year_of_birth", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "age", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "gender", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "race", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "ethnicity", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "sex_at_birth", "dataType": "INT64" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_procedure.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_procedure.json similarity index 82% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_procedure.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_procedure.json index cbeca40ca..fd3b0890d 100644 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_procedure.json +++ b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_procedure.json @@ -2,11 +2,11 @@ "name": "t_procedure", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_procedure_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_procedure_occurrence.json similarity index 59% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_procedure_occurrence.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_procedure_occurrence.json index ae09ad795..c1d8921c8 100644 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entity/t_procedure_occurrence.json +++ b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_procedure_occurrence.json @@ -2,13 +2,13 @@ "name": "t_procedure_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "procedure" }, - { "type": "SIMPLE", "name": "date" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "procedure", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_visit.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_visit.json similarity index 87% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_visit.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_visit.json index 1670f3b13..925efe4e9 100644 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_visit.json +++ b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_visit.json @@ -2,8 +2,8 @@ "name": "t_visit", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_visit_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_visit_occurrence.json similarity index 61% rename from service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_visit_occurrence.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_visit_occurrence.json index c023657a0..d86535110 100644 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/entity/t_visit_occurrence.json +++ b/service/src/main/resources/config/aou/test/SR2022Q4R6/entity/t_visit_occurrence.json @@ -2,13 +2,13 @@ "name": "t_visit_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "visit" }, - { "type": "SIMPLE", "name": "start_date" }, - { "type": "SIMPLE", "name": "end_date" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entitygroup/t_brand_ingredient.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entitygroup/t_brand_ingredient.json similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entitygroup/t_brand_ingredient.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entitygroup/t_brand_ingredient.json diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entitygroup/t_condition_person_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entitygroup/t_condition_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entitygroup/t_condition_person_occurrence.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entitygroup/t_condition_person_occurrence.json diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entitygroup/t_device_person_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entitygroup/t_device_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entitygroup/t_device_person_occurrence.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entitygroup/t_device_person_occurrence.json diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entitygroup/t_ingredient_person_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entitygroup/t_ingredient_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entitygroup/t_ingredient_person_occurrence.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entitygroup/t_ingredient_person_occurrence.json diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entitygroup/t_measurement_person_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entitygroup/t_measurement_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entitygroup/t_measurement_person_occurrence.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entitygroup/t_measurement_person_occurrence.json diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entitygroup/t_observation_person_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entitygroup/t_observation_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entitygroup/t_observation_person_occurrence.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entitygroup/t_observation_person_occurrence.json diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entitygroup/t_procedure_person_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entitygroup/t_procedure_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entitygroup/t_procedure_person_occurrence.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entitygroup/t_procedure_person_occurrence.json diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/entitygroup/t_visit_person_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/entitygroup/t_visit_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/entitygroup/t_visit_person_occurrence.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/entitygroup/t_visit_person_occurrence.json diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/SR2022Q4R6.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/SR2022Q4R6.json deleted file mode 100644 index 89fc76d36..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/SR2022Q4R6.json +++ /dev/null @@ -1,29 +0,0 @@ -{ - "name" : "SR2022Q4R6", - "dataPointers" : [ { - "type" : "BQ_DATASET", - "name" : "index_dataset", - "projectId" : "fc-aou-cdr-synth-test", - "datasetId" : "SR2022Q4R6", - "queryProjectId" : "fc-aou-cdr-synth-test", - "dataflowServiceAccountEmail" : "tanagra-indexing-runner@all-of-us-ehr-dev.iam.gserviceaccount.com", - "dataflowTempLocation" : "gs://all-of-us-ehr-dev-tanagra-indexing/SR2022Q4R6/tanagra_index_temp", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : true - }, { - "type" : "BQ_DATASET", - "name" : "omop_dataset", - "projectId" : "fc-aou-cdr-synth-test", - "datasetId" : "SR2022Q4R6", - "queryProjectId" : "fc-aou-cdr-synth-test", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : true - } ], - "entities" : [ "t_device.json", "t_visit_occurrence.json", "t_procedure_occurrence.json", "t_measurement_occurrence.json", "t_measurement.json", "t_condition_occurrence.json", "t_procedure.json", "t_ingredient.json", "t_ingredient_occurrence.json", "t_observation_occurrence.json", "t_brand.json", "t_observation.json", "t_condition.json", "t_device_occurrence.json", "t_person.json", "t_visit.json" ], - "entityGroups" : [ "t_procedure_person_occurrence.json", "t_visit_person_occurrence.json", "t_ingredient_person_occurrence.json", "t_device_person_occurrence.json", "t_condition_person_occurrence.json", "t_measurement_person_occurrence.json", "t_observation_person_occurrence.json", "t_brand_ingredient.json" ], - "primaryEntity" : "t_person", - "uiConfig" : "{ \"dataConfig\": { \"primaryEntity\": { \"displayName\": \"Person\", \"entity\": \"t_person\", \"key\": \"id\", \"classifications\": [ ] }, \"occurrences\": [ { \"id\": \"condition_occurrence\", \"displayName\": \"Condition Occurrences\", \"entity\": \"t_condition_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"condition\", \"attribute\": \"condition\", \"entity\": \"t_condition\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"procedure_occurrence\", \"displayName\": \"Procedure Occurrences\", \"entity\": \"t_procedure_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"procedure\", \"attribute\": \"procedure\", \"entity\": \"t_procedure\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"observation_occurrence\", \"displayName\": \"Observation Occurrence\", \"entity\": \"t_observation_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"observation\", \"attribute\": \"observation\", \"entity\": \"t_observation\", \"entityAttribute\": \"id\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"ingredient_occurrence\", \"displayName\": \"Drug Occurrence\", \"entity\": \"t_ingredient_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"ingredient\", \"attribute\": \"id\", \"entity\": \"t_ingredient\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" }, \"groupings\": [ { \"id\": \"brand\", \"entity\": \"t_brand\", \"defaultSort\": { \"attribute\": \"name\", \"direction\": \"ASC\" }, \"attributes\": [\"name\", \"id\", \"standard_concept\", \"concept_code\"] } ] } ] }, { \"id\": \"measurement_occurrence\", \"displayName\": \"Measurement Occurrence\", \"entity\": \"t_measurement_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"measurement\", \"attribute\": \"measurement\", \"entity\": \"t_measurement\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_item_count\", \"direction\": \"DESC\" } } ] } ] }, \"criteriaConfigs\": [ { \"type\": \"classification\", \"id\": \"tanagra-conditions\", \"title\": \"Condition\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Condition\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"condition_occurrence\", \"classification\": \"condition\", \"modifiers\": [ \"age_at_occurrence\", \"visit_type\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-procedures\", \"title\": \"Procedure\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Procedure\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"procedure_occurrence\", \"classification\": \"procedure\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"] }, { \"type\": \"classification\", \"id\": \"tanagra-observations\", \"title\": \"Observation\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"observation_occurrence\", \"classification\": \"observation\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"] }, { \"type\": \"classification\", \"id\": \"tanagra-drugs\", \"title\": \"Drug\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Drug\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"ingredient_occurrence\", \"classification\": \"ingredient\", \"modifiers\": [ \"age_at_occurrence\", \"visit_type\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-measurement\", \"title\": \"Labs and measurements\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_item_count\", \"width\": 120, \"title\": \"Count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Condition\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"measurement_occurrence\", \"classification\": \"measurement\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"], \"valueConfigs\": [ { \"title\": \"Categorical value\", \"attribute\": \"value_enum\" }, { \"title\": \"Numeric value\", \"attribute\": \"value_numeric\" } ] }, { \"type\": \"attribute\", \"id\": \"tanagra-ethnicity\", \"title\": \"Ethnicity\", \"category\": \"Program data\", \"attribute\": \"ethnicity\" }, { \"type\": \"attribute\", \"id\": \"tanagra-gender\", \"title\": \"Gender identity\", \"category\": \"Program data\", \"attribute\": \"gender\" }, { \"type\": \"attribute\", \"id\": \"tanagra-race\", \"title\": \"Race\", \"category\": \"Program data\", \"attribute\": \"race\" }, { \"type\": \"attribute\", \"id\": \"tanagra-age\", \"title\": \"Age\", \"category\": \"Program data\", \"attribute\": \"age\" } ], \"modifierConfigs\": [ { \"type\": \"unhinted-value\", \"id\": \"start_date_group_by_count\", \"title\": \"Occurrence count\", \"attribute\": \"start_date\", \"groupByCount\": true }, { \"type\": \"unhinted-value\", \"id\": \"date_group_by_count\", \"title\": \"Occurrence count\", \"attribute\": \"date\", \"groupByCount\": true }, { \"type\": \"attribute\", \"id\": \"visit_type\", \"title\": \"Visit type\", \"attribute\": \"visit_type\" }, { \"type\": \"attribute\", \"id\": \"age_at_occurrence\", \"title\": \"Age at occurrence\", \"attribute\": \"age_at_occurrence\" } ], \"demographicChartConfigs\": { \"groupByAttributes\": [\"gender\", \"race\", \"age\"], \"chartConfigs\": [ { \"title\": \"Gender identity\", \"primaryProperties\": [{ \"key\": \"gender\" }] }, { \"title\": \"Gender identity, Current age, Race\", \"primaryProperties\": [ { \"key\": \"gender\" }, { \"key\": \"age\", \"buckets\": [ { \"min\": 18, \"max\": 45, \"displayName\": \"18-44\" }, { \"min\": 45, \"max\": 65, \"displayName\": \"45-64\" }, { \"min\": 65, \"displayName\": \"65+\" } ] } ], \"stackedProperty\": { \"key\": \"race\" } } ] }, \"prepackagedConceptSets\": [ { \"id\": \"_demographics\", \"name\": \"Demographics\", \"occurrence\": \"\" }, { \"id\": \"_analgesics\", \"name\": \"Analgesics\", \"occurrence\": \"ingredient_occurrence\", \"filter\": { \"type\": \"CLASSIFICATION\", \"occurrenceId\": \"ingredient_occurrence\", \"classificationId\": \"ingredient\", \"keys\": [21604253] } } ], \"criteriaSearchConfig\": { \"criteriaTypeWidth\": 120, \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept Name\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up Count\" } ] }, \"cohortReviewConfig\": { \"participantsListColumns\": [ { \"key\": \"id\", \"width\": 100, \"title\": \"Id\" }, { \"key\": \"gender\", \"width\": 100, \"title\": \"Gender\" }, { \"key\": \"race\", \"width\": 100, \"title\": \"Race\" }, { \"key\": \"ethnicity\", \"width\": 100, \"title\": \"Ethnicity\" }, { \"key\": \"age\", \"width\": 60, \"title\": \"Year of Birth\" } ], \"attributes\": [ { \"title\": \"Gender\", \"key\": \"gender\" }, { \"title\": \"Age\", \"key\": \"age\" }, { \"title\": \"Race\", \"key\": \"race\" }, { \"title\": \"Ethnicity\", \"key\": \"ethnicity\" } ], \"pages\": [ { \"type\": \"occurrenceTable\", \"id\": \"condition\", \"title\": \"Conditions\", \"plugin\": { \"occurrence\": \"condition_occurrence\", \"columns\": [ { \"key\": \"condition\", \"width\": \"100%\", \"title\": \"Condition name\" }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\" }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\" } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"procedure\", \"title\": \"Procedures\", \"plugin\": { \"occurrence\": \"procedure_occurrence\", \"columns\": [ { \"key\": \"procedure\", \"width\": \"100%\", \"title\": \"Procedure name\" }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\" } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"observation\", \"title\": \"Observations\", \"plugin\": { \"occurrence\": \"observation_occurrence\", \"columns\": [ { \"key\": \"observation\", \"width\": \"100%\", \"title\": \"Observation name\" }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\" } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"ingredient\", \"title\": \"Drugs\", \"plugin\": { \"occurrence\": \"ingredient_occurrence\", \"columns\": [ { \"key\": \"ingredient\", \"width\": \"100%\", \"title\": \"Drug name\" }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\" }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\" } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"measurements\", \"title\": \"Labs and measurements\", \"plugin\": { \"occurrence\": \"measurement_occurrence\", \"columns\": [ { \"key\": \"measurement\", \"width\": \"100%\", \"title\": \"Lab/measurement name\" }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\" }, { \"key\": \"value_enum\", \"width\": 160, \"title\": \"Categorical value\" }, { \"key\": \"value_numeric\", \"width\": 160, \"title\": \"Numeric value\" }, { \"key\": \"unit\", \"width\": 160, \"title\": \"Unit\" } ] } } ] } } ", - "metadata" : { } -} diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_brand.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_brand.json deleted file mode 100644 index e31f880be..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_brand.json +++ /dev/null @@ -1,190 +0,0 @@ -{ - "name" : "t_brand", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Drug" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Brand Name" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "invalid_reason", - "runtimeCalculated" : false - }, - "operator" : "IS", - "value" : { } - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "RxNorm" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "RxNorm Extension" - } - } ] - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c ) AS textsearch JOIN `all-of-us-ehr-dev.SR2022Q4R6.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND c.concept_class_id = 'Brand Name' AND c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_brand" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_condition.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_condition.json deleted file mode 100644 index f2a0ab2d9..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_condition.json +++ /dev/null @@ -1,358 +0,0 @@ -{ - "name" : "t_condition", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 171331 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "PPI" - }, - "display" : "AllOfUs_PPI (Columbia)" - }, - "count" : 74 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CIEL" - }, - "display" : "Columbia International eHealth Laboratory (Columbia University)" - }, - "count" : 38818 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "Healthcare Common Procedure Coding System (CMS)" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HemOnc" - }, - "display" : "HemOnc" - }, - "count" : 240 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICDO3" - }, - "display" : "International Classification of Diseases for Oncology, Third Edition (WHO)" - }, - "count" : 62535 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS)" - }, - "count" : 15760 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "International Classification of Diseases, Tenth Revision, Clinical Modification (NCHS)" - }, - "count" : 90699 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Nebraska Lexicon" - }, - "display" : "Nebraska Lexicon" - }, - "count" : 151336 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OMOP Extension" - }, - "display" : "OMOP Extension (OHDSI)" - }, - "count" : 321 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 180133 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Condition" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c ) AS textsearch JOIN `all-of-us-ehr-dev.SR2022Q4R6.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Condition' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `all-of-us-ehr-dev.SR2022Q4R6.concept_relationship` cr JOIN `all-of-us-ehr-dev.SR2022Q4R6.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `all-of-us-ehr-dev.SR2022Q4R6.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Condition' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED' " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 441840 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_condition" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "t_condition_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "t_condition_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "t_condition" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_condition_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_condition_occurrence.json deleted file mode 100644 index 1b0c6b1cc..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_condition_occurrence.json +++ /dev/null @@ -1,212 +0,0 @@ -{ - "name" : "t_condition_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "condition", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 2.000023411E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020479.0, - "maxVal" : 1.5996259E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201235E7, - "maxVal" : 2.0435757E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "condition_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "condition_end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "condition_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "condition_source_concept_id", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "condition_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "condition_start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_condition_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_condition", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_device.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_device.json deleted file mode 100644 index 1eb2b8e16..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_device.json +++ /dev/null @@ -1,232 +0,0 @@ -{ - "name" : "t_device", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 218461 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "Current Procedural Terminology version 4 (AMA)" - }, - "count" : 24 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "Healthcare Common Procedure Coding System (CMS)" - }, - "count" : 4634 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10PCS" - }, - "display" : "ICD-10 Procedure Coding System (CMS)" - }, - "count" : 3 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NDC" - }, - "display" : "National Drug Code (FDA and manufacturers)" - }, - "count" : 11233 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 202567 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Device" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c ) AS textsearch JOIN `all-of-us-ehr-dev.SR2022Q4R6.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Device' AND c.standard_concept = 'S' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_device" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_device_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_device_occurrence.json deleted file mode 100644 index 75855f60f..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_device_occurrence.json +++ /dev/null @@ -1,185 +0,0 @@ -{ - "name" : "t_device_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 4.6274116E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020475.0, - "maxVal" : 1.5995732E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "device", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201235E7, - "maxVal" : 2.0435757E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "device_exposure" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "device_exposure_end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "device_source_concept_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "device_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "device_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "device_exposure_start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_device_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_device", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_ingredient.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_ingredient.json deleted file mode 100644 index 5d0422d6d..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_ingredient.json +++ /dev/null @@ -1,317 +0,0 @@ -{ - "name" : "t_ingredient", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 1983181 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 6509 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm" - }, - "display" : "RxNorm (NLM)" - }, - "count" : 148594 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm Extension" - }, - "display" : "RxNorm Extension (OHDSI)" - }, - "count" : 1834587 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ATC" - }, - "display" : "WHO Anatomic Therapeutic Chemical Classification" - }, - "count" : 6509 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT c.concept_id AS id, c.concept_name AS name, c.vocabulary_id, c.standard_concept, c.concept_code FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c WHERE c.domain_id = 'Drug' AND ( (c.vocabulary_id = 'ATC' AND c.standard_concept = 'C') OR (c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.standard_concept = 'S') ) " - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c ) AS textsearch JOIN `all-of-us-ehr-dev.SR2022Q4R6.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND ((c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.concept_class_id = 'Ingredient' AND c.standard_concept = 'S') OR (c.vocabulary_id = 'RxNorm' AND c.concept_class_id = 'Precise Ingredient') OR (c.vocabulary_id = 'ATC' AND c.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c.standard_concept = 'C')) " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child FROM `all-of-us-ehr-dev.SR2022Q4R6.concept_relationship` cr JOIN `all-of-us-ehr-dev.SR2022Q4R6.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `all-of-us-ehr-dev.SR2022Q4R6.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE c1.concept_id != c2.concept_id AND c1.domain_id = 'Drug' AND c2.domain_id = 'Drug' AND ( /* Populate Ingredients' ancestors', which are ATCs. See https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:atc#:~:text=the%20original%20ATC%20hierarchy%20is%20extended%20by%20Standard%20Drug%20Products%20of%20RxNorm%20and%20RxNorm%20Extension%20vocabularies%2C%20which%20are%20assigned%20to%20be%20descendants%20of%20the%205th%20ATC%20Classes. Eg: ATC 1st (highest ancestor) Subsumes ATC 2nd ATC 5th (direct parent of RxNorm) Maps to RxNorm */ (c1.vocabulary_id IN ('ATC') AND cr.relationship_id IN ('Subsumes', 'Maps to')) OR /* Populate Ingredients and their descendants: Branded Drug, Clinical Drug, etc. Ingredients and their descendants are RxNorm. drug_exposure contains Ingredients or their descendants. Use [1] and [2] to define hierarchy. Eg \"Marketed Product\" is most specific and is bottom of hierarchy. [1] https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:drug_exposure#:~:text=These%20are%20indicated,is%20available%20%E2%80%9CIngredient%E2%80%9D [2] https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:drug#:~:text=are%20not%20implemented.-,Relationships,-As%20usual%2C%20all */ ( c1.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c2.vocabulary_id IN ('RxNorm', 'RxNorm Extension') /* Only keep relationships where c1 is \"parent\" of c2 */ AND cr.relationship_id IN ('Constitutes', 'Contained in' , 'Has form', 'Has quantified form', 'RxNorm ing of', 'RxNorm inverse is a', 'Precise ing of') ) ) " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC 1st" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "C" - } - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 8 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_ingredient" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "t_ingredient_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "t_ingredient_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "t_ingredient" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 8 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_ingredient_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_ingredient_occurrence.json deleted file mode 100644 index 7665ba2e5..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_ingredient_occurrence.json +++ /dev/null @@ -1,256 +0,0 @@ -{ - "name" : "t_ingredient_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ingredient", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "refills", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -9.223372036854776E18, - "maxVal" : 10.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -9.223372036854776E18, - "maxVal" : 2.000007519E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020479.0, - "maxVal" : 1.5996253E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "days_supply", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -9.223372036854776E18, - "maxVal" : 180.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201235E7, - "maxVal" : 2.0435757E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "drug_exposure" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "drug_exposure_end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "drug_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "drug_source_concept_id", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "drug_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "drug_exposure_start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_ingredient_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "ingredient", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ingredient", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_measurement.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_measurement.json deleted file mode 100644 index 5a3eceae2..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_measurement.json +++ /dev/null @@ -1,410 +0,0 @@ -{ - "name" : "t_measurement", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 75626 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 41859 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "Logical Observation Identifiers Names and Codes (Regenstrief Institute)" - }, - "count" : 191836 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 29999 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Measurement" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "SNOMED" - } - } ] - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC" - } - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC Hierarchy" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC Component" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Lab Test" - } - } ] - } ] - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c ) AS textsearch JOIN `all-of-us-ehr-dev.SR2022Q4R6.concept` c ON c.concept_id = textsearch.id WHERE ((c.domain_id = 'Measurement' AND c.vocabulary_id = 'SNOMED') OR (c.vocabulary_id = 'LOINC' AND c.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test'))) " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `all-of-us-ehr-dev.SR2022Q4R6.concept_relationship` cr JOIN `all-of-us-ehr-dev.SR2022Q4R6.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `all-of-us-ehr-dev.SR2022Q4R6.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.vocabulary_id = c2.vocabulary_id AND ((c1.vocabulary_id = 'SNOMED' AND c1.domain_id = c2.domain_id AND c1.domain_id = 'Measurement') OR (c1.vocabulary_id = 'LOINC' AND c1.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test') AND c2.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test'))) " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Measurement" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "SNOMED" - } - } ] - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 36206173 - } - } ] - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 11 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_measurement" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "t_measurement_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "t_measurement_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "t_measurement" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 11 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_measurement_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_measurement_occurrence.json deleted file mode 100644 index 8df913266..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_measurement_occurrence.json +++ /dev/null @@ -1,241 +0,0 @@ -{ - "name" : "t_measurement_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -9.223372036854776E18, - "maxVal" : 3.040008559E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020475.0, - "maxVal" : 1.5996262E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_numeric", - "dataType" : "DOUBLE", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value_enum", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "measurement", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201234E7, - "maxVal" : 2.0435758E7 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "measurement" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "measurement_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "measurement_source_concept_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "measurement_id", - "runtimeCalculated" : false - } - }, - "value_numeric" : { - "value" : { - "column" : "value_as_number", - "runtimeCalculated" : false - } - }, - "value_enum" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "measurement" : { - "value" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "measurement_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "measurement_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_measurement_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value_numeric" : { - "value" : { - "column" : "value_numeric", - "runtimeCalculated" : false - } - }, - "value_enum" : { - "value" : { - "column" : "value_enum", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value_enum", - "runtimeCalculated" : false - } - }, - "measurement" : { - "value" : { - "column" : "measurement", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_measurement", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_observation.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_observation.json deleted file mode 100644 index 62269b19c..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_observation.json +++ /dev/null @@ -1,340 +0,0 @@ -{ - "name" : "t_observation", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 134800 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "APC" - }, - "display" : "Ambulatory Payment Classification (CMS)" - }, - "count" : 715 - }, { - "enumVal" : { - "value" : { - "stringVal" : "AoU_Custom" - }, - "display" : "AoU_Custom" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "AoU_General" - }, - "display" : "AoU_General" - }, - "count" : 13 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "Current Procedural Terminology version 4 (AMA)" - }, - "count" : 1092 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NAACCR" - }, - "display" : "Data Standards & Data Dictionary Volume II (NAACCR)" - }, - "count" : 96 - }, { - "enumVal" : { - "value" : { - "stringVal" : "DRG" - }, - "display" : "Diagnosis-related group (CMS)" - }, - "count" : 752 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "Healthcare Common Procedure Coding System (CMS)" - }, - "count" : 2667 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICDO3" - }, - "display" : "International Classification of Diseases for Oncology, Third Edition (WHO)" - }, - "count" : 49 - }, { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "Logical Observation Identifiers Names and Codes (Regenstrief Institute)" - }, - "count" : 10831 - }, { - "enumVal" : { - "value" : { - "stringVal" : "MDC" - }, - "display" : "Major Diagnostic Categories (CMS)" - }, - "count" : 26 - }, { - "enumVal" : { - "value" : { - "stringVal" : "PCORNet" - }, - "display" : "National Patient-Centered Clinical Research Network (PCORI)" - }, - "count" : 2 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NUCC" - }, - "display" : "National Uniform Claim Committee Health Care Provider Taxonomy Code Set (NUCC)" - }, - "count" : 4 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Nebraska Lexicon" - }, - "display" : "Nebraska Lexicon" - }, - "count" : 1004 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OMOP Extension" - }, - "display" : "OMOP Extension (OHDSI)" - }, - "count" : 136 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 117406 - }, { - "enumVal" : { - "value" : { - "stringVal" : "UB04 Pri Typ of Adm" - }, - "display" : "UB04 Claim Inpatient Admission Type Code (CMS)" - }, - "count" : 6 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Observation" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "PPI" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "Survey" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c ) AS textsearch JOIN `all-of-us-ehr-dev.SR2022Q4R6.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Observation' AND c.standard_concept = 'S' AND c.vocabulary_id != 'PPI' AND c.concept_class_id != 'Survey' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_observation" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_observation_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_observation_occurrence.json deleted file mode 100644 index 882b93e01..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_observation_occurrence.json +++ /dev/null @@ -1,493 +0,0 @@ -{ - "name" : "t_observation_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 4118133 - }, - "display" : "IU/L" - }, - "count" : 5 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 35289501 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4121007 - }, - "display" : "Seconds" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8799 - }, - "display" : "copies per milliliter" - }, - "count" : 231 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8512 - }, - "display" : "day" - }, - "count" : 2028 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9484 - }, - "display" : "degree" - }, - "count" : 55 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8653 - }, - "display" : "degree Celsius" - }, - "count" : 53 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8529 - }, - "display" : "index" - }, - "count" : 88 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8519 - }, - "display" : "liter" - }, - "count" : 15 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9546 - }, - "display" : "meter" - }, - "count" : 66 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4121396 - }, - "display" : "mg/dL" - }, - "count" : 26047 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8720 - }, - "display" : "microgram per gram" - }, - "count" : 23 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8587 - }, - "display" : "milliliter" - }, - "count" : 87 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8588 - }, - "display" : "millimeter" - }, - "count" : 55 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8876 - }, - "display" : "millimeter mercury column" - }, - "count" : 36 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8753 - }, - "display" : "millimole per liter" - }, - "count" : 22 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8931 - }, - "display" : "million per cubic millimeter" - }, - "count" : 957 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4118323 - }, - "display" : "mmHg" - }, - "count" : 63 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4122417 - }, - "display" : "ng/dL" - }, - "count" : 7 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9372 - }, - "display" : "ounce (apothecary)" - }, - "count" : 25481 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8647 - }, - "display" : "per microliter" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8554 - }, - "display" : "percent" - }, - "count" : 360 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4120725 - }, - "display" : "pg/mL" - }, - "count" : 1235 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8729 - }, - "display" : "picomole per liter" - }, - "count" : 3 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8555 - }, - "display" : "second" - }, - "count" : 7 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8525 - }, - "display" : "titer" - }, - "count" : 534 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4121397 - }, - "display" : "ug/dL" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8510 - }, - "display" : "unit" - }, - "count" : 908557 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8763 - }, - "display" : "unit per milliliter" - }, - "count" : 164 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9234 - }, - "display" : "volume percent" - }, - "count" : 7 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9448 - }, - "display" : "year" - }, - "count" : 129781 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -2.0, - "maxVal" : 2.000023487E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "observation", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_as_string", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020475.0, - "maxVal" : 1.5996262E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201234E7, - "maxVal" : 2.0435758E7 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "observation" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "observation_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "observation_source_concept_id", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "observation_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "observation_id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "observation_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_observation_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_observation", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_person.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_person.json deleted file mode 100644 index e6e651472..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_person.json +++ /dev/null @@ -1,382 +0,0 @@ -{ - "name" : "t_person", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "gender", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 45878463 - }, - "display" : "Female" - }, - "count" : 142307 - }, { - "enumVal" : { - "value" : { - "int64Val" : 45880669 - }, - "display" : "Male" - }, - "count" : 87099 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2000000002 - }, - "display" : "Not man only, not woman only, prefer not to answer, or skipped" - }, - "count" : 5119 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "race", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 2000000001 - }, - "display" : "Another single population" - }, - "count" : 5443 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8515 - }, - "display" : "Asian" - }, - "count" : 7476 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8516 - }, - "display" : "Black or African American" - }, - "count" : 46967 - }, { - "enumVal" : { - "value" : { - "int64Val" : 1177221 - }, - "display" : "I prefer not to answer" - }, - "count" : 1614 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2000000008 - }, - "display" : "More than one population" - }, - "count" : 10727 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 37524 - }, { - "enumVal" : { - "value" : { - "int64Val" : 45882607 - }, - "display" : "None of these" - }, - "count" : 2465 - }, { - "enumVal" : { - "value" : { - "int64Val" : 903096 - }, - "display" : "PMI: Skip" - }, - "count" : 1584 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8527 - }, - "display" : "White" - }, - "count" : 120725 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ethnicity", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 38003563 - }, - "display" : "Hispanic or Latino" - }, - "count" : 44673 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38003564 - }, - "display" : "Not Hispanic or Latino" - }, - "count" : 184189 - }, { - "enumVal" : { - "value" : { - "int64Val" : 903079 - }, - "display" : "PMI: Prefer Not To Answer" - }, - "count" : 1614 - }, { - "enumVal" : { - "value" : { - "int64Val" : 903096 - }, - "display" : "PMI: Skip" - }, - "count" : 1584 - }, { - "enumVal" : { - "value" : { - "int64Val" : 1586148 - }, - "display" : "What Race Ethnicity: Race Ethnicity None Of These" - }, - "count" : 2465 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "sex_at_birth", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 45878463 - }, - "display" : "Female" - }, - "count" : 143479 - }, { - "enumVal" : { - "value" : { - "int64Val" : 45880669 - }, - "display" : "Male" - }, - "count" : 87821 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 257 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2000000009 - }, - "display" : "Not male, not female, prefer not to answer, or skipped" - }, - "count" : 2968 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "age", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 22.0, - "maxVal" : 93.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "year_of_birth", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 1930.0, - "maxVal" : 2001.0 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "person" - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "gender_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "race_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "ethnicity_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "sex_at_birth" : { - "value" : { - "column" : "sex_at_birth_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "sex_at_birth_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "age" : { - "value" : { - "column" : "year_of_birth", - "sqlFunctionWrapper" : "EXTRACT(YEAR FROM CURRENT_DATE()) - ${fieldSql}", - "runtimeCalculated" : true - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_person" - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_gender", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_race", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ethnicity", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "sex_at_birth" : { - "value" : { - "column" : "sex_at_birth", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_sex_at_birth", - "runtimeCalculated" : false - } - }, - "age" : { - "value" : { - "column" : "age", - "sqlFunctionWrapper" : "EXTRACT(YEAR FROM CURRENT_DATE()) - ${fieldSql}", - "runtimeCalculated" : true - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_procedure.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_procedure.json deleted file mode 100644 index 156c6c947..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_procedure.json +++ /dev/null @@ -1,390 +0,0 @@ -{ - "name" : "t_procedure", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 266323 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 5756 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CIEL" - }, - "display" : "Columbia International eHealth Laboratory (Columbia University)" - }, - "count" : 648 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "Current Procedural Terminology version 4 (AMA)" - }, - "count" : 13409 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NAACCR" - }, - "display" : "Data Standards & Data Dictionary Volume II (NAACCR)" - }, - "count" : 710 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "Healthcare Common Procedure Coding System (CMS)" - }, - "count" : 1289 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HemOnc" - }, - "display" : "HemOnc" - }, - "count" : 99 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10PCS" - }, - "display" : "ICD-10 Procedure Coding System (CMS)" - }, - "count" : 194874 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS)" - }, - "count" : 177 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9Proc" - }, - "display" : "International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 3 (NCHS)" - }, - "count" : 4657 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "International Classification of Diseases, Tenth Revision, Clinical Modification (NCHS)" - }, - "count" : 7 - }, { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "Logical Observation Identifiers Names and Codes (Regenstrief Institute)" - }, - "count" : 9280 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Nebraska Lexicon" - }, - "display" : "Nebraska Lexicon" - }, - "count" : 72683 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OMOP Extension" - }, - "display" : "OMOP Extension (OHDSI)" - }, - "count" : 2 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 86910 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Procedure" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c ) AS textsearch JOIN `all-of-us-ehr-dev.SR2022Q4R6.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Procedure' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `all-of-us-ehr-dev.SR2022Q4R6.concept_relationship` cr JOIN `all-of-us-ehr-dev.SR2022Q4R6.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `all-of-us-ehr-dev.SR2022Q4R6.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Procedure' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED' " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 4322976 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_procedure" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "t_procedure_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "t_procedure_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "t_procedure" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_procedure_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_procedure_occurrence.json deleted file mode 100644 index e2dc63ee7..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_procedure_occurrence.json +++ /dev/null @@ -1,168 +0,0 @@ -{ - "name" : "t_procedure_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 2.000023474E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020476.0, - "maxVal" : 1.5996259E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "procedure", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201235E7, - "maxVal" : 2.0435757E7 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "procedure_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "procedure_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "procedure_source_concept_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "procedure_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "procedure_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_procedure_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_procedure", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_visit.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_visit.json deleted file mode 100644 index 39f561731..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_visit.json +++ /dev/null @@ -1,105 +0,0 @@ -{ - "name" : "t_visit", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Visit" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `all-of-us-ehr-dev.SR2022Q4R6.concept` c ) AS textsearch JOIN `all-of-us-ehr-dev.SR2022Q4R6.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Visit' AND c.standard_concept = 'S' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_visit" - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_visit_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_visit_occurrence.json deleted file mode 100644 index ccf7d7ecd..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entity/t_visit_occurrence.json +++ /dev/null @@ -1,367 +0,0 @@ -{ - "name" : "t_visit_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 5.542608719E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 21039000 - }, - "display" : "10 ML Morphine 0.2 MG/ML Prefilled Syringe Box of 10" - }, - "count" : 21 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21050000 - }, - "display" : "2000 ML benzyl benzoate 250 MG/ML Topical Solution" - }, - "count" : 60 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581478 - }, - "display" : "Ambulance Visit" - }, - "count" : 1746 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38004207 - }, - "display" : "Ambulatory Clinic / Center" - }, - "count" : 80437 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581479 - }, - "display" : "Ambulatory Rehabilitation Visit" - }, - "count" : 179 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21056626 - }, - "display" : "Amiodarone 50 MG/ML Oral Suspension" - }, - "count" : 10 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21090200 - }, - "display" : "Cholecalciferol 50000 UNT Oral Capsule [Aciferol D3] Box of 10 by Rhodes" - }, - "count" : 2 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21090300 - }, - "display" : "Chondroitin Sulfates 400 MG / Glucosamine 500 MG Oral Tablet [Joint-Flex] Box of 60" - }, - "count" : 32 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21036000 - }, - "display" : "Daptomycin 500 MG Injection Box of 1" - }, - "count" : 100 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21090500 - }, - "display" : "Diphenhydramine 25 MG Oral Tablet by Ennogen" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 439748 - }, { - "enumVal" : { - "value" : { - "int64Val" : 262 - }, - "display" : "Emergency Room and Inpatient Visit" - }, - "count" : 25323 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21090400 - }, - "display" : "Ergocalciferol 300000 UNT/ML Prefilled Syringe Box of 10" - }, - "count" : 75 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581476 - }, - "display" : "Home Visit" - }, - "count" : 40500 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 568911 - }, { - "enumVal" : { - "value" : { - "int64Val" : 32036 - }, - "display" : "Laboratory Visit" - }, - "count" : 1850 - }, { - "enumVal" : { - "value" : { - "int64Val" : 12 - }, - "display" : "Modifier" - }, - "count" : 30318 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1340218 - }, { - "enumVal" : { - "value" : { - "int64Val" : 42898160 - }, - "display" : "Non-hospital institution Visit" - }, - "count" : 22 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581477 - }, - "display" : "Office Visit" - }, - "count" : 629739 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814711 - }, - "display" : "Other ambulatory visit" - }, - "count" : 4720 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 9929594 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581458 - }, - "display" : "Pharmacy visit" - }, - "count" : 25279 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21033000 - }, - "display" : "Risperidone 0.5 MG Oral Tablet by Consilient" - }, - "count" : 17 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44818518 - }, - "display" : "Visit derived from EHR record" - }, - "count" : 856887 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201234E7, - "maxVal" : 2.0435758E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "visit_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "visit_end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "visit_source_concept_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "visit_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "visit_start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "t_visit_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "visit" : { - "value" : { - "column" : "visit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_brand_ingredient.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_brand_ingredient.json deleted file mode 100644 index e9161b6bb..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_brand_ingredient.json +++ /dev/null @@ -1,101 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "t_brand_ingredient", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "rawSql" : "/* 1. User searches for Brand Tylenol 2. User expands Tylenol to see which ingredients are in Tylenol 3. Ingredient Acetaminophen is shown Acetaminophen has over 300 descendants (eg \"acetaminophen 100 MG/ML Oral Suspension\"). Acetaminophen's concept_class_id is Ingredient; descendants' concept_class_ids are Clinical Drug Comp, Quant Clinical Drug, etc. Most descendants have a relationship with Brand Tylenol in concept_relationship. However, we only want to show Acetaminophen in step 3. So only keep relationships with concept_class_id=Ingredient. */ SELECT cr.* FROM `all-of-us-ehr-dev.SR2022Q4R6.concept_relationship` cr, `all-of-us-ehr-dev.SR2022Q4R6.concept` c2 WHERE cr.concept_id_2 = c2.concept_id AND c2.concept_class_id = 'Ingredient' " - }, - "idPairsIdA" : { - "column" : "concept_id_1", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "concept_id_2", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_t_brand_t_ingredient" - }, - "idPairsIdA" : { - "column" : "id_t_brand", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_brand" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "t_ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_brand_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_brand_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "t_ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_brand", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_brand", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "t_brand", - "itemsEntity" : "t_ingredient" -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_condition_person_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_condition_person_occurrence.json deleted file mode 100644 index b942859a6..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_condition_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "t_condition_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_t_condition_occurrence_t_condition" - }, - "idPairsIdA" : { - "column" : "id_t_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_condition", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_condition", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "t_condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_condition_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_condition_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "t_condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_condition_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_condition_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_condition", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "t_condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "t_condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_condition", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_condition_occurrence_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_condition_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "t_condition", - "occurrenceEntity" : "t_condition_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_device_person_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_device_person_occurrence.json deleted file mode 100644 index 3a6ad63d9..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_device_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "t_device_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_t_device_occurrence_t_device" - }, - "idPairsIdA" : { - "column" : "id_t_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_device", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_device", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_device_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_device_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_device", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_device", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_device_occurrence_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_device_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "t_device", - "occurrenceEntity" : "t_device_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_ingredient_person_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_ingredient_person_occurrence.json deleted file mode 100644 index 39d7e4aab..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_ingredient_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "t_ingredient_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_t_ingredient_occurrence_t_ingredient" - }, - "idPairsIdA" : { - "column" : "id_t_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "t_ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_ingredient_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_ingredient_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "t_ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_ingredient_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_ingredient", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "t_ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "t_ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_ingredient", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_ingredient_occurrence_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "t_ingredient", - "occurrenceEntity" : "t_ingredient_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_measurement_person_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_measurement_person_occurrence.json deleted file mode 100644 index 3533f504d..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_measurement_person_occurrence.json +++ /dev/null @@ -1,287 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "t_measurement_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_t_measurement_occurrence_t_measurement" - }, - "idPairsIdA" : { - "column" : "id_t_measurement_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_measurement", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_measurement_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_measurement", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_measurement", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "t_measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_measurement_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_measurement_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "t_measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_measurement_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_measurement_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_measurement_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_measurement", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "t_measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "t_measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_measurement", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_measurement", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_measurement_occurrence_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_measurement_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_measurement_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_measurement_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_measurement_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { - "modifiers" : { - "tablePointer" : { - "table" : "t_measurement_person_occurrence_modifiers" - }, - "fieldPointers" : { - "min" : { - "column" : "min", - "runtimeCalculated" : false - }, - "enum_count" : { - "column" : "enum_count", - "runtimeCalculated" : false - }, - "max" : { - "column" : "max", - "runtimeCalculated" : false - }, - "enum_display" : { - "column" : "enum_display", - "runtimeCalculated" : false - }, - "enum_value" : { - "column" : "enum_value", - "runtimeCalculated" : false - }, - "attribute_name" : { - "column" : "attribute_name", - "runtimeCalculated" : false - }, - "entity_id" : { - "column" : "entity_id", - "runtimeCalculated" : false - } - } - } - } - }, - "criteriaEntity" : "t_measurement", - "occurrenceEntity" : "t_measurement_occurrence", - "modifierAttributes" : [ "value_numeric", "value_enum" ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_observation_person_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_observation_person_occurrence.json deleted file mode 100644 index 13c5ccc71..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_observation_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "t_observation_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_t_observation_occurrence_t_observation" - }, - "idPairsIdA" : { - "column" : "id_t_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_observation", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_observation", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_observation_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_observation_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_observation", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_observation", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_observation_occurrence_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_observation_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "t_observation", - "occurrenceEntity" : "t_observation_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_procedure_person_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_procedure_person_occurrence.json deleted file mode 100644 index a56cf02b4..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_procedure_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "t_procedure_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_t_procedure_occurrence_t_procedure" - }, - "idPairsIdA" : { - "column" : "id_t_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_procedure", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_procedure", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "t_procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_procedure_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_procedure_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "t_procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_procedure_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_procedure", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "t_procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "t_procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_procedure", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_procedure_occurrence_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "t_procedure", - "occurrenceEntity" : "t_procedure_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_visit_person_occurrence.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_visit_person_occurrence.json deleted file mode 100644 index c3ed53b03..000000000 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/entitygroup/t_visit_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "t_visit_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_t_visit_occurrence_t_visit" - }, - "idPairsIdA" : { - "column" : "id_t_visit_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_visit", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_visit_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_visit", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_visit", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_visit" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_visit_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_visit_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_visit_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_visit", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_visit" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_visit", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_visit", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_t_visit_occurrence_t_person" - }, - "idPairsIdA" : { - "column" : "id_t_visit_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_t_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_visit_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "t_person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_t_visit_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_t_visit_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "t_visit", - "occurrenceEntity" : "t_visit_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_brand_all.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_brand_all.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_brand_all.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_brand_all.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_brand_ingredients.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_brand_ingredients.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_brand_ingredients.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_brand_ingredients.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_brand_textSearch.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_brand_textSearch.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_brand_textSearch.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_brand_textSearch.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_condition_occurrence_all.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_condition_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_condition_occurrence_all.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_condition_occurrence_all.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_condition_parentChild.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_condition_parentChild.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_condition_parentChild.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_condition_parentChild.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_condition_textSearch.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_condition_textSearch.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_condition_textSearch.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_condition_textSearch.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_device_occurrence_all.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_device_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_device_occurrence_all.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_device_occurrence_all.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_device_textSearch.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_device_textSearch.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_device_textSearch.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_device_textSearch.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_ingredient_all.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_ingredient_all.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_ingredient_all.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_ingredient_all.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_ingredient_occurrence_all.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_ingredient_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_ingredient_occurrence_all.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_ingredient_occurrence_all.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_ingredient_parentChild.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_ingredient_parentChild.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_ingredient_parentChild.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_ingredient_parentChild.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_ingredient_textSearch.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_ingredient_textSearch.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_ingredient_textSearch.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_ingredient_textSearch.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_measurement_occurrence_all.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_measurement_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_measurement_occurrence_all.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_measurement_occurrence_all.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_measurement_parentChild.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_measurement_parentChild.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_measurement_parentChild.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_measurement_parentChild.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_measurement_textSearch.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_measurement_textSearch.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_measurement_textSearch.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_measurement_textSearch.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_observation_occurrence_all.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_observation_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_observation_occurrence_all.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_observation_occurrence_all.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_observation_textSearch.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_observation_textSearch.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_observation_textSearch.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_observation_textSearch.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_person.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_person.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_person.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_person.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_procedure_occurrence_all.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_procedure_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_procedure_occurrence_all.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_procedure_occurrence_all.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_procedure_parentChild.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_procedure_parentChild.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_procedure_parentChild.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_procedure_parentChild.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_procedure_textSearch.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_procedure_textSearch.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_procedure_textSearch.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_procedure_textSearch.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_visit_occurrence_all.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_visit_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_visit_occurrence_all.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_visit_occurrence_all.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_visit_textSearch.sql b/service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_visit_textSearch.sql similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/sql/t_visit_textSearch.sql rename to service/src/main/resources/config/aou/test/SR2022Q4R6/sql/t_visit_textSearch.sql diff --git a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/ui/top_level.json b/service/src/main/resources/config/aou/test/SR2022Q4R6/ui/top_level.json similarity index 100% rename from service/src/main/resources/config/aou/test/SR2022Q4R6/original/ui/top_level.json rename to service/src/main/resources/config/aou/test/SR2022Q4R6/ui/top_level.json diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/aou_synthetic.json b/service/src/main/resources/config/broad/aou_synthetic/aou_synthetic.json similarity index 95% rename from service/src/main/resources/config/broad/aou_synthetic/original/aou_synthetic.json rename to service/src/main/resources/config/broad/aou_synthetic/aou_synthetic.json index 2e928432e..47caec116 100644 --- a/service/src/main/resources/config/broad/aou_synthetic/original/aou_synthetic.json +++ b/service/src/main/resources/config/broad/aou_synthetic/aou_synthetic.json @@ -8,7 +8,7 @@ { "type": "BQ_DATASET", "name": "index_dataset", "projectId": "broad-tanagra-dev", - "datasetId": "aousynthetic_index_031323" } ], + "datasetId": "aousynthetic_index_072623" } ], "entities": [ "brand.json", "condition.json", diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entity/brand.json b/service/src/main/resources/config/broad/aou_synthetic/entity/brand.json similarity index 86% rename from service/src/main/resources/config/broad/aou_synthetic/original/entity/brand.json rename to service/src/main/resources/config/broad/aou_synthetic/entity/brand.json index 8169d66fe..f58b7f515 100644 --- a/service/src/main/resources/config/broad/aou_synthetic/original/entity/brand.json +++ b/service/src/main/resources/config/broad/aou_synthetic/entity/brand.json @@ -2,10 +2,10 @@ "name": "brand", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entity/condition.json b/service/src/main/resources/config/broad/aou_synthetic/entity/condition.json similarity index 82% rename from service/src/main/resources/config/broad/aou_synthetic/original/entity/condition.json rename to service/src/main/resources/config/broad/aou_synthetic/entity/condition.json index be324f139..9e1c403ab 100644 --- a/service/src/main/resources/config/broad/aou_synthetic/original/entity/condition.json +++ b/service/src/main/resources/config/broad/aou_synthetic/entity/condition.json @@ -2,11 +2,11 @@ "name": "condition", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entity/condition_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/entity/condition_occurrence.json similarity index 55% rename from service/src/main/resources/config/broad/aou_synthetic/original/entity/condition_occurrence.json rename to service/src/main/resources/config/broad/aou_synthetic/entity/condition_occurrence.json index f5146304c..b2dde6b30 100644 --- a/service/src/main/resources/config/broad/aou_synthetic/original/entity/condition_occurrence.json +++ b/service/src/main/resources/config/broad/aou_synthetic/entity/condition_occurrence.json @@ -2,15 +2,15 @@ "name": "condition_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "condition" }, - { "type": "SIMPLE", "name": "start_date" }, - { "type": "SIMPLE", "name": "end_date" }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "condition", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entity/device.json b/service/src/main/resources/config/broad/aou_synthetic/entity/device.json similarity index 80% rename from service/src/main/resources/config/broad/aou_synthetic/original/entity/device.json rename to service/src/main/resources/config/broad/aou_synthetic/entity/device.json index 2806fa53a..ffa321805 100644 --- a/service/src/main/resources/config/broad/aou_synthetic/original/entity/device.json +++ b/service/src/main/resources/config/broad/aou_synthetic/entity/device.json @@ -2,11 +2,11 @@ "name": "device", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entity/device_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/entity/device_occurrence.json similarity index 58% rename from service/src/main/resources/config/verily/aou_synthetic/original/entity/device_occurrence.json rename to service/src/main/resources/config/broad/aou_synthetic/entity/device_occurrence.json index 8992ed405..03c74a8c3 100644 --- a/service/src/main/resources/config/verily/aou_synthetic/original/entity/device_occurrence.json +++ b/service/src/main/resources/config/broad/aou_synthetic/entity/device_occurrence.json @@ -2,14 +2,14 @@ "name": "device_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "device" }, - { "type": "SIMPLE", "name": "start_date" }, - { "type": "SIMPLE", "name": "end_date" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "device", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entity/ingredient.json b/service/src/main/resources/config/broad/aou_synthetic/entity/ingredient.json similarity index 84% rename from service/src/main/resources/config/broad/aou_synthetic/original/entity/ingredient.json rename to service/src/main/resources/config/broad/aou_synthetic/entity/ingredient.json index a557d47b7..b614560a0 100644 --- a/service/src/main/resources/config/broad/aou_synthetic/original/entity/ingredient.json +++ b/service/src/main/resources/config/broad/aou_synthetic/entity/ingredient.json @@ -2,11 +2,11 @@ "name": "ingredient", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entity/ingredient_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/entity/ingredient_occurrence.json similarity index 50% rename from service/src/main/resources/config/verily/aou_synthetic/original/entity/ingredient_occurrence.json rename to service/src/main/resources/config/broad/aou_synthetic/entity/ingredient_occurrence.json index 9d4e31f4b..bf5d0949a 100644 --- a/service/src/main/resources/config/verily/aou_synthetic/original/entity/ingredient_occurrence.json +++ b/service/src/main/resources/config/broad/aou_synthetic/entity/ingredient_occurrence.json @@ -2,17 +2,17 @@ "name": "ingredient_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "ingredient" }, - { "type": "SIMPLE", "name": "start_date" }, - { "type": "SIMPLE", "name": "end_date" }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "refills" }, - { "type": "SIMPLE", "name": "days_supply" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "ingredient", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "refills", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "days_supply", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entity/measurement.json b/service/src/main/resources/config/broad/aou_synthetic/entity/measurement.json similarity index 92% rename from service/src/main/resources/config/broad/aou_synthetic/original/entity/measurement.json rename to service/src/main/resources/config/broad/aou_synthetic/entity/measurement.json index 43ca17fca..67079d9fb 100644 --- a/service/src/main/resources/config/broad/aou_synthetic/original/entity/measurement.json +++ b/service/src/main/resources/config/broad/aou_synthetic/entity/measurement.json @@ -2,11 +2,11 @@ "name": "measurement", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entity/measurement_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/entity/measurement_occurrence.json similarity index 63% rename from service/src/main/resources/config/broad/aou_synthetic/original/entity/measurement_occurrence.json rename to service/src/main/resources/config/broad/aou_synthetic/entity/measurement_occurrence.json index 8d36bfb0c..0bd4d569d 100644 --- a/service/src/main/resources/config/broad/aou_synthetic/original/entity/measurement_occurrence.json +++ b/service/src/main/resources/config/broad/aou_synthetic/entity/measurement_occurrence.json @@ -2,16 +2,16 @@ "name": "measurement_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "measurement" }, - { "type": "SIMPLE", "name": "date" }, - { "type": "SIMPLE", "name": "value_numeric" }, - { "type": "KEY_AND_DISPLAY", "name": "value_enum" }, - { "type": "KEY_AND_DISPLAY", "name": "unit" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "measurement", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "value_numeric", "dataType": "DOUBLE" }, + { "type": "KEY_AND_DISPLAY", "name": "value_enum", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entity/observation.json b/service/src/main/resources/config/broad/aou_synthetic/entity/observation.json similarity index 83% rename from service/src/main/resources/config/verily/aou_synthetic/original/entity/observation.json rename to service/src/main/resources/config/broad/aou_synthetic/entity/observation.json index 4523ab033..372c3aed7 100644 --- a/service/src/main/resources/config/verily/aou_synthetic/original/entity/observation.json +++ b/service/src/main/resources/config/broad/aou_synthetic/entity/observation.json @@ -2,11 +2,11 @@ "name": "observation", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entity/observation_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/entity/observation_occurrence.json similarity index 62% rename from service/src/main/resources/config/verily/aou_synthetic/original/entity/observation_occurrence.json rename to service/src/main/resources/config/broad/aou_synthetic/entity/observation_occurrence.json index 0143edb84..550d9e61b 100644 --- a/service/src/main/resources/config/verily/aou_synthetic/original/entity/observation_occurrence.json +++ b/service/src/main/resources/config/broad/aou_synthetic/entity/observation_occurrence.json @@ -2,16 +2,16 @@ "name": "observation_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "observation" }, - { "type": "SIMPLE", "name": "date" }, - { "type": "SIMPLE", "name": "value_as_string" }, - { "type": "KEY_AND_DISPLAY", "name": "value" }, - { "type": "KEY_AND_DISPLAY", "name": "unit" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "observation", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "value_as_string", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "value", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entity/person.json b/service/src/main/resources/config/broad/aou_synthetic/entity/person.json similarity index 75% rename from service/src/main/resources/config/broad/aou_synthetic/original/entity/person.json rename to service/src/main/resources/config/broad/aou_synthetic/entity/person.json index aa7be3a45..3b457706d 100644 --- a/service/src/main/resources/config/broad/aou_synthetic/original/entity/person.json +++ b/service/src/main/resources/config/broad/aou_synthetic/entity/person.json @@ -2,12 +2,12 @@ "name": "person", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "year_of_birth" }, - { "type": "KEY_AND_DISPLAY", "name": "gender" }, - { "type": "KEY_AND_DISPLAY", "name": "race" }, - { "type": "KEY_AND_DISPLAY", "name": "ethnicity" }, - { "type": "KEY_AND_DISPLAY", "name": "sex_at_birth" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "year_of_birth", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "gender", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "race", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "ethnicity", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "sex_at_birth", "dataType": "INT64" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entity/procedure.json b/service/src/main/resources/config/broad/aou_synthetic/entity/procedure.json similarity index 82% rename from service/src/main/resources/config/verily/aou_synthetic/original/entity/procedure.json rename to service/src/main/resources/config/broad/aou_synthetic/entity/procedure.json index 6b60bb777..65d17c510 100644 --- a/service/src/main/resources/config/verily/aou_synthetic/original/entity/procedure.json +++ b/service/src/main/resources/config/broad/aou_synthetic/entity/procedure.json @@ -2,11 +2,11 @@ "name": "procedure", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entity/procedure_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/entity/procedure_occurrence.json similarity index 59% rename from service/src/main/resources/config/verily/aou_synthetic/original/entity/procedure_occurrence.json rename to service/src/main/resources/config/broad/aou_synthetic/entity/procedure_occurrence.json index 365672ade..c896a4a8a 100644 --- a/service/src/main/resources/config/verily/aou_synthetic/original/entity/procedure_occurrence.json +++ b/service/src/main/resources/config/broad/aou_synthetic/entity/procedure_occurrence.json @@ -2,13 +2,13 @@ "name": "procedure_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "procedure" }, - { "type": "SIMPLE", "name": "date" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "procedure", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entity/visit.json b/service/src/main/resources/config/broad/aou_synthetic/entity/visit.json similarity index 87% rename from service/src/main/resources/config/verily/aou_synthetic/original/entity/visit.json rename to service/src/main/resources/config/broad/aou_synthetic/entity/visit.json index 6cc2deb8e..410cf0be6 100644 --- a/service/src/main/resources/config/verily/aou_synthetic/original/entity/visit.json +++ b/service/src/main/resources/config/broad/aou_synthetic/entity/visit.json @@ -2,8 +2,8 @@ "name": "visit", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entity/visit_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/entity/visit_occurrence.json similarity index 61% rename from service/src/main/resources/config/verily/aou_synthetic/original/entity/visit_occurrence.json rename to service/src/main/resources/config/broad/aou_synthetic/entity/visit_occurrence.json index 6fd2b19a4..7616b9122 100644 --- a/service/src/main/resources/config/verily/aou_synthetic/original/entity/visit_occurrence.json +++ b/service/src/main/resources/config/broad/aou_synthetic/entity/visit_occurrence.json @@ -2,13 +2,13 @@ "name": "visit_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "visit" }, - { "type": "SIMPLE", "name": "start_date" }, - { "type": "SIMPLE", "name": "end_date" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE" }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entitygroup/brand_ingredient.json b/service/src/main/resources/config/broad/aou_synthetic/entitygroup/brand_ingredient.json similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/entitygroup/brand_ingredient.json rename to service/src/main/resources/config/broad/aou_synthetic/entitygroup/brand_ingredient.json diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entitygroup/condition_person_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/entitygroup/condition_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/entitygroup/condition_person_occurrence.json rename to service/src/main/resources/config/broad/aou_synthetic/entitygroup/condition_person_occurrence.json diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entitygroup/device_person_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/entitygroup/device_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/entitygroup/device_person_occurrence.json rename to service/src/main/resources/config/broad/aou_synthetic/entitygroup/device_person_occurrence.json diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entitygroup/ingredient_person_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/entitygroup/ingredient_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/entitygroup/ingredient_person_occurrence.json rename to service/src/main/resources/config/broad/aou_synthetic/entitygroup/ingredient_person_occurrence.json diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entitygroup/measurement_person_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/entitygroup/measurement_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/entitygroup/measurement_person_occurrence.json rename to service/src/main/resources/config/broad/aou_synthetic/entitygroup/measurement_person_occurrence.json diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entitygroup/observation_person_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/entitygroup/observation_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/entitygroup/observation_person_occurrence.json rename to service/src/main/resources/config/broad/aou_synthetic/entitygroup/observation_person_occurrence.json diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entitygroup/procedure_person_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/entitygroup/procedure_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/entitygroup/procedure_person_occurrence.json rename to service/src/main/resources/config/broad/aou_synthetic/entitygroup/procedure_person_occurrence.json diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entitygroup/visit_person_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/entitygroup/visit_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/entitygroup/visit_person_occurrence.json rename to service/src/main/resources/config/broad/aou_synthetic/entitygroup/visit_person_occurrence.json diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/aou_synthetic.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/aou_synthetic.json deleted file mode 100644 index dbae1aa7c..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/aou_synthetic.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "name" : "aou_synthetic", - "dataPointers" : [ { - "type" : "BQ_DATASET", - "name" : "index_dataset", - "projectId" : "broad-tanagra-dev", - "datasetId" : "aousynthetic_index_031323", - "queryProjectId" : "broad-tanagra-dev", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : true - }, { - "type" : "BQ_DATASET", - "name" : "omop_dataset", - "projectId" : "broad-tanagra-dev", - "datasetId" : "aou_synthetic_SR2019q4r4", - "queryProjectId" : "broad-tanagra-dev", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : true - } ], - "entities" : [ "measurement_occurrence.json", "condition_occurrence.json", "ingredient.json", "device_occurrence.json", "observation.json", "procedure.json", "measurement.json", "ingredient_occurrence.json", "condition.json", "person.json", "visit_occurrence.json", "observation_occurrence.json", "procedure_occurrence.json", "visit.json", "brand.json", "device.json" ], - "entityGroups" : [ "device_person_occurrence.json", "visit_person_occurrence.json", "condition_person_occurrence.json", "ingredient_person_occurrence.json", "observation_person_occurrence.json", "brand_ingredient.json", "measurement_person_occurrence.json", "procedure_person_occurrence.json" ], - "primaryEntity" : "person", - "uiConfig" : "{ \"dataConfig\": { \"primaryEntity\": { \"displayName\": \"Person\", \"entity\": \"person\", \"key\": \"id\" }, \"occurrences\": [ { \"id\": \"condition_occurrence\", \"displayName\": \"Condition Occurrences\", \"entity\": \"condition_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"condition\", \"attribute\": \"condition\", \"entity\": \"condition\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"procedure_occurrence\", \"displayName\": \"Procedure Occurrences\", \"entity\": \"procedure_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"procedure\", \"attribute\": \"procedure\", \"entity\": \"procedure\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"observation_occurrence\", \"displayName\": \"Observation Occurrence\", \"entity\": \"observation_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"observation\", \"attribute\": \"observation\", \"entity\": \"observation\", \"entityAttribute\": \"id\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"ingredient_occurrence\", \"displayName\": \"Drug Occurrence\", \"entity\": \"ingredient_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"ingredient\", \"attribute\": \"id\", \"entity\": \"ingredient\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" }, \"groupings\": [ { \"id\": \"brand\", \"entity\": \"brand\", \"defaultSort\": { \"attribute\": \"name\", \"direction\": \"ASC\" }, \"attributes\": [\"name\", \"id\", \"standard_concept\", \"concept_code\"] } ] } ] } ] }, \"criteriaConfigs\": [ { \"type\": \"classification\", \"id\": \"tanagra-conditions\", \"title\": \"Condition\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Condition\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"condition_occurrence\", \"classification\": \"condition\" }, { \"type\": \"classification\", \"id\": \"tanagra-procedures\", \"title\": \"Procedure\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Procedure\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"procedure_occurrence\", \"classification\": \"procedure\" }, { \"type\": \"classification\", \"id\": \"tanagra-observations\", \"title\": \"Observation\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"observation_occurrence\", \"classification\": \"observation\" }, { \"type\": \"classification\", \"id\": \"tanagra-drugs\", \"title\": \"Drug\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Drug\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"ingredient_occurrence\", \"classification\": \"ingredient\" }, { \"type\": \"attribute\", \"id\": \"tanagra-ethnicity\", \"title\": \"Ethnicity\", \"category\": \"Program data\", \"attribute\": \"ethnicity\" }, { \"type\": \"attribute\", \"id\": \"tanagra-gender\", \"title\": \"Gender identity\", \"category\": \"Program data\", \"attribute\": \"gender\" }, { \"type\": \"attribute\", \"id\": \"tanagra-race\", \"title\": \"Race\", \"category\": \"Program data\", \"attribute\": \"race\" }, { \"type\": \"attribute\", \"id\": \"tanagra-sex_at_birth\", \"title\": \"Sex assigned at birth\", \"category\": \"Program data\", \"attribute\": \"sex_at_birth\" }, { \"type\": \"attribute\", \"id\": \"tanagra-year_of_birth\", \"title\": \"Year of birth\", \"category\": \"Program data\", \"attribute\": \"year_of_birth\" } ], \"demographicChartConfigs\": { \"groupByAttributes\": [\"gender\", \"race\", \"year_of_birth\"], \"chartConfigs\": [ { \"title\": \"Gender identity\", \"primaryProperties\": [{ \"key\": \"gender\" }] }, { \"title\": \"Gender identity, Current age, Race\", \"primaryProperties\": [ { \"key\": \"gender\" }, { \"key\": \"age\", \"buckets\": [ { \"min\": 18, \"max\": 45, \"displayName\": \"18-44\" }, { \"min\": 45, \"max\": 65, \"displayName\": \"45-64\" }, { \"min\": 65, \"displayName\": \"65+\" } ] } ], \"stackedProperty\": { \"key\": \"race\" } } ] }, \"prepackagedConceptSets\": [ { \"id\": \"_demographics\", \"name\": \"Demographics\", \"occurrence\": \"\" }, { \"id\": \"_analgesics\", \"name\": \"Analgesics\", \"occurrence\": \"ingredient_occurrence\", \"filter\": { \"type\": \"CLASSIFICATION\", \"occurrenceId\": \"ingredient_occurrence\", \"classificationId\": \"ingredient\", \"keys\": [21604253] } } ], \"criteriaSearchConfig\": { \"criteriaTypeWidth\": 120, \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept Name\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up Count\" } ] }, \"cohortReviewConfig\": { \"participantsListColumns\": [ { \"key\": \"id\", \"width\": 100, \"title\": \"Id\" }, { \"key\": \"gender\", \"width\": 100, \"title\": \"Gender\" }, { \"key\": \"race\", \"width\": 100, \"title\": \"Race\" }, { \"key\": \"ethnicity\", \"width\": 100, \"title\": \"Ethnicity\" }, { \"key\": \"year_of_birth\", \"width\": 60, \"title\": \"Year of Birth\" } ], \"attributes\": [ { \"title\": \"Gender\", \"key\": \"gender\" }, { \"title\": \"Year of birth\", \"key\": \"year_of_birth\" }, { \"title\": \"Race\", \"key\": \"race\" }, { \"title\": \"Ethnicity\", \"key\": \"ethnicity\" } ], \"pages\": [ { \"type\": \"occurrenceTable\", \"id\": \"condition\", \"title\": \"Conditions\", \"plugin\": { \"occurrence\": \"condition_occurrence\", \"columns\": [ { \"key\": \"condition\", \"width\": \"100%\", \"title\": \"Condition name\", \"sortable\": true }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\", \"sortable\": true }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"procedure\", \"title\": \"Procedures\", \"plugin\": { \"occurrence\": \"procedure_occurrence\", \"columns\": [ { \"key\": \"procedure\", \"width\": \"100%\", \"title\": \"Procedure name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"observation\", \"title\": \"Observations\", \"plugin\": { \"occurrence\": \"observation_occurrence\", \"columns\": [ { \"key\": \"observation\", \"width\": \"100%\", \"title\": \"Observation name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\" , \"sortable\": true} ] } }, { \"type\": \"occurrenceTable\", \"id\": \"ingredient\", \"title\": \"Drugs\", \"plugin\": { \"occurrence\": \"ingredient_occurrence\", \"columns\": [ { \"key\": \"ingredient\", \"width\": \"100%\", \"title\": \"Drug name\", \"sortable\": true }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\", \"sortable\": true }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\", \"sortable\": true } ] } } ] } } ", - "metadata" : { } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/brand.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/brand.json deleted file mode 100644 index 80e50a277..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/brand.json +++ /dev/null @@ -1,190 +0,0 @@ -{ - "name" : "brand", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Drug" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Brand Name" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "invalid_reason", - "runtimeCalculated" : false - }, - "operator" : "IS", - "value" : { } - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "RxNorm" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "RxNorm Extension" - } - } ] - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT cs.concept_id AS id, cs.concept_synonym_name AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept_synonym` cs ) AS textsearch JOIN `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND c.concept_class_id = 'Brand Name' AND c.invalid_reason IS NULL AND c.vocabulary_id IN ('RxNorm', 'RxNorm Extension')" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "brand" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/condition.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/condition.json deleted file mode 100644 index 0554dfad5..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/condition.json +++ /dev/null @@ -1,334 +0,0 @@ -{ - "name" : "condition", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 172324 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "PPI" - }, - "display" : "AllOfUs_PPI (Columbia)" - }, - "count" : 74 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CIEL" - }, - "display" : "Columbia International eHealth Laboratory (Columbia University)" - }, - "count" : 38818 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "Healthcare Common Procedure Coding System (CMS)" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICDO3" - }, - "display" : "International Classification of Diseases for Oncology, Third Edition (WHO)" - }, - "count" : 61790 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS)" - }, - "count" : 15733 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "International Classification of Diseases, Tenth Revision, Clinical Modification (NCHS)" - }, - "count" : 90462 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 166684 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Condition" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT cs.concept_id AS id, cs.concept_synonym_name AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept_synonym` cs ) AS textsearch JOIN `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Condition' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept_relationship` cr JOIN `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Condition' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED'" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 441840 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "condition" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "condition_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "condition_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "condition" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/condition_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/condition_occurrence.json deleted file mode 100644 index 6c168de90..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/condition_occurrence.json +++ /dev/null @@ -1,212 +0,0 @@ -{ - "name" : "condition_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "condition", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 2.000023411E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020479.0, - "maxVal" : 1.5996259E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201235E7, - "maxVal" : 2.0435757E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "condition_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "condition_end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "condition_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "condition_source_concept_id", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "condition_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "condition_start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "condition_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_condition", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/device.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/device.json deleted file mode 100644 index c484d3045..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/device.json +++ /dev/null @@ -1,224 +0,0 @@ -{ - "name" : "device", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 214183 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "Current Procedural Terminology version 4 (AMA)" - }, - "count" : 24 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "Healthcare Common Procedure Coding System (CMS)" - }, - "count" : 4634 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NDC" - }, - "display" : "National Drug Code (FDA and manufacturers)" - }, - "count" : 10582 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 198943 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Device" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT cs.concept_id AS id, cs.concept_synonym_name AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept_synonym` cs ) AS textsearch JOIN `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Device' AND c.standard_concept = 'S'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "device" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/device_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/device_occurrence.json deleted file mode 100644 index 5b62b7ad0..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/device_occurrence.json +++ /dev/null @@ -1,185 +0,0 @@ -{ - "name" : "device_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 4.6274116E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020475.0, - "maxVal" : 1.5995732E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "device", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201235E7, - "maxVal" : 2.0435757E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "device_exposure" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "device_exposure_end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "device_source_concept_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "device_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "device_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "device_exposure_start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "device_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_device", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/ingredient.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/ingredient.json deleted file mode 100644 index f15e1b831..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/ingredient.json +++ /dev/null @@ -1,323 +0,0 @@ -{ - "name" : "ingredient", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 14566 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 6335 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm" - }, - "display" : "RxNorm (NLM)" - }, - "count" : 15575 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm Extension" - }, - "display" : "RxNorm Extension (OMOP)" - }, - "count" : 1978 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ATC" - }, - "display" : "WHO Anatomic Therapeutic Chemical Classification" - }, - "count" : 6335 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT c.concept_id AS id, c.concept_name AS name, c.vocabulary_id, c.standard_concept, c.concept_code FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c WHERE c.domain_id = 'Drug' AND ((c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.concept_class_id = 'Ingredient' AND c.standard_concept = 'S') OR (c.vocabulary_id = 'RxNorm' AND c.concept_class_id = 'Precise Ingredient') OR (c.vocabulary_id = 'ATC' AND c.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c.standard_concept = 'C'))" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT cs.concept_id AS id, cs.concept_synonym_name AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept_synonym` cs ) AS textsearch JOIN `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND ((c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.concept_class_id = 'Ingredient' AND c.standard_concept = 'S') OR (c.vocabulary_id = 'RxNorm' AND c.concept_class_id = 'Precise Ingredient') OR (c.vocabulary_id = 'ATC' AND c.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c.standard_concept = 'C'))" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept_relationship` cr JOIN `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id IN ('Has form', 'RxNorm - ATC', 'RxNorm - ATC name', 'Mapped from', 'Subsumes') AND c1.concept_id != c2.concept_id AND ((c1.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c1.concept_class_id = 'Ingredient' AND c1.standard_concept = 'S') OR (c1.vocabulary_id = 'RxNorm' AND c1.concept_class_id = 'Precise Ingredient') OR (c1.vocabulary_id = 'ATC' AND c1.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c1.standard_concept = 'C')) AND ((c2.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c2.concept_class_id = 'Ingredient' AND c2.standard_concept = 'S') OR (c2.vocabulary_id = 'RxNorm' AND c2.concept_class_id = 'Precise Ingredient') OR (c2.vocabulary_id = 'ATC' AND c2.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c2.standard_concept = 'C')) UNION ALL SELECT ca.ancestor_concept_id AS parent, ca.descendant_concept_id AS child, FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept_ancestor` ca JOIN `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c1 ON c1.concept_id = ca.ancestor_concept_id JOIN `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c2 ON c2.concept_id = ca.descendant_concept_id WHERE ca.min_levels_of_separation = 1 AND ca.max_levels_of_separation = 1 AND ((c1.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c1.concept_class_id = 'Ingredient' AND c1.standard_concept = 'S') OR (c1.vocabulary_id = 'RxNorm' AND c1.concept_class_id = 'Precise Ingredient') OR (c1.vocabulary_id = 'ATC' AND c1.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c1.standard_concept = 'C')) AND ((c2.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c2.concept_class_id = 'Ingredient' AND c2.standard_concept = 'S') OR (c2.vocabulary_id = 'RxNorm' AND c2.concept_class_id = 'Precise Ingredient') OR (c2.vocabulary_id = 'ATC' AND c2.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c2.standard_concept = 'C'))" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC 1st" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "C" - } - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 8 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "ingredient" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "ingredient_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "ingredient_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "ingredient" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 8 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/ingredient_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/ingredient_occurrence.json deleted file mode 100644 index 3b2f95e74..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/ingredient_occurrence.json +++ /dev/null @@ -1,256 +0,0 @@ -{ - "name" : "ingredient_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ingredient", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "refills", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -9.223372036854776E18, - "maxVal" : 10.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -9.223372036854776E18, - "maxVal" : 2.000007519E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020479.0, - "maxVal" : 1.5996253E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "days_supply", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -9.223372036854776E18, - "maxVal" : 180.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201235E7, - "maxVal" : 2.0435757E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "drug_exposure" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "drug_exposure_end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "drug_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "drug_source_concept_id", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "drug_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "drug_exposure_start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "ingredient_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "ingredient", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ingredient", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/measurement.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/measurement.json deleted file mode 100644 index 5aaacb7e3..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/measurement.json +++ /dev/null @@ -1,410 +0,0 @@ -{ - "name" : "measurement", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 67484 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 39415 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "Logical Observation Identifiers Names and Codes (Regenstrief Institute)" - }, - "count" : 183718 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 13963 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Measurement" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "SNOMED" - } - } ] - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC" - } - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC Hierarchy" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC Component" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Lab Test" - } - } ] - } ] - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT cs.concept_id AS id, cs.concept_synonym_name AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept_synonym` cs ) AS textsearch JOIN `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c ON c.concept_id = textsearch.id WHERE ((c.domain_id = 'Measurement' AND c.vocabulary_id = 'SNOMED') OR (c.vocabulary_id = 'LOINC' AND c.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test')))" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept_relationship` cr JOIN `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.vocabulary_id = c2.vocabulary_id AND ((c1.vocabulary_id = 'SNOMED' AND c1.domain_id = c2.domain_id AND c1.domain_id = 'Measurement') OR (c1.vocabulary_id = 'LOINC' AND c1.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test') AND c2.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test'))) " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Measurement" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "SNOMED" - } - } ] - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 36206173 - } - } ] - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 11 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "measurement" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "measurement_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "measurement_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "measurement" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 11 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/measurement_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/measurement_occurrence.json deleted file mode 100644 index 0c80b5716..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/measurement_occurrence.json +++ /dev/null @@ -1,241 +0,0 @@ -{ - "name" : "measurement_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -9.223372036854776E18, - "maxVal" : 3.040008559E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020475.0, - "maxVal" : 1.5996262E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_numeric", - "dataType" : "DOUBLE", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value_enum", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "measurement", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201234E7, - "maxVal" : 2.0435758E7 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "measurement" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "measurement_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "measurement_source_concept_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "measurement_id", - "runtimeCalculated" : false - } - }, - "value_numeric" : { - "value" : { - "column" : "value_as_number", - "runtimeCalculated" : false - } - }, - "value_enum" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "measurement" : { - "value" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "measurement_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "measurement_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "measurement_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value_numeric" : { - "value" : { - "column" : "value_numeric", - "runtimeCalculated" : false - } - }, - "value_enum" : { - "value" : { - "column" : "value_enum", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value_enum", - "runtimeCalculated" : false - } - }, - "measurement" : { - "value" : { - "column" : "measurement", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_measurement", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/observation.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/observation.json deleted file mode 100644 index 6f72b1ab9..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/observation.json +++ /dev/null @@ -1,300 +0,0 @@ -{ - "name" : "observation", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 142229 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "APC" - }, - "display" : "Ambulatory Payment Classification (CMS)" - }, - "count" : 715 - }, { - "enumVal" : { - "value" : { - "stringVal" : "AoU_General" - }, - "display" : "AoU_General" - }, - "count" : 11 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "Current Procedural Terminology version 4 (AMA)" - }, - "count" : 1083 - }, { - "enumVal" : { - "value" : { - "stringVal" : "DRG" - }, - "display" : "Diagnosis-related group (CMS)" - }, - "count" : 752 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "Healthcare Common Procedure Coding System (CMS)" - }, - "count" : 2667 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICDO3" - }, - "display" : "International Classification of Diseases for Oncology, Third Edition (WHO)" - }, - "count" : 398 - }, { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "Logical Observation Identifiers Names and Codes (Regenstrief Institute)" - }, - "count" : 6978 - }, { - "enumVal" : { - "value" : { - "stringVal" : "MDC" - }, - "display" : "Major Diagnostic Categories (CMS)" - }, - "count" : 26 - }, { - "enumVal" : { - "value" : { - "stringVal" : "PCORNet" - }, - "display" : "National Patient-Centered Clinical Research Network (PCORI)" - }, - "count" : 2 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NUCC" - }, - "display" : "National Uniform Claim Committee Health Care Provider Taxonomy Code Set (NUCC)" - }, - "count" : 4 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 128425 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Observation" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "PPI" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "Survey" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT cs.concept_id AS id, cs.concept_synonym_name AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept_synonym` cs ) AS textsearch JOIN `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Observation' AND c.standard_concept = 'S' AND c.vocabulary_id != 'PPI' AND c.concept_class_id != 'Survey'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "observation" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/observation_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/observation_occurrence.json deleted file mode 100644 index 5db43d181..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/observation_occurrence.json +++ /dev/null @@ -1,493 +0,0 @@ -{ - "name" : "observation_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 4118133 - }, - "display" : "IU/L" - }, - "count" : 5 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 35011492 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4121007 - }, - "display" : "Seconds" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8799 - }, - "display" : "copies per milliliter" - }, - "count" : 231 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8512 - }, - "display" : "day" - }, - "count" : 2028 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9484 - }, - "display" : "degree" - }, - "count" : 55 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8653 - }, - "display" : "degree Celsius" - }, - "count" : 53 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8529 - }, - "display" : "index" - }, - "count" : 88 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8519 - }, - "display" : "liter" - }, - "count" : 15 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9546 - }, - "display" : "meter" - }, - "count" : 66 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4121396 - }, - "display" : "mg/dL" - }, - "count" : 26047 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8720 - }, - "display" : "microgram per gram" - }, - "count" : 23 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8587 - }, - "display" : "milliliter" - }, - "count" : 87 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8588 - }, - "display" : "millimeter" - }, - "count" : 55 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8876 - }, - "display" : "millimeter mercury column" - }, - "count" : 36 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8753 - }, - "display" : "millimole per liter" - }, - "count" : 22 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8931 - }, - "display" : "million per cubic millimeter" - }, - "count" : 957 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4118323 - }, - "display" : "mmHg" - }, - "count" : 63 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4122417 - }, - "display" : "ng/dL" - }, - "count" : 7 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9372 - }, - "display" : "ounce (apothecary)" - }, - "count" : 25481 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8647 - }, - "display" : "per microliter" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8554 - }, - "display" : "percent" - }, - "count" : 360 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4120725 - }, - "display" : "pg/mL" - }, - "count" : 1235 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8729 - }, - "display" : "picomole per liter" - }, - "count" : 3 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8555 - }, - "display" : "second" - }, - "count" : 7 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8525 - }, - "display" : "titer" - }, - "count" : 534 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4121397 - }, - "display" : "ug/dL" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8510 - }, - "display" : "unit" - }, - "count" : 908557 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8763 - }, - "display" : "unit per milliliter" - }, - "count" : 164 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9234 - }, - "display" : "volume percent" - }, - "count" : 7 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9448 - }, - "display" : "year" - }, - "count" : 129781 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -2.0, - "maxVal" : 2.000023487E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "observation", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_as_string", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020475.0, - "maxVal" : 1.5996262E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201234E7, - "maxVal" : 2.0435758E7 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "observation" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "observation_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "observation_source_concept_id", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "observation_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "observation_id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "observation_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "observation_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_observation", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/person.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/person.json deleted file mode 100644 index 2fa9556eb..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/person.json +++ /dev/null @@ -1,358 +0,0 @@ -{ - "name" : "person", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "gender", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 45878463 - }, - "display" : "Female" - }, - "count" : 142307 - }, { - "enumVal" : { - "value" : { - "int64Val" : 45880669 - }, - "display" : "Male" - }, - "count" : 87099 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2000000002 - }, - "display" : "Not man only, not woman only, prefer not to answer, or skipped" - }, - "count" : 5119 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "race", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 2000000001 - }, - "display" : "Another single population" - }, - "count" : 5443 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8515 - }, - "display" : "Asian" - }, - "count" : 7476 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8516 - }, - "display" : "Black or African American" - }, - "count" : 46967 - }, { - "enumVal" : { - "value" : { - "int64Val" : 1177221 - }, - "display" : "I prefer not to answer" - }, - "count" : 1614 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2000000008 - }, - "display" : "More than one population" - }, - "count" : 10727 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 37524 - }, { - "enumVal" : { - "value" : { - "int64Val" : 45882607 - }, - "display" : "None of these" - }, - "count" : 2465 - }, { - "enumVal" : { - "value" : { - "int64Val" : 903096 - }, - "display" : "PMI: Skip" - }, - "count" : 1584 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8527 - }, - "display" : "White" - }, - "count" : 120725 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ethnicity", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 38003563 - }, - "display" : "Hispanic or Latino" - }, - "count" : 44673 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38003564 - }, - "display" : "Not Hispanic or Latino" - }, - "count" : 184189 - }, { - "enumVal" : { - "value" : { - "int64Val" : 903079 - }, - "display" : "PMI: Prefer Not To Answer" - }, - "count" : 1614 - }, { - "enumVal" : { - "value" : { - "int64Val" : 903096 - }, - "display" : "PMI: Skip" - }, - "count" : 1584 - }, { - "enumVal" : { - "value" : { - "int64Val" : 1586148 - }, - "display" : "What Race Ethnicity: Race Ethnicity None Of These" - }, - "count" : 2465 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "sex_at_birth", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 45878463 - }, - "display" : "Female" - }, - "count" : 143479 - }, { - "enumVal" : { - "value" : { - "int64Val" : 45880669 - }, - "display" : "Male" - }, - "count" : 87821 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 257 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2000000009 - }, - "display" : "Not male, not female, prefer not to answer, or skipped" - }, - "count" : 2968 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "year_of_birth", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 1930.0, - "maxVal" : 2001.0 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "person" - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "gender_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "race_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "ethnicity_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "sex_at_birth" : { - "value" : { - "column" : "sex_at_birth_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "sex_at_birth_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "person" - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_gender", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_race", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ethnicity", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "sex_at_birth" : { - "value" : { - "column" : "sex_at_birth", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_sex_at_birth", - "runtimeCalculated" : false - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/procedure.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/procedure.json deleted file mode 100644 index 6201ef06b..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/procedure.json +++ /dev/null @@ -1,350 +0,0 @@ -{ - "name" : "procedure", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 258789 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 3064 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CIEL" - }, - "display" : "Columbia International eHealth Laboratory (Columbia University)" - }, - "count" : 648 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "Current Procedural Terminology version 4 (AMA)" - }, - "count" : 13148 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "Healthcare Common Procedure Coding System (CMS)" - }, - "count" : 1289 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10PCS" - }, - "display" : "ICD-10 Procedure Coding System (CMS)" - }, - "count" : 193773 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS)" - }, - "count" : 283 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9Proc" - }, - "display" : "International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 3 (NCHS)" - }, - "count" : 4657 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "International Classification of Diseases, Tenth Revision, Clinical Modification (NCHS)" - }, - "count" : 9 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 78887 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Procedure" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT cs.concept_id AS id, cs.concept_synonym_name AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept_synonym` cs ) AS textsearch JOIN `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Procedure' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept_relationship` cr JOIN `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Procedure' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED'" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 4322976 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "procedure" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "procedure_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "procedure_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "procedure" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/procedure_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/procedure_occurrence.json deleted file mode 100644 index dac9a5514..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/procedure_occurrence.json +++ /dev/null @@ -1,168 +0,0 @@ -{ - "name" : "procedure_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 2.000023474E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020476.0, - "maxVal" : 1.5996259E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "procedure", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201235E7, - "maxVal" : 2.0435757E7 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "procedure_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "procedure_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "procedure_source_concept_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "procedure_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "procedure_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "procedure_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_procedure", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/visit.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/visit.json deleted file mode 100644 index 303a39e41..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/visit.json +++ /dev/null @@ -1,105 +0,0 @@ -{ - "name" : "visit", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Visit" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT cs.concept_id AS id, cs.concept_synonym_name AS text FROM `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept_synonym` cs ) AS textsearch JOIN `broad-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Visit' AND c.standard_concept = 'S'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "visit" - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/visit_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/visit_occurrence.json deleted file mode 100644 index b9335f9a7..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entity/visit_occurrence.json +++ /dev/null @@ -1,367 +0,0 @@ -{ - "name" : "visit_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 5.542608719E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 21039000 - }, - "display" : "10 ML Morphine 0.2 MG/ML Prefilled Syringe Box of 10" - }, - "count" : 21 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21050000 - }, - "display" : "2000 ML benzyl benzoate 250 MG/ML Topical Solution" - }, - "count" : 60 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581478 - }, - "display" : "Ambulance Visit" - }, - "count" : 1746 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38004207 - }, - "display" : "Ambulatory Clinic/Center" - }, - "count" : 80437 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581479 - }, - "display" : "Ambulatory Rehabilitation Visit" - }, - "count" : 179 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21056626 - }, - "display" : "Amiodarone 50 MG/ML Oral Suspension" - }, - "count" : 10 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21090200 - }, - "display" : "Cholecalciferol 50000 UNT Oral Capsule [Aciferol D3] Box of 10 by Rhodes" - }, - "count" : 2 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21090300 - }, - "display" : "Chondroitin Sulfates 400 MG / Glucosamine 500 MG Oral Tablet [Joint-Flex] Box of 60" - }, - "count" : 32 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21036000 - }, - "display" : "Daptomycin 500 MG Injection Box of 1" - }, - "count" : 100 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21090500 - }, - "display" : "Diphenhydramine 25 MG Oral Tablet by Ennogen" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 439748 - }, { - "enumVal" : { - "value" : { - "int64Val" : 262 - }, - "display" : "Emergency Room and Inpatient Visit" - }, - "count" : 25323 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21090400 - }, - "display" : "Ergocalciferol 300000 UNT/ML Prefilled Syringe Box of 10" - }, - "count" : 75 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581476 - }, - "display" : "Home Visit" - }, - "count" : 40500 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 568911 - }, { - "enumVal" : { - "value" : { - "int64Val" : 32036 - }, - "display" : "Laboratory Visit" - }, - "count" : 1850 - }, { - "enumVal" : { - "value" : { - "int64Val" : 12 - }, - "display" : "Modifier" - }, - "count" : 30318 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1340218 - }, { - "enumVal" : { - "value" : { - "int64Val" : 42898160 - }, - "display" : "Non-hospital institution Visit" - }, - "count" : 22 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581477 - }, - "display" : "Office Visit" - }, - "count" : 629739 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814711 - }, - "display" : "Other ambulatory visit" - }, - "count" : 4720 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 9929594 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581458 - }, - "display" : "Pharmacy visit" - }, - "count" : 25279 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21033000 - }, - "display" : "Risperidone 0.5 MG Oral Tablet by Consilient" - }, - "count" : 17 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44818518 - }, - "display" : "Visit derived from EHR record" - }, - "count" : 856887 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201234E7, - "maxVal" : 2.0435758E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "visit_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "visit_end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "visit_source_concept_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "visit_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "visit_start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "visit_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "visit" : { - "value" : { - "column" : "visit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/brand_ingredient.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/brand_ingredient.json deleted file mode 100644 index a0ad76e41..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/brand_ingredient.json +++ /dev/null @@ -1,101 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "brand_ingredient", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "concept_relationship" - }, - "idPairsIdA" : { - "column" : "concept_id_1", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "concept_id_2", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_brand_ingredient" - }, - "idPairsIdA" : { - "column" : "id_brand", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "brand" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_brand_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_brand_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_brand", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_brand", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "brand", - "itemsEntity" : "ingredient" -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/condition_person_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/condition_person_occurrence.json deleted file mode 100644 index a709ed653..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/condition_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "condition_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_condition_occurrence_condition" - }, - "idPairsIdA" : { - "column" : "id_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_condition", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_condition_person" - }, - "idPairsIdA" : { - "column" : "id_condition", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_condition_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "condition", - "occurrenceEntity" : "condition_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/device_person_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/device_person_occurrence.json deleted file mode 100644 index ff77e8f95..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/device_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "device_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_device_occurrence_device" - }, - "idPairsIdA" : { - "column" : "id_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_device", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_device_person" - }, - "idPairsIdA" : { - "column" : "id_device", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_device_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "device", - "occurrenceEntity" : "device_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/ingredient_person_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/ingredient_person_occurrence.json deleted file mode 100644 index 576ca9260..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/ingredient_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "ingredient_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_occurrence_ingredient" - }, - "idPairsIdA" : { - "column" : "id_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_person" - }, - "idPairsIdA" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "ingredient", - "occurrenceEntity" : "ingredient_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/measurement_person_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/measurement_person_occurrence.json deleted file mode 100644 index cb82b0df7..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/measurement_person_occurrence.json +++ /dev/null @@ -1,287 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "measurement_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_measurement_occurrence_measurement" - }, - "idPairsIdA" : { - "column" : "id_measurement_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_measurement", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_measurement_person" - }, - "idPairsIdA" : { - "column" : "id_measurement", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_measurement_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_measurement_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { - "modifiers" : { - "tablePointer" : { - "table" : "measurement_person_occurrence_modifiers" - }, - "fieldPointers" : { - "min" : { - "column" : "min", - "runtimeCalculated" : false - }, - "enum_count" : { - "column" : "enum_count", - "runtimeCalculated" : false - }, - "max" : { - "column" : "max", - "runtimeCalculated" : false - }, - "enum_display" : { - "column" : "enum_display", - "runtimeCalculated" : false - }, - "enum_value" : { - "column" : "enum_value", - "runtimeCalculated" : false - }, - "attribute_name" : { - "column" : "attribute_name", - "runtimeCalculated" : false - }, - "entity_id" : { - "column" : "entity_id", - "runtimeCalculated" : false - } - } - } - } - }, - "criteriaEntity" : "measurement", - "occurrenceEntity" : "measurement_occurrence", - "modifierAttributes" : [ "value_numeric", "value_enum" ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/observation_person_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/observation_person_occurrence.json deleted file mode 100644 index dad430b34..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/observation_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "observation_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_observation_occurrence_observation" - }, - "idPairsIdA" : { - "column" : "id_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_observation", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_observation_person" - }, - "idPairsIdA" : { - "column" : "id_observation", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_observation_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "observation", - "occurrenceEntity" : "observation_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/procedure_person_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/procedure_person_occurrence.json deleted file mode 100644 index be81091b7..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/procedure_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "procedure_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_procedure_occurrence_procedure" - }, - "idPairsIdA" : { - "column" : "id_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_procedure", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_procedure_person" - }, - "idPairsIdA" : { - "column" : "id_procedure", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_procedure_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "procedure", - "occurrenceEntity" : "procedure_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/visit_person_occurrence.json b/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/visit_person_occurrence.json deleted file mode 100644 index 1a4beff12..000000000 --- a/service/src/main/resources/config/broad/aou_synthetic/expanded/entitygroup/visit_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "visit_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_visit_occurrence_visit" - }, - "idPairsIdA" : { - "column" : "id_visit_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_visit", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_visit_person" - }, - "idPairsIdA" : { - "column" : "id_visit", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_visit_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_visit_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "visit", - "occurrenceEntity" : "visit_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/sql/brand_textSearch.sql b/service/src/main/resources/config/broad/aou_synthetic/sql/brand_textSearch.sql similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/sql/brand_textSearch.sql rename to service/src/main/resources/config/broad/aou_synthetic/sql/brand_textSearch.sql diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/sql/condition_parentChild.sql b/service/src/main/resources/config/broad/aou_synthetic/sql/condition_parentChild.sql similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/sql/condition_parentChild.sql rename to service/src/main/resources/config/broad/aou_synthetic/sql/condition_parentChild.sql diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/sql/condition_textSearch.sql b/service/src/main/resources/config/broad/aou_synthetic/sql/condition_textSearch.sql similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/sql/condition_textSearch.sql rename to service/src/main/resources/config/broad/aou_synthetic/sql/condition_textSearch.sql diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/sql/device_textSearch.sql b/service/src/main/resources/config/broad/aou_synthetic/sql/device_textSearch.sql similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/sql/device_textSearch.sql rename to service/src/main/resources/config/broad/aou_synthetic/sql/device_textSearch.sql diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/sql/ingredient_all.sql b/service/src/main/resources/config/broad/aou_synthetic/sql/ingredient_all.sql similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/sql/ingredient_all.sql rename to service/src/main/resources/config/broad/aou_synthetic/sql/ingredient_all.sql diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/sql/ingredient_parentChild.sql b/service/src/main/resources/config/broad/aou_synthetic/sql/ingredient_parentChild.sql similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/sql/ingredient_parentChild.sql rename to service/src/main/resources/config/broad/aou_synthetic/sql/ingredient_parentChild.sql diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/sql/ingredient_textSearch.sql b/service/src/main/resources/config/broad/aou_synthetic/sql/ingredient_textSearch.sql similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/sql/ingredient_textSearch.sql rename to service/src/main/resources/config/broad/aou_synthetic/sql/ingredient_textSearch.sql diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/sql/measurement_parentChild.sql b/service/src/main/resources/config/broad/aou_synthetic/sql/measurement_parentChild.sql similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/sql/measurement_parentChild.sql rename to service/src/main/resources/config/broad/aou_synthetic/sql/measurement_parentChild.sql diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/sql/measurement_textSearch.sql b/service/src/main/resources/config/broad/aou_synthetic/sql/measurement_textSearch.sql similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/sql/measurement_textSearch.sql rename to service/src/main/resources/config/broad/aou_synthetic/sql/measurement_textSearch.sql diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/sql/observation_textSearch.sql b/service/src/main/resources/config/broad/aou_synthetic/sql/observation_textSearch.sql similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/sql/observation_textSearch.sql rename to service/src/main/resources/config/broad/aou_synthetic/sql/observation_textSearch.sql diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/sql/procedure_parentChild.sql b/service/src/main/resources/config/broad/aou_synthetic/sql/procedure_parentChild.sql similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/sql/procedure_parentChild.sql rename to service/src/main/resources/config/broad/aou_synthetic/sql/procedure_parentChild.sql diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/sql/procedure_textSearch.sql b/service/src/main/resources/config/broad/aou_synthetic/sql/procedure_textSearch.sql similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/sql/procedure_textSearch.sql rename to service/src/main/resources/config/broad/aou_synthetic/sql/procedure_textSearch.sql diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/sql/visit_textSearch.sql b/service/src/main/resources/config/broad/aou_synthetic/sql/visit_textSearch.sql similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/sql/visit_textSearch.sql rename to service/src/main/resources/config/broad/aou_synthetic/sql/visit_textSearch.sql diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/ui/top_level.json b/service/src/main/resources/config/broad/aou_synthetic/ui/top_level.json similarity index 100% rename from service/src/main/resources/config/broad/aou_synthetic/original/ui/top_level.json rename to service/src/main/resources/config/broad/aou_synthetic/ui/top_level.json diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/cms_synpuf.json b/service/src/main/resources/config/broad/cms_synpuf/cms_synpuf.json similarity index 95% rename from service/src/main/resources/config/broad/cms_synpuf/original/cms_synpuf.json rename to service/src/main/resources/config/broad/cms_synpuf/cms_synpuf.json index dec2ff727..91406cbb4 100644 --- a/service/src/main/resources/config/broad/cms_synpuf/original/cms_synpuf.json +++ b/service/src/main/resources/config/broad/cms_synpuf/cms_synpuf.json @@ -9,7 +9,7 @@ { "type": "BQ_DATASET", "name": "index_dataset", "projectId": "broad-tanagra-dev", - "datasetId": "cmssynpuf_index_071923" } ], + "datasetId": "cmssynpuf_index_072623" } ], "entities": [ "brand.json", "condition.json", diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/brand.json b/service/src/main/resources/config/broad/cms_synpuf/entity/brand.json similarity index 69% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/brand.json rename to service/src/main/resources/config/broad/cms_synpuf/entity/brand.json index 0403f94a4..b91b1f66a 100644 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/brand.json +++ b/service/src/main/resources/config/broad/cms_synpuf/entity/brand.json @@ -2,10 +2,10 @@ "name": "brand", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/condition.json b/service/src/main/resources/config/broad/cms_synpuf/entity/condition.json similarity index 78% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/condition.json rename to service/src/main/resources/config/broad/cms_synpuf/entity/condition.json index 8d7f876d9..e8701cc41 100644 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/condition.json +++ b/service/src/main/resources/config/broad/cms_synpuf/entity/condition.json @@ -2,11 +2,11 @@ "name": "condition", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/cms_synpuf/entity/condition_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/entity/condition_occurrence.json new file mode 100644 index 000000000..b1651a33e --- /dev/null +++ b/service/src/main/resources/config/broad/cms_synpuf/entity/condition_occurrence.json @@ -0,0 +1,33 @@ +{ + "name": "condition_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "condition", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "condition_occurrence_all.sql" }, + "attributeMappings": { + "condition": { + "value": { "column": "condition_concept_id" }, + "display": { + "column": "condition_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/device.json b/service/src/main/resources/config/broad/cms_synpuf/entity/device.json similarity index 75% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/device.json rename to service/src/main/resources/config/broad/cms_synpuf/entity/device.json index 2e72d8d62..078cd332c 100644 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/device.json +++ b/service/src/main/resources/config/broad/cms_synpuf/entity/device.json @@ -2,11 +2,11 @@ "name": "device", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/cms_synpuf/entity/device_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/entity/device_occurrence.json new file mode 100644 index 000000000..b1569a268 --- /dev/null +++ b/service/src/main/resources/config/broad/cms_synpuf/entity/device_occurrence.json @@ -0,0 +1,32 @@ +{ + "name": "device_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "device", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "device_occurrence_all.sql" }, + "attributeMappings": { + "device": { + "value": { "column": "device_concept_id" }, + "display": { + "column": "device_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/ingredient.json b/service/src/main/resources/config/broad/cms_synpuf/entity/ingredient.json similarity index 81% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/ingredient.json rename to service/src/main/resources/config/broad/cms_synpuf/entity/ingredient.json index 0e7901ee5..59a4ddcc0 100644 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/ingredient.json +++ b/service/src/main/resources/config/broad/cms_synpuf/entity/ingredient.json @@ -2,11 +2,11 @@ "name": "ingredient", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/cms_synpuf/entity/ingredient_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/entity/ingredient_occurrence.json new file mode 100644 index 000000000..696b8fd95 --- /dev/null +++ b/service/src/main/resources/config/broad/cms_synpuf/entity/ingredient_occurrence.json @@ -0,0 +1,35 @@ +{ + "name": "ingredient_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "ingredient", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "refills", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "days_supply", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "ingredient_occurrence_all.sql" }, + "attributeMappings": { + "ingredient": { + "value": { "column": "drug_concept_id" }, + "display": { + "column": "drug_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/entity/observation.json b/service/src/main/resources/config/broad/cms_synpuf/entity/observation.json similarity index 79% rename from service/src/main/resources/config/broad/cms_synpuf/original/entity/observation.json rename to service/src/main/resources/config/broad/cms_synpuf/entity/observation.json index 668afebce..92f45b426 100644 --- a/service/src/main/resources/config/broad/cms_synpuf/original/entity/observation.json +++ b/service/src/main/resources/config/broad/cms_synpuf/entity/observation.json @@ -2,11 +2,11 @@ "name": "observation", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/entity/observation_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/entity/observation_occurrence.json similarity index 55% rename from service/src/main/resources/config/verily/cms_synpuf/original/entity/observation_occurrence.json rename to service/src/main/resources/config/broad/cms_synpuf/entity/observation_occurrence.json index a619f56ca..822933551 100644 --- a/service/src/main/resources/config/verily/cms_synpuf/original/entity/observation_occurrence.json +++ b/service/src/main/resources/config/broad/cms_synpuf/entity/observation_occurrence.json @@ -2,16 +2,16 @@ "name": "observation_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "observation" }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "value_as_string", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "value", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "unit", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "observation", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "value_as_string", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "value", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/entity/person.json b/service/src/main/resources/config/broad/cms_synpuf/entity/person.json similarity index 75% rename from service/src/main/resources/config/verily/cms_synpuf/original/entity/person.json rename to service/src/main/resources/config/broad/cms_synpuf/entity/person.json index 72d0994bf..ab41605d6 100644 --- a/service/src/main/resources/config/verily/cms_synpuf/original/entity/person.json +++ b/service/src/main/resources/config/broad/cms_synpuf/entity/person.json @@ -2,12 +2,12 @@ "name": "person", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "year_of_birth" }, - { "type": "SIMPLE", "name": "age" }, - { "type": "KEY_AND_DISPLAY", "name": "gender" }, - { "type": "KEY_AND_DISPLAY", "name": "race" }, - { "type": "KEY_AND_DISPLAY", "name": "ethnicity" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "year_of_birth", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "age", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "gender", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "race", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "ethnicity", "dataType": "INT64" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/entity/procedure.json b/service/src/main/resources/config/broad/cms_synpuf/entity/procedure.json similarity index 78% rename from service/src/main/resources/config/broad/cms_synpuf/original/entity/procedure.json rename to service/src/main/resources/config/broad/cms_synpuf/entity/procedure.json index 5b26c710e..b45e3d76c 100644 --- a/service/src/main/resources/config/broad/cms_synpuf/original/entity/procedure.json +++ b/service/src/main/resources/config/broad/cms_synpuf/entity/procedure.json @@ -2,11 +2,11 @@ "name": "procedure", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/cms_synpuf/entity/procedure_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/entity/procedure_occurrence.json new file mode 100644 index 000000000..83ae721c4 --- /dev/null +++ b/service/src/main/resources/config/broad/cms_synpuf/entity/procedure_occurrence.json @@ -0,0 +1,32 @@ +{ + "name": "procedure_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "procedure", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "procedure_occurrence_all.sql" }, + "attributeMappings": { + "procedure": { + "value": { "column": "procedure_concept_id" }, + "display": { + "column": "procedure_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "date": { "value": { "column": "procedure_dat" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/entitygroup/brand_ingredient.json b/service/src/main/resources/config/broad/cms_synpuf/entitygroup/brand_ingredient.json similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/entitygroup/brand_ingredient.json rename to service/src/main/resources/config/broad/cms_synpuf/entitygroup/brand_ingredient.json diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/entitygroup/condition_person_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/entitygroup/condition_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/entitygroup/condition_person_occurrence.json rename to service/src/main/resources/config/broad/cms_synpuf/entitygroup/condition_person_occurrence.json diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/entitygroup/device_person_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/entitygroup/device_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/entitygroup/device_person_occurrence.json rename to service/src/main/resources/config/broad/cms_synpuf/entitygroup/device_person_occurrence.json diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/entitygroup/ingredient_person_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/entitygroup/ingredient_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/entitygroup/ingredient_person_occurrence.json rename to service/src/main/resources/config/broad/cms_synpuf/entitygroup/ingredient_person_occurrence.json diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/entitygroup/observation_person_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/entitygroup/observation_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/entitygroup/observation_person_occurrence.json rename to service/src/main/resources/config/broad/cms_synpuf/entitygroup/observation_person_occurrence.json diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/entitygroup/procedure_person_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/entitygroup/procedure_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/entitygroup/procedure_person_occurrence.json rename to service/src/main/resources/config/broad/cms_synpuf/entitygroup/procedure_person_occurrence.json diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/cms_synpuf.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/cms_synpuf.json deleted file mode 100644 index 9f08ec8c9..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/cms_synpuf.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "name" : "cms_synpuf", - "dataPointers" : [ { - "type" : "BQ_DATASET", - "name" : "index_dataset", - "projectId" : "broad-tanagra-dev", - "datasetId" : "cmssynpuf_index_071923", - "queryProjectId" : "broad-tanagra-dev", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : true - }, { - "type" : "BQ_DATASET", - "name" : "omop_dataset", - "projectId" : "bigquery-public-data", - "datasetId" : "cms_synthetic_patient_data_omop", - "queryProjectId" : "broad-tanagra-dev", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : true - } ], - "entities" : [ "ingredient_occurrence.json", "condition.json", "condition_occurrence.json", "ingredient.json", "device_occurrence.json", "observation.json", "person.json", "observation_occurrence.json", "procedure.json", "procedure_occurrence.json", "brand.json", "device.json" ], - "entityGroups" : [ "device_person_occurrence.json", "condition_person_occurrence.json", "ingredient_person_occurrence.json", "observation_person_occurrence.json", "brand_ingredient.json", "procedure_person_occurrence.json" ], - "primaryEntity" : "person", - "uiConfig" : "{ \"dataConfig\": { \"primaryEntity\": { \"displayName\": \"Person\", \"entity\": \"person\", \"key\": \"id\" }, \"occurrences\": [ { \"id\": \"condition_occurrence\", \"displayName\": \"Condition Occurrences\", \"entity\": \"condition_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"condition\", \"attribute\": \"condition\", \"entity\": \"condition\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"procedure_occurrence\", \"displayName\": \"Procedure Occurrences\", \"entity\": \"procedure_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"procedure\", \"attribute\": \"procedure\", \"entity\": \"procedure\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"observation_occurrence\", \"displayName\": \"Observation Occurrence\", \"entity\": \"observation_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"observation\", \"attribute\": \"observation\", \"entity\": \"observation\", \"entityAttribute\": \"id\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"ingredient_occurrence\", \"displayName\": \"Drug Occurrence\", \"entity\": \"ingredient_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"ingredient\", \"attribute\": \"id\", \"entity\": \"ingredient\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" }, \"groupings\": [ { \"id\": \"brand\", \"entity\": \"brand\", \"defaultSort\": { \"attribute\": \"name\", \"direction\": \"ASC\" }, \"attributes\": [\"name\", \"id\", \"standard_concept\", \"concept_code\"] } ] } ] } ] }, \"criteriaConfigs\": [ { \"type\": \"classification\", \"id\": \"tanagra-conditions\", \"title\": \"Condition\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Condition\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"condition_occurrence\", \"classification\": \"condition\", \"modifiers\": [ \"age_at_occurrence\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-procedures\", \"title\": \"Procedure\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Procedure\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"procedure_occurrence\", \"classification\": \"procedure\", \"modifiers\": [\"age_at_occurrence\", \"date_group_by_count\"] }, { \"type\": \"classification\", \"id\": \"tanagra-observations\", \"title\": \"Observation\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"observation_occurrence\", \"classification\": \"observation\", \"modifiers\": [\"age_at_occurrence\", \"date_group_by_count\"] }, { \"type\": \"classification\", \"id\": \"tanagra-drugs\", \"title\": \"Drug\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Drug\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"ingredient_occurrence\", \"classification\": \"ingredient\", \"modifiers\": [ \"age_at_occurrence\", \"start_date_group_by_count\" ] }, { \"type\": \"attribute\", \"id\": \"tanagra-ethnicity\", \"title\": \"Ethnicity\", \"category\": \"Program data\", \"attribute\": \"ethnicity\" }, { \"type\": \"attribute\", \"id\": \"tanagra-gender\", \"title\": \"Gender identity\", \"category\": \"Program data\", \"attribute\": \"gender\" }, { \"type\": \"attribute\", \"id\": \"tanagra-race\", \"title\": \"Race\", \"category\": \"Program data\", \"attribute\": \"race\" }, { \"type\": \"attribute\", \"id\": \"tanagra-age\", \"title\": \"Age\", \"category\": \"Program data\", \"attribute\": \"age\" }, { \"type\": \"attribute\", \"id\": \"tanagra-sex_at_birth\", \"title\": \"Sex assigned at birth\", \"category\": \"Program data\", \"attribute\": \"sex_at_birth\" } ], \"modifierConfigs\": [ { \"type\": \"unhinted-value\", \"id\": \"start_date_group_by_count\", \"title\": \"Occurrence count\", \"attribute\": \"start_date\", \"groupByCount\": true }, { \"type\": \"unhinted-value\", \"id\": \"date_group_by_count\", \"title\": \"Occurrence count\", \"attribute\": \"date\", \"groupByCount\": true }, { \"type\": \"attribute\", \"id\": \"age_at_occurrence\", \"title\": \"Age at occurrence\", \"attribute\": \"age_at_occurrence\" } ], \"demographicChartConfigs\": { \"groupByAttributes\": [\"gender\", \"race\", \"age\"], \"chartConfigs\": [ { \"title\": \"Gender identity\", \"primaryProperties\": [{ \"key\": \"gender\" }] }, { \"title\": \"Gender identity, Current age, Race\", \"primaryProperties\": [ { \"key\": \"gender\" }, { \"key\": \"age\", \"buckets\": [ { \"min\": 18, \"max\": 45, \"displayName\": \"18-44\" }, { \"min\": 45, \"max\": 65, \"displayName\": \"45-64\" }, { \"min\": 65, \"displayName\": \"65+\" } ] } ], \"stackedProperty\": { \"key\": \"race\" } } ] }, \"prepackagedConceptSets\": [ { \"id\": \"_demographics\", \"name\": \"Demographics\", \"occurrence\": \"\" }, { \"id\": \"_analgesics\", \"name\": \"Analgesics\", \"occurrence\": \"ingredient_occurrence\", \"filter\": { \"type\": \"CLASSIFICATION\", \"occurrenceId\": \"ingredient_occurrence\", \"classificationId\": \"ingredient\", \"keys\": [21604253] } } ], \"criteriaSearchConfig\": { \"criteriaTypeWidth\": 120, \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept Name\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up Count\" } ] }, \"cohortReviewConfig\": { \"participantsListColumns\": [ { \"key\": \"id\", \"width\": 100, \"title\": \"Id\" }, { \"key\": \"gender\", \"width\": 100, \"title\": \"Gender\" }, { \"key\": \"race\", \"width\": 100, \"title\": \"Race\" }, { \"key\": \"ethnicity\", \"width\": 100, \"title\": \"Ethnicity\" }, { \"key\": \"age\", \"width\": 60, \"title\": \"Age\" } ], \"attributes\": [ { \"title\": \"Gender\", \"key\": \"gender\" }, { \"title\": \"Age\", \"key\": \"age\" }, { \"title\": \"Race\", \"key\": \"race\" }, { \"title\": \"Ethnicity\", \"key\": \"ethnicity\" } ], \"pages\": [ { \"type\": \"occurrenceTable\", \"id\": \"condition\", \"title\": \"Conditions\", \"plugin\": { \"occurrence\": \"condition_occurrence\", \"columns\": [ { \"key\": \"condition\", \"width\": \"100%\", \"title\": \"Condition name\", \"sortable\": true }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\", \"sortable\": true }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"procedure\", \"title\": \"Procedures\", \"plugin\": { \"occurrence\": \"procedure_occurrence\", \"columns\": [ { \"key\": \"procedure\", \"width\": \"100%\", \"title\": \"Procedure name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"observation\", \"title\": \"Observations\", \"plugin\": { \"occurrence\": \"observation_occurrence\", \"columns\": [ { \"key\": \"observation\", \"width\": \"100%\", \"title\": \"Observation name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"ingredient\", \"title\": \"Drugs\", \"plugin\": { \"occurrence\": \"ingredient_occurrence\", \"columns\": [ { \"key\": \"ingredient\", \"width\": \"100%\", \"title\": \"Drug name\", \"sortable\": true }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\", \"sortable\": true }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\", \"sortable\": true } ] } } ] } } ", - "metadata" : { } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/brand.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/brand.json deleted file mode 100644 index 65fb86c50..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/brand.json +++ /dev/null @@ -1,133 +0,0 @@ -{ - "name" : "brand", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT * FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` WHERE domain_id = 'Drug' AND concept_class_id = 'Brand Name' AND vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND DATE_DIFF(CAST(valid_end_date AS DATE), CURRENT_DATE(), DAY) > 0" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ) AS textsearch JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND c.concept_class_id = 'Brand Name' AND c.vocabulary_id IN ('RxNorm', 'RxNorm Extension')" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "brand" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/condition.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/condition.json deleted file mode 100644 index 27fbce0eb..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/condition.json +++ /dev/null @@ -1,299 +0,0 @@ -{ - "name" : "condition", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 97214 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "ICD10CM" - }, - "count" : 108038 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "ICD9CM" - }, - "count" : 16632 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 148722 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Condition" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ) AS textsearch JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Condition' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept_relationship` cr JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Condition' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED'" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 441840 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "condition" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "condition_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "condition_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "condition" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/condition_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/condition_occurrence.json deleted file mode 100644 index 195c36403..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/condition_occurrence.json +++ /dev/null @@ -1,202 +0,0 @@ -{ - "name" : "condition_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "condition", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 24.0, - "maxVal" : 101.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT co.condition_occurrence_id AS id, co.person_id, co.condition_concept_id, co.condition_start_date AS start_date, co.condition_end_date AS end_date, co.stop_reason, co.condition_source_value AS source_value, co.condition_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(co.condition_start_date, DATETIME(p.year_of_birth, p.month_of_birth, p.day_of_birth, 0, 0, 0), DAY) / 365.25) AS INT64) AS age_at_occurrence, FROM `bigquery-public-data.cms_synthetic_patient_data_omop.condition_occurrence` AS co JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.person` AS p ON p.person_id = co.person_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "condition_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "condition_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_condition", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/device.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/device.json deleted file mode 100644 index 25760fb08..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/device.json +++ /dev/null @@ -1,197 +0,0 @@ -{ - "name" : "device", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 18134 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 2828 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 15306 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Device" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ) AS textsearch JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Device' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "device" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/device_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/device_occurrence.json deleted file mode 100644 index 0bf7164ac..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/device_occurrence.json +++ /dev/null @@ -1,175 +0,0 @@ -{ - "name" : "device_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 24.0, - "maxVal" : 101.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "device", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT de.device_exposure_id AS id, de.person_id, de.device_concept_id, de.device_exposure_start_date AS start_date, de.device_exposure_end_date AS end_date, de.device_source_value AS source_value, de.device_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(de.device_exposure_start_date, DATETIME(p.year_of_birth, p.month_of_birth, p.day_of_birth, 0, 0, 0), DAY) / 365.25) AS INT64) AS age_at_occurrence, FROM `bigquery-public-data.cms_synthetic_patient_data_omop.device_exposure` AS de JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.person` AS p ON p.person_id = de.person_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "device_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "device_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_device", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/ingredient.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/ingredient.json deleted file mode 100644 index 11f68e969..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/ingredient.json +++ /dev/null @@ -1,312 +0,0 @@ -{ - "name" : "ingredient", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 1602994 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 43254 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "ATC" - }, - "display" : "ATC" - }, - "count" : 6129 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm" - }, - "display" : "RxNorm" - }, - "count" : 278569 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm Extension" - }, - "display" : "RxNorm Extension" - }, - "count" : 1650444 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT c.concept_id AS id, c.concept_name AS name, c.vocabulary_id, c.standard_concept, c.concept_code FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c WHERE c.domain_id = 'Drug' AND ( (c.vocabulary_id = 'ATC') OR (c.vocabulary_id IN ('RxNorm', 'RxNorm Extension')) ) " - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ) AS textsearch JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND ((c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.concept_class_id = 'Ingredient') OR (c.vocabulary_id = 'RxNorm' AND c.concept_class_id = 'Precise Ingredient') OR (c.vocabulary_id = 'ATC' AND c.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th'))) " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept_relationship` cr JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE c1.concept_id != c2.concept_id AND c1.domain_id = 'Drug' AND c2.domain_id = 'Drug' AND ( /* Populate Ingredients' ancestors', which are ATCs. See https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:atc#:~:text=the%20original%20ATC%20hierarchy%20is%20extended%20by%20Standard%20Drug%20Products%20of%20RxNorm%20and%20RxNorm%20Extension%20vocabularies%2C%20which%20are%20assigned%20to%20be%20descendants%20of%20the%205th%20ATC%20Classes. Eg: ATC 1st (highest ancestor) Subsumes ATC 2nd ATC 5th (direct parent of RxNorm) Maps to RxNorm */ (c1.vocabulary_id IN ('ATC') AND cr.relationship_id IN ('Subsumes', 'Maps to')) OR /* Populate Ingredients and their descendants: Branded Drug, Clinical Drug, etc. Ingredients and their descendants are RxNorm. drug_exposure contains Ingredients or their descendants. Use [1] and [2] to define hierarchy. Eg \"Marketed Product\" is most specific and is bottom of hierarchy. [1] https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:drug_exposure#:~:text=These%20are%20indicated,is%20available%20%E2%80%9CIngredient%E2%80%9D [2] https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:drug#:~:text=are%20not%20implemented.-,Relationships,-As%20usual%2C%20all */ ( c1.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c2.vocabulary_id IN ('RxNorm', 'RxNorm Extension') /* Only keep relationships where c1 is \"parent\" of c2 */ AND cr.relationship_id IN ('Constitutes', 'Contained in' , 'Has form', 'Has quantified form', 'RxNorm ing of', 'RxNorm inverse is a', 'Precise ing of') ) )" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC 1st" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "C" - } - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 15 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "ingredient" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "ingredient_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "ingredient_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "ingredient" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 15 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/ingredient_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/ingredient_occurrence.json deleted file mode 100644 index a906ce1f6..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/ingredient_occurrence.json +++ /dev/null @@ -1,236 +0,0 @@ -{ - "name" : "ingredient_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ingredient", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "refills", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 24.0, - "maxVal" : 101.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "days_supply", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT de.drug_exposure_id AS id, de.person_id, de.drug_concept_id, de.drug_exposure_start_date AS start_date, de.drug_exposure_end_date AS end_date, de.stop_reason, de.refills, de.days_supply, de.drug_source_value AS source_value, de.drug_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(de.drug_exposure_start_date, DATETIME(p.year_of_birth, p.month_of_birth, p.day_of_birth, 0, 0, 0), DAY) / 365.25) AS INT64) AS age_at_occurrence, FROM `bigquery-public-data.cms_synthetic_patient_data_omop.drug_exposure` AS de JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.person` AS p ON p.person_id = de.person_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "drug_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "ingredient_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "ingredient", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ingredient", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/observation.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/observation.json deleted file mode 100644 index f0782bf6e..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/observation.json +++ /dev/null @@ -1,233 +0,0 @@ -{ - "name" : "observation", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 149719 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "CPT4" - }, - "count" : 629 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 1489 - }, { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "LOINC" - }, - "count" : 16762 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 130839 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Observation" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "PPI" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "Survey" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ) AS textsearch JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Observation' AND c.vocabulary_id != 'PPI' AND c.concept_class_id != 'Survey' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "observation" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/observation_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/observation_occurrence.json deleted file mode 100644 index 36c8dd7cc..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/observation_occurrence.json +++ /dev/null @@ -1,231 +0,0 @@ -{ - "name" : "observation_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 24.0, - "maxVal" : 101.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "observation", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_as_string", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT o.observation_id AS id, o.person_id, o.observation_concept_id, o.observation_date, o.value_as_string, o.value_as_concept_id, o.unit_concept_id, o.observation_source_value AS source_value, o.observation_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(o.observation_date, DATETIME(p.year_of_birth, p.month_of_birth, p.day_of_birth, 0, 0, 0), DAY) / 365.25) AS INT64) AS age_at_occurrence, FROM `bigquery-public-data.cms_synthetic_patient_data_omop.observation` AS o JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.person` AS p ON p.person_id = o.person_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "observation_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "observation_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "observation_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_observation", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/person.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/person.json deleted file mode 100644 index 618513a15..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/person.json +++ /dev/null @@ -1,238 +0,0 @@ -{ - "name" : "person", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "gender", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 8532 - }, - "display" : "FEMALE" - }, - "count" : 1292861 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8507 - }, - "display" : "MALE" - }, - "count" : 1033995 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "race", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 8516 - }, - "display" : "Black or African American" - }, - "count" : 247723 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 152425 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8527 - }, - "display" : "White" - }, - "count" : 1926708 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ethnicity", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 38003563 - }, - "display" : "Hispanic or Latino" - }, - "count" : 54453 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38003564 - }, - "display" : "Not Hispanic or Latino" - }, - "count" : 2272403 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "age", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 40.0, - "maxVal" : 114.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "year_of_birth", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 1909.0, - "maxVal" : 1983.0 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT /* Can't do \"*\". During expansion, there's an error about person_id column being ambiguous. */ p.person_id, p.year_of_birth, DATETIME(p.year_of_birth, p.month_of_birth, p.day_of_birth, 0, 0, 0), p.gender_concept_id, p.race_concept_id, p.ethnicity_concept_id FROM `bigquery-public-data.cms_synthetic_patient_data_omop.person` p " - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "gender_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "race_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "ethnicity_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "age" : { - "value" : { - "column" : "year_of_birth", - "sqlFunctionWrapper" : "EXTRACT(YEAR FROM CURRENT_DATE()) - ${fieldSql}", - "runtimeCalculated" : true - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "person" - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_gender", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_race", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ethnicity", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "age" : { - "value" : { - "column" : "age", - "sqlFunctionWrapper" : "EXTRACT(YEAR FROM CURRENT_DATE()) - ${fieldSql}", - "runtimeCalculated" : true - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/procedure.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/procedure.json deleted file mode 100644 index 0062b8f21..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/procedure.json +++ /dev/null @@ -1,323 +0,0 @@ -{ - "name" : "procedure", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 61581 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 2990 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "CPT4" - }, - "count" : 13070 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 981 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "ICD10CM" - }, - "count" : 6 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "ICD9CM" - }, - "count" : 1318 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9Proc" - }, - "display" : "ICD9Proc" - }, - "count" : 4657 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 74959 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Procedure" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ) AS textsearch JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Procedure' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept_relationship` cr JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Procedure' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED'" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 4322976 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "procedure" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "procedure_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "procedure_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "procedure" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/procedure_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/procedure_occurrence.json deleted file mode 100644 index 57892dd4f..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/entity/procedure_occurrence.json +++ /dev/null @@ -1,158 +0,0 @@ -{ - "name" : "procedure_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 24.0, - "maxVal" : 101.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "procedure", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT po.procedure_occurrence_id AS id, po.person_id, po.procedure_concept_id, po.procedure_dat, po.procedure_source_value AS source_value, po.procedure_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(po.procedure_dat, DATETIME(p.year_of_birth, p.month_of_birth, p.day_of_birth, 0, 0, 0), DAY) / 365.25) AS INT64) AS age_at_occurrence, FROM `bigquery-public-data.cms_synthetic_patient_data_omop.procedure_occurrence` AS po JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.person` AS p ON p.person_id = po.person_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "procedure_dat", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "procedure_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "procedure_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_procedure", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/entitygroup/brand_ingredient.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/entitygroup/brand_ingredient.json deleted file mode 100644 index a0ad76e41..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/entitygroup/brand_ingredient.json +++ /dev/null @@ -1,101 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "brand_ingredient", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "concept_relationship" - }, - "idPairsIdA" : { - "column" : "concept_id_1", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "concept_id_2", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_brand_ingredient" - }, - "idPairsIdA" : { - "column" : "id_brand", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "brand" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_brand_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_brand_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_brand", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_brand", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "brand", - "itemsEntity" : "ingredient" -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/entitygroup/condition_person_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/entitygroup/condition_person_occurrence.json deleted file mode 100644 index a709ed653..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/entitygroup/condition_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "condition_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_condition_occurrence_condition" - }, - "idPairsIdA" : { - "column" : "id_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_condition", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_condition_person" - }, - "idPairsIdA" : { - "column" : "id_condition", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_condition_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "condition", - "occurrenceEntity" : "condition_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/entitygroup/device_person_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/entitygroup/device_person_occurrence.json deleted file mode 100644 index ff77e8f95..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/entitygroup/device_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "device_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_device_occurrence_device" - }, - "idPairsIdA" : { - "column" : "id_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_device", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_device_person" - }, - "idPairsIdA" : { - "column" : "id_device", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_device_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "device", - "occurrenceEntity" : "device_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/entitygroup/ingredient_person_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/entitygroup/ingredient_person_occurrence.json deleted file mode 100644 index 576ca9260..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/entitygroup/ingredient_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "ingredient_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_occurrence_ingredient" - }, - "idPairsIdA" : { - "column" : "id_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_person" - }, - "idPairsIdA" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "ingredient", - "occurrenceEntity" : "ingredient_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/entitygroup/observation_person_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/entitygroup/observation_person_occurrence.json deleted file mode 100644 index dad430b34..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/entitygroup/observation_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "observation_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_observation_occurrence_observation" - }, - "idPairsIdA" : { - "column" : "id_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_observation", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_observation_person" - }, - "idPairsIdA" : { - "column" : "id_observation", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_observation_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "observation", - "occurrenceEntity" : "observation_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/expanded/entitygroup/procedure_person_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/expanded/entitygroup/procedure_person_occurrence.json deleted file mode 100644 index be81091b7..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/expanded/entitygroup/procedure_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "procedure_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_procedure_occurrence_procedure" - }, - "idPairsIdA" : { - "column" : "id_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_procedure", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_procedure_person" - }, - "idPairsIdA" : { - "column" : "id_procedure", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_procedure_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "procedure", - "occurrenceEntity" : "procedure_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/entity/condition_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/original/entity/condition_occurrence.json deleted file mode 100644 index d41338a4f..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/original/entity/condition_occurrence.json +++ /dev/null @@ -1,33 +0,0 @@ -{ - "name": "condition_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "condition", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "condition_occurrence_all.sql" }, - "attributeMappings": { - "condition": { - "value": { "column": "condition_concept_id" }, - "display": { - "column": "condition_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/entity/device_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/original/entity/device_occurrence.json deleted file mode 100644 index 6674f3672..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/original/entity/device_occurrence.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "name": "device_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "device", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "device_occurrence_all.sql" }, - "attributeMappings": { - "device": { - "value": { "column": "device_concept_id" }, - "display": { - "column": "device_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/entity/ingredient_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/original/entity/ingredient_occurrence.json deleted file mode 100644 index 7be06f0ce..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/original/entity/ingredient_occurrence.json +++ /dev/null @@ -1,35 +0,0 @@ -{ - "name": "ingredient_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "ingredient", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "refills", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "days_supply", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "ingredient_occurrence_all.sql" }, - "attributeMappings": { - "ingredient": { - "value": { "column": "drug_concept_id" }, - "display": { - "column": "drug_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/entity/procedure_occurrence.json b/service/src/main/resources/config/broad/cms_synpuf/original/entity/procedure_occurrence.json deleted file mode 100644 index e7b248ce7..000000000 --- a/service/src/main/resources/config/broad/cms_synpuf/original/entity/procedure_occurrence.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "name": "procedure_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "procedure", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "procedure_occurrence_all.sql" }, - "attributeMappings": { - "procedure": { - "value": { "column": "procedure_concept_id" }, - "display": { - "column": "procedure_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "date": { "value": { "column": "procedure_dat" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/sql/brand_all.sql b/service/src/main/resources/config/broad/cms_synpuf/sql/brand_all.sql similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/sql/brand_all.sql rename to service/src/main/resources/config/broad/cms_synpuf/sql/brand_all.sql diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/sql/brand_ingredients.sql b/service/src/main/resources/config/broad/cms_synpuf/sql/brand_ingredients.sql similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/sql/brand_ingredients.sql rename to service/src/main/resources/config/broad/cms_synpuf/sql/brand_ingredients.sql diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/sql/brand_textSearch.sql b/service/src/main/resources/config/broad/cms_synpuf/sql/brand_textSearch.sql similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/sql/brand_textSearch.sql rename to service/src/main/resources/config/broad/cms_synpuf/sql/brand_textSearch.sql diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/sql/condition_occurrence_all.sql b/service/src/main/resources/config/broad/cms_synpuf/sql/condition_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/sql/condition_occurrence_all.sql rename to service/src/main/resources/config/broad/cms_synpuf/sql/condition_occurrence_all.sql diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/sql/condition_parentChild.sql b/service/src/main/resources/config/broad/cms_synpuf/sql/condition_parentChild.sql similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/sql/condition_parentChild.sql rename to service/src/main/resources/config/broad/cms_synpuf/sql/condition_parentChild.sql diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/sql/condition_textSearch.sql b/service/src/main/resources/config/broad/cms_synpuf/sql/condition_textSearch.sql similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/sql/condition_textSearch.sql rename to service/src/main/resources/config/broad/cms_synpuf/sql/condition_textSearch.sql diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/sql/device_occurrence_all.sql b/service/src/main/resources/config/broad/cms_synpuf/sql/device_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/sql/device_occurrence_all.sql rename to service/src/main/resources/config/broad/cms_synpuf/sql/device_occurrence_all.sql diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/sql/device_textSearch.sql b/service/src/main/resources/config/broad/cms_synpuf/sql/device_textSearch.sql similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/sql/device_textSearch.sql rename to service/src/main/resources/config/broad/cms_synpuf/sql/device_textSearch.sql diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/sql/ingredient_all.sql b/service/src/main/resources/config/broad/cms_synpuf/sql/ingredient_all.sql similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/sql/ingredient_all.sql rename to service/src/main/resources/config/broad/cms_synpuf/sql/ingredient_all.sql diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/sql/ingredient_occurrence_all.sql b/service/src/main/resources/config/broad/cms_synpuf/sql/ingredient_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/sql/ingredient_occurrence_all.sql rename to service/src/main/resources/config/broad/cms_synpuf/sql/ingredient_occurrence_all.sql diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/sql/ingredient_parentChild.sql b/service/src/main/resources/config/broad/cms_synpuf/sql/ingredient_parentChild.sql similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/sql/ingredient_parentChild.sql rename to service/src/main/resources/config/broad/cms_synpuf/sql/ingredient_parentChild.sql diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/sql/ingredient_textSearch.sql b/service/src/main/resources/config/broad/cms_synpuf/sql/ingredient_textSearch.sql similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/sql/ingredient_textSearch.sql rename to service/src/main/resources/config/broad/cms_synpuf/sql/ingredient_textSearch.sql diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/sql/observation_occurrence_all.sql b/service/src/main/resources/config/broad/cms_synpuf/sql/observation_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/sql/observation_occurrence_all.sql rename to service/src/main/resources/config/broad/cms_synpuf/sql/observation_occurrence_all.sql diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/sql/observation_textSearch.sql b/service/src/main/resources/config/broad/cms_synpuf/sql/observation_textSearch.sql similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/sql/observation_textSearch.sql rename to service/src/main/resources/config/broad/cms_synpuf/sql/observation_textSearch.sql diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/sql/person.sql b/service/src/main/resources/config/broad/cms_synpuf/sql/person.sql similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/sql/person.sql rename to service/src/main/resources/config/broad/cms_synpuf/sql/person.sql diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/sql/procedure_occurrence_all.sql b/service/src/main/resources/config/broad/cms_synpuf/sql/procedure_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/sql/procedure_occurrence_all.sql rename to service/src/main/resources/config/broad/cms_synpuf/sql/procedure_occurrence_all.sql diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/sql/procedure_parentChild.sql b/service/src/main/resources/config/broad/cms_synpuf/sql/procedure_parentChild.sql similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/sql/procedure_parentChild.sql rename to service/src/main/resources/config/broad/cms_synpuf/sql/procedure_parentChild.sql diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/sql/procedure_textSearch.sql b/service/src/main/resources/config/broad/cms_synpuf/sql/procedure_textSearch.sql similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/sql/procedure_textSearch.sql rename to service/src/main/resources/config/broad/cms_synpuf/sql/procedure_textSearch.sql diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/ui/top_level.json b/service/src/main/resources/config/broad/cms_synpuf/ui/top_level.json similarity index 100% rename from service/src/main/resources/config/broad/cms_synpuf/original/ui/top_level.json rename to service/src/main/resources/config/broad/cms_synpuf/ui/top_level.json diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/aou_synthetic.json b/service/src/main/resources/config/verily/aou_synthetic/aou_synthetic.json similarity index 96% rename from service/src/main/resources/config/verily/aou_synthetic/original/aou_synthetic.json rename to service/src/main/resources/config/verily/aou_synthetic/aou_synthetic.json index ab9169710..7a95b0594 100644 --- a/service/src/main/resources/config/verily/aou_synthetic/original/aou_synthetic.json +++ b/service/src/main/resources/config/verily/aou_synthetic/aou_synthetic.json @@ -9,7 +9,7 @@ { "type": "BQ_DATASET", "name": "index_dataset", "projectId": "verily-tanagra-dev", - "datasetId": "aousynthetic_index_011823", + "datasetId": "aousynthetic_index_072623", "dataflowServiceAccountEmail": "workflow-runner@verily-tanagra-dev.iam.gserviceaccount.com" } ], "entities": [ "brand.json", diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entity/brand.json b/service/src/main/resources/config/verily/aou_synthetic/entity/brand.json similarity index 86% rename from service/src/main/resources/config/verily/aou_synthetic/original/entity/brand.json rename to service/src/main/resources/config/verily/aou_synthetic/entity/brand.json index 8169d66fe..f58b7f515 100644 --- a/service/src/main/resources/config/verily/aou_synthetic/original/entity/brand.json +++ b/service/src/main/resources/config/verily/aou_synthetic/entity/brand.json @@ -2,10 +2,10 @@ "name": "brand", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entity/condition.json b/service/src/main/resources/config/verily/aou_synthetic/entity/condition.json similarity index 82% rename from service/src/main/resources/config/verily/aou_synthetic/original/entity/condition.json rename to service/src/main/resources/config/verily/aou_synthetic/entity/condition.json index be324f139..9e1c403ab 100644 --- a/service/src/main/resources/config/verily/aou_synthetic/original/entity/condition.json +++ b/service/src/main/resources/config/verily/aou_synthetic/entity/condition.json @@ -2,11 +2,11 @@ "name": "condition", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entity/condition_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/entity/condition_occurrence.json similarity index 55% rename from service/src/main/resources/config/verily/aou_synthetic/original/entity/condition_occurrence.json rename to service/src/main/resources/config/verily/aou_synthetic/entity/condition_occurrence.json index f5146304c..ecbac09e5 100644 --- a/service/src/main/resources/config/verily/aou_synthetic/original/entity/condition_occurrence.json +++ b/service/src/main/resources/config/verily/aou_synthetic/entity/condition_occurrence.json @@ -2,15 +2,15 @@ "name": "condition_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "condition" }, - { "type": "SIMPLE", "name": "start_date" }, - { "type": "SIMPLE", "name": "end_date" }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "condition", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "end_date", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entity/device.json b/service/src/main/resources/config/verily/aou_synthetic/entity/device.json similarity index 80% rename from service/src/main/resources/config/verily/aou_synthetic/original/entity/device.json rename to service/src/main/resources/config/verily/aou_synthetic/entity/device.json index 2806fa53a..ffa321805 100644 --- a/service/src/main/resources/config/verily/aou_synthetic/original/entity/device.json +++ b/service/src/main/resources/config/verily/aou_synthetic/entity/device.json @@ -2,11 +2,11 @@ "name": "device", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entity/device_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/entity/device_occurrence.json similarity index 57% rename from service/src/main/resources/config/broad/aou_synthetic/original/entity/device_occurrence.json rename to service/src/main/resources/config/verily/aou_synthetic/entity/device_occurrence.json index 8992ed405..25f72a151 100644 --- a/service/src/main/resources/config/broad/aou_synthetic/original/entity/device_occurrence.json +++ b/service/src/main/resources/config/verily/aou_synthetic/entity/device_occurrence.json @@ -2,14 +2,14 @@ "name": "device_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "device" }, - { "type": "SIMPLE", "name": "start_date" }, - { "type": "SIMPLE", "name": "end_date" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "device", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "end_date", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entity/ingredient.json b/service/src/main/resources/config/verily/aou_synthetic/entity/ingredient.json similarity index 84% rename from service/src/main/resources/config/verily/aou_synthetic/original/entity/ingredient.json rename to service/src/main/resources/config/verily/aou_synthetic/entity/ingredient.json index a557d47b7..b614560a0 100644 --- a/service/src/main/resources/config/verily/aou_synthetic/original/entity/ingredient.json +++ b/service/src/main/resources/config/verily/aou_synthetic/entity/ingredient.json @@ -2,11 +2,11 @@ "name": "ingredient", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entity/ingredient_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/entity/ingredient_occurrence.json similarity index 50% rename from service/src/main/resources/config/broad/aou_synthetic/original/entity/ingredient_occurrence.json rename to service/src/main/resources/config/verily/aou_synthetic/entity/ingredient_occurrence.json index 9d4e31f4b..c26202907 100644 --- a/service/src/main/resources/config/broad/aou_synthetic/original/entity/ingredient_occurrence.json +++ b/service/src/main/resources/config/verily/aou_synthetic/entity/ingredient_occurrence.json @@ -2,17 +2,17 @@ "name": "ingredient_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "ingredient" }, - { "type": "SIMPLE", "name": "start_date" }, - { "type": "SIMPLE", "name": "end_date" }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "refills" }, - { "type": "SIMPLE", "name": "days_supply" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "ingredient", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "end_date", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "refills", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "days_supply", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entity/measurement.json b/service/src/main/resources/config/verily/aou_synthetic/entity/measurement.json similarity index 92% rename from service/src/main/resources/config/verily/aou_synthetic/original/entity/measurement.json rename to service/src/main/resources/config/verily/aou_synthetic/entity/measurement.json index 43ca17fca..67079d9fb 100644 --- a/service/src/main/resources/config/verily/aou_synthetic/original/entity/measurement.json +++ b/service/src/main/resources/config/verily/aou_synthetic/entity/measurement.json @@ -2,11 +2,11 @@ "name": "measurement", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entity/measurement_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/entity/measurement_occurrence.json similarity index 63% rename from service/src/main/resources/config/verily/aou_synthetic/original/entity/measurement_occurrence.json rename to service/src/main/resources/config/verily/aou_synthetic/entity/measurement_occurrence.json index 8d36bfb0c..5b9efde7a 100644 --- a/service/src/main/resources/config/verily/aou_synthetic/original/entity/measurement_occurrence.json +++ b/service/src/main/resources/config/verily/aou_synthetic/entity/measurement_occurrence.json @@ -2,16 +2,16 @@ "name": "measurement_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "measurement" }, - { "type": "SIMPLE", "name": "date" }, - { "type": "SIMPLE", "name": "value_numeric" }, - { "type": "KEY_AND_DISPLAY", "name": "value_enum" }, - { "type": "KEY_AND_DISPLAY", "name": "unit" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "measurement", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "value_numeric", "dataType": "DOUBLE" }, + { "type": "KEY_AND_DISPLAY", "name": "value_enum", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entity/observation.json b/service/src/main/resources/config/verily/aou_synthetic/entity/observation.json similarity index 83% rename from service/src/main/resources/config/broad/aou_synthetic/original/entity/observation.json rename to service/src/main/resources/config/verily/aou_synthetic/entity/observation.json index 4523ab033..372c3aed7 100644 --- a/service/src/main/resources/config/broad/aou_synthetic/original/entity/observation.json +++ b/service/src/main/resources/config/verily/aou_synthetic/entity/observation.json @@ -2,11 +2,11 @@ "name": "observation", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entity/observation_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/entity/observation_occurrence.json similarity index 62% rename from service/src/main/resources/config/broad/aou_synthetic/original/entity/observation_occurrence.json rename to service/src/main/resources/config/verily/aou_synthetic/entity/observation_occurrence.json index 0143edb84..d1f9de6f8 100644 --- a/service/src/main/resources/config/broad/aou_synthetic/original/entity/observation_occurrence.json +++ b/service/src/main/resources/config/verily/aou_synthetic/entity/observation_occurrence.json @@ -2,16 +2,16 @@ "name": "observation_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "observation" }, - { "type": "SIMPLE", "name": "date" }, - { "type": "SIMPLE", "name": "value_as_string" }, - { "type": "KEY_AND_DISPLAY", "name": "value" }, - { "type": "KEY_AND_DISPLAY", "name": "unit" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "observation", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "value_as_string", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "value", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entity/person.json b/service/src/main/resources/config/verily/aou_synthetic/entity/person.json similarity index 75% rename from service/src/main/resources/config/verily/aou_synthetic/original/entity/person.json rename to service/src/main/resources/config/verily/aou_synthetic/entity/person.json index aa7be3a45..3b457706d 100644 --- a/service/src/main/resources/config/verily/aou_synthetic/original/entity/person.json +++ b/service/src/main/resources/config/verily/aou_synthetic/entity/person.json @@ -2,12 +2,12 @@ "name": "person", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "year_of_birth" }, - { "type": "KEY_AND_DISPLAY", "name": "gender" }, - { "type": "KEY_AND_DISPLAY", "name": "race" }, - { "type": "KEY_AND_DISPLAY", "name": "ethnicity" }, - { "type": "KEY_AND_DISPLAY", "name": "sex_at_birth" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "year_of_birth", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "gender", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "race", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "ethnicity", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "sex_at_birth", "dataType": "INT64" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entity/procedure.json b/service/src/main/resources/config/verily/aou_synthetic/entity/procedure.json similarity index 82% rename from service/src/main/resources/config/broad/aou_synthetic/original/entity/procedure.json rename to service/src/main/resources/config/verily/aou_synthetic/entity/procedure.json index 6b60bb777..65d17c510 100644 --- a/service/src/main/resources/config/broad/aou_synthetic/original/entity/procedure.json +++ b/service/src/main/resources/config/verily/aou_synthetic/entity/procedure.json @@ -2,11 +2,11 @@ "name": "procedure", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" }, - { "type": "KEY_AND_DISPLAY", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entity/procedure_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/entity/procedure_occurrence.json similarity index 58% rename from service/src/main/resources/config/broad/aou_synthetic/original/entity/procedure_occurrence.json rename to service/src/main/resources/config/verily/aou_synthetic/entity/procedure_occurrence.json index 365672ade..2f8d49cf9 100644 --- a/service/src/main/resources/config/broad/aou_synthetic/original/entity/procedure_occurrence.json +++ b/service/src/main/resources/config/verily/aou_synthetic/entity/procedure_occurrence.json @@ -2,13 +2,13 @@ "name": "procedure_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "procedure" }, - { "type": "SIMPLE", "name": "date" }, - { "type": "SIMPLE", "name": "visit_occurrence_id" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "procedure", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entity/visit.json b/service/src/main/resources/config/verily/aou_synthetic/entity/visit.json similarity index 87% rename from service/src/main/resources/config/broad/aou_synthetic/original/entity/visit.json rename to service/src/main/resources/config/verily/aou_synthetic/entity/visit.json index 6cc2deb8e..410cf0be6 100644 --- a/service/src/main/resources/config/broad/aou_synthetic/original/entity/visit.json +++ b/service/src/main/resources/config/verily/aou_synthetic/entity/visit.json @@ -2,8 +2,8 @@ "name": "visit", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/aou_synthetic/original/entity/visit_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/entity/visit_occurrence.json similarity index 61% rename from service/src/main/resources/config/broad/aou_synthetic/original/entity/visit_occurrence.json rename to service/src/main/resources/config/verily/aou_synthetic/entity/visit_occurrence.json index 6fd2b19a4..e0ee8df91 100644 --- a/service/src/main/resources/config/broad/aou_synthetic/original/entity/visit_occurrence.json +++ b/service/src/main/resources/config/verily/aou_synthetic/entity/visit_occurrence.json @@ -2,13 +2,13 @@ "name": "visit_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id" }, - { "type": "KEY_AND_DISPLAY", "name": "visit" }, - { "type": "SIMPLE", "name": "start_date" }, - { "type": "SIMPLE", "name": "end_date" }, - { "type": "SIMPLE", "name": "source_value" }, - { "type": "SIMPLE", "name": "source_criteria_id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "end_date", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entitygroup/brand_ingredient.json b/service/src/main/resources/config/verily/aou_synthetic/entitygroup/brand_ingredient.json similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/entitygroup/brand_ingredient.json rename to service/src/main/resources/config/verily/aou_synthetic/entitygroup/brand_ingredient.json diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entitygroup/condition_person_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/entitygroup/condition_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/entitygroup/condition_person_occurrence.json rename to service/src/main/resources/config/verily/aou_synthetic/entitygroup/condition_person_occurrence.json diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entitygroup/device_person_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/entitygroup/device_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/entitygroup/device_person_occurrence.json rename to service/src/main/resources/config/verily/aou_synthetic/entitygroup/device_person_occurrence.json diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entitygroup/ingredient_person_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/entitygroup/ingredient_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/entitygroup/ingredient_person_occurrence.json rename to service/src/main/resources/config/verily/aou_synthetic/entitygroup/ingredient_person_occurrence.json diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entitygroup/measurement_person_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/entitygroup/measurement_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/entitygroup/measurement_person_occurrence.json rename to service/src/main/resources/config/verily/aou_synthetic/entitygroup/measurement_person_occurrence.json diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entitygroup/observation_person_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/entitygroup/observation_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/entitygroup/observation_person_occurrence.json rename to service/src/main/resources/config/verily/aou_synthetic/entitygroup/observation_person_occurrence.json diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entitygroup/procedure_person_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/entitygroup/procedure_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/entitygroup/procedure_person_occurrence.json rename to service/src/main/resources/config/verily/aou_synthetic/entitygroup/procedure_person_occurrence.json diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/entitygroup/visit_person_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/entitygroup/visit_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/entitygroup/visit_person_occurrence.json rename to service/src/main/resources/config/verily/aou_synthetic/entitygroup/visit_person_occurrence.json diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/aou_synthetic.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/aou_synthetic.json deleted file mode 100644 index 0d86147ca..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/aou_synthetic.json +++ /dev/null @@ -1,28 +0,0 @@ -{ - "name" : "aou_synthetic", - "dataPointers" : [ { - "type" : "BQ_DATASET", - "name" : "index_dataset", - "projectId" : "verily-tanagra-dev", - "datasetId" : "aousynthetic_index_011823", - "queryProjectId" : "verily-tanagra-dev", - "dataflowServiceAccountEmail" : "workflow-runner@verily-tanagra-dev.iam.gserviceaccount.com", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : true - }, { - "type" : "BQ_DATASET", - "name" : "omop_dataset", - "projectId" : "verily-tanagra-dev", - "datasetId" : "aou_synthetic_SR2019q4r4", - "queryProjectId" : "verily-tanagra-dev", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : true - } ], - "entities" : [ "measurement_occurrence.json", "condition_occurrence.json", "ingredient.json", "device_occurrence.json", "observation.json", "procedure.json", "measurement.json", "ingredient_occurrence.json", "condition.json", "person.json", "visit_occurrence.json", "observation_occurrence.json", "procedure_occurrence.json", "visit.json", "brand.json", "device.json" ], - "entityGroups" : [ "device_person_occurrence.json", "visit_person_occurrence.json", "condition_person_occurrence.json", "ingredient_person_occurrence.json", "observation_person_occurrence.json", "brand_ingredient.json", "measurement_person_occurrence.json", "procedure_person_occurrence.json" ], - "primaryEntity" : "person", - "uiConfig" : "{ \"dataConfig\": { \"primaryEntity\": { \"displayName\": \"Person\", \"entity\": \"person\", \"key\": \"id\" }, \"occurrences\": [ { \"id\": \"condition_occurrence\", \"displayName\": \"Condition Occurrences\", \"entity\": \"condition_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"condition\", \"attribute\": \"condition\", \"entity\": \"condition\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"procedure_occurrence\", \"displayName\": \"Procedure Occurrences\", \"entity\": \"procedure_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"procedure\", \"attribute\": \"procedure\", \"entity\": \"procedure\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"observation_occurrence\", \"displayName\": \"Observation Occurrence\", \"entity\": \"observation_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"observation\", \"attribute\": \"observation\", \"entity\": \"observation\", \"entityAttribute\": \"id\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"ingredient_occurrence\", \"displayName\": \"Drug Occurrence\", \"entity\": \"ingredient_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"ingredient\", \"attribute\": \"id\", \"entity\": \"ingredient\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" }, \"groupings\": [ { \"id\": \"brand\", \"entity\": \"brand\", \"defaultSort\": { \"attribute\": \"name\", \"direction\": \"ASC\" }, \"attributes\": [\"name\", \"id\", \"standard_concept\", \"concept_code\"] } ] } ] } ] }, \"criteriaConfigs\": [ { \"type\": \"classification\", \"id\": \"tanagra-conditions\", \"title\": \"Condition\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Condition\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"condition_occurrence\", \"classification\": \"condition\" }, { \"type\": \"classification\", \"id\": \"tanagra-procedures\", \"title\": \"Procedure\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Procedure\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"procedure_occurrence\", \"classification\": \"procedure\" }, { \"type\": \"classification\", \"id\": \"tanagra-observations\", \"title\": \"Observation\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"observation_occurrence\", \"classification\": \"observation\" }, { \"type\": \"classification\", \"id\": \"tanagra-drugs\", \"title\": \"Drug\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Drug\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"ingredient_occurrence\", \"classification\": \"ingredient\" }, { \"type\": \"attribute\", \"id\": \"tanagra-ethnicity\", \"title\": \"Ethnicity\", \"category\": \"Program data\", \"attribute\": \"ethnicity\" }, { \"type\": \"attribute\", \"id\": \"tanagra-gender\", \"title\": \"Gender identity\", \"category\": \"Program data\", \"attribute\": \"gender\" }, { \"type\": \"attribute\", \"id\": \"tanagra-race\", \"title\": \"Race\", \"category\": \"Program data\", \"attribute\": \"race\" }, { \"type\": \"attribute\", \"id\": \"tanagra-sex_at_birth\", \"title\": \"Sex assigned at birth\", \"category\": \"Program data\", \"attribute\": \"sex_at_birth\" }, { \"type\": \"attribute\", \"id\": \"tanagra-year_of_birth\", \"title\": \"Year of birth\", \"category\": \"Program data\", \"attribute\": \"year_of_birth\" } ], \"demographicChartConfigs\": { \"groupByAttributes\": [\"gender\", \"race\", \"year_of_birth\"], \"chartConfigs\": [ { \"title\": \"Gender identity\", \"primaryProperties\": [{ \"key\": \"gender\" }] }, { \"title\": \"Gender identity, Current age, Race\", \"primaryProperties\": [ { \"key\": \"gender\" }, { \"key\": \"age\", \"buckets\": [ { \"min\": 18, \"max\": 45, \"displayName\": \"18-44\" }, { \"min\": 45, \"max\": 65, \"displayName\": \"45-64\" }, { \"min\": 65, \"displayName\": \"65+\" } ] } ], \"stackedProperty\": { \"key\": \"race\" } } ] }, \"prepackagedConceptSets\": [ { \"id\": \"_demographics\", \"name\": \"Demographics\", \"occurrence\": \"\" }, { \"id\": \"_analgesics\", \"name\": \"Analgesics\", \"occurrence\": \"ingredient_occurrence\", \"filter\": { \"type\": \"CLASSIFICATION\", \"occurrenceId\": \"ingredient_occurrence\", \"classificationId\": \"ingredient\", \"keys\": [21604253] } } ], \"criteriaSearchConfig\": { \"criteriaTypeWidth\": 120, \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept Name\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up Count\" } ] }, \"cohortReviewConfig\": { \"participantsListColumns\": [ { \"key\": \"id\", \"width\": 100, \"title\": \"Id\" }, { \"key\": \"gender\", \"width\": 100, \"title\": \"Gender\" }, { \"key\": \"race\", \"width\": 100, \"title\": \"Race\" }, { \"key\": \"ethnicity\", \"width\": 100, \"title\": \"Ethnicity\" }, { \"key\": \"year_of_birth\", \"width\": 60, \"title\": \"Year of Birth\" } ], \"attributes\": [ { \"title\": \"Gender\", \"key\": \"gender\" }, { \"title\": \"Year of birth\", \"key\": \"year_of_birth\" }, { \"title\": \"Race\", \"key\": \"race\" }, { \"title\": \"Ethnicity\", \"key\": \"ethnicity\" } ], \"pages\": [ { \"type\": \"occurrenceTable\", \"id\": \"condition\", \"title\": \"Conditions\", \"plugin\": { \"occurrence\": \"condition_occurrence\", \"columns\": [ { \"key\": \"condition\", \"width\": \"100%\", \"title\": \"Condition name\", \"sortable\": true }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\", \"sortable\": true }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"procedure\", \"title\": \"Procedures\", \"plugin\": { \"occurrence\": \"procedure_occurrence\", \"columns\": [ { \"key\": \"procedure\", \"width\": \"100%\", \"title\": \"Procedure name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"observation\", \"title\": \"Observations\", \"plugin\": { \"occurrence\": \"observation_occurrence\", \"columns\": [ { \"key\": \"observation\", \"width\": \"100%\", \"title\": \"Observation name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\" , \"sortable\": true} ] } }, { \"type\": \"occurrenceTable\", \"id\": \"ingredient\", \"title\": \"Drugs\", \"plugin\": { \"occurrence\": \"ingredient_occurrence\", \"columns\": [ { \"key\": \"ingredient\", \"width\": \"100%\", \"title\": \"Drug name\", \"sortable\": true }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\", \"sortable\": true }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\", \"sortable\": true } ] } } ] } } ", - "metadata" : { } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/brand.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/brand.json deleted file mode 100644 index 687808cd7..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/brand.json +++ /dev/null @@ -1,190 +0,0 @@ -{ - "name" : "brand", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Drug" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Brand Name" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "invalid_reason", - "runtimeCalculated" : false - }, - "operator" : "IS", - "value" : { } - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "RxNorm" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "RxNorm Extension" - } - } ] - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT cs.concept_id AS id, cs.concept_synonym_name AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept_synonym` cs ) AS textsearch JOIN `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND c.concept_class_id = 'Brand Name' AND c.invalid_reason IS NULL AND c.vocabulary_id IN ('RxNorm', 'RxNorm Extension')" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "brand" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/condition.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/condition.json deleted file mode 100644 index dbe85bc26..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/condition.json +++ /dev/null @@ -1,334 +0,0 @@ -{ - "name" : "condition", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 172324 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "PPI" - }, - "display" : "AllOfUs_PPI (Columbia)" - }, - "count" : 74 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CIEL" - }, - "display" : "Columbia International eHealth Laboratory (Columbia University)" - }, - "count" : 38818 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "Healthcare Common Procedure Coding System (CMS)" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICDO3" - }, - "display" : "International Classification of Diseases for Oncology, Third Edition (WHO)" - }, - "count" : 61790 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS)" - }, - "count" : 15733 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "International Classification of Diseases, Tenth Revision, Clinical Modification (NCHS)" - }, - "count" : 90462 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 166684 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Condition" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT cs.concept_id AS id, cs.concept_synonym_name AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept_synonym` cs ) AS textsearch JOIN `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Condition' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept_relationship` cr JOIN `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Condition' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED'" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 441840 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "condition" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "condition_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "condition_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "condition" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/condition_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/condition_occurrence.json deleted file mode 100644 index 579e6ce59..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/condition_occurrence.json +++ /dev/null @@ -1,212 +0,0 @@ -{ - "name" : "condition_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "condition", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 2.000023411E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020479.0, - "maxVal" : 1.5996259E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201235E7, - "maxVal" : 2.0435757E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "STRING", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "condition_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "condition_end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "condition_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "condition_source_concept_id", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "condition_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "condition_start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "condition_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_condition", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/device.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/device.json deleted file mode 100644 index 4b3770702..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/device.json +++ /dev/null @@ -1,224 +0,0 @@ -{ - "name" : "device", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 214183 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "Current Procedural Terminology version 4 (AMA)" - }, - "count" : 24 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "Healthcare Common Procedure Coding System (CMS)" - }, - "count" : 4634 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NDC" - }, - "display" : "National Drug Code (FDA and manufacturers)" - }, - "count" : 10582 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 198943 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Device" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT cs.concept_id AS id, cs.concept_synonym_name AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept_synonym` cs ) AS textsearch JOIN `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Device' AND c.standard_concept = 'S'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "device" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/device_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/device_occurrence.json deleted file mode 100644 index ef3353e20..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/device_occurrence.json +++ /dev/null @@ -1,185 +0,0 @@ -{ - "name" : "device_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 4.6274116E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020475.0, - "maxVal" : 1.5995732E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "device", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201235E7, - "maxVal" : 2.0435757E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "STRING", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "device_exposure" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "device_exposure_end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "device_source_concept_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "device_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "device_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "device_exposure_start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "device_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_device", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/ingredient.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/ingredient.json deleted file mode 100644 index cfad77d48..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/ingredient.json +++ /dev/null @@ -1,323 +0,0 @@ -{ - "name" : "ingredient", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 14566 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 6335 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm" - }, - "display" : "RxNorm (NLM)" - }, - "count" : 15575 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm Extension" - }, - "display" : "RxNorm Extension (OMOP)" - }, - "count" : 1978 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ATC" - }, - "display" : "WHO Anatomic Therapeutic Chemical Classification" - }, - "count" : 6335 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT c.concept_id AS id, c.concept_name AS name, c.vocabulary_id, c.standard_concept, c.concept_code FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c WHERE c.domain_id = 'Drug' AND ((c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.concept_class_id = 'Ingredient' AND c.standard_concept = 'S') OR (c.vocabulary_id = 'RxNorm' AND c.concept_class_id = 'Precise Ingredient') OR (c.vocabulary_id = 'ATC' AND c.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c.standard_concept = 'C'))" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT cs.concept_id AS id, cs.concept_synonym_name AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept_synonym` cs ) AS textsearch JOIN `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND ((c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.concept_class_id = 'Ingredient' AND c.standard_concept = 'S') OR (c.vocabulary_id = 'RxNorm' AND c.concept_class_id = 'Precise Ingredient') OR (c.vocabulary_id = 'ATC' AND c.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c.standard_concept = 'C'))" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept_relationship` cr JOIN `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id IN ('Has form', 'RxNorm - ATC', 'RxNorm - ATC name', 'Mapped from', 'Subsumes') AND c1.concept_id != c2.concept_id AND ((c1.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c1.concept_class_id = 'Ingredient' AND c1.standard_concept = 'S') OR (c1.vocabulary_id = 'RxNorm' AND c1.concept_class_id = 'Precise Ingredient') OR (c1.vocabulary_id = 'ATC' AND c1.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c1.standard_concept = 'C')) AND ((c2.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c2.concept_class_id = 'Ingredient' AND c2.standard_concept = 'S') OR (c2.vocabulary_id = 'RxNorm' AND c2.concept_class_id = 'Precise Ingredient') OR (c2.vocabulary_id = 'ATC' AND c2.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c2.standard_concept = 'C')) UNION ALL SELECT ca.ancestor_concept_id AS parent, ca.descendant_concept_id AS child, FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept_ancestor` ca JOIN `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c1 ON c1.concept_id = ca.ancestor_concept_id JOIN `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c2 ON c2.concept_id = ca.descendant_concept_id WHERE ca.min_levels_of_separation = 1 AND ca.max_levels_of_separation = 1 AND ((c1.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c1.concept_class_id = 'Ingredient' AND c1.standard_concept = 'S') OR (c1.vocabulary_id = 'RxNorm' AND c1.concept_class_id = 'Precise Ingredient') OR (c1.vocabulary_id = 'ATC' AND c1.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c1.standard_concept = 'C')) AND ((c2.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c2.concept_class_id = 'Ingredient' AND c2.standard_concept = 'S') OR (c2.vocabulary_id = 'RxNorm' AND c2.concept_class_id = 'Precise Ingredient') OR (c2.vocabulary_id = 'ATC' AND c2.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c2.standard_concept = 'C'))" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC 1st" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "C" - } - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 8 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "ingredient" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "ingredient_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "ingredient_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "ingredient" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 8 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/ingredient_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/ingredient_occurrence.json deleted file mode 100644 index 0f6e7dc7c..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/ingredient_occurrence.json +++ /dev/null @@ -1,256 +0,0 @@ -{ - "name" : "ingredient_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ingredient", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "refills", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -9.223372036854776E18, - "maxVal" : 10.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -9.223372036854776E18, - "maxVal" : 2.000007519E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020479.0, - "maxVal" : 1.5996253E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "days_supply", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -9.223372036854776E18, - "maxVal" : 180.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201235E7, - "maxVal" : 2.0435757E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "STRING", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "drug_exposure" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "drug_exposure_end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "drug_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "drug_source_concept_id", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "drug_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "drug_exposure_start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "ingredient_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "ingredient", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ingredient", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/measurement.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/measurement.json deleted file mode 100644 index 12e0a3267..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/measurement.json +++ /dev/null @@ -1,410 +0,0 @@ -{ - "name" : "measurement", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 67484 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 39415 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "Logical Observation Identifiers Names and Codes (Regenstrief Institute)" - }, - "count" : 183718 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 13963 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Measurement" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "SNOMED" - } - } ] - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC" - } - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC Hierarchy" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC Component" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Lab Test" - } - } ] - } ] - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT cs.concept_id AS id, cs.concept_synonym_name AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept_synonym` cs ) AS textsearch JOIN `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c ON c.concept_id = textsearch.id WHERE ((c.domain_id = 'Measurement' AND c.vocabulary_id = 'SNOMED') OR (c.vocabulary_id = 'LOINC' AND c.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test')))" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept_relationship` cr JOIN `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.vocabulary_id = c2.vocabulary_id AND ((c1.vocabulary_id = 'SNOMED' AND c1.domain_id = c2.domain_id AND c1.domain_id = 'Measurement') OR (c1.vocabulary_id = 'LOINC' AND c1.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test') AND c2.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test'))) " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Measurement" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "SNOMED" - } - } ] - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 36206173 - } - } ] - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 11 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "measurement" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "measurement_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "measurement_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "measurement" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 11 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/measurement_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/measurement_occurrence.json deleted file mode 100644 index b5d3b551a..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/measurement_occurrence.json +++ /dev/null @@ -1,241 +0,0 @@ -{ - "name" : "measurement_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -9.223372036854776E18, - "maxVal" : 3.040008559E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020475.0, - "maxVal" : 1.5996262E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_numeric", - "dataType" : "DOUBLE", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value_enum", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "measurement", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201234E7, - "maxVal" : 2.0435758E7 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "measurement" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "measurement_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "measurement_source_concept_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "measurement_id", - "runtimeCalculated" : false - } - }, - "value_numeric" : { - "value" : { - "column" : "value_as_number", - "runtimeCalculated" : false - } - }, - "value_enum" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "measurement" : { - "value" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "measurement_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "measurement_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "measurement_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value_numeric" : { - "value" : { - "column" : "value_numeric", - "runtimeCalculated" : false - } - }, - "value_enum" : { - "value" : { - "column" : "value_enum", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value_enum", - "runtimeCalculated" : false - } - }, - "measurement" : { - "value" : { - "column" : "measurement", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_measurement", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/observation.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/observation.json deleted file mode 100644 index 8f9517bb9..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/observation.json +++ /dev/null @@ -1,300 +0,0 @@ -{ - "name" : "observation", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 142229 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "APC" - }, - "display" : "Ambulatory Payment Classification (CMS)" - }, - "count" : 715 - }, { - "enumVal" : { - "value" : { - "stringVal" : "AoU_General" - }, - "display" : "AoU_General" - }, - "count" : 11 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "Current Procedural Terminology version 4 (AMA)" - }, - "count" : 1083 - }, { - "enumVal" : { - "value" : { - "stringVal" : "DRG" - }, - "display" : "Diagnosis-related group (CMS)" - }, - "count" : 752 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "Healthcare Common Procedure Coding System (CMS)" - }, - "count" : 2667 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICDO3" - }, - "display" : "International Classification of Diseases for Oncology, Third Edition (WHO)" - }, - "count" : 398 - }, { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "Logical Observation Identifiers Names and Codes (Regenstrief Institute)" - }, - "count" : 6978 - }, { - "enumVal" : { - "value" : { - "stringVal" : "MDC" - }, - "display" : "Major Diagnostic Categories (CMS)" - }, - "count" : 26 - }, { - "enumVal" : { - "value" : { - "stringVal" : "PCORNet" - }, - "display" : "National Patient-Centered Clinical Research Network (PCORI)" - }, - "count" : 2 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NUCC" - }, - "display" : "National Uniform Claim Committee Health Care Provider Taxonomy Code Set (NUCC)" - }, - "count" : 4 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 128425 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Observation" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "PPI" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "Survey" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT cs.concept_id AS id, cs.concept_synonym_name AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept_synonym` cs ) AS textsearch JOIN `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Observation' AND c.standard_concept = 'S' AND c.vocabulary_id != 'PPI' AND c.concept_class_id != 'Survey'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "observation" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/observation_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/observation_occurrence.json deleted file mode 100644 index fe42a567e..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/observation_occurrence.json +++ /dev/null @@ -1,493 +0,0 @@ -{ - "name" : "observation_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 4118133 - }, - "display" : "IU/L" - }, - "count" : 5 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 35011492 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4121007 - }, - "display" : "Seconds" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8799 - }, - "display" : "copies per milliliter" - }, - "count" : 231 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8512 - }, - "display" : "day" - }, - "count" : 2028 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9484 - }, - "display" : "degree" - }, - "count" : 55 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8653 - }, - "display" : "degree Celsius" - }, - "count" : 53 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8529 - }, - "display" : "index" - }, - "count" : 88 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8519 - }, - "display" : "liter" - }, - "count" : 15 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9546 - }, - "display" : "meter" - }, - "count" : 66 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4121396 - }, - "display" : "mg/dL" - }, - "count" : 26047 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8720 - }, - "display" : "microgram per gram" - }, - "count" : 23 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8587 - }, - "display" : "milliliter" - }, - "count" : 87 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8588 - }, - "display" : "millimeter" - }, - "count" : 55 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8876 - }, - "display" : "millimeter mercury column" - }, - "count" : 36 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8753 - }, - "display" : "millimole per liter" - }, - "count" : 22 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8931 - }, - "display" : "million per cubic millimeter" - }, - "count" : 957 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4118323 - }, - "display" : "mmHg" - }, - "count" : 63 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4122417 - }, - "display" : "ng/dL" - }, - "count" : 7 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9372 - }, - "display" : "ounce (apothecary)" - }, - "count" : 25481 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8647 - }, - "display" : "per microliter" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8554 - }, - "display" : "percent" - }, - "count" : 360 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4120725 - }, - "display" : "pg/mL" - }, - "count" : 1235 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8729 - }, - "display" : "picomole per liter" - }, - "count" : 3 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8555 - }, - "display" : "second" - }, - "count" : 7 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8525 - }, - "display" : "titer" - }, - "count" : 534 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4121397 - }, - "display" : "ug/dL" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8510 - }, - "display" : "unit" - }, - "count" : 908557 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8763 - }, - "display" : "unit per milliliter" - }, - "count" : 164 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9234 - }, - "display" : "volume percent" - }, - "count" : 7 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9448 - }, - "display" : "year" - }, - "count" : 129781 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -2.0, - "maxVal" : 2.000023487E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "observation", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_as_string", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020475.0, - "maxVal" : 1.5996262E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201234E7, - "maxVal" : 2.0435758E7 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "observation" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "observation_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "observation_source_concept_id", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "observation_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "observation_id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "observation_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "observation_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_observation", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/person.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/person.json deleted file mode 100644 index 2fa9556eb..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/person.json +++ /dev/null @@ -1,358 +0,0 @@ -{ - "name" : "person", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "gender", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 45878463 - }, - "display" : "Female" - }, - "count" : 142307 - }, { - "enumVal" : { - "value" : { - "int64Val" : 45880669 - }, - "display" : "Male" - }, - "count" : 87099 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2000000002 - }, - "display" : "Not man only, not woman only, prefer not to answer, or skipped" - }, - "count" : 5119 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "race", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 2000000001 - }, - "display" : "Another single population" - }, - "count" : 5443 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8515 - }, - "display" : "Asian" - }, - "count" : 7476 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8516 - }, - "display" : "Black or African American" - }, - "count" : 46967 - }, { - "enumVal" : { - "value" : { - "int64Val" : 1177221 - }, - "display" : "I prefer not to answer" - }, - "count" : 1614 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2000000008 - }, - "display" : "More than one population" - }, - "count" : 10727 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 37524 - }, { - "enumVal" : { - "value" : { - "int64Val" : 45882607 - }, - "display" : "None of these" - }, - "count" : 2465 - }, { - "enumVal" : { - "value" : { - "int64Val" : 903096 - }, - "display" : "PMI: Skip" - }, - "count" : 1584 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8527 - }, - "display" : "White" - }, - "count" : 120725 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ethnicity", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 38003563 - }, - "display" : "Hispanic or Latino" - }, - "count" : 44673 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38003564 - }, - "display" : "Not Hispanic or Latino" - }, - "count" : 184189 - }, { - "enumVal" : { - "value" : { - "int64Val" : 903079 - }, - "display" : "PMI: Prefer Not To Answer" - }, - "count" : 1614 - }, { - "enumVal" : { - "value" : { - "int64Val" : 903096 - }, - "display" : "PMI: Skip" - }, - "count" : 1584 - }, { - "enumVal" : { - "value" : { - "int64Val" : 1586148 - }, - "display" : "What Race Ethnicity: Race Ethnicity None Of These" - }, - "count" : 2465 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "sex_at_birth", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 45878463 - }, - "display" : "Female" - }, - "count" : 143479 - }, { - "enumVal" : { - "value" : { - "int64Val" : 45880669 - }, - "display" : "Male" - }, - "count" : 87821 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 257 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2000000009 - }, - "display" : "Not male, not female, prefer not to answer, or skipped" - }, - "count" : 2968 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "year_of_birth", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 1930.0, - "maxVal" : 2001.0 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "person" - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "gender_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "race_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "ethnicity_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "sex_at_birth" : { - "value" : { - "column" : "sex_at_birth_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "sex_at_birth_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "person" - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_gender", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_race", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ethnicity", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "sex_at_birth" : { - "value" : { - "column" : "sex_at_birth", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_sex_at_birth", - "runtimeCalculated" : false - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/procedure.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/procedure.json deleted file mode 100644 index 7b635c794..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/procedure.json +++ /dev/null @@ -1,350 +0,0 @@ -{ - "name" : "procedure", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 258789 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 3064 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CIEL" - }, - "display" : "Columbia International eHealth Laboratory (Columbia University)" - }, - "count" : 648 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "Current Procedural Terminology version 4 (AMA)" - }, - "count" : 13148 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "Healthcare Common Procedure Coding System (CMS)" - }, - "count" : 1289 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10PCS" - }, - "display" : "ICD-10 Procedure Coding System (CMS)" - }, - "count" : 193773 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS)" - }, - "count" : 283 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9Proc" - }, - "display" : "International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 3 (NCHS)" - }, - "count" : 4657 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "International Classification of Diseases, Tenth Revision, Clinical Modification (NCHS)" - }, - "count" : 9 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)" - }, - "count" : 78887 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Procedure" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "vocabulary_id", - "foreignTable" : "vocabulary", - "foreignKey" : "vocabulary_id", - "foreignColumn" : "vocabulary_name", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT cs.concept_id AS id, cs.concept_synonym_name AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept_synonym` cs ) AS textsearch JOIN `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Procedure' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept_relationship` cr JOIN `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Procedure' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED'" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 4322976 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "procedure" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "procedure_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "procedure_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "procedure" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/procedure_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/procedure_occurrence.json deleted file mode 100644 index cb7efa16d..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/procedure_occurrence.json +++ /dev/null @@ -1,168 +0,0 @@ -{ - "name" : "procedure_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 2.000023474E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2020476.0, - "maxVal" : 1.5996259E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "procedure", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201235E7, - "maxVal" : 2.0435757E7 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "procedure_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "procedure_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "procedure_source_concept_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "procedure_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "procedure_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "procedure_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_procedure", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/visit.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/visit.json deleted file mode 100644 index f5379ce8f..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/visit.json +++ /dev/null @@ -1,105 +0,0 @@ -{ - "name" : "visit", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Visit" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c UNION ALL SELECT cs.concept_id AS id, cs.concept_synonym_name AS text FROM `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept_synonym` cs ) AS textsearch JOIN `verily-tanagra-dev.aou_synthetic_SR2019q4r4.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Visit' AND c.standard_concept = 'S'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "visit" - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/visit_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/visit_occurrence.json deleted file mode 100644 index 59e2c122e..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entity/visit_occurrence.json +++ /dev/null @@ -1,367 +0,0 @@ -{ - "name" : "visit_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 5.542608719E9 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 21039000 - }, - "display" : "10 ML Morphine 0.2 MG/ML Prefilled Syringe Box of 10" - }, - "count" : 21 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21050000 - }, - "display" : "2000 ML benzyl benzoate 250 MG/ML Topical Solution" - }, - "count" : 60 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581478 - }, - "display" : "Ambulance Visit" - }, - "count" : 1746 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38004207 - }, - "display" : "Ambulatory Clinic/Center" - }, - "count" : 80437 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581479 - }, - "display" : "Ambulatory Rehabilitation Visit" - }, - "count" : 179 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21056626 - }, - "display" : "Amiodarone 50 MG/ML Oral Suspension" - }, - "count" : 10 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21090200 - }, - "display" : "Cholecalciferol 50000 UNT Oral Capsule [Aciferol D3] Box of 10 by Rhodes" - }, - "count" : 2 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21090300 - }, - "display" : "Chondroitin Sulfates 400 MG / Glucosamine 500 MG Oral Tablet [Joint-Flex] Box of 60" - }, - "count" : 32 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21036000 - }, - "display" : "Daptomycin 500 MG Injection Box of 1" - }, - "count" : 100 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21090500 - }, - "display" : "Diphenhydramine 25 MG Oral Tablet by Ennogen" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 439748 - }, { - "enumVal" : { - "value" : { - "int64Val" : 262 - }, - "display" : "Emergency Room and Inpatient Visit" - }, - "count" : 25323 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21090400 - }, - "display" : "Ergocalciferol 300000 UNT/ML Prefilled Syringe Box of 10" - }, - "count" : 75 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581476 - }, - "display" : "Home Visit" - }, - "count" : 40500 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 568911 - }, { - "enumVal" : { - "value" : { - "int64Val" : 32036 - }, - "display" : "Laboratory Visit" - }, - "count" : 1850 - }, { - "enumVal" : { - "value" : { - "int64Val" : 12 - }, - "display" : "Modifier" - }, - "count" : 30318 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1340218 - }, { - "enumVal" : { - "value" : { - "int64Val" : 42898160 - }, - "display" : "Non-hospital institution Visit" - }, - "count" : 22 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581477 - }, - "display" : "Office Visit" - }, - "count" : 629739 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814711 - }, - "display" : "Other ambulatory visit" - }, - "count" : 4720 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 9929594 - }, { - "enumVal" : { - "value" : { - "int64Val" : 581458 - }, - "display" : "Pharmacy visit" - }, - "count" : 25279 - }, { - "enumVal" : { - "value" : { - "int64Val" : 21033000 - }, - "display" : "Risperidone 0.5 MG Oral Tablet by Consilient" - }, - "count" : 17 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44818518 - }, - "display" : "Visit derived from EHR record" - }, - "count" : 856887 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 2.0201234E7, - "maxVal" : 2.0435758E7 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "STRING", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "visit_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "visit_end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "visit_source_concept_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "visit_source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "visit_start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "visit_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "visit" : { - "value" : { - "column" : "visit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/brand_ingredient.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/brand_ingredient.json deleted file mode 100644 index a0ad76e41..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/brand_ingredient.json +++ /dev/null @@ -1,101 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "brand_ingredient", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "concept_relationship" - }, - "idPairsIdA" : { - "column" : "concept_id_1", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "concept_id_2", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_brand_ingredient" - }, - "idPairsIdA" : { - "column" : "id_brand", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "brand" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_brand_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_brand_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_brand", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_brand", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "brand", - "itemsEntity" : "ingredient" -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/condition_person_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/condition_person_occurrence.json deleted file mode 100644 index a709ed653..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/condition_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "condition_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_condition_occurrence_condition" - }, - "idPairsIdA" : { - "column" : "id_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_condition", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_condition_person" - }, - "idPairsIdA" : { - "column" : "id_condition", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_condition_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "condition", - "occurrenceEntity" : "condition_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/device_person_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/device_person_occurrence.json deleted file mode 100644 index ff77e8f95..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/device_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "device_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_device_occurrence_device" - }, - "idPairsIdA" : { - "column" : "id_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_device", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_device_person" - }, - "idPairsIdA" : { - "column" : "id_device", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_device_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "device", - "occurrenceEntity" : "device_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/ingredient_person_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/ingredient_person_occurrence.json deleted file mode 100644 index 576ca9260..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/ingredient_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "ingredient_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_occurrence_ingredient" - }, - "idPairsIdA" : { - "column" : "id_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_person" - }, - "idPairsIdA" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "ingredient", - "occurrenceEntity" : "ingredient_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/measurement_person_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/measurement_person_occurrence.json deleted file mode 100644 index cb82b0df7..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/measurement_person_occurrence.json +++ /dev/null @@ -1,287 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "measurement_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_measurement_occurrence_measurement" - }, - "idPairsIdA" : { - "column" : "id_measurement_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_measurement", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_measurement_person" - }, - "idPairsIdA" : { - "column" : "id_measurement", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_measurement_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_measurement_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { - "modifiers" : { - "tablePointer" : { - "table" : "measurement_person_occurrence_modifiers" - }, - "fieldPointers" : { - "min" : { - "column" : "min", - "runtimeCalculated" : false - }, - "enum_count" : { - "column" : "enum_count", - "runtimeCalculated" : false - }, - "max" : { - "column" : "max", - "runtimeCalculated" : false - }, - "enum_display" : { - "column" : "enum_display", - "runtimeCalculated" : false - }, - "enum_value" : { - "column" : "enum_value", - "runtimeCalculated" : false - }, - "attribute_name" : { - "column" : "attribute_name", - "runtimeCalculated" : false - }, - "entity_id" : { - "column" : "entity_id", - "runtimeCalculated" : false - } - } - } - } - }, - "criteriaEntity" : "measurement", - "occurrenceEntity" : "measurement_occurrence", - "modifierAttributes" : [ "value_numeric", "value_enum" ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/observation_person_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/observation_person_occurrence.json deleted file mode 100644 index dad430b34..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/observation_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "observation_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_observation_occurrence_observation" - }, - "idPairsIdA" : { - "column" : "id_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_observation", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_observation_person" - }, - "idPairsIdA" : { - "column" : "id_observation", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_observation_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "observation", - "occurrenceEntity" : "observation_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/procedure_person_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/procedure_person_occurrence.json deleted file mode 100644 index be81091b7..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/procedure_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "procedure_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_procedure_occurrence_procedure" - }, - "idPairsIdA" : { - "column" : "id_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_procedure", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_procedure_person" - }, - "idPairsIdA" : { - "column" : "id_procedure", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_procedure_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "procedure", - "occurrenceEntity" : "procedure_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/visit_person_occurrence.json b/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/visit_person_occurrence.json deleted file mode 100644 index 1a4beff12..000000000 --- a/service/src/main/resources/config/verily/aou_synthetic/expanded/entitygroup/visit_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "visit_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_visit_occurrence_visit" - }, - "idPairsIdA" : { - "column" : "id_visit_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_visit", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_visit_person" - }, - "idPairsIdA" : { - "column" : "id_visit", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_visit_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_visit_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "visit", - "occurrenceEntity" : "visit_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/sql/brand_textSearch.sql b/service/src/main/resources/config/verily/aou_synthetic/sql/brand_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/sql/brand_textSearch.sql rename to service/src/main/resources/config/verily/aou_synthetic/sql/brand_textSearch.sql diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/sql/condition_parentChild.sql b/service/src/main/resources/config/verily/aou_synthetic/sql/condition_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/sql/condition_parentChild.sql rename to service/src/main/resources/config/verily/aou_synthetic/sql/condition_parentChild.sql diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/sql/condition_textSearch.sql b/service/src/main/resources/config/verily/aou_synthetic/sql/condition_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/sql/condition_textSearch.sql rename to service/src/main/resources/config/verily/aou_synthetic/sql/condition_textSearch.sql diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/sql/device_textSearch.sql b/service/src/main/resources/config/verily/aou_synthetic/sql/device_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/sql/device_textSearch.sql rename to service/src/main/resources/config/verily/aou_synthetic/sql/device_textSearch.sql diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/sql/ingredient_all.sql b/service/src/main/resources/config/verily/aou_synthetic/sql/ingredient_all.sql similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/sql/ingredient_all.sql rename to service/src/main/resources/config/verily/aou_synthetic/sql/ingredient_all.sql diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/sql/ingredient_parentChild.sql b/service/src/main/resources/config/verily/aou_synthetic/sql/ingredient_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/sql/ingredient_parentChild.sql rename to service/src/main/resources/config/verily/aou_synthetic/sql/ingredient_parentChild.sql diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/sql/ingredient_textSearch.sql b/service/src/main/resources/config/verily/aou_synthetic/sql/ingredient_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/sql/ingredient_textSearch.sql rename to service/src/main/resources/config/verily/aou_synthetic/sql/ingredient_textSearch.sql diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/sql/measurement_parentChild.sql b/service/src/main/resources/config/verily/aou_synthetic/sql/measurement_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/sql/measurement_parentChild.sql rename to service/src/main/resources/config/verily/aou_synthetic/sql/measurement_parentChild.sql diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/sql/measurement_textSearch.sql b/service/src/main/resources/config/verily/aou_synthetic/sql/measurement_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/sql/measurement_textSearch.sql rename to service/src/main/resources/config/verily/aou_synthetic/sql/measurement_textSearch.sql diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/sql/observation_textSearch.sql b/service/src/main/resources/config/verily/aou_synthetic/sql/observation_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/sql/observation_textSearch.sql rename to service/src/main/resources/config/verily/aou_synthetic/sql/observation_textSearch.sql diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/sql/procedure_parentChild.sql b/service/src/main/resources/config/verily/aou_synthetic/sql/procedure_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/sql/procedure_parentChild.sql rename to service/src/main/resources/config/verily/aou_synthetic/sql/procedure_parentChild.sql diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/sql/procedure_textSearch.sql b/service/src/main/resources/config/verily/aou_synthetic/sql/procedure_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/sql/procedure_textSearch.sql rename to service/src/main/resources/config/verily/aou_synthetic/sql/procedure_textSearch.sql diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/sql/visit_textSearch.sql b/service/src/main/resources/config/verily/aou_synthetic/sql/visit_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/sql/visit_textSearch.sql rename to service/src/main/resources/config/verily/aou_synthetic/sql/visit_textSearch.sql diff --git a/service/src/main/resources/config/verily/aou_synthetic/original/ui/top_level.json b/service/src/main/resources/config/verily/aou_synthetic/ui/top_level.json similarity index 100% rename from service/src/main/resources/config/verily/aou_synthetic/original/ui/top_level.json rename to service/src/main/resources/config/verily/aou_synthetic/ui/top_level.json diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/cms_synpuf.json b/service/src/main/resources/config/verily/cms_synpuf/cms_synpuf.json similarity index 96% rename from service/src/main/resources/config/verily/cms_synpuf/original/cms_synpuf.json rename to service/src/main/resources/config/verily/cms_synpuf/cms_synpuf.json index 158a7de38..9b224c307 100644 --- a/service/src/main/resources/config/verily/cms_synpuf/original/cms_synpuf.json +++ b/service/src/main/resources/config/verily/cms_synpuf/cms_synpuf.json @@ -9,7 +9,7 @@ { "type": "BQ_DATASET", "name": "index_dataset", "projectId": "verily-tanagra-dev", - "datasetId": "cmssynpuf_index_071923", + "datasetId": "cmssynpuf_index_072623", "dataflowServiceAccountEmail": "workflow-runner@verily-tanagra-dev.iam.gserviceaccount.com" } ], "entities": [ "brand.json", diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/entity/brand.json b/service/src/main/resources/config/verily/cms_synpuf/entity/brand.json similarity index 69% rename from service/src/main/resources/config/broad/cms_synpuf/original/entity/brand.json rename to service/src/main/resources/config/verily/cms_synpuf/entity/brand.json index 0403f94a4..b91b1f66a 100644 --- a/service/src/main/resources/config/broad/cms_synpuf/original/entity/brand.json +++ b/service/src/main/resources/config/verily/cms_synpuf/entity/brand.json @@ -2,10 +2,10 @@ "name": "brand", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/sdd/original/entity/condition.json b/service/src/main/resources/config/verily/cms_synpuf/entity/condition.json similarity index 78% rename from service/src/main/resources/config/verily/sdd/original/entity/condition.json rename to service/src/main/resources/config/verily/cms_synpuf/entity/condition.json index 8d7f876d9..e8701cc41 100644 --- a/service/src/main/resources/config/verily/sdd/original/entity/condition.json +++ b/service/src/main/resources/config/verily/cms_synpuf/entity/condition.json @@ -2,11 +2,11 @@ "name": "condition", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/cms_synpuf/entity/condition_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/entity/condition_occurrence.json new file mode 100644 index 000000000..b1651a33e --- /dev/null +++ b/service/src/main/resources/config/verily/cms_synpuf/entity/condition_occurrence.json @@ -0,0 +1,33 @@ +{ + "name": "condition_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "condition", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "condition_occurrence_all.sql" }, + "attributeMappings": { + "condition": { + "value": { "column": "condition_concept_id" }, + "display": { + "column": "condition_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/sdd/original/entity/device.json b/service/src/main/resources/config/verily/cms_synpuf/entity/device.json similarity index 75% rename from service/src/main/resources/config/verily/sdd/original/entity/device.json rename to service/src/main/resources/config/verily/cms_synpuf/entity/device.json index 2e72d8d62..078cd332c 100644 --- a/service/src/main/resources/config/verily/sdd/original/entity/device.json +++ b/service/src/main/resources/config/verily/cms_synpuf/entity/device.json @@ -2,11 +2,11 @@ "name": "device", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/cms_synpuf/entity/device_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/entity/device_occurrence.json new file mode 100644 index 000000000..b1569a268 --- /dev/null +++ b/service/src/main/resources/config/verily/cms_synpuf/entity/device_occurrence.json @@ -0,0 +1,32 @@ +{ + "name": "device_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "device", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "device_occurrence_all.sql" }, + "attributeMappings": { + "device": { + "value": { "column": "device_concept_id" }, + "display": { + "column": "device_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/entity/ingredient.json b/service/src/main/resources/config/verily/cms_synpuf/entity/ingredient.json similarity index 81% rename from service/src/main/resources/config/verily/cms_synpuf/original/entity/ingredient.json rename to service/src/main/resources/config/verily/cms_synpuf/entity/ingredient.json index 0e7901ee5..59a4ddcc0 100644 --- a/service/src/main/resources/config/verily/cms_synpuf/original/entity/ingredient.json +++ b/service/src/main/resources/config/verily/cms_synpuf/entity/ingredient.json @@ -2,11 +2,11 @@ "name": "ingredient", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/cms_synpuf/entity/ingredient_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/entity/ingredient_occurrence.json new file mode 100644 index 000000000..696b8fd95 --- /dev/null +++ b/service/src/main/resources/config/verily/cms_synpuf/entity/ingredient_occurrence.json @@ -0,0 +1,35 @@ +{ + "name": "ingredient_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "ingredient", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "refills", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "days_supply", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "ingredient_occurrence_all.sql" }, + "attributeMappings": { + "ingredient": { + "value": { "column": "drug_concept_id" }, + "display": { + "column": "drug_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/observation.json b/service/src/main/resources/config/verily/cms_synpuf/entity/observation.json similarity index 79% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/observation.json rename to service/src/main/resources/config/verily/cms_synpuf/entity/observation.json index 668afebce..92f45b426 100644 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/observation.json +++ b/service/src/main/resources/config/verily/cms_synpuf/entity/observation.json @@ -2,11 +2,11 @@ "name": "observation", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/entity/observation_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/entity/observation_occurrence.json similarity index 55% rename from service/src/main/resources/config/broad/cms_synpuf/original/entity/observation_occurrence.json rename to service/src/main/resources/config/verily/cms_synpuf/entity/observation_occurrence.json index a619f56ca..822933551 100644 --- a/service/src/main/resources/config/broad/cms_synpuf/original/entity/observation_occurrence.json +++ b/service/src/main/resources/config/verily/cms_synpuf/entity/observation_occurrence.json @@ -2,16 +2,16 @@ "name": "observation_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "observation" }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "value_as_string", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "value", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "unit", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "observation", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "value_as_string", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "value", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/entity/person.json b/service/src/main/resources/config/verily/cms_synpuf/entity/person.json similarity index 75% rename from service/src/main/resources/config/broad/cms_synpuf/original/entity/person.json rename to service/src/main/resources/config/verily/cms_synpuf/entity/person.json index 72d0994bf..ab41605d6 100644 --- a/service/src/main/resources/config/broad/cms_synpuf/original/entity/person.json +++ b/service/src/main/resources/config/verily/cms_synpuf/entity/person.json @@ -2,12 +2,12 @@ "name": "person", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "year_of_birth" }, - { "type": "SIMPLE", "name": "age" }, - { "type": "KEY_AND_DISPLAY", "name": "gender" }, - { "type": "KEY_AND_DISPLAY", "name": "race" }, - { "type": "KEY_AND_DISPLAY", "name": "ethnicity" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "year_of_birth", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "age", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "gender", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "race", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "ethnicity", "dataType": "INT64" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/procedure.json b/service/src/main/resources/config/verily/cms_synpuf/entity/procedure.json similarity index 78% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/procedure.json rename to service/src/main/resources/config/verily/cms_synpuf/entity/procedure.json index 5b26c710e..b45e3d76c 100644 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/procedure.json +++ b/service/src/main/resources/config/verily/cms_synpuf/entity/procedure.json @@ -2,11 +2,11 @@ "name": "procedure", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/cms_synpuf/entity/procedure_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/entity/procedure_occurrence.json new file mode 100644 index 000000000..83ae721c4 --- /dev/null +++ b/service/src/main/resources/config/verily/cms_synpuf/entity/procedure_occurrence.json @@ -0,0 +1,32 @@ +{ + "name": "procedure_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "procedure", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "procedure_occurrence_all.sql" }, + "attributeMappings": { + "procedure": { + "value": { "column": "procedure_concept_id" }, + "display": { + "column": "procedure_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "date": { "value": { "column": "procedure_dat" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/entitygroup/brand_ingredient.json b/service/src/main/resources/config/verily/cms_synpuf/entitygroup/brand_ingredient.json similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/entitygroup/brand_ingredient.json rename to service/src/main/resources/config/verily/cms_synpuf/entitygroup/brand_ingredient.json diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/entitygroup/condition_person_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/entitygroup/condition_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/entitygroup/condition_person_occurrence.json rename to service/src/main/resources/config/verily/cms_synpuf/entitygroup/condition_person_occurrence.json diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/entitygroup/device_person_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/entitygroup/device_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/entitygroup/device_person_occurrence.json rename to service/src/main/resources/config/verily/cms_synpuf/entitygroup/device_person_occurrence.json diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/entitygroup/ingredient_person_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/entitygroup/ingredient_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/entitygroup/ingredient_person_occurrence.json rename to service/src/main/resources/config/verily/cms_synpuf/entitygroup/ingredient_person_occurrence.json diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/entitygroup/observation_person_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/entitygroup/observation_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/entitygroup/observation_person_occurrence.json rename to service/src/main/resources/config/verily/cms_synpuf/entitygroup/observation_person_occurrence.json diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/entitygroup/procedure_person_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/entitygroup/procedure_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/entitygroup/procedure_person_occurrence.json rename to service/src/main/resources/config/verily/cms_synpuf/entitygroup/procedure_person_occurrence.json diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/cms_synpuf.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/cms_synpuf.json deleted file mode 100644 index 493b631df..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/cms_synpuf.json +++ /dev/null @@ -1,28 +0,0 @@ -{ - "name" : "cms_synpuf", - "dataPointers" : [ { - "type" : "BQ_DATASET", - "name" : "index_dataset", - "projectId" : "verily-tanagra-dev", - "datasetId" : "cmssynpuf_index_071923", - "queryProjectId" : "verily-tanagra-dev", - "dataflowServiceAccountEmail" : "workflow-runner@verily-tanagra-dev.iam.gserviceaccount.com", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : true - }, { - "type" : "BQ_DATASET", - "name" : "omop_dataset", - "projectId" : "bigquery-public-data", - "datasetId" : "cms_synthetic_patient_data_omop", - "queryProjectId" : "verily-tanagra-dev", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : true - } ], - "entities" : [ "ingredient_occurrence.json", "condition.json", "condition_occurrence.json", "ingredient.json", "device_occurrence.json", "observation.json", "person.json", "observation_occurrence.json", "procedure.json", "procedure_occurrence.json", "brand.json", "device.json" ], - "entityGroups" : [ "device_person_occurrence.json", "condition_person_occurrence.json", "ingredient_person_occurrence.json", "observation_person_occurrence.json", "brand_ingredient.json", "procedure_person_occurrence.json" ], - "primaryEntity" : "person", - "uiConfig" : "{ \"dataConfig\": { \"primaryEntity\": { \"displayName\": \"Person\", \"entity\": \"person\", \"key\": \"id\" }, \"occurrences\": [ { \"id\": \"condition_occurrence\", \"displayName\": \"Condition Occurrences\", \"entity\": \"condition_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"condition\", \"attribute\": \"condition\", \"entity\": \"condition\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"procedure_occurrence\", \"displayName\": \"Procedure Occurrences\", \"entity\": \"procedure_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"procedure\", \"attribute\": \"procedure\", \"entity\": \"procedure\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"observation_occurrence\", \"displayName\": \"Observation Occurrence\", \"entity\": \"observation_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"observation\", \"attribute\": \"observation\", \"entity\": \"observation\", \"entityAttribute\": \"id\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"ingredient_occurrence\", \"displayName\": \"Drug Occurrence\", \"entity\": \"ingredient_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"ingredient\", \"attribute\": \"id\", \"entity\": \"ingredient\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" }, \"groupings\": [ { \"id\": \"brand\", \"entity\": \"brand\", \"defaultSort\": { \"attribute\": \"name\", \"direction\": \"ASC\" }, \"attributes\": [\"name\", \"id\", \"standard_concept\", \"concept_code\"] } ] } ] } ] }, \"criteriaConfigs\": [ { \"type\": \"classification\", \"id\": \"tanagra-conditions\", \"title\": \"Condition\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Condition\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"condition_occurrence\", \"classification\": \"condition\", \"modifiers\": [ \"age_at_occurrence\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-procedures\", \"title\": \"Procedure\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Procedure\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"procedure_occurrence\", \"classification\": \"procedure\", \"modifiers\": [\"age_at_occurrence\", \"date_group_by_count\"] }, { \"type\": \"classification\", \"id\": \"tanagra-observations\", \"title\": \"Observation\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"observation_occurrence\", \"classification\": \"observation\", \"modifiers\": [\"age_at_occurrence\", \"date_group_by_count\"] }, { \"type\": \"classification\", \"id\": \"tanagra-drugs\", \"title\": \"Drug\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Drug\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"ingredient_occurrence\", \"classification\": \"ingredient\", \"modifiers\": [ \"age_at_occurrence\", \"start_date_group_by_count\" ] }, { \"type\": \"attribute\", \"id\": \"tanagra-ethnicity\", \"title\": \"Ethnicity\", \"category\": \"Program data\", \"attribute\": \"ethnicity\" }, { \"type\": \"attribute\", \"id\": \"tanagra-gender\", \"title\": \"Gender identity\", \"category\": \"Program data\", \"attribute\": \"gender\" }, { \"type\": \"attribute\", \"id\": \"tanagra-race\", \"title\": \"Race\", \"category\": \"Program data\", \"attribute\": \"race\" }, { \"type\": \"attribute\", \"id\": \"tanagra-age\", \"title\": \"Age\", \"category\": \"Program data\", \"attribute\": \"age\" }, { \"type\": \"attribute\", \"id\": \"tanagra-sex_at_birth\", \"title\": \"Sex assigned at birth\", \"category\": \"Program data\", \"attribute\": \"sex_at_birth\" } ], \"modifierConfigs\": [ { \"type\": \"unhinted-value\", \"id\": \"start_date_group_by_count\", \"title\": \"Occurrence count\", \"attribute\": \"start_date\", \"groupByCount\": true }, { \"type\": \"unhinted-value\", \"id\": \"date_group_by_count\", \"title\": \"Occurrence count\", \"attribute\": \"date\", \"groupByCount\": true }, { \"type\": \"attribute\", \"id\": \"age_at_occurrence\", \"title\": \"Age at occurrence\", \"attribute\": \"age_at_occurrence\" } ], \"demographicChartConfigs\": { \"groupByAttributes\": [\"gender\", \"race\", \"age\"], \"chartConfigs\": [ { \"title\": \"Gender identity\", \"primaryProperties\": [{ \"key\": \"gender\" }] }, { \"title\": \"Gender identity, Current age, Race\", \"primaryProperties\": [ { \"key\": \"gender\" }, { \"key\": \"age\", \"buckets\": [ { \"min\": 18, \"max\": 45, \"displayName\": \"18-44\" }, { \"min\": 45, \"max\": 65, \"displayName\": \"45-64\" }, { \"min\": 65, \"displayName\": \"65+\" } ] } ], \"stackedProperty\": { \"key\": \"race\" } } ] }, \"prepackagedConceptSets\": [ { \"id\": \"_demographics\", \"name\": \"Demographics\", \"occurrence\": \"\" }, { \"id\": \"_analgesics\", \"name\": \"Analgesics\", \"occurrence\": \"ingredient_occurrence\", \"filter\": { \"type\": \"CLASSIFICATION\", \"occurrenceId\": \"ingredient_occurrence\", \"classificationId\": \"ingredient\", \"keys\": [21604253] } } ], \"criteriaSearchConfig\": { \"criteriaTypeWidth\": 120, \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept Name\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up Count\" } ] }, \"cohortReviewConfig\": { \"participantsListColumns\": [ { \"key\": \"id\", \"width\": 100, \"title\": \"Id\" }, { \"key\": \"gender\", \"width\": 100, \"title\": \"Gender\" }, { \"key\": \"race\", \"width\": 100, \"title\": \"Race\" }, { \"key\": \"ethnicity\", \"width\": 100, \"title\": \"Ethnicity\" }, { \"key\": \"age\", \"width\": 60, \"title\": \"Age\" } ], \"attributes\": [ { \"title\": \"Gender\", \"key\": \"gender\" }, { \"title\": \"Age\", \"key\": \"age\" }, { \"title\": \"Race\", \"key\": \"race\" }, { \"title\": \"Ethnicity\", \"key\": \"ethnicity\" } ], \"pages\": [ { \"type\": \"occurrenceTable\", \"id\": \"condition\", \"title\": \"Conditions\", \"plugin\": { \"occurrence\": \"condition_occurrence\", \"columns\": [ { \"key\": \"condition\", \"width\": \"100%\", \"title\": \"Condition name\", \"sortable\": true }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\", \"sortable\": true }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"procedure\", \"title\": \"Procedures\", \"plugin\": { \"occurrence\": \"procedure_occurrence\", \"columns\": [ { \"key\": \"procedure\", \"width\": \"100%\", \"title\": \"Procedure name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"observation\", \"title\": \"Observations\", \"plugin\": { \"occurrence\": \"observation_occurrence\", \"columns\": [ { \"key\": \"observation\", \"width\": \"100%\", \"title\": \"Observation name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"ingredient\", \"title\": \"Drugs\", \"plugin\": { \"occurrence\": \"ingredient_occurrence\", \"columns\": [ { \"key\": \"ingredient\", \"width\": \"100%\", \"title\": \"Drug name\", \"sortable\": true }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\", \"sortable\": true }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\", \"sortable\": true } ] } } ] } } ", - "metadata" : { } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/brand.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/brand.json deleted file mode 100644 index 65fb86c50..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/brand.json +++ /dev/null @@ -1,133 +0,0 @@ -{ - "name" : "brand", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT * FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` WHERE domain_id = 'Drug' AND concept_class_id = 'Brand Name' AND vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND DATE_DIFF(CAST(valid_end_date AS DATE), CURRENT_DATE(), DAY) > 0" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ) AS textsearch JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND c.concept_class_id = 'Brand Name' AND c.vocabulary_id IN ('RxNorm', 'RxNorm Extension')" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "brand" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/condition.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/condition.json deleted file mode 100644 index 27fbce0eb..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/condition.json +++ /dev/null @@ -1,299 +0,0 @@ -{ - "name" : "condition", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 97214 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "ICD10CM" - }, - "count" : 108038 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "ICD9CM" - }, - "count" : 16632 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 148722 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Condition" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ) AS textsearch JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Condition' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept_relationship` cr JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Condition' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED'" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 441840 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "condition" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "condition_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "condition_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "condition" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/condition_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/condition_occurrence.json deleted file mode 100644 index 195c36403..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/condition_occurrence.json +++ /dev/null @@ -1,202 +0,0 @@ -{ - "name" : "condition_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "condition", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 24.0, - "maxVal" : 101.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT co.condition_occurrence_id AS id, co.person_id, co.condition_concept_id, co.condition_start_date AS start_date, co.condition_end_date AS end_date, co.stop_reason, co.condition_source_value AS source_value, co.condition_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(co.condition_start_date, DATETIME(p.year_of_birth, p.month_of_birth, p.day_of_birth, 0, 0, 0), DAY) / 365.25) AS INT64) AS age_at_occurrence, FROM `bigquery-public-data.cms_synthetic_patient_data_omop.condition_occurrence` AS co JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.person` AS p ON p.person_id = co.person_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "condition_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "condition_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_condition", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/device.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/device.json deleted file mode 100644 index 25760fb08..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/device.json +++ /dev/null @@ -1,197 +0,0 @@ -{ - "name" : "device", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 18134 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 2828 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 15306 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Device" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ) AS textsearch JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Device' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "device" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/device_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/device_occurrence.json deleted file mode 100644 index 0bf7164ac..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/device_occurrence.json +++ /dev/null @@ -1,175 +0,0 @@ -{ - "name" : "device_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 24.0, - "maxVal" : 101.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "device", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT de.device_exposure_id AS id, de.person_id, de.device_concept_id, de.device_exposure_start_date AS start_date, de.device_exposure_end_date AS end_date, de.device_source_value AS source_value, de.device_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(de.device_exposure_start_date, DATETIME(p.year_of_birth, p.month_of_birth, p.day_of_birth, 0, 0, 0), DAY) / 365.25) AS INT64) AS age_at_occurrence, FROM `bigquery-public-data.cms_synthetic_patient_data_omop.device_exposure` AS de JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.person` AS p ON p.person_id = de.person_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "device_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "device_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_device", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/ingredient.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/ingredient.json deleted file mode 100644 index 11f68e969..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/ingredient.json +++ /dev/null @@ -1,312 +0,0 @@ -{ - "name" : "ingredient", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 1602994 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 43254 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "ATC" - }, - "display" : "ATC" - }, - "count" : 6129 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm" - }, - "display" : "RxNorm" - }, - "count" : 278569 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm Extension" - }, - "display" : "RxNorm Extension" - }, - "count" : 1650444 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT c.concept_id AS id, c.concept_name AS name, c.vocabulary_id, c.standard_concept, c.concept_code FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c WHERE c.domain_id = 'Drug' AND ( (c.vocabulary_id = 'ATC') OR (c.vocabulary_id IN ('RxNorm', 'RxNorm Extension')) ) " - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ) AS textsearch JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND ((c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.concept_class_id = 'Ingredient') OR (c.vocabulary_id = 'RxNorm' AND c.concept_class_id = 'Precise Ingredient') OR (c.vocabulary_id = 'ATC' AND c.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th'))) " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept_relationship` cr JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE c1.concept_id != c2.concept_id AND c1.domain_id = 'Drug' AND c2.domain_id = 'Drug' AND ( /* Populate Ingredients' ancestors', which are ATCs. See https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:atc#:~:text=the%20original%20ATC%20hierarchy%20is%20extended%20by%20Standard%20Drug%20Products%20of%20RxNorm%20and%20RxNorm%20Extension%20vocabularies%2C%20which%20are%20assigned%20to%20be%20descendants%20of%20the%205th%20ATC%20Classes. Eg: ATC 1st (highest ancestor) Subsumes ATC 2nd ATC 5th (direct parent of RxNorm) Maps to RxNorm */ (c1.vocabulary_id IN ('ATC') AND cr.relationship_id IN ('Subsumes', 'Maps to')) OR /* Populate Ingredients and their descendants: Branded Drug, Clinical Drug, etc. Ingredients and their descendants are RxNorm. drug_exposure contains Ingredients or their descendants. Use [1] and [2] to define hierarchy. Eg \"Marketed Product\" is most specific and is bottom of hierarchy. [1] https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:drug_exposure#:~:text=These%20are%20indicated,is%20available%20%E2%80%9CIngredient%E2%80%9D [2] https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:drug#:~:text=are%20not%20implemented.-,Relationships,-As%20usual%2C%20all */ ( c1.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c2.vocabulary_id IN ('RxNorm', 'RxNorm Extension') /* Only keep relationships where c1 is \"parent\" of c2 */ AND cr.relationship_id IN ('Constitutes', 'Contained in' , 'Has form', 'Has quantified form', 'RxNorm ing of', 'RxNorm inverse is a', 'Precise ing of') ) )" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC 1st" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "C" - } - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 15 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "ingredient" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "ingredient_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "ingredient_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "ingredient" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 15 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/ingredient_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/ingredient_occurrence.json deleted file mode 100644 index a906ce1f6..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/ingredient_occurrence.json +++ /dev/null @@ -1,236 +0,0 @@ -{ - "name" : "ingredient_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ingredient", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "refills", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 24.0, - "maxVal" : 101.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "days_supply", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT de.drug_exposure_id AS id, de.person_id, de.drug_concept_id, de.drug_exposure_start_date AS start_date, de.drug_exposure_end_date AS end_date, de.stop_reason, de.refills, de.days_supply, de.drug_source_value AS source_value, de.drug_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(de.drug_exposure_start_date, DATETIME(p.year_of_birth, p.month_of_birth, p.day_of_birth, 0, 0, 0), DAY) / 365.25) AS INT64) AS age_at_occurrence, FROM `bigquery-public-data.cms_synthetic_patient_data_omop.drug_exposure` AS de JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.person` AS p ON p.person_id = de.person_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "drug_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "ingredient_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "ingredient", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ingredient", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/observation.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/observation.json deleted file mode 100644 index f0782bf6e..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/observation.json +++ /dev/null @@ -1,233 +0,0 @@ -{ - "name" : "observation", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 149719 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "CPT4" - }, - "count" : 629 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 1489 - }, { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "LOINC" - }, - "count" : 16762 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 130839 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Observation" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "PPI" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "Survey" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ) AS textsearch JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Observation' AND c.vocabulary_id != 'PPI' AND c.concept_class_id != 'Survey' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "observation" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/observation_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/observation_occurrence.json deleted file mode 100644 index 36c8dd7cc..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/observation_occurrence.json +++ /dev/null @@ -1,231 +0,0 @@ -{ - "name" : "observation_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 24.0, - "maxVal" : 101.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "observation", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_as_string", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT o.observation_id AS id, o.person_id, o.observation_concept_id, o.observation_date, o.value_as_string, o.value_as_concept_id, o.unit_concept_id, o.observation_source_value AS source_value, o.observation_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(o.observation_date, DATETIME(p.year_of_birth, p.month_of_birth, p.day_of_birth, 0, 0, 0), DAY) / 365.25) AS INT64) AS age_at_occurrence, FROM `bigquery-public-data.cms_synthetic_patient_data_omop.observation` AS o JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.person` AS p ON p.person_id = o.person_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "observation_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "observation_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "observation_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_observation", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/person.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/person.json deleted file mode 100644 index 618513a15..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/person.json +++ /dev/null @@ -1,238 +0,0 @@ -{ - "name" : "person", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "gender", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 8532 - }, - "display" : "FEMALE" - }, - "count" : 1292861 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8507 - }, - "display" : "MALE" - }, - "count" : 1033995 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "race", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 8516 - }, - "display" : "Black or African American" - }, - "count" : 247723 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 152425 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8527 - }, - "display" : "White" - }, - "count" : 1926708 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ethnicity", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 38003563 - }, - "display" : "Hispanic or Latino" - }, - "count" : 54453 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38003564 - }, - "display" : "Not Hispanic or Latino" - }, - "count" : 2272403 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "age", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 40.0, - "maxVal" : 114.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "year_of_birth", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 1909.0, - "maxVal" : 1983.0 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT /* Can't do \"*\". During expansion, there's an error about person_id column being ambiguous. */ p.person_id, p.year_of_birth, DATETIME(p.year_of_birth, p.month_of_birth, p.day_of_birth, 0, 0, 0), p.gender_concept_id, p.race_concept_id, p.ethnicity_concept_id FROM `bigquery-public-data.cms_synthetic_patient_data_omop.person` p " - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "gender_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "race_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "ethnicity_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "age" : { - "value" : { - "column" : "year_of_birth", - "sqlFunctionWrapper" : "EXTRACT(YEAR FROM CURRENT_DATE()) - ${fieldSql}", - "runtimeCalculated" : true - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "person" - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_gender", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_race", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ethnicity", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "age" : { - "value" : { - "column" : "age", - "sqlFunctionWrapper" : "EXTRACT(YEAR FROM CURRENT_DATE()) - ${fieldSql}", - "runtimeCalculated" : true - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/procedure.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/procedure.json deleted file mode 100644 index 0062b8f21..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/procedure.json +++ /dev/null @@ -1,323 +0,0 @@ -{ - "name" : "procedure", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 61581 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 2990 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "CPT4" - }, - "count" : 13070 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 981 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "ICD10CM" - }, - "count" : 6 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "ICD9CM" - }, - "count" : 1318 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9Proc" - }, - "display" : "ICD9Proc" - }, - "count" : 4657 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 74959 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Procedure" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ) AS textsearch JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Procedure' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `bigquery-public-data.cms_synthetic_patient_data_omop.concept_relationship` cr JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Procedure' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED'" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 4322976 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "procedure" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "procedure_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "procedure_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "procedure" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/procedure_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/procedure_occurrence.json deleted file mode 100644 index 57892dd4f..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/entity/procedure_occurrence.json +++ /dev/null @@ -1,158 +0,0 @@ -{ - "name" : "procedure_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 24.0, - "maxVal" : 101.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "procedure", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT po.procedure_occurrence_id AS id, po.person_id, po.procedure_concept_id, po.procedure_dat, po.procedure_source_value AS source_value, po.procedure_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(po.procedure_dat, DATETIME(p.year_of_birth, p.month_of_birth, p.day_of_birth, 0, 0, 0), DAY) / 365.25) AS INT64) AS age_at_occurrence, FROM `bigquery-public-data.cms_synthetic_patient_data_omop.procedure_occurrence` AS po JOIN `bigquery-public-data.cms_synthetic_patient_data_omop.person` AS p ON p.person_id = po.person_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "procedure_dat", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "procedure_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "procedure_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_procedure", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/entitygroup/brand_ingredient.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/entitygroup/brand_ingredient.json deleted file mode 100644 index a0ad76e41..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/entitygroup/brand_ingredient.json +++ /dev/null @@ -1,101 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "brand_ingredient", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "concept_relationship" - }, - "idPairsIdA" : { - "column" : "concept_id_1", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "concept_id_2", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_brand_ingredient" - }, - "idPairsIdA" : { - "column" : "id_brand", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "brand" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_brand_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_brand_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_brand", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_brand", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "brand", - "itemsEntity" : "ingredient" -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/entitygroup/condition_person_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/entitygroup/condition_person_occurrence.json deleted file mode 100644 index a709ed653..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/entitygroup/condition_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "condition_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_condition_occurrence_condition" - }, - "idPairsIdA" : { - "column" : "id_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_condition", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_condition_person" - }, - "idPairsIdA" : { - "column" : "id_condition", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_condition_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "condition", - "occurrenceEntity" : "condition_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/entitygroup/device_person_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/entitygroup/device_person_occurrence.json deleted file mode 100644 index ff77e8f95..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/entitygroup/device_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "device_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_device_occurrence_device" - }, - "idPairsIdA" : { - "column" : "id_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_device", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_device_person" - }, - "idPairsIdA" : { - "column" : "id_device", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_device_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "device", - "occurrenceEntity" : "device_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/entitygroup/ingredient_person_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/entitygroup/ingredient_person_occurrence.json deleted file mode 100644 index 576ca9260..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/entitygroup/ingredient_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "ingredient_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_occurrence_ingredient" - }, - "idPairsIdA" : { - "column" : "id_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_person" - }, - "idPairsIdA" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "ingredient", - "occurrenceEntity" : "ingredient_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/entitygroup/observation_person_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/entitygroup/observation_person_occurrence.json deleted file mode 100644 index dad430b34..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/entitygroup/observation_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "observation_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_observation_occurrence_observation" - }, - "idPairsIdA" : { - "column" : "id_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_observation", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_observation_person" - }, - "idPairsIdA" : { - "column" : "id_observation", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_observation_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "observation", - "occurrenceEntity" : "observation_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/expanded/entitygroup/procedure_person_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/expanded/entitygroup/procedure_person_occurrence.json deleted file mode 100644 index be81091b7..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/expanded/entitygroup/procedure_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "procedure_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_procedure_occurrence_procedure" - }, - "idPairsIdA" : { - "column" : "id_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_procedure", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_procedure_person" - }, - "idPairsIdA" : { - "column" : "id_procedure", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_procedure_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "procedure", - "occurrenceEntity" : "procedure_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/entity/condition_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/original/entity/condition_occurrence.json deleted file mode 100644 index d41338a4f..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/original/entity/condition_occurrence.json +++ /dev/null @@ -1,33 +0,0 @@ -{ - "name": "condition_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "condition", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "condition_occurrence_all.sql" }, - "attributeMappings": { - "condition": { - "value": { "column": "condition_concept_id" }, - "display": { - "column": "condition_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/entity/device_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/original/entity/device_occurrence.json deleted file mode 100644 index 6674f3672..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/original/entity/device_occurrence.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "name": "device_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "device", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "device_occurrence_all.sql" }, - "attributeMappings": { - "device": { - "value": { "column": "device_concept_id" }, - "display": { - "column": "device_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/entity/ingredient_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/original/entity/ingredient_occurrence.json deleted file mode 100644 index 7be06f0ce..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/original/entity/ingredient_occurrence.json +++ /dev/null @@ -1,35 +0,0 @@ -{ - "name": "ingredient_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "ingredient", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "refills", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "days_supply", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "ingredient_occurrence_all.sql" }, - "attributeMappings": { - "ingredient": { - "value": { "column": "drug_concept_id" }, - "display": { - "column": "drug_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/entity/procedure_occurrence.json b/service/src/main/resources/config/verily/cms_synpuf/original/entity/procedure_occurrence.json deleted file mode 100644 index e7b248ce7..000000000 --- a/service/src/main/resources/config/verily/cms_synpuf/original/entity/procedure_occurrence.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "name": "procedure_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "procedure", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "procedure_occurrence_all.sql" }, - "attributeMappings": { - "procedure": { - "value": { "column": "procedure_concept_id" }, - "display": { - "column": "procedure_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "date": { "value": { "column": "procedure_dat" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/sql/brand_all.sql b/service/src/main/resources/config/verily/cms_synpuf/sql/brand_all.sql similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/sql/brand_all.sql rename to service/src/main/resources/config/verily/cms_synpuf/sql/brand_all.sql diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/sql/brand_ingredients.sql b/service/src/main/resources/config/verily/cms_synpuf/sql/brand_ingredients.sql similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/sql/brand_ingredients.sql rename to service/src/main/resources/config/verily/cms_synpuf/sql/brand_ingredients.sql diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/sql/brand_textSearch.sql b/service/src/main/resources/config/verily/cms_synpuf/sql/brand_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/sql/brand_textSearch.sql rename to service/src/main/resources/config/verily/cms_synpuf/sql/brand_textSearch.sql diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/sql/condition_occurrence_all.sql b/service/src/main/resources/config/verily/cms_synpuf/sql/condition_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/sql/condition_occurrence_all.sql rename to service/src/main/resources/config/verily/cms_synpuf/sql/condition_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/sql/condition_parentChild.sql b/service/src/main/resources/config/verily/cms_synpuf/sql/condition_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/sql/condition_parentChild.sql rename to service/src/main/resources/config/verily/cms_synpuf/sql/condition_parentChild.sql diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/sql/condition_textSearch.sql b/service/src/main/resources/config/verily/cms_synpuf/sql/condition_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/sql/condition_textSearch.sql rename to service/src/main/resources/config/verily/cms_synpuf/sql/condition_textSearch.sql diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/sql/device_occurrence_all.sql b/service/src/main/resources/config/verily/cms_synpuf/sql/device_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/sql/device_occurrence_all.sql rename to service/src/main/resources/config/verily/cms_synpuf/sql/device_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/sql/device_textSearch.sql b/service/src/main/resources/config/verily/cms_synpuf/sql/device_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/sql/device_textSearch.sql rename to service/src/main/resources/config/verily/cms_synpuf/sql/device_textSearch.sql diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/sql/ingredient_all.sql b/service/src/main/resources/config/verily/cms_synpuf/sql/ingredient_all.sql similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/sql/ingredient_all.sql rename to service/src/main/resources/config/verily/cms_synpuf/sql/ingredient_all.sql diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/sql/ingredient_occurrence_all.sql b/service/src/main/resources/config/verily/cms_synpuf/sql/ingredient_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/sql/ingredient_occurrence_all.sql rename to service/src/main/resources/config/verily/cms_synpuf/sql/ingredient_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/sql/ingredient_parentChild.sql b/service/src/main/resources/config/verily/cms_synpuf/sql/ingredient_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/sql/ingredient_parentChild.sql rename to service/src/main/resources/config/verily/cms_synpuf/sql/ingredient_parentChild.sql diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/sql/ingredient_textSearch.sql b/service/src/main/resources/config/verily/cms_synpuf/sql/ingredient_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/sql/ingredient_textSearch.sql rename to service/src/main/resources/config/verily/cms_synpuf/sql/ingredient_textSearch.sql diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/sql/observation_occurrence_all.sql b/service/src/main/resources/config/verily/cms_synpuf/sql/observation_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/sql/observation_occurrence_all.sql rename to service/src/main/resources/config/verily/cms_synpuf/sql/observation_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/sql/observation_textSearch.sql b/service/src/main/resources/config/verily/cms_synpuf/sql/observation_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/sql/observation_textSearch.sql rename to service/src/main/resources/config/verily/cms_synpuf/sql/observation_textSearch.sql diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/sql/person.sql b/service/src/main/resources/config/verily/cms_synpuf/sql/person.sql similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/sql/person.sql rename to service/src/main/resources/config/verily/cms_synpuf/sql/person.sql diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/sql/procedure_occurrence_all.sql b/service/src/main/resources/config/verily/cms_synpuf/sql/procedure_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/sql/procedure_occurrence_all.sql rename to service/src/main/resources/config/verily/cms_synpuf/sql/procedure_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/sql/procedure_parentChild.sql b/service/src/main/resources/config/verily/cms_synpuf/sql/procedure_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/sql/procedure_parentChild.sql rename to service/src/main/resources/config/verily/cms_synpuf/sql/procedure_parentChild.sql diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/sql/procedure_textSearch.sql b/service/src/main/resources/config/verily/cms_synpuf/sql/procedure_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/sql/procedure_textSearch.sql rename to service/src/main/resources/config/verily/cms_synpuf/sql/procedure_textSearch.sql diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/ui/top_level.json b/service/src/main/resources/config/verily/cms_synpuf/ui/top_level.json similarity index 100% rename from service/src/main/resources/config/verily/cms_synpuf/original/ui/top_level.json rename to service/src/main/resources/config/verily/cms_synpuf/ui/top_level.json diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/entity/brand.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/brand.json similarity index 69% rename from service/src/main/resources/config/verily/cms_synpuf/original/entity/brand.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/brand.json index 0403f94a4..b91b1f66a 100644 --- a/service/src/main/resources/config/verily/cms_synpuf/original/entity/brand.json +++ b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/brand.json @@ -2,10 +2,10 @@ "name": "brand", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/entity/condition.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/condition.json similarity index 78% rename from service/src/main/resources/config/verily/cms_synpuf/original/entity/condition.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/condition.json index 8d7f876d9..e8701cc41 100644 --- a/service/src/main/resources/config/verily/cms_synpuf/original/entity/condition.json +++ b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/condition.json @@ -2,11 +2,11 @@ "name": "condition", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/condition_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/condition_occurrence.json new file mode 100644 index 000000000..da2c2bb90 --- /dev/null +++ b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/condition_occurrence.json @@ -0,0 +1,42 @@ +{ + "name": "condition_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "condition", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_value", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "condition_occurrence_all.sql" }, + "attributeMappings": { + "condition": { + "value": { "column": "condition_concept_id" }, + "display": { + "column": "condition_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/entity/device.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/device.json similarity index 75% rename from service/src/main/resources/config/verily/cms_synpuf/original/entity/device.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/device.json index 2e72d8d62..078cd332c 100644 --- a/service/src/main/resources/config/verily/cms_synpuf/original/entity/device.json +++ b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/device.json @@ -2,11 +2,11 @@ "name": "device", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/device_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/device_occurrence.json new file mode 100644 index 000000000..f1212d800 --- /dev/null +++ b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/device_occurrence.json @@ -0,0 +1,41 @@ +{ + "name": "device_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "device", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "device_occurrence_all.sql" }, + "attributeMappings": { + "device": { + "value": { "column": "device_concept_id" }, + "display": { + "column": "device_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/sdd/original/entity/ingredient.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/ingredient.json similarity index 81% rename from service/src/main/resources/config/verily/sdd/original/entity/ingredient.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/ingredient.json index 0e7901ee5..59a4ddcc0 100644 --- a/service/src/main/resources/config/verily/sdd/original/entity/ingredient.json +++ b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/ingredient.json @@ -2,11 +2,11 @@ "name": "ingredient", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/ingredient_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/ingredient_occurrence.json new file mode 100644 index 000000000..07888a044 --- /dev/null +++ b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/ingredient_occurrence.json @@ -0,0 +1,44 @@ +{ + "name": "ingredient_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "ingredient", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "refills", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "days_supply", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "source_value", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "ingredient_occurrence_all.sql" }, + "attributeMappings": { + "ingredient": { + "value": { "column": "drug_concept_id" }, + "display": { + "column": "drug_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/measurement.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/measurement.json similarity index 90% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entity/measurement.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/measurement.json index 70324f369..f71f480d4 100644 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/measurement.json +++ b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/measurement.json @@ -2,11 +2,11 @@ "name": "measurement", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/sdd/original/entity/measurement_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/measurement_occurrence.json similarity index 55% rename from service/src/main/resources/config/verily/sdd/original/entity/measurement_occurrence.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/measurement_occurrence.json index cc142dabb..081cef822 100644 --- a/service/src/main/resources/config/verily/sdd/original/entity/measurement_occurrence.json +++ b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/measurement_occurrence.json @@ -2,18 +2,18 @@ "name": "measurement_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "measurement", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "value_numeric", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "value_enum", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "unit", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "measurement", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "value_numeric", "dataType": "DOUBLE", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "value_enum", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/entity/observation.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/observation.json similarity index 79% rename from service/src/main/resources/config/verily/cms_synpuf/original/entity/observation.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/observation.json index 668afebce..92f45b426 100644 --- a/service/src/main/resources/config/verily/cms_synpuf/original/entity/observation.json +++ b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/observation.json @@ -2,11 +2,11 @@ "name": "observation", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/sdd/original/entity/observation_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/observation_occurrence.json similarity index 55% rename from service/src/main/resources/config/verily/sdd/original/entity/observation_occurrence.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/observation_occurrence.json index c1709a63a..e60191dab 100644 --- a/service/src/main/resources/config/verily/sdd/original/entity/observation_occurrence.json +++ b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/observation_occurrence.json @@ -2,18 +2,18 @@ "name": "observation_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "observation" }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "value_as_string", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "value", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "unit", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "observation", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "value_as_string", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "value", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/person.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/person.json similarity index 75% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/person.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/person.json index 0ccb5282b..6f5ed26aa 100644 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/person.json +++ b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/person.json @@ -2,12 +2,12 @@ "name": "person", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "year_of_birth" }, - { "type": "SIMPLE", "name": "age" }, - { "type": "KEY_AND_DISPLAY", "name": "gender" }, - { "type": "KEY_AND_DISPLAY", "name": "race" }, - { "type": "KEY_AND_DISPLAY", "name": "ethnicity" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "year_of_birth", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "age", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "gender", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "race", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "ethnicity", "dataType": "INT64" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/verily/sdd/original/entity/procedure.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/procedure.json similarity index 78% rename from service/src/main/resources/config/verily/sdd/original/entity/procedure.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/procedure.json index 5b26c710e..b45e3d76c 100644 --- a/service/src/main/resources/config/verily/sdd/original/entity/procedure.json +++ b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/procedure.json @@ -2,11 +2,11 @@ "name": "procedure", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/procedure_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/procedure_occurrence.json similarity index 51% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entity/procedure_occurrence.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/procedure_occurrence.json index 6d1d61acc..54f261a97 100644 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/procedure_occurrence.json +++ b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/procedure_occurrence.json @@ -2,15 +2,15 @@ "name": "procedure_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "procedure", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "procedure", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/visit.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/visit.json similarity index 85% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/visit.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/visit.json index 0b9a91bde..68bcc9d58 100644 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/visit.json +++ b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/visit.json @@ -2,8 +2,8 @@ "name": "visit", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/visit_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/visit_occurrence.json new file mode 100644 index 000000000..9cd8fcdbd --- /dev/null +++ b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entity/visit_occurrence.json @@ -0,0 +1,32 @@ +{ + "name": "visit_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "visit_occurrence_all.sql" }, + "attributeMappings": { + "visit": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entitygroup/brand_ingredient.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entitygroup/brand_ingredient.json similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entitygroup/brand_ingredient.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entitygroup/brand_ingredient.json diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entitygroup/condition_person_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entitygroup/condition_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entitygroup/condition_person_occurrence.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entitygroup/condition_person_occurrence.json diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entitygroup/device_person_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entitygroup/device_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entitygroup/device_person_occurrence.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entitygroup/device_person_occurrence.json diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entitygroup/ingredient_person_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entitygroup/ingredient_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entitygroup/ingredient_person_occurrence.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entitygroup/ingredient_person_occurrence.json diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entitygroup/measurement_person_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entitygroup/measurement_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entitygroup/measurement_person_occurrence.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entitygroup/measurement_person_occurrence.json diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entitygroup/observation_person_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entitygroup/observation_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entitygroup/observation_person_occurrence.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entitygroup/observation_person_occurrence.json diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entitygroup/procedure_person_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entitygroup/procedure_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entitygroup/procedure_person_occurrence.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entitygroup/procedure_person_occurrence.json diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entitygroup/visit_person_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/entitygroup/visit_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entitygroup/visit_person_occurrence.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/entitygroup/visit_person_occurrence.json diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/brand.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/brand.json deleted file mode 100644 index 8f6d6a970..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/brand.json +++ /dev/null @@ -1,133 +0,0 @@ -{ - "name" : "brand", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT * FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` WHERE domain_id = 'Drug' AND concept_class_id = 'Brand Name' AND vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND DATE_DIFF(CAST(valid_end_date AS DATE), CURRENT_DATE(), DAY) > 0" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c ) AS textsearch JOIN `verily-tanagra-dev.pilot_synthea_2022q3.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND c.concept_class_id = 'Brand Name' AND c.vocabulary_id IN ('RxNorm', 'RxNorm Extension')" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "brand" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/condition.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/condition.json deleted file mode 100644 index 19e3c38b3..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/condition.json +++ /dev/null @@ -1,299 +0,0 @@ -{ - "name" : "condition", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 97214 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "ICD10CM" - }, - "count" : 108038 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "ICD9CM" - }, - "count" : 16632 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 148722 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Condition" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c ) AS textsearch JOIN `verily-tanagra-dev.pilot_synthea_2022q3.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Condition' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept_relationship` cr JOIN `verily-tanagra-dev.pilot_synthea_2022q3.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `verily-tanagra-dev.pilot_synthea_2022q3.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Condition' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED'" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 441840 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "condition" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "condition_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "condition_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "condition" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/condition_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/condition_occurrence.json deleted file mode 100644 index 562e26663..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/condition_occurrence.json +++ /dev/null @@ -1,275 +0,0 @@ -{ - "name" : "condition_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "condition", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 107.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 1158 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 706 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 17297 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT co.condition_occurrence_id AS id, co.person_id, co.condition_concept_id, co.condition_start_date AS start_date, co.condition_end_date AS end_date, co.stop_reason, co.condition_source_value AS source_value, co.condition_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(co.condition_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, co.visit_occurrence_id, vo.visit_concept_id FROM `verily-tanagra-dev.pilot_synthea_2022q3.condition_occurrence` AS co JOIN `verily-tanagra-dev.pilot_synthea_2022q3.person` AS p ON p.person_id = co.person_id LEFT JOIN `verily-tanagra-dev.pilot_synthea_2022q3.visit_occurrence` AS vo ON vo.visit_occurrence_id = co.visit_occurrence_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "condition_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "condition_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_condition", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/device.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/device.json deleted file mode 100644 index d6ca37ae0..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/device.json +++ /dev/null @@ -1,197 +0,0 @@ -{ - "name" : "device", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 18134 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 2828 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 15306 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Device" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c ) AS textsearch JOIN `verily-tanagra-dev.pilot_synthea_2022q3.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Device' AND c.standard_concept = 'S'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "device" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/device_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/device_occurrence.json deleted file mode 100644 index 17fe46c89..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/device_occurrence.json +++ /dev/null @@ -1,248 +0,0 @@ -{ - "name" : "device_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 91.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 112 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 209 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 713 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "device", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT de.device_exposure_id AS id, de.person_id, de.device_concept_id, de.device_exposure_start_date AS start_date, de.device_exposure_end_date AS end_date, de.device_source_value AS source_value, de.device_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(de.device_exposure_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, de.visit_occurrence_id, vo.visit_concept_id FROM `verily-tanagra-dev.pilot_synthea_2022q3.device_exposure` AS de JOIN `verily-tanagra-dev.pilot_synthea_2022q3.person` AS p ON p.person_id = de.person_id LEFT JOIN `verily-tanagra-dev.pilot_synthea_2022q3.visit_occurrence` AS vo ON vo.visit_occurrence_id = de.visit_occurrence_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "device_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "device_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_device", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/ingredient.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/ingredient.json deleted file mode 100644 index 1f91a44b7..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/ingredient.json +++ /dev/null @@ -1,306 +0,0 @@ -{ - "name" : "ingredient", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 1602994 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 6082 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "ATC" - }, - "display" : "ATC" - }, - "count" : 6082 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm" - }, - "display" : "RxNorm" - }, - "count" : 146228 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm Extension" - }, - "display" : "RxNorm Extension" - }, - "count" : 1456766 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT c.concept_id AS id, c.concept_name AS name, c.vocabulary_id, c.standard_concept, c.concept_code FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c WHERE c.domain_id = 'Drug' AND ( (c.vocabulary_id = 'ATC' AND c.standard_concept = 'C') OR (c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.standard_concept = 'S') )" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c ) AS textsearch JOIN `verily-tanagra-dev.pilot_synthea_2022q3.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND ((c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.concept_class_id = 'Ingredient' AND c.standard_concept = 'S') OR (c.vocabulary_id = 'RxNorm' AND c.concept_class_id = 'Precise Ingredient') OR (c.vocabulary_id = 'ATC' AND c.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c.standard_concept = 'C'))" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept_relationship` cr JOIN `verily-tanagra-dev.pilot_synthea_2022q3.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `verily-tanagra-dev.pilot_synthea_2022q3.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE c1.concept_id != c2.concept_id AND c1.domain_id = 'Drug' AND c2.domain_id = 'Drug' AND ( /* Populate Ingredients' ancestors', which are ATCs. See https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:atc#:~:text=the%20original%20ATC%20hierarchy%20is%20extended%20by%20Standard%20Drug%20Products%20of%20RxNorm%20and%20RxNorm%20Extension%20vocabularies%2C%20which%20are%20assigned%20to%20be%20descendants%20of%20the%205th%20ATC%20Classes. Eg: ATC 1st (highest ancestor) Subsumes ATC 2nd ATC 5th (direct parent of RxNorm) Maps to RxNorm */ (c1.vocabulary_id IN ('ATC') AND cr.relationship_id IN ('Subsumes', 'Maps to')) OR /* Populate Ingredients and their descendants: Branded Drug, Clinical Drug, etc. Ingredients and their descendants are RxNorm. drug_exposure contains Ingredients or their descendants. Use [1] and [2] to define hierarchy. Eg \"Marketed Product\" is most specific and is bottom of hierarchy. [1] https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:drug_exposure#:~:text=These%20are%20indicated,is%20available%20%E2%80%9CIngredient%E2%80%9D [2] https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:drug#:~:text=are%20not%20implemented.-,Relationships,-As%20usual%2C%20all */ ( c1.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c2.vocabulary_id IN ('RxNorm', 'RxNorm Extension') /* Only keep relationships where c1 is \"parent\" of c2 */ AND cr.relationship_id IN ('Constitutes', 'Contained in' , 'Has form', 'Has quantified form', 'RxNorm ing of', 'RxNorm inverse is a', 'Precise ing of') ) )" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC 1st" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "C" - } - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 15 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "ingredient" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "ingredient_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "ingredient_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "ingredient" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 15 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/ingredient_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/ingredient_occurrence.json deleted file mode 100644 index d6098d6a6..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/ingredient_occurrence.json +++ /dev/null @@ -1,319 +0,0 @@ -{ - "name" : "ingredient_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ingredient", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 1219 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 2272 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 77306 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "days_supply", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -6.0, - "maxVal" : 21639.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "refills", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 0.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 108.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT de.drug_exposure_id AS id, de.person_id, de.drug_concept_id, de.drug_exposure_start_date AS start_date, de.drug_exposure_end_date AS end_date, de.stop_reason, de.refills, de.days_supply, de.drug_source_value AS source_value, de.drug_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(de.drug_exposure_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, de.visit_occurrence_id, vo.visit_concept_id FROM `verily-tanagra-dev.pilot_synthea_2022q3.drug_exposure` AS de JOIN `verily-tanagra-dev.pilot_synthea_2022q3.person` AS p ON p.person_id = de.person_id LEFT JOIN `verily-tanagra-dev.pilot_synthea_2022q3.visit_occurrence` AS vo ON vo.visit_occurrence_id = de.visit_occurrence_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "drug_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "ingredient_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "ingredient", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ingredient", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/measurement.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/measurement.json deleted file mode 100644 index 1cb4ef56d..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/measurement.json +++ /dev/null @@ -1,399 +0,0 @@ -{ - "name" : "measurement", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 61650 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 38036 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "LOINC" - }, - "count" : 91968 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 11020 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Measurement" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "SNOMED" - } - } ] - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC" - } - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC Hierarchy" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC Component" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Lab Test" - } - } ] - } ] - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c ) AS textsearch JOIN `verily-tanagra-dev.pilot_synthea_2022q3.concept` c ON c.concept_id = textsearch.id WHERE ((c.domain_id = 'Measurement' AND c.vocabulary_id = 'SNOMED') OR (c.vocabulary_id = 'LOINC' AND c.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test')))" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept_relationship` cr JOIN `verily-tanagra-dev.pilot_synthea_2022q3.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `verily-tanagra-dev.pilot_synthea_2022q3.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.vocabulary_id = c2.vocabulary_id AND ((c1.vocabulary_id = 'SNOMED' AND c1.domain_id = c2.domain_id AND c1.domain_id = 'Measurement') OR (c1.vocabulary_id = 'LOINC' AND c1.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test') AND c2.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test'))) " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Measurement" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "SNOMED" - } - } ] - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 36206173 - } - } ] - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 11 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "measurement" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "measurement_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "measurement_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "measurement" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 11 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/measurement_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/measurement_occurrence.json deleted file mode 100644 index 662e61400..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/measurement_occurrence.json +++ /dev/null @@ -1,304 +0,0 @@ -{ - "name" : "measurement_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 108.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 3241 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 33322 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 270774 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_numeric", - "dataType" : "DOUBLE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value_enum", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "measurement", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT mo.measurement_id AS id, mo.person_id, mo.measurement_concept_id, mo.measurement_date, mo.value_as_number AS value_numeric, mo.value_as_concept_id, mo.unit_concept_id, mo.measurement_source_value AS source_value, mo.measurement_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(mo.measurement_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, mo.visit_occurrence_id, vo.visit_concept_id FROM `verily-tanagra-dev.pilot_synthea_2022q3.measurement` AS mo JOIN `verily-tanagra-dev.pilot_synthea_2022q3.person` AS p ON p.person_id = mo.person_id LEFT JOIN `verily-tanagra-dev.pilot_synthea_2022q3.visit_occurrence` AS vo ON vo.visit_occurrence_id = mo.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "measurement_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value_numeric" : { - "value" : { - "column" : "value_numeric", - "runtimeCalculated" : false - } - }, - "value_enum" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "measurement" : { - "value" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "measurement_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "measurement_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value_numeric" : { - "value" : { - "column" : "value_numeric", - "runtimeCalculated" : false - } - }, - "value_enum" : { - "value" : { - "column" : "value_enum", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value_enum", - "runtimeCalculated" : false - } - }, - "measurement" : { - "value" : { - "column" : "measurement", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_measurement", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/observation.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/observation.json deleted file mode 100644 index 766359d1e..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/observation.json +++ /dev/null @@ -1,233 +0,0 @@ -{ - "name" : "observation", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 149719 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "CPT4" - }, - "count" : 629 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 1489 - }, { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "LOINC" - }, - "count" : 16762 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 130839 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Observation" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "PPI" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "Survey" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c ) AS textsearch JOIN `verily-tanagra-dev.pilot_synthea_2022q3.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Observation' AND c.standard_concept = 'S' AND c.vocabulary_id != 'PPI' AND c.concept_class_id != 'Survey'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "observation" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/observation_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/observation_occurrence.json deleted file mode 100644 index 76e85618a..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/observation_occurrence.json +++ /dev/null @@ -1,836 +0,0 @@ -{ - "name" : "observation_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 108.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "observation", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 3037141 - }, - "display" : "Abuse Status [OMAHA]" - }, - "count" : 65 - }, { - "enumVal" : { - "value" : { - "int64Val" : 40759918 - }, - "display" : "Address" - }, - "count" : 9622 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4138133 - }, - "display" : "Animal dander" - }, - "count" : 184 - }, { - "enumVal" : { - "value" : { - "int64Val" : 40766240 - }, - "display" : "Are you covered by health insurance or some other kind of health care plan [PhenX]" - }, - "count" : 65 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4122068 - }, - "display" : "Bee venom" - }, - "count" : 52 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4060985 - }, - "display" : "Body mass index 30+ - obesity" - }, - "count" : 946 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4256640 - }, - "display" : "Body mass index 40+ - severely obese" - }, - "count" : 16 - }, { - "enumVal" : { - "value" : { - "int64Val" : 40771960 - }, - "display" : "Cause of death [US Standard Certificate of Death]" - }, - "count" : 179 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4290627 - }, - "display" : "Cow's milk" - }, - "count" : 42 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4008008 - }, - "display" : "Eggs" - }, - "count" : 40 - }, { - "enumVal" : { - "value" : { - "int64Val" : 40770471 - }, - "display" : "Employment status - current [Reported]" - }, - "count" : 9622 - }, { - "enumVal" : { - "value" : { - "int64Val" : 40762524 - }, - "display" : "Fall risk level [Morse Fall Scale]" - }, - "count" : 2037 - }, { - "enumVal" : { - "value" : { - "int64Val" : 40762523 - }, - "display" : "Fall risk total [Morse Fall Scale]" - }, - "count" : 2037 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4053118 - }, - "display" : "Full-time employment" - }, - "count" : 30026 - }, { - "enumVal" : { - "value" : { - "int64Val" : 42868746 - }, - "display" : "Generalized anxiety disorder 7 item (GAD-7) total score [Reported.PHQ]" - }, - "count" : 4981 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4117479 - }, - "display" : "Grass pollen" - }, - "count" : 148 - }, { - "enumVal" : { - "value" : { - "int64Val" : 40758406 - }, - "display" : "HIV status" - }, - "count" : 65 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4145802 - }, - "display" : "Has a criminal record" - }, - "count" : 490 - }, { - "enumVal" : { - "value" : { - "int64Val" : 42528763 - }, - "display" : "Highest level of education - Reported" - }, - "count" : 9622 - }, { - "enumVal" : { - "value" : { - "int64Val" : 40759172 - }, - "display" : "Hispanic or Latino" - }, - "count" : 9622 - }, { - "enumVal" : { - "value" : { - "int64Val" : 3051031 - }, - "display" : "History of Hospitalizations+Outpatient visits Narrative" - }, - "count" : 65 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4323766 - }, - "display" : "History of amputation of foot" - }, - "count" : 4 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4323208 - }, - "display" : "History of appendectomy" - }, - "count" : 106 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4324181 - }, - "display" : "History of cardiac arrest" - }, - "count" : 98 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4163874 - }, - "display" : "History of myocardial infarction" - }, - "count" : 62 - }, { - "enumVal" : { - "value" : { - "int64Val" : 45766064 - }, - "display" : "History of single seizure" - }, - "count" : 72 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4139934 - }, - "display" : "Homeless" - }, - "count" : 14 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4125382 - }, - "display" : "House dust mite" - }, - "count" : 142 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4022661 - }, - "display" : "Housing problem" - }, - "count" : 306 - }, { - "enumVal" : { - "value" : { - "int64Val" : 42869557 - }, - "display" : "Housing status" - }, - "count" : 9687 - }, { - "enumVal" : { - "value" : { - "int64Val" : 40766239 - }, - "display" : "How many people are living or staying at this address [#] [PhenX]" - }, - "count" : 9622 - }, { - "enumVal" : { - "value" : { - "int64Val" : 37017222 - }, - "display" : "Lack of access to transportation" - }, - "count" : 238 - }, { - "enumVal" : { - "value" : { - "int64Val" : 40758030 - }, - "display" : "Language.preferred" - }, - "count" : 9622 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4008070 - }, - "display" : "Latex" - }, - "count" : 62 - }, { - "enumVal" : { - "value" : { - "int64Val" : 46235010 - }, - "display" : "Mental health Outpatient Note" - }, - "count" : 44 - }, { - "enumVal" : { - "value" : { - "int64Val" : 42529398 - }, - "display" : "Mental health Telehealth Note" - }, - "count" : 43 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4224654 - }, - "display" : "Mold" - }, - "count" : 176 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4072733 - }, - "display" : "Only received primary school education" - }, - "count" : 226 - }, { - "enumVal" : { - "value" : { - "int64Val" : 3034263 - }, - "display" : "Pain severity - Reported" - }, - "count" : 1386 - }, { - "enumVal" : { - "value" : { - "int64Val" : 46235652 - }, - "display" : "Pain severity in the past week - 0-10 numeric rating [Reported]" - }, - "count" : 522 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4059634 - }, - "display" : "Part-time employment" - }, - "count" : 5608 - }, { - "enumVal" : { - "value" : { - "int64Val" : 40758879 - }, - "display" : "Patient Health Questionnaire 2 item (PHQ-2) total score [Reported]" - }, - "count" : 7514 - }, { - "enumVal" : { - "value" : { - "int64Val" : 3042932 - }, - "display" : "Patient Health Questionnaire 9 item (PHQ-9) total score [Reported]" - }, - "count" : 443 - }, { - "enumVal" : { - "value" : { - "int64Val" : 46235654 - }, - "display" : "Primary insurance" - }, - "count" : 9622 - }, { - "enumVal" : { - "value" : { - "int64Val" : 3046853 - }, - "display" : "Race" - }, - "count" : 9622 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4076230 - }, - "display" : "Received higher education" - }, - "count" : 1134 - }, { - "enumVal" : { - "value" : { - "int64Val" : 40488824 - }, - "display" : "Refugee" - }, - "count" : 140 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4313322 - }, - "display" : "Reports of violence in the environment" - }, - "count" : 1150 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4074924 - }, - "display" : "Served in armed forces" - }, - "count" : 146 - }, { - "enumVal" : { - "value" : { - "int64Val" : 46235214 - }, - "display" : "Sexual orientation" - }, - "count" : 65 - }, { - "enumVal" : { - "value" : { - "int64Val" : 42709996 - }, - "display" : "Smokes tobacco daily" - }, - "count" : 26 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4106307 - }, - "display" : "Soya bean" - }, - "count" : 34 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4038238 - }, - "display" : "Suspected lung cancer" - }, - "count" : 32 - }, { - "enumVal" : { - "value" : { - "int64Val" : 46234710 - }, - "display" : "Symptom" - }, - "count" : 240 - }, { - "enumVal" : { - "value" : { - "int64Val" : 43054909 - }, - "display" : "Tobacco smoking status NHIS" - }, - "count" : 12938 - }, { - "enumVal" : { - "value" : { - "int64Val" : 46235357 - }, - "display" : "Total score [AUDIT-C]" - }, - "count" : 3015 - }, { - "enumVal" : { - "value" : { - "int64Val" : 42529243 - }, - "display" : "Total score [DAST-10]" - }, - "count" : 3006 - }, { - "enumVal" : { - "value" : { - "int64Val" : 46234808 - }, - "display" : "Total score [HARK]" - }, - "count" : 2935 - }, { - "enumVal" : { - "value" : { - "int64Val" : 42869860 - }, - "display" : "Total score [MMSE]" - }, - "count" : 86 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4141789 - }, - "display" : "Transport problems" - }, - "count" : 236 - }, { - "enumVal" : { - "value" : { - "int64Val" : 36713251 - }, - "display" : "Tree nut" - }, - "count" : 46 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4121085 - }, - "display" : "Unable to swallow saliva" - }, - "count" : 4 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4251171 - }, - "display" : "Unemployed" - }, - "count" : 128 - }, { - "enumVal" : { - "value" : { - "int64Val" : 40766311 - }, - "display" : "What was your best estimate of the total income of all family members from all sources, before taxes, in last year [PhenX]" - }, - "count" : 9622 - }, { - "enumVal" : { - "value" : { - "int64Val" : 4261709 - }, - "display" : "Wheat" - }, - "count" : 62 - }, { - "enumVal" : { - "value" : { - "int64Val" : 46235507 - }, - "display" : "Within the last year, have you been afraid of your partner or ex-partner [HARK]" - }, - "count" : 9622 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_as_string", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 780 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 3092 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 285915 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT o.observation_id AS id, o.person_id, o.observation_concept_id, o.observation_date, o.value_as_string, o.value_as_concept_id, o.unit_concept_id, o.observation_source_value AS source_value, o.observation_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(o.observation_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, o.visit_occurrence_id, vo.visit_concept_id FROM `verily-tanagra-dev.pilot_synthea_2022q3.observation` AS o JOIN `verily-tanagra-dev.pilot_synthea_2022q3.person` AS p ON p.person_id = o.person_id LEFT JOIN `verily-tanagra-dev.pilot_synthea_2022q3.visit_occurrence` AS vo ON vo.visit_occurrence_id = o.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "observation_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "observation_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "observation_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_observation", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/person.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/person.json deleted file mode 100644 index f684802c7..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/person.json +++ /dev/null @@ -1,246 +0,0 @@ -{ - "name" : "person", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "gender", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 8532 - }, - "display" : "FEMALE" - }, - "count" : 538 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8507 - }, - "display" : "MALE" - }, - "count" : 647 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "race", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 8515 - }, - "display" : "Asian" - }, - "count" : 78 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8516 - }, - "display" : "Black or African American" - }, - "count" : 98 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 44 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8527 - }, - "display" : "White" - }, - "count" : 965 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ethnicity", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 38003563 - }, - "display" : "Hispanic or Latino" - }, - "count" : 143 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38003564 - }, - "display" : "Not Hispanic or Latino" - }, - "count" : 1042 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "age", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 1.0, - "maxVal" : 110.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "year_of_birth", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 1913.0, - "maxVal" : 2022.0 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "person" - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "gender_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "race_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "ethnicity_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "age" : { - "value" : { - "column" : "birth_datetime", - "sqlFunctionWrapper" : "CAST(FLOOR(TIMESTAMP_DIFF(CURRENT_TIMESTAMP(), ${fieldSql}, DAY) / 365.25) AS INT64)", - "runtimeCalculated" : true - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "person" - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_gender", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_race", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ethnicity", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "age" : { - "value" : { - "column" : "age", - "sqlFunctionWrapper" : "CAST(FLOOR(TIMESTAMP_DIFF(CURRENT_TIMESTAMP(), ${fieldSql}, DAY) / 365.25) AS INT64)", - "runtimeCalculated" : true - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/procedure.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/procedure.json deleted file mode 100644 index d41a83b1e..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/procedure.json +++ /dev/null @@ -1,323 +0,0 @@ -{ - "name" : "procedure", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 61581 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 2990 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "CPT4" - }, - "count" : 13070 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 981 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "ICD10CM" - }, - "count" : 6 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "ICD9CM" - }, - "count" : 1318 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9Proc" - }, - "display" : "ICD9Proc" - }, - "count" : 4657 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 74959 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Procedure" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c ) AS textsearch JOIN `verily-tanagra-dev.pilot_synthea_2022q3.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Procedure' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept_relationship` cr JOIN `verily-tanagra-dev.pilot_synthea_2022q3.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `verily-tanagra-dev.pilot_synthea_2022q3.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Procedure' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED'" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 4322976 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "procedure" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "procedure_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "procedure_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "procedure" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/procedure_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/procedure_occurrence.json deleted file mode 100644 index f48fba53f..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/procedure_occurrence.json +++ /dev/null @@ -1,231 +0,0 @@ -{ - "name" : "procedure_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 108.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 1547 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 3825 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 49493 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "procedure", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT po.procedure_occurrence_id AS id, po.person_id, po.procedure_concept_id, po.procedure_date, po.procedure_source_value AS source_value, po.procedure_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(po.procedure_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, po.visit_occurrence_id, vo.visit_concept_id FROM `verily-tanagra-dev.pilot_synthea_2022q3.procedure_occurrence` AS po JOIN `verily-tanagra-dev.pilot_synthea_2022q3.person` AS p ON p.person_id = po.person_id LEFT JOIN `verily-tanagra-dev.pilot_synthea_2022q3.visit_occurrence` AS vo ON vo.visit_occurrence_id = po.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "procedure_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "procedure_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "procedure_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_procedure", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/visit.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/visit.json deleted file mode 100644 index 69f7de8e8..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/visit.json +++ /dev/null @@ -1,105 +0,0 @@ -{ - "name" : "visit", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Visit" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept` c ) AS textsearch JOIN `verily-tanagra-dev.pilot_synthea_2022q3.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Visit' AND c.standard_concept = 'S'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "visit" - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/visit_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/visit_occurrence.json deleted file mode 100644 index a6ae18d3c..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entity/visit_occurrence.json +++ /dev/null @@ -1,203 +0,0 @@ -{ - "name" : "visit_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 108.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 2088 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 2041 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 55578 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT vo.visit_occurrence_id AS id, vo.person_id, vo.visit_concept_id, vo.visit_start_date AS start_date, vo.visit_end_date AS end_date, vo.visit_source_value AS source_value, vo.visit_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(vo.visit_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence FROM `verily-tanagra-dev.pilot_synthea_2022q3.visit_occurrence` AS vo JOIN `verily-tanagra-dev.pilot_synthea_2022q3.person` AS p ON p.person_id = vo.person_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "visit" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "visit_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "visit" : { - "value" : { - "column" : "visit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/brand_ingredient.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/brand_ingredient.json deleted file mode 100644 index 1e846b59c..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/brand_ingredient.json +++ /dev/null @@ -1,101 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "brand_ingredient", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "rawSql" : "/* 1. User searches for Brand Tylenol 2. User expands Tylenol to see which ingredients are in Tylenol 3. Ingredient Acetaminophen is shown Acetaminophen has over 300 descendants (eg \"acetaminophen 100 MG/ML Oral Suspension\"). Acetaminophen's concept_class_id is Ingredient; descendants' concept_class_ids are Clinical Drug Comp, Quant Clinical Drug, etc. Most descendants have a relationship with Brand Tylenol in concept_relationship. However, we only want to show Acetaminophen in step 3. So only keep relationships with concept_class_id=Ingredient. */ SELECT cr.* FROM `verily-tanagra-dev.pilot_synthea_2022q3.concept_relationship` cr, `verily-tanagra-dev.pilot_synthea_2022q3.concept` c2 WHERE cr.concept_id_2 = c2.concept_id AND c2.concept_class_id = 'Ingredient'" - }, - "idPairsIdA" : { - "column" : "concept_id_1", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "concept_id_2", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_brand_ingredient" - }, - "idPairsIdA" : { - "column" : "id_brand", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "brand" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_brand_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_brand_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_brand", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_brand", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "brand", - "itemsEntity" : "ingredient" -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/condition_person_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/condition_person_occurrence.json deleted file mode 100644 index a709ed653..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/condition_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "condition_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_condition_occurrence_condition" - }, - "idPairsIdA" : { - "column" : "id_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_condition", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_condition_person" - }, - "idPairsIdA" : { - "column" : "id_condition", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_condition_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "condition", - "occurrenceEntity" : "condition_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/device_person_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/device_person_occurrence.json deleted file mode 100644 index ff77e8f95..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/device_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "device_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_device_occurrence_device" - }, - "idPairsIdA" : { - "column" : "id_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_device", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_device_person" - }, - "idPairsIdA" : { - "column" : "id_device", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_device_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "device", - "occurrenceEntity" : "device_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/ingredient_person_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/ingredient_person_occurrence.json deleted file mode 100644 index 576ca9260..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/ingredient_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "ingredient_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_occurrence_ingredient" - }, - "idPairsIdA" : { - "column" : "id_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_person" - }, - "idPairsIdA" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "ingredient", - "occurrenceEntity" : "ingredient_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/measurement_person_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/measurement_person_occurrence.json deleted file mode 100644 index cb82b0df7..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/measurement_person_occurrence.json +++ /dev/null @@ -1,287 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "measurement_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_measurement_occurrence_measurement" - }, - "idPairsIdA" : { - "column" : "id_measurement_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_measurement", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_measurement_person" - }, - "idPairsIdA" : { - "column" : "id_measurement", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_measurement_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_measurement_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { - "modifiers" : { - "tablePointer" : { - "table" : "measurement_person_occurrence_modifiers" - }, - "fieldPointers" : { - "min" : { - "column" : "min", - "runtimeCalculated" : false - }, - "enum_count" : { - "column" : "enum_count", - "runtimeCalculated" : false - }, - "max" : { - "column" : "max", - "runtimeCalculated" : false - }, - "enum_display" : { - "column" : "enum_display", - "runtimeCalculated" : false - }, - "enum_value" : { - "column" : "enum_value", - "runtimeCalculated" : false - }, - "attribute_name" : { - "column" : "attribute_name", - "runtimeCalculated" : false - }, - "entity_id" : { - "column" : "entity_id", - "runtimeCalculated" : false - } - } - } - } - }, - "criteriaEntity" : "measurement", - "occurrenceEntity" : "measurement_occurrence", - "modifierAttributes" : [ "value_numeric", "value_enum" ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/observation_person_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/observation_person_occurrence.json deleted file mode 100644 index dad430b34..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/observation_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "observation_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_observation_occurrence_observation" - }, - "idPairsIdA" : { - "column" : "id_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_observation", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_observation_person" - }, - "idPairsIdA" : { - "column" : "id_observation", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_observation_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "observation", - "occurrenceEntity" : "observation_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/procedure_person_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/procedure_person_occurrence.json deleted file mode 100644 index be81091b7..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/procedure_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "procedure_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_procedure_occurrence_procedure" - }, - "idPairsIdA" : { - "column" : "id_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_procedure", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_procedure_person" - }, - "idPairsIdA" : { - "column" : "id_procedure", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_procedure_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "procedure", - "occurrenceEntity" : "procedure_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/visit_person_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/visit_person_occurrence.json deleted file mode 100644 index 1a4beff12..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/entitygroup/visit_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "visit_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_visit_occurrence_visit" - }, - "idPairsIdA" : { - "column" : "id_visit_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_visit", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_visit_person" - }, - "idPairsIdA" : { - "column" : "id_visit", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_visit_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_visit_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "visit", - "occurrenceEntity" : "visit_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/pilot_synthea_2022q3.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/pilot_synthea_2022q3.json deleted file mode 100644 index 6baf3b0aa..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/expanded/pilot_synthea_2022q3.json +++ /dev/null @@ -1,29 +0,0 @@ -{ - "name" : "pilot_synthea_2022q3", - "dataPointers" : [ { - "type" : "BQ_DATASET", - "name" : "index_dataset", - "projectId" : "verily-tanagra-dev", - "datasetId" : "pilot_synthea2022q3_index_051923", - "queryProjectId" : "verily-tanagra-dev", - "dataflowServiceAccountEmail" : "workflow-runner@verily-tanagra-dev.iam.gserviceaccount.com", - "dataflowTempLocation" : "gs://dataflow-staging-us-central1-694046000181/temp/", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : false - }, { - "type" : "BQ_DATASET", - "name" : "omop_dataset", - "projectId" : "verily-tanagra-dev", - "datasetId" : "pilot_synthea_2022q3", - "queryProjectId" : "verily-tanagra-dev", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : true - } ], - "entities" : [ "measurement_occurrence.json", "condition_occurrence.json", "ingredient.json", "device_occurrence.json", "observation.json", "procedure.json", "measurement.json", "ingredient_occurrence.json", "condition.json", "person.json", "visit_occurrence.json", "observation_occurrence.json", "procedure_occurrence.json", "visit.json", "brand.json", "device.json" ], - "entityGroups" : [ "device_person_occurrence.json", "visit_person_occurrence.json", "condition_person_occurrence.json", "ingredient_person_occurrence.json", "observation_person_occurrence.json", "brand_ingredient.json", "measurement_person_occurrence.json", "procedure_person_occurrence.json" ], - "primaryEntity" : "person", - "uiConfig" : "{ \"dataConfig\": { \"primaryEntity\": { \"displayName\": \"Person\", \"entity\": \"person\", \"key\": \"id\", \"classifications\": [] }, \"occurrences\": [ { \"id\": \"condition_occurrence\", \"displayName\": \"Condition Occurrences\", \"entity\": \"condition_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"condition\", \"attribute\": \"condition\", \"entity\": \"condition\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"procedure_occurrence\", \"displayName\": \"Procedure Occurrences\", \"entity\": \"procedure_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"procedure\", \"attribute\": \"procedure\", \"entity\": \"procedure\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"observation_occurrence\", \"displayName\": \"Observation Occurrence\", \"entity\": \"observation_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"observation\", \"attribute\": \"observation\", \"entity\": \"observation\", \"entityAttribute\": \"id\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"ingredient_occurrence\", \"displayName\": \"Drug Occurrence\", \"entity\": \"ingredient_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"ingredient\", \"attribute\": \"id\", \"entity\": \"ingredient\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" }, \"groupings\": [ { \"id\": \"brand\", \"entity\": \"brand\", \"defaultSort\": { \"attribute\": \"name\", \"direction\": \"ASC\" }, \"attributes\": [\"name\", \"id\", \"standard_concept\", \"concept_code\"] } ] } ] }, { \"id\": \"measurement_occurrence\", \"displayName\": \"Measurement Occurrence\", \"entity\": \"measurement_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"measurement\", \"attribute\": \"measurement\", \"entity\": \"measurement\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_item_count\", \"direction\": \"DESC\" } } ] } ] }, \"criteriaConfigs\": [ { \"type\": \"classification\", \"id\": \"tanagra-conditions\", \"title\": \"Condition\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Condition\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"condition_occurrence\", \"classification\": \"condition\", \"modifiers\": [ \"age_at_occurrence\", \"visit_type\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-procedures\", \"title\": \"Procedure\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Procedure\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"procedure_occurrence\", \"classification\": \"procedure\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"] }, { \"type\": \"classification\", \"id\": \"tanagra-observations\", \"title\": \"Observation\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"observation_occurrence\", \"classification\": \"observation\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"] }, { \"type\": \"classification\", \"id\": \"tanagra-drugs\", \"title\": \"Drug\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Drug\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"ingredient_occurrence\", \"classification\": \"ingredient\", \"modifiers\": [ \"age_at_occurrence\", \"visit_type\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-measurement\", \"title\": \"Labs and measurements\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_item_count\", \"width\": 120, \"title\": \"Count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Condition\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"measurement_occurrence\", \"classification\": \"measurement\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"], \"valueConfigs\": [ { \"title\": \"Categorical value\", \"attribute\": \"value_enum\" }, { \"title\": \"Numeric value\", \"attribute\": \"value_numeric\" } ] }, { \"type\": \"attribute\", \"id\": \"tanagra-ethnicity\", \"title\": \"Ethnicity\", \"category\": \"Program data\", \"attribute\": \"ethnicity\" }, { \"type\": \"attribute\", \"id\": \"tanagra-gender\", \"title\": \"Gender identity\", \"category\": \"Program data\", \"attribute\": \"gender\" }, { \"type\": \"attribute\", \"id\": \"tanagra-race\", \"title\": \"Race\", \"category\": \"Program data\", \"attribute\": \"race\" }, { \"type\": \"attribute\", \"id\": \"tanagra-age\", \"title\": \"Age\", \"category\": \"Program data\", \"attribute\": \"age\" } ], \"modifierConfigs\": [ { \"type\": \"unhinted-value\", \"id\": \"start_date_group_by_count\", \"title\": \"Occurrence count\", \"attribute\": \"start_date\", \"groupByCount\": true }, { \"type\": \"unhinted-value\", \"id\": \"date_group_by_count\", \"title\": \"Occurrence count\", \"attribute\": \"date\", \"groupByCount\": true }, { \"type\": \"attribute\", \"id\": \"visit_type\", \"title\": \"Visit type\", \"attribute\": \"visit_type\" }, { \"type\": \"attribute\", \"id\": \"age_at_occurrence\", \"title\": \"Age at occurrence\", \"attribute\": \"age_at_occurrence\" } ], \"demographicChartConfigs\": { \"groupByAttributes\": [\"gender\", \"race\", \"age\"], \"chartConfigs\": [ { \"title\": \"Gender identity\", \"primaryProperties\": [{ \"key\": \"gender\" }] }, { \"title\": \"Gender identity, Current age, Race\", \"primaryProperties\": [ { \"key\": \"gender\" }, { \"key\": \"age\", \"buckets\": [ { \"min\": 18, \"max\": 45, \"displayName\": \"18-44\" }, { \"min\": 45, \"max\": 65, \"displayName\": \"45-64\" }, { \"min\": 65, \"displayName\": \"65+\" } ] } ], \"stackedProperty\": { \"key\": \"race\" } } ] }, \"prepackagedConceptSets\": [ { \"id\": \"_demographics\", \"name\": \"Demographics\", \"occurrence\": \"\" }, { \"id\": \"_analgesics\", \"name\": \"Analgesics\", \"occurrence\": \"ingredient_occurrence\", \"filter\": { \"type\": \"CLASSIFICATION\", \"occurrenceId\": \"ingredient_occurrence\", \"classificationId\": \"ingredient\", \"keys\": [21604253] } } ], \"criteriaSearchConfig\": { \"criteriaTypeWidth\": 120, \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept Name\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up Count\" } ] }, \"cohortReviewConfig\": { \"participantsListColumns\": [ { \"key\": \"id\", \"width\": 100, \"title\": \"Id\" }, { \"key\": \"gender\", \"width\": 100, \"title\": \"Gender\" }, { \"key\": \"race\", \"width\": 100, \"title\": \"Race\" }, { \"key\": \"ethnicity\", \"width\": 100, \"title\": \"Ethnicity\" }, { \"key\": \"age\", \"width\": 60, \"title\": \"Year of Birth\" } ], \"attributes\": [ { \"title\": \"Gender\", \"key\": \"gender\" }, { \"title\": \"Age\", \"key\": \"age\" }, { \"title\": \"Race\", \"key\": \"race\" }, { \"title\": \"Ethnicity\", \"key\": \"ethnicity\" } ], \"pages\": [ { \"type\": \"occurrenceTable\", \"id\": \"condition\", \"title\": \"Conditions\", \"plugin\": { \"occurrence\": \"condition_occurrence\", \"columns\": [ { \"key\": \"condition\", \"width\": \"100%\", \"title\": \"Condition name\", \"sortable\": true }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\", \"sortable\": true }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"procedure\", \"title\": \"Procedures\", \"plugin\": { \"occurrence\": \"procedure_occurrence\", \"columns\": [ { \"key\": \"procedure\", \"width\": \"100%\", \"title\": \"Procedure name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"observation\", \"title\": \"Observations\", \"plugin\": { \"occurrence\": \"observation_occurrence\", \"columns\": [ { \"key\": \"observation\", \"width\": \"100%\", \"title\": \"Observation name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"ingredient\", \"title\": \"Drugs\", \"plugin\": { \"occurrence\": \"ingredient_occurrence\", \"columns\": [ { \"key\": \"ingredient\", \"width\": \"100%\", \"title\": \"Drug name\", \"sortable\": true }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\", \"sortable\": true }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"measurements\", \"title\": \"Labs and measurements\", \"plugin\": { \"occurrence\": \"measurement_occurrence\", \"columns\": [ { \"key\": \"measurement\", \"width\": \"100%\", \"title\": \"Lab/measurement name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true }, { \"key\": \"value_enum\", \"width\": 160, \"title\": \"Categorical value\", \"sortable\": true }, { \"key\": \"value_numeric\", \"width\": 160, \"title\": \"Numeric value\", \"sortable\": true }, { \"key\": \"unit\", \"width\": 160, \"title\": \"Unit\", \"sortable\": true } ] } } ] } } ", - "metadata" : { } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/condition_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/condition_occurrence.json deleted file mode 100644 index 5734966fc..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/condition_occurrence.json +++ /dev/null @@ -1,42 +0,0 @@ -{ - "name": "condition_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "condition", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "condition_occurrence_all.sql" }, - "attributeMappings": { - "condition": { - "value": { "column": "condition_concept_id" }, - "display": { - "column": "condition_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/device_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/device_occurrence.json deleted file mode 100644 index ffcfbb5fc..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/device_occurrence.json +++ /dev/null @@ -1,41 +0,0 @@ -{ - "name": "device_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "device", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "device_occurrence_all.sql" }, - "attributeMappings": { - "device": { - "value": { "column": "device_concept_id" }, - "display": { - "column": "device_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/ingredient_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/ingredient_occurrence.json deleted file mode 100644 index 6e4263d3a..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/ingredient_occurrence.json +++ /dev/null @@ -1,44 +0,0 @@ -{ - "name": "ingredient_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "ingredient", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "refills" }, - { "type": "SIMPLE", "name": "days_supply" }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "ingredient_occurrence_all.sql" }, - "attributeMappings": { - "ingredient": { - "value": { "column": "drug_concept_id" }, - "display": { - "column": "drug_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/visit_occurrence.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/visit_occurrence.json deleted file mode 100644 index cff5a1628..000000000 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/visit_occurrence.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "name": "visit_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit" }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "visit_occurrence_all.sql" }, - "attributeMappings": { - "visit": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/pilot_synthea_2022q3.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/pilot_synthea_2022q3.json similarity index 96% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/pilot_synthea_2022q3.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/pilot_synthea_2022q3.json index 9cd39e074..2a45fcf1d 100644 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/pilot_synthea_2022q3.json +++ b/service/src/main/resources/config/verily/pilot_synthea_2022q3/pilot_synthea_2022q3.json @@ -10,7 +10,7 @@ { "type": "BQ_DATASET", "name": "index_dataset", "projectId": "verily-tanagra-dev", - "datasetId": "pilot_synthea2022q3_index_051923", + "datasetId": "pilot_synthea2022q3_index_072623", "dataflowServiceAccountEmail": "workflow-runner@verily-tanagra-dev.iam.gserviceaccount.com", "dataflowTempLocation": "gs://dataflow-staging-us-central1-694046000181/temp/", "dataflowRegion": "us-central1", diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/brand_all.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/brand_all.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/brand_all.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/brand_all.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/brand_ingredients.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/brand_ingredients.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/brand_ingredients.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/brand_ingredients.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/brand_textSearch.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/brand_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/brand_textSearch.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/brand_textSearch.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/condition_occurrence_all.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/condition_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/condition_occurrence_all.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/condition_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/condition_parentChild.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/condition_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/condition_parentChild.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/condition_parentChild.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/condition_textSearch.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/condition_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/condition_textSearch.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/condition_textSearch.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/device_occurrence_all.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/device_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/device_occurrence_all.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/device_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/device_textSearch.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/device_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/device_textSearch.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/device_textSearch.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/ingredient_all.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/ingredient_all.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/ingredient_all.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/ingredient_all.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/ingredient_occurrence_all.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/ingredient_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/ingredient_occurrence_all.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/ingredient_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/ingredient_parentChild.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/ingredient_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/ingredient_parentChild.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/ingredient_parentChild.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/ingredient_textSearch.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/ingredient_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/ingredient_textSearch.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/ingredient_textSearch.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/measurement_occurrence_all.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/measurement_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/measurement_occurrence_all.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/measurement_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/measurement_parentChild.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/measurement_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/measurement_parentChild.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/measurement_parentChild.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/measurement_textSearch.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/measurement_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/measurement_textSearch.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/measurement_textSearch.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/observation_occurrence_all.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/observation_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/observation_occurrence_all.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/observation_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/observation_textSearch.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/observation_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/observation_textSearch.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/observation_textSearch.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/procedure_occurrence_all.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/procedure_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/procedure_occurrence_all.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/procedure_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/procedure_parentChild.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/procedure_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/procedure_parentChild.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/procedure_parentChild.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/procedure_textSearch.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/procedure_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/procedure_textSearch.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/procedure_textSearch.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/visit_occurrence_all.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/visit_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/visit_occurrence_all.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/visit_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/visit_textSearch.sql b/service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/visit_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/sql/visit_textSearch.sql rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/sql/visit_textSearch.sql diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/ui/top_level.json b/service/src/main/resources/config/verily/pilot_synthea_2022q3/ui/top_level.json similarity index 100% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/ui/top_level.json rename to service/src/main/resources/config/verily/pilot_synthea_2022q3/ui/top_level.json diff --git a/service/src/main/resources/config/verily/sdd/original/entity/brand.json b/service/src/main/resources/config/verily/sdd/entity/brand.json similarity index 69% rename from service/src/main/resources/config/verily/sdd/original/entity/brand.json rename to service/src/main/resources/config/verily/sdd/entity/brand.json index 0403f94a4..b91b1f66a 100644 --- a/service/src/main/resources/config/verily/sdd/original/entity/brand.json +++ b/service/src/main/resources/config/verily/sdd/entity/brand.json @@ -2,10 +2,10 @@ "name": "brand", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/entity/condition.json b/service/src/main/resources/config/verily/sdd/entity/condition.json similarity index 78% rename from service/src/main/resources/config/broad/cms_synpuf/original/entity/condition.json rename to service/src/main/resources/config/verily/sdd/entity/condition.json index 8d7f876d9..e8701cc41 100644 --- a/service/src/main/resources/config/broad/cms_synpuf/original/entity/condition.json +++ b/service/src/main/resources/config/verily/sdd/entity/condition.json @@ -2,11 +2,11 @@ "name": "condition", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/sdd/entity/condition_occurrence.json b/service/src/main/resources/config/verily/sdd/entity/condition_occurrence.json new file mode 100644 index 000000000..43d6ea3bf --- /dev/null +++ b/service/src/main/resources/config/verily/sdd/entity/condition_occurrence.json @@ -0,0 +1,42 @@ +{ + "name": "condition_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "condition", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "condition_occurrence_all.sql" }, + "attributeMappings": { + "condition": { + "value": { "column": "condition_concept_id" }, + "display": { + "column": "condition_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/entity/device.json b/service/src/main/resources/config/verily/sdd/entity/device.json similarity index 75% rename from service/src/main/resources/config/broad/cms_synpuf/original/entity/device.json rename to service/src/main/resources/config/verily/sdd/entity/device.json index 2e72d8d62..078cd332c 100644 --- a/service/src/main/resources/config/broad/cms_synpuf/original/entity/device.json +++ b/service/src/main/resources/config/verily/sdd/entity/device.json @@ -2,11 +2,11 @@ "name": "device", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/sdd/entity/device_occurrence.json b/service/src/main/resources/config/verily/sdd/entity/device_occurrence.json new file mode 100644 index 000000000..5bbd49b98 --- /dev/null +++ b/service/src/main/resources/config/verily/sdd/entity/device_occurrence.json @@ -0,0 +1,41 @@ +{ + "name": "device_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "device", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "device_occurrence_all.sql" }, + "attributeMappings": { + "device": { + "value": { "column": "device_concept_id" }, + "display": { + "column": "device_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/genotyping.json b/service/src/main/resources/config/verily/sdd/entity/genotyping.json similarity index 83% rename from service/src/main/resources/config/vumc/sdd/original/entity/genotyping.json rename to service/src/main/resources/config/verily/sdd/entity/genotyping.json index da41c742c..9ad082975 100644 --- a/service/src/main/resources/config/vumc/sdd/original/entity/genotyping.json +++ b/service/src/main/resources/config/verily/sdd/entity/genotyping.json @@ -2,8 +2,8 @@ "name": "genotyping", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/broad/cms_synpuf/original/entity/ingredient.json b/service/src/main/resources/config/verily/sdd/entity/ingredient.json similarity index 81% rename from service/src/main/resources/config/broad/cms_synpuf/original/entity/ingredient.json rename to service/src/main/resources/config/verily/sdd/entity/ingredient.json index 0e7901ee5..59a4ddcc0 100644 --- a/service/src/main/resources/config/broad/cms_synpuf/original/entity/ingredient.json +++ b/service/src/main/resources/config/verily/sdd/entity/ingredient.json @@ -2,11 +2,11 @@ "name": "ingredient", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/sdd/entity/ingredient_occurrence.json b/service/src/main/resources/config/verily/sdd/entity/ingredient_occurrence.json new file mode 100644 index 000000000..04f5eff91 --- /dev/null +++ b/service/src/main/resources/config/verily/sdd/entity/ingredient_occurrence.json @@ -0,0 +1,44 @@ +{ + "name": "ingredient_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "ingredient", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "refills", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "days_supply", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "ingredient_occurrence_all.sql" }, + "attributeMappings": { + "ingredient": { + "value": { "column": "drug_concept_id" }, + "display": { + "column": "drug_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/measurement.json b/service/src/main/resources/config/verily/sdd/entity/measurement.json similarity index 90% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/measurement.json rename to service/src/main/resources/config/verily/sdd/entity/measurement.json index 70324f369..f71f480d4 100644 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/measurement.json +++ b/service/src/main/resources/config/verily/sdd/entity/measurement.json @@ -2,11 +2,11 @@ "name": "measurement", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/measurement_occurrence.json b/service/src/main/resources/config/verily/sdd/entity/measurement_occurrence.json similarity index 55% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entity/measurement_occurrence.json rename to service/src/main/resources/config/verily/sdd/entity/measurement_occurrence.json index cc142dabb..081cef822 100644 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/measurement_occurrence.json +++ b/service/src/main/resources/config/verily/sdd/entity/measurement_occurrence.json @@ -2,18 +2,18 @@ "name": "measurement_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "measurement", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "value_numeric", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "value_enum", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "unit", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "measurement", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "value_numeric", "dataType": "DOUBLE", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "value_enum", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/note.json b/service/src/main/resources/config/verily/sdd/entity/note.json similarity index 81% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entity/note.json rename to service/src/main/resources/config/verily/sdd/entity/note.json index e21370c93..a73afb9de 100644 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/note.json +++ b/service/src/main/resources/config/verily/sdd/entity/note.json @@ -2,10 +2,10 @@ "name": "note", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/sdd/entity/note_occurrence.json b/service/src/main/resources/config/verily/sdd/entity/note_occurrence.json new file mode 100644 index 000000000..70d6913cf --- /dev/null +++ b/service/src/main/resources/config/verily/sdd/entity/note_occurrence.json @@ -0,0 +1,42 @@ +{ + "name": "note_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "note", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "title", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "text", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "note_occurrence_all.sql" }, + "attributeMappings": { + "date": { "value": { "column": "note_date" } }, + "note": { + "value": { "column": "note_type_concept_id" }, + "display": { + "column": "note_type_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/sdd/original/entity/observation.json b/service/src/main/resources/config/verily/sdd/entity/observation.json similarity index 79% rename from service/src/main/resources/config/verily/sdd/original/entity/observation.json rename to service/src/main/resources/config/verily/sdd/entity/observation.json index 668afebce..92f45b426 100644 --- a/service/src/main/resources/config/verily/sdd/original/entity/observation.json +++ b/service/src/main/resources/config/verily/sdd/entity/observation.json @@ -2,11 +2,11 @@ "name": "observation", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/observation_occurrence.json b/service/src/main/resources/config/verily/sdd/entity/observation_occurrence.json similarity index 55% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entity/observation_occurrence.json rename to service/src/main/resources/config/verily/sdd/entity/observation_occurrence.json index c1709a63a..e60191dab 100644 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/observation_occurrence.json +++ b/service/src/main/resources/config/verily/sdd/entity/observation_occurrence.json @@ -2,18 +2,18 @@ "name": "observation_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "observation" }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "value_as_string", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "value", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "unit", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "observation", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "value_as_string", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "value", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/person.json b/service/src/main/resources/config/verily/sdd/entity/person.json similarity index 60% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/person.json rename to service/src/main/resources/config/verily/sdd/entity/person.json index 06a1770c9..a68df85fb 100644 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/person.json +++ b/service/src/main/resources/config/verily/sdd/entity/person.json @@ -2,17 +2,17 @@ "name": "person", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "year_of_birth" }, - { "type": "SIMPLE", "name": "age" }, - { "type": "KEY_AND_DISPLAY", "name": "gender" }, - { "type": "KEY_AND_DISPLAY", "name": "race" }, - { "type": "KEY_AND_DISPLAY", "name": "ethnicity" }, - { "type": "SIMPLE", "name": "has_biovu_sample" }, - { "type": "SIMPLE", "name": "biovu_sample_dna_yield" }, - { "type": "SIMPLE", "name": "biovu_sample_is_compromised" }, - { "type": "SIMPLE", "name": "biovu_sample_is_nonshippable" }, - { "type": "SIMPLE", "name": "biovu_sample_has_plasma" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "year_of_birth", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "age", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "gender", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "race", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "ethnicity", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "has_biovu_sample", "dataType": "BOOLEAN" }, + { "type": "SIMPLE", "name": "biovu_sample_dna_yield", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "biovu_sample_is_compromised", "dataType": "BOOLEAN" }, + { "type": "SIMPLE", "name": "biovu_sample_is_nonshippable", "dataType": "BOOLEAN" }, + { "type": "SIMPLE", "name": "biovu_sample_has_plasma", "dataType": "BOOLEAN" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/verily/cms_synpuf/original/entity/procedure.json b/service/src/main/resources/config/verily/sdd/entity/procedure.json similarity index 78% rename from service/src/main/resources/config/verily/cms_synpuf/original/entity/procedure.json rename to service/src/main/resources/config/verily/sdd/entity/procedure.json index 5b26c710e..b45e3d76c 100644 --- a/service/src/main/resources/config/verily/cms_synpuf/original/entity/procedure.json +++ b/service/src/main/resources/config/verily/sdd/entity/procedure.json @@ -2,11 +2,11 @@ "name": "procedure", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/procedure_occurrence.json b/service/src/main/resources/config/verily/sdd/entity/procedure_occurrence.json similarity index 51% rename from service/src/main/resources/config/vumc/sdd/original/entity/procedure_occurrence.json rename to service/src/main/resources/config/verily/sdd/entity/procedure_occurrence.json index 6d1d61acc..40651ca30 100644 --- a/service/src/main/resources/config/vumc/sdd/original/entity/procedure_occurrence.json +++ b/service/src/main/resources/config/verily/sdd/entity/procedure_occurrence.json @@ -2,15 +2,15 @@ "name": "procedure_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "procedure", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "procedure", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/snp.json b/service/src/main/resources/config/verily/sdd/entity/snp.json similarity index 85% rename from service/src/main/resources/config/vumc/sdd/original/entity/snp.json rename to service/src/main/resources/config/verily/sdd/entity/snp.json index f51c0976a..31efb7e94 100644 --- a/service/src/main/resources/config/vumc/sdd/original/entity/snp.json +++ b/service/src/main/resources/config/verily/sdd/entity/snp.json @@ -2,7 +2,7 @@ "name": "snp", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/sdd/original/entity/visit.json b/service/src/main/resources/config/verily/sdd/entity/visit.json similarity index 85% rename from service/src/main/resources/config/verily/sdd/original/entity/visit.json rename to service/src/main/resources/config/verily/sdd/entity/visit.json index 0b9a91bde..68bcc9d58 100644 --- a/service/src/main/resources/config/verily/sdd/original/entity/visit.json +++ b/service/src/main/resources/config/verily/sdd/entity/visit.json @@ -2,8 +2,8 @@ "name": "visit", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/sdd/entity/visit_occurrence.json b/service/src/main/resources/config/verily/sdd/entity/visit_occurrence.json new file mode 100644 index 000000000..9cd8fcdbd --- /dev/null +++ b/service/src/main/resources/config/verily/sdd/entity/visit_occurrence.json @@ -0,0 +1,32 @@ +{ + "name": "visit_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "visit_occurrence_all.sql" }, + "attributeMappings": { + "visit": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/sdd/original/entitygroup/brand_ingredient.json b/service/src/main/resources/config/verily/sdd/entitygroup/brand_ingredient.json similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/entitygroup/brand_ingredient.json rename to service/src/main/resources/config/verily/sdd/entitygroup/brand_ingredient.json diff --git a/service/src/main/resources/config/verily/sdd/original/entitygroup/condition_person_occurrence.json b/service/src/main/resources/config/verily/sdd/entitygroup/condition_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/entitygroup/condition_person_occurrence.json rename to service/src/main/resources/config/verily/sdd/entitygroup/condition_person_occurrence.json diff --git a/service/src/main/resources/config/verily/sdd/original/entitygroup/device_person_occurrence.json b/service/src/main/resources/config/verily/sdd/entitygroup/device_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/entitygroup/device_person_occurrence.json rename to service/src/main/resources/config/verily/sdd/entitygroup/device_person_occurrence.json diff --git a/service/src/main/resources/config/verily/sdd/original/entitygroup/genotyping_person.json b/service/src/main/resources/config/verily/sdd/entitygroup/genotyping_person.json similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/entitygroup/genotyping_person.json rename to service/src/main/resources/config/verily/sdd/entitygroup/genotyping_person.json diff --git a/service/src/main/resources/config/verily/sdd/original/entitygroup/ingredient_person_occurrence.json b/service/src/main/resources/config/verily/sdd/entitygroup/ingredient_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/entitygroup/ingredient_person_occurrence.json rename to service/src/main/resources/config/verily/sdd/entitygroup/ingredient_person_occurrence.json diff --git a/service/src/main/resources/config/verily/sdd/original/entitygroup/measurement_person_occurrence.json b/service/src/main/resources/config/verily/sdd/entitygroup/measurement_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/entitygroup/measurement_person_occurrence.json rename to service/src/main/resources/config/verily/sdd/entitygroup/measurement_person_occurrence.json diff --git a/service/src/main/resources/config/verily/sdd/original/entitygroup/note_person_occurrence.json b/service/src/main/resources/config/verily/sdd/entitygroup/note_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/entitygroup/note_person_occurrence.json rename to service/src/main/resources/config/verily/sdd/entitygroup/note_person_occurrence.json diff --git a/service/src/main/resources/config/verily/sdd/original/entitygroup/observation_person_occurrence.json b/service/src/main/resources/config/verily/sdd/entitygroup/observation_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/entitygroup/observation_person_occurrence.json rename to service/src/main/resources/config/verily/sdd/entitygroup/observation_person_occurrence.json diff --git a/service/src/main/resources/config/verily/sdd/original/entitygroup/procedure_person_occurrence.json b/service/src/main/resources/config/verily/sdd/entitygroup/procedure_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/entitygroup/procedure_person_occurrence.json rename to service/src/main/resources/config/verily/sdd/entitygroup/procedure_person_occurrence.json diff --git a/service/src/main/resources/config/verily/sdd/original/entitygroup/snp_person.json b/service/src/main/resources/config/verily/sdd/entitygroup/snp_person.json similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/entitygroup/snp_person.json rename to service/src/main/resources/config/verily/sdd/entitygroup/snp_person.json diff --git a/service/src/main/resources/config/verily/sdd/original/entitygroup/visit_person_occurrence.json b/service/src/main/resources/config/verily/sdd/entitygroup/visit_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/entitygroup/visit_person_occurrence.json rename to service/src/main/resources/config/verily/sdd/entitygroup/visit_person_occurrence.json diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/brand.json b/service/src/main/resources/config/verily/sdd/expanded/entity/brand.json deleted file mode 100644 index ebb136c03..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/brand.json +++ /dev/null @@ -1,135 +0,0 @@ -{ - "name" : "brand", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "" - }, - "display" : "Unknown" - }, - "count" : 82839 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT * FROM `victr-tanagra-test.sd_static.concept` WHERE domain_id = 'Drug' AND concept_class_id = 'Brand Name' AND vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND DATE_DIFF(valid_end_date, CURRENT_DATE(), DAY) > 0" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_static.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_static.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND c.concept_class_id = 'Brand Name' AND c.vocabulary_id IN ('RxNorm', 'RxNorm Extension')" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "brand" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/condition.json b/service/src/main/resources/config/verily/sdd/expanded/entity/condition.json deleted file mode 100644 index e289b79ff..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/condition.json +++ /dev/null @@ -1,461 +0,0 @@ -{ - "name" : "condition", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 174148 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 384 - }, { - "enumVal" : { - "value" : { - "stringVal" : "" - }, - "display" : "Unknown" - }, - "count" : 523932 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CIEL" - }, - "display" : "CIEL" - }, - "count" : 38818 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CIM10" - }, - "display" : "CIM10" - }, - "count" : 10867 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Cohort" - }, - "display" : "Cohort" - }, - "count" : 66 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HemOnc" - }, - "display" : "HemOnc" - }, - "count" : 219 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10" - }, - "display" : "ICD10" - }, - "count" : 15017 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "ICD10CM" - }, - "count" : 90542 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CN" - }, - "display" : "ICD10CN" - }, - "count" : 31794 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10GM" - }, - "display" : "ICD10GM" - }, - "count" : 16006 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "ICD9CM" - }, - "count" : 15760 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICDO3" - }, - "display" : "ICDO3" - }, - "count" : 62410 - }, { - "enumVal" : { - "value" : { - "stringVal" : "KCD7" - }, - "display" : "KCD7" - }, - "count" : 20743 - }, { - "enumVal" : { - "value" : { - "stringVal" : "MeSH" - }, - "display" : "MeSH" - }, - "count" : 6795 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Nebraska Lexicon" - }, - "display" : "Nebraska Lexicon" - }, - "count" : 151336 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OMOP Extension" - }, - "display" : "OMOP Extension" - }, - "count" : 7 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPCS4" - }, - "display" : "OPCS4" - }, - "count" : 6 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OXMIS" - }, - "display" : "OXMIS" - }, - "count" : 5704 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OncoTree" - }, - "display" : "OncoTree" - }, - "count" : 869 - }, { - "enumVal" : { - "value" : { - "stringVal" : "PPI" - }, - "display" : "PPI" - }, - "count" : 74 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Read" - }, - "display" : "Read" - }, - "count" : 47736 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SMQ" - }, - "display" : "SMQ" - }, - "count" : 324 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 180133 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED Veterinary" - }, - "display" : "SNOMED Veterinary" - }, - "count" : 3237 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Condition" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_static.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_static.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Condition' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `victr-tanagra-test.sd_static.concept_relationship` cr JOIN `victr-tanagra-test.sd_static.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `victr-tanagra-test.sd_static.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Condition' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED'" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 441840 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "condition" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "condition_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "condition_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "condition" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/condition_occurrence.json b/service/src/main/resources/config/verily/sdd/expanded/entity/condition_occurrence.json deleted file mode 100644 index 5ead0db13..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/condition_occurrence.json +++ /dev/null @@ -1,283 +0,0 @@ -{ - "name" : "condition_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "condition", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -977.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 8278785 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 52395118 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 3007838 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 137386512 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT co.condition_occurrence_id AS id, co.person_id, co.condition_concept_id, co.condition_start_date AS start_date, co.condition_end_date AS end_date, co.stop_reason, co.condition_source_value AS source_value, co.condition_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(co.condition_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, co.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_static.condition_occurrence` AS co JOIN `victr-tanagra-test.sd_static.person` AS p ON p.person_id = co.person_id LEFT JOIN `victr-tanagra-test.sd_static.visit_occurrence` AS vo ON vo.visit_occurrence_id = co.visit_occurrence_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "condition_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "condition_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_condition", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/device.json b/service/src/main/resources/config/verily/sdd/expanded/entity/device.json deleted file mode 100644 index f3f972937..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/device.json +++ /dev/null @@ -1,285 +0,0 @@ -{ - "name" : "device", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 245402 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "AMT" - }, - "display" : "AMT" - }, - "count" : 2945 - }, { - "enumVal" : { - "value" : { - "stringVal" : "BDPM" - }, - "display" : "BDPM" - }, - "count" : 1106 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "CPT4" - }, - "count" : 24 - }, { - "enumVal" : { - "value" : { - "stringVal" : "GGR" - }, - "display" : "GGR" - }, - "count" : 596 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 4634 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10PCS" - }, - "display" : "ICD10PCS" - }, - "count" : 3 - }, { - "enumVal" : { - "value" : { - "stringVal" : "JMDC" - }, - "display" : "JMDC" - }, - "count" : 1313 - }, { - "enumVal" : { - "value" : { - "stringVal" : "KDC" - }, - "display" : "KDC" - }, - "count" : 112 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NDC" - }, - "display" : "NDC" - }, - "count" : 10963 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPCS4" - }, - "display" : "OPCS4" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 202567 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED Veterinary" - }, - "display" : "SNOMED Veterinary" - }, - "count" : 67 - }, { - "enumVal" : { - "value" : { - "stringVal" : "dm+d" - }, - "display" : "dm+d" - }, - "count" : 21071 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Device" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_static.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_static.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Device' AND c.standard_concept = 'S'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "device" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/device_occurrence.json b/service/src/main/resources/config/verily/sdd/expanded/entity/device_occurrence.json deleted file mode 100644 index 2793a3402..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/device_occurrence.json +++ /dev/null @@ -1,256 +0,0 @@ -{ - "name" : "device_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -4.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 99792 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 928353 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 830 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 1931949 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "device", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT de.device_exposure_id AS id, de.person_id, de.device_concept_id, de.device_exposure_start_date AS start_date, de.device_exposure_end_date AS end_date, de.device_source_value AS source_value, de.device_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(de.device_exposure_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, de.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_static.device_exposure` AS de JOIN `victr-tanagra-test.sd_static.person` AS p ON p.person_id = de.person_id LEFT JOIN `victr-tanagra-test.sd_static.visit_occurrence` AS vo ON vo.visit_occurrence_id = de.visit_occurrence_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "device_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "device_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_device", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/genotyping.json b/service/src/main/resources/config/verily/sdd/expanded/entity/genotyping.json deleted file mode 100644 index 6550c6a0a..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/genotyping.json +++ /dev/null @@ -1,149 +0,0 @@ -{ - "name" : "genotyping", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "/* platform_id column has type NUMERIC. This causes index column to be FLOAT. Currently indexing doesn't handle floats properly, so change column to INTEGER. */ SELECT CAST(platform_id as INT64) AS platform_id, assay_name as assay_name FROM `victr-tanagra-test.sd_static.platform` UNION ALL /* Add some rows to get hierarchy to work. Parent ids are defined in genotype_criteria, criteria_meta_seq column. criteria_meta_seq is not in the same \"ID space\" as platform_id. Tanagra requres parent id to be in same \"ID space\" as platform_id. So create artificial platform_ids for parents. */ (SELECT 101 AS platform_id, 'GWAS Platforms' AS assay_name UNION ALL SELECT 102, 'Non-GWAS and Targeted Genotyping Platforms' UNION ALL SELECT 103, 'Sequencing Platforms') " - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "assay_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "platform_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "attributes" : [ "id", "name" ] - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT /* Use parent ids defined in platform.sql */ parent_seq + 100 AS parent, CAST(platform_id as INT64) AS child FROM `victr-tanagra-test.sd_static.genotype_criteria` g, `victr-tanagra-test.sd_static.platform` p WHERE g.name = p.assay_name " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "rawSql" : "/* Match the platform ids in platform.sql */ SELECT 101 AS id UNION ALL SELECT 102 UNION ALL SELECT 103 " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 1 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "genotyping" - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "genotyping_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "genotyping_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "genotyping" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 1 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/ingredient.json b/service/src/main/resources/config/verily/sdd/expanded/entity/ingredient.json deleted file mode 100644 index c46893302..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/ingredient.json +++ /dev/null @@ -1,306 +0,0 @@ -{ - "name" : "ingredient", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 1921307 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 6335 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "ATC" - }, - "display" : "ATC" - }, - "count" : 6335 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm" - }, - "display" : "RxNorm" - }, - "count" : 147265 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm Extension" - }, - "display" : "RxNorm Extension" - }, - "count" : 1774042 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT c.concept_id AS id, c.concept_name AS name, c.vocabulary_id, c.standard_concept, c.concept_code FROM `victr-tanagra-test.sd_static.concept` c WHERE c.domain_id = 'Drug' AND ( (c.vocabulary_id = 'ATC' AND c.standard_concept = 'C') OR (c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.standard_concept = 'S') )" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_static.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_static.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND ((c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.concept_class_id = 'Ingredient' AND c.standard_concept = 'S') OR (c.vocabulary_id = 'RxNorm' AND c.concept_class_id = 'Precise Ingredient') OR (c.vocabulary_id = 'ATC' AND c.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c.standard_concept = 'C'))" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child FROM `victr-tanagra-test.sd_static.concept_relationship` cr JOIN `victr-tanagra-test.sd_static.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `victr-tanagra-test.sd_static.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE c1.concept_id != c2.concept_id AND c1.domain_id = 'Drug' AND c2.domain_id = 'Drug' AND ( /* Populate Ingredients' ancestors', which are ATCs. See https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:atc#:~:text=the%20original%20ATC%20hierarchy%20is%20extended%20by%20Standard%20Drug%20Products%20of%20RxNorm%20and%20RxNorm%20Extension%20vocabularies%2C%20which%20are%20assigned%20to%20be%20descendants%20of%20the%205th%20ATC%20Classes. Eg: ATC 1st (highest ancestor) Subsumes ATC 2nd ATC 5th (direct parent of RxNorm) Maps to RxNorm */ (c1.vocabulary_id IN ('ATC') AND cr.relationship_id IN ('Subsumes', 'Maps to')) OR /* Populate Ingredients and their descendants: Branded Drug, Clinical Drug, etc. Ingredients and their descendants are RxNorm. drug_exposure contains Ingredients or their descendants. Use [1] and [2] to define hierarchy. Eg \"Marketed Product\" is most specific and is bottom of hierarchy. [1] https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:drug_exposure#:~:text=These%20are%20indicated,is%20available%20%E2%80%9CIngredient%E2%80%9D [2] https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:drug#:~:text=are%20not%20implemented.-,Relationships,-As%20usual%2C%20all */ ( c1.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c2.vocabulary_id IN ('RxNorm', 'RxNorm Extension') /* Only keep relationships where c1 is \"parent\" of c2 */ AND cr.relationship_id IN ('Constitutes', 'Contained in' , 'Has form', 'Has quantified form', 'RxNorm ing of', 'RxNorm inverse is a', 'Precise ing of') ) )" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC 1st" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "C" - } - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 15 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "ingredient" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "ingredient_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "ingredient_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "ingredient" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 15 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/ingredient_occurrence.json b/service/src/main/resources/config/verily/sdd/expanded/entity/ingredient_occurrence.json deleted file mode 100644 index c0621be80..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/ingredient_occurrence.json +++ /dev/null @@ -1,543 +0,0 @@ -{ - "name" : "ingredient_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ingredient", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Allergic res" - }, - "display" : "Allergic res" - }, - "count" : 4846 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Alternate tx" - }, - "display" : "Alternate tx" - }, - "count" : 84029 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Anes Stop" - }, - "display" : "Anes Stop" - }, - "count" : 2863009 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Availability" - }, - "display" : "Availability" - }, - "count" : 6600 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CONTACT " - }, - "display" : "CONTACT " - }, - "count" : 614 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Cleanup" - }, - "display" : "Cleanup" - }, - "count" : 399229 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Cost of medi" - }, - "display" : "Cost of medi" - }, - "count" : 9054 - }, { - "enumVal" : { - "value" : { - "stringVal" : "DC'd by othr" - }, - "display" : "DC'd by othr" - }, - "count" : 164096 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Dose adjustm" - }, - "display" : "Dose adjustm" - }, - "count" : 110534 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Drug interac" - }, - "display" : "Drug interac" - }, - "count" : 1982 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Duplicate or" - }, - "display" : "Duplicate or" - }, - "count" : 523173 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Error" - }, - "display" : "Error" - }, - "count" : 238189 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Expired" - }, - "display" : "Expired" - }, - "count" : 151543 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Formulary" - }, - "display" : "Formulary" - }, - "count" : 25726 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NON-ADHEREN" - }, - "display" : "NON-ADHEREN" - }, - "count" : 9253 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Other" - }, - "display" : "Other" - }, - "count" : 195756 - }, { - "enumVal" : { - "value" : { - "stringVal" : "PATIENT DISC" - }, - "display" : "PATIENT DISC" - }, - "count" : 6654423 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Paradoxical " - }, - "display" : "Paradoxical " - }, - "count" : 275 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Pregnancy" - }, - "display" : "Pregnancy" - }, - "count" : 1116 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RETURNED TO " - }, - "display" : "RETURNED TO " - }, - "count" : 19246 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Reorder" - }, - "display" : "Reorder" - }, - "count" : 4317260 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SE" - }, - "display" : "SE" - }, - "count" : 40002 - }, { - "enumVal" : { - "value" : { - "stringVal" : "STOP TAKING " - }, - "display" : "STOP TAKING " - }, - "count" : 402507 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SURGERY" - }, - "display" : "SURGERY" - }, - "count" : 921 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Stop Med" - }, - "display" : "Stop Med" - }, - "count" : 123398 - }, { - "enumVal" : { - "value" : { - "stringVal" : "TRANSFER" - }, - "display" : "TRANSFER" - }, - "count" : 571939 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Therapy comp" - }, - "display" : "Therapy comp" - }, - "count" : 2198773 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 6103937 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 185294420 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 286446 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 42337392 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "days_supply", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 1.0, - "maxVal" : 36135.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "refills", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 365.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -2005.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT de.drug_exposure_id AS id, de.person_id, de.drug_concept_id, de.drug_exposure_start_date AS start_date, de.drug_exposure_end_date AS end_date, de.stop_reason, de.refills, de.days_supply, de.drug_source_value AS source_value, de.drug_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(de.drug_exposure_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, de.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_static.drug_exposure` AS de JOIN `victr-tanagra-test.sd_static.person` AS p ON p.person_id = de.person_id LEFT JOIN `victr-tanagra-test.sd_static.visit_occurrence` AS vo ON vo.visit_occurrence_id = de.visit_occurrence_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "drug_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "ingredient_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "ingredient", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ingredient", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/measurement.json b/service/src/main/resources/config/verily/sdd/expanded/entity/measurement.json deleted file mode 100644 index bac646402..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/measurement.json +++ /dev/null @@ -1,409 +0,0 @@ -{ - "name" : "measurement", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 73948 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 40193 - }, { - "enumVal" : { - "value" : { - "stringVal" : "" - }, - "display" : "Unknown" - }, - "count" : 101999 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NULL" - }, - "display" : "Unknown" - }, - "count" : 9 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "LOINC" - }, - "count" : 186150 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 29999 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Measurement" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "SNOMED" - } - } ] - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC" - } - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC Hierarchy" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC Component" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Lab Test" - } - } ] - } ] - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_static.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_static.concept` c ON c.concept_id = textsearch.id WHERE ((c.domain_id = 'Measurement' AND c.vocabulary_id = 'SNOMED') OR (c.vocabulary_id = 'LOINC' AND c.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test')))" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `victr-tanagra-test.sd_static.concept_relationship` cr JOIN `victr-tanagra-test.sd_static.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `victr-tanagra-test.sd_static.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.vocabulary_id = c2.vocabulary_id AND ((c1.vocabulary_id = 'SNOMED' AND c1.domain_id = c2.domain_id AND c1.domain_id = 'Measurement') OR (c1.vocabulary_id = 'LOINC' AND c1.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test') AND c2.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test'))) " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Measurement" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "SNOMED" - } - } ] - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 36206173 - } - } ] - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 11 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "measurement" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "measurement_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "measurement_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "measurement" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 11 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/measurement_occurrence.json b/service/src/main/resources/config/verily/sdd/expanded/entity/measurement_occurrence.json deleted file mode 100644 index 39a1bf898..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/measurement_occurrence.json +++ /dev/null @@ -1,312 +0,0 @@ -{ - "name" : "measurement_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -1765.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 33250279 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 502984032 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 2421169 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 231277325 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_numeric", - "dataType" : "DOUBLE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value_enum", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "measurement", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT mo.measurement_id AS id, mo.person_id, mo.measurement_concept_id, mo.measurement_date, mo.value_as_number AS value_numeric, mo.value_as_concept_id, mo.unit_concept_id, mo.measurement_source_value AS source_value, mo.measurement_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(mo.measurement_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, mo.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_static.measurement` AS mo JOIN `victr-tanagra-test.sd_static.person` AS p ON p.person_id = mo.person_id LEFT JOIN `victr-tanagra-test.sd_static.visit_occurrence` AS vo ON vo.visit_occurrence_id = mo.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "measurement_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value_numeric" : { - "value" : { - "column" : "value_numeric", - "runtimeCalculated" : false - } - }, - "value_enum" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "measurement" : { - "value" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "measurement_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "measurement_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value_numeric" : { - "value" : { - "column" : "value_numeric", - "runtimeCalculated" : false - } - }, - "value_enum" : { - "value" : { - "column" : "value_enum", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value_enum", - "runtimeCalculated" : false - } - }, - "measurement" : { - "value" : { - "column" : "measurement", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_measurement", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/note.json b/service/src/main/resources/config/verily/sdd/expanded/entity/note.json deleted file mode 100644 index d187aacd5..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/note.json +++ /dev/null @@ -1,195 +0,0 @@ -{ - "name" : "note", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "None" - }, - "display" : "None" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Note Type" - }, - "display" : "Note Type" - }, - "count" : 10 - }, { - "enumVal" : { - "value" : { - "stringVal" : "VUMC Note Type" - }, - "display" : "VUMC Note Type" - }, - "count" : 3 - }, { - "enumVal" : { - "value" : { - "stringVal" : "VUMC PSS Type" - }, - "display" : "VUMC PSS Type" - }, - "count" : 1 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 0 - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Note Type" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "VUMC Note Type" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "VUMC PSS Type" - } - } ] - } - }, - "attributeMappings" : { - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_static.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_static.concept` c ON c.concept_id = textsearch.id WHERE c.vocabulary_id IN ('Note Type', 'VUMC Note Type', 'VUMC PSS Type') OR c.concept_id = 0" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "note" - }, - "attributeMappings" : { - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/note_occurrence.json b/service/src/main/resources/config/verily/sdd/expanded/entity/note_occurrence.json deleted file mode 100644 index 2952b5c9b..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/note_occurrence.json +++ /dev/null @@ -1,380 +0,0 @@ -{ - "name" : "note_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "note", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 44814638 - }, - "display" : "Admission note" - }, - "count" : 2211781 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814643 - }, - "display" : "Ancillary report" - }, - "count" : 11923399 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814637 - }, - "display" : "Discharge summary" - }, - "count" : 5590516 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2003594153 - }, - "display" : "ECG_IMPRESSION" - }, - "count" : 1993820 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814646 - }, - "display" : "Emergency department note" - }, - "count" : 2970051 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814639 - }, - "display" : "Inpatient note" - }, - "count" : 15472924 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 6844205 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814645 - }, - "display" : "Note" - }, - "count" : 68281428 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814644 - }, - "display" : "Nursing report" - }, - "count" : 6777679 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814640 - }, - "display" : "Outpatient note" - }, - "count" : 69556237 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2002404173 - }, - "display" : "PL_PROBLEM LIST" - }, - "count" : 679215564 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814642 - }, - "display" : "Pathology report" - }, - "count" : 2697212 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2002603124 - }, - "display" : "Pss Problem snomed data" - }, - "count" : 29508422 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814641 - }, - "display" : "Radiology report" - }, - "count" : 16997484 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2004084156 - }, - "display" : "VUMC forms data" - }, - "count" : 479294 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -1611.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 1516005 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 16924704 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1275410 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 25879317 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "text", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "title", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT n.note_id AS id, n.person_id, n.note_type_concept_id, n.note_date, n.note_title AS title, n.note_text AS text, n.note_source_value AS source_value, CAST(FLOOR(TIMESTAMP_DIFF(n.note_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, n.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_static.note` AS n JOIN `victr-tanagra-test.sd_static.person` AS p ON p.person_id = n.person_id LEFT JOIN `victr-tanagra-test.sd_static.visit_occurrence` AS vo ON vo.visit_occurrence_id = n.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "note_date", - "runtimeCalculated" : false - } - }, - "note" : { - "value" : { - "column" : "note_type_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "note_type_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "text" : { - "value" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "title" : { - "value" : { - "column" : "title", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "note_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "note" : { - "value" : { - "column" : "note", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_note", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "text" : { - "value" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "title" : { - "value" : { - "column" : "title", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/observation.json b/service/src/main/resources/config/verily/sdd/expanded/entity/observation.json deleted file mode 100644 index 6ad73cc2a..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/observation.json +++ /dev/null @@ -1,337 +0,0 @@ -{ - "name" : "observation", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 162296 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "APC" - }, - "display" : "APC" - }, - "count" : 715 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "CPT4" - }, - "count" : 1083 - }, { - "enumVal" : { - "value" : { - "stringVal" : "DRG" - }, - "display" : "DRG" - }, - "count" : 752 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 2667 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICDO3" - }, - "display" : "ICDO3" - }, - "count" : 49 - }, { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "LOINC" - }, - "count" : 7087 - }, { - "enumVal" : { - "value" : { - "stringVal" : "MDC" - }, - "display" : "MDC" - }, - "count" : 26 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NAACCR" - }, - "display" : "NAACCR" - }, - "count" : 96 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NUCC" - }, - "display" : "NUCC" - }, - "count" : 4 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Nebraska Lexicon" - }, - "display" : "Nebraska Lexicon" - }, - "count" : 1004 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OMOP Extension" - }, - "display" : "OMOP Extension" - }, - "count" : 107 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPCS4" - }, - "display" : "OPCS4" - }, - "count" : 56 - }, { - "enumVal" : { - "value" : { - "stringVal" : "PCORNet" - }, - "display" : "PCORNet" - }, - "count" : 2 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 117406 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED Veterinary" - }, - "display" : "SNOMED Veterinary" - }, - "count" : 27401 - }, { - "enumVal" : { - "value" : { - "stringVal" : "UB04 Pri Typ of Adm" - }, - "display" : "UB04 Pri Typ of Adm" - }, - "count" : 6 - }, { - "enumVal" : { - "value" : { - "stringVal" : "UK Biobank" - }, - "display" : "UK Biobank" - }, - "count" : 3835 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Observation" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "PPI" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "Survey" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_static.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_static.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Observation' AND c.standard_concept = 'S' AND c.vocabulary_id != 'PPI' AND c.concept_class_id != 'Survey'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "observation" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/observation_occurrence.json b/service/src/main/resources/config/verily/sdd/expanded/entity/observation_occurrence.json deleted file mode 100644 index e9deef974..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/observation_occurrence.json +++ /dev/null @@ -1,312 +0,0 @@ -{ - "name" : "observation_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -977.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "observation", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_as_string", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 3576917 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 8957833 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 803664 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 57751171 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT o.observation_id AS id, o.person_id, o.observation_concept_id, o.observation_date, o.value_as_string, o.value_as_concept_id, o.unit_concept_id, o.observation_source_value AS source_value, o.observation_source_concept_id AS source_criteria_id, CAST(FLOOR(DATE_DIFF(o.observation_date, CAST(p.birth_datetime AS DATE), DAY) / 365.25) AS INT64) AS age_at_occurrence, o.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_static.observation` AS o JOIN `victr-tanagra-test.sd_static.person` AS p ON p.person_id = o.person_id LEFT JOIN `victr-tanagra-test.sd_static.visit_occurrence` AS vo ON vo.visit_occurrence_id = o.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "observation_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "observation_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "observation_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_observation", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/person.json b/service/src/main/resources/config/verily/sdd/expanded/entity/person.json deleted file mode 100644 index 1ac7aa1d0..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/person.json +++ /dev/null @@ -1,360 +0,0 @@ -{ - "name" : "person", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "gender", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 8532 - }, - "display" : "FEMALE" - }, - "count" : 1850236 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8507 - }, - "display" : "MALE" - }, - "count" : 1594485 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 4177 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "race", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 8657 - }, - "display" : "American Indian or Alaska Native" - }, - "count" : 4572 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8515 - }, - "display" : "Asian" - }, - "count" : 45958 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38003598 - }, - "display" : "Black" - }, - "count" : 327829 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 953870 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8527 - }, - "display" : "White" - }, - "count" : 2116669 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ethnicity", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 38003563 - }, - "display" : "Hispanic or Latino" - }, - "count" : 113110 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 960195 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38003564 - }, - "display" : "Not Hispanic or Latino" - }, - "count" : 2375593 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "biovu_sample_has_plasma", - "dataType" : "BOOLEAN", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "biovu_sample_dna_yield", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -99999.0, - "maxVal" : 500.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "biovu_sample_is_compromised", - "dataType" : "BOOLEAN", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "age", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -971.0, - "maxVal" : 224.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "has_biovu_sample", - "dataType" : "BOOLEAN", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "biovu_sample_is_nonshippable", - "dataType" : "BOOLEAN", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "year_of_birth", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 1799.0, - "maxVal" : 2993.0 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT /* Can't do \"*\". During expansion, there's an error about person_id column being ambiguous. */ p.person_id, p.year_of_birth, p.birth_datetime, p.gender_concept_id, p.race_concept_id, p.ethnicity_concept_id, /* Add BioVU sample columns. The way x_biovu_sample_status is created, there should be at most one row per person. */ EXISTS (SELECT 1 FROM `victr-tanagra-test.sd_static.x_biovu_sample_status` x WHERE p.person_id = x.person_id) AS has_biovu_sample, x.dna_yield_ind AS biovu_sample_dna_yield, /* As a courtesy, convert string fields to boolean: 0 -> No, 1 -> Yes */ CASE WHEN x.compromise_ind = '1' THEN true WHEN x.compromise_ind = '0' THEN false ELSE null END AS biovu_sample_is_compromised, CASE WHEN x.nonshippable_ind = '1' THEN true WHEN x.nonshippable_ind = '0' THEN false ELSE null END AS biovu_sample_is_nonshippable, CASE WHEN x.plasma_ind = '1' THEN true WHEN x.plasma_ind = '0' THEN false ELSE null END AS biovu_sample_has_plasma FROM `victr-tanagra-test.sd_static.person` p LEFT OUTER JOIN ( /* Get rid of duplicate rows in x_biovu_sample_status. For example, person 4587323 has 11 duplicate rows. This returns just 1 row for each person. */ WITH x_biovu_sample_status AS ( SELECT *, ROW_NUMBER() OVER(PARTITION BY person_id) AS rn FROM `victr-tanagra-test.sd_static.x_biovu_sample_status` ) SELECT * FROM x_biovu_sample_status WHERE rn = 1 ) x ON p.person_id = x.person_id " - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "gender_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "race_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "ethnicity_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "biovu_sample_has_plasma" : { - "value" : { - "column" : "biovu_sample_has_plasma", - "runtimeCalculated" : false - } - }, - "biovu_sample_dna_yield" : { - "value" : { - "column" : "biovu_sample_dna_yield", - "runtimeCalculated" : false - } - }, - "biovu_sample_is_compromised" : { - "value" : { - "column" : "biovu_sample_is_compromised", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "age" : { - "value" : { - "column" : "birth_datetime", - "sqlFunctionWrapper" : "CAST(FLOOR(TIMESTAMP_DIFF(CURRENT_TIMESTAMP(), ${fieldSql}, DAY) / 365.25) AS INT64)", - "runtimeCalculated" : true - } - }, - "has_biovu_sample" : { - "value" : { - "column" : "has_biovu_sample", - "runtimeCalculated" : false - } - }, - "biovu_sample_is_nonshippable" : { - "value" : { - "column" : "biovu_sample_is_nonshippable", - "runtimeCalculated" : false - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "person" - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_gender", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_race", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ethnicity", - "runtimeCalculated" : false - } - }, - "biovu_sample_has_plasma" : { - "value" : { - "column" : "biovu_sample_has_plasma", - "runtimeCalculated" : false - } - }, - "biovu_sample_dna_yield" : { - "value" : { - "column" : "biovu_sample_dna_yield", - "runtimeCalculated" : false - } - }, - "biovu_sample_is_compromised" : { - "value" : { - "column" : "biovu_sample_is_compromised", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "age" : { - "value" : { - "column" : "age", - "sqlFunctionWrapper" : "CAST(FLOOR(TIMESTAMP_DIFF(CURRENT_TIMESTAMP(), ${fieldSql}, DAY) / 365.25) AS INT64)", - "runtimeCalculated" : true - } - }, - "has_biovu_sample" : { - "value" : { - "column" : "has_biovu_sample", - "runtimeCalculated" : false - } - }, - "biovu_sample_is_nonshippable" : { - "value" : { - "column" : "biovu_sample_is_nonshippable", - "runtimeCalculated" : false - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/procedure.json b/service/src/main/resources/config/verily/sdd/expanded/entity/procedure.json deleted file mode 100644 index 86b4983b7..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/procedure.json +++ /dev/null @@ -1,485 +0,0 @@ -{ - "name" : "procedure", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 262341 - }, { - "enumVal" : { - "value" : { - "stringVal" : "" - }, - "display" : "Unknown" - }, - "count" : 458585 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 3064 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CCAM" - }, - "display" : "CCAM" - }, - "count" : 10206 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CIEL" - }, - "display" : "CIEL" - }, - "count" : 648 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CIM10" - }, - "display" : "CIM10" - }, - "count" : 195 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "CPT4" - }, - "count" : 13143 - }, { - "enumVal" : { - "value" : { - "stringVal" : "EDI" - }, - "display" : "EDI" - }, - "count" : 249785 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 1289 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HemOnc" - }, - "display" : "HemOnc" - }, - "count" : 92 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10" - }, - "display" : "ICD10" - }, - "count" : 161 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "ICD10CM" - }, - "count" : 6 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CN" - }, - "display" : "ICD10CN" - }, - "count" : 386 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10GM" - }, - "display" : "ICD10GM" - }, - "count" : 157 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10PCS" - }, - "display" : "ICD10PCS" - }, - "count" : 194874 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "ICD9CM" - }, - "count" : 177 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9Proc" - }, - "display" : "ICD9Proc" - }, - "count" : 4657 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9ProcCN" - }, - "display" : "ICD9ProcCN" - }, - "count" : 13385 - }, { - "enumVal" : { - "value" : { - "stringVal" : "KCD7" - }, - "display" : "KCD7" - }, - "count" : 165 - }, { - "enumVal" : { - "value" : { - "stringVal" : "MeSH" - }, - "display" : "MeSH" - }, - "count" : 951 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NAACCR" - }, - "display" : "NAACCR" - }, - "count" : 710 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Nebraska Lexicon" - }, - "display" : "Nebraska Lexicon" - }, - "count" : 72683 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OMOP Extension" - }, - "display" : "OMOP Extension" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPCS4" - }, - "display" : "OPCS4" - }, - "count" : 9750 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPS" - }, - "display" : "OPS" - }, - "count" : 41101 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OXMIS" - }, - "display" : "OXMIS" - }, - "count" : 1193 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Read" - }, - "display" : "Read" - }, - "count" : 20973 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 86910 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED Veterinary" - }, - "display" : "SNOMED Veterinary" - }, - "count" : 392 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Procedure" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_static.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_static.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Procedure' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `victr-tanagra-test.sd_static.concept_relationship` cr JOIN `victr-tanagra-test.sd_static.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `victr-tanagra-test.sd_static.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Procedure' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED'" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 4322976 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "procedure" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "procedure_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "procedure_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "procedure" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/procedure_occurrence.json b/service/src/main/resources/config/verily/sdd/expanded/entity/procedure_occurrence.json deleted file mode 100644 index 6696f0ac0..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/procedure_occurrence.json +++ /dev/null @@ -1,239 +0,0 @@ -{ - "name" : "procedure_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -96.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 6819652 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 30613368 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 813264 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 82908869 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "procedure", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT po.procedure_occurrence_id AS id, po.person_id, po.procedure_concept_id, po.procedure_date, po.procedure_source_value AS source_value, po.procedure_source_concept_id AS source_criteria_id, CAST(FLOOR(DATE_DIFF(po.procedure_date, CAST(p.birth_datetime AS DATE), DAY) / 365.25) AS INT64) AS age_at_occurrence, po.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_static.procedure_occurrence` AS po JOIN `victr-tanagra-test.sd_static.person` AS p ON p.person_id = po.person_id LEFT JOIN `victr-tanagra-test.sd_static.visit_occurrence` AS vo ON vo.visit_occurrence_id = po.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "procedure_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "procedure_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "procedure_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_procedure", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/snp.json b/service/src/main/resources/config/verily/sdd/expanded/entity/snp.json deleted file mode 100644 index e6eb94ef2..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/snp.json +++ /dev/null @@ -1,49 +0,0 @@ -{ - "name" : "snp", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "STRING", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT DISTINCT snp FROM `victr-tanagra-test.sd_static.x_snp` ORDER BY snp " - }, - "attributeMappings" : { - "id" : { - "value" : { - "column" : "snp", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "attributes" : [ "id" ] - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "snp" - }, - "attributeMappings" : { - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/visit.json b/service/src/main/resources/config/verily/sdd/expanded/entity/visit.json deleted file mode 100644 index 716ebc81a..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/visit.json +++ /dev/null @@ -1,105 +0,0 @@ -{ - "name" : "visit", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Visit" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_static.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_static.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Visit' AND c.standard_concept = 'S'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "visit" - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entity/visit_occurrence.json b/service/src/main/resources/config/verily/sdd/expanded/entity/visit_occurrence.json deleted file mode 100644 index 2a0a707cd..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entity/visit_occurrence.json +++ /dev/null @@ -1,211 +0,0 @@ -{ - "name" : "visit_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -977.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 1690886 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 3078021 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1077644 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 57044408 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT vo.visit_occurrence_id AS id, vo.person_id, vo.visit_concept_id, vo.visit_start_date AS start_date, vo.visit_end_date AS end_date, vo.visit_source_value AS source_value, vo.visit_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(vo.visit_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence FROM `victr-tanagra-test.sd_static.visit_occurrence` AS vo JOIN `victr-tanagra-test.sd_static.person` AS p ON p.person_id = vo.person_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "visit" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "visit_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "visit" : { - "value" : { - "column" : "visit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/brand_ingredient.json b/service/src/main/resources/config/verily/sdd/expanded/entitygroup/brand_ingredient.json deleted file mode 100644 index 3edaee58d..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/brand_ingredient.json +++ /dev/null @@ -1,101 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "brand_ingredient", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "rawSql" : "/* 1. User searches for Brand Tylenol 2. User expands Tylenol to see which ingredients are in Tylenol 3. Ingredient Acetaminophen is shown Acetaminophen has over 300 descendants (eg \"acetaminophen 100 MG/ML Oral Suspension\"). Acetaminophen's concept_class_id is Ingredient; descendants' concept_class_ids are Clinical Drug Comp, Quant Clinical Drug, etc. Most descendants have a relationship with Brand Tylenol in concept_relationship. However, we only want to show Acetaminophen in step 3. So only keep relationships with concept_class_id=Ingredient. */ SELECT cr.* FROM `victr-tanagra-test.sd_static.concept_relationship` cr, `victr-tanagra-test.sd_static.concept` c2 WHERE cr.concept_id_2 = c2.concept_id AND c2.concept_class_id = 'Ingredient'" - }, - "idPairsIdA" : { - "column" : "concept_id_1", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "concept_id_2", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_brand_ingredient" - }, - "idPairsIdA" : { - "column" : "id_brand", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "brand" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_brand_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_brand_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_brand", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_brand", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "brand", - "itemsEntity" : "ingredient" -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/condition_person_occurrence.json b/service/src/main/resources/config/verily/sdd/expanded/entitygroup/condition_person_occurrence.json deleted file mode 100644 index a709ed653..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/condition_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "condition_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_condition_occurrence_condition" - }, - "idPairsIdA" : { - "column" : "id_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_condition", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_condition_person" - }, - "idPairsIdA" : { - "column" : "id_condition", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_condition_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "condition", - "occurrenceEntity" : "condition_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/device_person_occurrence.json b/service/src/main/resources/config/verily/sdd/expanded/entitygroup/device_person_occurrence.json deleted file mode 100644 index ff77e8f95..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/device_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "device_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_device_occurrence_device" - }, - "idPairsIdA" : { - "column" : "id_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_device", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_device_person" - }, - "idPairsIdA" : { - "column" : "id_device", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_device_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "device", - "occurrenceEntity" : "device_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/genotyping_person.json b/service/src/main/resources/config/verily/sdd/expanded/entitygroup/genotyping_person.json deleted file mode 100644 index fb3cbb2ce..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/genotyping_person.json +++ /dev/null @@ -1,101 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "genotyping_person", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "rawSql" : "/* platform_id column has type NUMERIC. This causes index column to be FLOAT. Currently indexing doesn't handle floats properly, so change column to INTEGER. */ SELECT genotype_result_id AS genotype_result_id, person_id, CAST(platform_id as INT64) as platform_id FROM `victr-tanagra-test.sd_static.genotype_result` " - }, - "idPairsIdA" : { - "column" : "platform_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_genotyping_person" - }, - "idPairsIdA" : { - "column" : "id_genotyping", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "genotyping" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "genotyping" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_genotyping", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_genotyping", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "genotyping", - "itemsEntity" : "person" -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/ingredient_person_occurrence.json b/service/src/main/resources/config/verily/sdd/expanded/entitygroup/ingredient_person_occurrence.json deleted file mode 100644 index 576ca9260..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/ingredient_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "ingredient_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_occurrence_ingredient" - }, - "idPairsIdA" : { - "column" : "id_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_person" - }, - "idPairsIdA" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "ingredient", - "occurrenceEntity" : "ingredient_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/measurement_person_occurrence.json b/service/src/main/resources/config/verily/sdd/expanded/entitygroup/measurement_person_occurrence.json deleted file mode 100644 index cb82b0df7..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/measurement_person_occurrence.json +++ /dev/null @@ -1,287 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "measurement_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_measurement_occurrence_measurement" - }, - "idPairsIdA" : { - "column" : "id_measurement_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_measurement", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_measurement_person" - }, - "idPairsIdA" : { - "column" : "id_measurement", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_measurement_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_measurement_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { - "modifiers" : { - "tablePointer" : { - "table" : "measurement_person_occurrence_modifiers" - }, - "fieldPointers" : { - "min" : { - "column" : "min", - "runtimeCalculated" : false - }, - "enum_count" : { - "column" : "enum_count", - "runtimeCalculated" : false - }, - "max" : { - "column" : "max", - "runtimeCalculated" : false - }, - "enum_display" : { - "column" : "enum_display", - "runtimeCalculated" : false - }, - "enum_value" : { - "column" : "enum_value", - "runtimeCalculated" : false - }, - "attribute_name" : { - "column" : "attribute_name", - "runtimeCalculated" : false - }, - "entity_id" : { - "column" : "entity_id", - "runtimeCalculated" : false - } - } - } - } - }, - "criteriaEntity" : "measurement", - "occurrenceEntity" : "measurement_occurrence", - "modifierAttributes" : [ "value_numeric", "value_enum" ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/note_person_occurrence.json b/service/src/main/resources/config/verily/sdd/expanded/entitygroup/note_person_occurrence.json deleted file mode 100644 index dd4403308..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/note_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "note_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "note" - }, - "idPairsIdA" : { - "column" : "note_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "note_type_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "note" - }, - "idPairsIdA" : { - "column" : "note_type_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "note" - }, - "idPairsIdA" : { - "column" : "note_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_note_occurrence_note" - }, - "idPairsIdA" : { - "column" : "id_note_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_note", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "note_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_note", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_note", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "note" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_note_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_note_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_note_person" - }, - "idPairsIdA" : { - "column" : "id_note", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "note" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_note", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_note", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_note_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_note_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "note_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_note_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_note_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "note", - "occurrenceEntity" : "note_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/observation_person_occurrence.json b/service/src/main/resources/config/verily/sdd/expanded/entitygroup/observation_person_occurrence.json deleted file mode 100644 index dad430b34..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/observation_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "observation_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_observation_occurrence_observation" - }, - "idPairsIdA" : { - "column" : "id_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_observation", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_observation_person" - }, - "idPairsIdA" : { - "column" : "id_observation", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_observation_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "observation", - "occurrenceEntity" : "observation_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/procedure_person_occurrence.json b/service/src/main/resources/config/verily/sdd/expanded/entitygroup/procedure_person_occurrence.json deleted file mode 100644 index be81091b7..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/procedure_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "procedure_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_procedure_occurrence_procedure" - }, - "idPairsIdA" : { - "column" : "id_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_procedure", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_procedure_person" - }, - "idPairsIdA" : { - "column" : "id_procedure", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_procedure_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "procedure", - "occurrenceEntity" : "procedure_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/snp_person.json b/service/src/main/resources/config/verily/sdd/expanded/entitygroup/snp_person.json deleted file mode 100644 index 6eb9e54df..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/snp_person.json +++ /dev/null @@ -1,84 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "snp_person", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "x_snp" - }, - "idPairsIdA" : { - "column" : "snp", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_snp_person" - }, - "idPairsIdA" : { - "column" : "id_snp", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "snp" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_snp", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_snp", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "snp", - "itemsEntity" : "person" -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/visit_person_occurrence.json b/service/src/main/resources/config/verily/sdd/expanded/entitygroup/visit_person_occurrence.json deleted file mode 100644 index 1a4beff12..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/entitygroup/visit_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "visit_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_visit_occurrence_visit" - }, - "idPairsIdA" : { - "column" : "id_visit_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_visit", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_visit_person" - }, - "idPairsIdA" : { - "column" : "id_visit", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_visit_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_visit_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "visit", - "occurrenceEntity" : "visit_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/expanded/sdd.json b/service/src/main/resources/config/verily/sdd/expanded/sdd.json deleted file mode 100644 index da3cea827..000000000 --- a/service/src/main/resources/config/verily/sdd/expanded/sdd.json +++ /dev/null @@ -1,29 +0,0 @@ -{ - "name" : "sdd", - "dataPointers" : [ { - "type" : "BQ_DATASET", - "name" : "index_dataset", - "projectId" : "verily-tanagra-dev", - "datasetId" : "sdstatic_index_051623", - "queryProjectId" : "verily-tanagra-dev", - "dataflowServiceAccountEmail" : "backend-default@verily-tanagra-dev.iam.gserviceaccount.com", - "dataflowTempLocation" : "gs://dataflow-staging-us-central1-694046000181/temp/", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : false - }, { - "type" : "BQ_DATASET", - "name" : "omop_dataset", - "projectId" : "victr-tanagra-test", - "datasetId" : "sd_static", - "queryProjectId" : "victr-tanagra-test", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : true - } ], - "entities" : [ "measurement_occurrence.json", "note.json", "condition_occurrence.json", "ingredient.json", "device_occurrence.json", "observation.json", "genotyping.json", "procedure.json", "measurement.json", "ingredient_occurrence.json", "condition.json", "snp.json", "person.json", "visit_occurrence.json", "observation_occurrence.json", "procedure_occurrence.json", "visit.json", "brand.json", "device.json", "note_occurrence.json" ], - "entityGroups" : [ "device_person_occurrence.json", "genotyping_person.json", "visit_person_occurrence.json", "condition_person_occurrence.json", "snp_person.json", "note_person_occurrence.json", "ingredient_person_occurrence.json", "observation_person_occurrence.json", "brand_ingredient.json", "measurement_person_occurrence.json", "procedure_person_occurrence.json" ], - "primaryEntity" : "person", - "uiConfig" : "{ \"dataConfig\": { \"primaryEntity\": { \"displayName\": \"Person\", \"entity\": \"person\", \"key\": \"id\", \"classifications\": [ { \"id\": \"snp\", \"attribute\": \"id\", \"entity\": \"snp\", \"entityAttribute\": \"id\", \"defaultSort\": { \"attribute\": \"id\", \"direction\": \"ASC\" } }, { \"id\": \"genotyping\", \"attribute\": \"id\", \"entity\": \"genotyping\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"name\", \"direction\": \"ASC\" } } ] }, \"occurrences\": [ { \"id\": \"condition_occurrence\", \"displayName\": \"Condition Occurrences\", \"entity\": \"condition_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"condition\", \"attribute\": \"condition\", \"entity\": \"condition\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"procedure_occurrence\", \"displayName\": \"Procedure Occurrences\", \"entity\": \"procedure_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"procedure\", \"attribute\": \"procedure\", \"entity\": \"procedure\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"observation_occurrence\", \"displayName\": \"Observation Occurrence\", \"entity\": \"observation_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"observation\", \"attribute\": \"observation\", \"entity\": \"observation\", \"entityAttribute\": \"id\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"ingredient_occurrence\", \"displayName\": \"Drug Occurrence\", \"entity\": \"ingredient_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"ingredient\", \"attribute\": \"id\", \"entity\": \"ingredient\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" }, \"groupings\": [ { \"id\": \"brand\", \"entity\": \"brand\", \"defaultSort\": { \"attribute\": \"name\", \"direction\": \"ASC\" }, \"attributes\": [\"name\", \"id\", \"standard_concept\", \"concept_code\"] } ] } ] }, { \"id\": \"note_occurrence\", \"displayName\": \"Documents\", \"entity\": \"note_occurrence\", \"key\": \"id\" }, { \"id\": \"measurement_occurrence\", \"displayName\": \"Measurement Occurrence\", \"entity\": \"measurement_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"measurement\", \"attribute\": \"measurement\", \"entity\": \"measurement\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_item_count\", \"direction\": \"DESC\" } } ] } ] }, \"criteriaConfigs\": [ { \"type\": \"classification\", \"id\": \"tanagra-conditions\", \"title\": \"Condition\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Condition\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"condition_occurrence\", \"classification\": \"condition\", \"modifiers\": [ \"age_at_occurrence\", \"visit_type\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-procedures\", \"title\": \"Procedure\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Procedure\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"procedure_occurrence\", \"classification\": \"procedure\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"] }, { \"type\": \"classification\", \"id\": \"tanagra-observations\", \"title\": \"Observation\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"observation_occurrence\", \"classification\": \"observation\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"] }, { \"type\": \"classification\", \"id\": \"tanagra-drugs\", \"title\": \"Drug\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Drug\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"ingredient_occurrence\", \"classification\": \"ingredient\", \"modifiers\": [ \"age_at_occurrence\", \"visit_type\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-genotyping\", \"title\": \"Genotyping platform\", \"category\": \"Demographics\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Genotyping platform\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Genotyping platform\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Id\" } ], \"occurrence\": \"\", \"classification\": \"genotyping\" }, { \"type\": \"classification\", \"id\": \"tanagra-measurement\", \"title\": \"Labs and measurements\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_item_count\", \"width\": 120, \"title\": \"Count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Condition\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"measurement_occurrence\", \"classification\": \"measurement\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"], \"valueConfigs\": [ { \"title\": \"Categorical value\", \"attribute\": \"value_enum\" }, { \"title\": \"Numeric value\", \"attribute\": \"value_numeric\" } ] }, { \"type\": \"attribute\", \"id\": \"tanagra-ethnicity\", \"title\": \"Ethnicity\", \"category\": \"Demographics\", \"attribute\": \"ethnicity\" }, { \"type\": \"attribute\", \"id\": \"tanagra-gender\", \"title\": \"Gender identity\", \"category\": \"Demographics\", \"attribute\": \"gender\" }, { \"type\": \"attribute\", \"id\": \"tanagra-race\", \"title\": \"Race\", \"category\": \"Demographics\", \"attribute\": \"race\" }, { \"type\": \"attribute\", \"id\": \"tanagra-age\", \"title\": \"Age\", \"category\": \"Demographics\", \"attribute\": \"age\" }, { \"type\": \"search\", \"id\": \"tanagra-documents\", \"title\": \"Documents\", \"conceptSet\": true, \"category\": \"Domains\", \"occurrenceId\": \"note_occurrence\", \"searchAttribute\": \"title\", \"categoryAttribute\": \"note\", \"modifiers\": [ \"age_at_occurrence\", \"visit_type\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-snp\", \"title\": \"SNP variant\", \"category\": \"Demographics\", \"columns\": [{ \"key\": \"id\", \"width\": \"100%\", \"title\": \"SNP variant\" }], \"occurrence\": \"\", \"classification\": \"snp\" }, { \"type\": \"biovu\", \"id\": \"biovu\", \"title\": \"BioVU Samples\", \"category\": \"BioVU\" } ], \"modifierConfigs\": [ { \"type\": \"unhinted-value\", \"id\": \"start_date_group_by_count\", \"title\": \"Occurrence count\", \"attribute\": \"start_date\", \"groupByCount\": true }, { \"type\": \"unhinted-value\", \"id\": \"date_group_by_count\", \"title\": \"Occurrence count\", \"attribute\": \"date\", \"groupByCount\": true }, { \"type\": \"attribute\", \"id\": \"visit_type\", \"title\": \"Visit type\", \"attribute\": \"visit_type\" }, { \"type\": \"attribute\", \"id\": \"age_at_occurrence\", \"title\": \"Age at occurrence\", \"attribute\": \"age_at_occurrence\" } ], \"demographicChartConfigs\": { \"groupByAttributes\": [\"gender\", \"race\", \"age\"], \"chartConfigs\": [ { \"title\": \"Gender identity\", \"primaryProperties\": [{ \"key\": \"gender\" }] }, { \"title\": \"Gender identity, Current age, Race\", \"primaryProperties\": [ { \"key\": \"gender\" }, { \"key\": \"age\", \"buckets\": [ { \"min\": 18, \"max\": 45, \"displayName\": \"18-44\" }, { \"min\": 45, \"max\": 65, \"displayName\": \"45-64\" }, { \"min\": 65, \"displayName\": \"65+\" } ] } ], \"stackedProperty\": { \"key\": \"race\" } } ] }, \"prepackagedConceptSets\": [ { \"id\": \"_demographics\", \"name\": \"Demographics\", \"occurrence\": \"\" }, { \"id\": \"_analgesics\", \"name\": \"Analgesics\", \"occurrence\": \"ingredient_occurrence\", \"filter\": { \"type\": \"CLASSIFICATION\", \"occurrenceId\": \"ingredient_occurrence\", \"classificationId\": \"ingredient\", \"keys\": [21604253] } } ], \"criteriaSearchConfig\": { \"criteriaTypeWidth\": 120, \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept Name\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up Count\" } ] }, \"cohortReviewConfig\": { \"participantsListColumns\": [ { \"key\": \"id\", \"width\": 100, \"title\": \"Id\" }, { \"key\": \"gender\", \"width\": 100, \"title\": \"Gender\" }, { \"key\": \"race\", \"width\": 100, \"title\": \"Race\" }, { \"key\": \"ethnicity\", \"width\": 100, \"title\": \"Ethnicity\" }, { \"key\": \"age\", \"width\": 60, \"title\": \"Year of Birth\" } ], \"attributes\": [ { \"title\": \"Gender\", \"key\": \"gender\" }, { \"title\": \"Age\", \"key\": \"age\" }, { \"title\": \"Race\", \"key\": \"race\" }, { \"title\": \"Ethnicity\", \"key\": \"ethnicity\" } ], \"pages\": [ { \"type\": \"occurrenceTable\", \"id\": \"condition\", \"title\": \"Conditions\", \"plugin\": { \"occurrence\": \"condition_occurrence\", \"columns\": [ { \"key\": \"condition\", \"width\": \"100%\", \"title\": \"Condition name\", \"sortable\": true }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\", \"sortable\": true }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"procedure\", \"title\": \"Procedures\", \"plugin\": { \"occurrence\": \"procedure_occurrence\", \"columns\": [ { \"key\": \"procedure\", \"width\": \"100%\", \"title\": \"Procedure name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"observation\", \"title\": \"Observations\", \"plugin\": { \"occurrence\": \"observation_occurrence\", \"columns\": [ { \"key\": \"observation\", \"width\": \"100%\", \"title\": \"Observation name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"ingredient\", \"title\": \"Drugs\", \"plugin\": { \"occurrence\": \"ingredient_occurrence\", \"columns\": [ { \"key\": \"ingredient\", \"width\": \"100%\", \"title\": \"Drug name\", \"sortable\": true }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\", \"sortable\": true }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"measurements\", \"title\": \"Labs and measurements\", \"plugin\": { \"occurrence\": \"measurement_occurrence\", \"columns\": [ { \"key\": \"measurement\", \"width\": \"100%\", \"title\": \"Lab/measurement name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true }, { \"key\": \"value_enum\", \"width\": 160, \"title\": \"Categorical value\", \"sortable\": true }, { \"key\": \"value_numeric\", \"width\": 160, \"title\": \"Numeric value\", \"sortable\": true }, { \"key\": \"unit\", \"width\": 160, \"title\": \"Unit\", \"sortable\": true } ] } }, { \"type\": \"textSearch\", \"id\": \"notes\", \"title\": \"Documents\", \"plugin\": { \"occurrence\": \"note_occurrence\", \"title\": \"title\", \"subtitles\": [\"note\", \"date\"], \"text\": \"text\", \"categoryAttribute\": \"note\", \"sortOrder\": { \"attribute\": \"date\", \"direction\": \"ASC\" } } } ] } } ", - "metadata" : { } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd/original/entity/condition_occurrence.json b/service/src/main/resources/config/verily/sdd/original/entity/condition_occurrence.json deleted file mode 100644 index 5734966fc..000000000 --- a/service/src/main/resources/config/verily/sdd/original/entity/condition_occurrence.json +++ /dev/null @@ -1,42 +0,0 @@ -{ - "name": "condition_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "condition", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "condition_occurrence_all.sql" }, - "attributeMappings": { - "condition": { - "value": { "column": "condition_concept_id" }, - "display": { - "column": "condition_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/sdd/original/entity/device_occurrence.json b/service/src/main/resources/config/verily/sdd/original/entity/device_occurrence.json deleted file mode 100644 index ffcfbb5fc..000000000 --- a/service/src/main/resources/config/verily/sdd/original/entity/device_occurrence.json +++ /dev/null @@ -1,41 +0,0 @@ -{ - "name": "device_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "device", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "device_occurrence_all.sql" }, - "attributeMappings": { - "device": { - "value": { "column": "device_concept_id" }, - "display": { - "column": "device_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/sdd/original/entity/ingredient_occurrence.json b/service/src/main/resources/config/verily/sdd/original/entity/ingredient_occurrence.json deleted file mode 100644 index 6e4263d3a..000000000 --- a/service/src/main/resources/config/verily/sdd/original/entity/ingredient_occurrence.json +++ /dev/null @@ -1,44 +0,0 @@ -{ - "name": "ingredient_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "ingredient", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "refills" }, - { "type": "SIMPLE", "name": "days_supply" }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "ingredient_occurrence_all.sql" }, - "attributeMappings": { - "ingredient": { - "value": { "column": "drug_concept_id" }, - "display": { - "column": "drug_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/sdd/original/entity/note_occurrence.json b/service/src/main/resources/config/verily/sdd/original/entity/note_occurrence.json deleted file mode 100644 index 4ea519ebd..000000000 --- a/service/src/main/resources/config/verily/sdd/original/entity/note_occurrence.json +++ /dev/null @@ -1,42 +0,0 @@ -{ - "name": "note_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "note" }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "title", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "text", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "note_occurrence_all.sql" }, - "attributeMappings": { - "date": { "value": { "column": "note_date" } }, - "note": { - "value": { "column": "note_type_concept_id" }, - "display": { - "column": "note_type_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/sdd/original/entity/visit_occurrence.json b/service/src/main/resources/config/verily/sdd/original/entity/visit_occurrence.json deleted file mode 100644 index cff5a1628..000000000 --- a/service/src/main/resources/config/verily/sdd/original/entity/visit_occurrence.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "name": "visit_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit" }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "visit_occurrence_all.sql" }, - "attributeMappings": { - "visit": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/sdd/original/sdd.json b/service/src/main/resources/config/verily/sdd/sdd.json similarity index 94% rename from service/src/main/resources/config/verily/sdd/original/sdd.json rename to service/src/main/resources/config/verily/sdd/sdd.json index 71351151e..9d780eb5c 100644 --- a/service/src/main/resources/config/verily/sdd/original/sdd.json +++ b/service/src/main/resources/config/verily/sdd/sdd.json @@ -9,7 +9,7 @@ { "type": "BQ_DATASET", "name": "index_dataset", "projectId": "verily-tanagra-dev", - "datasetId": "sdstatic_index_051623", + "datasetId": "sdstatic_index_072623", "dataflowServiceAccountEmail": "backend-default@verily-tanagra-dev.iam.gserviceaccount.com", "dataflowTempLocation": "gs://dataflow-staging-us-central1-694046000181/temp/", "dataflowRegion": "us-central1", @@ -34,7 +34,6 @@ "person.json", "procedure.json", "procedure_occurrence.json", - "snp.json", "visit.json", "visit_occurrence.json" ], "primaryEntity": "person", @@ -48,7 +47,6 @@ "note_person_occurrence.json", "observation_person_occurrence.json", "procedure_person_occurrence.json", - "snp_person.json", "visit_person_occurrence.json" ], "uiConfigFile": "top_level.json" diff --git a/service/src/main/resources/config/verily/sdd/original/sql/brand_all.sql b/service/src/main/resources/config/verily/sdd/sql/brand_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/brand_all.sql rename to service/src/main/resources/config/verily/sdd/sql/brand_all.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/brand_ingredients.sql b/service/src/main/resources/config/verily/sdd/sql/brand_ingredients.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/brand_ingredients.sql rename to service/src/main/resources/config/verily/sdd/sql/brand_ingredients.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/brand_textSearch.sql b/service/src/main/resources/config/verily/sdd/sql/brand_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/brand_textSearch.sql rename to service/src/main/resources/config/verily/sdd/sql/brand_textSearch.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/condition_occurrence_all.sql b/service/src/main/resources/config/verily/sdd/sql/condition_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/condition_occurrence_all.sql rename to service/src/main/resources/config/verily/sdd/sql/condition_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/condition_parentChild.sql b/service/src/main/resources/config/verily/sdd/sql/condition_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/condition_parentChild.sql rename to service/src/main/resources/config/verily/sdd/sql/condition_parentChild.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/condition_textSearch.sql b/service/src/main/resources/config/verily/sdd/sql/condition_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/condition_textSearch.sql rename to service/src/main/resources/config/verily/sdd/sql/condition_textSearch.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/device_occurrence_all.sql b/service/src/main/resources/config/verily/sdd/sql/device_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/device_occurrence_all.sql rename to service/src/main/resources/config/verily/sdd/sql/device_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/device_textSearch.sql b/service/src/main/resources/config/verily/sdd/sql/device_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/device_textSearch.sql rename to service/src/main/resources/config/verily/sdd/sql/device_textSearch.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/genotype_result.sql b/service/src/main/resources/config/verily/sdd/sql/genotype_result.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/genotype_result.sql rename to service/src/main/resources/config/verily/sdd/sql/genotype_result.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/genotyping_parentChild.sql b/service/src/main/resources/config/verily/sdd/sql/genotyping_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/genotyping_parentChild.sql rename to service/src/main/resources/config/verily/sdd/sql/genotyping_parentChild.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/genotyping_rootNodesFilter.sql b/service/src/main/resources/config/verily/sdd/sql/genotyping_rootNodesFilter.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/genotyping_rootNodesFilter.sql rename to service/src/main/resources/config/verily/sdd/sql/genotyping_rootNodesFilter.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/ingredient_all.sql b/service/src/main/resources/config/verily/sdd/sql/ingredient_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/ingredient_all.sql rename to service/src/main/resources/config/verily/sdd/sql/ingredient_all.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/ingredient_occurrence_all.sql b/service/src/main/resources/config/verily/sdd/sql/ingredient_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/ingredient_occurrence_all.sql rename to service/src/main/resources/config/verily/sdd/sql/ingredient_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/ingredient_parentChild.sql b/service/src/main/resources/config/verily/sdd/sql/ingredient_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/ingredient_parentChild.sql rename to service/src/main/resources/config/verily/sdd/sql/ingredient_parentChild.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/ingredient_textSearch.sql b/service/src/main/resources/config/verily/sdd/sql/ingredient_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/ingredient_textSearch.sql rename to service/src/main/resources/config/verily/sdd/sql/ingredient_textSearch.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/measurement_occurrence_all.sql b/service/src/main/resources/config/verily/sdd/sql/measurement_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/measurement_occurrence_all.sql rename to service/src/main/resources/config/verily/sdd/sql/measurement_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/measurement_parentChild.sql b/service/src/main/resources/config/verily/sdd/sql/measurement_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/measurement_parentChild.sql rename to service/src/main/resources/config/verily/sdd/sql/measurement_parentChild.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/measurement_textSearch.sql b/service/src/main/resources/config/verily/sdd/sql/measurement_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/measurement_textSearch.sql rename to service/src/main/resources/config/verily/sdd/sql/measurement_textSearch.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/note_occurrence_all.sql b/service/src/main/resources/config/verily/sdd/sql/note_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/note_occurrence_all.sql rename to service/src/main/resources/config/verily/sdd/sql/note_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/note_textSearch.sql b/service/src/main/resources/config/verily/sdd/sql/note_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/note_textSearch.sql rename to service/src/main/resources/config/verily/sdd/sql/note_textSearch.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/observation_occurrence_all.sql b/service/src/main/resources/config/verily/sdd/sql/observation_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/observation_occurrence_all.sql rename to service/src/main/resources/config/verily/sdd/sql/observation_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/observation_textSearch.sql b/service/src/main/resources/config/verily/sdd/sql/observation_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/observation_textSearch.sql rename to service/src/main/resources/config/verily/sdd/sql/observation_textSearch.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/person.sql b/service/src/main/resources/config/verily/sdd/sql/person.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/person.sql rename to service/src/main/resources/config/verily/sdd/sql/person.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/platform.sql b/service/src/main/resources/config/verily/sdd/sql/platform.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/platform.sql rename to service/src/main/resources/config/verily/sdd/sql/platform.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/procedure_occurrence_all.sql b/service/src/main/resources/config/verily/sdd/sql/procedure_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/procedure_occurrence_all.sql rename to service/src/main/resources/config/verily/sdd/sql/procedure_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/procedure_parentChild.sql b/service/src/main/resources/config/verily/sdd/sql/procedure_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/procedure_parentChild.sql rename to service/src/main/resources/config/verily/sdd/sql/procedure_parentChild.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/procedure_textSearch.sql b/service/src/main/resources/config/verily/sdd/sql/procedure_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/procedure_textSearch.sql rename to service/src/main/resources/config/verily/sdd/sql/procedure_textSearch.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/visit_occurrence_all.sql b/service/src/main/resources/config/verily/sdd/sql/visit_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/visit_occurrence_all.sql rename to service/src/main/resources/config/verily/sdd/sql/visit_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/visit_textSearch.sql b/service/src/main/resources/config/verily/sdd/sql/visit_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/visit_textSearch.sql rename to service/src/main/resources/config/verily/sdd/sql/visit_textSearch.sql diff --git a/service/src/main/resources/config/verily/sdd/original/sql/x_snp.sql b/service/src/main/resources/config/verily/sdd/sql/x_snp.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd/original/sql/x_snp.sql rename to service/src/main/resources/config/verily/sdd/sql/x_snp.sql diff --git a/service/src/main/resources/config/verily/sdd/original/ui/top_level.json b/service/src/main/resources/config/verily/sdd/ui/top_level.json similarity index 98% rename from service/src/main/resources/config/verily/sdd/original/ui/top_level.json rename to service/src/main/resources/config/verily/sdd/ui/top_level.json index 9d9ffe627..b99f202df 100644 --- a/service/src/main/resources/config/verily/sdd/original/ui/top_level.json +++ b/service/src/main/resources/config/verily/sdd/ui/top_level.json @@ -5,16 +5,6 @@ "entity": "person", "key": "id", "classifications": [ - { - "id": "snp", - "attribute": "id", - "entity": "snp", - "entityAttribute": "id", - "defaultSort": { - "attribute": "id", - "direction": "ASC" - } - }, { "id": "genotyping", "attribute": "id", diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/entity/brand.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/brand.json new file mode 100644 index 000000000..b91b1f66a --- /dev/null +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/brand.json @@ -0,0 +1,29 @@ +{ + "name": "brand", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "rawSqlFile": "brand_all.sql" + }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "brand_textSearch.sql" } } } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/entity/condition.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/condition.json new file mode 100644 index 000000000..e8701cc41 --- /dev/null +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/condition.json @@ -0,0 +1,51 @@ +{ + "name": "condition", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "table": "concept", + "filter": { + "type": "BINARY", + "field": { "column": "domain_id" }, + "operator": "EQUALS", + "value": { "stringVal": "Condition" } } }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } }, + "vocabulary": { "value": { "column": "vocabulary_id" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "condition_textSearch.sql" } } }, + "hierarchyMappings": { + "standard": { + "childParent": { + "tablePointer": { "rawSqlFile": "condition_parentChild.sql" } + }, + "rootNodesFilter": { + "tablePointer": { + "table": "concept", + "filter": { "type": "BINARY", "field": { "column": "concept_id" }, "operator": "EQUALS", "value": { "int64Val": 441840 } } }, + "fieldPointers": { + "id": { "column": "concept_id" } + } + }, + "maxHierarchyDepth": 20 + } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/entity/condition_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/condition_occurrence.json new file mode 100644 index 000000000..4d9166cbf --- /dev/null +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/condition_occurrence.json @@ -0,0 +1,42 @@ +{ + "name": "condition_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "condition", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "condition_occurrence_all.sql" }, + "attributeMappings": { + "condition": { + "value": { "column": "condition_concept_id" }, + "display": { + "column": "condition_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/entity/device.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/device.json new file mode 100644 index 000000000..078cd332c --- /dev/null +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/device.json @@ -0,0 +1,43 @@ +{ + "name": "device", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "table": "concept", + "filter": { + "type": "BOOLEAN_AND_OR", + "operator": "AND", + "subfilters": [ + { "type": "BINARY", + "field": { "column": "domain_id" }, + "operator": "EQUALS", + "value": { "stringVal": "Device" } }, + { "type": "BINARY", + "field": { "column": "standard_concept" }, + "operator": "EQUALS", + "value": { "stringVal": "S" } } + ] } }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } }, + "vocabulary": { "value": { "column": "vocabulary_id" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "device_textSearch.sql" } } } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/entity/device_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/device_occurrence.json new file mode 100644 index 000000000..5691bd575 --- /dev/null +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/device_occurrence.json @@ -0,0 +1,41 @@ +{ + "name": "device_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "device", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "device_occurrence_all.sql" }, + "attributeMappings": { + "device": { + "value": { "column": "device_concept_id" }, + "display": { + "column": "device_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/genotyping.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/genotyping.json similarity index 83% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/genotyping.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entity/genotyping.json index e8fa76c2d..9c2739273 100644 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/genotyping.json +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/genotyping.json @@ -2,8 +2,8 @@ "name": "genotyping", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/entity/ingredient.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/ingredient.json new file mode 100644 index 000000000..59a4ddcc0 --- /dev/null +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/ingredient.json @@ -0,0 +1,58 @@ +{ + "name": "ingredient", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "ingredient_all.sql" }, + "attributeMappings": { + "vocabulary": { "value": { "column": "vocabulary_id" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "ingredient_textSearch.sql" } } }, + "hierarchyMappings": { + "standard": { + "childParent": { + "tablePointer": { "rawSqlFile": "ingredient_parentChild.sql" } + }, + "rootNodesFilter": { + "tablePointer": { + "table": "concept", + "filter": { + "type": "BOOLEAN_AND_OR", + "operator": "AND", + "subfilters": [ + { "type": "BINARY", + "field": { "column": "vocabulary_id" }, + "operator": "EQUALS", + "value": { "stringVal": "ATC" } }, + { "type": "BINARY", + "field": { "column": "concept_class_id" }, + "operator": "EQUALS", + "value": { "stringVal": "ATC 1st" } }, + { "type": "BINARY", + "field": { "column": "standard_concept" }, + "operator": "EQUALS", + "value": { "stringVal": "C" } } ] } }, + "fieldPointers": { + "id": { "column": "concept_id" } + } + }, + "maxHierarchyDepth": 15 + } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/entity/ingredient_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/ingredient_occurrence.json new file mode 100644 index 000000000..27470b70b --- /dev/null +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/ingredient_occurrence.json @@ -0,0 +1,44 @@ +{ + "name": "ingredient_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "ingredient", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "refills", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "days_supply", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "ingredient_occurrence_all.sql" }, + "attributeMappings": { + "ingredient": { + "value": { "column": "drug_concept_id" }, + "display": { + "column": "drug_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/sdd/original/entity/measurement.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/measurement.json similarity index 90% rename from service/src/main/resources/config/verily/sdd/original/entity/measurement.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entity/measurement.json index 70324f369..f71f480d4 100644 --- a/service/src/main/resources/config/verily/sdd/original/entity/measurement.json +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/measurement.json @@ -2,11 +2,11 @@ "name": "measurement", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/measurement_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/measurement_occurrence.json similarity index 55% rename from service/src/main/resources/config/vumc/sdd/original/entity/measurement_occurrence.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entity/measurement_occurrence.json index cc142dabb..2fcd3d557 100644 --- a/service/src/main/resources/config/vumc/sdd/original/entity/measurement_occurrence.json +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/measurement_occurrence.json @@ -2,18 +2,18 @@ "name": "measurement_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "measurement", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "value_numeric", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "value_enum", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "unit", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "measurement", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "value_numeric", "dataType": "DOUBLE", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "value_enum", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/note.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/note.json similarity index 81% rename from service/src/main/resources/config/vumc/sdd/original/entity/note.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entity/note.json index e21370c93..a73afb9de 100644 --- a/service/src/main/resources/config/vumc/sdd/original/entity/note.json +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/note.json @@ -2,10 +2,10 @@ "name": "note", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/entity/note_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/note_occurrence.json new file mode 100644 index 000000000..06c084e35 --- /dev/null +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/note_occurrence.json @@ -0,0 +1,42 @@ +{ + "name": "note_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "note", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "title", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "text", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "note_occurrence_all.sql" }, + "attributeMappings": { + "date": { "value": { "column": "note_date" } }, + "note": { + "value": { "column": "note_type_concept_id" }, + "display": { + "column": "note_type_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/entity/observation.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/observation.json new file mode 100644 index 000000000..92f45b426 --- /dev/null +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/observation.json @@ -0,0 +1,51 @@ +{ + "name": "observation", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "table": "concept", + "filter": { + "type": "BOOLEAN_AND_OR", + "operator": "AND", + "subfilters": [ + { "type": "BINARY", + "field": { "column": "domain_id" }, + "operator": "EQUALS", + "value": { "stringVal": "Observation" } }, + { "type": "BINARY", + "field": { "column": "standard_concept" }, + "operator": "EQUALS", + "value": { "stringVal": "S" } }, + { "type": "BINARY", + "field": { "column": "vocabulary_id" }, + "operator": "NOT_EQUALS", + "value": { "stringVal": "PPI" } }, + { "type": "BINARY", + "field": { "column": "concept_class_id" }, + "operator": "NOT_EQUALS", + "value": { "stringVal": "Survey" } } + ] } }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } }, + "vocabulary": { "value": { "column": "vocabulary_id" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "observation_textSearch.sql" } } } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/observation_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/observation_occurrence.json similarity index 55% rename from service/src/main/resources/config/vumc/sdd/original/entity/observation_occurrence.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entity/observation_occurrence.json index c1709a63a..da8e8c476 100644 --- a/service/src/main/resources/config/vumc/sdd/original/entity/observation_occurrence.json +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/observation_occurrence.json @@ -2,18 +2,18 @@ "name": "observation_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "observation" }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "value_as_string", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "value", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "unit", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "observation", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "value_as_string", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "value", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/verily/sdd/original/entity/person.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/person.json similarity index 60% rename from service/src/main/resources/config/verily/sdd/original/entity/person.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entity/person.json index 06a1770c9..a68df85fb 100644 --- a/service/src/main/resources/config/verily/sdd/original/entity/person.json +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/person.json @@ -2,17 +2,17 @@ "name": "person", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "year_of_birth" }, - { "type": "SIMPLE", "name": "age" }, - { "type": "KEY_AND_DISPLAY", "name": "gender" }, - { "type": "KEY_AND_DISPLAY", "name": "race" }, - { "type": "KEY_AND_DISPLAY", "name": "ethnicity" }, - { "type": "SIMPLE", "name": "has_biovu_sample" }, - { "type": "SIMPLE", "name": "biovu_sample_dna_yield" }, - { "type": "SIMPLE", "name": "biovu_sample_is_compromised" }, - { "type": "SIMPLE", "name": "biovu_sample_is_nonshippable" }, - { "type": "SIMPLE", "name": "biovu_sample_has_plasma" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "year_of_birth", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "age", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "gender", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "race", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "ethnicity", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "has_biovu_sample", "dataType": "BOOLEAN" }, + { "type": "SIMPLE", "name": "biovu_sample_dna_yield", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "biovu_sample_is_compromised", "dataType": "BOOLEAN" }, + { "type": "SIMPLE", "name": "biovu_sample_is_nonshippable", "dataType": "BOOLEAN" }, + { "type": "SIMPLE", "name": "biovu_sample_has_plasma", "dataType": "BOOLEAN" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/entity/procedure.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/procedure.json new file mode 100644 index 000000000..b45e3d76c --- /dev/null +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/procedure.json @@ -0,0 +1,51 @@ +{ + "name": "procedure", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "table": "concept", + "filter": { + "type": "BINARY", + "field": { "column": "domain_id" }, + "operator": "EQUALS", + "value": { "stringVal": "Procedure" } } }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } }, + "vocabulary": { "value": { "column": "vocabulary_id" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "procedure_textSearch.sql" } } }, + "hierarchyMappings": { + "standard": { + "childParent": { + "tablePointer": { "rawSqlFile": "procedure_parentChild.sql" } + }, + "rootNodesFilter": { + "tablePointer": { + "table": "concept", + "filter": { "type": "BINARY", "field": { "column": "concept_id" }, "operator": "EQUALS", "value": { "int64Val": 4322976 } } }, + "fieldPointers": { + "id": { "column": "concept_id" } + } + }, + "maxHierarchyDepth": 19 + } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/procedure_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/procedure_occurrence.json similarity index 51% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/procedure_occurrence.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entity/procedure_occurrence.json index 6d1d61acc..fdc4cc913 100644 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/procedure_occurrence.json +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/procedure_occurrence.json @@ -2,15 +2,15 @@ "name": "procedure_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "procedure", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "procedure", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/snp.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/snp.json similarity index 77% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entity/snp.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entity/snp.json index 5e9df59ef..86b0d95b0 100644 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/snp.json +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/snp.json @@ -2,8 +2,8 @@ "name": "snp", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/entity/visit.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/visit.json new file mode 100644 index 000000000..68bcc9d58 --- /dev/null +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/visit.json @@ -0,0 +1,33 @@ +{ + "name": "visit", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "table": "concept", + "filter": { + "type": "BOOLEAN_AND_OR", + "operator": "AND", + "subfilters": [ + { "type": "BINARY", + "field": { "column": "domain_id" }, + "operator": "EQUALS", + "value": { "stringVal": "Visit" } }, + { "type": "BINARY", + "field": { "column": "standard_concept" }, + "operator": "EQUALS", + "value": { "stringVal": "S" } } ] } }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "visit_textSearch.sql" } } } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/entity/visit_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/entity/visit_occurrence.json new file mode 100644 index 000000000..4c91db3ae --- /dev/null +++ b/service/src/main/resources/config/verily/sdd_refresh0323/entity/visit_occurrence.json @@ -0,0 +1,32 @@ +{ + "name": "visit_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "visit_occurrence_all.sql" }, + "attributeMappings": { + "visit": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/brand_ingredient.json b/service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/brand_ingredient.json similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/brand_ingredient.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/brand_ingredient.json diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/condition_person_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/condition_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/condition_person_occurrence.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/condition_person_occurrence.json diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/device_person_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/device_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/device_person_occurrence.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/device_person_occurrence.json diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/genotyping_person.json b/service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/genotyping_person.json similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/genotyping_person.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/genotyping_person.json diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/ingredient_person_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/ingredient_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/ingredient_person_occurrence.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/ingredient_person_occurrence.json diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/measurement_person_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/measurement_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/measurement_person_occurrence.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/measurement_person_occurrence.json diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/note_person_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/note_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/note_person_occurrence.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/note_person_occurrence.json diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/observation_person_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/observation_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/observation_person_occurrence.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/observation_person_occurrence.json diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/procedure_person_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/procedure_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/procedure_person_occurrence.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/procedure_person_occurrence.json diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/snp_person.json b/service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/snp_person.json similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/snp_person.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/snp_person.json diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/visit_person_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/visit_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entitygroup/visit_person_occurrence.json rename to service/src/main/resources/config/verily/sdd_refresh0323/entitygroup/visit_person_occurrence.json diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/brand.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/brand.json deleted file mode 100644 index aac74b038..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/brand.json +++ /dev/null @@ -1,141 +0,0 @@ -{ - "name" : "brand", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "" - }, - "display" : "Unknown" - }, - "count" : 7 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT * FROM `victr-tanagra-test.sd_20230328.concept` WHERE domain_id = 'Drug' AND concept_class_id = 'Brand Name' AND vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND DATE_DIFF(CAST(valid_end_date AS DATE), CURRENT_DATE(), DAY) > 0" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_20230328.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_20230328.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND c.concept_class_id = 'Brand Name' AND c.vocabulary_id IN ('RxNorm', 'RxNorm Extension')" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "brand" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/condition.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/condition.json deleted file mode 100644 index c119911e7..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/condition.json +++ /dev/null @@ -1,459 +0,0 @@ -{ - "name" : "condition", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 174148 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 384 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CIEL" - }, - "display" : "CIEL" - }, - "count" : 38818 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CIM10" - }, - "display" : "CIM10" - }, - "count" : 10867 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Cohort" - }, - "display" : "Cohort" - }, - "count" : 66 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HemOnc" - }, - "display" : "HemOnc" - }, - "count" : 219 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10" - }, - "display" : "ICD10" - }, - "count" : 15017 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "ICD10CM" - }, - "count" : 90542 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CN" - }, - "display" : "ICD10CN" - }, - "count" : 31794 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10GM" - }, - "display" : "ICD10GM" - }, - "count" : 16006 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "ICD9CM" - }, - "count" : 15760 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICDO3" - }, - "display" : "ICDO3" - }, - "count" : 62410 - }, { - "enumVal" : { - "value" : { - "stringVal" : "KCD7" - }, - "display" : "KCD7" - }, - "count" : 20743 - }, { - "enumVal" : { - "value" : { - "stringVal" : "MeSH" - }, - "display" : "MeSH" - }, - "count" : 6795 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Nebraska Lexicon" - }, - "display" : "Nebraska Lexicon" - }, - "count" : 151336 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OMOP Extension" - }, - "display" : "OMOP Extension" - }, - "count" : 7 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPCS4" - }, - "display" : "OPCS4" - }, - "count" : 6 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OXMIS" - }, - "display" : "OXMIS" - }, - "count" : 5704 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OncoTree" - }, - "display" : "OncoTree" - }, - "count" : 869 - }, { - "enumVal" : { - "value" : { - "stringVal" : "PPI" - }, - "display" : "PPI" - }, - "count" : 74 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Read" - }, - "display" : "Read" - }, - "count" : 47736 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SMQ" - }, - "display" : "SMQ" - }, - "count" : 324 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 180133 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED Veterinary" - }, - "display" : "SNOMED Veterinary" - }, - "count" : 3237 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Condition" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_20230328.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_20230328.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Condition' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `victr-tanagra-test.sd_20230328.concept_relationship` cr JOIN `victr-tanagra-test.sd_20230328.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `victr-tanagra-test.sd_20230328.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Condition' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED'" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 441840 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "condition" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "condition_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "condition_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "condition" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/condition_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/condition_occurrence.json deleted file mode 100644 index b1009e345..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/condition_occurrence.json +++ /dev/null @@ -1,283 +0,0 @@ -{ - "name" : "condition_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "condition", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -977.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 9117630 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 57159530 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 3963125 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 158270179 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT co.condition_occurrence_id AS id, co.person_id, co.condition_concept_id, co.condition_start_date AS start_date, co.condition_end_date AS end_date, co.stop_reason, co.condition_source_value AS source_value, co.condition_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(co.condition_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, co.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_20230328.condition_occurrence` AS co JOIN `victr-tanagra-test.sd_20230328.person` AS p ON p.person_id = co.person_id LEFT JOIN `victr-tanagra-test.sd_20230328.visit_occurrence` AS vo ON vo.visit_occurrence_id = co.visit_occurrence_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "condition_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "condition_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_condition", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/device.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/device.json deleted file mode 100644 index 65f7f4871..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/device.json +++ /dev/null @@ -1,285 +0,0 @@ -{ - "name" : "device", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 245402 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "AMT" - }, - "display" : "AMT" - }, - "count" : 2945 - }, { - "enumVal" : { - "value" : { - "stringVal" : "BDPM" - }, - "display" : "BDPM" - }, - "count" : 1106 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "CPT4" - }, - "count" : 24 - }, { - "enumVal" : { - "value" : { - "stringVal" : "GGR" - }, - "display" : "GGR" - }, - "count" : 596 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 4634 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10PCS" - }, - "display" : "ICD10PCS" - }, - "count" : 3 - }, { - "enumVal" : { - "value" : { - "stringVal" : "JMDC" - }, - "display" : "JMDC" - }, - "count" : 1313 - }, { - "enumVal" : { - "value" : { - "stringVal" : "KDC" - }, - "display" : "KDC" - }, - "count" : 112 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NDC" - }, - "display" : "NDC" - }, - "count" : 10963 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPCS4" - }, - "display" : "OPCS4" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 202567 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED Veterinary" - }, - "display" : "SNOMED Veterinary" - }, - "count" : 67 - }, { - "enumVal" : { - "value" : { - "stringVal" : "dm+d" - }, - "display" : "dm+d" - }, - "count" : 21071 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Device" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_20230328.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_20230328.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Device' AND c.standard_concept = 'S'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "device" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/device_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/device_occurrence.json deleted file mode 100644 index 4510cd078..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/device_occurrence.json +++ /dev/null @@ -1,256 +0,0 @@ -{ - "name" : "device_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -4.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 116800 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 935607 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1719 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 2120916 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "device", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT de.device_exposure_id AS id, de.person_id, de.device_concept_id, de.device_exposure_start_date AS start_date, de.device_exposure_end_date AS end_date, de.device_source_value AS source_value, de.device_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(de.device_exposure_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, de.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_20230328.device_exposure` AS de JOIN `victr-tanagra-test.sd_20230328.person` AS p ON p.person_id = de.person_id LEFT JOIN `victr-tanagra-test.sd_20230328.visit_occurrence` AS vo ON vo.visit_occurrence_id = de.visit_occurrence_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "device_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "device_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_device", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/genotyping.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/genotyping.json deleted file mode 100644 index 1fc374b02..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/genotyping.json +++ /dev/null @@ -1,149 +0,0 @@ -{ - "name" : "genotyping", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "/* platform_id column has type NUMERIC. This causes index column to be FLOAT. Currently indexing doesn't handle floats properly, so change column to INTEGER. */ SELECT CAST(platform_id as INT64) AS platform_id, assay_name as assay_name FROM `victr-tanagra-test.sd_20230328.platform` UNION ALL /* Add some rows to get hierarchy to work. Parent ids are defined in genotype_criteria, criteria_meta_seq column. criteria_meta_seq is not in the same \"ID space\" as platform_id. Tanagra requres parent id to be in same \"ID space\" as platform_id. So create artificial platform_ids for parents. */ (SELECT 101 AS platform_id, 'GWAS Platforms' AS assay_name UNION ALL SELECT 102, 'Non-GWAS and Targeted Genotyping Platforms' UNION ALL SELECT 103, 'Sequencing Platforms') " - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "assay_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "platform_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "attributes" : [ "id", "name" ] - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT /* Use parent ids defined in platform.sql */ parent_seq + 100 AS parent, CAST(platform_id as INT64) AS child FROM `victr-tanagra-test.sd_20230328.genotype_criteria` g, `victr-tanagra-test.sd_20230328.platform` p WHERE g.name = p.assay_name " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "rawSql" : "/* Match the platform ids in platform.sql */ SELECT 101 AS id UNION ALL SELECT 102 UNION ALL SELECT 103 " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 1 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "genotyping" - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "genotyping_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "genotyping_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "genotyping" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 1 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/ingredient.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/ingredient.json deleted file mode 100644 index 33ca6e8d5..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/ingredient.json +++ /dev/null @@ -1,306 +0,0 @@ -{ - "name" : "ingredient", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 1921307 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 6335 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "ATC" - }, - "display" : "ATC" - }, - "count" : 6335 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm" - }, - "display" : "RxNorm" - }, - "count" : 147265 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm Extension" - }, - "display" : "RxNorm Extension" - }, - "count" : 1774042 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT c.concept_id AS id, c.concept_name AS name, c.vocabulary_id, c.standard_concept, c.concept_code FROM `victr-tanagra-test.sd_20230328.concept` c WHERE c.domain_id = 'Drug' AND ( (c.vocabulary_id = 'ATC' AND c.standard_concept = 'C') OR (c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.standard_concept = 'S') )" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_20230328.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_20230328.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND ((c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.concept_class_id = 'Ingredient' AND c.standard_concept = 'S') OR (c.vocabulary_id = 'RxNorm' AND c.concept_class_id = 'Precise Ingredient') OR (c.vocabulary_id = 'ATC' AND c.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c.standard_concept = 'C'))" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child FROM `victr-tanagra-test.sd_20230328.concept_relationship` cr JOIN `victr-tanagra-test.sd_20230328.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `victr-tanagra-test.sd_20230328.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE c1.concept_id != c2.concept_id AND c1.domain_id = 'Drug' AND c2.domain_id = 'Drug' AND ( /* Populate Ingredients' ancestors', which are ATCs. See https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:atc#:~:text=the%20original%20ATC%20hierarchy%20is%20extended%20by%20Standard%20Drug%20Products%20of%20RxNorm%20and%20RxNorm%20Extension%20vocabularies%2C%20which%20are%20assigned%20to%20be%20descendants%20of%20the%205th%20ATC%20Classes. Eg: ATC 1st (highest ancestor) Subsumes ATC 2nd ATC 5th (direct parent of RxNorm) Maps to RxNorm */ (c1.vocabulary_id IN ('ATC') AND cr.relationship_id IN ('Subsumes', 'Maps to')) OR /* Populate Ingredients and their descendants: Branded Drug, Clinical Drug, etc. Ingredients and their descendants are RxNorm. drug_exposure contains Ingredients or their descendants. Use [1] and [2] to define hierarchy. Eg \"Marketed Product\" is most specific and is bottom of hierarchy. [1] https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:drug_exposure#:~:text=These%20are%20indicated,is%20available%20%E2%80%9CIngredient%E2%80%9D [2] https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:drug#:~:text=are%20not%20implemented.-,Relationships,-As%20usual%2C%20all */ ( c1.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c2.vocabulary_id IN ('RxNorm', 'RxNorm Extension') /* Only keep relationships where c1 is \"parent\" of c2 */ AND cr.relationship_id IN ('Constitutes', 'Contained in' , 'Has form', 'Has quantified form', 'RxNorm ing of', 'RxNorm inverse is a', 'Precise ing of') ) )" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC 1st" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "C" - } - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 15 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "ingredient" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "ingredient_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "ingredient_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "ingredient" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 15 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/ingredient_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/ingredient_occurrence.json deleted file mode 100644 index f20e2a223..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/ingredient_occurrence.json +++ /dev/null @@ -1,543 +0,0 @@ -{ - "name" : "ingredient_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ingredient", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Allergic res" - }, - "display" : "Allergic res" - }, - "count" : 6246 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Alternate tx" - }, - "display" : "Alternate tx" - }, - "count" : 115351 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Anes Stop" - }, - "display" : "Anes Stop" - }, - "count" : 3911532 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Availability" - }, - "display" : "Availability" - }, - "count" : 9361 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CONTACT " - }, - "display" : "CONTACT " - }, - "count" : 858 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Cleanup" - }, - "display" : "Cleanup" - }, - "count" : 892415 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Cost of medi" - }, - "display" : "Cost of medi" - }, - "count" : 12304 - }, { - "enumVal" : { - "value" : { - "stringVal" : "DC'd by othr" - }, - "display" : "DC'd by othr" - }, - "count" : 222665 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Dose adjustm" - }, - "display" : "Dose adjustm" - }, - "count" : 163200 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Drug interac" - }, - "display" : "Drug interac" - }, - "count" : 2748 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Duplicate or" - }, - "display" : "Duplicate or" - }, - "count" : 602987 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Error" - }, - "display" : "Error" - }, - "count" : 319842 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Expired" - }, - "display" : "Expired" - }, - "count" : 165053 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Formulary" - }, - "display" : "Formulary" - }, - "count" : 34057 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NON-ADHEREN" - }, - "display" : "NON-ADHEREN" - }, - "count" : 11216 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Other" - }, - "display" : "Other" - }, - "count" : 240539 - }, { - "enumVal" : { - "value" : { - "stringVal" : "PATIENT DISC" - }, - "display" : "PATIENT DISC" - }, - "count" : 9038687 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Paradoxical" - }, - "display" : "Paradoxical" - }, - "count" : 343 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Pregnancy" - }, - "display" : "Pregnancy" - }, - "count" : 1330 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RETURNED TO " - }, - "display" : "RETURNED TO " - }, - "count" : 23983 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Reorder" - }, - "display" : "Reorder" - }, - "count" : 5801736 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SE" - }, - "display" : "SE" - }, - "count" : 47335 - }, { - "enumVal" : { - "value" : { - "stringVal" : "STOP TAKING " - }, - "display" : "STOP TAKING " - }, - "count" : 547157 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SURGERY" - }, - "display" : "SURGERY" - }, - "count" : 1049 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Stop Med" - }, - "display" : "Stop Med" - }, - "count" : 352498 - }, { - "enumVal" : { - "value" : { - "stringVal" : "TRANSFER" - }, - "display" : "TRANSFER" - }, - "count" : 797968 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Therapy comp" - }, - "display" : "Therapy comp" - }, - "count" : 2998407 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 7158852 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 213493259 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 348634 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 53088542 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "days_supply", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 1.0, - "maxVal" : 36135.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "refills", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 365.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -1000.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT de.drug_exposure_id AS id, de.person_id, de.drug_concept_id, de.drug_exposure_start_date AS start_date, de.drug_exposure_end_date AS end_date, de.stop_reason, de.refills, de.days_supply, de.drug_source_value AS source_value, de.drug_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(de.drug_exposure_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, de.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_20230328.drug_exposure` AS de JOIN `victr-tanagra-test.sd_20230328.person` AS p ON p.person_id = de.person_id LEFT JOIN `victr-tanagra-test.sd_20230328.visit_occurrence` AS vo ON vo.visit_occurrence_id = de.visit_occurrence_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "drug_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "ingredient_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "ingredient", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ingredient", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/measurement.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/measurement.json deleted file mode 100644 index 2706a9943..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/measurement.json +++ /dev/null @@ -1,407 +0,0 @@ -{ - "name" : "measurement", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 73948 - }, { - "enumVal" : { - "value" : { - "stringVal" : "" - }, - "display" : "Unknown" - }, - "count" : 9 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 40193 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "LOINC" - }, - "count" : 186150 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 29999 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Measurement" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "SNOMED" - } - } ] - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC" - } - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC Hierarchy" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC Component" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Lab Test" - } - } ] - } ] - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_20230328.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_20230328.concept` c ON c.concept_id = textsearch.id WHERE ((c.domain_id = 'Measurement' AND c.vocabulary_id = 'SNOMED') OR (c.vocabulary_id = 'LOINC' AND c.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test')))" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `victr-tanagra-test.sd_20230328.concept_relationship` cr JOIN `victr-tanagra-test.sd_20230328.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `victr-tanagra-test.sd_20230328.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.vocabulary_id = c2.vocabulary_id AND ((c1.vocabulary_id = 'SNOMED' AND c1.domain_id = c2.domain_id AND c1.domain_id = 'Measurement') OR (c1.vocabulary_id = 'LOINC' AND c1.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test') AND c2.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test'))) " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Measurement" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "SNOMED" - } - } ] - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 36206173 - } - } ] - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 11 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "measurement" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "measurement_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "measurement_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "measurement" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 11 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/measurement_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/measurement_occurrence.json deleted file mode 100644 index a6eb0a0d1..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/measurement_occurrence.json +++ /dev/null @@ -1,312 +0,0 @@ -{ - "name" : "measurement_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -1765.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 42914672 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 641606490 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 2817948 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 302941126 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_numeric", - "dataType" : "DOUBLE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value_enum", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "measurement", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT mo.measurement_id AS id, mo.person_id, mo.measurement_concept_id, mo.measurement_date, mo.value_as_number AS value_numeric, mo.value_as_concept_id, mo.unit_concept_id, mo.measurement_source_value AS source_value, mo.measurement_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(mo.measurement_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, mo.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_20230328.measurement` AS mo JOIN `victr-tanagra-test.sd_20230328.person` AS p ON p.person_id = mo.person_id LEFT JOIN `victr-tanagra-test.sd_20230328.visit_occurrence` AS vo ON vo.visit_occurrence_id = mo.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "measurement_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value_numeric" : { - "value" : { - "column" : "value_numeric", - "runtimeCalculated" : false - } - }, - "value_enum" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "measurement" : { - "value" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "measurement_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "measurement_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value_numeric" : { - "value" : { - "column" : "value_numeric", - "runtimeCalculated" : false - } - }, - "value_enum" : { - "value" : { - "column" : "value_enum", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value_enum", - "runtimeCalculated" : false - } - }, - "measurement" : { - "value" : { - "column" : "measurement", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_measurement", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/note.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/note.json deleted file mode 100644 index a25a251a5..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/note.json +++ /dev/null @@ -1,195 +0,0 @@ -{ - "name" : "note", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "None" - }, - "display" : "None" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Note Type" - }, - "display" : "Note Type" - }, - "count" : 10 - }, { - "enumVal" : { - "value" : { - "stringVal" : "VUMC Note Type" - }, - "display" : "VUMC Note Type" - }, - "count" : 3 - }, { - "enumVal" : { - "value" : { - "stringVal" : "VUMC PSS Type" - }, - "display" : "VUMC PSS Type" - }, - "count" : 1 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 0 - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Note Type" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "VUMC Note Type" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "VUMC PSS Type" - } - } ] - } - }, - "attributeMappings" : { - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_20230328.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_20230328.concept` c ON c.concept_id = textsearch.id WHERE c.vocabulary_id IN ('Note Type', 'VUMC Note Type', 'VUMC PSS Type') OR c.concept_id = 0" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "note" - }, - "attributeMappings" : { - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/note_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/note_occurrence.json deleted file mode 100644 index 09e65181f..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/note_occurrence.json +++ /dev/null @@ -1,380 +0,0 @@ -{ - "name" : "note_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "note", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 44814638 - }, - "display" : "Admission note" - }, - "count" : 2442874 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814643 - }, - "display" : "Ancillary report" - }, - "count" : 11932638 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814637 - }, - "display" : "Discharge summary" - }, - "count" : 5844946 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2003594153 - }, - "display" : "ECG_IMPRESSION" - }, - "count" : 2133266 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814646 - }, - "display" : "Emergency department note" - }, - "count" : 3497555 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814639 - }, - "display" : "Inpatient note" - }, - "count" : 19765349 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 9356183 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814645 - }, - "display" : "Note" - }, - "count" : 76574511 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814644 - }, - "display" : "Nursing report" - }, - "count" : 6939641 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814640 - }, - "display" : "Outpatient note" - }, - "count" : 87119775 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2002404173 - }, - "display" : "PL_PROBLEM LIST" - }, - "count" : 537792653 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814642 - }, - "display" : "Pathology report" - }, - "count" : 2188991 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2002603124 - }, - "display" : "Pss Problem snomed data" - }, - "count" : 29685278 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814641 - }, - "display" : "Radiology report" - }, - "count" : 18457033 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2004084156 - }, - "display" : "VUMC forms data" - }, - "count" : 1317981 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -1646.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 2415239 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 22246659 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1812247 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 33946457 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "text", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "title", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT n.note_id AS id, n.person_id, n.note_type_concept_id, n.note_date, n.note_title AS title, n.note_text AS text, n.note_source_value AS source_value, CAST(FLOOR(TIMESTAMP_DIFF(n.note_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, n.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_20230328.note` AS n JOIN `victr-tanagra-test.sd_20230328.person` AS p ON p.person_id = n.person_id LEFT JOIN `victr-tanagra-test.sd_20230328.visit_occurrence` AS vo ON vo.visit_occurrence_id = n.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "note_date", - "runtimeCalculated" : false - } - }, - "note" : { - "value" : { - "column" : "note_type_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "note_type_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "text" : { - "value" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "title" : { - "value" : { - "column" : "title", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "note_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "note" : { - "value" : { - "column" : "note", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_note", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "text" : { - "value" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "title" : { - "value" : { - "column" : "title", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/observation.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/observation.json deleted file mode 100644 index cf6238dcd..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/observation.json +++ /dev/null @@ -1,337 +0,0 @@ -{ - "name" : "observation", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 162296 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "APC" - }, - "display" : "APC" - }, - "count" : 715 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "CPT4" - }, - "count" : 1083 - }, { - "enumVal" : { - "value" : { - "stringVal" : "DRG" - }, - "display" : "DRG" - }, - "count" : 752 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 2667 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICDO3" - }, - "display" : "ICDO3" - }, - "count" : 49 - }, { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "LOINC" - }, - "count" : 7087 - }, { - "enumVal" : { - "value" : { - "stringVal" : "MDC" - }, - "display" : "MDC" - }, - "count" : 26 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NAACCR" - }, - "display" : "NAACCR" - }, - "count" : 96 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NUCC" - }, - "display" : "NUCC" - }, - "count" : 4 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Nebraska Lexicon" - }, - "display" : "Nebraska Lexicon" - }, - "count" : 1004 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OMOP Extension" - }, - "display" : "OMOP Extension" - }, - "count" : 107 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPCS4" - }, - "display" : "OPCS4" - }, - "count" : 56 - }, { - "enumVal" : { - "value" : { - "stringVal" : "PCORNet" - }, - "display" : "PCORNet" - }, - "count" : 2 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 117406 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED Veterinary" - }, - "display" : "SNOMED Veterinary" - }, - "count" : 27401 - }, { - "enumVal" : { - "value" : { - "stringVal" : "UB04 Pri Typ of Adm" - }, - "display" : "UB04 Pri Typ of Adm" - }, - "count" : 6 - }, { - "enumVal" : { - "value" : { - "stringVal" : "UK Biobank" - }, - "display" : "UK Biobank" - }, - "count" : 3835 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Observation" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "PPI" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "Survey" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_20230328.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_20230328.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Observation' AND c.standard_concept = 'S' AND c.vocabulary_id != 'PPI' AND c.concept_class_id != 'Survey'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "observation" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/observation_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/observation_occurrence.json deleted file mode 100644 index 704e54191..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/observation_occurrence.json +++ /dev/null @@ -1,312 +0,0 @@ -{ - "name" : "observation_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -977.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "observation", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_as_string", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 4017765 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 10358821 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1121298 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 67445573 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT o.observation_id AS id, o.person_id, o.observation_concept_id, o.observation_date, o.value_as_string, o.value_as_concept_id, o.unit_concept_id, o.observation_source_value AS source_value, o.observation_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(o.observation_date, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, o.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_20230328.observation` AS o JOIN `victr-tanagra-test.sd_20230328.person` AS p ON p.person_id = o.person_id LEFT JOIN `victr-tanagra-test.sd_20230328.visit_occurrence` AS vo ON vo.visit_occurrence_id = o.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "observation_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "observation_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "observation_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_observation", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/person.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/person.json deleted file mode 100644 index 023e47eb3..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/person.json +++ /dev/null @@ -1,360 +0,0 @@ -{ - "name" : "person", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "gender", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 8532 - }, - "display" : "FEMALE" - }, - "count" : 1940496 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8507 - }, - "display" : "MALE" - }, - "count" : 1673369 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 4273 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "race", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 8657 - }, - "display" : "American Indian or Alaska Native" - }, - "count" : 5078 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8515 - }, - "display" : "Asian" - }, - "count" : 48897 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38003598 - }, - "display" : "Black" - }, - "count" : 343615 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1000410 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8527 - }, - "display" : "White" - }, - "count" : 2220138 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ethnicity", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 38003563 - }, - "display" : "Hispanic or Latino" - }, - "count" : 123186 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1027401 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38003564 - }, - "display" : "Not Hispanic or Latino" - }, - "count" : 2467551 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "biovu_sample_has_plasma", - "dataType" : "BOOLEAN", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "biovu_sample_dna_yield", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 500.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "biovu_sample_is_compromised", - "dataType" : "BOOLEAN", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "age", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -971.0, - "maxVal" : 224.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "has_biovu_sample", - "dataType" : "BOOLEAN", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "biovu_sample_is_nonshippable", - "dataType" : "BOOLEAN", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "year_of_birth", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 1799.0, - "maxVal" : 2993.0 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT /* Can't do \"*\". During expansion, there's an error about person_id column being ambiguous. */ p.person_id, p.year_of_birth, p.birth_datetime, p.gender_concept_id, p.race_concept_id, p.ethnicity_concept_id, /* Add BioVU sample columns. The way x_biovu_sample_status is created, there should be at most one row per person. */ EXISTS (SELECT 1 FROM `victr-tanagra-test.sd_20230328.x_biovu_sample_status` x WHERE p.person_id = x.person_id) AS has_biovu_sample, x.dna_yield_ind AS biovu_sample_dna_yield, /* As a courtesy, convert string fields to boolean: 0 -> No, 1 -> Yes */ CASE WHEN x.compromise_ind = '1' THEN true WHEN x.compromise_ind = '0' THEN false ELSE null END AS biovu_sample_is_compromised, CASE WHEN x.nonshippable_ind = '1' THEN true WHEN x.nonshippable_ind = '0' THEN false ELSE null END AS biovu_sample_is_nonshippable, CASE WHEN x.plasma_ind = '1' THEN true WHEN x.plasma_ind = '0' THEN false ELSE null END AS biovu_sample_has_plasma FROM `victr-tanagra-test.sd_20230328.person` p LEFT OUTER JOIN ( /* Get rid of duplicate rows in x_biovu_sample_status. For example, person 4587323 has 11 duplicate rows. This returns just 1 row for each person. */ WITH x_biovu_sample_status AS ( SELECT *, ROW_NUMBER() OVER(PARTITION BY person_id) AS rn FROM `victr-tanagra-test.sd_20230328.x_biovu_sample_status` ) SELECT * FROM x_biovu_sample_status WHERE rn = 1 ) x ON p.person_id = x.person_id " - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "gender_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "race_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "ethnicity_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "biovu_sample_has_plasma" : { - "value" : { - "column" : "biovu_sample_has_plasma", - "runtimeCalculated" : false - } - }, - "biovu_sample_dna_yield" : { - "value" : { - "column" : "biovu_sample_dna_yield", - "runtimeCalculated" : false - } - }, - "biovu_sample_is_compromised" : { - "value" : { - "column" : "biovu_sample_is_compromised", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "age" : { - "value" : { - "column" : "birth_datetime", - "sqlFunctionWrapper" : "CAST(FLOOR(TIMESTAMP_DIFF(CURRENT_TIMESTAMP(), ${fieldSql}, DAY) / 365.25) AS INT64)", - "runtimeCalculated" : true - } - }, - "has_biovu_sample" : { - "value" : { - "column" : "has_biovu_sample", - "runtimeCalculated" : false - } - }, - "biovu_sample_is_nonshippable" : { - "value" : { - "column" : "biovu_sample_is_nonshippable", - "runtimeCalculated" : false - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "person" - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_gender", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_race", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ethnicity", - "runtimeCalculated" : false - } - }, - "biovu_sample_has_plasma" : { - "value" : { - "column" : "biovu_sample_has_plasma", - "runtimeCalculated" : false - } - }, - "biovu_sample_dna_yield" : { - "value" : { - "column" : "biovu_sample_dna_yield", - "runtimeCalculated" : false - } - }, - "biovu_sample_is_compromised" : { - "value" : { - "column" : "biovu_sample_is_compromised", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "age" : { - "value" : { - "column" : "age", - "sqlFunctionWrapper" : "CAST(FLOOR(TIMESTAMP_DIFF(CURRENT_TIMESTAMP(), ${fieldSql}, DAY) / 365.25) AS INT64)", - "runtimeCalculated" : true - } - }, - "has_biovu_sample" : { - "value" : { - "column" : "has_biovu_sample", - "runtimeCalculated" : false - } - }, - "biovu_sample_is_nonshippable" : { - "value" : { - "column" : "biovu_sample_is_nonshippable", - "runtimeCalculated" : false - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/procedure.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/procedure.json deleted file mode 100644 index 1c48b48ca..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/procedure.json +++ /dev/null @@ -1,483 +0,0 @@ -{ - "name" : "procedure", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 262341 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 3064 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CCAM" - }, - "display" : "CCAM" - }, - "count" : 10206 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CIEL" - }, - "display" : "CIEL" - }, - "count" : 648 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CIM10" - }, - "display" : "CIM10" - }, - "count" : 195 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "CPT4" - }, - "count" : 13143 - }, { - "enumVal" : { - "value" : { - "stringVal" : "EDI" - }, - "display" : "EDI" - }, - "count" : 249785 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 1289 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HemOnc" - }, - "display" : "HemOnc" - }, - "count" : 92 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10" - }, - "display" : "ICD10" - }, - "count" : 161 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "ICD10CM" - }, - "count" : 6 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CN" - }, - "display" : "ICD10CN" - }, - "count" : 386 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10GM" - }, - "display" : "ICD10GM" - }, - "count" : 157 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10PCS" - }, - "display" : "ICD10PCS" - }, - "count" : 194874 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "ICD9CM" - }, - "count" : 177 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9Proc" - }, - "display" : "ICD9Proc" - }, - "count" : 4657 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9ProcCN" - }, - "display" : "ICD9ProcCN" - }, - "count" : 13385 - }, { - "enumVal" : { - "value" : { - "stringVal" : "KCD7" - }, - "display" : "KCD7" - }, - "count" : 165 - }, { - "enumVal" : { - "value" : { - "stringVal" : "MeSH" - }, - "display" : "MeSH" - }, - "count" : 951 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NAACCR" - }, - "display" : "NAACCR" - }, - "count" : 710 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Nebraska Lexicon" - }, - "display" : "Nebraska Lexicon" - }, - "count" : 72683 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OMOP Extension" - }, - "display" : "OMOP Extension" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPCS4" - }, - "display" : "OPCS4" - }, - "count" : 9750 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPS" - }, - "display" : "OPS" - }, - "count" : 41101 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OXMIS" - }, - "display" : "OXMIS" - }, - "count" : 1193 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Read" - }, - "display" : "Read" - }, - "count" : 20973 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 86910 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED Veterinary" - }, - "display" : "SNOMED Veterinary" - }, - "count" : 392 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Procedure" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_20230328.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_20230328.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Procedure' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `victr-tanagra-test.sd_20230328.concept_relationship` cr JOIN `victr-tanagra-test.sd_20230328.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `victr-tanagra-test.sd_20230328.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Procedure' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED'" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 4322976 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "procedure" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "procedure_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "procedure_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "procedure" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/procedure_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/procedure_occurrence.json deleted file mode 100644 index 51a12c619..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/procedure_occurrence.json +++ /dev/null @@ -1,239 +0,0 @@ -{ - "name" : "procedure_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -96.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 7621518 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 32528299 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1120517 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 90242249 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "procedure", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT po.procedure_occurrence_id AS id, po.person_id, po.procedure_concept_id, po.procedure_date, po.procedure_source_value AS source_value, po.procedure_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(po.procedure_date, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, po.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_20230328.procedure_occurrence` AS po JOIN `victr-tanagra-test.sd_20230328.person` AS p ON p.person_id = po.person_id LEFT JOIN `victr-tanagra-test.sd_20230328.visit_occurrence` AS vo ON vo.visit_occurrence_id = po.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "procedure_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "procedure_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "procedure_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_procedure", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/snp.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/snp.json deleted file mode 100644 index ebf05408e..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/snp.json +++ /dev/null @@ -1,66 +0,0 @@ -{ - "name" : "snp", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT crit_noid.snp_id, ROW_NUMBER() OVER (ORDER BY crit_noid.snp_id) AS row_num FROM ( SELECT DISTINCT snp_id FROM `victr-tanagra-test.sd_20230328.x_snp` ) AS crit_noid " - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "snp_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "row_num", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "attributes" : [ "id" ] - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "snp" - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/visit.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/visit.json deleted file mode 100644 index 4dc0f54d1..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/visit.json +++ /dev/null @@ -1,105 +0,0 @@ -{ - "name" : "visit", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Visit" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_20230328.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_20230328.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Visit' AND c.standard_concept = 'S'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "visit" - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/visit_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/visit_occurrence.json deleted file mode 100644 index 7ec5b89d7..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entity/visit_occurrence.json +++ /dev/null @@ -1,211 +0,0 @@ -{ - "name" : "visit_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -977.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 1854114 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 3830834 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1527518 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 61824433 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT vo.visit_occurrence_id AS id, vo.person_id, vo.visit_concept_id, vo.visit_start_date AS start_date, vo.visit_end_date AS end_date, vo.visit_source_value AS source_value, vo.visit_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(vo.visit_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence FROM `victr-tanagra-test.sd_20230328.visit_occurrence` AS vo JOIN `victr-tanagra-test.sd_20230328.person` AS p ON p.person_id = vo.person_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "visit" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "visit_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "visit" : { - "value" : { - "column" : "visit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/brand_ingredient.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/brand_ingredient.json deleted file mode 100644 index 381d393df..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/brand_ingredient.json +++ /dev/null @@ -1,101 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "brand_ingredient", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "rawSql" : "/* 1. User searches for Brand Tylenol 2. User expands Tylenol to see which ingredients are in Tylenol 3. Ingredient Acetaminophen is shown Acetaminophen has over 300 descendants (eg \"acetaminophen 100 MG/ML Oral Suspension\"). Acetaminophen's concept_class_id is Ingredient; descendants' concept_class_ids are Clinical Drug Comp, Quant Clinical Drug, etc. Most descendants have a relationship with Brand Tylenol in concept_relationship. However, we only want to show Acetaminophen in step 3. So only keep relationships with concept_class_id=Ingredient. */ SELECT cr.* FROM `victr-tanagra-test.sd_20230328.concept_relationship` cr, `victr-tanagra-test.sd_20230328.concept` c2 WHERE cr.concept_id_2 = c2.concept_id AND c2.concept_class_id = 'Ingredient'" - }, - "idPairsIdA" : { - "column" : "concept_id_1", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "concept_id_2", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_brand_ingredient" - }, - "idPairsIdA" : { - "column" : "id_brand", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "brand" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_brand_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_brand_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_brand", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_brand", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "brand", - "itemsEntity" : "ingredient" -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/condition_person_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/condition_person_occurrence.json deleted file mode 100644 index a709ed653..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/condition_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "condition_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_condition_occurrence_condition" - }, - "idPairsIdA" : { - "column" : "id_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_condition", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_condition_person" - }, - "idPairsIdA" : { - "column" : "id_condition", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_condition_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "condition", - "occurrenceEntity" : "condition_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/device_person_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/device_person_occurrence.json deleted file mode 100644 index ff77e8f95..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/device_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "device_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_device_occurrence_device" - }, - "idPairsIdA" : { - "column" : "id_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_device", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_device_person" - }, - "idPairsIdA" : { - "column" : "id_device", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_device_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "device", - "occurrenceEntity" : "device_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/genotyping_person.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/genotyping_person.json deleted file mode 100644 index 313074da0..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/genotyping_person.json +++ /dev/null @@ -1,101 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "genotyping_person", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "rawSql" : "/* platform_id column has type NUMERIC. This causes index column to be FLOAT. Currently indexing doesn't handle floats properly, so change column to INTEGER. */ SELECT genotype_result_id AS genotype_result_id, person_id, CAST(platform_id as INT64) as platform_id FROM `victr-tanagra-test.sd_20230328.x_genotype_result` " - }, - "idPairsIdA" : { - "column" : "platform_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_genotyping_person" - }, - "idPairsIdA" : { - "column" : "id_genotyping", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "genotyping" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "genotyping" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_genotyping", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_genotyping", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "genotyping", - "itemsEntity" : "person" -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/ingredient_person_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/ingredient_person_occurrence.json deleted file mode 100644 index 576ca9260..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/ingredient_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "ingredient_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_occurrence_ingredient" - }, - "idPairsIdA" : { - "column" : "id_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_person" - }, - "idPairsIdA" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "ingredient", - "occurrenceEntity" : "ingredient_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/measurement_person_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/measurement_person_occurrence.json deleted file mode 100644 index cb82b0df7..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/measurement_person_occurrence.json +++ /dev/null @@ -1,287 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "measurement_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_measurement_occurrence_measurement" - }, - "idPairsIdA" : { - "column" : "id_measurement_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_measurement", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_measurement_person" - }, - "idPairsIdA" : { - "column" : "id_measurement", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_measurement_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_measurement_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { - "modifiers" : { - "tablePointer" : { - "table" : "measurement_person_occurrence_modifiers" - }, - "fieldPointers" : { - "min" : { - "column" : "min", - "runtimeCalculated" : false - }, - "enum_count" : { - "column" : "enum_count", - "runtimeCalculated" : false - }, - "max" : { - "column" : "max", - "runtimeCalculated" : false - }, - "enum_display" : { - "column" : "enum_display", - "runtimeCalculated" : false - }, - "enum_value" : { - "column" : "enum_value", - "runtimeCalculated" : false - }, - "attribute_name" : { - "column" : "attribute_name", - "runtimeCalculated" : false - }, - "entity_id" : { - "column" : "entity_id", - "runtimeCalculated" : false - } - } - } - } - }, - "criteriaEntity" : "measurement", - "occurrenceEntity" : "measurement_occurrence", - "modifierAttributes" : [ "value_numeric", "value_enum" ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/note_person_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/note_person_occurrence.json deleted file mode 100644 index dd4403308..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/note_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "note_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "note" - }, - "idPairsIdA" : { - "column" : "note_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "note_type_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "note" - }, - "idPairsIdA" : { - "column" : "note_type_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "note" - }, - "idPairsIdA" : { - "column" : "note_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_note_occurrence_note" - }, - "idPairsIdA" : { - "column" : "id_note_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_note", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "note_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_note", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_note", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "note" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_note_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_note_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_note_person" - }, - "idPairsIdA" : { - "column" : "id_note", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "note" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_note", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_note", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_note_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_note_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "note_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_note_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_note_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "note", - "occurrenceEntity" : "note_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/observation_person_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/observation_person_occurrence.json deleted file mode 100644 index dad430b34..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/observation_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "observation_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_observation_occurrence_observation" - }, - "idPairsIdA" : { - "column" : "id_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_observation", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_observation_person" - }, - "idPairsIdA" : { - "column" : "id_observation", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_observation_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "observation", - "occurrenceEntity" : "observation_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/procedure_person_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/procedure_person_occurrence.json deleted file mode 100644 index be81091b7..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/procedure_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "procedure_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_procedure_occurrence_procedure" - }, - "idPairsIdA" : { - "column" : "id_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_procedure", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_procedure_person" - }, - "idPairsIdA" : { - "column" : "id_procedure", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_procedure_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "procedure", - "occurrenceEntity" : "procedure_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/snp_person.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/snp_person.json deleted file mode 100644 index 639ba08fd..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/snp_person.json +++ /dev/null @@ -1,84 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "snp_person", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "rawSql" : "SELECT crit.row_num, occ.snp_id, occ.person_id FROM `victr-tanagra-test.sd_20230328.x_snp` AS occ JOIN ( SELECT crit_noid.snp_id, ROW_NUMBER() OVER (ORDER BY crit_noid.snp_id) AS row_num FROM ( SELECT DISTINCT snp_id FROM `victr-tanagra-test.sd_20230328.x_snp` ) AS crit_noid ) AS crit ON crit.snp_id = occ.snp_id " - }, - "idPairsIdA" : { - "column" : "row_num", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_snp_person" - }, - "idPairsIdA" : { - "column" : "id_snp", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "snp" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_snp", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_snp", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "snp", - "itemsEntity" : "person" -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/visit_person_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/visit_person_occurrence.json deleted file mode 100644 index 1a4beff12..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/entitygroup/visit_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "visit_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_visit_occurrence_visit" - }, - "idPairsIdA" : { - "column" : "id_visit_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_visit", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_visit_person" - }, - "idPairsIdA" : { - "column" : "id_visit", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_visit_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_visit_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "visit", - "occurrenceEntity" : "visit_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/sdd_refresh0323.json b/service/src/main/resources/config/verily/sdd_refresh0323/expanded/sdd_refresh0323.json deleted file mode 100644 index 3c46e251b..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/expanded/sdd_refresh0323.json +++ /dev/null @@ -1,29 +0,0 @@ -{ - "name" : "sdd_refresh0323", - "dataPointers" : [ { - "type" : "BQ_DATASET", - "name" : "index_dataset", - "projectId" : "verily-tanagra-dev", - "datasetId" : "sd20230328_index_051823", - "queryProjectId" : "verily-tanagra-dev", - "dataflowServiceAccountEmail" : "backend-default@verily-tanagra-dev.iam.gserviceaccount.com", - "dataflowTempLocation" : "gs://dataflow-staging-us-east1-694046000181/temp/", - "dataflowRegion" : "us-east1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : false - }, { - "type" : "BQ_DATASET", - "name" : "omop_dataset", - "projectId" : "victr-tanagra-test", - "datasetId" : "sd_20230328", - "queryProjectId" : "victr-tanagra-test", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : true - } ], - "entities" : [ "measurement_occurrence.json", "note.json", "condition_occurrence.json", "ingredient.json", "device_occurrence.json", "observation.json", "genotyping.json", "procedure.json", "measurement.json", "ingredient_occurrence.json", "condition.json", "snp.json", "person.json", "visit_occurrence.json", "observation_occurrence.json", "procedure_occurrence.json", "visit.json", "brand.json", "device.json", "note_occurrence.json" ], - "entityGroups" : [ "device_person_occurrence.json", "genotyping_person.json", "visit_person_occurrence.json", "condition_person_occurrence.json", "snp_person.json", "note_person_occurrence.json", "ingredient_person_occurrence.json", "observation_person_occurrence.json", "brand_ingredient.json", "measurement_person_occurrence.json", "procedure_person_occurrence.json" ], - "primaryEntity" : "person", - "uiConfig" : "{ \"dataConfig\": { \"primaryEntity\": { \"displayName\": \"Person\", \"entity\": \"person\", \"key\": \"id\", \"classifications\": [ { \"id\": \"snp\", \"attribute\": \"id\", \"entity\": \"snp\", \"entityAttribute\": \"id\", \"defaultSort\": { \"attribute\": \"id\", \"direction\": \"ASC\" } }, { \"id\": \"genotyping\", \"attribute\": \"id\", \"entity\": \"genotyping\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"name\", \"direction\": \"ASC\" } } ] }, \"occurrences\": [ { \"id\": \"condition_occurrence\", \"displayName\": \"Condition Occurrences\", \"entity\": \"condition_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"condition\", \"attribute\": \"condition\", \"entity\": \"condition\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"procedure_occurrence\", \"displayName\": \"Procedure Occurrences\", \"entity\": \"procedure_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"procedure\", \"attribute\": \"procedure\", \"entity\": \"procedure\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"observation_occurrence\", \"displayName\": \"Observation Occurrence\", \"entity\": \"observation_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"observation\", \"attribute\": \"observation\", \"entity\": \"observation\", \"entityAttribute\": \"id\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"ingredient_occurrence\", \"displayName\": \"Drug Occurrence\", \"entity\": \"ingredient_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"ingredient\", \"attribute\": \"id\", \"entity\": \"ingredient\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" }, \"groupings\": [ { \"id\": \"brand\", \"entity\": \"brand\", \"defaultSort\": { \"attribute\": \"name\", \"direction\": \"ASC\" }, \"attributes\": [\"name\", \"id\", \"standard_concept\", \"concept_code\"] } ] } ] }, { \"id\": \"note_occurrence\", \"displayName\": \"Documents\", \"entity\": \"note_occurrence\", \"key\": \"id\" }, { \"id\": \"measurement_occurrence\", \"displayName\": \"Measurement Occurrence\", \"entity\": \"measurement_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"measurement\", \"attribute\": \"measurement\", \"entity\": \"measurement\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_item_count\", \"direction\": \"DESC\" } } ] } ] }, \"criteriaConfigs\": [ { \"type\": \"classification\", \"id\": \"tanagra-conditions\", \"title\": \"Condition\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Condition\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"condition_occurrence\", \"classification\": \"condition\", \"modifiers\": [ \"age_at_occurrence\", \"visit_type\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-procedures\", \"title\": \"Procedure\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Procedure\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"procedure_occurrence\", \"classification\": \"procedure\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"] }, { \"type\": \"classification\", \"id\": \"tanagra-observations\", \"title\": \"Observation\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"observation_occurrence\", \"classification\": \"observation\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"] }, { \"type\": \"classification\", \"id\": \"tanagra-drugs\", \"title\": \"Drug\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Drug\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"ingredient_occurrence\", \"classification\": \"ingredient\", \"modifiers\": [ \"age_at_occurrence\", \"visit_type\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-genotyping\", \"title\": \"Genotyping platform\", \"category\": \"Demographics\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Genotyping platform\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Genotyping platform\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Id\" } ], \"occurrence\": \"\", \"classification\": \"genotyping\" }, { \"type\": \"classification\", \"id\": \"tanagra-measurement\", \"title\": \"Labs and measurements\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_item_count\", \"width\": 120, \"title\": \"Count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Condition\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"measurement_occurrence\", \"classification\": \"measurement\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"], \"valueConfigs\": [ { \"title\": \"Categorical value\", \"attribute\": \"value_enum\" }, { \"title\": \"Numeric value\", \"attribute\": \"value_numeric\" } ] }, { \"type\": \"attribute\", \"id\": \"tanagra-ethnicity\", \"title\": \"Ethnicity\", \"category\": \"Demographics\", \"attribute\": \"ethnicity\" }, { \"type\": \"attribute\", \"id\": \"tanagra-gender\", \"title\": \"Gender identity\", \"category\": \"Demographics\", \"attribute\": \"gender\" }, { \"type\": \"attribute\", \"id\": \"tanagra-race\", \"title\": \"Race\", \"category\": \"Demographics\", \"attribute\": \"race\" }, { \"type\": \"attribute\", \"id\": \"tanagra-age\", \"title\": \"Age\", \"category\": \"Demographics\", \"attribute\": \"age\" }, { \"type\": \"search\", \"id\": \"tanagra-documents\", \"title\": \"Documents\", \"conceptSet\": true, \"category\": \"Domains\", \"occurrenceId\": \"note_occurrence\", \"searchAttribute\": \"title\", \"categoryAttribute\": \"note\", \"modifiers\": [ \"age_at_occurrence\", \"visit_type\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-snp\", \"title\": \"SNP variant\", \"category\": \"Demographics\", \"columns\": [{ \"key\": \"name\", \"width\": \"100%\", \"title\": \"SNP variant\" }], \"occurrence\": \"\", \"classification\": \"snp\" }, { \"type\": \"biovu\", \"id\": \"biovu\", \"title\": \"BioVU Samples\", \"category\": \"BioVU\" } ], \"modifierConfigs\": [ { \"type\": \"unhinted-value\", \"id\": \"start_date_group_by_count\", \"title\": \"Occurrence count\", \"attribute\": \"start_date\", \"groupByCount\": true }, { \"type\": \"unhinted-value\", \"id\": \"date_group_by_count\", \"title\": \"Occurrence count\", \"attribute\": \"date\", \"groupByCount\": true }, { \"type\": \"attribute\", \"id\": \"visit_type\", \"title\": \"Visit type\", \"attribute\": \"visit_type\" }, { \"type\": \"attribute\", \"id\": \"age_at_occurrence\", \"title\": \"Age at occurrence\", \"attribute\": \"age_at_occurrence\" } ], \"demographicChartConfigs\": { \"groupByAttributes\": [\"gender\", \"race\", \"age\"], \"chartConfigs\": [ { \"title\": \"Gender identity\", \"primaryProperties\": [{ \"key\": \"gender\" }] }, { \"title\": \"Gender identity, Current age, Race\", \"primaryProperties\": [ { \"key\": \"gender\" }, { \"key\": \"age\", \"buckets\": [ { \"min\": 18, \"max\": 45, \"displayName\": \"18-44\" }, { \"min\": 45, \"max\": 65, \"displayName\": \"45-64\" }, { \"min\": 65, \"displayName\": \"65+\" } ] } ], \"stackedProperty\": { \"key\": \"race\" } } ] }, \"prepackagedConceptSets\": [ { \"id\": \"_demographics\", \"name\": \"Demographics\", \"occurrence\": \"\" }, { \"id\": \"_analgesics\", \"name\": \"Analgesics\", \"occurrence\": \"ingredient_occurrence\", \"filter\": { \"type\": \"CLASSIFICATION\", \"occurrenceId\": \"ingredient_occurrence\", \"classificationId\": \"ingredient\", \"keys\": [21604253] } } ], \"criteriaSearchConfig\": { \"criteriaTypeWidth\": 120, \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept Name\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up Count\" } ] }, \"cohortReviewConfig\": { \"participantsListColumns\": [ { \"key\": \"id\", \"width\": 100, \"title\": \"Id\" }, { \"key\": \"gender\", \"width\": 100, \"title\": \"Gender\" }, { \"key\": \"race\", \"width\": 100, \"title\": \"Race\" }, { \"key\": \"ethnicity\", \"width\": 100, \"title\": \"Ethnicity\" }, { \"key\": \"age\", \"width\": 60, \"title\": \"Year of Birth\" } ], \"attributes\": [ { \"title\": \"Gender\", \"key\": \"gender\" }, { \"title\": \"Age\", \"key\": \"age\" }, { \"title\": \"Race\", \"key\": \"race\" }, { \"title\": \"Ethnicity\", \"key\": \"ethnicity\" } ], \"pages\": [ { \"type\": \"occurrenceTable\", \"id\": \"condition\", \"title\": \"Conditions\", \"plugin\": { \"occurrence\": \"condition_occurrence\", \"columns\": [ { \"key\": \"condition\", \"width\": \"100%\", \"title\": \"Condition name\", \"sortable\": true }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\", \"sortable\": true }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"procedure\", \"title\": \"Procedures\", \"plugin\": { \"occurrence\": \"procedure_occurrence\", \"columns\": [ { \"key\": \"procedure\", \"width\": \"100%\", \"title\": \"Procedure name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"observation\", \"title\": \"Observations\", \"plugin\": { \"occurrence\": \"observation_occurrence\", \"columns\": [ { \"key\": \"observation\", \"width\": \"100%\", \"title\": \"Observation name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"ingredient\", \"title\": \"Drugs\", \"plugin\": { \"occurrence\": \"ingredient_occurrence\", \"columns\": [ { \"key\": \"ingredient\", \"width\": \"100%\", \"title\": \"Drug name\", \"sortable\": true }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\", \"sortable\": true }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"measurements\", \"title\": \"Labs and measurements\", \"plugin\": { \"occurrence\": \"measurement_occurrence\", \"columns\": [ { \"key\": \"measurement\", \"width\": \"100%\", \"title\": \"Lab/measurement name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true }, { \"key\": \"value_enum\", \"width\": 160, \"title\": \"Categorical value\", \"sortable\": true }, { \"key\": \"value_numeric\", \"width\": 160, \"title\": \"Numeric value\", \"sortable\": true }, { \"key\": \"unit\", \"width\": 160, \"title\": \"Unit\", \"sortable\": true } ] } }, { \"type\": \"textSearch\", \"id\": \"notes\", \"title\": \"Documents\", \"plugin\": { \"occurrence\": \"note_occurrence\", \"title\": \"title\", \"subtitles\": [\"note\", \"date\"], \"text\": \"text\", \"categoryAttribute\": \"note\", \"sortOrder\": { \"attribute\": \"date\", \"direction\": \"ASC\" } } } ] } } ", - "metadata" : { } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/brand.json b/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/brand.json deleted file mode 100644 index 0403f94a4..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/brand.json +++ /dev/null @@ -1,29 +0,0 @@ -{ - "name": "brand", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "rawSqlFile": "brand_all.sql" - }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "brand_textSearch.sql" } } } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/condition.json b/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/condition.json deleted file mode 100644 index 8d7f876d9..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/condition.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "name": "condition", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "table": "concept", - "filter": { - "type": "BINARY", - "field": { "column": "domain_id" }, - "operator": "EQUALS", - "value": { "stringVal": "Condition" } } }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } }, - "vocabulary": { "value": { "column": "vocabulary_id" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "condition_textSearch.sql" } } }, - "hierarchyMappings": { - "standard": { - "childParent": { - "tablePointer": { "rawSqlFile": "condition_parentChild.sql" } - }, - "rootNodesFilter": { - "tablePointer": { - "table": "concept", - "filter": { "type": "BINARY", "field": { "column": "concept_id" }, "operator": "EQUALS", "value": { "int64Val": 441840 } } }, - "fieldPointers": { - "id": { "column": "concept_id" } - } - }, - "maxHierarchyDepth": 20 - } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/condition_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/condition_occurrence.json deleted file mode 100644 index 5734966fc..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/condition_occurrence.json +++ /dev/null @@ -1,42 +0,0 @@ -{ - "name": "condition_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "condition", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "condition_occurrence_all.sql" }, - "attributeMappings": { - "condition": { - "value": { "column": "condition_concept_id" }, - "display": { - "column": "condition_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/device.json b/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/device.json deleted file mode 100644 index 2e72d8d62..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/device.json +++ /dev/null @@ -1,43 +0,0 @@ -{ - "name": "device", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "table": "concept", - "filter": { - "type": "BOOLEAN_AND_OR", - "operator": "AND", - "subfilters": [ - { "type": "BINARY", - "field": { "column": "domain_id" }, - "operator": "EQUALS", - "value": { "stringVal": "Device" } }, - { "type": "BINARY", - "field": { "column": "standard_concept" }, - "operator": "EQUALS", - "value": { "stringVal": "S" } } - ] } }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } }, - "vocabulary": { "value": { "column": "vocabulary_id" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "device_textSearch.sql" } } } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/device_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/device_occurrence.json deleted file mode 100644 index ffcfbb5fc..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/device_occurrence.json +++ /dev/null @@ -1,41 +0,0 @@ -{ - "name": "device_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "device", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "device_occurrence_all.sql" }, - "attributeMappings": { - "device": { - "value": { "column": "device_concept_id" }, - "display": { - "column": "device_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/ingredient.json b/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/ingredient.json deleted file mode 100644 index 0e7901ee5..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/ingredient.json +++ /dev/null @@ -1,58 +0,0 @@ -{ - "name": "ingredient", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "ingredient_all.sql" }, - "attributeMappings": { - "vocabulary": { "value": { "column": "vocabulary_id" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "ingredient_textSearch.sql" } } }, - "hierarchyMappings": { - "standard": { - "childParent": { - "tablePointer": { "rawSqlFile": "ingredient_parentChild.sql" } - }, - "rootNodesFilter": { - "tablePointer": { - "table": "concept", - "filter": { - "type": "BOOLEAN_AND_OR", - "operator": "AND", - "subfilters": [ - { "type": "BINARY", - "field": { "column": "vocabulary_id" }, - "operator": "EQUALS", - "value": { "stringVal": "ATC" } }, - { "type": "BINARY", - "field": { "column": "concept_class_id" }, - "operator": "EQUALS", - "value": { "stringVal": "ATC 1st" } }, - { "type": "BINARY", - "field": { "column": "standard_concept" }, - "operator": "EQUALS", - "value": { "stringVal": "C" } } ] } }, - "fieldPointers": { - "id": { "column": "concept_id" } - } - }, - "maxHierarchyDepth": 15 - } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/ingredient_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/ingredient_occurrence.json deleted file mode 100644 index 6e4263d3a..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/ingredient_occurrence.json +++ /dev/null @@ -1,44 +0,0 @@ -{ - "name": "ingredient_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "ingredient", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "refills" }, - { "type": "SIMPLE", "name": "days_supply" }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "ingredient_occurrence_all.sql" }, - "attributeMappings": { - "ingredient": { - "value": { "column": "drug_concept_id" }, - "display": { - "column": "drug_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/note_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/note_occurrence.json deleted file mode 100644 index 4ea519ebd..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/note_occurrence.json +++ /dev/null @@ -1,42 +0,0 @@ -{ - "name": "note_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "note" }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "title", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "text", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "note_occurrence_all.sql" }, - "attributeMappings": { - "date": { "value": { "column": "note_date" } }, - "note": { - "value": { "column": "note_type_concept_id" }, - "display": { - "column": "note_type_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/observation.json b/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/observation.json deleted file mode 100644 index 668afebce..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/observation.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "name": "observation", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "table": "concept", - "filter": { - "type": "BOOLEAN_AND_OR", - "operator": "AND", - "subfilters": [ - { "type": "BINARY", - "field": { "column": "domain_id" }, - "operator": "EQUALS", - "value": { "stringVal": "Observation" } }, - { "type": "BINARY", - "field": { "column": "standard_concept" }, - "operator": "EQUALS", - "value": { "stringVal": "S" } }, - { "type": "BINARY", - "field": { "column": "vocabulary_id" }, - "operator": "NOT_EQUALS", - "value": { "stringVal": "PPI" } }, - { "type": "BINARY", - "field": { "column": "concept_class_id" }, - "operator": "NOT_EQUALS", - "value": { "stringVal": "Survey" } } - ] } }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } }, - "vocabulary": { "value": { "column": "vocabulary_id" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "observation_textSearch.sql" } } } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/procedure.json b/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/procedure.json deleted file mode 100644 index 5b26c710e..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/procedure.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "name": "procedure", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "table": "concept", - "filter": { - "type": "BINARY", - "field": { "column": "domain_id" }, - "operator": "EQUALS", - "value": { "stringVal": "Procedure" } } }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } }, - "vocabulary": { "value": { "column": "vocabulary_id" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "procedure_textSearch.sql" } } }, - "hierarchyMappings": { - "standard": { - "childParent": { - "tablePointer": { "rawSqlFile": "procedure_parentChild.sql" } - }, - "rootNodesFilter": { - "tablePointer": { - "table": "concept", - "filter": { "type": "BINARY", "field": { "column": "concept_id" }, "operator": "EQUALS", "value": { "int64Val": 4322976 } } }, - "fieldPointers": { - "id": { "column": "concept_id" } - } - }, - "maxHierarchyDepth": 19 - } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/visit.json b/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/visit.json deleted file mode 100644 index 0b9a91bde..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/visit.json +++ /dev/null @@ -1,33 +0,0 @@ -{ - "name": "visit", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "table": "concept", - "filter": { - "type": "BOOLEAN_AND_OR", - "operator": "AND", - "subfilters": [ - { "type": "BINARY", - "field": { "column": "domain_id" }, - "operator": "EQUALS", - "value": { "stringVal": "Visit" } }, - { "type": "BINARY", - "field": { "column": "standard_concept" }, - "operator": "EQUALS", - "value": { "stringVal": "S" } } ] } }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "visit_textSearch.sql" } } } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/visit_occurrence.json b/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/visit_occurrence.json deleted file mode 100644 index cff5a1628..000000000 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/visit_occurrence.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "name": "visit_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit" }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "visit_occurrence_all.sql" }, - "attributeMappings": { - "visit": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sdd_refresh0323.json b/service/src/main/resources/config/verily/sdd_refresh0323/sdd_refresh0323.json similarity index 97% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sdd_refresh0323.json rename to service/src/main/resources/config/verily/sdd_refresh0323/sdd_refresh0323.json index 960e2ef02..f63247ae9 100644 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/sdd_refresh0323.json +++ b/service/src/main/resources/config/verily/sdd_refresh0323/sdd_refresh0323.json @@ -9,7 +9,7 @@ { "type": "BQ_DATASET", "name": "index_dataset", "projectId": "verily-tanagra-dev", - "datasetId": "sd20230328_index_051823", + "datasetId": "sd20230328_index_072623", "dataflowServiceAccountEmail": "backend-default@verily-tanagra-dev.iam.gserviceaccount.com", "dataflowTempLocation": "gs://dataflow-staging-us-east1-694046000181/temp/", "dataflowRegion": "us-east1", diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/brand_all.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/brand_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/brand_all.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/brand_all.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/brand_ingredients.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/brand_ingredients.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/brand_ingredients.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/brand_ingredients.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/brand_textSearch.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/brand_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/brand_textSearch.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/brand_textSearch.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/condition_occurrence_all.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/condition_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/condition_occurrence_all.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/condition_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/condition_parentChild.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/condition_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/condition_parentChild.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/condition_parentChild.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/condition_textSearch.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/condition_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/condition_textSearch.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/condition_textSearch.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/device_occurrence_all.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/device_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/device_occurrence_all.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/device_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/device_textSearch.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/device_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/device_textSearch.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/device_textSearch.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/genotype_result.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/genotype_result.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/genotype_result.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/genotype_result.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/genotyping_all.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/genotyping_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/genotyping_all.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/genotyping_all.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/genotyping_parentChild.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/genotyping_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/genotyping_parentChild.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/genotyping_parentChild.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/genotyping_rootNodesFilter.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/genotyping_rootNodesFilter.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/genotyping_rootNodesFilter.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/genotyping_rootNodesFilter.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/ingredient_all.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/ingredient_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/ingredient_all.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/ingredient_all.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/ingredient_occurrence_all.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/ingredient_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/ingredient_occurrence_all.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/ingredient_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/ingredient_parentChild.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/ingredient_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/ingredient_parentChild.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/ingredient_parentChild.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/ingredient_textSearch.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/ingredient_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/ingredient_textSearch.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/ingredient_textSearch.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/measurement_occurrence_all.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/measurement_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/measurement_occurrence_all.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/measurement_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/measurement_parentChild.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/measurement_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/measurement_parentChild.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/measurement_parentChild.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/measurement_textSearch.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/measurement_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/measurement_textSearch.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/measurement_textSearch.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/note_occurrence_all.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/note_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/note_occurrence_all.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/note_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/note_textSearch.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/note_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/note_textSearch.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/note_textSearch.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/observation_occurrence_all.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/observation_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/observation_occurrence_all.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/observation_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/observation_textSearch.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/observation_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/observation_textSearch.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/observation_textSearch.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/person.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/person.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/person.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/person.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/procedure_occurrence_all.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/procedure_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/procedure_occurrence_all.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/procedure_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/procedure_parentChild.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/procedure_parentChild.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/procedure_parentChild.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/procedure_parentChild.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/procedure_textSearch.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/procedure_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/procedure_textSearch.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/procedure_textSearch.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/snp_all.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/snp_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/snp_all.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/snp_all.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/snp_occurrence_all.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/snp_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/snp_occurrence_all.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/snp_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/visit_occurrence_all.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/visit_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/visit_occurrence_all.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/visit_occurrence_all.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/sql/visit_textSearch.sql b/service/src/main/resources/config/verily/sdd_refresh0323/sql/visit_textSearch.sql similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/sql/visit_textSearch.sql rename to service/src/main/resources/config/verily/sdd_refresh0323/sql/visit_textSearch.sql diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/ui/top_level.json b/service/src/main/resources/config/verily/sdd_refresh0323/ui/top_level.json similarity index 100% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/ui/top_level.json rename to service/src/main/resources/config/verily/sdd_refresh0323/ui/top_level.json diff --git a/service/src/main/resources/config/vumc/sdd/entity/brand.json b/service/src/main/resources/config/vumc/sdd/entity/brand.json new file mode 100644 index 000000000..b91b1f66a --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd/entity/brand.json @@ -0,0 +1,29 @@ +{ + "name": "brand", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "rawSqlFile": "brand_all.sql" + }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "brand_textSearch.sql" } } } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/entity/condition.json b/service/src/main/resources/config/vumc/sdd/entity/condition.json new file mode 100644 index 000000000..e8701cc41 --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd/entity/condition.json @@ -0,0 +1,51 @@ +{ + "name": "condition", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "table": "concept", + "filter": { + "type": "BINARY", + "field": { "column": "domain_id" }, + "operator": "EQUALS", + "value": { "stringVal": "Condition" } } }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } }, + "vocabulary": { "value": { "column": "vocabulary_id" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "condition_textSearch.sql" } } }, + "hierarchyMappings": { + "standard": { + "childParent": { + "tablePointer": { "rawSqlFile": "condition_parentChild.sql" } + }, + "rootNodesFilter": { + "tablePointer": { + "table": "concept", + "filter": { "type": "BINARY", "field": { "column": "concept_id" }, "operator": "EQUALS", "value": { "int64Val": 441840 } } }, + "fieldPointers": { + "id": { "column": "concept_id" } + } + }, + "maxHierarchyDepth": 20 + } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/vumc/sdd/entity/condition_occurrence.json b/service/src/main/resources/config/vumc/sdd/entity/condition_occurrence.json new file mode 100644 index 000000000..43d6ea3bf --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd/entity/condition_occurrence.json @@ -0,0 +1,42 @@ +{ + "name": "condition_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "condition", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "condition_occurrence_all.sql" }, + "attributeMappings": { + "condition": { + "value": { "column": "condition_concept_id" }, + "display": { + "column": "condition_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/vumc/sdd/entity/device.json b/service/src/main/resources/config/vumc/sdd/entity/device.json new file mode 100644 index 000000000..078cd332c --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd/entity/device.json @@ -0,0 +1,43 @@ +{ + "name": "device", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "table": "concept", + "filter": { + "type": "BOOLEAN_AND_OR", + "operator": "AND", + "subfilters": [ + { "type": "BINARY", + "field": { "column": "domain_id" }, + "operator": "EQUALS", + "value": { "stringVal": "Device" } }, + { "type": "BINARY", + "field": { "column": "standard_concept" }, + "operator": "EQUALS", + "value": { "stringVal": "S" } } + ] } }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } }, + "vocabulary": { "value": { "column": "vocabulary_id" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "device_textSearch.sql" } } } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/entity/device_occurrence.json b/service/src/main/resources/config/vumc/sdd/entity/device_occurrence.json new file mode 100644 index 000000000..5bbd49b98 --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd/entity/device_occurrence.json @@ -0,0 +1,41 @@ +{ + "name": "device_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "device", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "device_occurrence_all.sql" }, + "attributeMappings": { + "device": { + "value": { "column": "device_concept_id" }, + "display": { + "column": "device_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/sdd/original/entity/genotyping.json b/service/src/main/resources/config/vumc/sdd/entity/genotyping.json similarity index 83% rename from service/src/main/resources/config/verily/sdd/original/entity/genotyping.json rename to service/src/main/resources/config/vumc/sdd/entity/genotyping.json index da41c742c..9ad082975 100644 --- a/service/src/main/resources/config/verily/sdd/original/entity/genotyping.json +++ b/service/src/main/resources/config/vumc/sdd/entity/genotyping.json @@ -2,8 +2,8 @@ "name": "genotyping", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/vumc/sdd/entity/ingredient.json b/service/src/main/resources/config/vumc/sdd/entity/ingredient.json new file mode 100644 index 000000000..59a4ddcc0 --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd/entity/ingredient.json @@ -0,0 +1,58 @@ +{ + "name": "ingredient", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "ingredient_all.sql" }, + "attributeMappings": { + "vocabulary": { "value": { "column": "vocabulary_id" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "ingredient_textSearch.sql" } } }, + "hierarchyMappings": { + "standard": { + "childParent": { + "tablePointer": { "rawSqlFile": "ingredient_parentChild.sql" } + }, + "rootNodesFilter": { + "tablePointer": { + "table": "concept", + "filter": { + "type": "BOOLEAN_AND_OR", + "operator": "AND", + "subfilters": [ + { "type": "BINARY", + "field": { "column": "vocabulary_id" }, + "operator": "EQUALS", + "value": { "stringVal": "ATC" } }, + { "type": "BINARY", + "field": { "column": "concept_class_id" }, + "operator": "EQUALS", + "value": { "stringVal": "ATC 1st" } }, + { "type": "BINARY", + "field": { "column": "standard_concept" }, + "operator": "EQUALS", + "value": { "stringVal": "C" } } ] } }, + "fieldPointers": { + "id": { "column": "concept_id" } + } + }, + "maxHierarchyDepth": 15 + } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/vumc/sdd/entity/ingredient_occurrence.json b/service/src/main/resources/config/vumc/sdd/entity/ingredient_occurrence.json new file mode 100644 index 000000000..04f5eff91 --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd/entity/ingredient_occurrence.json @@ -0,0 +1,44 @@ +{ + "name": "ingredient_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "ingredient", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "refills", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "days_supply", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "ingredient_occurrence_all.sql" }, + "attributeMappings": { + "ingredient": { + "value": { "column": "drug_concept_id" }, + "display": { + "column": "drug_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/measurement.json b/service/src/main/resources/config/vumc/sdd/entity/measurement.json similarity index 90% rename from service/src/main/resources/config/vumc/sdd/original/entity/measurement.json rename to service/src/main/resources/config/vumc/sdd/entity/measurement.json index 70324f369..f71f480d4 100644 --- a/service/src/main/resources/config/vumc/sdd/original/entity/measurement.json +++ b/service/src/main/resources/config/vumc/sdd/entity/measurement.json @@ -2,11 +2,11 @@ "name": "measurement", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/measurement_occurrence.json b/service/src/main/resources/config/vumc/sdd/entity/measurement_occurrence.json similarity index 55% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/measurement_occurrence.json rename to service/src/main/resources/config/vumc/sdd/entity/measurement_occurrence.json index cc142dabb..081cef822 100644 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/measurement_occurrence.json +++ b/service/src/main/resources/config/vumc/sdd/entity/measurement_occurrence.json @@ -2,18 +2,18 @@ "name": "measurement_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "measurement", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "value_numeric", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "value_enum", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "unit", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "measurement", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "value_numeric", "dataType": "DOUBLE", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "value_enum", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/note.json b/service/src/main/resources/config/vumc/sdd/entity/note.json similarity index 81% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/note.json rename to service/src/main/resources/config/vumc/sdd/entity/note.json index e21370c93..a73afb9de 100644 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/note.json +++ b/service/src/main/resources/config/vumc/sdd/entity/note.json @@ -2,10 +2,10 @@ "name": "note", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/vumc/sdd/entity/note_occurrence.json b/service/src/main/resources/config/vumc/sdd/entity/note_occurrence.json new file mode 100644 index 000000000..70d6913cf --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd/entity/note_occurrence.json @@ -0,0 +1,42 @@ +{ + "name": "note_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "note", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "title", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "text", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "note_occurrence_all.sql" }, + "attributeMappings": { + "date": { "value": { "column": "note_date" } }, + "note": { + "value": { "column": "note_type_concept_id" }, + "display": { + "column": "note_type_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/vumc/sdd/entity/observation.json b/service/src/main/resources/config/vumc/sdd/entity/observation.json new file mode 100644 index 000000000..92f45b426 --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd/entity/observation.json @@ -0,0 +1,51 @@ +{ + "name": "observation", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "table": "concept", + "filter": { + "type": "BOOLEAN_AND_OR", + "operator": "AND", + "subfilters": [ + { "type": "BINARY", + "field": { "column": "domain_id" }, + "operator": "EQUALS", + "value": { "stringVal": "Observation" } }, + { "type": "BINARY", + "field": { "column": "standard_concept" }, + "operator": "EQUALS", + "value": { "stringVal": "S" } }, + { "type": "BINARY", + "field": { "column": "vocabulary_id" }, + "operator": "NOT_EQUALS", + "value": { "stringVal": "PPI" } }, + { "type": "BINARY", + "field": { "column": "concept_class_id" }, + "operator": "NOT_EQUALS", + "value": { "stringVal": "Survey" } } + ] } }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } }, + "vocabulary": { "value": { "column": "vocabulary_id" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "observation_textSearch.sql" } } } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} \ No newline at end of file diff --git a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/observation_occurrence.json b/service/src/main/resources/config/vumc/sdd/entity/observation_occurrence.json similarity index 55% rename from service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/observation_occurrence.json rename to service/src/main/resources/config/vumc/sdd/entity/observation_occurrence.json index c1709a63a..e60191dab 100644 --- a/service/src/main/resources/config/verily/pilot_synthea_2022q3/original/entity/observation_occurrence.json +++ b/service/src/main/resources/config/vumc/sdd/entity/observation_occurrence.json @@ -2,18 +2,18 @@ "name": "observation_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "observation" }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "value_as_string", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "value", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "unit", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "observation", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "value_as_string", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "value", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/person.json b/service/src/main/resources/config/vumc/sdd/entity/person.json similarity index 60% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entity/person.json rename to service/src/main/resources/config/vumc/sdd/entity/person.json index 06a1770c9..a68df85fb 100644 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/person.json +++ b/service/src/main/resources/config/vumc/sdd/entity/person.json @@ -2,17 +2,17 @@ "name": "person", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "year_of_birth" }, - { "type": "SIMPLE", "name": "age" }, - { "type": "KEY_AND_DISPLAY", "name": "gender" }, - { "type": "KEY_AND_DISPLAY", "name": "race" }, - { "type": "KEY_AND_DISPLAY", "name": "ethnicity" }, - { "type": "SIMPLE", "name": "has_biovu_sample" }, - { "type": "SIMPLE", "name": "biovu_sample_dna_yield" }, - { "type": "SIMPLE", "name": "biovu_sample_is_compromised" }, - { "type": "SIMPLE", "name": "biovu_sample_is_nonshippable" }, - { "type": "SIMPLE", "name": "biovu_sample_has_plasma" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "year_of_birth", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "age", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "gender", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "race", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "ethnicity", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "has_biovu_sample", "dataType": "BOOLEAN" }, + { "type": "SIMPLE", "name": "biovu_sample_dna_yield", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "biovu_sample_is_compromised", "dataType": "BOOLEAN" }, + { "type": "SIMPLE", "name": "biovu_sample_is_nonshippable", "dataType": "BOOLEAN" }, + { "type": "SIMPLE", "name": "biovu_sample_has_plasma", "dataType": "BOOLEAN" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/vumc/sdd/entity/procedure.json b/service/src/main/resources/config/vumc/sdd/entity/procedure.json new file mode 100644 index 000000000..b45e3d76c --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd/entity/procedure.json @@ -0,0 +1,51 @@ +{ + "name": "procedure", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "table": "concept", + "filter": { + "type": "BINARY", + "field": { "column": "domain_id" }, + "operator": "EQUALS", + "value": { "stringVal": "Procedure" } } }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } }, + "vocabulary": { "value": { "column": "vocabulary_id" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "procedure_textSearch.sql" } } }, + "hierarchyMappings": { + "standard": { + "childParent": { + "tablePointer": { "rawSqlFile": "procedure_parentChild.sql" } + }, + "rootNodesFilter": { + "tablePointer": { + "table": "concept", + "filter": { "type": "BINARY", "field": { "column": "concept_id" }, "operator": "EQUALS", "value": { "int64Val": 4322976 } } }, + "fieldPointers": { + "id": { "column": "concept_id" } + } + }, + "maxHierarchyDepth": 19 + } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/sdd/original/entity/procedure_occurrence.json b/service/src/main/resources/config/vumc/sdd/entity/procedure_occurrence.json similarity index 51% rename from service/src/main/resources/config/verily/sdd/original/entity/procedure_occurrence.json rename to service/src/main/resources/config/vumc/sdd/entity/procedure_occurrence.json index 6d1d61acc..40651ca30 100644 --- a/service/src/main/resources/config/verily/sdd/original/entity/procedure_occurrence.json +++ b/service/src/main/resources/config/vumc/sdd/entity/procedure_occurrence.json @@ -2,15 +2,15 @@ "name": "procedure_occurrence", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "procedure", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "procedure", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/verily/sdd/original/entity/snp.json b/service/src/main/resources/config/vumc/sdd/entity/snp.json similarity index 85% rename from service/src/main/resources/config/verily/sdd/original/entity/snp.json rename to service/src/main/resources/config/vumc/sdd/entity/snp.json index f51c0976a..31efb7e94 100644 --- a/service/src/main/resources/config/verily/sdd/original/entity/snp.json +++ b/service/src/main/resources/config/vumc/sdd/entity/snp.json @@ -2,7 +2,7 @@ "name": "snp", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/vumc/sdd/entity/visit.json b/service/src/main/resources/config/vumc/sdd/entity/visit.json new file mode 100644 index 000000000..68bcc9d58 --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd/entity/visit.json @@ -0,0 +1,33 @@ +{ + "name": "visit", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "table": "concept", + "filter": { + "type": "BOOLEAN_AND_OR", + "operator": "AND", + "subfilters": [ + { "type": "BINARY", + "field": { "column": "domain_id" }, + "operator": "EQUALS", + "value": { "stringVal": "Visit" } }, + { "type": "BINARY", + "field": { "column": "standard_concept" }, + "operator": "EQUALS", + "value": { "stringVal": "S" } } ] } }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "visit_textSearch.sql" } } } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/entity/visit_occurrence.json b/service/src/main/resources/config/vumc/sdd/entity/visit_occurrence.json new file mode 100644 index 000000000..9cd8fcdbd --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd/entity/visit_occurrence.json @@ -0,0 +1,32 @@ +{ + "name": "visit_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "DATE", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "visit_occurrence_all.sql" }, + "attributeMappings": { + "visit": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/vumc/sdd/original/entitygroup/brand_ingredient.json b/service/src/main/resources/config/vumc/sdd/entitygroup/brand_ingredient.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/entitygroup/brand_ingredient.json rename to service/src/main/resources/config/vumc/sdd/entitygroup/brand_ingredient.json diff --git a/service/src/main/resources/config/vumc/sdd/original/entitygroup/condition_person_occurrence.json b/service/src/main/resources/config/vumc/sdd/entitygroup/condition_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/entitygroup/condition_person_occurrence.json rename to service/src/main/resources/config/vumc/sdd/entitygroup/condition_person_occurrence.json diff --git a/service/src/main/resources/config/vumc/sdd/original/entitygroup/device_person_occurrence.json b/service/src/main/resources/config/vumc/sdd/entitygroup/device_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/entitygroup/device_person_occurrence.json rename to service/src/main/resources/config/vumc/sdd/entitygroup/device_person_occurrence.json diff --git a/service/src/main/resources/config/vumc/sdd/original/entitygroup/genotyping_person.json b/service/src/main/resources/config/vumc/sdd/entitygroup/genotyping_person.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/entitygroup/genotyping_person.json rename to service/src/main/resources/config/vumc/sdd/entitygroup/genotyping_person.json diff --git a/service/src/main/resources/config/vumc/sdd/original/entitygroup/ingredient_person_occurrence.json b/service/src/main/resources/config/vumc/sdd/entitygroup/ingredient_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/entitygroup/ingredient_person_occurrence.json rename to service/src/main/resources/config/vumc/sdd/entitygroup/ingredient_person_occurrence.json diff --git a/service/src/main/resources/config/vumc/sdd/original/entitygroup/measurement_person_occurrence.json b/service/src/main/resources/config/vumc/sdd/entitygroup/measurement_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/entitygroup/measurement_person_occurrence.json rename to service/src/main/resources/config/vumc/sdd/entitygroup/measurement_person_occurrence.json diff --git a/service/src/main/resources/config/vumc/sdd/original/entitygroup/note_person_occurrence.json b/service/src/main/resources/config/vumc/sdd/entitygroup/note_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/entitygroup/note_person_occurrence.json rename to service/src/main/resources/config/vumc/sdd/entitygroup/note_person_occurrence.json diff --git a/service/src/main/resources/config/vumc/sdd/original/entitygroup/observation_person_occurrence.json b/service/src/main/resources/config/vumc/sdd/entitygroup/observation_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/entitygroup/observation_person_occurrence.json rename to service/src/main/resources/config/vumc/sdd/entitygroup/observation_person_occurrence.json diff --git a/service/src/main/resources/config/vumc/sdd/original/entitygroup/procedure_person_occurrence.json b/service/src/main/resources/config/vumc/sdd/entitygroup/procedure_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/entitygroup/procedure_person_occurrence.json rename to service/src/main/resources/config/vumc/sdd/entitygroup/procedure_person_occurrence.json diff --git a/service/src/main/resources/config/vumc/sdd/original/entitygroup/snp_person.json b/service/src/main/resources/config/vumc/sdd/entitygroup/snp_person.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/entitygroup/snp_person.json rename to service/src/main/resources/config/vumc/sdd/entitygroup/snp_person.json diff --git a/service/src/main/resources/config/vumc/sdd/original/entitygroup/visit_person_occurrence.json b/service/src/main/resources/config/vumc/sdd/entitygroup/visit_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/entitygroup/visit_person_occurrence.json rename to service/src/main/resources/config/vumc/sdd/entitygroup/visit_person_occurrence.json diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/brand.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/brand.json deleted file mode 100644 index ebb136c03..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/brand.json +++ /dev/null @@ -1,135 +0,0 @@ -{ - "name" : "brand", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "" - }, - "display" : "Unknown" - }, - "count" : 82839 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT * FROM `victr-tanagra-test.sd_static.concept` WHERE domain_id = 'Drug' AND concept_class_id = 'Brand Name' AND vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND DATE_DIFF(valid_end_date, CURRENT_DATE(), DAY) > 0" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_static.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_static.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND c.concept_class_id = 'Brand Name' AND c.vocabulary_id IN ('RxNorm', 'RxNorm Extension')" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "brand" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/condition.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/condition.json deleted file mode 100644 index e289b79ff..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/condition.json +++ /dev/null @@ -1,461 +0,0 @@ -{ - "name" : "condition", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 174148 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 384 - }, { - "enumVal" : { - "value" : { - "stringVal" : "" - }, - "display" : "Unknown" - }, - "count" : 523932 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CIEL" - }, - "display" : "CIEL" - }, - "count" : 38818 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CIM10" - }, - "display" : "CIM10" - }, - "count" : 10867 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Cohort" - }, - "display" : "Cohort" - }, - "count" : 66 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HemOnc" - }, - "display" : "HemOnc" - }, - "count" : 219 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10" - }, - "display" : "ICD10" - }, - "count" : 15017 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "ICD10CM" - }, - "count" : 90542 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CN" - }, - "display" : "ICD10CN" - }, - "count" : 31794 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10GM" - }, - "display" : "ICD10GM" - }, - "count" : 16006 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "ICD9CM" - }, - "count" : 15760 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICDO3" - }, - "display" : "ICDO3" - }, - "count" : 62410 - }, { - "enumVal" : { - "value" : { - "stringVal" : "KCD7" - }, - "display" : "KCD7" - }, - "count" : 20743 - }, { - "enumVal" : { - "value" : { - "stringVal" : "MeSH" - }, - "display" : "MeSH" - }, - "count" : 6795 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Nebraska Lexicon" - }, - "display" : "Nebraska Lexicon" - }, - "count" : 151336 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OMOP Extension" - }, - "display" : "OMOP Extension" - }, - "count" : 7 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPCS4" - }, - "display" : "OPCS4" - }, - "count" : 6 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OXMIS" - }, - "display" : "OXMIS" - }, - "count" : 5704 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OncoTree" - }, - "display" : "OncoTree" - }, - "count" : 869 - }, { - "enumVal" : { - "value" : { - "stringVal" : "PPI" - }, - "display" : "PPI" - }, - "count" : 74 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Read" - }, - "display" : "Read" - }, - "count" : 47736 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SMQ" - }, - "display" : "SMQ" - }, - "count" : 324 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 180133 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED Veterinary" - }, - "display" : "SNOMED Veterinary" - }, - "count" : 3237 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Condition" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_static.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_static.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Condition' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `victr-tanagra-test.sd_static.concept_relationship` cr JOIN `victr-tanagra-test.sd_static.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `victr-tanagra-test.sd_static.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Condition' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED'" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 441840 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "condition" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "condition_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "condition_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "condition" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/condition_occurrence.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/condition_occurrence.json deleted file mode 100644 index 5ead0db13..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/condition_occurrence.json +++ /dev/null @@ -1,283 +0,0 @@ -{ - "name" : "condition_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "condition", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -977.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 8278785 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 52395118 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 3007838 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 137386512 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT co.condition_occurrence_id AS id, co.person_id, co.condition_concept_id, co.condition_start_date AS start_date, co.condition_end_date AS end_date, co.stop_reason, co.condition_source_value AS source_value, co.condition_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(co.condition_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, co.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_static.condition_occurrence` AS co JOIN `victr-tanagra-test.sd_static.person` AS p ON p.person_id = co.person_id LEFT JOIN `victr-tanagra-test.sd_static.visit_occurrence` AS vo ON vo.visit_occurrence_id = co.visit_occurrence_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "condition_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "condition_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_condition", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/device.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/device.json deleted file mode 100644 index f3f972937..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/device.json +++ /dev/null @@ -1,285 +0,0 @@ -{ - "name" : "device", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 245402 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "AMT" - }, - "display" : "AMT" - }, - "count" : 2945 - }, { - "enumVal" : { - "value" : { - "stringVal" : "BDPM" - }, - "display" : "BDPM" - }, - "count" : 1106 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "CPT4" - }, - "count" : 24 - }, { - "enumVal" : { - "value" : { - "stringVal" : "GGR" - }, - "display" : "GGR" - }, - "count" : 596 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 4634 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10PCS" - }, - "display" : "ICD10PCS" - }, - "count" : 3 - }, { - "enumVal" : { - "value" : { - "stringVal" : "JMDC" - }, - "display" : "JMDC" - }, - "count" : 1313 - }, { - "enumVal" : { - "value" : { - "stringVal" : "KDC" - }, - "display" : "KDC" - }, - "count" : 112 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NDC" - }, - "display" : "NDC" - }, - "count" : 10963 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPCS4" - }, - "display" : "OPCS4" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 202567 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED Veterinary" - }, - "display" : "SNOMED Veterinary" - }, - "count" : 67 - }, { - "enumVal" : { - "value" : { - "stringVal" : "dm+d" - }, - "display" : "dm+d" - }, - "count" : 21071 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Device" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_static.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_static.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Device' AND c.standard_concept = 'S'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "device" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/device_occurrence.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/device_occurrence.json deleted file mode 100644 index 2793a3402..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/device_occurrence.json +++ /dev/null @@ -1,256 +0,0 @@ -{ - "name" : "device_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -4.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 99792 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 928353 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 830 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 1931949 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "device", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT de.device_exposure_id AS id, de.person_id, de.device_concept_id, de.device_exposure_start_date AS start_date, de.device_exposure_end_date AS end_date, de.device_source_value AS source_value, de.device_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(de.device_exposure_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, de.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_static.device_exposure` AS de JOIN `victr-tanagra-test.sd_static.person` AS p ON p.person_id = de.person_id LEFT JOIN `victr-tanagra-test.sd_static.visit_occurrence` AS vo ON vo.visit_occurrence_id = de.visit_occurrence_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "device_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "device_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_device", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/genotyping.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/genotyping.json deleted file mode 100644 index 6550c6a0a..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/genotyping.json +++ /dev/null @@ -1,149 +0,0 @@ -{ - "name" : "genotyping", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "/* platform_id column has type NUMERIC. This causes index column to be FLOAT. Currently indexing doesn't handle floats properly, so change column to INTEGER. */ SELECT CAST(platform_id as INT64) AS platform_id, assay_name as assay_name FROM `victr-tanagra-test.sd_static.platform` UNION ALL /* Add some rows to get hierarchy to work. Parent ids are defined in genotype_criteria, criteria_meta_seq column. criteria_meta_seq is not in the same \"ID space\" as platform_id. Tanagra requres parent id to be in same \"ID space\" as platform_id. So create artificial platform_ids for parents. */ (SELECT 101 AS platform_id, 'GWAS Platforms' AS assay_name UNION ALL SELECT 102, 'Non-GWAS and Targeted Genotyping Platforms' UNION ALL SELECT 103, 'Sequencing Platforms') " - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "assay_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "platform_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "attributes" : [ "id", "name" ] - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT /* Use parent ids defined in platform.sql */ parent_seq + 100 AS parent, CAST(platform_id as INT64) AS child FROM `victr-tanagra-test.sd_static.genotype_criteria` g, `victr-tanagra-test.sd_static.platform` p WHERE g.name = p.assay_name " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "rawSql" : "/* Match the platform ids in platform.sql */ SELECT 101 AS id UNION ALL SELECT 102 UNION ALL SELECT 103 " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 1 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "genotyping" - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "genotyping_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "genotyping_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "genotyping" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 1 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/ingredient.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/ingredient.json deleted file mode 100644 index c46893302..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/ingredient.json +++ /dev/null @@ -1,306 +0,0 @@ -{ - "name" : "ingredient", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 1921307 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 6335 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "ATC" - }, - "display" : "ATC" - }, - "count" : 6335 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm" - }, - "display" : "RxNorm" - }, - "count" : 147265 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm Extension" - }, - "display" : "RxNorm Extension" - }, - "count" : 1774042 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT c.concept_id AS id, c.concept_name AS name, c.vocabulary_id, c.standard_concept, c.concept_code FROM `victr-tanagra-test.sd_static.concept` c WHERE c.domain_id = 'Drug' AND ( (c.vocabulary_id = 'ATC' AND c.standard_concept = 'C') OR (c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.standard_concept = 'S') )" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_static.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_static.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND ((c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.concept_class_id = 'Ingredient' AND c.standard_concept = 'S') OR (c.vocabulary_id = 'RxNorm' AND c.concept_class_id = 'Precise Ingredient') OR (c.vocabulary_id = 'ATC' AND c.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c.standard_concept = 'C'))" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child FROM `victr-tanagra-test.sd_static.concept_relationship` cr JOIN `victr-tanagra-test.sd_static.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `victr-tanagra-test.sd_static.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE c1.concept_id != c2.concept_id AND c1.domain_id = 'Drug' AND c2.domain_id = 'Drug' AND ( /* Populate Ingredients' ancestors', which are ATCs. See https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:atc#:~:text=the%20original%20ATC%20hierarchy%20is%20extended%20by%20Standard%20Drug%20Products%20of%20RxNorm%20and%20RxNorm%20Extension%20vocabularies%2C%20which%20are%20assigned%20to%20be%20descendants%20of%20the%205th%20ATC%20Classes. Eg: ATC 1st (highest ancestor) Subsumes ATC 2nd ATC 5th (direct parent of RxNorm) Maps to RxNorm */ (c1.vocabulary_id IN ('ATC') AND cr.relationship_id IN ('Subsumes', 'Maps to')) OR /* Populate Ingredients and their descendants: Branded Drug, Clinical Drug, etc. Ingredients and their descendants are RxNorm. drug_exposure contains Ingredients or their descendants. Use [1] and [2] to define hierarchy. Eg \"Marketed Product\" is most specific and is bottom of hierarchy. [1] https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:drug_exposure#:~:text=These%20are%20indicated,is%20available%20%E2%80%9CIngredient%E2%80%9D [2] https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:drug#:~:text=are%20not%20implemented.-,Relationships,-As%20usual%2C%20all */ ( c1.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c2.vocabulary_id IN ('RxNorm', 'RxNorm Extension') /* Only keep relationships where c1 is \"parent\" of c2 */ AND cr.relationship_id IN ('Constitutes', 'Contained in' , 'Has form', 'Has quantified form', 'RxNorm ing of', 'RxNorm inverse is a', 'Precise ing of') ) )" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC 1st" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "C" - } - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 15 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "ingredient" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "ingredient_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "ingredient_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "ingredient" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 15 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/ingredient_occurrence.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/ingredient_occurrence.json deleted file mode 100644 index c0621be80..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/ingredient_occurrence.json +++ /dev/null @@ -1,543 +0,0 @@ -{ - "name" : "ingredient_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ingredient", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Allergic res" - }, - "display" : "Allergic res" - }, - "count" : 4846 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Alternate tx" - }, - "display" : "Alternate tx" - }, - "count" : 84029 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Anes Stop" - }, - "display" : "Anes Stop" - }, - "count" : 2863009 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Availability" - }, - "display" : "Availability" - }, - "count" : 6600 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CONTACT " - }, - "display" : "CONTACT " - }, - "count" : 614 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Cleanup" - }, - "display" : "Cleanup" - }, - "count" : 399229 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Cost of medi" - }, - "display" : "Cost of medi" - }, - "count" : 9054 - }, { - "enumVal" : { - "value" : { - "stringVal" : "DC'd by othr" - }, - "display" : "DC'd by othr" - }, - "count" : 164096 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Dose adjustm" - }, - "display" : "Dose adjustm" - }, - "count" : 110534 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Drug interac" - }, - "display" : "Drug interac" - }, - "count" : 1982 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Duplicate or" - }, - "display" : "Duplicate or" - }, - "count" : 523173 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Error" - }, - "display" : "Error" - }, - "count" : 238189 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Expired" - }, - "display" : "Expired" - }, - "count" : 151543 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Formulary" - }, - "display" : "Formulary" - }, - "count" : 25726 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NON-ADHEREN" - }, - "display" : "NON-ADHEREN" - }, - "count" : 9253 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Other" - }, - "display" : "Other" - }, - "count" : 195756 - }, { - "enumVal" : { - "value" : { - "stringVal" : "PATIENT DISC" - }, - "display" : "PATIENT DISC" - }, - "count" : 6654423 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Paradoxical " - }, - "display" : "Paradoxical " - }, - "count" : 275 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Pregnancy" - }, - "display" : "Pregnancy" - }, - "count" : 1116 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RETURNED TO " - }, - "display" : "RETURNED TO " - }, - "count" : 19246 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Reorder" - }, - "display" : "Reorder" - }, - "count" : 4317260 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SE" - }, - "display" : "SE" - }, - "count" : 40002 - }, { - "enumVal" : { - "value" : { - "stringVal" : "STOP TAKING " - }, - "display" : "STOP TAKING " - }, - "count" : 402507 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SURGERY" - }, - "display" : "SURGERY" - }, - "count" : 921 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Stop Med" - }, - "display" : "Stop Med" - }, - "count" : 123398 - }, { - "enumVal" : { - "value" : { - "stringVal" : "TRANSFER" - }, - "display" : "TRANSFER" - }, - "count" : 571939 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Therapy comp" - }, - "display" : "Therapy comp" - }, - "count" : 2198773 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 6103937 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 185294420 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 286446 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 42337392 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "days_supply", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 1.0, - "maxVal" : 36135.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "refills", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 365.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -2005.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT de.drug_exposure_id AS id, de.person_id, de.drug_concept_id, de.drug_exposure_start_date AS start_date, de.drug_exposure_end_date AS end_date, de.stop_reason, de.refills, de.days_supply, de.drug_source_value AS source_value, de.drug_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(de.drug_exposure_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, de.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_static.drug_exposure` AS de JOIN `victr-tanagra-test.sd_static.person` AS p ON p.person_id = de.person_id LEFT JOIN `victr-tanagra-test.sd_static.visit_occurrence` AS vo ON vo.visit_occurrence_id = de.visit_occurrence_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "drug_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "ingredient_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "ingredient", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ingredient", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/measurement.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/measurement.json deleted file mode 100644 index bac646402..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/measurement.json +++ /dev/null @@ -1,409 +0,0 @@ -{ - "name" : "measurement", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 73948 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 40193 - }, { - "enumVal" : { - "value" : { - "stringVal" : "" - }, - "display" : "Unknown" - }, - "count" : 101999 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NULL" - }, - "display" : "Unknown" - }, - "count" : 9 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "LOINC" - }, - "count" : 186150 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 29999 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Measurement" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "SNOMED" - } - } ] - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC" - } - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC Hierarchy" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC Component" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Lab Test" - } - } ] - } ] - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_static.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_static.concept` c ON c.concept_id = textsearch.id WHERE ((c.domain_id = 'Measurement' AND c.vocabulary_id = 'SNOMED') OR (c.vocabulary_id = 'LOINC' AND c.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test')))" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `victr-tanagra-test.sd_static.concept_relationship` cr JOIN `victr-tanagra-test.sd_static.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `victr-tanagra-test.sd_static.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.vocabulary_id = c2.vocabulary_id AND ((c1.vocabulary_id = 'SNOMED' AND c1.domain_id = c2.domain_id AND c1.domain_id = 'Measurement') OR (c1.vocabulary_id = 'LOINC' AND c1.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test') AND c2.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test'))) " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Measurement" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "SNOMED" - } - } ] - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 36206173 - } - } ] - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 11 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "measurement" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "measurement_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "measurement_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "measurement" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 11 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/measurement_occurrence.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/measurement_occurrence.json deleted file mode 100644 index 39a1bf898..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/measurement_occurrence.json +++ /dev/null @@ -1,312 +0,0 @@ -{ - "name" : "measurement_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -1765.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 33250279 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 502984032 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 2421169 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 231277325 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_numeric", - "dataType" : "DOUBLE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value_enum", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "measurement", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT mo.measurement_id AS id, mo.person_id, mo.measurement_concept_id, mo.measurement_date, mo.value_as_number AS value_numeric, mo.value_as_concept_id, mo.unit_concept_id, mo.measurement_source_value AS source_value, mo.measurement_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(mo.measurement_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, mo.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_static.measurement` AS mo JOIN `victr-tanagra-test.sd_static.person` AS p ON p.person_id = mo.person_id LEFT JOIN `victr-tanagra-test.sd_static.visit_occurrence` AS vo ON vo.visit_occurrence_id = mo.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "measurement_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value_numeric" : { - "value" : { - "column" : "value_numeric", - "runtimeCalculated" : false - } - }, - "value_enum" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "measurement" : { - "value" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "measurement_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "measurement_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value_numeric" : { - "value" : { - "column" : "value_numeric", - "runtimeCalculated" : false - } - }, - "value_enum" : { - "value" : { - "column" : "value_enum", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value_enum", - "runtimeCalculated" : false - } - }, - "measurement" : { - "value" : { - "column" : "measurement", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_measurement", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/note.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/note.json deleted file mode 100644 index d187aacd5..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/note.json +++ /dev/null @@ -1,195 +0,0 @@ -{ - "name" : "note", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "None" - }, - "display" : "None" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Note Type" - }, - "display" : "Note Type" - }, - "count" : 10 - }, { - "enumVal" : { - "value" : { - "stringVal" : "VUMC Note Type" - }, - "display" : "VUMC Note Type" - }, - "count" : 3 - }, { - "enumVal" : { - "value" : { - "stringVal" : "VUMC PSS Type" - }, - "display" : "VUMC PSS Type" - }, - "count" : 1 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 0 - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Note Type" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "VUMC Note Type" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "VUMC PSS Type" - } - } ] - } - }, - "attributeMappings" : { - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_static.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_static.concept` c ON c.concept_id = textsearch.id WHERE c.vocabulary_id IN ('Note Type', 'VUMC Note Type', 'VUMC PSS Type') OR c.concept_id = 0" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "note" - }, - "attributeMappings" : { - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/note_occurrence.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/note_occurrence.json deleted file mode 100644 index 2952b5c9b..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/note_occurrence.json +++ /dev/null @@ -1,380 +0,0 @@ -{ - "name" : "note_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "note", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 44814638 - }, - "display" : "Admission note" - }, - "count" : 2211781 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814643 - }, - "display" : "Ancillary report" - }, - "count" : 11923399 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814637 - }, - "display" : "Discharge summary" - }, - "count" : 5590516 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2003594153 - }, - "display" : "ECG_IMPRESSION" - }, - "count" : 1993820 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814646 - }, - "display" : "Emergency department note" - }, - "count" : 2970051 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814639 - }, - "display" : "Inpatient note" - }, - "count" : 15472924 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 6844205 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814645 - }, - "display" : "Note" - }, - "count" : 68281428 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814644 - }, - "display" : "Nursing report" - }, - "count" : 6777679 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814640 - }, - "display" : "Outpatient note" - }, - "count" : 69556237 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2002404173 - }, - "display" : "PL_PROBLEM LIST" - }, - "count" : 679215564 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814642 - }, - "display" : "Pathology report" - }, - "count" : 2697212 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2002603124 - }, - "display" : "Pss Problem snomed data" - }, - "count" : 29508422 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814641 - }, - "display" : "Radiology report" - }, - "count" : 16997484 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2004084156 - }, - "display" : "VUMC forms data" - }, - "count" : 479294 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -1611.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 1516005 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 16924704 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1275410 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 25879317 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "text", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "title", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT n.note_id AS id, n.person_id, n.note_type_concept_id, n.note_date, n.note_title AS title, n.note_text AS text, n.note_source_value AS source_value, CAST(FLOOR(TIMESTAMP_DIFF(n.note_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, n.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_static.note` AS n JOIN `victr-tanagra-test.sd_static.person` AS p ON p.person_id = n.person_id LEFT JOIN `victr-tanagra-test.sd_static.visit_occurrence` AS vo ON vo.visit_occurrence_id = n.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "note_date", - "runtimeCalculated" : false - } - }, - "note" : { - "value" : { - "column" : "note_type_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "note_type_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "text" : { - "value" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "title" : { - "value" : { - "column" : "title", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "note_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "note" : { - "value" : { - "column" : "note", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_note", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "text" : { - "value" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "title" : { - "value" : { - "column" : "title", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/observation.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/observation.json deleted file mode 100644 index 6ad73cc2a..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/observation.json +++ /dev/null @@ -1,337 +0,0 @@ -{ - "name" : "observation", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 162296 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "APC" - }, - "display" : "APC" - }, - "count" : 715 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "CPT4" - }, - "count" : 1083 - }, { - "enumVal" : { - "value" : { - "stringVal" : "DRG" - }, - "display" : "DRG" - }, - "count" : 752 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 2667 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICDO3" - }, - "display" : "ICDO3" - }, - "count" : 49 - }, { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "LOINC" - }, - "count" : 7087 - }, { - "enumVal" : { - "value" : { - "stringVal" : "MDC" - }, - "display" : "MDC" - }, - "count" : 26 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NAACCR" - }, - "display" : "NAACCR" - }, - "count" : 96 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NUCC" - }, - "display" : "NUCC" - }, - "count" : 4 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Nebraska Lexicon" - }, - "display" : "Nebraska Lexicon" - }, - "count" : 1004 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OMOP Extension" - }, - "display" : "OMOP Extension" - }, - "count" : 107 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPCS4" - }, - "display" : "OPCS4" - }, - "count" : 56 - }, { - "enumVal" : { - "value" : { - "stringVal" : "PCORNet" - }, - "display" : "PCORNet" - }, - "count" : 2 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 117406 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED Veterinary" - }, - "display" : "SNOMED Veterinary" - }, - "count" : 27401 - }, { - "enumVal" : { - "value" : { - "stringVal" : "UB04 Pri Typ of Adm" - }, - "display" : "UB04 Pri Typ of Adm" - }, - "count" : 6 - }, { - "enumVal" : { - "value" : { - "stringVal" : "UK Biobank" - }, - "display" : "UK Biobank" - }, - "count" : 3835 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Observation" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "PPI" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "Survey" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_static.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_static.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Observation' AND c.standard_concept = 'S' AND c.vocabulary_id != 'PPI' AND c.concept_class_id != 'Survey'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "observation" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/observation_occurrence.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/observation_occurrence.json deleted file mode 100644 index e9deef974..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/observation_occurrence.json +++ /dev/null @@ -1,312 +0,0 @@ -{ - "name" : "observation_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -977.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "observation", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_as_string", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 3576917 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 8957833 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 803664 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 57751171 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT o.observation_id AS id, o.person_id, o.observation_concept_id, o.observation_date, o.value_as_string, o.value_as_concept_id, o.unit_concept_id, o.observation_source_value AS source_value, o.observation_source_concept_id AS source_criteria_id, CAST(FLOOR(DATE_DIFF(o.observation_date, CAST(p.birth_datetime AS DATE), DAY) / 365.25) AS INT64) AS age_at_occurrence, o.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_static.observation` AS o JOIN `victr-tanagra-test.sd_static.person` AS p ON p.person_id = o.person_id LEFT JOIN `victr-tanagra-test.sd_static.visit_occurrence` AS vo ON vo.visit_occurrence_id = o.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "observation_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "observation_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "observation_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_observation", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/person.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/person.json deleted file mode 100644 index 1ac7aa1d0..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/person.json +++ /dev/null @@ -1,360 +0,0 @@ -{ - "name" : "person", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "gender", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 8532 - }, - "display" : "FEMALE" - }, - "count" : 1850236 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8507 - }, - "display" : "MALE" - }, - "count" : 1594485 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 4177 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "race", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 8657 - }, - "display" : "American Indian or Alaska Native" - }, - "count" : 4572 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8515 - }, - "display" : "Asian" - }, - "count" : 45958 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38003598 - }, - "display" : "Black" - }, - "count" : 327829 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 953870 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8527 - }, - "display" : "White" - }, - "count" : 2116669 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ethnicity", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 38003563 - }, - "display" : "Hispanic or Latino" - }, - "count" : 113110 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 960195 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38003564 - }, - "display" : "Not Hispanic or Latino" - }, - "count" : 2375593 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "biovu_sample_has_plasma", - "dataType" : "BOOLEAN", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "biovu_sample_dna_yield", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -99999.0, - "maxVal" : 500.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "biovu_sample_is_compromised", - "dataType" : "BOOLEAN", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "age", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -971.0, - "maxVal" : 224.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "has_biovu_sample", - "dataType" : "BOOLEAN", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "biovu_sample_is_nonshippable", - "dataType" : "BOOLEAN", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "year_of_birth", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 1799.0, - "maxVal" : 2993.0 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT /* Can't do \"*\". During expansion, there's an error about person_id column being ambiguous. */ p.person_id, p.year_of_birth, p.birth_datetime, p.gender_concept_id, p.race_concept_id, p.ethnicity_concept_id, /* Add BioVU sample columns. The way x_biovu_sample_status is created, there should be at most one row per person. */ EXISTS (SELECT 1 FROM `victr-tanagra-test.sd_static.x_biovu_sample_status` x WHERE p.person_id = x.person_id) AS has_biovu_sample, x.dna_yield_ind AS biovu_sample_dna_yield, /* As a courtesy, convert string fields to boolean: 0 -> No, 1 -> Yes */ CASE WHEN x.compromise_ind = '1' THEN true WHEN x.compromise_ind = '0' THEN false ELSE null END AS biovu_sample_is_compromised, CASE WHEN x.nonshippable_ind = '1' THEN true WHEN x.nonshippable_ind = '0' THEN false ELSE null END AS biovu_sample_is_nonshippable, CASE WHEN x.plasma_ind = '1' THEN true WHEN x.plasma_ind = '0' THEN false ELSE null END AS biovu_sample_has_plasma FROM `victr-tanagra-test.sd_static.person` p LEFT OUTER JOIN ( /* Get rid of duplicate rows in x_biovu_sample_status. For example, person 4587323 has 11 duplicate rows. This returns just 1 row for each person. */ WITH x_biovu_sample_status AS ( SELECT *, ROW_NUMBER() OVER(PARTITION BY person_id) AS rn FROM `victr-tanagra-test.sd_static.x_biovu_sample_status` ) SELECT * FROM x_biovu_sample_status WHERE rn = 1 ) x ON p.person_id = x.person_id " - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "gender_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "race_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "ethnicity_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "biovu_sample_has_plasma" : { - "value" : { - "column" : "biovu_sample_has_plasma", - "runtimeCalculated" : false - } - }, - "biovu_sample_dna_yield" : { - "value" : { - "column" : "biovu_sample_dna_yield", - "runtimeCalculated" : false - } - }, - "biovu_sample_is_compromised" : { - "value" : { - "column" : "biovu_sample_is_compromised", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "age" : { - "value" : { - "column" : "birth_datetime", - "sqlFunctionWrapper" : "CAST(FLOOR(TIMESTAMP_DIFF(CURRENT_TIMESTAMP(), ${fieldSql}, DAY) / 365.25) AS INT64)", - "runtimeCalculated" : true - } - }, - "has_biovu_sample" : { - "value" : { - "column" : "has_biovu_sample", - "runtimeCalculated" : false - } - }, - "biovu_sample_is_nonshippable" : { - "value" : { - "column" : "biovu_sample_is_nonshippable", - "runtimeCalculated" : false - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "person" - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_gender", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_race", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ethnicity", - "runtimeCalculated" : false - } - }, - "biovu_sample_has_plasma" : { - "value" : { - "column" : "biovu_sample_has_plasma", - "runtimeCalculated" : false - } - }, - "biovu_sample_dna_yield" : { - "value" : { - "column" : "biovu_sample_dna_yield", - "runtimeCalculated" : false - } - }, - "biovu_sample_is_compromised" : { - "value" : { - "column" : "biovu_sample_is_compromised", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "age" : { - "value" : { - "column" : "age", - "sqlFunctionWrapper" : "CAST(FLOOR(TIMESTAMP_DIFF(CURRENT_TIMESTAMP(), ${fieldSql}, DAY) / 365.25) AS INT64)", - "runtimeCalculated" : true - } - }, - "has_biovu_sample" : { - "value" : { - "column" : "has_biovu_sample", - "runtimeCalculated" : false - } - }, - "biovu_sample_is_nonshippable" : { - "value" : { - "column" : "biovu_sample_is_nonshippable", - "runtimeCalculated" : false - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/procedure.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/procedure.json deleted file mode 100644 index 86b4983b7..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/procedure.json +++ /dev/null @@ -1,485 +0,0 @@ -{ - "name" : "procedure", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 262341 - }, { - "enumVal" : { - "value" : { - "stringVal" : "" - }, - "display" : "Unknown" - }, - "count" : 458585 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 3064 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CCAM" - }, - "display" : "CCAM" - }, - "count" : 10206 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CIEL" - }, - "display" : "CIEL" - }, - "count" : 648 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CIM10" - }, - "display" : "CIM10" - }, - "count" : 195 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "CPT4" - }, - "count" : 13143 - }, { - "enumVal" : { - "value" : { - "stringVal" : "EDI" - }, - "display" : "EDI" - }, - "count" : 249785 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 1289 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HemOnc" - }, - "display" : "HemOnc" - }, - "count" : 92 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10" - }, - "display" : "ICD10" - }, - "count" : 161 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "ICD10CM" - }, - "count" : 6 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CN" - }, - "display" : "ICD10CN" - }, - "count" : 386 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10GM" - }, - "display" : "ICD10GM" - }, - "count" : 157 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10PCS" - }, - "display" : "ICD10PCS" - }, - "count" : 194874 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "ICD9CM" - }, - "count" : 177 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9Proc" - }, - "display" : "ICD9Proc" - }, - "count" : 4657 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9ProcCN" - }, - "display" : "ICD9ProcCN" - }, - "count" : 13385 - }, { - "enumVal" : { - "value" : { - "stringVal" : "KCD7" - }, - "display" : "KCD7" - }, - "count" : 165 - }, { - "enumVal" : { - "value" : { - "stringVal" : "MeSH" - }, - "display" : "MeSH" - }, - "count" : 951 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NAACCR" - }, - "display" : "NAACCR" - }, - "count" : 710 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Nebraska Lexicon" - }, - "display" : "Nebraska Lexicon" - }, - "count" : 72683 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OMOP Extension" - }, - "display" : "OMOP Extension" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPCS4" - }, - "display" : "OPCS4" - }, - "count" : 9750 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPS" - }, - "display" : "OPS" - }, - "count" : 41101 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OXMIS" - }, - "display" : "OXMIS" - }, - "count" : 1193 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Read" - }, - "display" : "Read" - }, - "count" : 20973 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 86910 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED Veterinary" - }, - "display" : "SNOMED Veterinary" - }, - "count" : 392 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Procedure" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_static.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_static.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Procedure' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `victr-tanagra-test.sd_static.concept_relationship` cr JOIN `victr-tanagra-test.sd_static.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `victr-tanagra-test.sd_static.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Procedure' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED'" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 4322976 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "procedure" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "procedure_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "procedure_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "procedure" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/procedure_occurrence.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/procedure_occurrence.json deleted file mode 100644 index 6696f0ac0..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/procedure_occurrence.json +++ /dev/null @@ -1,239 +0,0 @@ -{ - "name" : "procedure_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -96.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 6819652 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 30613368 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 813264 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 82908869 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "procedure", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT po.procedure_occurrence_id AS id, po.person_id, po.procedure_concept_id, po.procedure_date, po.procedure_source_value AS source_value, po.procedure_source_concept_id AS source_criteria_id, CAST(FLOOR(DATE_DIFF(po.procedure_date, CAST(p.birth_datetime AS DATE), DAY) / 365.25) AS INT64) AS age_at_occurrence, po.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_static.procedure_occurrence` AS po JOIN `victr-tanagra-test.sd_static.person` AS p ON p.person_id = po.person_id LEFT JOIN `victr-tanagra-test.sd_static.visit_occurrence` AS vo ON vo.visit_occurrence_id = po.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "procedure_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "procedure_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "procedure_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_procedure", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/snp.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/snp.json deleted file mode 100644 index e6eb94ef2..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/snp.json +++ /dev/null @@ -1,49 +0,0 @@ -{ - "name" : "snp", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "STRING", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT DISTINCT snp FROM `victr-tanagra-test.sd_static.x_snp` ORDER BY snp " - }, - "attributeMappings" : { - "id" : { - "value" : { - "column" : "snp", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "attributes" : [ "id" ] - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "snp" - }, - "attributeMappings" : { - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/visit.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/visit.json deleted file mode 100644 index 716ebc81a..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/visit.json +++ /dev/null @@ -1,105 +0,0 @@ -{ - "name" : "visit", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Visit" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_static.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_static.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_static.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Visit' AND c.standard_concept = 'S'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "visit" - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entity/visit_occurrence.json b/service/src/main/resources/config/vumc/sdd/expanded/entity/visit_occurrence.json deleted file mode 100644 index 2a0a707cd..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entity/visit_occurrence.json +++ /dev/null @@ -1,211 +0,0 @@ -{ - "name" : "visit_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -977.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 1690886 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 3078021 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1077644 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 57044408 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "DATE", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT vo.visit_occurrence_id AS id, vo.person_id, vo.visit_concept_id, vo.visit_start_date AS start_date, vo.visit_end_date AS end_date, vo.visit_source_value AS source_value, vo.visit_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(vo.visit_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence FROM `victr-tanagra-test.sd_static.visit_occurrence` AS vo JOIN `victr-tanagra-test.sd_static.person` AS p ON p.person_id = vo.person_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "visit" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "visit_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "visit" : { - "value" : { - "column" : "visit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/brand_ingredient.json b/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/brand_ingredient.json deleted file mode 100644 index 3edaee58d..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/brand_ingredient.json +++ /dev/null @@ -1,101 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "brand_ingredient", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "rawSql" : "/* 1. User searches for Brand Tylenol 2. User expands Tylenol to see which ingredients are in Tylenol 3. Ingredient Acetaminophen is shown Acetaminophen has over 300 descendants (eg \"acetaminophen 100 MG/ML Oral Suspension\"). Acetaminophen's concept_class_id is Ingredient; descendants' concept_class_ids are Clinical Drug Comp, Quant Clinical Drug, etc. Most descendants have a relationship with Brand Tylenol in concept_relationship. However, we only want to show Acetaminophen in step 3. So only keep relationships with concept_class_id=Ingredient. */ SELECT cr.* FROM `victr-tanagra-test.sd_static.concept_relationship` cr, `victr-tanagra-test.sd_static.concept` c2 WHERE cr.concept_id_2 = c2.concept_id AND c2.concept_class_id = 'Ingredient'" - }, - "idPairsIdA" : { - "column" : "concept_id_1", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "concept_id_2", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_brand_ingredient" - }, - "idPairsIdA" : { - "column" : "id_brand", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "brand" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_brand_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_brand_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_brand", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_brand", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "brand", - "itemsEntity" : "ingredient" -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/condition_person_occurrence.json b/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/condition_person_occurrence.json deleted file mode 100644 index a709ed653..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/condition_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "condition_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_condition_occurrence_condition" - }, - "idPairsIdA" : { - "column" : "id_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_condition", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_condition_person" - }, - "idPairsIdA" : { - "column" : "id_condition", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_condition_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "condition", - "occurrenceEntity" : "condition_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/device_person_occurrence.json b/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/device_person_occurrence.json deleted file mode 100644 index ff77e8f95..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/device_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "device_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_device_occurrence_device" - }, - "idPairsIdA" : { - "column" : "id_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_device", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_device_person" - }, - "idPairsIdA" : { - "column" : "id_device", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_device_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "device", - "occurrenceEntity" : "device_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/genotyping_person.json b/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/genotyping_person.json deleted file mode 100644 index fb3cbb2ce..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/genotyping_person.json +++ /dev/null @@ -1,101 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "genotyping_person", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "rawSql" : "/* platform_id column has type NUMERIC. This causes index column to be FLOAT. Currently indexing doesn't handle floats properly, so change column to INTEGER. */ SELECT genotype_result_id AS genotype_result_id, person_id, CAST(platform_id as INT64) as platform_id FROM `victr-tanagra-test.sd_static.genotype_result` " - }, - "idPairsIdA" : { - "column" : "platform_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_genotyping_person" - }, - "idPairsIdA" : { - "column" : "id_genotyping", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "genotyping" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "genotyping" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_genotyping", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_genotyping", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "genotyping", - "itemsEntity" : "person" -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/ingredient_person_occurrence.json b/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/ingredient_person_occurrence.json deleted file mode 100644 index 576ca9260..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/ingredient_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "ingredient_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_occurrence_ingredient" - }, - "idPairsIdA" : { - "column" : "id_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_person" - }, - "idPairsIdA" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "ingredient", - "occurrenceEntity" : "ingredient_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/measurement_person_occurrence.json b/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/measurement_person_occurrence.json deleted file mode 100644 index cb82b0df7..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/measurement_person_occurrence.json +++ /dev/null @@ -1,287 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "measurement_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_measurement_occurrence_measurement" - }, - "idPairsIdA" : { - "column" : "id_measurement_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_measurement", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_measurement_person" - }, - "idPairsIdA" : { - "column" : "id_measurement", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_measurement_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_measurement_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { - "modifiers" : { - "tablePointer" : { - "table" : "measurement_person_occurrence_modifiers" - }, - "fieldPointers" : { - "min" : { - "column" : "min", - "runtimeCalculated" : false - }, - "enum_count" : { - "column" : "enum_count", - "runtimeCalculated" : false - }, - "max" : { - "column" : "max", - "runtimeCalculated" : false - }, - "enum_display" : { - "column" : "enum_display", - "runtimeCalculated" : false - }, - "enum_value" : { - "column" : "enum_value", - "runtimeCalculated" : false - }, - "attribute_name" : { - "column" : "attribute_name", - "runtimeCalculated" : false - }, - "entity_id" : { - "column" : "entity_id", - "runtimeCalculated" : false - } - } - } - } - }, - "criteriaEntity" : "measurement", - "occurrenceEntity" : "measurement_occurrence", - "modifierAttributes" : [ "value_numeric", "value_enum" ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/note_person_occurrence.json b/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/note_person_occurrence.json deleted file mode 100644 index dd4403308..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/note_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "note_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "note" - }, - "idPairsIdA" : { - "column" : "note_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "note_type_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "note" - }, - "idPairsIdA" : { - "column" : "note_type_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "note" - }, - "idPairsIdA" : { - "column" : "note_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_note_occurrence_note" - }, - "idPairsIdA" : { - "column" : "id_note_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_note", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "note_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_note", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_note", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "note" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_note_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_note_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_note_person" - }, - "idPairsIdA" : { - "column" : "id_note", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "note" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_note", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_note", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_note_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_note_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "note_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_note_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_note_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "note", - "occurrenceEntity" : "note_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/observation_person_occurrence.json b/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/observation_person_occurrence.json deleted file mode 100644 index dad430b34..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/observation_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "observation_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_observation_occurrence_observation" - }, - "idPairsIdA" : { - "column" : "id_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_observation", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_observation_person" - }, - "idPairsIdA" : { - "column" : "id_observation", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_observation_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "observation", - "occurrenceEntity" : "observation_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/procedure_person_occurrence.json b/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/procedure_person_occurrence.json deleted file mode 100644 index be81091b7..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/procedure_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "procedure_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_procedure_occurrence_procedure" - }, - "idPairsIdA" : { - "column" : "id_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_procedure", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_procedure_person" - }, - "idPairsIdA" : { - "column" : "id_procedure", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_procedure_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "procedure", - "occurrenceEntity" : "procedure_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/snp_person.json b/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/snp_person.json deleted file mode 100644 index 6eb9e54df..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/snp_person.json +++ /dev/null @@ -1,84 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "snp_person", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "x_snp" - }, - "idPairsIdA" : { - "column" : "snp", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_snp_person" - }, - "idPairsIdA" : { - "column" : "id_snp", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "snp" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_snp", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_snp", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "snp", - "itemsEntity" : "person" -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/visit_person_occurrence.json b/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/visit_person_occurrence.json deleted file mode 100644 index 1a4beff12..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/entitygroup/visit_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "visit_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_visit_occurrence_visit" - }, - "idPairsIdA" : { - "column" : "id_visit_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_visit", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_visit_person" - }, - "idPairsIdA" : { - "column" : "id_visit", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_visit_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_visit_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "visit", - "occurrenceEntity" : "visit_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/expanded/sdd.json b/service/src/main/resources/config/vumc/sdd/expanded/sdd.json deleted file mode 100644 index 0da49fc36..000000000 --- a/service/src/main/resources/config/vumc/sdd/expanded/sdd.json +++ /dev/null @@ -1,29 +0,0 @@ -{ - "name" : "sdd", - "dataPointers" : [ { - "type" : "BQ_DATASET", - "name" : "index_dataset", - "projectId" : "victr-tanagra-test", - "datasetId" : "sdstatic_index", - "queryProjectId" : "victr-tanagra-test", - "dataflowServiceAccountEmail" : "tanagra-indexing-runner@victr-tanagra-test.iam.gserviceaccount.com", - "dataflowTempLocation" : "gs://dataflow-indexing-victr-tanagra-test/temp/", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : true - }, { - "type" : "BQ_DATASET", - "name" : "omop_dataset", - "projectId" : "victr-tanagra-test", - "datasetId" : "sd_static", - "queryProjectId" : "victr-tanagra-test", - "dataflowRegion" : "us-central1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : true - } ], - "entities" : [ "measurement_occurrence.json", "note.json", "condition_occurrence.json", "ingredient.json", "device_occurrence.json", "observation.json", "genotyping.json", "procedure.json", "measurement.json", "ingredient_occurrence.json", "condition.json", "snp.json", "person.json", "visit_occurrence.json", "observation_occurrence.json", "procedure_occurrence.json", "visit.json", "brand.json", "device.json", "note_occurrence.json" ], - "entityGroups" : [ "device_person_occurrence.json", "genotyping_person.json", "visit_person_occurrence.json", "condition_person_occurrence.json", "snp_person.json", "note_person_occurrence.json", "ingredient_person_occurrence.json", "observation_person_occurrence.json", "brand_ingredient.json", "measurement_person_occurrence.json", "procedure_person_occurrence.json" ], - "primaryEntity" : "person", - "uiConfig" : "{ \"dataConfig\": { \"primaryEntity\": { \"displayName\": \"Person\", \"entity\": \"person\", \"key\": \"id\", \"classifications\": [ { \"id\": \"snp\", \"attribute\": \"id\", \"entity\": \"snp\", \"entityAttribute\": \"id\", \"defaultSort\": { \"attribute\": \"id\", \"direction\": \"ASC\" } }, { \"id\": \"genotyping\", \"attribute\": \"id\", \"entity\": \"genotyping\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"name\", \"direction\": \"ASC\" } } ] }, \"occurrences\": [ { \"id\": \"condition_occurrence\", \"displayName\": \"Condition Occurrences\", \"entity\": \"condition_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"condition\", \"attribute\": \"condition\", \"entity\": \"condition\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"procedure_occurrence\", \"displayName\": \"Procedure Occurrences\", \"entity\": \"procedure_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"procedure\", \"attribute\": \"procedure\", \"entity\": \"procedure\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"observation_occurrence\", \"displayName\": \"Observation Occurrence\", \"entity\": \"observation_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"observation\", \"attribute\": \"observation\", \"entity\": \"observation\", \"entityAttribute\": \"id\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"ingredient_occurrence\", \"displayName\": \"Drug Occurrence\", \"entity\": \"ingredient_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"ingredient\", \"attribute\": \"id\", \"entity\": \"ingredient\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" }, \"groupings\": [ { \"id\": \"brand\", \"entity\": \"brand\", \"defaultSort\": { \"attribute\": \"name\", \"direction\": \"ASC\" }, \"attributes\": [\"name\", \"id\", \"standard_concept\", \"concept_code\"] } ] } ] }, { \"id\": \"note_occurrence\", \"displayName\": \"Documents\", \"entity\": \"note_occurrence\", \"key\": \"id\" }, { \"id\": \"measurement_occurrence\", \"displayName\": \"Measurement Occurrence\", \"entity\": \"measurement_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"measurement\", \"attribute\": \"measurement\", \"entity\": \"measurement\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_item_count\", \"direction\": \"DESC\" } } ] } ] }, \"criteriaConfigs\": [ { \"type\": \"classification\", \"id\": \"tanagra-conditions\", \"title\": \"Condition\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Condition\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"condition_occurrence\", \"classification\": \"condition\", \"modifiers\": [ \"age_at_occurrence\", \"visit_type\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-procedures\", \"title\": \"Procedure\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Procedure\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"procedure_occurrence\", \"classification\": \"procedure\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"] }, { \"type\": \"classification\", \"id\": \"tanagra-observations\", \"title\": \"Observation\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"observation_occurrence\", \"classification\": \"observation\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"] }, { \"type\": \"classification\", \"id\": \"tanagra-drugs\", \"title\": \"Drug\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Drug\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"ingredient_occurrence\", \"classification\": \"ingredient\", \"modifiers\": [ \"age_at_occurrence\", \"visit_type\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-genotyping\", \"title\": \"Genotyping platform\", \"category\": \"Demographics\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Genotyping platform\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Genotyping platform\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Id\" } ], \"occurrence\": \"\", \"classification\": \"genotyping\" }, { \"type\": \"classification\", \"id\": \"tanagra-measurement\", \"title\": \"Labs and measurements\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_item_count\", \"width\": 120, \"title\": \"Count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Condition\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"measurement_occurrence\", \"classification\": \"measurement\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"], \"valueConfigs\": [ { \"title\": \"Categorical value\", \"attribute\": \"value_enum\" }, { \"title\": \"Numeric value\", \"attribute\": \"value_numeric\" } ] }, { \"type\": \"attribute\", \"id\": \"tanagra-ethnicity\", \"title\": \"Ethnicity\", \"category\": \"Demographics\", \"attribute\": \"ethnicity\" }, { \"type\": \"attribute\", \"id\": \"tanagra-gender\", \"title\": \"Gender identity\", \"category\": \"Demographics\", \"attribute\": \"gender\" }, { \"type\": \"attribute\", \"id\": \"tanagra-race\", \"title\": \"Race\", \"category\": \"Demographics\", \"attribute\": \"race\" }, { \"type\": \"attribute\", \"id\": \"tanagra-age\", \"title\": \"Age\", \"category\": \"Demographics\", \"attribute\": \"age\" }, { \"type\": \"search\", \"id\": \"tanagra-documents\", \"title\": \"Documents\", \"conceptSet\": true, \"category\": \"Domains\", \"occurrenceId\": \"note_occurrence\", \"searchAttribute\": \"title\", \"categoryAttribute\": \"note\", \"modifiers\": [ \"age_at_occurrence\", \"visit_type\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-snp\", \"title\": \"SNP variant\", \"category\": \"Demographics\", \"columns\": [{ \"key\": \"id\", \"width\": \"100%\", \"title\": \"SNP variant\" }], \"occurrence\": \"\", \"classification\": \"snp\" }, { \"type\": \"biovu\", \"id\": \"biovu\", \"title\": \"BioVU Samples\", \"category\": \"BioVU\" } ], \"modifierConfigs\": [ { \"type\": \"unhinted-value\", \"id\": \"start_date_group_by_count\", \"title\": \"Occurrence count\", \"attribute\": \"start_date\", \"groupByCount\": true }, { \"type\": \"unhinted-value\", \"id\": \"date_group_by_count\", \"title\": \"Occurrence count\", \"attribute\": \"date\", \"groupByCount\": true }, { \"type\": \"attribute\", \"id\": \"visit_type\", \"title\": \"Visit type\", \"attribute\": \"visit_type\" }, { \"type\": \"attribute\", \"id\": \"age_at_occurrence\", \"title\": \"Age at occurrence\", \"attribute\": \"age_at_occurrence\" } ], \"demographicChartConfigs\": { \"groupByAttributes\": [\"gender\", \"race\", \"age\"], \"chartConfigs\": [ { \"title\": \"Gender identity\", \"primaryProperties\": [{ \"key\": \"gender\" }] }, { \"title\": \"Gender identity, Current age, Race\", \"primaryProperties\": [ { \"key\": \"gender\" }, { \"key\": \"age\", \"buckets\": [ { \"min\": 18, \"max\": 45, \"displayName\": \"18-44\" }, { \"min\": 45, \"max\": 65, \"displayName\": \"45-64\" }, { \"min\": 65, \"displayName\": \"65+\" } ] } ], \"stackedProperty\": { \"key\": \"race\" } } ] }, \"prepackagedConceptSets\": [ { \"id\": \"_demographics\", \"name\": \"Demographics\", \"occurrence\": \"\" }, { \"id\": \"_analgesics\", \"name\": \"Analgesics\", \"occurrence\": \"ingredient_occurrence\", \"filter\": { \"type\": \"CLASSIFICATION\", \"occurrenceId\": \"ingredient_occurrence\", \"classificationId\": \"ingredient\", \"keys\": [21604253] } } ], \"criteriaSearchConfig\": { \"criteriaTypeWidth\": 120, \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept Name\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up Count\" } ] }, \"cohortReviewConfig\": { \"participantsListColumns\": [ { \"key\": \"id\", \"width\": 100, \"title\": \"Id\" }, { \"key\": \"gender\", \"width\": 100, \"title\": \"Gender\" }, { \"key\": \"race\", \"width\": 100, \"title\": \"Race\" }, { \"key\": \"ethnicity\", \"width\": 100, \"title\": \"Ethnicity\" }, { \"key\": \"age\", \"width\": 60, \"title\": \"Year of Birth\" } ], \"attributes\": [ { \"title\": \"Gender\", \"key\": \"gender\" }, { \"title\": \"Age\", \"key\": \"age\" }, { \"title\": \"Race\", \"key\": \"race\" }, { \"title\": \"Ethnicity\", \"key\": \"ethnicity\" } ], \"pages\": [ { \"type\": \"occurrenceTable\", \"id\": \"condition\", \"title\": \"Conditions\", \"plugin\": { \"occurrence\": \"condition_occurrence\", \"columns\": [ { \"key\": \"condition\", \"width\": \"100%\", \"title\": \"Condition name\", \"sortable\": true }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\", \"sortable\": true }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"procedure\", \"title\": \"Procedures\", \"plugin\": { \"occurrence\": \"procedure_occurrence\", \"columns\": [ { \"key\": \"procedure\", \"width\": \"100%\", \"title\": \"Procedure name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"observation\", \"title\": \"Observations\", \"plugin\": { \"occurrence\": \"observation_occurrence\", \"columns\": [ { \"key\": \"observation\", \"width\": \"100%\", \"title\": \"Observation name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"ingredient\", \"title\": \"Drugs\", \"plugin\": { \"occurrence\": \"ingredient_occurrence\", \"columns\": [ { \"key\": \"ingredient\", \"width\": \"100%\", \"title\": \"Drug name\", \"sortable\": true }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\", \"sortable\": true }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"measurements\", \"title\": \"Labs and measurements\", \"plugin\": { \"occurrence\": \"measurement_occurrence\", \"columns\": [ { \"key\": \"measurement\", \"width\": \"100%\", \"title\": \"Lab/measurement name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true }, { \"key\": \"value_enum\", \"width\": 160, \"title\": \"Categorical value\", \"sortable\": true }, { \"key\": \"value_numeric\", \"width\": 160, \"title\": \"Numeric value\", \"sortable\": true }, { \"key\": \"unit\", \"width\": 160, \"title\": \"Unit\", \"sortable\": true } ] } }, { \"type\": \"textSearch\", \"id\": \"notes\", \"title\": \"Documents\", \"plugin\": { \"occurrence\": \"note_occurrence\", \"title\": \"title\", \"subtitles\": [\"note\", \"date\"], \"text\": \"text\", \"categoryAttribute\": \"note\", \"sortOrder\": { \"attribute\": \"date\", \"direction\": \"ASC\" } } } ] } } ", - "metadata" : { } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/brand.json b/service/src/main/resources/config/vumc/sdd/original/entity/brand.json deleted file mode 100644 index 0403f94a4..000000000 --- a/service/src/main/resources/config/vumc/sdd/original/entity/brand.json +++ /dev/null @@ -1,29 +0,0 @@ -{ - "name": "brand", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "rawSqlFile": "brand_all.sql" - }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "brand_textSearch.sql" } } } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/condition.json b/service/src/main/resources/config/vumc/sdd/original/entity/condition.json deleted file mode 100644 index 8d7f876d9..000000000 --- a/service/src/main/resources/config/vumc/sdd/original/entity/condition.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "name": "condition", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "table": "concept", - "filter": { - "type": "BINARY", - "field": { "column": "domain_id" }, - "operator": "EQUALS", - "value": { "stringVal": "Condition" } } }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } }, - "vocabulary": { "value": { "column": "vocabulary_id" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "condition_textSearch.sql" } } }, - "hierarchyMappings": { - "standard": { - "childParent": { - "tablePointer": { "rawSqlFile": "condition_parentChild.sql" } - }, - "rootNodesFilter": { - "tablePointer": { - "table": "concept", - "filter": { "type": "BINARY", "field": { "column": "concept_id" }, "operator": "EQUALS", "value": { "int64Val": 441840 } } }, - "fieldPointers": { - "id": { "column": "concept_id" } - } - }, - "maxHierarchyDepth": 20 - } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/condition_occurrence.json b/service/src/main/resources/config/vumc/sdd/original/entity/condition_occurrence.json deleted file mode 100644 index 5734966fc..000000000 --- a/service/src/main/resources/config/vumc/sdd/original/entity/condition_occurrence.json +++ /dev/null @@ -1,42 +0,0 @@ -{ - "name": "condition_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "condition", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "condition_occurrence_all.sql" }, - "attributeMappings": { - "condition": { - "value": { "column": "condition_concept_id" }, - "display": { - "column": "condition_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/device.json b/service/src/main/resources/config/vumc/sdd/original/entity/device.json deleted file mode 100644 index 2e72d8d62..000000000 --- a/service/src/main/resources/config/vumc/sdd/original/entity/device.json +++ /dev/null @@ -1,43 +0,0 @@ -{ - "name": "device", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "table": "concept", - "filter": { - "type": "BOOLEAN_AND_OR", - "operator": "AND", - "subfilters": [ - { "type": "BINARY", - "field": { "column": "domain_id" }, - "operator": "EQUALS", - "value": { "stringVal": "Device" } }, - { "type": "BINARY", - "field": { "column": "standard_concept" }, - "operator": "EQUALS", - "value": { "stringVal": "S" } } - ] } }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } }, - "vocabulary": { "value": { "column": "vocabulary_id" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "device_textSearch.sql" } } } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/device_occurrence.json b/service/src/main/resources/config/vumc/sdd/original/entity/device_occurrence.json deleted file mode 100644 index ffcfbb5fc..000000000 --- a/service/src/main/resources/config/vumc/sdd/original/entity/device_occurrence.json +++ /dev/null @@ -1,41 +0,0 @@ -{ - "name": "device_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "device", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "device_occurrence_all.sql" }, - "attributeMappings": { - "device": { - "value": { "column": "device_concept_id" }, - "display": { - "column": "device_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/ingredient.json b/service/src/main/resources/config/vumc/sdd/original/entity/ingredient.json deleted file mode 100644 index 0e7901ee5..000000000 --- a/service/src/main/resources/config/vumc/sdd/original/entity/ingredient.json +++ /dev/null @@ -1,58 +0,0 @@ -{ - "name": "ingredient", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "ingredient_all.sql" }, - "attributeMappings": { - "vocabulary": { "value": { "column": "vocabulary_id" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "ingredient_textSearch.sql" } } }, - "hierarchyMappings": { - "standard": { - "childParent": { - "tablePointer": { "rawSqlFile": "ingredient_parentChild.sql" } - }, - "rootNodesFilter": { - "tablePointer": { - "table": "concept", - "filter": { - "type": "BOOLEAN_AND_OR", - "operator": "AND", - "subfilters": [ - { "type": "BINARY", - "field": { "column": "vocabulary_id" }, - "operator": "EQUALS", - "value": { "stringVal": "ATC" } }, - { "type": "BINARY", - "field": { "column": "concept_class_id" }, - "operator": "EQUALS", - "value": { "stringVal": "ATC 1st" } }, - { "type": "BINARY", - "field": { "column": "standard_concept" }, - "operator": "EQUALS", - "value": { "stringVal": "C" } } ] } }, - "fieldPointers": { - "id": { "column": "concept_id" } - } - }, - "maxHierarchyDepth": 15 - } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/ingredient_occurrence.json b/service/src/main/resources/config/vumc/sdd/original/entity/ingredient_occurrence.json deleted file mode 100644 index 6e4263d3a..000000000 --- a/service/src/main/resources/config/vumc/sdd/original/entity/ingredient_occurrence.json +++ /dev/null @@ -1,44 +0,0 @@ -{ - "name": "ingredient_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "ingredient", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "refills" }, - { "type": "SIMPLE", "name": "days_supply" }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "ingredient_occurrence_all.sql" }, - "attributeMappings": { - "ingredient": { - "value": { "column": "drug_concept_id" }, - "display": { - "column": "drug_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/note_occurrence.json b/service/src/main/resources/config/vumc/sdd/original/entity/note_occurrence.json deleted file mode 100644 index 4ea519ebd..000000000 --- a/service/src/main/resources/config/vumc/sdd/original/entity/note_occurrence.json +++ /dev/null @@ -1,42 +0,0 @@ -{ - "name": "note_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "note" }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "title", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "text", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "note_occurrence_all.sql" }, - "attributeMappings": { - "date": { "value": { "column": "note_date" } }, - "note": { - "value": { "column": "note_type_concept_id" }, - "display": { - "column": "note_type_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/observation.json b/service/src/main/resources/config/vumc/sdd/original/entity/observation.json deleted file mode 100644 index 668afebce..000000000 --- a/service/src/main/resources/config/vumc/sdd/original/entity/observation.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "name": "observation", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "table": "concept", - "filter": { - "type": "BOOLEAN_AND_OR", - "operator": "AND", - "subfilters": [ - { "type": "BINARY", - "field": { "column": "domain_id" }, - "operator": "EQUALS", - "value": { "stringVal": "Observation" } }, - { "type": "BINARY", - "field": { "column": "standard_concept" }, - "operator": "EQUALS", - "value": { "stringVal": "S" } }, - { "type": "BINARY", - "field": { "column": "vocabulary_id" }, - "operator": "NOT_EQUALS", - "value": { "stringVal": "PPI" } }, - { "type": "BINARY", - "field": { "column": "concept_class_id" }, - "operator": "NOT_EQUALS", - "value": { "stringVal": "Survey" } } - ] } }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } }, - "vocabulary": { "value": { "column": "vocabulary_id" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "observation_textSearch.sql" } } } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/procedure.json b/service/src/main/resources/config/vumc/sdd/original/entity/procedure.json deleted file mode 100644 index 5b26c710e..000000000 --- a/service/src/main/resources/config/vumc/sdd/original/entity/procedure.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "name": "procedure", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "table": "concept", - "filter": { - "type": "BINARY", - "field": { "column": "domain_id" }, - "operator": "EQUALS", - "value": { "stringVal": "Procedure" } } }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } }, - "vocabulary": { "value": { "column": "vocabulary_id" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "procedure_textSearch.sql" } } }, - "hierarchyMappings": { - "standard": { - "childParent": { - "tablePointer": { "rawSqlFile": "procedure_parentChild.sql" } - }, - "rootNodesFilter": { - "tablePointer": { - "table": "concept", - "filter": { "type": "BINARY", "field": { "column": "concept_id" }, "operator": "EQUALS", "value": { "int64Val": 4322976 } } }, - "fieldPointers": { - "id": { "column": "concept_id" } - } - }, - "maxHierarchyDepth": 19 - } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/visit.json b/service/src/main/resources/config/vumc/sdd/original/entity/visit.json deleted file mode 100644 index 0b9a91bde..000000000 --- a/service/src/main/resources/config/vumc/sdd/original/entity/visit.json +++ /dev/null @@ -1,33 +0,0 @@ -{ - "name": "visit", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "table": "concept", - "filter": { - "type": "BOOLEAN_AND_OR", - "operator": "AND", - "subfilters": [ - { "type": "BINARY", - "field": { "column": "domain_id" }, - "operator": "EQUALS", - "value": { "stringVal": "Visit" } }, - { "type": "BINARY", - "field": { "column": "standard_concept" }, - "operator": "EQUALS", - "value": { "stringVal": "S" } } ] } }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "visit_textSearch.sql" } } } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/visit_occurrence.json b/service/src/main/resources/config/vumc/sdd/original/entity/visit_occurrence.json deleted file mode 100644 index cff5a1628..000000000 --- a/service/src/main/resources/config/vumc/sdd/original/entity/visit_occurrence.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "name": "visit_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit" }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "visit_occurrence_all.sql" }, - "attributeMappings": { - "visit": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd/original/sdd.json b/service/src/main/resources/config/vumc/sdd/sdd.json similarity index 97% rename from service/src/main/resources/config/vumc/sdd/original/sdd.json rename to service/src/main/resources/config/vumc/sdd/sdd.json index 6f583c704..40345a9e4 100644 --- a/service/src/main/resources/config/vumc/sdd/original/sdd.json +++ b/service/src/main/resources/config/vumc/sdd/sdd.json @@ -32,7 +32,6 @@ "person.json", "procedure.json", "procedure_occurrence.json", - "snp.json", "visit.json", "visit_occurrence.json" ], "primaryEntity": "person", @@ -46,7 +45,6 @@ "note_person_occurrence.json", "observation_person_occurrence.json", "procedure_person_occurrence.json", - "snp_person.json", "visit_person_occurrence.json" ], "uiConfigFile": "top_level.json" diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/brand_all.sql b/service/src/main/resources/config/vumc/sdd/sql/brand_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/brand_all.sql rename to service/src/main/resources/config/vumc/sdd/sql/brand_all.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/brand_ingredients.sql b/service/src/main/resources/config/vumc/sdd/sql/brand_ingredients.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/brand_ingredients.sql rename to service/src/main/resources/config/vumc/sdd/sql/brand_ingredients.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/brand_textSearch.sql b/service/src/main/resources/config/vumc/sdd/sql/brand_textSearch.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/brand_textSearch.sql rename to service/src/main/resources/config/vumc/sdd/sql/brand_textSearch.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/condition_occurrence_all.sql b/service/src/main/resources/config/vumc/sdd/sql/condition_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/condition_occurrence_all.sql rename to service/src/main/resources/config/vumc/sdd/sql/condition_occurrence_all.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/condition_parentChild.sql b/service/src/main/resources/config/vumc/sdd/sql/condition_parentChild.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/condition_parentChild.sql rename to service/src/main/resources/config/vumc/sdd/sql/condition_parentChild.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/condition_textSearch.sql b/service/src/main/resources/config/vumc/sdd/sql/condition_textSearch.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/condition_textSearch.sql rename to service/src/main/resources/config/vumc/sdd/sql/condition_textSearch.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/device_occurrence_all.sql b/service/src/main/resources/config/vumc/sdd/sql/device_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/device_occurrence_all.sql rename to service/src/main/resources/config/vumc/sdd/sql/device_occurrence_all.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/device_textSearch.sql b/service/src/main/resources/config/vumc/sdd/sql/device_textSearch.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/device_textSearch.sql rename to service/src/main/resources/config/vumc/sdd/sql/device_textSearch.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/genotype_result.sql b/service/src/main/resources/config/vumc/sdd/sql/genotype_result.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/genotype_result.sql rename to service/src/main/resources/config/vumc/sdd/sql/genotype_result.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/genotyping_parentChild.sql b/service/src/main/resources/config/vumc/sdd/sql/genotyping_parentChild.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/genotyping_parentChild.sql rename to service/src/main/resources/config/vumc/sdd/sql/genotyping_parentChild.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/genotyping_rootNodesFilter.sql b/service/src/main/resources/config/vumc/sdd/sql/genotyping_rootNodesFilter.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/genotyping_rootNodesFilter.sql rename to service/src/main/resources/config/vumc/sdd/sql/genotyping_rootNodesFilter.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/ingredient_all.sql b/service/src/main/resources/config/vumc/sdd/sql/ingredient_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/ingredient_all.sql rename to service/src/main/resources/config/vumc/sdd/sql/ingredient_all.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/ingredient_occurrence_all.sql b/service/src/main/resources/config/vumc/sdd/sql/ingredient_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/ingredient_occurrence_all.sql rename to service/src/main/resources/config/vumc/sdd/sql/ingredient_occurrence_all.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/ingredient_parentChild.sql b/service/src/main/resources/config/vumc/sdd/sql/ingredient_parentChild.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/ingredient_parentChild.sql rename to service/src/main/resources/config/vumc/sdd/sql/ingredient_parentChild.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/ingredient_textSearch.sql b/service/src/main/resources/config/vumc/sdd/sql/ingredient_textSearch.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/ingredient_textSearch.sql rename to service/src/main/resources/config/vumc/sdd/sql/ingredient_textSearch.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/measurement_occurrence_all.sql b/service/src/main/resources/config/vumc/sdd/sql/measurement_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/measurement_occurrence_all.sql rename to service/src/main/resources/config/vumc/sdd/sql/measurement_occurrence_all.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/measurement_parentChild.sql b/service/src/main/resources/config/vumc/sdd/sql/measurement_parentChild.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/measurement_parentChild.sql rename to service/src/main/resources/config/vumc/sdd/sql/measurement_parentChild.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/measurement_textSearch.sql b/service/src/main/resources/config/vumc/sdd/sql/measurement_textSearch.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/measurement_textSearch.sql rename to service/src/main/resources/config/vumc/sdd/sql/measurement_textSearch.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/note_occurrence_all.sql b/service/src/main/resources/config/vumc/sdd/sql/note_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/note_occurrence_all.sql rename to service/src/main/resources/config/vumc/sdd/sql/note_occurrence_all.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/note_textSearch.sql b/service/src/main/resources/config/vumc/sdd/sql/note_textSearch.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/note_textSearch.sql rename to service/src/main/resources/config/vumc/sdd/sql/note_textSearch.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/observation_occurrence_all.sql b/service/src/main/resources/config/vumc/sdd/sql/observation_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/observation_occurrence_all.sql rename to service/src/main/resources/config/vumc/sdd/sql/observation_occurrence_all.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/observation_textSearch.sql b/service/src/main/resources/config/vumc/sdd/sql/observation_textSearch.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/observation_textSearch.sql rename to service/src/main/resources/config/vumc/sdd/sql/observation_textSearch.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/person.sql b/service/src/main/resources/config/vumc/sdd/sql/person.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/person.sql rename to service/src/main/resources/config/vumc/sdd/sql/person.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/platform.sql b/service/src/main/resources/config/vumc/sdd/sql/platform.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/platform.sql rename to service/src/main/resources/config/vumc/sdd/sql/platform.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/procedure_occurrence_all.sql b/service/src/main/resources/config/vumc/sdd/sql/procedure_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/procedure_occurrence_all.sql rename to service/src/main/resources/config/vumc/sdd/sql/procedure_occurrence_all.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/procedure_parentChild.sql b/service/src/main/resources/config/vumc/sdd/sql/procedure_parentChild.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/procedure_parentChild.sql rename to service/src/main/resources/config/vumc/sdd/sql/procedure_parentChild.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/procedure_textSearch.sql b/service/src/main/resources/config/vumc/sdd/sql/procedure_textSearch.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/procedure_textSearch.sql rename to service/src/main/resources/config/vumc/sdd/sql/procedure_textSearch.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/visit_occurrence_all.sql b/service/src/main/resources/config/vumc/sdd/sql/visit_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/visit_occurrence_all.sql rename to service/src/main/resources/config/vumc/sdd/sql/visit_occurrence_all.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/visit_textSearch.sql b/service/src/main/resources/config/vumc/sdd/sql/visit_textSearch.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/visit_textSearch.sql rename to service/src/main/resources/config/vumc/sdd/sql/visit_textSearch.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/sql/x_snp.sql b/service/src/main/resources/config/vumc/sdd/sql/x_snp.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd/original/sql/x_snp.sql rename to service/src/main/resources/config/vumc/sdd/sql/x_snp.sql diff --git a/service/src/main/resources/config/vumc/sdd/original/ui/top_level.json b/service/src/main/resources/config/vumc/sdd/ui/top_level.json similarity index 98% rename from service/src/main/resources/config/vumc/sdd/original/ui/top_level.json rename to service/src/main/resources/config/vumc/sdd/ui/top_level.json index 9d9ffe627..b99f202df 100644 --- a/service/src/main/resources/config/vumc/sdd/original/ui/top_level.json +++ b/service/src/main/resources/config/vumc/sdd/ui/top_level.json @@ -5,16 +5,6 @@ "entity": "person", "key": "id", "classifications": [ - { - "id": "snp", - "attribute": "id", - "entity": "snp", - "entityAttribute": "id", - "defaultSort": { - "attribute": "id", - "direction": "ASC" - } - }, { "id": "genotyping", "attribute": "id", diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/entity/brand.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/brand.json new file mode 100644 index 000000000..b91b1f66a --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/brand.json @@ -0,0 +1,29 @@ +{ + "name": "brand", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "rawSqlFile": "brand_all.sql" + }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "brand_textSearch.sql" } } } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/entity/condition.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/condition.json new file mode 100644 index 000000000..e8701cc41 --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/condition.json @@ -0,0 +1,51 @@ +{ + "name": "condition", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "table": "concept", + "filter": { + "type": "BINARY", + "field": { "column": "domain_id" }, + "operator": "EQUALS", + "value": { "stringVal": "Condition" } } }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } }, + "vocabulary": { "value": { "column": "vocabulary_id" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "condition_textSearch.sql" } } }, + "hierarchyMappings": { + "standard": { + "childParent": { + "tablePointer": { "rawSqlFile": "condition_parentChild.sql" } + }, + "rootNodesFilter": { + "tablePointer": { + "table": "concept", + "filter": { "type": "BINARY", "field": { "column": "concept_id" }, "operator": "EQUALS", "value": { "int64Val": 441840 } } }, + "fieldPointers": { + "id": { "column": "concept_id" } + } + }, + "maxHierarchyDepth": 20 + } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/entity/condition_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/condition_occurrence.json new file mode 100644 index 000000000..4d9166cbf --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/condition_occurrence.json @@ -0,0 +1,42 @@ +{ + "name": "condition_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "condition", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "condition_occurrence_all.sql" }, + "attributeMappings": { + "condition": { + "value": { "column": "condition_concept_id" }, + "display": { + "column": "condition_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/entity/device.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/device.json new file mode 100644 index 000000000..078cd332c --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/device.json @@ -0,0 +1,43 @@ +{ + "name": "device", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "table": "concept", + "filter": { + "type": "BOOLEAN_AND_OR", + "operator": "AND", + "subfilters": [ + { "type": "BINARY", + "field": { "column": "domain_id" }, + "operator": "EQUALS", + "value": { "stringVal": "Device" } }, + { "type": "BINARY", + "field": { "column": "standard_concept" }, + "operator": "EQUALS", + "value": { "stringVal": "S" } } + ] } }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } }, + "vocabulary": { "value": { "column": "vocabulary_id" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "device_textSearch.sql" } } } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/entity/device_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/device_occurrence.json new file mode 100644 index 000000000..5691bd575 --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/device_occurrence.json @@ -0,0 +1,41 @@ +{ + "name": "device_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "device", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "device_occurrence_all.sql" }, + "attributeMappings": { + "device": { + "value": { "column": "device_concept_id" }, + "display": { + "column": "device_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/genotyping.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/genotyping.json similarity index 83% rename from service/src/main/resources/config/verily/sdd_refresh0323/original/entity/genotyping.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entity/genotyping.json index e8fa76c2d..9c2739273 100644 --- a/service/src/main/resources/config/verily/sdd_refresh0323/original/entity/genotyping.json +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/genotyping.json @@ -2,8 +2,8 @@ "name": "genotyping", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/entity/ingredient.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/ingredient.json new file mode 100644 index 000000000..59a4ddcc0 --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/ingredient.json @@ -0,0 +1,58 @@ +{ + "name": "ingredient", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "ingredient_all.sql" }, + "attributeMappings": { + "vocabulary": { "value": { "column": "vocabulary_id" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "ingredient_textSearch.sql" } } }, + "hierarchyMappings": { + "standard": { + "childParent": { + "tablePointer": { "rawSqlFile": "ingredient_parentChild.sql" } + }, + "rootNodesFilter": { + "tablePointer": { + "table": "concept", + "filter": { + "type": "BOOLEAN_AND_OR", + "operator": "AND", + "subfilters": [ + { "type": "BINARY", + "field": { "column": "vocabulary_id" }, + "operator": "EQUALS", + "value": { "stringVal": "ATC" } }, + { "type": "BINARY", + "field": { "column": "concept_class_id" }, + "operator": "EQUALS", + "value": { "stringVal": "ATC 1st" } }, + { "type": "BINARY", + "field": { "column": "standard_concept" }, + "operator": "EQUALS", + "value": { "stringVal": "C" } } ] } }, + "fieldPointers": { + "id": { "column": "concept_id" } + } + }, + "maxHierarchyDepth": 15 + } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/entity/ingredient_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/ingredient_occurrence.json new file mode 100644 index 000000000..27470b70b --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/ingredient_occurrence.json @@ -0,0 +1,44 @@ +{ + "name": "ingredient_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "ingredient", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "start_date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "stop_reason", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "refills", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "days_supply", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "ingredient_occurrence_all.sql" }, + "attributeMappings": { + "ingredient": { + "value": { "column": "drug_concept_id" }, + "display": { + "column": "drug_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/entity/measurement.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/measurement.json new file mode 100644 index 000000000..f71f480d4 --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/measurement.json @@ -0,0 +1,109 @@ +{ + "name": "measurement", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "table": "concept", + "filter": { + "type": "BOOLEAN_AND_OR", + "operator": "OR", + "subfilters": [ + { "type": "BOOLEAN_AND_OR", + "operator": "AND", + "subfilters": [ + { "type": "BINARY", + "field": { "column": "domain_id" }, + "operator": "EQUALS", + "value": { "stringVal": "Measurement" } }, + { "type": "BINARY", + "field": { "column": "vocabulary_id" }, + "operator": "EQUALS", + "value": { "stringVal": "SNOMED" } } ] }, + { "type": "BOOLEAN_AND_OR", + "operator": "AND", + "subfilters": [ + { "type": "BINARY", + "field": { "column": "vocabulary_id" }, + "operator": "EQUALS", + "value": { "stringVal": "LOINC" } }, + { "type": "BOOLEAN_AND_OR", + "operator": "OR", + "subfilters": [ + { "type": "BINARY", + "field": { "column": "concept_class_id" }, + "operator": "EQUALS", + "value": { "stringVal": "LOINC Hierarchy" } }, + { "type": "BINARY", + "field": { "column": "concept_class_id" }, + "operator": "EQUALS", + "value": { "stringVal": "LOINC Component" } }, + { "type": "BINARY", + "field": { "column": "concept_class_id" }, + "operator": "EQUALS", + "value": { "stringVal": "Lab Test" } } + ] } ] } ] } }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } }, + "vocabulary": { "value": { "column": "vocabulary_id" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "measurement_textSearch.sql" } } }, + "hierarchyMappings": { + "standard": { + "childParent": { + "tablePointer": { "rawSqlFile": "measurement_parentChild.sql" } + }, + "rootNodesFilter": { + "tablePointer": { + "table": "concept", + "filter": { + "type": "BOOLEAN_AND_OR", + "operator": "OR", + "subfilters": [ + { "type": "BOOLEAN_AND_OR", + "operator": "AND", + "subfilters": [ + { "type": "BINARY", + "field": { "column": "domain_id" }, + "operator": "EQUALS", + "value": { "stringVal": "Measurement" } }, + { "type": "BINARY", + "field": { "column": "vocabulary_id" }, + "operator": "EQUALS", + "value": { "stringVal": "SNOMED" } } ] }, + { "type": "BOOLEAN_AND_OR", + "operator": "AND", + "subfilters": [ + { "type": "BINARY", + "field": { "column": "vocabulary_id" }, + "operator": "EQUALS", + "value": { "stringVal": "LOINC" } }, + { "type": "BINARY", + "field": { "column": "concept_id" }, + "operator": "EQUALS", + "value": { "int64Val": 36206173 } } ] } ] } }, + "fieldPointers": { + "id": { "column": "concept_id" } + } + }, + "maxHierarchyDepth": 11 + } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/entity/measurement_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/measurement_occurrence.json new file mode 100644 index 000000000..2fcd3d557 --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/measurement_occurrence.json @@ -0,0 +1,58 @@ +{ + "name": "measurement_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "measurement", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "value_numeric", "dataType": "DOUBLE", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "value_enum", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "measurement_occurrence_all.sql" }, + "attributeMappings": { + "measurement": { + "value": { "column": "measurement_concept_id" }, + "display": { + "column": "measurement_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "date": { "value": { "column": "measurement_date" } }, + "value_enum": { + "value": { "column": "value_as_concept_id" }, + "display": { + "column": "value_as_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "unit": { + "value": { "column": "unit_concept_id" }, + "display": { + "column": "unit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/verily/sdd/original/entity/note.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/note.json similarity index 81% rename from service/src/main/resources/config/verily/sdd/original/entity/note.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entity/note.json index e21370c93..a73afb9de 100644 --- a/service/src/main/resources/config/verily/sdd/original/entity/note.json +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/note.json @@ -2,10 +2,10 @@ "name": "note", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], "sourceDataMapping": { "dataPointer": "omop_dataset", diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/entity/note_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/note_occurrence.json new file mode 100644 index 000000000..06c084e35 --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/note_occurrence.json @@ -0,0 +1,42 @@ +{ + "name": "note_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "note", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "title", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "text", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "note_occurrence_all.sql" }, + "attributeMappings": { + "date": { "value": { "column": "note_date" } }, + "note": { + "value": { "column": "note_type_concept_id" }, + "display": { + "column": "note_type_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/entity/observation.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/observation.json new file mode 100644 index 000000000..92f45b426 --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/observation.json @@ -0,0 +1,51 @@ +{ + "name": "observation", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "table": "concept", + "filter": { + "type": "BOOLEAN_AND_OR", + "operator": "AND", + "subfilters": [ + { "type": "BINARY", + "field": { "column": "domain_id" }, + "operator": "EQUALS", + "value": { "stringVal": "Observation" } }, + { "type": "BINARY", + "field": { "column": "standard_concept" }, + "operator": "EQUALS", + "value": { "stringVal": "S" } }, + { "type": "BINARY", + "field": { "column": "vocabulary_id" }, + "operator": "NOT_EQUALS", + "value": { "stringVal": "PPI" } }, + { "type": "BINARY", + "field": { "column": "concept_class_id" }, + "operator": "NOT_EQUALS", + "value": { "stringVal": "Survey" } } + ] } }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } }, + "vocabulary": { "value": { "column": "vocabulary_id" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "observation_textSearch.sql" } } } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/entity/observation_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/observation_occurrence.json new file mode 100644 index 000000000..da8e8c476 --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/observation_occurrence.json @@ -0,0 +1,58 @@ +{ + "name": "observation_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "observation", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "value_as_string", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "value", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "unit", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "observation_occurrence_all.sql" }, + "attributeMappings": { + "observation": { + "value": { "column": "observation_concept_id" }, + "display": { + "column": "observation_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "date": { "value": { "column": "observation_date" } }, + "value": { + "value": { "column": "value_as_concept_id" }, + "display": { + "column": "value_as_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "unit": { + "value": { "column": "unit_concept_id" }, + "display": { + "column": "unit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/vumc/sdd/original/entity/person.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/person.json similarity index 60% rename from service/src/main/resources/config/vumc/sdd/original/entity/person.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entity/person.json index 06a1770c9..a68df85fb 100644 --- a/service/src/main/resources/config/vumc/sdd/original/entity/person.json +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/person.json @@ -2,17 +2,17 @@ "name": "person", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "year_of_birth" }, - { "type": "SIMPLE", "name": "age" }, - { "type": "KEY_AND_DISPLAY", "name": "gender" }, - { "type": "KEY_AND_DISPLAY", "name": "race" }, - { "type": "KEY_AND_DISPLAY", "name": "ethnicity" }, - { "type": "SIMPLE", "name": "has_biovu_sample" }, - { "type": "SIMPLE", "name": "biovu_sample_dna_yield" }, - { "type": "SIMPLE", "name": "biovu_sample_is_compromised" }, - { "type": "SIMPLE", "name": "biovu_sample_is_nonshippable" }, - { "type": "SIMPLE", "name": "biovu_sample_has_plasma" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "year_of_birth", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "age", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "gender", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "race", "dataType": "INT64" }, + { "type": "KEY_AND_DISPLAY", "name": "ethnicity", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "has_biovu_sample", "dataType": "BOOLEAN" }, + { "type": "SIMPLE", "name": "biovu_sample_dna_yield", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "biovu_sample_is_compromised", "dataType": "BOOLEAN" }, + { "type": "SIMPLE", "name": "biovu_sample_is_nonshippable", "dataType": "BOOLEAN" }, + { "type": "SIMPLE", "name": "biovu_sample_has_plasma", "dataType": "BOOLEAN" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/entity/procedure.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/procedure.json new file mode 100644 index 000000000..b45e3d76c --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/procedure.json @@ -0,0 +1,51 @@ +{ + "name": "procedure", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "vocabulary", "dataType": "STRING" }, + { "type": "KEY_AND_DISPLAY", "name": "standard_concept", "dataType": "STRING" }, + { "type": "SIMPLE", "name": "concept_code", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "table": "concept", + "filter": { + "type": "BINARY", + "field": { "column": "domain_id" }, + "operator": "EQUALS", + "value": { "stringVal": "Procedure" } } }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } }, + "vocabulary": { "value": { "column": "vocabulary_id" } }, + "standard_concept": { + "value": { "column": "standard_concept" }, + "display": { + "column": "standard_concept", + "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "procedure_textSearch.sql" } } }, + "hierarchyMappings": { + "standard": { + "childParent": { + "tablePointer": { "rawSqlFile": "procedure_parentChild.sql" } + }, + "rootNodesFilter": { + "tablePointer": { + "table": "concept", + "filter": { "type": "BINARY", "field": { "column": "concept_id" }, "operator": "EQUALS", "value": { "int64Val": 4322976 } } }, + "fieldPointers": { + "id": { "column": "concept_id" } + } + }, + "maxHierarchyDepth": 19 + } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/entity/procedure_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/procedure_occurrence.json new file mode 100644 index 000000000..fdc4cc913 --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/procedure_occurrence.json @@ -0,0 +1,41 @@ +{ + "name": "procedure_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "procedure", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "visit_occurrence_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit_type", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "procedure_occurrence_all.sql" }, + "attributeMappings": { + "procedure": { + "value": { "column": "procedure_concept_id" }, + "display": { + "column": "procedure_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } }, + "date": { "value": { "column": "procedure_date" } }, + "visit_type": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/snp.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/snp.json similarity index 77% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/snp.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entity/snp.json index 5e9df59ef..86b0d95b0 100644 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/snp.json +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/snp.json @@ -2,8 +2,8 @@ "name": "snp", "idAttribute": "id", "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name" } + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING" } ], "sourceDataMapping": { diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/entity/visit.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/visit.json new file mode 100644 index 000000000..68bcc9d58 --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/visit.json @@ -0,0 +1,33 @@ +{ + "name": "visit", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "name", "dataType": "STRING", "displayHintTypes": ["NONE"] } ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { + "table": "concept", + "filter": { + "type": "BOOLEAN_AND_OR", + "operator": "AND", + "subfilters": [ + { "type": "BINARY", + "field": { "column": "domain_id" }, + "operator": "EQUALS", + "value": { "stringVal": "Visit" } }, + { "type": "BINARY", + "field": { "column": "standard_concept" }, + "operator": "EQUALS", + "value": { "stringVal": "S" } } ] } }, + "attributeMappings": { + "id": { "value": { "column": "concept_id" } }, + "name": { "value": { "column": "concept_name" } } }, + "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "visit_textSearch.sql" } } } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/entity/visit_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/visit_occurrence.json new file mode 100644 index 000000000..4c91db3ae --- /dev/null +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/visit_occurrence.json @@ -0,0 +1,32 @@ +{ + "name": "visit_occurrence", + "idAttribute": "id", + "attributes": [ + { "type": "SIMPLE", "name": "id", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "person_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "KEY_AND_DISPLAY", "name": "visit", "dataType": "INT64" }, + { "type": "SIMPLE", "name": "start_date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "end_date", "dataType": "TIMESTAMP", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_value", "dataType": "STRING", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "source_criteria_id", "dataType": "INT64", "displayHintTypes": ["NONE"] }, + { "type": "SIMPLE", "name": "age_at_occurrence", "dataType": "INT64" } + ], + + "sourceDataMapping": { + "dataPointer": "omop_dataset", + "tablePointer": { "rawSqlFile": "visit_occurrence_all.sql" }, + "attributeMappings": { + "visit": { + "value": { "column": "visit_concept_id" }, + "display": { + "column": "visit_concept_id", + "foreignTable": "concept", + "foreignKey": "concept_id", + "foreignColumn": "concept_name" } } + } + }, + + "indexDataMapping": { + "dataPointer": "index_dataset" + } +} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/brand_ingredient.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/brand_ingredient.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/brand_ingredient.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/brand_ingredient.json diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/condition_person_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/condition_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/condition_person_occurrence.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/condition_person_occurrence.json diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/device_person_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/device_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/device_person_occurrence.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/device_person_occurrence.json diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/genotyping_person.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/genotyping_person.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/genotyping_person.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/genotyping_person.json diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/ingredient_person_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/ingredient_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/ingredient_person_occurrence.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/ingredient_person_occurrence.json diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/measurement_person_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/measurement_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/measurement_person_occurrence.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/measurement_person_occurrence.json diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/note_person_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/note_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/note_person_occurrence.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/note_person_occurrence.json diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/observation_person_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/observation_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/observation_person_occurrence.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/observation_person_occurrence.json diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/procedure_person_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/procedure_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/procedure_person_occurrence.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/procedure_person_occurrence.json diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/snp_person.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/snp_person.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/snp_person.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/snp_person.json diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/visit_person_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/visit_person_occurrence.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entitygroup/visit_person_occurrence.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entitygroup/visit_person_occurrence.json diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/brand.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/brand.json deleted file mode 100644 index aac74b038..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/brand.json +++ /dev/null @@ -1,141 +0,0 @@ -{ - "name" : "brand", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "" - }, - "display" : "Unknown" - }, - "count" : 7 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT * FROM `victr-tanagra-test.sd_20230328.concept` WHERE domain_id = 'Drug' AND concept_class_id = 'Brand Name' AND vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND DATE_DIFF(CAST(valid_end_date AS DATE), CURRENT_DATE(), DAY) > 0" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_20230328.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_20230328.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND c.concept_class_id = 'Brand Name' AND c.vocabulary_id IN ('RxNorm', 'RxNorm Extension')" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "brand" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/condition.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/condition.json deleted file mode 100644 index c119911e7..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/condition.json +++ /dev/null @@ -1,459 +0,0 @@ -{ - "name" : "condition", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 174148 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 384 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CIEL" - }, - "display" : "CIEL" - }, - "count" : 38818 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CIM10" - }, - "display" : "CIM10" - }, - "count" : 10867 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Cohort" - }, - "display" : "Cohort" - }, - "count" : 66 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HemOnc" - }, - "display" : "HemOnc" - }, - "count" : 219 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10" - }, - "display" : "ICD10" - }, - "count" : 15017 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "ICD10CM" - }, - "count" : 90542 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CN" - }, - "display" : "ICD10CN" - }, - "count" : 31794 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10GM" - }, - "display" : "ICD10GM" - }, - "count" : 16006 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "ICD9CM" - }, - "count" : 15760 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICDO3" - }, - "display" : "ICDO3" - }, - "count" : 62410 - }, { - "enumVal" : { - "value" : { - "stringVal" : "KCD7" - }, - "display" : "KCD7" - }, - "count" : 20743 - }, { - "enumVal" : { - "value" : { - "stringVal" : "MeSH" - }, - "display" : "MeSH" - }, - "count" : 6795 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Nebraska Lexicon" - }, - "display" : "Nebraska Lexicon" - }, - "count" : 151336 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OMOP Extension" - }, - "display" : "OMOP Extension" - }, - "count" : 7 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPCS4" - }, - "display" : "OPCS4" - }, - "count" : 6 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OXMIS" - }, - "display" : "OXMIS" - }, - "count" : 5704 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OncoTree" - }, - "display" : "OncoTree" - }, - "count" : 869 - }, { - "enumVal" : { - "value" : { - "stringVal" : "PPI" - }, - "display" : "PPI" - }, - "count" : 74 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Read" - }, - "display" : "Read" - }, - "count" : 47736 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SMQ" - }, - "display" : "SMQ" - }, - "count" : 324 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 180133 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED Veterinary" - }, - "display" : "SNOMED Veterinary" - }, - "count" : 3237 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Condition" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_20230328.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_20230328.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Condition' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `victr-tanagra-test.sd_20230328.concept_relationship` cr JOIN `victr-tanagra-test.sd_20230328.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `victr-tanagra-test.sd_20230328.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Condition' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED'" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 441840 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "condition" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "condition_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "condition_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "condition" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 20 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/condition_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/condition_occurrence.json deleted file mode 100644 index b1009e345..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/condition_occurrence.json +++ /dev/null @@ -1,283 +0,0 @@ -{ - "name" : "condition_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "condition", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -977.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 9117630 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 57159530 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 3963125 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 158270179 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT co.condition_occurrence_id AS id, co.person_id, co.condition_concept_id, co.condition_start_date AS start_date, co.condition_end_date AS end_date, co.stop_reason, co.condition_source_value AS source_value, co.condition_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(co.condition_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, co.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_20230328.condition_occurrence` AS co JOIN `victr-tanagra-test.sd_20230328.person` AS p ON p.person_id = co.person_id LEFT JOIN `victr-tanagra-test.sd_20230328.visit_occurrence` AS vo ON vo.visit_occurrence_id = co.visit_occurrence_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "condition_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "condition_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "condition" : { - "value" : { - "column" : "condition", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_condition", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/device.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/device.json deleted file mode 100644 index 65f7f4871..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/device.json +++ /dev/null @@ -1,285 +0,0 @@ -{ - "name" : "device", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 245402 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "AMT" - }, - "display" : "AMT" - }, - "count" : 2945 - }, { - "enumVal" : { - "value" : { - "stringVal" : "BDPM" - }, - "display" : "BDPM" - }, - "count" : 1106 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "CPT4" - }, - "count" : 24 - }, { - "enumVal" : { - "value" : { - "stringVal" : "GGR" - }, - "display" : "GGR" - }, - "count" : 596 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 4634 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10PCS" - }, - "display" : "ICD10PCS" - }, - "count" : 3 - }, { - "enumVal" : { - "value" : { - "stringVal" : "JMDC" - }, - "display" : "JMDC" - }, - "count" : 1313 - }, { - "enumVal" : { - "value" : { - "stringVal" : "KDC" - }, - "display" : "KDC" - }, - "count" : 112 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NDC" - }, - "display" : "NDC" - }, - "count" : 10963 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPCS4" - }, - "display" : "OPCS4" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 202567 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED Veterinary" - }, - "display" : "SNOMED Veterinary" - }, - "count" : 67 - }, { - "enumVal" : { - "value" : { - "stringVal" : "dm+d" - }, - "display" : "dm+d" - }, - "count" : 21071 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Device" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_20230328.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_20230328.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Device' AND c.standard_concept = 'S'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "device" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/device_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/device_occurrence.json deleted file mode 100644 index 4510cd078..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/device_occurrence.json +++ /dev/null @@ -1,256 +0,0 @@ -{ - "name" : "device_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -4.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 116800 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 935607 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1719 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 2120916 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "device", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT de.device_exposure_id AS id, de.person_id, de.device_concept_id, de.device_exposure_start_date AS start_date, de.device_exposure_end_date AS end_date, de.device_source_value AS source_value, de.device_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(de.device_exposure_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, de.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_20230328.device_exposure` AS de JOIN `victr-tanagra-test.sd_20230328.person` AS p ON p.person_id = de.person_id LEFT JOIN `victr-tanagra-test.sd_20230328.visit_occurrence` AS vo ON vo.visit_occurrence_id = de.visit_occurrence_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "device_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "device_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "device" : { - "value" : { - "column" : "device", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_device", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/genotyping.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/genotyping.json deleted file mode 100644 index 1fc374b02..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/genotyping.json +++ /dev/null @@ -1,149 +0,0 @@ -{ - "name" : "genotyping", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "/* platform_id column has type NUMERIC. This causes index column to be FLOAT. Currently indexing doesn't handle floats properly, so change column to INTEGER. */ SELECT CAST(platform_id as INT64) AS platform_id, assay_name as assay_name FROM `victr-tanagra-test.sd_20230328.platform` UNION ALL /* Add some rows to get hierarchy to work. Parent ids are defined in genotype_criteria, criteria_meta_seq column. criteria_meta_seq is not in the same \"ID space\" as platform_id. Tanagra requres parent id to be in same \"ID space\" as platform_id. So create artificial platform_ids for parents. */ (SELECT 101 AS platform_id, 'GWAS Platforms' AS assay_name UNION ALL SELECT 102, 'Non-GWAS and Targeted Genotyping Platforms' UNION ALL SELECT 103, 'Sequencing Platforms') " - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "assay_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "platform_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "attributes" : [ "id", "name" ] - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT /* Use parent ids defined in platform.sql */ parent_seq + 100 AS parent, CAST(platform_id as INT64) AS child FROM `victr-tanagra-test.sd_20230328.genotype_criteria` g, `victr-tanagra-test.sd_20230328.platform` p WHERE g.name = p.assay_name " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "rawSql" : "/* Match the platform ids in platform.sql */ SELECT 101 AS id UNION ALL SELECT 102 UNION ALL SELECT 103 " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 1 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "genotyping" - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "genotyping_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "genotyping_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "genotyping" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 1 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/ingredient.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/ingredient.json deleted file mode 100644 index 33ca6e8d5..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/ingredient.json +++ /dev/null @@ -1,306 +0,0 @@ -{ - "name" : "ingredient", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 1921307 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 6335 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "ATC" - }, - "display" : "ATC" - }, - "count" : 6335 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm" - }, - "display" : "RxNorm" - }, - "count" : 147265 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RxNorm Extension" - }, - "display" : "RxNorm Extension" - }, - "count" : 1774042 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT c.concept_id AS id, c.concept_name AS name, c.vocabulary_id, c.standard_concept, c.concept_code FROM `victr-tanagra-test.sd_20230328.concept` c WHERE c.domain_id = 'Drug' AND ( (c.vocabulary_id = 'ATC' AND c.standard_concept = 'C') OR (c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.standard_concept = 'S') )" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_20230328.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_20230328.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Drug' AND ((c.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c.concept_class_id = 'Ingredient' AND c.standard_concept = 'S') OR (c.vocabulary_id = 'RxNorm' AND c.concept_class_id = 'Precise Ingredient') OR (c.vocabulary_id = 'ATC' AND c.concept_class_id IN ('ATC 1st', 'ATC 2nd', 'ATC 3rd', 'ATC 4th', 'ATC 5th') AND c.standard_concept = 'C'))" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child FROM `victr-tanagra-test.sd_20230328.concept_relationship` cr JOIN `victr-tanagra-test.sd_20230328.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `victr-tanagra-test.sd_20230328.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE c1.concept_id != c2.concept_id AND c1.domain_id = 'Drug' AND c2.domain_id = 'Drug' AND ( /* Populate Ingredients' ancestors', which are ATCs. See https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:atc#:~:text=the%20original%20ATC%20hierarchy%20is%20extended%20by%20Standard%20Drug%20Products%20of%20RxNorm%20and%20RxNorm%20Extension%20vocabularies%2C%20which%20are%20assigned%20to%20be%20descendants%20of%20the%205th%20ATC%20Classes. Eg: ATC 1st (highest ancestor) Subsumes ATC 2nd ATC 5th (direct parent of RxNorm) Maps to RxNorm */ (c1.vocabulary_id IN ('ATC') AND cr.relationship_id IN ('Subsumes', 'Maps to')) OR /* Populate Ingredients and their descendants: Branded Drug, Clinical Drug, etc. Ingredients and their descendants are RxNorm. drug_exposure contains Ingredients or their descendants. Use [1] and [2] to define hierarchy. Eg \"Marketed Product\" is most specific and is bottom of hierarchy. [1] https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:drug_exposure#:~:text=These%20are%20indicated,is%20available%20%E2%80%9CIngredient%E2%80%9D [2] https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:drug#:~:text=are%20not%20implemented.-,Relationships,-As%20usual%2C%20all */ ( c1.vocabulary_id IN ('RxNorm', 'RxNorm Extension') AND c2.vocabulary_id IN ('RxNorm', 'RxNorm Extension') /* Only keep relationships where c1 is \"parent\" of c2 */ AND cr.relationship_id IN ('Constitutes', 'Contained in' , 'Has form', 'Has quantified form', 'RxNorm ing of', 'RxNorm inverse is a', 'Precise ing of') ) )" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "ATC 1st" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "C" - } - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 15 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "ingredient" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "ingredient_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "ingredient_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "ingredient" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 15 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/ingredient_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/ingredient_occurrence.json deleted file mode 100644 index f20e2a223..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/ingredient_occurrence.json +++ /dev/null @@ -1,543 +0,0 @@ -{ - "name" : "ingredient_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ingredient", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "stop_reason", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : null - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Allergic res" - }, - "display" : "Allergic res" - }, - "count" : 6246 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Alternate tx" - }, - "display" : "Alternate tx" - }, - "count" : 115351 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Anes Stop" - }, - "display" : "Anes Stop" - }, - "count" : 3911532 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Availability" - }, - "display" : "Availability" - }, - "count" : 9361 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CONTACT " - }, - "display" : "CONTACT " - }, - "count" : 858 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Cleanup" - }, - "display" : "Cleanup" - }, - "count" : 892415 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Cost of medi" - }, - "display" : "Cost of medi" - }, - "count" : 12304 - }, { - "enumVal" : { - "value" : { - "stringVal" : "DC'd by othr" - }, - "display" : "DC'd by othr" - }, - "count" : 222665 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Dose adjustm" - }, - "display" : "Dose adjustm" - }, - "count" : 163200 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Drug interac" - }, - "display" : "Drug interac" - }, - "count" : 2748 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Duplicate or" - }, - "display" : "Duplicate or" - }, - "count" : 602987 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Error" - }, - "display" : "Error" - }, - "count" : 319842 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Expired" - }, - "display" : "Expired" - }, - "count" : 165053 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Formulary" - }, - "display" : "Formulary" - }, - "count" : 34057 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NON-ADHEREN" - }, - "display" : "NON-ADHEREN" - }, - "count" : 11216 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Other" - }, - "display" : "Other" - }, - "count" : 240539 - }, { - "enumVal" : { - "value" : { - "stringVal" : "PATIENT DISC" - }, - "display" : "PATIENT DISC" - }, - "count" : 9038687 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Paradoxical" - }, - "display" : "Paradoxical" - }, - "count" : 343 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Pregnancy" - }, - "display" : "Pregnancy" - }, - "count" : 1330 - }, { - "enumVal" : { - "value" : { - "stringVal" : "RETURNED TO " - }, - "display" : "RETURNED TO " - }, - "count" : 23983 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Reorder" - }, - "display" : "Reorder" - }, - "count" : 5801736 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SE" - }, - "display" : "SE" - }, - "count" : 47335 - }, { - "enumVal" : { - "value" : { - "stringVal" : "STOP TAKING " - }, - "display" : "STOP TAKING " - }, - "count" : 547157 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SURGERY" - }, - "display" : "SURGERY" - }, - "count" : 1049 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Stop Med" - }, - "display" : "Stop Med" - }, - "count" : 352498 - }, { - "enumVal" : { - "value" : { - "stringVal" : "TRANSFER" - }, - "display" : "TRANSFER" - }, - "count" : 797968 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Therapy comp" - }, - "display" : "Therapy comp" - }, - "count" : 2998407 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 7158852 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 213493259 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 348634 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 53088542 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "days_supply", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 1.0, - "maxVal" : 36135.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "refills", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 365.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -1000.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT de.drug_exposure_id AS id, de.person_id, de.drug_concept_id, de.drug_exposure_start_date AS start_date, de.drug_exposure_end_date AS end_date, de.stop_reason, de.refills, de.days_supply, de.drug_source_value AS source_value, de.drug_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(de.drug_exposure_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, de.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_20230328.drug_exposure` AS de JOIN `victr-tanagra-test.sd_20230328.person` AS p ON p.person_id = de.person_id LEFT JOIN `victr-tanagra-test.sd_20230328.visit_occurrence` AS vo ON vo.visit_occurrence_id = de.visit_occurrence_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "drug_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "ingredient_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "ingredient" : { - "value" : { - "column" : "ingredient", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ingredient", - "runtimeCalculated" : false - } - }, - "stop_reason" : { - "value" : { - "column" : "stop_reason", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "days_supply" : { - "value" : { - "column" : "days_supply", - "runtimeCalculated" : false - } - }, - "refills" : { - "value" : { - "column" : "refills", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/measurement.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/measurement.json deleted file mode 100644 index 2706a9943..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/measurement.json +++ /dev/null @@ -1,407 +0,0 @@ -{ - "name" : "measurement", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 73948 - }, { - "enumVal" : { - "value" : { - "stringVal" : "" - }, - "display" : "Unknown" - }, - "count" : 9 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 40193 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "LOINC" - }, - "count" : 186150 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 29999 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Measurement" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "SNOMED" - } - } ] - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC" - } - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC Hierarchy" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC Component" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Lab Test" - } - } ] - } ] - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_20230328.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_20230328.concept` c ON c.concept_id = textsearch.id WHERE ((c.domain_id = 'Measurement' AND c.vocabulary_id = 'SNOMED') OR (c.vocabulary_id = 'LOINC' AND c.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test')))" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `victr-tanagra-test.sd_20230328.concept_relationship` cr JOIN `victr-tanagra-test.sd_20230328.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `victr-tanagra-test.sd_20230328.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.vocabulary_id = c2.vocabulary_id AND ((c1.vocabulary_id = 'SNOMED' AND c1.domain_id = c2.domain_id AND c1.domain_id = 'Measurement') OR (c1.vocabulary_id = 'LOINC' AND c1.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test') AND c2.concept_class_id IN ('LOINC Hierarchy', 'LOINC Component', 'Lab Test'))) " - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Measurement" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "SNOMED" - } - } ] - }, { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "LOINC" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 36206173 - } - } ] - } ] - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 11 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "measurement" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "measurement_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "measurement_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "measurement" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 11 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/measurement_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/measurement_occurrence.json deleted file mode 100644 index a6eb0a0d1..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/measurement_occurrence.json +++ /dev/null @@ -1,312 +0,0 @@ -{ - "name" : "measurement_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -1765.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 42914672 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 641606490 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 2817948 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 302941126 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_numeric", - "dataType" : "DOUBLE", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value_enum", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "measurement", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT mo.measurement_id AS id, mo.person_id, mo.measurement_concept_id, mo.measurement_date, mo.value_as_number AS value_numeric, mo.value_as_concept_id, mo.unit_concept_id, mo.measurement_source_value AS source_value, mo.measurement_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(mo.measurement_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, mo.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_20230328.measurement` AS mo JOIN `victr-tanagra-test.sd_20230328.person` AS p ON p.person_id = mo.person_id LEFT JOIN `victr-tanagra-test.sd_20230328.visit_occurrence` AS vo ON vo.visit_occurrence_id = mo.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "measurement_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value_numeric" : { - "value" : { - "column" : "value_numeric", - "runtimeCalculated" : false - } - }, - "value_enum" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "measurement" : { - "value" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "measurement_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "measurement_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value_numeric" : { - "value" : { - "column" : "value_numeric", - "runtimeCalculated" : false - } - }, - "value_enum" : { - "value" : { - "column" : "value_enum", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value_enum", - "runtimeCalculated" : false - } - }, - "measurement" : { - "value" : { - "column" : "measurement", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_measurement", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/note.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/note.json deleted file mode 100644 index a25a251a5..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/note.json +++ /dev/null @@ -1,195 +0,0 @@ -{ - "name" : "note", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "None" - }, - "display" : "None" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Note Type" - }, - "display" : "Note Type" - }, - "count" : 10 - }, { - "enumVal" : { - "value" : { - "stringVal" : "VUMC Note Type" - }, - "display" : "VUMC Note Type" - }, - "count" : 3 - }, { - "enumVal" : { - "value" : { - "stringVal" : "VUMC PSS Type" - }, - "display" : "VUMC PSS Type" - }, - "count" : 1 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "OR", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 0 - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Note Type" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "VUMC Note Type" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "VUMC PSS Type" - } - } ] - } - }, - "attributeMappings" : { - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_20230328.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_20230328.concept` c ON c.concept_id = textsearch.id WHERE c.vocabulary_id IN ('Note Type', 'VUMC Note Type', 'VUMC PSS Type') OR c.concept_id = 0" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "note" - }, - "attributeMappings" : { - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/note_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/note_occurrence.json deleted file mode 100644 index 09e65181f..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/note_occurrence.json +++ /dev/null @@ -1,380 +0,0 @@ -{ - "name" : "note_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "note", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 44814638 - }, - "display" : "Admission note" - }, - "count" : 2442874 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814643 - }, - "display" : "Ancillary report" - }, - "count" : 11932638 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814637 - }, - "display" : "Discharge summary" - }, - "count" : 5844946 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2003594153 - }, - "display" : "ECG_IMPRESSION" - }, - "count" : 2133266 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814646 - }, - "display" : "Emergency department note" - }, - "count" : 3497555 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814639 - }, - "display" : "Inpatient note" - }, - "count" : 19765349 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 9356183 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814645 - }, - "display" : "Note" - }, - "count" : 76574511 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814644 - }, - "display" : "Nursing report" - }, - "count" : 6939641 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814640 - }, - "display" : "Outpatient note" - }, - "count" : 87119775 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2002404173 - }, - "display" : "PL_PROBLEM LIST" - }, - "count" : 537792653 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814642 - }, - "display" : "Pathology report" - }, - "count" : 2188991 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2002603124 - }, - "display" : "Pss Problem snomed data" - }, - "count" : 29685278 - }, { - "enumVal" : { - "value" : { - "int64Val" : 44814641 - }, - "display" : "Radiology report" - }, - "count" : 18457033 - }, { - "enumVal" : { - "value" : { - "int64Val" : 2004084156 - }, - "display" : "VUMC forms data" - }, - "count" : 1317981 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -1646.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 2415239 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 22246659 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1812247 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 33946457 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "text", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "title", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT n.note_id AS id, n.person_id, n.note_type_concept_id, n.note_date, n.note_title AS title, n.note_text AS text, n.note_source_value AS source_value, CAST(FLOOR(TIMESTAMP_DIFF(n.note_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, n.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_20230328.note` AS n JOIN `victr-tanagra-test.sd_20230328.person` AS p ON p.person_id = n.person_id LEFT JOIN `victr-tanagra-test.sd_20230328.visit_occurrence` AS vo ON vo.visit_occurrence_id = n.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "note_date", - "runtimeCalculated" : false - } - }, - "note" : { - "value" : { - "column" : "note_type_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "note_type_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "text" : { - "value" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "title" : { - "value" : { - "column" : "title", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "note_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "note" : { - "value" : { - "column" : "note", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_note", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "text" : { - "value" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "title" : { - "value" : { - "column" : "title", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/observation.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/observation.json deleted file mode 100644 index cf6238dcd..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/observation.json +++ /dev/null @@ -1,337 +0,0 @@ -{ - "name" : "observation", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 162296 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "APC" - }, - "display" : "APC" - }, - "count" : 715 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "CPT4" - }, - "count" : 1083 - }, { - "enumVal" : { - "value" : { - "stringVal" : "DRG" - }, - "display" : "DRG" - }, - "count" : 752 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 2667 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICDO3" - }, - "display" : "ICDO3" - }, - "count" : 49 - }, { - "enumVal" : { - "value" : { - "stringVal" : "LOINC" - }, - "display" : "LOINC" - }, - "count" : 7087 - }, { - "enumVal" : { - "value" : { - "stringVal" : "MDC" - }, - "display" : "MDC" - }, - "count" : 26 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NAACCR" - }, - "display" : "NAACCR" - }, - "count" : 96 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NUCC" - }, - "display" : "NUCC" - }, - "count" : 4 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Nebraska Lexicon" - }, - "display" : "Nebraska Lexicon" - }, - "count" : 1004 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OMOP Extension" - }, - "display" : "OMOP Extension" - }, - "count" : 107 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPCS4" - }, - "display" : "OPCS4" - }, - "count" : 56 - }, { - "enumVal" : { - "value" : { - "stringVal" : "PCORNet" - }, - "display" : "PCORNet" - }, - "count" : 2 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 117406 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED Veterinary" - }, - "display" : "SNOMED Veterinary" - }, - "count" : 27401 - }, { - "enumVal" : { - "value" : { - "stringVal" : "UB04 Pri Typ of Adm" - }, - "display" : "UB04 Pri Typ of Adm" - }, - "count" : 6 - }, { - "enumVal" : { - "value" : { - "stringVal" : "UK Biobank" - }, - "display" : "UK Biobank" - }, - "count" : 3835 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Observation" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "PPI" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "concept_class_id", - "runtimeCalculated" : false - }, - "operator" : "NOT_EQUALS", - "value" : { - "stringVal" : "Survey" - } - } ] - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_20230328.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_20230328.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Observation' AND c.standard_concept = 'S' AND c.vocabulary_id != 'PPI' AND c.concept_class_id != 'Survey'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "observation" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/observation_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/observation_occurrence.json deleted file mode 100644 index 704e54191..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/observation_occurrence.json +++ /dev/null @@ -1,312 +0,0 @@ -{ - "name" : "observation_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "unit", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -977.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "observation", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "value_as_string", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 4017765 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 10358821 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1121298 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 67445573 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "value", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT o.observation_id AS id, o.person_id, o.observation_concept_id, o.observation_date, o.value_as_string, o.value_as_concept_id, o.unit_concept_id, o.observation_source_value AS source_value, o.observation_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(o.observation_date, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, o.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_20230328.observation` AS o JOIN `victr-tanagra-test.sd_20230328.person` AS p ON p.person_id = o.person_id LEFT JOIN `victr-tanagra-test.sd_20230328.visit_occurrence` AS vo ON vo.visit_occurrence_id = o.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "observation_date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "unit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "observation_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value_as_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "value_as_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "observation_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "unit" : { - "value" : { - "column" : "unit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_unit", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "observation" : { - "value" : { - "column" : "observation", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_observation", - "runtimeCalculated" : false - } - }, - "value_as_string" : { - "value" : { - "column" : "value_as_string", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "value" : { - "value" : { - "column" : "value", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_value", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/person.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/person.json deleted file mode 100644 index 023e47eb3..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/person.json +++ /dev/null @@ -1,360 +0,0 @@ -{ - "name" : "person", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "gender", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 8532 - }, - "display" : "FEMALE" - }, - "count" : 1940496 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8507 - }, - "display" : "MALE" - }, - "count" : 1673369 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 4273 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "race", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 8657 - }, - "display" : "American Indian or Alaska Native" - }, - "count" : 5078 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8515 - }, - "display" : "Asian" - }, - "count" : 48897 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38003598 - }, - "display" : "Black" - }, - "count" : 343615 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1000410 - }, { - "enumVal" : { - "value" : { - "int64Val" : 8527 - }, - "display" : "White" - }, - "count" : 2220138 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "ethnicity", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 38003563 - }, - "display" : "Hispanic or Latino" - }, - "count" : 123186 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1027401 - }, { - "enumVal" : { - "value" : { - "int64Val" : 38003564 - }, - "display" : "Not Hispanic or Latino" - }, - "count" : 2467551 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "biovu_sample_has_plasma", - "dataType" : "BOOLEAN", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "biovu_sample_dna_yield", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 0.0, - "maxVal" : 500.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "biovu_sample_is_compromised", - "dataType" : "BOOLEAN", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "age", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -971.0, - "maxVal" : 224.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "has_biovu_sample", - "dataType" : "BOOLEAN", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "biovu_sample_is_nonshippable", - "dataType" : "BOOLEAN", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "year_of_birth", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : 1799.0, - "maxVal" : 2993.0 - }, - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT /* Can't do \"*\". During expansion, there's an error about person_id column being ambiguous. */ p.person_id, p.year_of_birth, p.birth_datetime, p.gender_concept_id, p.race_concept_id, p.ethnicity_concept_id, /* Add BioVU sample columns. The way x_biovu_sample_status is created, there should be at most one row per person. */ EXISTS (SELECT 1 FROM `victr-tanagra-test.sd_20230328.x_biovu_sample_status` x WHERE p.person_id = x.person_id) AS has_biovu_sample, x.dna_yield_ind AS biovu_sample_dna_yield, /* As a courtesy, convert string fields to boolean: 0 -> No, 1 -> Yes */ CASE WHEN x.compromise_ind = '1' THEN true WHEN x.compromise_ind = '0' THEN false ELSE null END AS biovu_sample_is_compromised, CASE WHEN x.nonshippable_ind = '1' THEN true WHEN x.nonshippable_ind = '0' THEN false ELSE null END AS biovu_sample_is_nonshippable, CASE WHEN x.plasma_ind = '1' THEN true WHEN x.plasma_ind = '0' THEN false ELSE null END AS biovu_sample_has_plasma FROM `victr-tanagra-test.sd_20230328.person` p LEFT OUTER JOIN ( /* Get rid of duplicate rows in x_biovu_sample_status. For example, person 4587323 has 11 duplicate rows. This returns just 1 row for each person. */ WITH x_biovu_sample_status AS ( SELECT *, ROW_NUMBER() OVER(PARTITION BY person_id) AS rn FROM `victr-tanagra-test.sd_20230328.x_biovu_sample_status` ) SELECT * FROM x_biovu_sample_status WHERE rn = 1 ) x ON p.person_id = x.person_id " - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "gender_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "race_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "ethnicity_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "biovu_sample_has_plasma" : { - "value" : { - "column" : "biovu_sample_has_plasma", - "runtimeCalculated" : false - } - }, - "biovu_sample_dna_yield" : { - "value" : { - "column" : "biovu_sample_dna_yield", - "runtimeCalculated" : false - } - }, - "biovu_sample_is_compromised" : { - "value" : { - "column" : "biovu_sample_is_compromised", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "age" : { - "value" : { - "column" : "birth_datetime", - "sqlFunctionWrapper" : "CAST(FLOOR(TIMESTAMP_DIFF(CURRENT_TIMESTAMP(), ${fieldSql}, DAY) / 365.25) AS INT64)", - "runtimeCalculated" : true - } - }, - "has_biovu_sample" : { - "value" : { - "column" : "has_biovu_sample", - "runtimeCalculated" : false - } - }, - "biovu_sample_is_nonshippable" : { - "value" : { - "column" : "biovu_sample_is_nonshippable", - "runtimeCalculated" : false - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "person" - }, - "attributeMappings" : { - "gender" : { - "value" : { - "column" : "gender", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_gender", - "runtimeCalculated" : false - } - }, - "race" : { - "value" : { - "column" : "race", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_race", - "runtimeCalculated" : false - } - }, - "ethnicity" : { - "value" : { - "column" : "ethnicity", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_ethnicity", - "runtimeCalculated" : false - } - }, - "biovu_sample_has_plasma" : { - "value" : { - "column" : "biovu_sample_has_plasma", - "runtimeCalculated" : false - } - }, - "biovu_sample_dna_yield" : { - "value" : { - "column" : "biovu_sample_dna_yield", - "runtimeCalculated" : false - } - }, - "biovu_sample_is_compromised" : { - "value" : { - "column" : "biovu_sample_is_compromised", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "age" : { - "value" : { - "column" : "age", - "sqlFunctionWrapper" : "CAST(FLOOR(TIMESTAMP_DIFF(CURRENT_TIMESTAMP(), ${fieldSql}, DAY) / 365.25) AS INT64)", - "runtimeCalculated" : true - } - }, - "has_biovu_sample" : { - "value" : { - "column" : "has_biovu_sample", - "runtimeCalculated" : false - } - }, - "biovu_sample_is_nonshippable" : { - "value" : { - "column" : "biovu_sample_is_nonshippable", - "runtimeCalculated" : false - } - }, - "year_of_birth" : { - "value" : { - "column" : "year_of_birth", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/procedure.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/procedure.json deleted file mode 100644 index 1c48b48ca..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/procedure.json +++ /dev/null @@ -1,483 +0,0 @@ -{ - "name" : "procedure", - "idAttribute" : "id", - "attributes" : [ { - "type" : "KEY_AND_DISPLAY", - "name" : "standard_concept", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { }, - "display" : "Source" - }, - "count" : 0 - }, { - "enumVal" : { - "value" : { - "stringVal" : "S" - }, - "display" : "Standard" - }, - "count" : 262341 - }, { - "enumVal" : { - "value" : { - "stringVal" : "C" - }, - "display" : "Unknown" - }, - "count" : 3064 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "vocabulary", - "dataType" : "STRING", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "stringVal" : "CCAM" - }, - "display" : "CCAM" - }, - "count" : 10206 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CIEL" - }, - "display" : "CIEL" - }, - "count" : 648 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CIM10" - }, - "display" : "CIM10" - }, - "count" : 195 - }, { - "enumVal" : { - "value" : { - "stringVal" : "CPT4" - }, - "display" : "CPT4" - }, - "count" : 13143 - }, { - "enumVal" : { - "value" : { - "stringVal" : "EDI" - }, - "display" : "EDI" - }, - "count" : 249785 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HCPCS" - }, - "display" : "HCPCS" - }, - "count" : 1289 - }, { - "enumVal" : { - "value" : { - "stringVal" : "HemOnc" - }, - "display" : "HemOnc" - }, - "count" : 92 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10" - }, - "display" : "ICD10" - }, - "count" : 161 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CM" - }, - "display" : "ICD10CM" - }, - "count" : 6 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10CN" - }, - "display" : "ICD10CN" - }, - "count" : 386 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10GM" - }, - "display" : "ICD10GM" - }, - "count" : 157 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD10PCS" - }, - "display" : "ICD10PCS" - }, - "count" : 194874 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9CM" - }, - "display" : "ICD9CM" - }, - "count" : 177 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9Proc" - }, - "display" : "ICD9Proc" - }, - "count" : 4657 - }, { - "enumVal" : { - "value" : { - "stringVal" : "ICD9ProcCN" - }, - "display" : "ICD9ProcCN" - }, - "count" : 13385 - }, { - "enumVal" : { - "value" : { - "stringVal" : "KCD7" - }, - "display" : "KCD7" - }, - "count" : 165 - }, { - "enumVal" : { - "value" : { - "stringVal" : "MeSH" - }, - "display" : "MeSH" - }, - "count" : 951 - }, { - "enumVal" : { - "value" : { - "stringVal" : "NAACCR" - }, - "display" : "NAACCR" - }, - "count" : 710 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Nebraska Lexicon" - }, - "display" : "Nebraska Lexicon" - }, - "count" : 72683 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OMOP Extension" - }, - "display" : "OMOP Extension" - }, - "count" : 1 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPCS4" - }, - "display" : "OPCS4" - }, - "count" : 9750 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OPS" - }, - "display" : "OPS" - }, - "count" : 41101 - }, { - "enumVal" : { - "value" : { - "stringVal" : "OXMIS" - }, - "display" : "OXMIS" - }, - "count" : 1193 - }, { - "enumVal" : { - "value" : { - "stringVal" : "Read" - }, - "display" : "Read" - }, - "count" : 20973 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED" - }, - "display" : "SNOMED" - }, - "count" : 86910 - }, { - "enumVal" : { - "value" : { - "stringVal" : "SNOMED Veterinary" - }, - "display" : "SNOMED Veterinary" - }, - "count" : 392 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "concept_code", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Procedure" - } - } - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "standard_concept", - "sqlFunctionWrapper" : "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary_id", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_20230328.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_20230328.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Procedure' " - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "rawSql" : "SELECT cr.concept_id_1 AS parent, cr.concept_id_2 AS child, FROM `victr-tanagra-test.sd_20230328.concept_relationship` cr JOIN `victr-tanagra-test.sd_20230328.concept` c1 ON c1.concept_id = cr.concept_id_1 JOIN `victr-tanagra-test.sd_20230328.concept` c2 ON c2.concept_id = cr.concept_id_2 WHERE cr.relationship_id = 'Subsumes' AND c1.domain_id = c2.domain_id AND c2.domain_id = 'Procedure' AND c1.vocabulary_id = c2.vocabulary_id AND c2.vocabulary_id = 'SNOMED'" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "rootNodesFilter" : { - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BINARY", - "field" : { - "column" : "concept_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "int64Val" : 4322976 - } - } - }, - "fieldPointers" : { - "id" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "procedure" - }, - "attributeMappings" : { - "standard_concept" : { - "value" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_standard_concept", - "runtimeCalculated" : false - } - }, - "vocabulary" : { - "value" : { - "column" : "vocabulary", - "runtimeCalculated" : false - } - }, - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "concept_code" : { - "value" : { - "column" : "concept_code", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { - "standard" : { - "childParent" : { - "tablePointer" : { - "table" : "procedure_standard_childParent" - }, - "fieldPointers" : { - "parent" : { - "column" : "parent", - "runtimeCalculated" : false - }, - "child" : { - "column" : "child", - "runtimeCalculated" : false - } - } - }, - "ancestorDescendant" : { - "tablePointer" : { - "table" : "procedure_standard_ancestorDescendant" - }, - "fieldPointers" : { - "ancestor" : { - "column" : "ancestor", - "runtimeCalculated" : false - }, - "descendant" : { - "column" : "descendant", - "runtimeCalculated" : false - } - } - }, - "pathNumChildren" : { - "tablePointer" : { - "table" : "procedure" - }, - "fieldPointers" : { - "path" : { - "column" : "t_standard_path", - "runtimeCalculated" : false - }, - "num_children" : { - "column" : "t_standard_num_children", - "runtimeCalculated" : false - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "maxHierarchyDepth" : 19 - } - } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/procedure_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/procedure_occurrence.json deleted file mode 100644 index 51a12c619..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/procedure_occurrence.json +++ /dev/null @@ -1,239 +0,0 @@ -{ - "name" : "procedure_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -96.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "visit_occurrence_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit_type", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 7621518 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 32528299 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1120517 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 90242249 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "procedure", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT po.procedure_occurrence_id AS id, po.person_id, po.procedure_concept_id, po.procedure_date, po.procedure_source_value AS source_value, po.procedure_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(po.procedure_date, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence, po.visit_occurrence_id, vo.visit_concept_id FROM `victr-tanagra-test.sd_20230328.procedure_occurrence` AS po JOIN `victr-tanagra-test.sd_20230328.person` AS p ON p.person_id = po.person_id LEFT JOIN `victr-tanagra-test.sd_20230328.visit_occurrence` AS vo ON vo.visit_occurrence_id = po.visit_occurrence_id " - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "procedure_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "procedure_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "procedure_occurrence" - }, - "attributeMappings" : { - "date" : { - "value" : { - "column" : "date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "visit_occurrence_id" : { - "value" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - } - }, - "visit_type" : { - "value" : { - "column" : "visit_type", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit_type", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "procedure" : { - "value" : { - "column" : "procedure", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_procedure", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/snp.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/snp.json deleted file mode 100644 index ebf05408e..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/snp.json +++ /dev/null @@ -1,66 +0,0 @@ -{ - "name" : "snp", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT crit_noid.snp_id, ROW_NUMBER() OVER (ORDER BY crit_noid.snp_id) AS row_num FROM ( SELECT DISTINCT snp_id FROM `victr-tanagra-test.sd_20230328.x_snp` ) AS crit_noid " - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "snp_id", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "row_num", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "attributes" : [ "id" ] - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "snp" - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/visit.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/visit.json deleted file mode 100644 index 4dc0f54d1..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/visit.json +++ /dev/null @@ -1,105 +0,0 @@ -{ - "name" : "visit", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "name", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "table" : "concept", - "filter" : { - "type" : "BOOLEAN_AND_OR", - "operator" : "AND", - "subfilters" : [ { - "type" : "BINARY", - "field" : { - "column" : "domain_id", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "Visit" - } - }, { - "type" : "BINARY", - "field" : { - "column" : "standard_concept", - "runtimeCalculated" : false - }, - "operator" : "EQUALS", - "value" : { - "stringVal" : "S" - } - } ] - } - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "concept_name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "concept_id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchStringTable" : { - "tablePointer" : { - "rawSql" : "SELECT textsearch.id, textsearch.text FROM ( SELECT c.concept_id AS id, c.concept_name AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, CAST(c.concept_id AS STRING) AS text FROM `victr-tanagra-test.sd_20230328.concept` c UNION ALL SELECT c.concept_id AS id, c.concept_code AS text FROM `victr-tanagra-test.sd_20230328.concept` c ) AS textsearch JOIN `victr-tanagra-test.sd_20230328.concept` c ON c.concept_id = textsearch.id WHERE c.domain_id = 'Visit' AND c.standard_concept = 'S'" - }, - "fieldPointers" : { - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "text" : { - "column" : "text", - "runtimeCalculated" : false - } - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "visit" - }, - "attributeMappings" : { - "name" : { - "value" : { - "column" : "name", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - } - }, - "textSearchMapping" : { - "searchString" : { - "column" : "text", - "runtimeCalculated" : false - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/visit_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/visit_occurrence.json deleted file mode 100644 index 7ec5b89d7..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entity/visit_occurrence.json +++ /dev/null @@ -1,211 +0,0 @@ -{ - "name" : "visit_occurrence", - "idAttribute" : "id", - "attributes" : [ { - "type" : "SIMPLE", - "name" : "end_date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "source_criteria_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "age_at_occurrence", - "dataType" : "INT64", - "displayHint" : { - "type" : "RANGE", - "minVal" : -977.0, - "maxVal" : 89.0 - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "id", - "dataType" : "INT64", - "displayHintTypes" : [ ] - }, { - "type" : "KEY_AND_DISPLAY", - "name" : "visit", - "dataType" : "INT64", - "displayHint" : { - "type" : "ENUM", - "enumVals" : [ { - "enumVal" : { - "value" : { - "int64Val" : 9203 - }, - "display" : "Emergency Room Visit" - }, - "count" : 1854114 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9201 - }, - "display" : "Inpatient Visit" - }, - "count" : 3830834 - }, { - "enumVal" : { - "value" : { - "int64Val" : 0 - }, - "display" : "No matching concept" - }, - "count" : 1527518 - }, { - "enumVal" : { - "value" : { - "int64Val" : 9202 - }, - "display" : "Outpatient Visit" - }, - "count" : 61824433 - } ] - }, - "displayHintTypes" : [ ] - }, { - "type" : "SIMPLE", - "name" : "source_value", - "dataType" : "STRING", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "person_id", - "dataType" : "INT64", - "displayHintTypes" : [ "NONE" ] - }, { - "type" : "SIMPLE", - "name" : "start_date", - "dataType" : "TIMESTAMP", - "displayHintTypes" : [ "NONE" ] - } ], - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "tablePointer" : { - "rawSql" : "SELECT vo.visit_occurrence_id AS id, vo.person_id, vo.visit_concept_id, vo.visit_start_date AS start_date, vo.visit_end_date AS end_date, vo.visit_source_value AS source_value, vo.visit_source_concept_id AS source_criteria_id, CAST(FLOOR(TIMESTAMP_DIFF(vo.visit_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence FROM `victr-tanagra-test.sd_20230328.visit_occurrence` AS vo JOIN `victr-tanagra-test.sd_20230328.person` AS p ON p.person_id = vo.person_id " - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "visit" : { - "value" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "display" : { - "column" : "visit_concept_id", - "foreignTable" : "concept", - "foreignKey" : "concept_id", - "foreignColumn" : "concept_name", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "tablePointer" : { - "table" : "visit_occurrence" - }, - "attributeMappings" : { - "end_date" : { - "value" : { - "column" : "end_date", - "runtimeCalculated" : false - } - }, - "source_criteria_id" : { - "value" : { - "column" : "source_criteria_id", - "runtimeCalculated" : false - } - }, - "age_at_occurrence" : { - "value" : { - "column" : "age_at_occurrence", - "runtimeCalculated" : false - } - }, - "id" : { - "value" : { - "column" : "id", - "runtimeCalculated" : false - } - }, - "visit" : { - "value" : { - "column" : "visit", - "runtimeCalculated" : false - }, - "display" : { - "column" : "t_display_visit", - "runtimeCalculated" : false - } - }, - "source_value" : { - "value" : { - "column" : "source_value", - "runtimeCalculated" : false - } - }, - "person_id" : { - "value" : { - "column" : "person_id", - "runtimeCalculated" : false - } - }, - "start_date" : { - "value" : { - "column" : "start_date", - "runtimeCalculated" : false - } - } - }, - "hierarchyMappings" : { } - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/brand_ingredient.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/brand_ingredient.json deleted file mode 100644 index 381d393df..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/brand_ingredient.json +++ /dev/null @@ -1,101 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "brand_ingredient", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "rawSql" : "/* 1. User searches for Brand Tylenol 2. User expands Tylenol to see which ingredients are in Tylenol 3. Ingredient Acetaminophen is shown Acetaminophen has over 300 descendants (eg \"acetaminophen 100 MG/ML Oral Suspension\"). Acetaminophen's concept_class_id is Ingredient; descendants' concept_class_ids are Clinical Drug Comp, Quant Clinical Drug, etc. Most descendants have a relationship with Brand Tylenol in concept_relationship. However, we only want to show Acetaminophen in step 3. So only keep relationships with concept_class_id=Ingredient. */ SELECT cr.* FROM `victr-tanagra-test.sd_20230328.concept_relationship` cr, `victr-tanagra-test.sd_20230328.concept` c2 WHERE cr.concept_id_2 = c2.concept_id AND c2.concept_class_id = 'Ingredient'" - }, - "idPairsIdA" : { - "column" : "concept_id_1", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "concept_id_2", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_brand_ingredient" - }, - "idPairsIdA" : { - "column" : "id_brand", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "brand" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_brand_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_brand_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_brand", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_brand", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "brand", - "itemsEntity" : "ingredient" -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/condition_person_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/condition_person_occurrence.json deleted file mode 100644 index a709ed653..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/condition_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "condition_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "condition_occurrence" - }, - "idPairsIdA" : { - "column" : "condition_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_condition_occurrence_condition" - }, - "idPairsIdA" : { - "column" : "id_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_condition", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_condition_person" - }, - "idPairsIdA" : { - "column" : "id_condition", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "condition" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_condition_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_condition_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "condition_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_condition_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_condition_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "condition", - "occurrenceEntity" : "condition_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/device_person_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/device_person_occurrence.json deleted file mode 100644 index ff77e8f95..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/device_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "device_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "device_exposure" - }, - "idPairsIdA" : { - "column" : "device_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_device_occurrence_device" - }, - "idPairsIdA" : { - "column" : "id_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_device", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_device_person" - }, - "idPairsIdA" : { - "column" : "id_device", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_device_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_device_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "device_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_device_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_device_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "device", - "occurrenceEntity" : "device_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/genotyping_person.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/genotyping_person.json deleted file mode 100644 index 313074da0..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/genotyping_person.json +++ /dev/null @@ -1,101 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "genotyping_person", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "rawSql" : "/* platform_id column has type NUMERIC. This causes index column to be FLOAT. Currently indexing doesn't handle floats properly, so change column to INTEGER. */ SELECT genotype_result_id AS genotype_result_id, person_id, CAST(platform_id as INT64) as platform_id FROM `victr-tanagra-test.sd_20230328.x_genotype_result` " - }, - "idPairsIdA" : { - "column" : "platform_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_genotyping_person" - }, - "idPairsIdA" : { - "column" : "id_genotyping", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "genotyping" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "genotyping" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_genotyping", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_genotyping", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "genotyping", - "itemsEntity" : "person" -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/ingredient_person_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/ingredient_person_occurrence.json deleted file mode 100644 index 576ca9260..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/ingredient_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "ingredient_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "drug_exposure" - }, - "idPairsIdA" : { - "column" : "drug_exposure_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_occurrence_ingredient" - }, - "idPairsIdA" : { - "column" : "id_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_person" - }, - "idPairsIdA" : { - "column" : "id_ingredient", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_ingredient_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_ingredient_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "ingredient_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_ingredient_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_ingredient_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "ingredient", - "occurrenceEntity" : "ingredient_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/measurement_person_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/measurement_person_occurrence.json deleted file mode 100644 index cb82b0df7..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/measurement_person_occurrence.json +++ /dev/null @@ -1,287 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "measurement_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "measurement" - }, - "idPairsIdA" : { - "column" : "measurement_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_measurement_occurrence_measurement" - }, - "idPairsIdA" : { - "column" : "id_measurement_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_measurement", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_measurement_person" - }, - "idPairsIdA" : { - "column" : "id_measurement", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_measurement_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_measurement_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "measurement_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_measurement_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_measurement_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { - "modifiers" : { - "tablePointer" : { - "table" : "measurement_person_occurrence_modifiers" - }, - "fieldPointers" : { - "min" : { - "column" : "min", - "runtimeCalculated" : false - }, - "enum_count" : { - "column" : "enum_count", - "runtimeCalculated" : false - }, - "max" : { - "column" : "max", - "runtimeCalculated" : false - }, - "enum_display" : { - "column" : "enum_display", - "runtimeCalculated" : false - }, - "enum_value" : { - "column" : "enum_value", - "runtimeCalculated" : false - }, - "attribute_name" : { - "column" : "attribute_name", - "runtimeCalculated" : false - }, - "entity_id" : { - "column" : "entity_id", - "runtimeCalculated" : false - } - } - } - } - }, - "criteriaEntity" : "measurement", - "occurrenceEntity" : "measurement_occurrence", - "modifierAttributes" : [ "value_numeric", "value_enum" ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/note_person_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/note_person_occurrence.json deleted file mode 100644 index dd4403308..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/note_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "note_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "note" - }, - "idPairsIdA" : { - "column" : "note_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "note_type_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "note" - }, - "idPairsIdA" : { - "column" : "note_type_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "note" - }, - "idPairsIdA" : { - "column" : "note_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_note_occurrence_note" - }, - "idPairsIdA" : { - "column" : "id_note_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_note", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "note_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_note", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_note", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "note" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_note_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_note_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_note_person" - }, - "idPairsIdA" : { - "column" : "id_note", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "note" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_note", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_note", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_note_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_note_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "note_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_note_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_note_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "note", - "occurrenceEntity" : "note_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/observation_person_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/observation_person_occurrence.json deleted file mode 100644 index dad430b34..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/observation_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "observation_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "observation" - }, - "idPairsIdA" : { - "column" : "observation_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_observation_occurrence_observation" - }, - "idPairsIdA" : { - "column" : "id_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_observation", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_observation_person" - }, - "idPairsIdA" : { - "column" : "id_observation", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_observation_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_observation_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "observation_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_observation_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_observation_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "observation", - "occurrenceEntity" : "observation_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/procedure_person_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/procedure_person_occurrence.json deleted file mode 100644 index be81091b7..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/procedure_person_occurrence.json +++ /dev/null @@ -1,251 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "procedure_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "procedure_occurrence" - }, - "idPairsIdA" : { - "column" : "procedure_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_procedure_occurrence_procedure" - }, - "idPairsIdA" : { - "column" : "id_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_procedure", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "standard" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_procedure_person" - }, - "idPairsIdA" : { - "column" : "id_procedure", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "standard" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person_standard", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person_standard", - "runtimeCalculated" : false - } - }, - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_procedure_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_procedure_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "procedure_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_procedure_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_procedure_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "procedure", - "occurrenceEntity" : "procedure_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/snp_person.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/snp_person.json deleted file mode 100644 index 639ba08fd..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/snp_person.json +++ /dev/null @@ -1,84 +0,0 @@ -{ - "type" : "GROUP_ITEMS", - "name" : "snp_person", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "rawSql" : "SELECT crit.row_num, occ.snp_id, occ.person_id FROM `victr-tanagra-test.sd_20230328.x_snp` AS occ JOIN ( SELECT crit_noid.snp_id, ROW_NUMBER() OVER (ORDER BY crit_noid.snp_id) AS row_num FROM ( SELECT DISTINCT snp_id FROM `victr-tanagra-test.sd_20230328.x_snp` ) AS crit_noid ) AS crit ON crit.snp_id = occ.snp_id " - }, - "idPairsIdA" : { - "column" : "row_num", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "groupToItems" : { - "idPairsTable" : { - "table" : "idpairs_snp_person" - }, - "idPairsIdA" : { - "column" : "id_snp", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "snp" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_snp", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_snp", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "groupEntity" : "snp", - "itemsEntity" : "person" -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/visit_person_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/visit_person_occurrence.json deleted file mode 100644 index 1a4beff12..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/entitygroup/visit_person_occurrence.json +++ /dev/null @@ -1,217 +0,0 @@ -{ - "type" : "CRITERIA_OCCURRENCE", - "name" : "visit_person_occurrence", - "sourceDataMapping" : { - "dataPointer" : "omop_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_concept_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "visit_occurrence" - }, - "idPairsIdA" : { - "column" : "visit_occurrence_id", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "person_id", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { }, - "rollupInformationMapB" : { } - } - }, - "auxiliaryDataMappings" : { } - }, - "indexDataMapping" : { - "dataPointer" : "index_dataset", - "relationshipMappings" : { - "occurrenceToCriteria" : { - "idPairsTable" : { - "table" : "idpairs_visit_occurrence_visit" - }, - "idPairsIdA" : { - "column" : "id_visit_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_visit", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit_occurrence", - "runtimeCalculated" : false - } - } - } - }, - "criteriaToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_visit_person" - }, - "idPairsIdA" : { - "column" : "id_visit", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit", - "runtimeCalculated" : false - } - } - } - }, - "occurrenceToPrimary" : { - "idPairsTable" : { - "table" : "idpairs_visit_occurrence_person" - }, - "idPairsIdA" : { - "column" : "id_visit_occurrence", - "runtimeCalculated" : false - }, - "idPairsIdB" : { - "column" : "id_person", - "runtimeCalculated" : false - }, - "rollupInformationMapA" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "visit_occurrence" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_person", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_person", - "runtimeCalculated" : false - } - } - }, - "rollupInformationMapB" : { - "NO_HIERARCHY" : { - "table" : { - "table" : "person" - }, - "id" : { - "column" : "id", - "runtimeCalculated" : false - }, - "count" : { - "column" : "t_count_visit_occurrence", - "runtimeCalculated" : false - }, - "displayHints" : { - "column" : "t_displayhints_visit_occurrence", - "runtimeCalculated" : false - } - } - } - } - }, - "auxiliaryDataMappings" : { } - }, - "criteriaEntity" : "visit", - "occurrenceEntity" : "visit_occurrence", - "modifierAttributes" : [ ] -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/sdd_refresh0323.json b/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/sdd_refresh0323.json deleted file mode 100644 index 0d8b8a80a..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/expanded/sdd_refresh0323.json +++ /dev/null @@ -1,29 +0,0 @@ -{ - "name" : "sdd_refresh0323", - "dataPointers" : [ { - "type" : "BQ_DATASET", - "name" : "index_dataset", - "projectId" : "victr-tanagra-deploytest", - "datasetId" : "sd_20230328_indexes", - "queryProjectId" : "victr-tanagra-deploytest", - "dataflowServiceAccountEmail" : "victr-tanagra-deploytest@appspot.gserviceaccount.com", - "dataflowTempLocation" : "gs://dataflow-indexing-victr-tanagra-deploytest/temp/", - "dataflowRegion" : "us-east1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : false - }, { - "type" : "BQ_DATASET", - "name" : "omop_dataset", - "projectId" : "victr-tanagra-test", - "datasetId" : "sd_20230328", - "queryProjectId" : "victr-tanagra-test", - "dataflowRegion" : "us-east1", - "dataflowWorkerMachineType" : "n1-standard-4", - "dataflowUsePublicIps" : true - } ], - "entities" : [ "measurement_occurrence.json", "note.json", "condition_occurrence.json", "ingredient.json", "device_occurrence.json", "observation.json", "genotyping.json", "procedure.json", "measurement.json", "ingredient_occurrence.json", "condition.json", "snp.json", "person.json", "visit_occurrence.json", "observation_occurrence.json", "procedure_occurrence.json", "visit.json", "brand.json", "device.json", "note_occurrence.json" ], - "entityGroups" : [ "device_person_occurrence.json", "genotyping_person.json", "visit_person_occurrence.json", "condition_person_occurrence.json", "snp_person.json", "note_person_occurrence.json", "ingredient_person_occurrence.json", "observation_person_occurrence.json", "brand_ingredient.json", "measurement_person_occurrence.json", "procedure_person_occurrence.json" ], - "primaryEntity" : "person", - "uiConfig" : "{ \"dataConfig\": { \"primaryEntity\": { \"displayName\": \"Person\", \"entity\": \"person\", \"key\": \"id\", \"classifications\": [ { \"id\": \"snp\", \"attribute\": \"id\", \"entity\": \"snp\", \"entityAttribute\": \"id\", \"defaultSort\": { \"attribute\": \"id\", \"direction\": \"ASC\" } }, { \"id\": \"genotyping\", \"attribute\": \"id\", \"entity\": \"genotyping\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"name\", \"direction\": \"ASC\" } } ] }, \"occurrences\": [ { \"id\": \"condition_occurrence\", \"displayName\": \"Condition Occurrences\", \"entity\": \"condition_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"condition\", \"attribute\": \"condition\", \"entity\": \"condition\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"procedure_occurrence\", \"displayName\": \"Procedure Occurrences\", \"entity\": \"procedure_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"procedure\", \"attribute\": \"procedure\", \"entity\": \"procedure\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"observation_occurrence\", \"displayName\": \"Observation Occurrence\", \"entity\": \"observation_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"observation\", \"attribute\": \"observation\", \"entity\": \"observation\", \"entityAttribute\": \"id\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" } } ] }, { \"id\": \"ingredient_occurrence\", \"displayName\": \"Drug Occurrence\", \"entity\": \"ingredient_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"ingredient\", \"attribute\": \"id\", \"entity\": \"ingredient\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_rollup_count\", \"direction\": \"DESC\" }, \"groupings\": [ { \"id\": \"brand\", \"entity\": \"brand\", \"defaultSort\": { \"attribute\": \"name\", \"direction\": \"ASC\" }, \"attributes\": [\"name\", \"id\", \"standard_concept\", \"concept_code\"] } ] } ] }, { \"id\": \"note_occurrence\", \"displayName\": \"Documents\", \"entity\": \"note_occurrence\", \"key\": \"id\" }, { \"id\": \"measurement_occurrence\", \"displayName\": \"Measurement Occurrence\", \"entity\": \"measurement_occurrence\", \"key\": \"id\", \"classifications\": [ { \"id\": \"measurement\", \"attribute\": \"measurement\", \"entity\": \"measurement\", \"entityAttribute\": \"id\", \"hierarchy\": \"standard\", \"defaultSort\": { \"attribute\": \"t_item_count\", \"direction\": \"DESC\" } } ] } ] }, \"criteriaConfigs\": [ { \"type\": \"classification\", \"id\": \"tanagra-conditions\", \"title\": \"Condition\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Condition\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"condition_occurrence\", \"classification\": \"condition\", \"modifiers\": [ \"age_at_occurrence\", \"visit_type\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-procedures\", \"title\": \"Procedure\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Procedure\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"procedure_occurrence\", \"classification\": \"procedure\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"] }, { \"type\": \"classification\", \"id\": \"tanagra-observations\", \"title\": \"Observation\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"observation_occurrence\", \"classification\": \"observation\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"] }, { \"type\": \"classification\", \"id\": \"tanagra-drugs\", \"title\": \"Drug\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Drug\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"ingredient_occurrence\", \"classification\": \"ingredient\", \"modifiers\": [ \"age_at_occurrence\", \"visit_type\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-genotyping\", \"title\": \"Genotyping platform\", \"category\": \"Demographics\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Genotyping platform\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Genotyping platform\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Id\" } ], \"occurrence\": \"\", \"classification\": \"genotyping\" }, { \"type\": \"classification\", \"id\": \"tanagra-measurement\", \"title\": \"Labs and measurements\", \"conceptSet\": true, \"category\": \"Domains\", \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept name\" }, { \"key\": \"id\", \"width\": 100, \"title\": \"Concept ID\" }, { \"key\": \"standard_concept\", \"width\": 120, \"title\": \"Source/standard\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_item_count\", \"width\": 120, \"title\": \"Count\" } ], \"hierarchyColumns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Condition\" }, { \"key\": \"id\", \"width\": 120, \"title\": \"Concept ID\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up count\" } ], \"occurrence\": \"measurement_occurrence\", \"classification\": \"measurement\", \"modifiers\": [\"age_at_occurrence\", \"visit_type\", \"date_group_by_count\"], \"valueConfigs\": [ { \"title\": \"Categorical value\", \"attribute\": \"value_enum\" }, { \"title\": \"Numeric value\", \"attribute\": \"value_numeric\" } ] }, { \"type\": \"attribute\", \"id\": \"tanagra-ethnicity\", \"title\": \"Ethnicity\", \"category\": \"Demographics\", \"attribute\": \"ethnicity\" }, { \"type\": \"attribute\", \"id\": \"tanagra-gender\", \"title\": \"Gender identity\", \"category\": \"Demographics\", \"attribute\": \"gender\" }, { \"type\": \"attribute\", \"id\": \"tanagra-race\", \"title\": \"Race\", \"category\": \"Demographics\", \"attribute\": \"race\" }, { \"type\": \"attribute\", \"id\": \"tanagra-age\", \"title\": \"Age\", \"category\": \"Demographics\", \"attribute\": \"age\" }, { \"type\": \"search\", \"id\": \"tanagra-documents\", \"title\": \"Documents\", \"conceptSet\": true, \"category\": \"Domains\", \"occurrenceId\": \"note_occurrence\", \"searchAttribute\": \"title\", \"categoryAttribute\": \"note\", \"modifiers\": [ \"age_at_occurrence\", \"visit_type\", \"start_date_group_by_count\" ] }, { \"type\": \"classification\", \"id\": \"tanagra-snp\", \"title\": \"SNP variant\", \"category\": \"Demographics\", \"columns\": [{ \"key\": \"name\", \"width\": \"100%\", \"title\": \"SNP variant\" }], \"occurrence\": \"\", \"classification\": \"snp\" }, { \"type\": \"biovu\", \"id\": \"biovu\", \"title\": \"BioVU Samples\", \"category\": \"BioVU\" } ], \"modifierConfigs\": [ { \"type\": \"unhinted-value\", \"id\": \"start_date_group_by_count\", \"title\": \"Occurrence count\", \"attribute\": \"start_date\", \"groupByCount\": true }, { \"type\": \"unhinted-value\", \"id\": \"date_group_by_count\", \"title\": \"Occurrence count\", \"attribute\": \"date\", \"groupByCount\": true }, { \"type\": \"attribute\", \"id\": \"visit_type\", \"title\": \"Visit type\", \"attribute\": \"visit_type\" }, { \"type\": \"attribute\", \"id\": \"age_at_occurrence\", \"title\": \"Age at occurrence\", \"attribute\": \"age_at_occurrence\" } ], \"demographicChartConfigs\": { \"groupByAttributes\": [\"gender\", \"race\", \"age\"], \"chartConfigs\": [ { \"title\": \"Gender identity\", \"primaryProperties\": [{ \"key\": \"gender\" }] }, { \"title\": \"Gender identity, Current age, Race\", \"primaryProperties\": [ { \"key\": \"gender\" }, { \"key\": \"age\", \"buckets\": [ { \"min\": 18, \"max\": 45, \"displayName\": \"18-44\" }, { \"min\": 45, \"max\": 65, \"displayName\": \"45-64\" }, { \"min\": 65, \"displayName\": \"65+\" } ] } ], \"stackedProperty\": { \"key\": \"race\" } } ] }, \"prepackagedConceptSets\": [ { \"id\": \"_demographics\", \"name\": \"Demographics\", \"occurrence\": \"\" }, { \"id\": \"_analgesics\", \"name\": \"Analgesics\", \"occurrence\": \"ingredient_occurrence\", \"filter\": { \"type\": \"CLASSIFICATION\", \"occurrenceId\": \"ingredient_occurrence\", \"classificationId\": \"ingredient\", \"keys\": [21604253] } } ], \"criteriaSearchConfig\": { \"criteriaTypeWidth\": 120, \"columns\": [ { \"key\": \"name\", \"width\": \"100%\", \"title\": \"Concept Name\" }, { \"key\": \"vocabulary_t_value\", \"width\": 120, \"title\": \"Vocab\" }, { \"key\": \"concept_code\", \"width\": 120, \"title\": \"Code\" }, { \"key\": \"t_rollup_count\", \"width\": 120, \"title\": \"Roll-up Count\" } ] }, \"cohortReviewConfig\": { \"participantsListColumns\": [ { \"key\": \"id\", \"width\": 100, \"title\": \"Id\" }, { \"key\": \"gender\", \"width\": 100, \"title\": \"Gender\" }, { \"key\": \"race\", \"width\": 100, \"title\": \"Race\" }, { \"key\": \"ethnicity\", \"width\": 100, \"title\": \"Ethnicity\" }, { \"key\": \"age\", \"width\": 60, \"title\": \"Year of Birth\" } ], \"attributes\": [ { \"title\": \"Gender\", \"key\": \"gender\" }, { \"title\": \"Age\", \"key\": \"age\" }, { \"title\": \"Race\", \"key\": \"race\" }, { \"title\": \"Ethnicity\", \"key\": \"ethnicity\" } ], \"pages\": [ { \"type\": \"occurrenceTable\", \"id\": \"condition\", \"title\": \"Conditions\", \"plugin\": { \"occurrence\": \"condition_occurrence\", \"columns\": [ { \"key\": \"condition\", \"width\": \"100%\", \"title\": \"Condition name\", \"sortable\": true }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\", \"sortable\": true }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"procedure\", \"title\": \"Procedures\", \"plugin\": { \"occurrence\": \"procedure_occurrence\", \"columns\": [ { \"key\": \"procedure\", \"width\": \"100%\", \"title\": \"Procedure name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"observation\", \"title\": \"Observations\", \"plugin\": { \"occurrence\": \"observation_occurrence\", \"columns\": [ { \"key\": \"observation\", \"width\": \"100%\", \"title\": \"Observation name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"ingredient\", \"title\": \"Drugs\", \"plugin\": { \"occurrence\": \"ingredient_occurrence\", \"columns\": [ { \"key\": \"ingredient\", \"width\": \"100%\", \"title\": \"Drug name\", \"sortable\": true }, { \"key\": \"start_date\", \"width\": 200, \"title\": \"Start date\", \"sortable\": true }, { \"key\": \"end_date\", \"width\": 200, \"title\": \"End date\", \"sortable\": true } ] } }, { \"type\": \"occurrenceTable\", \"id\": \"measurements\", \"title\": \"Labs and measurements\", \"plugin\": { \"occurrence\": \"measurement_occurrence\", \"columns\": [ { \"key\": \"measurement\", \"width\": \"100%\", \"title\": \"Lab/measurement name\", \"sortable\": true }, { \"key\": \"date\", \"width\": 200, \"title\": \"Date\", \"sortable\": true }, { \"key\": \"value_enum\", \"width\": 160, \"title\": \"Categorical value\", \"sortable\": true }, { \"key\": \"value_numeric\", \"width\": 160, \"title\": \"Numeric value\", \"sortable\": true }, { \"key\": \"unit\", \"width\": 160, \"title\": \"Unit\", \"sortable\": true } ] } }, { \"type\": \"textSearch\", \"id\": \"notes\", \"title\": \"Documents\", \"plugin\": { \"occurrence\": \"note_occurrence\", \"title\": \"title\", \"subtitles\": [\"note\", \"date\"], \"text\": \"text\", \"categoryAttribute\": \"note\", \"sortOrder\": { \"attribute\": \"date\", \"direction\": \"ASC\" } } } ] } } ", - "metadata" : { } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/brand.json b/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/brand.json deleted file mode 100644 index 0403f94a4..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/brand.json +++ /dev/null @@ -1,29 +0,0 @@ -{ - "name": "brand", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "rawSqlFile": "brand_all.sql" - }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "brand_textSearch.sql" } } } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/condition.json b/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/condition.json deleted file mode 100644 index 8d7f876d9..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/condition.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "name": "condition", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "table": "concept", - "filter": { - "type": "BINARY", - "field": { "column": "domain_id" }, - "operator": "EQUALS", - "value": { "stringVal": "Condition" } } }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } }, - "vocabulary": { "value": { "column": "vocabulary_id" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "condition_textSearch.sql" } } }, - "hierarchyMappings": { - "standard": { - "childParent": { - "tablePointer": { "rawSqlFile": "condition_parentChild.sql" } - }, - "rootNodesFilter": { - "tablePointer": { - "table": "concept", - "filter": { "type": "BINARY", "field": { "column": "concept_id" }, "operator": "EQUALS", "value": { "int64Val": 441840 } } }, - "fieldPointers": { - "id": { "column": "concept_id" } - } - }, - "maxHierarchyDepth": 20 - } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/condition_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/condition_occurrence.json deleted file mode 100644 index 5734966fc..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/condition_occurrence.json +++ /dev/null @@ -1,42 +0,0 @@ -{ - "name": "condition_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "condition", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "condition_occurrence_all.sql" }, - "attributeMappings": { - "condition": { - "value": { "column": "condition_concept_id" }, - "display": { - "column": "condition_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/device.json b/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/device.json deleted file mode 100644 index 2e72d8d62..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/device.json +++ /dev/null @@ -1,43 +0,0 @@ -{ - "name": "device", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "table": "concept", - "filter": { - "type": "BOOLEAN_AND_OR", - "operator": "AND", - "subfilters": [ - { "type": "BINARY", - "field": { "column": "domain_id" }, - "operator": "EQUALS", - "value": { "stringVal": "Device" } }, - { "type": "BINARY", - "field": { "column": "standard_concept" }, - "operator": "EQUALS", - "value": { "stringVal": "S" } } - ] } }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } }, - "vocabulary": { "value": { "column": "vocabulary_id" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "device_textSearch.sql" } } } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/device_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/device_occurrence.json deleted file mode 100644 index ffcfbb5fc..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/device_occurrence.json +++ /dev/null @@ -1,41 +0,0 @@ -{ - "name": "device_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "device", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "device_occurrence_all.sql" }, - "attributeMappings": { - "device": { - "value": { "column": "device_concept_id" }, - "display": { - "column": "device_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/ingredient.json b/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/ingredient.json deleted file mode 100644 index 0e7901ee5..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/ingredient.json +++ /dev/null @@ -1,58 +0,0 @@ -{ - "name": "ingredient", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "ingredient_all.sql" }, - "attributeMappings": { - "vocabulary": { "value": { "column": "vocabulary_id" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "ingredient_textSearch.sql" } } }, - "hierarchyMappings": { - "standard": { - "childParent": { - "tablePointer": { "rawSqlFile": "ingredient_parentChild.sql" } - }, - "rootNodesFilter": { - "tablePointer": { - "table": "concept", - "filter": { - "type": "BOOLEAN_AND_OR", - "operator": "AND", - "subfilters": [ - { "type": "BINARY", - "field": { "column": "vocabulary_id" }, - "operator": "EQUALS", - "value": { "stringVal": "ATC" } }, - { "type": "BINARY", - "field": { "column": "concept_class_id" }, - "operator": "EQUALS", - "value": { "stringVal": "ATC 1st" } }, - { "type": "BINARY", - "field": { "column": "standard_concept" }, - "operator": "EQUALS", - "value": { "stringVal": "C" } } ] } }, - "fieldPointers": { - "id": { "column": "concept_id" } - } - }, - "maxHierarchyDepth": 15 - } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/ingredient_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/ingredient_occurrence.json deleted file mode 100644 index 6e4263d3a..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/ingredient_occurrence.json +++ /dev/null @@ -1,44 +0,0 @@ -{ - "name": "ingredient_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "ingredient", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "stop_reason" }, - { "type": "SIMPLE", "name": "refills" }, - { "type": "SIMPLE", "name": "days_supply" }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "ingredient_occurrence_all.sql" }, - "attributeMappings": { - "ingredient": { - "value": { "column": "drug_concept_id" }, - "display": { - "column": "drug_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/measurement.json b/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/measurement.json deleted file mode 100644 index 70324f369..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/measurement.json +++ /dev/null @@ -1,109 +0,0 @@ -{ - "name": "measurement", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "table": "concept", - "filter": { - "type": "BOOLEAN_AND_OR", - "operator": "OR", - "subfilters": [ - { "type": "BOOLEAN_AND_OR", - "operator": "AND", - "subfilters": [ - { "type": "BINARY", - "field": { "column": "domain_id" }, - "operator": "EQUALS", - "value": { "stringVal": "Measurement" } }, - { "type": "BINARY", - "field": { "column": "vocabulary_id" }, - "operator": "EQUALS", - "value": { "stringVal": "SNOMED" } } ] }, - { "type": "BOOLEAN_AND_OR", - "operator": "AND", - "subfilters": [ - { "type": "BINARY", - "field": { "column": "vocabulary_id" }, - "operator": "EQUALS", - "value": { "stringVal": "LOINC" } }, - { "type": "BOOLEAN_AND_OR", - "operator": "OR", - "subfilters": [ - { "type": "BINARY", - "field": { "column": "concept_class_id" }, - "operator": "EQUALS", - "value": { "stringVal": "LOINC Hierarchy" } }, - { "type": "BINARY", - "field": { "column": "concept_class_id" }, - "operator": "EQUALS", - "value": { "stringVal": "LOINC Component" } }, - { "type": "BINARY", - "field": { "column": "concept_class_id" }, - "operator": "EQUALS", - "value": { "stringVal": "Lab Test" } } - ] } ] } ] } }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } }, - "vocabulary": { "value": { "column": "vocabulary_id" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "measurement_textSearch.sql" } } }, - "hierarchyMappings": { - "standard": { - "childParent": { - "tablePointer": { "rawSqlFile": "measurement_parentChild.sql" } - }, - "rootNodesFilter": { - "tablePointer": { - "table": "concept", - "filter": { - "type": "BOOLEAN_AND_OR", - "operator": "OR", - "subfilters": [ - { "type": "BOOLEAN_AND_OR", - "operator": "AND", - "subfilters": [ - { "type": "BINARY", - "field": { "column": "domain_id" }, - "operator": "EQUALS", - "value": { "stringVal": "Measurement" } }, - { "type": "BINARY", - "field": { "column": "vocabulary_id" }, - "operator": "EQUALS", - "value": { "stringVal": "SNOMED" } } ] }, - { "type": "BOOLEAN_AND_OR", - "operator": "AND", - "subfilters": [ - { "type": "BINARY", - "field": { "column": "vocabulary_id" }, - "operator": "EQUALS", - "value": { "stringVal": "LOINC" } }, - { "type": "BINARY", - "field": { "column": "concept_id" }, - "operator": "EQUALS", - "value": { "int64Val": 36206173 } } ] } ] } }, - "fieldPointers": { - "id": { "column": "concept_id" } - } - }, - "maxHierarchyDepth": 11 - } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/measurement_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/measurement_occurrence.json deleted file mode 100644 index cc142dabb..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/measurement_occurrence.json +++ /dev/null @@ -1,58 +0,0 @@ -{ - "name": "measurement_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "measurement", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "value_numeric", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "value_enum", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "unit", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "measurement_occurrence_all.sql" }, - "attributeMappings": { - "measurement": { - "value": { "column": "measurement_concept_id" }, - "display": { - "column": "measurement_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "date": { "value": { "column": "measurement_date" } }, - "value_enum": { - "value": { "column": "value_as_concept_id" }, - "display": { - "column": "value_as_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "unit": { - "value": { "column": "unit_concept_id" }, - "display": { - "column": "unit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/note_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/note_occurrence.json deleted file mode 100644 index 4ea519ebd..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/note_occurrence.json +++ /dev/null @@ -1,42 +0,0 @@ -{ - "name": "note_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "note" }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "title", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "text", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "note_occurrence_all.sql" }, - "attributeMappings": { - "date": { "value": { "column": "note_date" } }, - "note": { - "value": { "column": "note_type_concept_id" }, - "display": { - "column": "note_type_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/observation.json b/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/observation.json deleted file mode 100644 index 668afebce..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/observation.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "name": "observation", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "table": "concept", - "filter": { - "type": "BOOLEAN_AND_OR", - "operator": "AND", - "subfilters": [ - { "type": "BINARY", - "field": { "column": "domain_id" }, - "operator": "EQUALS", - "value": { "stringVal": "Observation" } }, - { "type": "BINARY", - "field": { "column": "standard_concept" }, - "operator": "EQUALS", - "value": { "stringVal": "S" } }, - { "type": "BINARY", - "field": { "column": "vocabulary_id" }, - "operator": "NOT_EQUALS", - "value": { "stringVal": "PPI" } }, - { "type": "BINARY", - "field": { "column": "concept_class_id" }, - "operator": "NOT_EQUALS", - "value": { "stringVal": "Survey" } } - ] } }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } }, - "vocabulary": { "value": { "column": "vocabulary_id" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "observation_textSearch.sql" } } } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/observation_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/observation_occurrence.json deleted file mode 100644 index c1709a63a..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/observation_occurrence.json +++ /dev/null @@ -1,58 +0,0 @@ -{ - "name": "observation_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "observation" }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "value_as_string", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "value", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "unit", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "observation_occurrence_all.sql" }, - "attributeMappings": { - "observation": { - "value": { "column": "observation_concept_id" }, - "display": { - "column": "observation_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "date": { "value": { "column": "observation_date" } }, - "value": { - "value": { "column": "value_as_concept_id" }, - "display": { - "column": "value_as_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "unit": { - "value": { "column": "unit_concept_id" }, - "display": { - "column": "unit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/procedure.json b/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/procedure.json deleted file mode 100644 index 5b26c710e..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/procedure.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "name": "procedure", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "vocabulary" }, - { "type": "KEY_AND_DISPLAY", "name": "standard_concept" }, - { "type": "SIMPLE", "name": "concept_code", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "table": "concept", - "filter": { - "type": "BINARY", - "field": { "column": "domain_id" }, - "operator": "EQUALS", - "value": { "stringVal": "Procedure" } } }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } }, - "vocabulary": { "value": { "column": "vocabulary_id" } }, - "standard_concept": { - "value": { "column": "standard_concept" }, - "display": { - "column": "standard_concept", - "sqlFunctionWrapper": "(CASE WHEN ${fieldSql} IS NULL THEN 'Source' WHEN ${fieldSql} = 'S' THEN 'Standard' ELSE 'Unknown' END)" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "procedure_textSearch.sql" } } }, - "hierarchyMappings": { - "standard": { - "childParent": { - "tablePointer": { "rawSqlFile": "procedure_parentChild.sql" } - }, - "rootNodesFilter": { - "tablePointer": { - "table": "concept", - "filter": { "type": "BINARY", "field": { "column": "concept_id" }, "operator": "EQUALS", "value": { "int64Val": 4322976 } } }, - "fieldPointers": { - "id": { "column": "concept_id" } - } - }, - "maxHierarchyDepth": 19 - } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/procedure_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/procedure_occurrence.json deleted file mode 100644 index 6d1d61acc..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/procedure_occurrence.json +++ /dev/null @@ -1,41 +0,0 @@ -{ - "name": "procedure_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "procedure", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" }, - { "type": "SIMPLE", "name": "visit_occurrence_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit_type" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "procedure_occurrence_all.sql" }, - "attributeMappings": { - "procedure": { - "value": { "column": "procedure_concept_id" }, - "display": { - "column": "procedure_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } }, - "date": { "value": { "column": "procedure_date" } }, - "visit_type": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/visit.json b/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/visit.json deleted file mode 100644 index 0b9a91bde..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/visit.json +++ /dev/null @@ -1,33 +0,0 @@ -{ - "name": "visit", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "name", "displayHintTypes": ["NONE"] } ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { - "table": "concept", - "filter": { - "type": "BOOLEAN_AND_OR", - "operator": "AND", - "subfilters": [ - { "type": "BINARY", - "field": { "column": "domain_id" }, - "operator": "EQUALS", - "value": { "stringVal": "Visit" } }, - { "type": "BINARY", - "field": { "column": "standard_concept" }, - "operator": "EQUALS", - "value": { "stringVal": "S" } } ] } }, - "attributeMappings": { - "id": { "value": { "column": "concept_id" } }, - "name": { "value": { "column": "concept_name" } } }, - "textSearchMapping": { "searchStringTable": { "tablePointer": { "rawSqlFile": "visit_textSearch.sql" } } } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} \ No newline at end of file diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/visit_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/visit_occurrence.json deleted file mode 100644 index cff5a1628..000000000 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/visit_occurrence.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "name": "visit_occurrence", - "idAttribute": "id", - "attributes": [ - { "type": "SIMPLE", "name": "id" }, - { "type": "SIMPLE", "name": "person_id", "displayHintTypes": ["NONE"] }, - { "type": "KEY_AND_DISPLAY", "name": "visit" }, - { "type": "SIMPLE", "name": "start_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "end_date", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_value", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "source_criteria_id", "displayHintTypes": ["NONE"] }, - { "type": "SIMPLE", "name": "age_at_occurrence" } - ], - - "sourceDataMapping": { - "dataPointer": "omop_dataset", - "tablePointer": { "rawSqlFile": "visit_occurrence_all.sql" }, - "attributeMappings": { - "visit": { - "value": { "column": "visit_concept_id" }, - "display": { - "column": "visit_concept_id", - "foreignTable": "concept", - "foreignKey": "concept_id", - "foreignColumn": "concept_name" } } - } - }, - - "indexDataMapping": { - "dataPointer": "index_dataset" - } -} diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sdd_refresh0323.json b/service/src/main/resources/config/vumc/sdd_refresh0323/sdd_refresh0323.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sdd_refresh0323.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/sdd_refresh0323.json diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/brand_all.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/brand_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/brand_all.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/brand_all.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/brand_ingredients.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/brand_ingredients.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/brand_ingredients.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/brand_ingredients.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/brand_textSearch.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/brand_textSearch.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/brand_textSearch.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/brand_textSearch.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/condition_occurrence_all.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/condition_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/condition_occurrence_all.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/condition_occurrence_all.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/condition_parentChild.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/condition_parentChild.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/condition_parentChild.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/condition_parentChild.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/condition_textSearch.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/condition_textSearch.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/condition_textSearch.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/condition_textSearch.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/device_occurrence_all.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/device_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/device_occurrence_all.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/device_occurrence_all.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/device_textSearch.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/device_textSearch.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/device_textSearch.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/device_textSearch.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/genotype_result.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/genotype_result.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/genotype_result.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/genotype_result.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/genotyping_all.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/genotyping_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/genotyping_all.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/genotyping_all.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/genotyping_parentChild.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/genotyping_parentChild.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/genotyping_parentChild.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/genotyping_parentChild.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/genotyping_rootNodesFilter.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/genotyping_rootNodesFilter.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/genotyping_rootNodesFilter.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/genotyping_rootNodesFilter.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/ingredient_all.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/ingredient_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/ingredient_all.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/ingredient_all.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/ingredient_occurrence_all.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/ingredient_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/ingredient_occurrence_all.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/ingredient_occurrence_all.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/ingredient_parentChild.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/ingredient_parentChild.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/ingredient_parentChild.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/ingredient_parentChild.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/ingredient_textSearch.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/ingredient_textSearch.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/ingredient_textSearch.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/ingredient_textSearch.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/measurement_occurrence_all.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/measurement_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/measurement_occurrence_all.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/measurement_occurrence_all.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/measurement_parentChild.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/measurement_parentChild.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/measurement_parentChild.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/measurement_parentChild.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/measurement_textSearch.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/measurement_textSearch.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/measurement_textSearch.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/measurement_textSearch.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/note_occurrence_all.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/note_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/note_occurrence_all.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/note_occurrence_all.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/note_textSearch.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/note_textSearch.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/note_textSearch.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/note_textSearch.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/observation_occurrence_all.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/observation_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/observation_occurrence_all.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/observation_occurrence_all.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/observation_textSearch.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/observation_textSearch.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/observation_textSearch.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/observation_textSearch.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/person.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/person.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/person.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/person.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/procedure_occurrence_all.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/procedure_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/procedure_occurrence_all.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/procedure_occurrence_all.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/procedure_parentChild.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/procedure_parentChild.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/procedure_parentChild.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/procedure_parentChild.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/procedure_textSearch.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/procedure_textSearch.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/procedure_textSearch.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/procedure_textSearch.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/snp_all.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/snp_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/snp_all.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/snp_all.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/snp_occurrence_all.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/snp_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/snp_occurrence_all.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/snp_occurrence_all.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/visit_occurrence_all.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/visit_occurrence_all.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/visit_occurrence_all.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/visit_occurrence_all.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/visit_textSearch.sql b/service/src/main/resources/config/vumc/sdd_refresh0323/sql/visit_textSearch.sql similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/sql/visit_textSearch.sql rename to service/src/main/resources/config/vumc/sdd_refresh0323/sql/visit_textSearch.sql diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/ui/top_level.json b/service/src/main/resources/config/vumc/sdd_refresh0323/ui/top_level.json similarity index 100% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/ui/top_level.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/ui/top_level.json diff --git a/service/src/test/java/bio/terra/tanagra/api/sdd/SddSnpTest.java b/service/src/test/java/bio/terra/tanagra/api/sdd/SddSnpTest.java index a4debcc24..f118744d7 100644 --- a/service/src/test/java/bio/terra/tanagra/api/sdd/SddSnpTest.java +++ b/service/src/test/java/bio/terra/tanagra/api/sdd/SddSnpTest.java @@ -3,8 +3,10 @@ import bio.terra.tanagra.api.BaseQueriesTest; import java.io.IOException; import java.util.List; +import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; +@Disabled("SDD underlay is out-of-date. Need to update this test to use SDD_REFRESH0323 instead.") public class SddSnpTest extends BaseQueriesTest { @Override protected String getUnderlayName() { diff --git a/service/src/test/java/bio/terra/tanagra/underlayspecific/BaseHintsTest.java b/service/src/test/java/bio/terra/tanagra/underlayspecific/BaseHintsTest.java new file mode 100644 index 000000000..fadc42ef0 --- /dev/null +++ b/service/src/test/java/bio/terra/tanagra/underlayspecific/BaseHintsTest.java @@ -0,0 +1,79 @@ +package bio.terra.tanagra.underlayspecific; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +import bio.terra.tanagra.app.Main; +import bio.terra.tanagra.query.Literal; +import bio.terra.tanagra.service.QuerysService; +import bio.terra.tanagra.service.UnderlaysService; +import bio.terra.tanagra.service.instances.EntityHintRequest; +import bio.terra.tanagra.service.instances.EntityHintResult; +import bio.terra.tanagra.underlay.Attribute; +import bio.terra.tanagra.underlay.DisplayHint; +import bio.terra.tanagra.underlay.displayhint.EnumVal; +import bio.terra.tanagra.underlay.displayhint.EnumVals; +import java.util.*; +import org.junit.jupiter.api.Tag; +import org.junit.jupiter.api.extension.ExtendWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.ActiveProfiles; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit.jupiter.SpringExtension; + +/** + * Utility methods for testing the values of display hints computed across all entity instances + * (e.g. enum values for person.gender). + */ +@ExtendWith(SpringExtension.class) +@ContextConfiguration(classes = Main.class) +@SpringBootTest +@ActiveProfiles("test") +@Tag("requires-cloud-access") +public abstract class BaseHintsTest { + @Autowired protected UnderlaysService underlaysService; + @Autowired protected QuerysService querysService; + + protected abstract String getUnderlayName(); + + protected void assertEntityLevelHintsMatch( + String entityName, Map expectedHints) { + EntityHintRequest entityHintRequest = + new EntityHintRequest.Builder() + .entity(underlaysService.getEntity(getUnderlayName(), entityName)) + .build(); + assertHintsMatch(entityHintRequest, expectedHints); + } + + protected void assertInstanceLevelHintsMatch( + String entityName, + String relatedEntityName, + Literal relatedEntityId, + Map expectedHints) { + EntityHintRequest entityHintRequest = + new EntityHintRequest.Builder() + .entity(underlaysService.getEntity(getUnderlayName(), entityName)) + .relatedEntity(underlaysService.getEntity(getUnderlayName(), relatedEntityName)) + .relatedEntityId(relatedEntityId) + .build(); + assertHintsMatch(entityHintRequest, expectedHints); + } + + private void assertHintsMatch( + EntityHintRequest entityHintRequest, Map expectedHints) { + EntityHintResult entityHintResult = querysService.listEntityHints(entityHintRequest); + + for (Map.Entry expected : expectedHints.entrySet()) { + Attribute attr = entityHintRequest.getEntity().getAttribute(expected.getKey()); + DisplayHint actual = entityHintResult.getHintMap().get(attr); + assertEquals(expected.getValue(), actual); + } + } + + protected static EnumVals buildEnumVals(List enumVals) { + List modifiableList = new ArrayList<>(enumVals); + modifiableList.sort( + Comparator.comparing(ev -> String.valueOf(ev.getValueDisplay().getDisplay()))); + return new EnumVals(modifiableList); + } +} diff --git a/service/src/test/java/bio/terra/tanagra/underlayspecific/broad/CmsSynpufHintsTest.java b/service/src/test/java/bio/terra/tanagra/underlayspecific/broad/CmsSynpufHintsTest.java new file mode 100644 index 000000000..c50d08e5e --- /dev/null +++ b/service/src/test/java/bio/terra/tanagra/underlayspecific/broad/CmsSynpufHintsTest.java @@ -0,0 +1,53 @@ +package bio.terra.tanagra.underlayspecific.broad; + +import bio.terra.tanagra.query.Literal; +import bio.terra.tanagra.underlay.DisplayHint; +import bio.terra.tanagra.underlay.ValueDisplay; +import bio.terra.tanagra.underlay.displayhint.EnumVal; +import bio.terra.tanagra.underlay.displayhint.NumericRange; +import bio.terra.tanagra.underlayspecific.BaseHintsTest; +import java.util.List; +import java.util.Map; +import org.junit.jupiter.api.Tag; +import org.junit.jupiter.api.Test; + +@Tag("broad-underlays") +public class CmsSynpufHintsTest extends BaseHintsTest { + + @Override + protected String getUnderlayName() { + return "cms_synpuf"; + } + + @Test + void personEntityLevel() { + Map expectedHints = + Map.of( + "gender", + buildEnumVals( + List.of( + new EnumVal(new ValueDisplay(new Literal(8_532L), "FEMALE"), 1_292_861), + new EnumVal(new ValueDisplay(new Literal(8_507L), "MALE"), 1_033_995))), + "race", + buildEnumVals( + List.of( + new EnumVal( + new ValueDisplay(new Literal(8_516L), "Black or African American"), + 247_723), + new EnumVal( + new ValueDisplay(new Literal(0L), "No matching concept"), 152_425), + new EnumVal(new ValueDisplay(new Literal(8_527L), "White"), 1_926_708))), + "ethnicity", + buildEnumVals( + List.of( + new EnumVal( + new ValueDisplay(new Literal(38_003_563L), "Hispanic or Latino"), + 54_453), + new EnumVal( + new ValueDisplay(new Literal(38_003_564L), "Not Hispanic or Latino"), + 2_272_403))), + "age", new NumericRange(40.0, 114.0), + "year_of_birth", new NumericRange(1909.0, 1983.0)); + assertEntityLevelHintsMatch("person", expectedHints); + } +} diff --git a/service/src/test/resources/application-test.yaml b/service/src/test/resources/application-test.yaml index 61e6b3656..d648a58d7 100644 --- a/service/src/test/resources/application-test.yaml +++ b/service/src/test/resources/application-test.yaml @@ -1,7 +1,6 @@ tanagra: underlay: - # TODO: Separate out test profiles per env. For now, this works because we're just generate SQL strings, and not using credentials to actually run the queries against BQ. - files: [ "broad/aou_synthetic/expanded/aou_synthetic.json", "broad/cms_synpuf/expanded/cms_synpuf.json", "verily/sdd/expanded/sdd.json" ] + files: [ "broad/cms_synpuf/cms_synpuf.json", "broad/aou_synthetic/aou_synthetic.json", "verily/sdd/sdd.json" ] feature: artifact-storage-enabled: true diff --git a/service/src/test/resources/sql/aousynthetic/brand-noFilter.sql b/service/src/test/resources/sql/aousynthetic/brand-noFilter.sql index bf4cfb250..ff0471aea 100644 --- a/service/src/test/resources/sql/aousynthetic/brand-noFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/brand-noFilter.sql @@ -1 +1 @@ -SELECT b.concept_code AS concept_code, b.id AS id, b.name AS name, b.standard_concept AS standard_concept, b.t_display_standard_concept AS t_display_standard_concept FROM `broad-tanagra-dev.aousynthetic_index_031323`.brand AS b LIMIT 30 +SELECT b.concept_code AS concept_code, b.id AS id, b.name AS name, b.standard_concept AS standard_concept, b.t_display_standard_concept AS t_display_standard_concept FROM `broad-tanagra-dev.aousynthetic_index_072623`.brand AS b LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/brand-textFilter.sql b/service/src/test/resources/sql/aousynthetic/brand-textFilter.sql index e41069b14..6b6927b5b 100644 --- a/service/src/test/resources/sql/aousynthetic/brand-textFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/brand-textFilter.sql @@ -1 +1 @@ -SELECT b.concept_code AS concept_code, b.id AS id, b.name AS name, b.standard_concept AS standard_concept, b.t_display_standard_concept AS t_display_standard_concept FROM `broad-tanagra-dev.aousynthetic_index_031323`.brand AS b WHERE CONTAINS_SUBSTR(b.text, 'paracetamol') LIMIT 30 +SELECT b.concept_code AS concept_code, b.id AS id, b.name AS name, b.standard_concept AS standard_concept, b.t_display_standard_concept AS t_display_standard_concept FROM `broad-tanagra-dev.aousynthetic_index_072623`.brand AS b WHERE CONTAINS_SUBSTR(b.text, 'paracetamol') LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/condition-noFilter.sql b/service/src/test/resources/sql/aousynthetic/condition-noFilter.sql index f1f380046..7e74c9806 100644 --- a/service/src/test/resources/sql/aousynthetic/condition-noFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/condition-noFilter.sql @@ -1 +1 @@ -SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, c.t_display_vocabulary AS t_display_vocabulary, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition AS c LIMIT 30 +SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, c.t_display_vocabulary AS t_display_vocabulary, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition AS c LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/condition-standard-diabetes-hierarchyAncestorFilter.sql b/service/src/test/resources/sql/aousynthetic/condition-standard-diabetes-hierarchyAncestorFilter.sql index f41ba8bda..863b40297 100644 --- a/service/src/test/resources/sql/aousynthetic/condition-standard-diabetes-hierarchyAncestorFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/condition-standard-diabetes-hierarchyAncestorFilter.sql @@ -1 +1 @@ -SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, c.t_display_vocabulary AS t_display_vocabulary, (c.t_standard_path IS NOT NULL) AS t_standard_is_member, (c.t_standard_path IS NOT NULL AND c.t_standard_path='') AS t_standard_is_root, c.t_standard_num_children AS t_standard_num_children, c.t_standard_path AS t_standard_path, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition AS c WHERE (c.id IN (SELECT c.descendant FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition_standard_ancestorDescendant AS c WHERE c.ancestor = 201826) OR c.id = 201826) LIMIT 30 +SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, c.t_display_vocabulary AS t_display_vocabulary, (c.t_standard_path IS NOT NULL) AS t_standard_is_member, (c.t_standard_path IS NOT NULL AND c.t_standard_path='') AS t_standard_is_root, c.t_standard_num_children AS t_standard_num_children, c.t_standard_path AS t_standard_path, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition AS c WHERE (c.id IN (SELECT c.descendant FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition_standard_ancestorDescendant AS c WHERE c.ancestor = 201826) OR c.id = 201826) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/condition-standard-diabetes-hierarchyParentFilter.sql b/service/src/test/resources/sql/aousynthetic/condition-standard-diabetes-hierarchyParentFilter.sql index 85e61222a..9eded3c99 100644 --- a/service/src/test/resources/sql/aousynthetic/condition-standard-diabetes-hierarchyParentFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/condition-standard-diabetes-hierarchyParentFilter.sql @@ -1 +1 @@ -SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, c.t_display_vocabulary AS t_display_vocabulary, (c.t_standard_path IS NOT NULL) AS t_standard_is_member, (c.t_standard_path IS NOT NULL AND c.t_standard_path='') AS t_standard_is_root, c.t_standard_num_children AS t_standard_num_children, c.t_standard_path AS t_standard_path, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition AS c WHERE c.id IN (SELECT c.child FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition_standard_childParent AS c WHERE c.parent = 201826) LIMIT 30 +SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, c.t_display_vocabulary AS t_display_vocabulary, (c.t_standard_path IS NOT NULL) AS t_standard_is_member, (c.t_standard_path IS NOT NULL AND c.t_standard_path='') AS t_standard_is_root, c.t_standard_num_children AS t_standard_num_children, c.t_standard_path AS t_standard_path, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition AS c WHERE c.id IN (SELECT c.child FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition_standard_childParent AS c WHERE c.parent = 201826) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/condition-standard-hierarchyMemberFilter.sql b/service/src/test/resources/sql/aousynthetic/condition-standard-hierarchyMemberFilter.sql index 8f5c5aed1..ddac40977 100644 --- a/service/src/test/resources/sql/aousynthetic/condition-standard-hierarchyMemberFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/condition-standard-hierarchyMemberFilter.sql @@ -1 +1 @@ -SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, c.t_display_vocabulary AS t_display_vocabulary, (c.t_standard_path IS NOT NULL) AS t_standard_is_member, (c.t_standard_path IS NOT NULL AND c.t_standard_path='') AS t_standard_is_root, c.t_standard_num_children AS t_standard_num_children, c.t_standard_path AS t_standard_path, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition AS c WHERE c.t_standard_path IS NOT NULL LIMIT 30 +SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, c.t_display_vocabulary AS t_display_vocabulary, (c.t_standard_path IS NOT NULL) AS t_standard_is_member, (c.t_standard_path IS NOT NULL AND c.t_standard_path='') AS t_standard_is_root, c.t_standard_num_children AS t_standard_num_children, c.t_standard_path AS t_standard_path, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition AS c WHERE c.t_standard_path IS NOT NULL LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/condition-standard-hierarchyRootFilter.sql b/service/src/test/resources/sql/aousynthetic/condition-standard-hierarchyRootFilter.sql index 0a13b1616..8c5465215 100644 --- a/service/src/test/resources/sql/aousynthetic/condition-standard-hierarchyRootFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/condition-standard-hierarchyRootFilter.sql @@ -1 +1 @@ -SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, c.t_display_vocabulary AS t_display_vocabulary, (c.t_standard_path IS NOT NULL) AS t_standard_is_member, (c.t_standard_path IS NOT NULL AND c.t_standard_path='') AS t_standard_is_root, c.t_standard_num_children AS t_standard_num_children, c.t_standard_path AS t_standard_path, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition AS c WHERE c.t_standard_path = '' LIMIT 30 +SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, c.t_display_vocabulary AS t_display_vocabulary, (c.t_standard_path IS NOT NULL) AS t_standard_is_member, (c.t_standard_path IS NOT NULL AND c.t_standard_path='') AS t_standard_is_root, c.t_standard_num_children AS t_standard_num_children, c.t_standard_path AS t_standard_path, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition AS c WHERE c.t_standard_path = '' LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/condition-textFilter.sql b/service/src/test/resources/sql/aousynthetic/condition-textFilter.sql index fa5474ba7..3bf1d2569 100644 --- a/service/src/test/resources/sql/aousynthetic/condition-textFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/condition-textFilter.sql @@ -1 +1 @@ -SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, c.t_display_vocabulary AS t_display_vocabulary, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition AS c WHERE CONTAINS_SUBSTR(c.text, 'sense of smell absent') LIMIT 30 +SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, c.t_display_vocabulary AS t_display_vocabulary, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition AS c WHERE CONTAINS_SUBSTR(c.text, 'sense of smell absent') LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/conditionoccurrence-diabetes.sql b/service/src/test/resources/sql/aousynthetic/conditionoccurrence-diabetes.sql index c33aef70c..a6a90e190 100644 --- a/service/src/test/resources/sql/aousynthetic/conditionoccurrence-diabetes.sql +++ b/service/src/test/resources/sql/aousynthetic/conditionoccurrence-diabetes.sql @@ -1 +1 @@ -SELECT c.condition AS condition, c.end_date AS end_date, c.id AS id, c.person_id AS person_id, c.source_criteria_id AS source_criteria_id, c.source_value AS source_value, c.start_date AS start_date, c.stop_reason AS stop_reason, c.t_display_condition AS t_display_condition, c.visit_occurrence_id AS visit_occurrence_id FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_condition_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition AS c WHERE c.id = 201826)))))) LIMIT 30 +SELECT c.condition AS condition, c.end_date AS end_date, c.id AS id, c.person_id AS person_id, c.source_criteria_id AS source_criteria_id, c.source_value AS source_value, c.start_date AS start_date, c.stop_reason AS stop_reason, c.t_display_condition AS t_display_condition, c.visit_occurrence_id AS visit_occurrence_id FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_condition_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition AS c WHERE c.id = 201826)))))) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/conditionoccurrence-diabetesAndSepsis.sql b/service/src/test/resources/sql/aousynthetic/conditionoccurrence-diabetesAndSepsis.sql index e6358fc89..30a4ca1e7 100644 --- a/service/src/test/resources/sql/aousynthetic/conditionoccurrence-diabetesAndSepsis.sql +++ b/service/src/test/resources/sql/aousynthetic/conditionoccurrence-diabetesAndSepsis.sql @@ -1 +1 @@ -SELECT c.condition AS condition, c.end_date AS end_date, c.id AS id, c.person_id AS person_id, c.source_criteria_id AS source_criteria_id, c.source_value AS source_value, c.start_date AS start_date, c.stop_reason AS stop_reason, c.t_display_condition AS t_display_condition, c.visit_occurrence_id AS visit_occurrence_id FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_condition_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p WHERE (p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition AS c WHERE c.id = 201826)))) AND p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition AS c WHERE c.id = 132797))))))) LIMIT 30 +SELECT c.condition AS condition, c.end_date AS end_date, c.id AS id, c.person_id AS person_id, c.source_criteria_id AS source_criteria_id, c.source_value AS source_value, c.start_date AS start_date, c.stop_reason AS stop_reason, c.t_display_condition AS t_display_condition, c.visit_occurrence_id AS visit_occurrence_id FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_condition_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p WHERE (p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition AS c WHERE c.id = 201826)))) AND p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition AS c WHERE c.id = 132797))))))) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/device-noFilter.sql b/service/src/test/resources/sql/aousynthetic/device-noFilter.sql index e4c4e2e99..8141f1baa 100644 --- a/service/src/test/resources/sql/aousynthetic/device-noFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/device-noFilter.sql @@ -1 +1 @@ -SELECT d.concept_code AS concept_code, d.id AS id, d.name AS name, d.standard_concept AS standard_concept, d.t_display_standard_concept AS t_display_standard_concept, d.t_display_vocabulary AS t_display_vocabulary, d.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.device AS d LIMIT 30 +SELECT d.concept_code AS concept_code, d.id AS id, d.name AS name, d.standard_concept AS standard_concept, d.t_display_standard_concept AS t_display_standard_concept, d.t_display_vocabulary AS t_display_vocabulary, d.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.device AS d LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/device-textFilter.sql b/service/src/test/resources/sql/aousynthetic/device-textFilter.sql index a8339cf77..a6e8e0523 100644 --- a/service/src/test/resources/sql/aousynthetic/device-textFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/device-textFilter.sql @@ -1 +1 @@ -SELECT d.concept_code AS concept_code, d.id AS id, d.name AS name, d.standard_concept AS standard_concept, d.t_display_standard_concept AS t_display_standard_concept, d.t_display_vocabulary AS t_display_vocabulary, d.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.device AS d WHERE CONTAINS_SUBSTR(d.text, 'hearing aid') LIMIT 30 +SELECT d.concept_code AS concept_code, d.id AS id, d.name AS name, d.standard_concept AS standard_concept, d.t_display_standard_concept AS t_display_standard_concept, d.t_display_vocabulary AS t_display_vocabulary, d.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.device AS d WHERE CONTAINS_SUBSTR(d.text, 'hearing aid') LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/deviceoccurrence-longLegCast.sql b/service/src/test/resources/sql/aousynthetic/deviceoccurrence-longLegCast.sql index c1eb0a612..8a7cf6492 100644 --- a/service/src/test/resources/sql/aousynthetic/deviceoccurrence-longLegCast.sql +++ b/service/src/test/resources/sql/aousynthetic/deviceoccurrence-longLegCast.sql @@ -1 +1 @@ -SELECT d.device AS device, d.end_date AS end_date, d.id AS id, d.person_id AS person_id, d.source_criteria_id AS source_criteria_id, d.source_value AS source_value, d.start_date AS start_date, d.t_display_device AS t_display_device, d.visit_occurrence_id AS visit_occurrence_id FROM `broad-tanagra-dev.aousynthetic_index_031323`.device_occurrence AS d WHERE d.id IN (SELECT i.id_device_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_device_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_device_occurrence_person AS i WHERE i.id_device_occurrence IN (SELECT d.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.device_occurrence AS d WHERE d.id IN (SELECT i.id_device_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_device_occurrence_device AS i WHERE i.id_device IN (SELECT d.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.device AS d WHERE d.id = 4038664)))))) LIMIT 30 +SELECT d.device AS device, d.end_date AS end_date, d.id AS id, d.person_id AS person_id, d.source_criteria_id AS source_criteria_id, d.source_value AS source_value, d.start_date AS start_date, d.t_display_device AS t_display_device, d.visit_occurrence_id AS visit_occurrence_id FROM `broad-tanagra-dev.aousynthetic_index_072623`.device_occurrence AS d WHERE d.id IN (SELECT i.id_device_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_device_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_device_occurrence_person AS i WHERE i.id_device_occurrence IN (SELECT d.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.device_occurrence AS d WHERE d.id IN (SELECT i.id_device_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_device_occurrence_device AS i WHERE i.id_device IN (SELECT d.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.device AS d WHERE d.id = 4038664)))))) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/ingredient-noFilter.sql b/service/src/test/resources/sql/aousynthetic/ingredient-noFilter.sql index 1f53b6bc4..d2445db36 100644 --- a/service/src/test/resources/sql/aousynthetic/ingredient-noFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/ingredient-noFilter.sql @@ -1 +1 @@ -SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.t_display_vocabulary AS t_display_vocabulary, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.ingredient AS i LIMIT 30 +SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.t_display_vocabulary AS t_display_vocabulary, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.ingredient AS i LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/ingredient-relationshipFilter.sql b/service/src/test/resources/sql/aousynthetic/ingredient-relationshipFilter.sql index efdb48878..b78b48835 100644 --- a/service/src/test/resources/sql/aousynthetic/ingredient-relationshipFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/ingredient-relationshipFilter.sql @@ -1 +1 @@ -SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.t_display_vocabulary AS t_display_vocabulary, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.ingredient AS i WHERE i.id IN (SELECT i.id_ingredient FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_brand_ingredient AS i WHERE i.id_brand IN (SELECT b.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.brand AS b WHERE b.id = 19082059)) LIMIT 30 +SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.t_display_vocabulary AS t_display_vocabulary, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.ingredient AS i WHERE i.id IN (SELECT i.id_ingredient FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_brand_ingredient AS i WHERE i.id_brand IN (SELECT b.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.brand AS b WHERE b.id = 19082059)) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/ingredient-standard-cardiacPreparations-hierarchyAncestorFilter.sql b/service/src/test/resources/sql/aousynthetic/ingredient-standard-cardiacPreparations-hierarchyAncestorFilter.sql index 0f7521891..8d71222f0 100644 --- a/service/src/test/resources/sql/aousynthetic/ingredient-standard-cardiacPreparations-hierarchyAncestorFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/ingredient-standard-cardiacPreparations-hierarchyAncestorFilter.sql @@ -1 +1 @@ -SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.t_display_vocabulary AS t_display_vocabulary, (i.t_standard_path IS NOT NULL) AS t_standard_is_member, (i.t_standard_path IS NOT NULL AND i.t_standard_path='') AS t_standard_is_root, i.t_standard_num_children AS t_standard_num_children, i.t_standard_path AS t_standard_path, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.ingredient AS i WHERE (i.id IN (SELECT i.descendant FROM `broad-tanagra-dev.aousynthetic_index_031323`.ingredient_standard_ancestorDescendant AS i WHERE i.ancestor = 21600360) OR i.id = 21600360) LIMIT 30 +SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.t_display_vocabulary AS t_display_vocabulary, (i.t_standard_path IS NOT NULL) AS t_standard_is_member, (i.t_standard_path IS NOT NULL AND i.t_standard_path='') AS t_standard_is_root, i.t_standard_num_children AS t_standard_num_children, i.t_standard_path AS t_standard_path, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.ingredient AS i WHERE (i.id IN (SELECT i.descendant FROM `broad-tanagra-dev.aousynthetic_index_072623`.ingredient_standard_ancestorDescendant AS i WHERE i.ancestor = 21600360) OR i.id = 21600360) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/ingredient-standard-hierarchyMemberFilter.sql b/service/src/test/resources/sql/aousynthetic/ingredient-standard-hierarchyMemberFilter.sql index 744a0fbd8..255aa5c76 100644 --- a/service/src/test/resources/sql/aousynthetic/ingredient-standard-hierarchyMemberFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/ingredient-standard-hierarchyMemberFilter.sql @@ -1 +1 @@ -SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.t_display_vocabulary AS t_display_vocabulary, (i.t_standard_path IS NOT NULL) AS t_standard_is_member, (i.t_standard_path IS NOT NULL AND i.t_standard_path='') AS t_standard_is_root, i.t_standard_num_children AS t_standard_num_children, i.t_standard_path AS t_standard_path, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.ingredient AS i WHERE i.t_standard_path IS NOT NULL LIMIT 30 +SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.t_display_vocabulary AS t_display_vocabulary, (i.t_standard_path IS NOT NULL) AS t_standard_is_member, (i.t_standard_path IS NOT NULL AND i.t_standard_path='') AS t_standard_is_root, i.t_standard_num_children AS t_standard_num_children, i.t_standard_path AS t_standard_path, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.ingredient AS i WHERE i.t_standard_path IS NOT NULL LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/ingredient-standard-hierarchyRootFilter.sql b/service/src/test/resources/sql/aousynthetic/ingredient-standard-hierarchyRootFilter.sql index 4c7c0ce68..ac78e44c4 100644 --- a/service/src/test/resources/sql/aousynthetic/ingredient-standard-hierarchyRootFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/ingredient-standard-hierarchyRootFilter.sql @@ -1 +1 @@ -SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.t_display_vocabulary AS t_display_vocabulary, (i.t_standard_path IS NOT NULL) AS t_standard_is_member, (i.t_standard_path IS NOT NULL AND i.t_standard_path='') AS t_standard_is_root, i.t_standard_num_children AS t_standard_num_children, i.t_standard_path AS t_standard_path, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.ingredient AS i WHERE i.t_standard_path = '' LIMIT 30 +SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.t_display_vocabulary AS t_display_vocabulary, (i.t_standard_path IS NOT NULL) AS t_standard_is_member, (i.t_standard_path IS NOT NULL AND i.t_standard_path='') AS t_standard_is_root, i.t_standard_num_children AS t_standard_num_children, i.t_standard_path AS t_standard_path, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.ingredient AS i WHERE i.t_standard_path = '' LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/ingredient-standard-opioids-hierarchyParentFilter.sql b/service/src/test/resources/sql/aousynthetic/ingredient-standard-opioids-hierarchyParentFilter.sql index b13baf446..387a1da33 100644 --- a/service/src/test/resources/sql/aousynthetic/ingredient-standard-opioids-hierarchyParentFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/ingredient-standard-opioids-hierarchyParentFilter.sql @@ -1 +1 @@ -SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.t_display_vocabulary AS t_display_vocabulary, (i.t_standard_path IS NOT NULL) AS t_standard_is_member, (i.t_standard_path IS NOT NULL AND i.t_standard_path='') AS t_standard_is_root, i.t_standard_num_children AS t_standard_num_children, i.t_standard_path AS t_standard_path, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.ingredient AS i WHERE i.id IN (SELECT i.child FROM `broad-tanagra-dev.aousynthetic_index_031323`.ingredient_standard_childParent AS i WHERE i.parent = 21603396) LIMIT 30 +SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.t_display_vocabulary AS t_display_vocabulary, (i.t_standard_path IS NOT NULL) AS t_standard_is_member, (i.t_standard_path IS NOT NULL AND i.t_standard_path='') AS t_standard_is_root, i.t_standard_num_children AS t_standard_num_children, i.t_standard_path AS t_standard_path, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.ingredient AS i WHERE i.id IN (SELECT i.child FROM `broad-tanagra-dev.aousynthetic_index_072623`.ingredient_standard_childParent AS i WHERE i.parent = 21603396) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/ingredient-textFilter.sql b/service/src/test/resources/sql/aousynthetic/ingredient-textFilter.sql index a709daf2b..82a78eaa8 100644 --- a/service/src/test/resources/sql/aousynthetic/ingredient-textFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/ingredient-textFilter.sql @@ -1 +1 @@ -SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.t_display_vocabulary AS t_display_vocabulary, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.ingredient AS i WHERE CONTAINS_SUBSTR(i.text, 'alcohol') LIMIT 30 +SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.t_display_vocabulary AS t_display_vocabulary, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.ingredient AS i WHERE CONTAINS_SUBSTR(i.text, 'alcohol') LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/ingredientoccurrence-ibuprofen.sql b/service/src/test/resources/sql/aousynthetic/ingredientoccurrence-ibuprofen.sql index 1da65c1c4..783f90759 100644 --- a/service/src/test/resources/sql/aousynthetic/ingredientoccurrence-ibuprofen.sql +++ b/service/src/test/resources/sql/aousynthetic/ingredientoccurrence-ibuprofen.sql @@ -1 +1 @@ -SELECT i.days_supply AS days_supply, i.end_date AS end_date, i.id AS id, i.ingredient AS ingredient, i.person_id AS person_id, i.refills AS refills, i.source_criteria_id AS source_criteria_id, i.source_value AS source_value, i.start_date AS start_date, i.stop_reason AS stop_reason, i.t_display_ingredient AS t_display_ingredient, i.visit_occurrence_id AS visit_occurrence_id FROM `broad-tanagra-dev.aousynthetic_index_031323`.ingredient_occurrence AS i WHERE i.id IN (SELECT i.id_ingredient_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_ingredient_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_ingredient_occurrence_person AS i WHERE i.id_ingredient_occurrence IN (SELECT i.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.ingredient_occurrence AS i WHERE i.id IN (SELECT i.id_ingredient_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_ingredient_occurrence_ingredient AS i WHERE i.id_ingredient IN (SELECT i.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.ingredient AS i WHERE i.id = 1177480)))))) LIMIT 30 +SELECT i.days_supply AS days_supply, i.end_date AS end_date, i.id AS id, i.ingredient AS ingredient, i.person_id AS person_id, i.refills AS refills, i.source_criteria_id AS source_criteria_id, i.source_value AS source_value, i.start_date AS start_date, i.stop_reason AS stop_reason, i.t_display_ingredient AS t_display_ingredient, i.visit_occurrence_id AS visit_occurrence_id FROM `broad-tanagra-dev.aousynthetic_index_072623`.ingredient_occurrence AS i WHERE i.id IN (SELECT i.id_ingredient_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_ingredient_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_ingredient_occurrence_person AS i WHERE i.id_ingredient_occurrence IN (SELECT i.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.ingredient_occurrence AS i WHERE i.id IN (SELECT i.id_ingredient_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_ingredient_occurrence_ingredient AS i WHERE i.id_ingredient IN (SELECT i.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.ingredient AS i WHERE i.id = 1177480)))))) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/measurement-hierarchyRootFilterLOINC.sql b/service/src/test/resources/sql/aousynthetic/measurement-hierarchyRootFilterLOINC.sql index d0059fb04..12140bd9d 100644 --- a/service/src/test/resources/sql/aousynthetic/measurement-hierarchyRootFilterLOINC.sql +++ b/service/src/test/resources/sql/aousynthetic/measurement-hierarchyRootFilterLOINC.sql @@ -1 +1 @@ -SELECT m.concept_code AS concept_code, m.id AS id, m.name AS name, m.standard_concept AS standard_concept, m.t_display_standard_concept AS t_display_standard_concept, m.t_display_vocabulary AS t_display_vocabulary, (m.t_standard_path IS NOT NULL) AS t_standard_is_member, (m.t_standard_path IS NOT NULL AND m.t_standard_path='') AS t_standard_is_root, m.t_standard_num_children AS t_standard_num_children, m.t_standard_path AS t_standard_path, m.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.measurement AS m WHERE (m.t_standard_path = '' AND m.vocabulary = 'LOINC') LIMIT 30 +SELECT m.concept_code AS concept_code, m.id AS id, m.name AS name, m.standard_concept AS standard_concept, m.t_display_standard_concept AS t_display_standard_concept, m.t_display_vocabulary AS t_display_vocabulary, (m.t_standard_path IS NOT NULL) AS t_standard_is_member, (m.t_standard_path IS NOT NULL AND m.t_standard_path='') AS t_standard_is_root, m.t_standard_num_children AS t_standard_num_children, m.t_standard_path AS t_standard_path, m.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.measurement AS m WHERE (m.t_standard_path = '' AND m.vocabulary = 'LOINC') LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/measurement-hierarchyRootFilterSNOMED.sql b/service/src/test/resources/sql/aousynthetic/measurement-hierarchyRootFilterSNOMED.sql index 368454c77..30afb25a6 100644 --- a/service/src/test/resources/sql/aousynthetic/measurement-hierarchyRootFilterSNOMED.sql +++ b/service/src/test/resources/sql/aousynthetic/measurement-hierarchyRootFilterSNOMED.sql @@ -1 +1 @@ -SELECT m.concept_code AS concept_code, m.id AS id, m.name AS name, m.standard_concept AS standard_concept, m.t_display_standard_concept AS t_display_standard_concept, m.t_display_vocabulary AS t_display_vocabulary, (m.t_standard_path IS NOT NULL) AS t_standard_is_member, (m.t_standard_path IS NOT NULL AND m.t_standard_path='') AS t_standard_is_root, m.t_standard_num_children AS t_standard_num_children, m.t_standard_path AS t_standard_path, m.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.measurement AS m WHERE (m.t_standard_path = '' AND m.vocabulary = 'SNOMED') LIMIT 30 +SELECT m.concept_code AS concept_code, m.id AS id, m.name AS name, m.standard_concept AS standard_concept, m.t_display_standard_concept AS t_display_standard_concept, m.t_display_vocabulary AS t_display_vocabulary, (m.t_standard_path IS NOT NULL) AS t_standard_is_member, (m.t_standard_path IS NOT NULL AND m.t_standard_path='') AS t_standard_is_root, m.t_standard_num_children AS t_standard_num_children, m.t_standard_path AS t_standard_path, m.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.measurement AS m WHERE (m.t_standard_path = '' AND m.vocabulary = 'SNOMED') LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/measurement-noFilter.sql b/service/src/test/resources/sql/aousynthetic/measurement-noFilter.sql index 02c3764bc..60f77a840 100644 --- a/service/src/test/resources/sql/aousynthetic/measurement-noFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/measurement-noFilter.sql @@ -1 +1 @@ -SELECT m.concept_code AS concept_code, m.id AS id, m.name AS name, m.standard_concept AS standard_concept, m.t_display_standard_concept AS t_display_standard_concept, m.t_display_vocabulary AS t_display_vocabulary, m.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.measurement AS m LIMIT 30 +SELECT m.concept_code AS concept_code, m.id AS id, m.name AS name, m.standard_concept AS standard_concept, m.t_display_standard_concept AS t_display_standard_concept, m.t_display_vocabulary AS t_display_vocabulary, m.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.measurement AS m LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/measurement-standard-glucoseTolerance-hierarchyAncestorFilter.sql b/service/src/test/resources/sql/aousynthetic/measurement-standard-glucoseTolerance-hierarchyAncestorFilter.sql index 1c4831b50..871ef65d2 100644 --- a/service/src/test/resources/sql/aousynthetic/measurement-standard-glucoseTolerance-hierarchyAncestorFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/measurement-standard-glucoseTolerance-hierarchyAncestorFilter.sql @@ -1 +1 @@ -SELECT m.concept_code AS concept_code, m.id AS id, m.name AS name, m.standard_concept AS standard_concept, m.t_display_standard_concept AS t_display_standard_concept, m.t_display_vocabulary AS t_display_vocabulary, (m.t_standard_path IS NOT NULL) AS t_standard_is_member, (m.t_standard_path IS NOT NULL AND m.t_standard_path='') AS t_standard_is_root, m.t_standard_num_children AS t_standard_num_children, m.t_standard_path AS t_standard_path, m.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.measurement AS m WHERE (m.id IN (SELECT m.descendant FROM `broad-tanagra-dev.aousynthetic_index_031323`.measurement_standard_ancestorDescendant AS m WHERE m.ancestor = 37048668) OR m.id = 37048668) LIMIT 30 +SELECT m.concept_code AS concept_code, m.id AS id, m.name AS name, m.standard_concept AS standard_concept, m.t_display_standard_concept AS t_display_standard_concept, m.t_display_vocabulary AS t_display_vocabulary, (m.t_standard_path IS NOT NULL) AS t_standard_is_member, (m.t_standard_path IS NOT NULL AND m.t_standard_path='') AS t_standard_is_root, m.t_standard_num_children AS t_standard_num_children, m.t_standard_path AS t_standard_path, m.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.measurement AS m WHERE (m.id IN (SELECT m.descendant FROM `broad-tanagra-dev.aousynthetic_index_072623`.measurement_standard_ancestorDescendant AS m WHERE m.ancestor = 37048668) OR m.id = 37048668) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/measurement-standard-glucoseTolerance-hierarchyParentFilter.sql b/service/src/test/resources/sql/aousynthetic/measurement-standard-glucoseTolerance-hierarchyParentFilter.sql index d059e56d0..3aaf7fbda 100644 --- a/service/src/test/resources/sql/aousynthetic/measurement-standard-glucoseTolerance-hierarchyParentFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/measurement-standard-glucoseTolerance-hierarchyParentFilter.sql @@ -1 +1 @@ -SELECT m.concept_code AS concept_code, m.id AS id, m.name AS name, m.standard_concept AS standard_concept, m.t_display_standard_concept AS t_display_standard_concept, m.t_display_vocabulary AS t_display_vocabulary, (m.t_standard_path IS NOT NULL) AS t_standard_is_member, (m.t_standard_path IS NOT NULL AND m.t_standard_path='') AS t_standard_is_root, m.t_standard_num_children AS t_standard_num_children, m.t_standard_path AS t_standard_path, m.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.measurement AS m WHERE m.id IN (SELECT m.child FROM `broad-tanagra-dev.aousynthetic_index_031323`.measurement_standard_childParent AS m WHERE m.parent = 37072239) LIMIT 30 +SELECT m.concept_code AS concept_code, m.id AS id, m.name AS name, m.standard_concept AS standard_concept, m.t_display_standard_concept AS t_display_standard_concept, m.t_display_vocabulary AS t_display_vocabulary, (m.t_standard_path IS NOT NULL) AS t_standard_is_member, (m.t_standard_path IS NOT NULL AND m.t_standard_path='') AS t_standard_is_root, m.t_standard_num_children AS t_standard_num_children, m.t_standard_path AS t_standard_path, m.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.measurement AS m WHERE m.id IN (SELECT m.child FROM `broad-tanagra-dev.aousynthetic_index_072623`.measurement_standard_childParent AS m WHERE m.parent = 37072239) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/measurement-textFilter.sql b/service/src/test/resources/sql/aousynthetic/measurement-textFilter.sql index 17faa7d2b..5d7f578e2 100644 --- a/service/src/test/resources/sql/aousynthetic/measurement-textFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/measurement-textFilter.sql @@ -1 +1 @@ -SELECT m.concept_code AS concept_code, m.id AS id, m.name AS name, m.standard_concept AS standard_concept, m.t_display_standard_concept AS t_display_standard_concept, m.t_display_vocabulary AS t_display_vocabulary, m.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.measurement AS m WHERE CONTAINS_SUBSTR(m.text, 'hematocrit') LIMIT 30 +SELECT m.concept_code AS concept_code, m.id AS id, m.name AS name, m.standard_concept AS standard_concept, m.t_display_standard_concept AS t_display_standard_concept, m.t_display_vocabulary AS t_display_vocabulary, m.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.measurement AS m WHERE CONTAINS_SUBSTR(m.text, 'hematocrit') LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/measurementoccurrence-hematocrit.sql b/service/src/test/resources/sql/aousynthetic/measurementoccurrence-hematocrit.sql index f9736938f..4a3dcec57 100644 --- a/service/src/test/resources/sql/aousynthetic/measurementoccurrence-hematocrit.sql +++ b/service/src/test/resources/sql/aousynthetic/measurementoccurrence-hematocrit.sql @@ -1 +1 @@ -SELECT m.date AS date, m.id AS id, m.measurement AS measurement, m.person_id AS person_id, m.source_criteria_id AS source_criteria_id, m.source_value AS source_value, m.t_display_measurement AS t_display_measurement, m.t_display_unit AS t_display_unit, m.t_display_value_enum AS t_display_value_enum, m.unit AS unit, m.value_enum AS value_enum, m.value_numeric AS value_numeric, m.visit_occurrence_id AS visit_occurrence_id FROM `broad-tanagra-dev.aousynthetic_index_031323`.measurement_occurrence AS m WHERE m.id IN (SELECT i.id_measurement_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_measurement_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_measurement_occurrence_person AS i WHERE i.id_measurement_occurrence IN (SELECT m.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.measurement_occurrence AS m WHERE m.id IN (SELECT i.id_measurement_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_measurement_occurrence_measurement AS i WHERE i.id_measurement IN (SELECT m.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.measurement AS m WHERE m.id = 3009542)))))) LIMIT 30 +SELECT m.date AS date, m.id AS id, m.measurement AS measurement, m.person_id AS person_id, m.source_criteria_id AS source_criteria_id, m.source_value AS source_value, m.t_display_measurement AS t_display_measurement, m.t_display_unit AS t_display_unit, m.t_display_value_enum AS t_display_value_enum, m.unit AS unit, m.value_enum AS value_enum, m.value_numeric AS value_numeric, m.visit_occurrence_id AS visit_occurrence_id FROM `broad-tanagra-dev.aousynthetic_index_072623`.measurement_occurrence AS m WHERE m.id IN (SELECT i.id_measurement_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_measurement_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_measurement_occurrence_person AS i WHERE i.id_measurement_occurrence IN (SELECT m.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.measurement_occurrence AS m WHERE m.id IN (SELECT i.id_measurement_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_measurement_occurrence_measurement AS i WHERE i.id_measurement IN (SELECT m.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.measurement AS m WHERE m.id = 3009542)))))) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/observation-noFilter.sql b/service/src/test/resources/sql/aousynthetic/observation-noFilter.sql index ee4392bf9..00d1482d7 100644 --- a/service/src/test/resources/sql/aousynthetic/observation-noFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/observation-noFilter.sql @@ -1 +1 @@ -SELECT o.concept_code AS concept_code, o.id AS id, o.name AS name, o.standard_concept AS standard_concept, o.t_display_standard_concept AS t_display_standard_concept, o.t_display_vocabulary AS t_display_vocabulary, o.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.observation AS o LIMIT 30 +SELECT o.concept_code AS concept_code, o.id AS id, o.name AS name, o.standard_concept AS standard_concept, o.t_display_standard_concept AS t_display_standard_concept, o.t_display_vocabulary AS t_display_vocabulary, o.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.observation AS o LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/observation-textFilter.sql b/service/src/test/resources/sql/aousynthetic/observation-textFilter.sql index d666d2e5a..74a0a4a6a 100644 --- a/service/src/test/resources/sql/aousynthetic/observation-textFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/observation-textFilter.sql @@ -1 +1 @@ -SELECT o.concept_code AS concept_code, o.id AS id, o.name AS name, o.standard_concept AS standard_concept, o.t_display_standard_concept AS t_display_standard_concept, o.t_display_vocabulary AS t_display_vocabulary, o.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.observation AS o WHERE CONTAINS_SUBSTR(o.text, 'smoke') LIMIT 30 +SELECT o.concept_code AS concept_code, o.id AS id, o.name AS name, o.standard_concept AS standard_concept, o.t_display_standard_concept AS t_display_standard_concept, o.t_display_vocabulary AS t_display_vocabulary, o.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.observation AS o WHERE CONTAINS_SUBSTR(o.text, 'smoke') LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/observationoccurrence-vaccineRefusal.sql b/service/src/test/resources/sql/aousynthetic/observationoccurrence-vaccineRefusal.sql index a040a591a..f2ddb06b6 100644 --- a/service/src/test/resources/sql/aousynthetic/observationoccurrence-vaccineRefusal.sql +++ b/service/src/test/resources/sql/aousynthetic/observationoccurrence-vaccineRefusal.sql @@ -1 +1 @@ -SELECT o.date AS date, o.id AS id, o.observation AS observation, o.person_id AS person_id, o.source_criteria_id AS source_criteria_id, o.source_value AS source_value, o.t_display_observation AS t_display_observation, o.t_display_unit AS t_display_unit, o.t_display_value AS t_display_value, o.unit AS unit, o.value AS value, o.value_as_string AS value_as_string, o.visit_occurrence_id AS visit_occurrence_id FROM `broad-tanagra-dev.aousynthetic_index_031323`.observation_occurrence AS o WHERE o.id IN (SELECT i.id_observation_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_observation_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_observation_occurrence_person AS i WHERE i.id_observation_occurrence IN (SELECT o.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.observation_occurrence AS o WHERE o.id IN (SELECT i.id_observation_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_observation_occurrence_observation AS i WHERE i.id_observation IN (SELECT o.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.observation AS o WHERE o.id = 43531662)))))) LIMIT 30 +SELECT o.date AS date, o.id AS id, o.observation AS observation, o.person_id AS person_id, o.source_criteria_id AS source_criteria_id, o.source_value AS source_value, o.t_display_observation AS t_display_observation, o.t_display_unit AS t_display_unit, o.t_display_value AS t_display_value, o.unit AS unit, o.value AS value, o.value_as_string AS value_as_string, o.visit_occurrence_id AS visit_occurrence_id FROM `broad-tanagra-dev.aousynthetic_index_072623`.observation_occurrence AS o WHERE o.id IN (SELECT i.id_observation_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_observation_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_observation_occurrence_person AS i WHERE i.id_observation_occurrence IN (SELECT o.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.observation_occurrence AS o WHERE o.id IN (SELECT i.id_observation_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_observation_occurrence_observation AS i WHERE i.id_observation IN (SELECT o.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.observation AS o WHERE o.id = 43531662)))))) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/person-all-count.sql b/service/src/test/resources/sql/aousynthetic/person-all-count.sql index 441b686d0..36fde29fa 100644 --- a/service/src/test/resources/sql/aousynthetic/person-all-count.sql +++ b/service/src/test/resources/sql/aousynthetic/person-all-count.sql @@ -1 +1 @@ -SELECT COUNT(p.id) AS t_count FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p +SELECT COUNT(p.id) AS t_count FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p diff --git a/service/src/test/resources/sql/aousynthetic/person-diabetes-count.sql b/service/src/test/resources/sql/aousynthetic/person-diabetes-count.sql index 16c85949f..2c9ac1dc7 100644 --- a/service/src/test/resources/sql/aousynthetic/person-diabetes-count.sql +++ b/service/src/test/resources/sql/aousynthetic/person-diabetes-count.sql @@ -1 +1 @@ -SELECT p.gender AS gender, p.race AS race, COUNT(p.id) AS t_count, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition AS c WHERE c.id = 201826)))) GROUP BY gender, t_display_gender, race, t_display_race ORDER BY gender ASC, t_display_gender ASC, race ASC, t_display_race ASC +SELECT p.gender AS gender, p.race AS race, COUNT(p.id) AS t_count, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition AS c WHERE c.id = 201826)))) GROUP BY gender, t_display_gender, race, t_display_race ORDER BY gender ASC, t_display_gender ASC, race ASC, t_display_race ASC diff --git a/service/src/test/resources/sql/aousynthetic/person-diabetes-numOccurrenceDates.sql b/service/src/test/resources/sql/aousynthetic/person-diabetes-numOccurrenceDates.sql index 37f7b7843..1485169dc 100644 --- a/service/src/test/resources/sql/aousynthetic/person-diabetes-numOccurrenceDates.sql +++ b/service/src/test/resources/sql/aousynthetic/person-diabetes-numOccurrenceDates.sql @@ -1 +1 @@ -SELECT p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.sex_at_birth AS sex_at_birth, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.t_display_sex_at_birth AS t_display_sex_at_birth, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p WHERE p.id IN (SELECT x.person_id FROM (SELECT c.condition AS condition, c.person_id AS person_id, c.t_display_condition AS t_display_condition FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition AS c WHERE c.id = 201826)) GROUP BY person_id, condition, t_display_condition) AS x GROUP BY x.person_id HAVING COUNT(*) > 1) LIMIT 30 +SELECT p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.sex_at_birth AS sex_at_birth, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.t_display_sex_at_birth AS t_display_sex_at_birth, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p WHERE p.id IN (SELECT x.person_id FROM (SELECT c.condition AS condition, c.person_id AS person_id, c.t_display_condition AS t_display_condition FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition AS c WHERE c.id = 201826)) GROUP BY person_id, condition, t_display_condition) AS x GROUP BY x.person_id HAVING COUNT(*) > 1) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/person-diabetes.sql b/service/src/test/resources/sql/aousynthetic/person-diabetes.sql index 9dabd5419..29396d5f1 100644 --- a/service/src/test/resources/sql/aousynthetic/person-diabetes.sql +++ b/service/src/test/resources/sql/aousynthetic/person-diabetes.sql @@ -1 +1 @@ -SELECT p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.sex_at_birth AS sex_at_birth, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.t_display_sex_at_birth AS t_display_sex_at_birth, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.condition AS c WHERE c.id = 201826)))) LIMIT 30 +SELECT p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.sex_at_birth AS sex_at_birth, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.t_display_sex_at_birth AS t_display_sex_at_birth, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.condition AS c WHERE c.id = 201826)))) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/person-genderRace-count.sql b/service/src/test/resources/sql/aousynthetic/person-genderRace-count.sql index 8306cb0a3..6796c71a0 100644 --- a/service/src/test/resources/sql/aousynthetic/person-genderRace-count.sql +++ b/service/src/test/resources/sql/aousynthetic/person-genderRace-count.sql @@ -1 +1 @@ -SELECT p.gender AS gender, p.race AS race, COUNT(p.id) AS t_count, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p GROUP BY gender, t_display_gender, race, t_display_race ORDER BY gender ASC, t_display_gender ASC, race ASC, t_display_race ASC +SELECT p.gender AS gender, p.race AS race, COUNT(p.id) AS t_count, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p GROUP BY gender, t_display_gender, race, t_display_race ORDER BY gender ASC, t_display_gender ASC, race ASC, t_display_race ASC diff --git a/service/src/test/resources/sql/aousynthetic/person-hematocrit.sql b/service/src/test/resources/sql/aousynthetic/person-hematocrit.sql index e9285c60b..2226c4a3d 100644 --- a/service/src/test/resources/sql/aousynthetic/person-hematocrit.sql +++ b/service/src/test/resources/sql/aousynthetic/person-hematocrit.sql @@ -1 +1 @@ -SELECT p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.sex_at_birth AS sex_at_birth, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.t_display_sex_at_birth AS t_display_sex_at_birth, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_measurement_occurrence_person AS i WHERE i.id_measurement_occurrence IN (SELECT m.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.measurement_occurrence AS m WHERE m.id IN (SELECT i.id_measurement_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_measurement_occurrence_measurement AS i WHERE i.id_measurement IN (SELECT m.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.measurement AS m WHERE m.id = 3009542)))) LIMIT 30 +SELECT p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.sex_at_birth AS sex_at_birth, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.t_display_sex_at_birth AS t_display_sex_at_birth, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_measurement_occurrence_person AS i WHERE i.id_measurement_occurrence IN (SELECT m.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.measurement_occurrence AS m WHERE m.id IN (SELECT i.id_measurement_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_measurement_occurrence_measurement AS i WHERE i.id_measurement IN (SELECT m.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.measurement AS m WHERE m.id = 3009542)))) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/person-ibuprofen.sql b/service/src/test/resources/sql/aousynthetic/person-ibuprofen.sql index 2e70ca822..98b61538c 100644 --- a/service/src/test/resources/sql/aousynthetic/person-ibuprofen.sql +++ b/service/src/test/resources/sql/aousynthetic/person-ibuprofen.sql @@ -1 +1 @@ -SELECT p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.sex_at_birth AS sex_at_birth, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.t_display_sex_at_birth AS t_display_sex_at_birth, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_ingredient_occurrence_person AS i WHERE i.id_ingredient_occurrence IN (SELECT i.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.ingredient_occurrence AS i WHERE i.id IN (SELECT i.id_ingredient_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_ingredient_occurrence_ingredient AS i WHERE i.id_ingredient IN (SELECT i.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.ingredient AS i WHERE i.id = 1177480)))) LIMIT 30 +SELECT p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.sex_at_birth AS sex_at_birth, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.t_display_sex_at_birth AS t_display_sex_at_birth, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_ingredient_occurrence_person AS i WHERE i.id_ingredient_occurrence IN (SELECT i.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.ingredient_occurrence AS i WHERE i.id IN (SELECT i.id_ingredient_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_ingredient_occurrence_ingredient AS i WHERE i.id_ingredient IN (SELECT i.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.ingredient AS i WHERE i.id = 1177480)))) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/person-longLegCast.sql b/service/src/test/resources/sql/aousynthetic/person-longLegCast.sql index 9958142e8..20ee0828f 100644 --- a/service/src/test/resources/sql/aousynthetic/person-longLegCast.sql +++ b/service/src/test/resources/sql/aousynthetic/person-longLegCast.sql @@ -1 +1 @@ -SELECT p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.sex_at_birth AS sex_at_birth, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.t_display_sex_at_birth AS t_display_sex_at_birth, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_device_occurrence_person AS i WHERE i.id_device_occurrence IN (SELECT d.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.device_occurrence AS d WHERE d.id IN (SELECT i.id_device_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_device_occurrence_device AS i WHERE i.id_device IN (SELECT d.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.device AS d WHERE d.id = 4038664)))) LIMIT 30 +SELECT p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.sex_at_birth AS sex_at_birth, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.t_display_sex_at_birth AS t_display_sex_at_birth, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_device_occurrence_person AS i WHERE i.id_device_occurrence IN (SELECT d.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.device_occurrence AS d WHERE d.id IN (SELECT i.id_device_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_device_occurrence_device AS i WHERE i.id_device IN (SELECT d.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.device AS d WHERE d.id = 4038664)))) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/person-mammogram.sql b/service/src/test/resources/sql/aousynthetic/person-mammogram.sql index d9104906d..0abb01800 100644 --- a/service/src/test/resources/sql/aousynthetic/person-mammogram.sql +++ b/service/src/test/resources/sql/aousynthetic/person-mammogram.sql @@ -1 +1 @@ -SELECT p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.sex_at_birth AS sex_at_birth, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.t_display_sex_at_birth AS t_display_sex_at_birth, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_procedure_occurrence_person AS i WHERE i.id_procedure_occurrence IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.procedure_occurrence AS p WHERE p.id IN (SELECT i.id_procedure_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_procedure_occurrence_procedure AS i WHERE i.id_procedure IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.procedure AS p WHERE p.id = 4324693)))) LIMIT 30 +SELECT p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.sex_at_birth AS sex_at_birth, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.t_display_sex_at_birth AS t_display_sex_at_birth, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_procedure_occurrence_person AS i WHERE i.id_procedure_occurrence IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.procedure_occurrence AS p WHERE p.id IN (SELECT i.id_procedure_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_procedure_occurrence_procedure AS i WHERE i.id_procedure IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.procedure AS p WHERE p.id = 4324693)))) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/person-noFilter.sql b/service/src/test/resources/sql/aousynthetic/person-noFilter.sql index 68ec37731..01fd717af 100644 --- a/service/src/test/resources/sql/aousynthetic/person-noFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/person-noFilter.sql @@ -1 +1 @@ -SELECT p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.sex_at_birth AS sex_at_birth, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.t_display_sex_at_birth AS t_display_sex_at_birth, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p LIMIT 30 +SELECT p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.sex_at_birth AS sex_at_birth, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.t_display_sex_at_birth AS t_display_sex_at_birth, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/person-outpatient.sql b/service/src/test/resources/sql/aousynthetic/person-outpatient.sql index 89b5f5752..fbf3c1f40 100644 --- a/service/src/test/resources/sql/aousynthetic/person-outpatient.sql +++ b/service/src/test/resources/sql/aousynthetic/person-outpatient.sql @@ -1 +1 @@ -SELECT p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.sex_at_birth AS sex_at_birth, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.t_display_sex_at_birth AS t_display_sex_at_birth, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_visit_occurrence_person AS i WHERE i.id_visit_occurrence IN (SELECT v.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.visit_occurrence AS v WHERE v.id IN (SELECT i.id_visit_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_visit_occurrence_visit AS i WHERE i.id_visit IN (SELECT v.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.visit AS v WHERE v.id = 9202)))) LIMIT 30 +SELECT p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.sex_at_birth AS sex_at_birth, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.t_display_sex_at_birth AS t_display_sex_at_birth, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_visit_occurrence_person AS i WHERE i.id_visit_occurrence IN (SELECT v.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.visit_occurrence AS v WHERE v.id IN (SELECT i.id_visit_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_visit_occurrence_visit AS i WHERE i.id_visit IN (SELECT v.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.visit AS v WHERE v.id = 9202)))) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/person-vaccineRefusal.sql b/service/src/test/resources/sql/aousynthetic/person-vaccineRefusal.sql index 070c78e6e..1f23b9d72 100644 --- a/service/src/test/resources/sql/aousynthetic/person-vaccineRefusal.sql +++ b/service/src/test/resources/sql/aousynthetic/person-vaccineRefusal.sql @@ -1 +1 @@ -SELECT p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.sex_at_birth AS sex_at_birth, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.t_display_sex_at_birth AS t_display_sex_at_birth, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_observation_occurrence_person AS i WHERE i.id_observation_occurrence IN (SELECT o.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.observation_occurrence AS o WHERE o.id IN (SELECT i.id_observation_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_observation_occurrence_observation AS i WHERE i.id_observation IN (SELECT o.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.observation AS o WHERE o.id = 43531662)))) LIMIT 30 +SELECT p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.sex_at_birth AS sex_at_birth, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.t_display_sex_at_birth AS t_display_sex_at_birth, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_observation_occurrence_person AS i WHERE i.id_observation_occurrence IN (SELECT o.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.observation_occurrence AS o WHERE o.id IN (SELECT i.id_observation_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_observation_occurrence_observation AS i WHERE i.id_observation IN (SELECT o.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.observation AS o WHERE o.id = 43531662)))) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/procedure-noFilter.sql b/service/src/test/resources/sql/aousynthetic/procedure-noFilter.sql index 67bb438cf..d0cfb3e13 100644 --- a/service/src/test/resources/sql/aousynthetic/procedure-noFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/procedure-noFilter.sql @@ -1 +1 @@ -SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, p.t_display_vocabulary AS t_display_vocabulary, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.procedure AS p LIMIT 30 +SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, p.t_display_vocabulary AS t_display_vocabulary, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.procedure AS p LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/procedure-standard-hierarchyMemberFilter.sql b/service/src/test/resources/sql/aousynthetic/procedure-standard-hierarchyMemberFilter.sql index 9529de096..df0fa883c 100644 --- a/service/src/test/resources/sql/aousynthetic/procedure-standard-hierarchyMemberFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/procedure-standard-hierarchyMemberFilter.sql @@ -1 +1 @@ -SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, p.t_display_vocabulary AS t_display_vocabulary, (p.t_standard_path IS NOT NULL) AS t_standard_is_member, (p.t_standard_path IS NOT NULL AND p.t_standard_path='') AS t_standard_is_root, p.t_standard_num_children AS t_standard_num_children, p.t_standard_path AS t_standard_path, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.procedure AS p WHERE p.t_standard_path IS NOT NULL LIMIT 30 +SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, p.t_display_vocabulary AS t_display_vocabulary, (p.t_standard_path IS NOT NULL) AS t_standard_is_member, (p.t_standard_path IS NOT NULL AND p.t_standard_path='') AS t_standard_is_root, p.t_standard_num_children AS t_standard_num_children, p.t_standard_path AS t_standard_path, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.procedure AS p WHERE p.t_standard_path IS NOT NULL LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/procedure-standard-hierarchyRootFilter.sql b/service/src/test/resources/sql/aousynthetic/procedure-standard-hierarchyRootFilter.sql index 6a426c5c5..10756e1fc 100644 --- a/service/src/test/resources/sql/aousynthetic/procedure-standard-hierarchyRootFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/procedure-standard-hierarchyRootFilter.sql @@ -1 +1 @@ -SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, p.t_display_vocabulary AS t_display_vocabulary, (p.t_standard_path IS NOT NULL) AS t_standard_is_member, (p.t_standard_path IS NOT NULL AND p.t_standard_path='') AS t_standard_is_root, p.t_standard_num_children AS t_standard_num_children, p.t_standard_path AS t_standard_path, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.procedure AS p WHERE p.t_standard_path = '' LIMIT 30 +SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, p.t_display_vocabulary AS t_display_vocabulary, (p.t_standard_path IS NOT NULL) AS t_standard_is_member, (p.t_standard_path IS NOT NULL AND p.t_standard_path='') AS t_standard_is_root, p.t_standard_num_children AS t_standard_num_children, p.t_standard_path AS t_standard_path, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.procedure AS p WHERE p.t_standard_path = '' LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/procedure-standard-mumpsVaccination-hierarchyParentFilter.sql b/service/src/test/resources/sql/aousynthetic/procedure-standard-mumpsVaccination-hierarchyParentFilter.sql index b38161587..0c1bcdc0a 100644 --- a/service/src/test/resources/sql/aousynthetic/procedure-standard-mumpsVaccination-hierarchyParentFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/procedure-standard-mumpsVaccination-hierarchyParentFilter.sql @@ -1 +1 @@ -SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, p.t_display_vocabulary AS t_display_vocabulary, (p.t_standard_path IS NOT NULL) AS t_standard_is_member, (p.t_standard_path IS NOT NULL AND p.t_standard_path='') AS t_standard_is_root, p.t_standard_num_children AS t_standard_num_children, p.t_standard_path AS t_standard_path, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.procedure AS p WHERE p.id IN (SELECT p.child FROM `broad-tanagra-dev.aousynthetic_index_031323`.procedure_standard_childParent AS p WHERE p.parent = 4179181) LIMIT 30 +SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, p.t_display_vocabulary AS t_display_vocabulary, (p.t_standard_path IS NOT NULL) AS t_standard_is_member, (p.t_standard_path IS NOT NULL AND p.t_standard_path='') AS t_standard_is_root, p.t_standard_num_children AS t_standard_num_children, p.t_standard_path AS t_standard_path, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.procedure AS p WHERE p.id IN (SELECT p.child FROM `broad-tanagra-dev.aousynthetic_index_072623`.procedure_standard_childParent AS p WHERE p.parent = 4179181) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/procedure-standard-viralImmunization-hierarchyAncestorFilter.sql b/service/src/test/resources/sql/aousynthetic/procedure-standard-viralImmunization-hierarchyAncestorFilter.sql index a639a6785..dadd59c7f 100644 --- a/service/src/test/resources/sql/aousynthetic/procedure-standard-viralImmunization-hierarchyAncestorFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/procedure-standard-viralImmunization-hierarchyAncestorFilter.sql @@ -1 +1 @@ -SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, p.t_display_vocabulary AS t_display_vocabulary, (p.t_standard_path IS NOT NULL) AS t_standard_is_member, (p.t_standard_path IS NOT NULL AND p.t_standard_path='') AS t_standard_is_root, p.t_standard_num_children AS t_standard_num_children, p.t_standard_path AS t_standard_path, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.procedure AS p WHERE (p.id IN (SELECT p.descendant FROM `broad-tanagra-dev.aousynthetic_index_031323`.procedure_standard_ancestorDescendant AS p WHERE p.ancestor = 4176720) OR p.id = 4176720) LIMIT 30 +SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, p.t_display_vocabulary AS t_display_vocabulary, (p.t_standard_path IS NOT NULL) AS t_standard_is_member, (p.t_standard_path IS NOT NULL AND p.t_standard_path='') AS t_standard_is_root, p.t_standard_num_children AS t_standard_num_children, p.t_standard_path AS t_standard_path, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.procedure AS p WHERE (p.id IN (SELECT p.descendant FROM `broad-tanagra-dev.aousynthetic_index_072623`.procedure_standard_ancestorDescendant AS p WHERE p.ancestor = 4176720) OR p.id = 4176720) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/procedure-textFilter.sql b/service/src/test/resources/sql/aousynthetic/procedure-textFilter.sql index 992c9568b..68732d990 100644 --- a/service/src/test/resources/sql/aousynthetic/procedure-textFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/procedure-textFilter.sql @@ -1 +1 @@ -SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, p.t_display_vocabulary AS t_display_vocabulary, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_031323`.procedure AS p WHERE CONTAINS_SUBSTR(p.text, 'mammogram') LIMIT 30 +SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, p.t_display_vocabulary AS t_display_vocabulary, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.aousynthetic_index_072623`.procedure AS p WHERE CONTAINS_SUBSTR(p.text, 'mammogram') LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/procedureoccurrence-mammogram.sql b/service/src/test/resources/sql/aousynthetic/procedureoccurrence-mammogram.sql index 6b7dca532..d0ac56809 100644 --- a/service/src/test/resources/sql/aousynthetic/procedureoccurrence-mammogram.sql +++ b/service/src/test/resources/sql/aousynthetic/procedureoccurrence-mammogram.sql @@ -1 +1 @@ -SELECT p.date AS date, p.id AS id, p.person_id AS person_id, p.procedure AS procedure, p.source_criteria_id AS source_criteria_id, p.source_value AS source_value, p.t_display_procedure AS t_display_procedure, p.visit_occurrence_id AS visit_occurrence_id FROM `broad-tanagra-dev.aousynthetic_index_031323`.procedure_occurrence AS p WHERE p.id IN (SELECT i.id_procedure_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_procedure_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_procedure_occurrence_person AS i WHERE i.id_procedure_occurrence IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.procedure_occurrence AS p WHERE p.id IN (SELECT i.id_procedure_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_procedure_occurrence_procedure AS i WHERE i.id_procedure IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.procedure AS p WHERE p.id = 4324693)))))) LIMIT 30 +SELECT p.date AS date, p.id AS id, p.person_id AS person_id, p.procedure AS procedure, p.source_criteria_id AS source_criteria_id, p.source_value AS source_value, p.t_display_procedure AS t_display_procedure, p.visit_occurrence_id AS visit_occurrence_id FROM `broad-tanagra-dev.aousynthetic_index_072623`.procedure_occurrence AS p WHERE p.id IN (SELECT i.id_procedure_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_procedure_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_procedure_occurrence_person AS i WHERE i.id_procedure_occurrence IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.procedure_occurrence AS p WHERE p.id IN (SELECT i.id_procedure_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_procedure_occurrence_procedure AS i WHERE i.id_procedure IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.procedure AS p WHERE p.id = 4324693)))))) LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/visit-noFilter.sql b/service/src/test/resources/sql/aousynthetic/visit-noFilter.sql index e41d6d99a..4f257a1c6 100644 --- a/service/src/test/resources/sql/aousynthetic/visit-noFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/visit-noFilter.sql @@ -1 +1 @@ -SELECT v.id AS id, v.name AS name FROM `broad-tanagra-dev.aousynthetic_index_031323`.visit AS v LIMIT 30 +SELECT v.id AS id, v.name AS name FROM `broad-tanagra-dev.aousynthetic_index_072623`.visit AS v LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/visit-textFilter.sql b/service/src/test/resources/sql/aousynthetic/visit-textFilter.sql index 22647ce15..aac5d0b03 100644 --- a/service/src/test/resources/sql/aousynthetic/visit-textFilter.sql +++ b/service/src/test/resources/sql/aousynthetic/visit-textFilter.sql @@ -1 +1 @@ -SELECT v.id AS id, v.name AS name FROM `broad-tanagra-dev.aousynthetic_index_031323`.visit AS v WHERE CONTAINS_SUBSTR(v.text, 'ambul') LIMIT 30 +SELECT v.id AS id, v.name AS name FROM `broad-tanagra-dev.aousynthetic_index_072623`.visit AS v WHERE CONTAINS_SUBSTR(v.text, 'ambul') LIMIT 30 diff --git a/service/src/test/resources/sql/aousynthetic/visitoccurrence-outpatient.sql b/service/src/test/resources/sql/aousynthetic/visitoccurrence-outpatient.sql index 166f67907..98814a767 100644 --- a/service/src/test/resources/sql/aousynthetic/visitoccurrence-outpatient.sql +++ b/service/src/test/resources/sql/aousynthetic/visitoccurrence-outpatient.sql @@ -1 +1 @@ -SELECT v.end_date AS end_date, v.id AS id, v.person_id AS person_id, v.source_criteria_id AS source_criteria_id, v.source_value AS source_value, v.start_date AS start_date, v.t_display_visit AS t_display_visit, v.visit AS visit FROM `broad-tanagra-dev.aousynthetic_index_031323`.visit_occurrence AS v WHERE v.id IN (SELECT i.id_visit_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_visit_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_visit_occurrence_person AS i WHERE i.id_visit_occurrence IN (SELECT v.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.visit_occurrence AS v WHERE v.id IN (SELECT i.id_visit_occurrence FROM `broad-tanagra-dev.aousynthetic_index_031323`.idpairs_visit_occurrence_visit AS i WHERE i.id_visit IN (SELECT v.id FROM `broad-tanagra-dev.aousynthetic_index_031323`.visit AS v WHERE v.id = 9202)))))) LIMIT 30 +SELECT v.end_date AS end_date, v.id AS id, v.person_id AS person_id, v.source_criteria_id AS source_criteria_id, v.source_value AS source_value, v.start_date AS start_date, v.t_display_visit AS t_display_visit, v.visit AS visit FROM `broad-tanagra-dev.aousynthetic_index_072623`.visit_occurrence AS v WHERE v.id IN (SELECT i.id_visit_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_visit_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_visit_occurrence_person AS i WHERE i.id_visit_occurrence IN (SELECT v.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.visit_occurrence AS v WHERE v.id IN (SELECT i.id_visit_occurrence FROM `broad-tanagra-dev.aousynthetic_index_072623`.idpairs_visit_occurrence_visit AS i WHERE i.id_visit IN (SELECT v.id FROM `broad-tanagra-dev.aousynthetic_index_072623`.visit AS v WHERE v.id = 9202)))))) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/brand-noFilter.sql b/service/src/test/resources/sql/cmssynpuf/brand-noFilter.sql index d460feb55..8899422db 100644 --- a/service/src/test/resources/sql/cmssynpuf/brand-noFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/brand-noFilter.sql @@ -1 +1 @@ -SELECT b.concept_code AS concept_code, b.id AS id, b.name AS name, b.standard_concept AS standard_concept, b.t_display_standard_concept AS t_display_standard_concept FROM `broad-tanagra-dev.cmssynpuf_index_071923`.brand AS b LIMIT 30 +SELECT b.concept_code AS concept_code, b.id AS id, b.name AS name, b.standard_concept AS standard_concept, b.t_display_standard_concept AS t_display_standard_concept FROM `broad-tanagra-dev.cmssynpuf_index_072623`.brand AS b LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/brand-textFilter.sql b/service/src/test/resources/sql/cmssynpuf/brand-textFilter.sql index ac5d65bfe..281e55169 100644 --- a/service/src/test/resources/sql/cmssynpuf/brand-textFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/brand-textFilter.sql @@ -1 +1 @@ -SELECT b.concept_code AS concept_code, b.id AS id, b.name AS name, b.standard_concept AS standard_concept, b.t_display_standard_concept AS t_display_standard_concept FROM `broad-tanagra-dev.cmssynpuf_index_071923`.brand AS b WHERE CONTAINS_SUBSTR(b.text, 'paracetamol') LIMIT 30 +SELECT b.concept_code AS concept_code, b.id AS id, b.name AS name, b.standard_concept AS standard_concept, b.t_display_standard_concept AS t_display_standard_concept FROM `broad-tanagra-dev.cmssynpuf_index_072623`.brand AS b WHERE CONTAINS_SUBSTR(b.text, 'paracetamol') LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/condition-noFilter.sql b/service/src/test/resources/sql/cmssynpuf/condition-noFilter.sql index fe9c968a0..d12ed0c92 100644 --- a/service/src/test/resources/sql/cmssynpuf/condition-noFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/condition-noFilter.sql @@ -1 +1 @@ -SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition AS c LIMIT 30 +SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition AS c LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/condition-standard-diabetes-hierarchyAncestorFilter.sql b/service/src/test/resources/sql/cmssynpuf/condition-standard-diabetes-hierarchyAncestorFilter.sql index b30e9c32a..855426688 100644 --- a/service/src/test/resources/sql/cmssynpuf/condition-standard-diabetes-hierarchyAncestorFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/condition-standard-diabetes-hierarchyAncestorFilter.sql @@ -1 +1 @@ -SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, (c.t_standard_path IS NOT NULL) AS t_standard_is_member, (c.t_standard_path IS NOT NULL AND c.t_standard_path='') AS t_standard_is_root, c.t_standard_num_children AS t_standard_num_children, c.t_standard_path AS t_standard_path, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition AS c WHERE (c.id IN (SELECT c.descendant FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition_standard_ancestorDescendant AS c WHERE c.ancestor = 201826) OR c.id = 201826) LIMIT 30 +SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, (c.t_standard_path IS NOT NULL) AS t_standard_is_member, (c.t_standard_path IS NOT NULL AND c.t_standard_path='') AS t_standard_is_root, c.t_standard_num_children AS t_standard_num_children, c.t_standard_path AS t_standard_path, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition AS c WHERE (c.id IN (SELECT c.descendant FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition_standard_ancestorDescendant AS c WHERE c.ancestor = 201826) OR c.id = 201826) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/condition-standard-diabetes-hierarchyParentFilter.sql b/service/src/test/resources/sql/cmssynpuf/condition-standard-diabetes-hierarchyParentFilter.sql index 3089bacec..76afaf4df 100644 --- a/service/src/test/resources/sql/cmssynpuf/condition-standard-diabetes-hierarchyParentFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/condition-standard-diabetes-hierarchyParentFilter.sql @@ -1 +1 @@ -SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, (c.t_standard_path IS NOT NULL) AS t_standard_is_member, (c.t_standard_path IS NOT NULL AND c.t_standard_path='') AS t_standard_is_root, c.t_standard_num_children AS t_standard_num_children, c.t_standard_path AS t_standard_path, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition AS c WHERE c.id IN (SELECT c.child FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition_standard_childParent AS c WHERE c.parent = 201826) LIMIT 30 +SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, (c.t_standard_path IS NOT NULL) AS t_standard_is_member, (c.t_standard_path IS NOT NULL AND c.t_standard_path='') AS t_standard_is_root, c.t_standard_num_children AS t_standard_num_children, c.t_standard_path AS t_standard_path, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition AS c WHERE c.id IN (SELECT c.child FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition_standard_childParent AS c WHERE c.parent = 201826) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/condition-standard-hierarchyMemberFilter.sql b/service/src/test/resources/sql/cmssynpuf/condition-standard-hierarchyMemberFilter.sql index f9c95795d..f56c84975 100644 --- a/service/src/test/resources/sql/cmssynpuf/condition-standard-hierarchyMemberFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/condition-standard-hierarchyMemberFilter.sql @@ -1 +1 @@ -SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, (c.t_standard_path IS NOT NULL) AS t_standard_is_member, (c.t_standard_path IS NOT NULL AND c.t_standard_path='') AS t_standard_is_root, c.t_standard_num_children AS t_standard_num_children, c.t_standard_path AS t_standard_path, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition AS c WHERE c.t_standard_path IS NOT NULL LIMIT 30 +SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, (c.t_standard_path IS NOT NULL) AS t_standard_is_member, (c.t_standard_path IS NOT NULL AND c.t_standard_path='') AS t_standard_is_root, c.t_standard_num_children AS t_standard_num_children, c.t_standard_path AS t_standard_path, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition AS c WHERE c.t_standard_path IS NOT NULL LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/condition-standard-hierarchyRootFilter.sql b/service/src/test/resources/sql/cmssynpuf/condition-standard-hierarchyRootFilter.sql index c130a3c22..37d313eed 100644 --- a/service/src/test/resources/sql/cmssynpuf/condition-standard-hierarchyRootFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/condition-standard-hierarchyRootFilter.sql @@ -1 +1 @@ -SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, (c.t_standard_path IS NOT NULL) AS t_standard_is_member, (c.t_standard_path IS NOT NULL AND c.t_standard_path='') AS t_standard_is_root, c.t_standard_num_children AS t_standard_num_children, c.t_standard_path AS t_standard_path, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition AS c WHERE c.t_standard_path = '' LIMIT 30 +SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, (c.t_standard_path IS NOT NULL) AS t_standard_is_member, (c.t_standard_path IS NOT NULL AND c.t_standard_path='') AS t_standard_is_root, c.t_standard_num_children AS t_standard_num_children, c.t_standard_path AS t_standard_path, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition AS c WHERE c.t_standard_path = '' LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/condition-textFilter.sql b/service/src/test/resources/sql/cmssynpuf/condition-textFilter.sql index 04f3d80ac..7a12b8fea 100644 --- a/service/src/test/resources/sql/cmssynpuf/condition-textFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/condition-textFilter.sql @@ -1 +1 @@ -SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition AS c WHERE CONTAINS_SUBSTR(c.text, 'sense of smell absent') LIMIT 30 +SELECT c.concept_code AS concept_code, c.id AS id, c.name AS name, c.standard_concept AS standard_concept, c.t_display_standard_concept AS t_display_standard_concept, c.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition AS c WHERE CONTAINS_SUBSTR(c.text, 'sense of smell absent') LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/conditionoccurrence-diabetes.sql b/service/src/test/resources/sql/cmssynpuf/conditionoccurrence-diabetes.sql index d5788a320..092f7a528 100644 --- a/service/src/test/resources/sql/cmssynpuf/conditionoccurrence-diabetes.sql +++ b/service/src/test/resources/sql/cmssynpuf/conditionoccurrence-diabetes.sql @@ -1 +1 @@ -SELECT c.age_at_occurrence AS age_at_occurrence, c.condition AS condition, c.end_date AS end_date, c.id AS id, c.person_id AS person_id, c.source_criteria_id AS source_criteria_id, c.source_value AS source_value, c.start_date AS start_date, c.stop_reason AS stop_reason, c.t_display_condition AS t_display_condition FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_condition_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition AS c WHERE c.id = 201826)))))) LIMIT 30 +SELECT c.age_at_occurrence AS age_at_occurrence, c.condition AS condition, c.end_date AS end_date, c.id AS id, c.person_id AS person_id, c.source_criteria_id AS source_criteria_id, c.source_value AS source_value, c.start_date AS start_date, c.stop_reason AS stop_reason, c.t_display_condition AS t_display_condition FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_condition_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition AS c WHERE c.id = 201826)))))) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/conditionoccurrence-diabetesAndSepsis.sql b/service/src/test/resources/sql/cmssynpuf/conditionoccurrence-diabetesAndSepsis.sql index 2d2d5e99c..fb3d028f2 100644 --- a/service/src/test/resources/sql/cmssynpuf/conditionoccurrence-diabetesAndSepsis.sql +++ b/service/src/test/resources/sql/cmssynpuf/conditionoccurrence-diabetesAndSepsis.sql @@ -1 +1 @@ -SELECT c.age_at_occurrence AS age_at_occurrence, c.condition AS condition, c.end_date AS end_date, c.id AS id, c.person_id AS person_id, c.source_criteria_id AS source_criteria_id, c.source_value AS source_value, c.start_date AS start_date, c.stop_reason AS stop_reason, c.t_display_condition AS t_display_condition FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_condition_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.person AS p WHERE (p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition AS c WHERE c.id = 201826)))) AND p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition AS c WHERE c.id = 132797))))))) LIMIT 30 +SELECT c.age_at_occurrence AS age_at_occurrence, c.condition AS condition, c.end_date AS end_date, c.id AS id, c.person_id AS person_id, c.source_criteria_id AS source_criteria_id, c.source_value AS source_value, c.start_date AS start_date, c.stop_reason AS stop_reason, c.t_display_condition AS t_display_condition FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_condition_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.person AS p WHERE (p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition AS c WHERE c.id = 201826)))) AND p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition AS c WHERE c.id = 132797))))))) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/device-noFilter.sql b/service/src/test/resources/sql/cmssynpuf/device-noFilter.sql index f3020e7f6..06082bcc3 100644 --- a/service/src/test/resources/sql/cmssynpuf/device-noFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/device-noFilter.sql @@ -1 +1 @@ -SELECT d.concept_code AS concept_code, d.id AS id, d.name AS name, d.standard_concept AS standard_concept, d.t_display_standard_concept AS t_display_standard_concept, d.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.device AS d LIMIT 30 +SELECT d.concept_code AS concept_code, d.id AS id, d.name AS name, d.standard_concept AS standard_concept, d.t_display_standard_concept AS t_display_standard_concept, d.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.device AS d LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/device-textFilter.sql b/service/src/test/resources/sql/cmssynpuf/device-textFilter.sql index eafe71466..25ab489b2 100644 --- a/service/src/test/resources/sql/cmssynpuf/device-textFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/device-textFilter.sql @@ -1 +1 @@ -SELECT d.concept_code AS concept_code, d.id AS id, d.name AS name, d.standard_concept AS standard_concept, d.t_display_standard_concept AS t_display_standard_concept, d.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.device AS d WHERE CONTAINS_SUBSTR(d.text, 'hearing aid') LIMIT 30 +SELECT d.concept_code AS concept_code, d.id AS id, d.name AS name, d.standard_concept AS standard_concept, d.t_display_standard_concept AS t_display_standard_concept, d.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.device AS d WHERE CONTAINS_SUBSTR(d.text, 'hearing aid') LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/deviceoccurrence-longLegCast.sql b/service/src/test/resources/sql/cmssynpuf/deviceoccurrence-longLegCast.sql index 7bf4a30c4..5a309867a 100644 --- a/service/src/test/resources/sql/cmssynpuf/deviceoccurrence-longLegCast.sql +++ b/service/src/test/resources/sql/cmssynpuf/deviceoccurrence-longLegCast.sql @@ -1 +1 @@ -SELECT d.age_at_occurrence AS age_at_occurrence, d.device AS device, d.end_date AS end_date, d.id AS id, d.person_id AS person_id, d.source_criteria_id AS source_criteria_id, d.source_value AS source_value, d.start_date AS start_date, d.t_display_device AS t_display_device FROM `broad-tanagra-dev.cmssynpuf_index_071923`.device_occurrence AS d WHERE d.id IN (SELECT i.id_device_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_device_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_device_occurrence_person AS i WHERE i.id_device_occurrence IN (SELECT d.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.device_occurrence AS d WHERE d.id IN (SELECT i.id_device_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_device_occurrence_device AS i WHERE i.id_device IN (SELECT d.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.device AS d WHERE d.id = 4038664)))))) LIMIT 30 +SELECT d.age_at_occurrence AS age_at_occurrence, d.device AS device, d.end_date AS end_date, d.id AS id, d.person_id AS person_id, d.source_criteria_id AS source_criteria_id, d.source_value AS source_value, d.start_date AS start_date, d.t_display_device AS t_display_device FROM `broad-tanagra-dev.cmssynpuf_index_072623`.device_occurrence AS d WHERE d.id IN (SELECT i.id_device_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_device_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_device_occurrence_person AS i WHERE i.id_device_occurrence IN (SELECT d.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.device_occurrence AS d WHERE d.id IN (SELECT i.id_device_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_device_occurrence_device AS i WHERE i.id_device IN (SELECT d.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.device AS d WHERE d.id = 4038664)))))) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/ingredient-noFilter.sql b/service/src/test/resources/sql/cmssynpuf/ingredient-noFilter.sql index a83fe5b45..58e20d177 100644 --- a/service/src/test/resources/sql/cmssynpuf/ingredient-noFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/ingredient-noFilter.sql @@ -1 +1 @@ -SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.ingredient AS i LIMIT 30 +SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.ingredient AS i LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/ingredient-relationshipFilter.sql b/service/src/test/resources/sql/cmssynpuf/ingredient-relationshipFilter.sql index be0e7c35c..117feff44 100644 --- a/service/src/test/resources/sql/cmssynpuf/ingredient-relationshipFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/ingredient-relationshipFilter.sql @@ -1 +1 @@ -SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.ingredient AS i WHERE i.id IN (SELECT i.id_ingredient FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_brand_ingredient AS i WHERE i.id_brand IN (SELECT b.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.brand AS b WHERE b.id = 19082059)) LIMIT 30 +SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.ingredient AS i WHERE i.id IN (SELECT i.id_ingredient FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_brand_ingredient AS i WHERE i.id_brand IN (SELECT b.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.brand AS b WHERE b.id = 19082059)) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/ingredient-standard-cardiacPreparations-hierarchyAncestorFilter.sql b/service/src/test/resources/sql/cmssynpuf/ingredient-standard-cardiacPreparations-hierarchyAncestorFilter.sql index e371c70ba..b49330ab3 100644 --- a/service/src/test/resources/sql/cmssynpuf/ingredient-standard-cardiacPreparations-hierarchyAncestorFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/ingredient-standard-cardiacPreparations-hierarchyAncestorFilter.sql @@ -1 +1 @@ -SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, (i.t_standard_path IS NOT NULL) AS t_standard_is_member, (i.t_standard_path IS NOT NULL AND i.t_standard_path='') AS t_standard_is_root, i.t_standard_num_children AS t_standard_num_children, i.t_standard_path AS t_standard_path, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.ingredient AS i WHERE (i.id IN (SELECT i.descendant FROM `broad-tanagra-dev.cmssynpuf_index_071923`.ingredient_standard_ancestorDescendant AS i WHERE i.ancestor = 21600360) OR i.id = 21600360) LIMIT 30 +SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, (i.t_standard_path IS NOT NULL) AS t_standard_is_member, (i.t_standard_path IS NOT NULL AND i.t_standard_path='') AS t_standard_is_root, i.t_standard_num_children AS t_standard_num_children, i.t_standard_path AS t_standard_path, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.ingredient AS i WHERE (i.id IN (SELECT i.descendant FROM `broad-tanagra-dev.cmssynpuf_index_072623`.ingredient_standard_ancestorDescendant AS i WHERE i.ancestor = 21600360) OR i.id = 21600360) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/ingredient-standard-hierarchyMemberFilter.sql b/service/src/test/resources/sql/cmssynpuf/ingredient-standard-hierarchyMemberFilter.sql index be2a10696..66b70fc3e 100644 --- a/service/src/test/resources/sql/cmssynpuf/ingredient-standard-hierarchyMemberFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/ingredient-standard-hierarchyMemberFilter.sql @@ -1 +1 @@ -SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, (i.t_standard_path IS NOT NULL) AS t_standard_is_member, (i.t_standard_path IS NOT NULL AND i.t_standard_path='') AS t_standard_is_root, i.t_standard_num_children AS t_standard_num_children, i.t_standard_path AS t_standard_path, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.ingredient AS i WHERE i.t_standard_path IS NOT NULL LIMIT 30 +SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, (i.t_standard_path IS NOT NULL) AS t_standard_is_member, (i.t_standard_path IS NOT NULL AND i.t_standard_path='') AS t_standard_is_root, i.t_standard_num_children AS t_standard_num_children, i.t_standard_path AS t_standard_path, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.ingredient AS i WHERE i.t_standard_path IS NOT NULL LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/ingredient-standard-hierarchyRootFilter.sql b/service/src/test/resources/sql/cmssynpuf/ingredient-standard-hierarchyRootFilter.sql index 87f66ea71..8042c232e 100644 --- a/service/src/test/resources/sql/cmssynpuf/ingredient-standard-hierarchyRootFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/ingredient-standard-hierarchyRootFilter.sql @@ -1 +1 @@ -SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, (i.t_standard_path IS NOT NULL) AS t_standard_is_member, (i.t_standard_path IS NOT NULL AND i.t_standard_path='') AS t_standard_is_root, i.t_standard_num_children AS t_standard_num_children, i.t_standard_path AS t_standard_path, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.ingredient AS i WHERE i.t_standard_path = '' LIMIT 30 +SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, (i.t_standard_path IS NOT NULL) AS t_standard_is_member, (i.t_standard_path IS NOT NULL AND i.t_standard_path='') AS t_standard_is_root, i.t_standard_num_children AS t_standard_num_children, i.t_standard_path AS t_standard_path, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.ingredient AS i WHERE i.t_standard_path = '' LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/ingredient-standard-opioids-hierarchyParentFilter.sql b/service/src/test/resources/sql/cmssynpuf/ingredient-standard-opioids-hierarchyParentFilter.sql index 1b4788d15..ff1c91623 100644 --- a/service/src/test/resources/sql/cmssynpuf/ingredient-standard-opioids-hierarchyParentFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/ingredient-standard-opioids-hierarchyParentFilter.sql @@ -1 +1 @@ -SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, (i.t_standard_path IS NOT NULL) AS t_standard_is_member, (i.t_standard_path IS NOT NULL AND i.t_standard_path='') AS t_standard_is_root, i.t_standard_num_children AS t_standard_num_children, i.t_standard_path AS t_standard_path, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.ingredient AS i WHERE i.id IN (SELECT i.child FROM `broad-tanagra-dev.cmssynpuf_index_071923`.ingredient_standard_childParent AS i WHERE i.parent = 21603396) LIMIT 30 +SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, (i.t_standard_path IS NOT NULL) AS t_standard_is_member, (i.t_standard_path IS NOT NULL AND i.t_standard_path='') AS t_standard_is_root, i.t_standard_num_children AS t_standard_num_children, i.t_standard_path AS t_standard_path, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.ingredient AS i WHERE i.id IN (SELECT i.child FROM `broad-tanagra-dev.cmssynpuf_index_072623`.ingredient_standard_childParent AS i WHERE i.parent = 21603396) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/ingredient-textFilter.sql b/service/src/test/resources/sql/cmssynpuf/ingredient-textFilter.sql index e1961ea9a..5edc919e7 100644 --- a/service/src/test/resources/sql/cmssynpuf/ingredient-textFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/ingredient-textFilter.sql @@ -1 +1 @@ -SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.ingredient AS i WHERE CONTAINS_SUBSTR(i.text, 'alcohol') LIMIT 30 +SELECT i.concept_code AS concept_code, i.id AS id, i.name AS name, i.standard_concept AS standard_concept, i.t_display_standard_concept AS t_display_standard_concept, i.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.ingredient AS i WHERE CONTAINS_SUBSTR(i.text, 'alcohol') LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/ingredientoccurrence-ibuprofen.sql b/service/src/test/resources/sql/cmssynpuf/ingredientoccurrence-ibuprofen.sql index b937f2a17..e21a458dd 100644 --- a/service/src/test/resources/sql/cmssynpuf/ingredientoccurrence-ibuprofen.sql +++ b/service/src/test/resources/sql/cmssynpuf/ingredientoccurrence-ibuprofen.sql @@ -1 +1 @@ -SELECT i.age_at_occurrence AS age_at_occurrence, i.days_supply AS days_supply, i.end_date AS end_date, i.id AS id, i.ingredient AS ingredient, i.person_id AS person_id, i.refills AS refills, i.source_criteria_id AS source_criteria_id, i.source_value AS source_value, i.start_date AS start_date, i.stop_reason AS stop_reason, i.t_display_ingredient AS t_display_ingredient FROM `broad-tanagra-dev.cmssynpuf_index_071923`.ingredient_occurrence AS i WHERE i.id IN (SELECT i.id_ingredient_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_ingredient_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_ingredient_occurrence_person AS i WHERE i.id_ingredient_occurrence IN (SELECT i.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.ingredient_occurrence AS i WHERE i.id IN (SELECT i.id_ingredient_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_ingredient_occurrence_ingredient AS i WHERE i.id_ingredient IN (SELECT i.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.ingredient AS i WHERE i.id = 1177480)))))) LIMIT 30 +SELECT i.age_at_occurrence AS age_at_occurrence, i.days_supply AS days_supply, i.end_date AS end_date, i.id AS id, i.ingredient AS ingredient, i.person_id AS person_id, i.refills AS refills, i.source_criteria_id AS source_criteria_id, i.source_value AS source_value, i.start_date AS start_date, i.stop_reason AS stop_reason, i.t_display_ingredient AS t_display_ingredient FROM `broad-tanagra-dev.cmssynpuf_index_072623`.ingredient_occurrence AS i WHERE i.id IN (SELECT i.id_ingredient_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_ingredient_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_ingredient_occurrence_person AS i WHERE i.id_ingredient_occurrence IN (SELECT i.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.ingredient_occurrence AS i WHERE i.id IN (SELECT i.id_ingredient_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_ingredient_occurrence_ingredient AS i WHERE i.id_ingredient IN (SELECT i.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.ingredient AS i WHERE i.id = 1177480)))))) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/observation-noFilter.sql b/service/src/test/resources/sql/cmssynpuf/observation-noFilter.sql index 6f3dab503..e3758b0a8 100644 --- a/service/src/test/resources/sql/cmssynpuf/observation-noFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/observation-noFilter.sql @@ -1 +1 @@ -SELECT o.concept_code AS concept_code, o.id AS id, o.name AS name, o.standard_concept AS standard_concept, o.t_display_standard_concept AS t_display_standard_concept, o.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.observation AS o LIMIT 30 +SELECT o.concept_code AS concept_code, o.id AS id, o.name AS name, o.standard_concept AS standard_concept, o.t_display_standard_concept AS t_display_standard_concept, o.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.observation AS o LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/observation-textFilter.sql b/service/src/test/resources/sql/cmssynpuf/observation-textFilter.sql index 6b880197c..41c03370b 100644 --- a/service/src/test/resources/sql/cmssynpuf/observation-textFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/observation-textFilter.sql @@ -1 +1 @@ -SELECT o.concept_code AS concept_code, o.id AS id, o.name AS name, o.standard_concept AS standard_concept, o.t_display_standard_concept AS t_display_standard_concept, o.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.observation AS o WHERE CONTAINS_SUBSTR(o.text, 'smoke') LIMIT 30 +SELECT o.concept_code AS concept_code, o.id AS id, o.name AS name, o.standard_concept AS standard_concept, o.t_display_standard_concept AS t_display_standard_concept, o.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.observation AS o WHERE CONTAINS_SUBSTR(o.text, 'smoke') LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/observationoccurrence-vaccineRefusal.sql b/service/src/test/resources/sql/cmssynpuf/observationoccurrence-vaccineRefusal.sql index 72a8e4870..2157b9998 100644 --- a/service/src/test/resources/sql/cmssynpuf/observationoccurrence-vaccineRefusal.sql +++ b/service/src/test/resources/sql/cmssynpuf/observationoccurrence-vaccineRefusal.sql @@ -1 +1 @@ -SELECT o.age_at_occurrence AS age_at_occurrence, o.date AS date, o.id AS id, o.observation AS observation, o.person_id AS person_id, o.source_criteria_id AS source_criteria_id, o.source_value AS source_value, o.t_display_observation AS t_display_observation, o.t_display_unit AS t_display_unit, o.t_display_value AS t_display_value, o.unit AS unit, o.value AS value, o.value_as_string AS value_as_string FROM `broad-tanagra-dev.cmssynpuf_index_071923`.observation_occurrence AS o WHERE o.id IN (SELECT i.id_observation_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_observation_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_observation_occurrence_person AS i WHERE i.id_observation_occurrence IN (SELECT o.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.observation_occurrence AS o WHERE o.id IN (SELECT i.id_observation_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_observation_occurrence_observation AS i WHERE i.id_observation IN (SELECT o.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.observation AS o WHERE o.id = 43531662)))))) LIMIT 30 +SELECT o.age_at_occurrence AS age_at_occurrence, o.date AS date, o.id AS id, o.observation AS observation, o.person_id AS person_id, o.source_criteria_id AS source_criteria_id, o.source_value AS source_value, o.t_display_observation AS t_display_observation, o.t_display_unit AS t_display_unit, o.t_display_value AS t_display_value, o.unit AS unit, o.value AS value, o.value_as_string AS value_as_string FROM `broad-tanagra-dev.cmssynpuf_index_072623`.observation_occurrence AS o WHERE o.id IN (SELECT i.id_observation_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_observation_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_observation_occurrence_person AS i WHERE i.id_observation_occurrence IN (SELECT o.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.observation_occurrence AS o WHERE o.id IN (SELECT i.id_observation_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_observation_occurrence_observation AS i WHERE i.id_observation IN (SELECT o.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.observation AS o WHERE o.id = 43531662)))))) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/person-all-count.sql b/service/src/test/resources/sql/cmssynpuf/person-all-count.sql index 9a4241fd1..92d5eb82c 100644 --- a/service/src/test/resources/sql/cmssynpuf/person-all-count.sql +++ b/service/src/test/resources/sql/cmssynpuf/person-all-count.sql @@ -1 +1 @@ -SELECT COUNT(p.id) AS t_count FROM `broad-tanagra-dev.cmssynpuf_index_071923`.person AS p +SELECT COUNT(p.id) AS t_count FROM `broad-tanagra-dev.cmssynpuf_index_072623`.person AS p diff --git a/service/src/test/resources/sql/cmssynpuf/person-diabetes-count.sql b/service/src/test/resources/sql/cmssynpuf/person-diabetes-count.sql index 8f467437e..10d54b8aa 100644 --- a/service/src/test/resources/sql/cmssynpuf/person-diabetes-count.sql +++ b/service/src/test/resources/sql/cmssynpuf/person-diabetes-count.sql @@ -1 +1 @@ -SELECT p.gender AS gender, p.race AS race, COUNT(p.id) AS t_count, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race FROM `broad-tanagra-dev.cmssynpuf_index_071923`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition AS c WHERE c.id = 201826)))) GROUP BY gender, t_display_gender, race, t_display_race ORDER BY gender ASC, t_display_gender ASC, race ASC, t_display_race ASC +SELECT p.gender AS gender, p.race AS race, COUNT(p.id) AS t_count, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race FROM `broad-tanagra-dev.cmssynpuf_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition AS c WHERE c.id = 201826)))) GROUP BY gender, t_display_gender, race, t_display_race ORDER BY gender ASC, t_display_gender ASC, race ASC, t_display_race ASC diff --git a/service/src/test/resources/sql/cmssynpuf/person-diabetes-numOccurrenceDates.sql b/service/src/test/resources/sql/cmssynpuf/person-diabetes-numOccurrenceDates.sql index 03271003f..1e64b9674 100644 --- a/service/src/test/resources/sql/cmssynpuf/person-diabetes-numOccurrenceDates.sql +++ b/service/src/test/resources/sql/cmssynpuf/person-diabetes-numOccurrenceDates.sql @@ -1 +1 @@ -SELECT EXTRACT(YEAR FROM CURRENT_DATE()) - p.age AS age, p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.cmssynpuf_index_071923`.person AS p WHERE p.id IN (SELECT x.person_id FROM (SELECT c.condition AS condition, c.person_id AS person_id, c.t_display_condition AS t_display_condition FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition AS c WHERE c.id = 201826)) GROUP BY person_id, condition, t_display_condition) AS x GROUP BY x.person_id HAVING COUNT(*) > 1) LIMIT 30 +SELECT EXTRACT(YEAR FROM CURRENT_DATE()) - p.age AS age, p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.cmssynpuf_index_072623`.person AS p WHERE p.id IN (SELECT x.person_id FROM (SELECT c.condition AS condition, c.person_id AS person_id, c.t_display_condition AS t_display_condition FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition AS c WHERE c.id = 201826)) GROUP BY person_id, condition, t_display_condition) AS x GROUP BY x.person_id HAVING COUNT(*) > 1) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/person-diabetes.sql b/service/src/test/resources/sql/cmssynpuf/person-diabetes.sql index 2f6fd3f23..eeea9c1ef 100644 --- a/service/src/test/resources/sql/cmssynpuf/person-diabetes.sql +++ b/service/src/test/resources/sql/cmssynpuf/person-diabetes.sql @@ -1 +1 @@ -SELECT EXTRACT(YEAR FROM CURRENT_DATE()) - p.age AS age, p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.cmssynpuf_index_071923`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.condition AS c WHERE c.id = 201826)))) LIMIT 30 +SELECT EXTRACT(YEAR FROM CURRENT_DATE()) - p.age AS age, p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.cmssynpuf_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_condition_occurrence_person AS i WHERE i.id_condition_occurrence IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition_occurrence AS c WHERE c.id IN (SELECT i.id_condition_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_condition_occurrence_condition AS i WHERE i.id_condition IN (SELECT c.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.condition AS c WHERE c.id = 201826)))) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/person-genderRace-count.sql b/service/src/test/resources/sql/cmssynpuf/person-genderRace-count.sql index dbd1d0769..1a9e71d68 100644 --- a/service/src/test/resources/sql/cmssynpuf/person-genderRace-count.sql +++ b/service/src/test/resources/sql/cmssynpuf/person-genderRace-count.sql @@ -1 +1 @@ -SELECT p.gender AS gender, p.race AS race, COUNT(p.id) AS t_count, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race FROM `broad-tanagra-dev.cmssynpuf_index_071923`.person AS p GROUP BY gender, t_display_gender, race, t_display_race ORDER BY gender ASC, t_display_gender ASC, race ASC, t_display_race ASC +SELECT p.gender AS gender, p.race AS race, COUNT(p.id) AS t_count, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race FROM `broad-tanagra-dev.cmssynpuf_index_072623`.person AS p GROUP BY gender, t_display_gender, race, t_display_race ORDER BY gender ASC, t_display_gender ASC, race ASC, t_display_race ASC diff --git a/service/src/test/resources/sql/cmssynpuf/person-ibuprofen.sql b/service/src/test/resources/sql/cmssynpuf/person-ibuprofen.sql index 3a8223740..10666db93 100644 --- a/service/src/test/resources/sql/cmssynpuf/person-ibuprofen.sql +++ b/service/src/test/resources/sql/cmssynpuf/person-ibuprofen.sql @@ -1 +1 @@ -SELECT EXTRACT(YEAR FROM CURRENT_DATE()) - p.age AS age, p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.cmssynpuf_index_071923`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_ingredient_occurrence_person AS i WHERE i.id_ingredient_occurrence IN (SELECT i.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.ingredient_occurrence AS i WHERE i.id IN (SELECT i.id_ingredient_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_ingredient_occurrence_ingredient AS i WHERE i.id_ingredient IN (SELECT i.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.ingredient AS i WHERE i.id = 1177480)))) LIMIT 30 +SELECT EXTRACT(YEAR FROM CURRENT_DATE()) - p.age AS age, p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.cmssynpuf_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_ingredient_occurrence_person AS i WHERE i.id_ingredient_occurrence IN (SELECT i.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.ingredient_occurrence AS i WHERE i.id IN (SELECT i.id_ingredient_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_ingredient_occurrence_ingredient AS i WHERE i.id_ingredient IN (SELECT i.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.ingredient AS i WHERE i.id = 1177480)))) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/person-longLegCast.sql b/service/src/test/resources/sql/cmssynpuf/person-longLegCast.sql index 6572d1714..e01fa1e1c 100644 --- a/service/src/test/resources/sql/cmssynpuf/person-longLegCast.sql +++ b/service/src/test/resources/sql/cmssynpuf/person-longLegCast.sql @@ -1 +1 @@ -SELECT EXTRACT(YEAR FROM CURRENT_DATE()) - p.age AS age, p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.cmssynpuf_index_071923`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_device_occurrence_person AS i WHERE i.id_device_occurrence IN (SELECT d.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.device_occurrence AS d WHERE d.id IN (SELECT i.id_device_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_device_occurrence_device AS i WHERE i.id_device IN (SELECT d.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.device AS d WHERE d.id = 4038664)))) LIMIT 30 +SELECT EXTRACT(YEAR FROM CURRENT_DATE()) - p.age AS age, p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.cmssynpuf_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_device_occurrence_person AS i WHERE i.id_device_occurrence IN (SELECT d.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.device_occurrence AS d WHERE d.id IN (SELECT i.id_device_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_device_occurrence_device AS i WHERE i.id_device IN (SELECT d.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.device AS d WHERE d.id = 4038664)))) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/person-mammogram.sql b/service/src/test/resources/sql/cmssynpuf/person-mammogram.sql index 09545f99a..9b2b8fb2a 100644 --- a/service/src/test/resources/sql/cmssynpuf/person-mammogram.sql +++ b/service/src/test/resources/sql/cmssynpuf/person-mammogram.sql @@ -1 +1 @@ -SELECT EXTRACT(YEAR FROM CURRENT_DATE()) - p.age AS age, p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.cmssynpuf_index_071923`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_procedure_occurrence_person AS i WHERE i.id_procedure_occurrence IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.procedure_occurrence AS p WHERE p.id IN (SELECT i.id_procedure_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_procedure_occurrence_procedure AS i WHERE i.id_procedure IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.procedure AS p WHERE p.id = 4324693)))) LIMIT 30 +SELECT EXTRACT(YEAR FROM CURRENT_DATE()) - p.age AS age, p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.cmssynpuf_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_procedure_occurrence_person AS i WHERE i.id_procedure_occurrence IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.procedure_occurrence AS p WHERE p.id IN (SELECT i.id_procedure_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_procedure_occurrence_procedure AS i WHERE i.id_procedure IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.procedure AS p WHERE p.id = 4324693)))) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/person-noFilter.sql b/service/src/test/resources/sql/cmssynpuf/person-noFilter.sql index 2b617cb35..61c6fbb5a 100644 --- a/service/src/test/resources/sql/cmssynpuf/person-noFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/person-noFilter.sql @@ -1 +1 @@ -SELECT EXTRACT(YEAR FROM CURRENT_DATE()) - p.age AS age, p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.cmssynpuf_index_071923`.person AS p LIMIT 30 +SELECT EXTRACT(YEAR FROM CURRENT_DATE()) - p.age AS age, p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.cmssynpuf_index_072623`.person AS p LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/person-vaccineRefusal.sql b/service/src/test/resources/sql/cmssynpuf/person-vaccineRefusal.sql index 5c7b46971..48297ee82 100644 --- a/service/src/test/resources/sql/cmssynpuf/person-vaccineRefusal.sql +++ b/service/src/test/resources/sql/cmssynpuf/person-vaccineRefusal.sql @@ -1 +1 @@ -SELECT EXTRACT(YEAR FROM CURRENT_DATE()) - p.age AS age, p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.cmssynpuf_index_071923`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_observation_occurrence_person AS i WHERE i.id_observation_occurrence IN (SELECT o.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.observation_occurrence AS o WHERE o.id IN (SELECT i.id_observation_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_observation_occurrence_observation AS i WHERE i.id_observation IN (SELECT o.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.observation AS o WHERE o.id = 43531662)))) LIMIT 30 +SELECT EXTRACT(YEAR FROM CURRENT_DATE()) - p.age AS age, p.ethnicity AS ethnicity, p.gender AS gender, p.id AS id, p.race AS race, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.year_of_birth AS year_of_birth FROM `broad-tanagra-dev.cmssynpuf_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_observation_occurrence_person AS i WHERE i.id_observation_occurrence IN (SELECT o.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.observation_occurrence AS o WHERE o.id IN (SELECT i.id_observation_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_observation_occurrence_observation AS i WHERE i.id_observation IN (SELECT o.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.observation AS o WHERE o.id = 43531662)))) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/procedure-noFilter.sql b/service/src/test/resources/sql/cmssynpuf/procedure-noFilter.sql index f95692561..f885dc177 100644 --- a/service/src/test/resources/sql/cmssynpuf/procedure-noFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/procedure-noFilter.sql @@ -1 +1 @@ -SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.procedure AS p LIMIT 30 +SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.procedure AS p LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/procedure-standard-hierarchyMemberFilter.sql b/service/src/test/resources/sql/cmssynpuf/procedure-standard-hierarchyMemberFilter.sql index 134fb6c3f..70cfab056 100644 --- a/service/src/test/resources/sql/cmssynpuf/procedure-standard-hierarchyMemberFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/procedure-standard-hierarchyMemberFilter.sql @@ -1 +1 @@ -SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, (p.t_standard_path IS NOT NULL) AS t_standard_is_member, (p.t_standard_path IS NOT NULL AND p.t_standard_path='') AS t_standard_is_root, p.t_standard_num_children AS t_standard_num_children, p.t_standard_path AS t_standard_path, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.procedure AS p WHERE p.t_standard_path IS NOT NULL LIMIT 30 +SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, (p.t_standard_path IS NOT NULL) AS t_standard_is_member, (p.t_standard_path IS NOT NULL AND p.t_standard_path='') AS t_standard_is_root, p.t_standard_num_children AS t_standard_num_children, p.t_standard_path AS t_standard_path, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.procedure AS p WHERE p.t_standard_path IS NOT NULL LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/procedure-standard-hierarchyRootFilter.sql b/service/src/test/resources/sql/cmssynpuf/procedure-standard-hierarchyRootFilter.sql index b1e4b8d35..328821146 100644 --- a/service/src/test/resources/sql/cmssynpuf/procedure-standard-hierarchyRootFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/procedure-standard-hierarchyRootFilter.sql @@ -1 +1 @@ -SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, (p.t_standard_path IS NOT NULL) AS t_standard_is_member, (p.t_standard_path IS NOT NULL AND p.t_standard_path='') AS t_standard_is_root, p.t_standard_num_children AS t_standard_num_children, p.t_standard_path AS t_standard_path, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.procedure AS p WHERE p.t_standard_path = '' LIMIT 30 +SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, (p.t_standard_path IS NOT NULL) AS t_standard_is_member, (p.t_standard_path IS NOT NULL AND p.t_standard_path='') AS t_standard_is_root, p.t_standard_num_children AS t_standard_num_children, p.t_standard_path AS t_standard_path, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.procedure AS p WHERE p.t_standard_path = '' LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/procedure-standard-mumpsVaccination-hierarchyParentFilter.sql b/service/src/test/resources/sql/cmssynpuf/procedure-standard-mumpsVaccination-hierarchyParentFilter.sql index cea69ac0a..c9a256c06 100644 --- a/service/src/test/resources/sql/cmssynpuf/procedure-standard-mumpsVaccination-hierarchyParentFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/procedure-standard-mumpsVaccination-hierarchyParentFilter.sql @@ -1 +1 @@ -SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, (p.t_standard_path IS NOT NULL) AS t_standard_is_member, (p.t_standard_path IS NOT NULL AND p.t_standard_path='') AS t_standard_is_root, p.t_standard_num_children AS t_standard_num_children, p.t_standard_path AS t_standard_path, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.procedure AS p WHERE p.id IN (SELECT p.child FROM `broad-tanagra-dev.cmssynpuf_index_071923`.procedure_standard_childParent AS p WHERE p.parent = 4179181) LIMIT 30 +SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, (p.t_standard_path IS NOT NULL) AS t_standard_is_member, (p.t_standard_path IS NOT NULL AND p.t_standard_path='') AS t_standard_is_root, p.t_standard_num_children AS t_standard_num_children, p.t_standard_path AS t_standard_path, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.procedure AS p WHERE p.id IN (SELECT p.child FROM `broad-tanagra-dev.cmssynpuf_index_072623`.procedure_standard_childParent AS p WHERE p.parent = 4179181) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/procedure-standard-viralImmunization-hierarchyAncestorFilter.sql b/service/src/test/resources/sql/cmssynpuf/procedure-standard-viralImmunization-hierarchyAncestorFilter.sql index 8324eda31..3b176fb9d 100644 --- a/service/src/test/resources/sql/cmssynpuf/procedure-standard-viralImmunization-hierarchyAncestorFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/procedure-standard-viralImmunization-hierarchyAncestorFilter.sql @@ -1 +1 @@ -SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, (p.t_standard_path IS NOT NULL) AS t_standard_is_member, (p.t_standard_path IS NOT NULL AND p.t_standard_path='') AS t_standard_is_root, p.t_standard_num_children AS t_standard_num_children, p.t_standard_path AS t_standard_path, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.procedure AS p WHERE (p.id IN (SELECT p.descendant FROM `broad-tanagra-dev.cmssynpuf_index_071923`.procedure_standard_ancestorDescendant AS p WHERE p.ancestor = 4176720) OR p.id = 4176720) LIMIT 30 +SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, (p.t_standard_path IS NOT NULL) AS t_standard_is_member, (p.t_standard_path IS NOT NULL AND p.t_standard_path='') AS t_standard_is_root, p.t_standard_num_children AS t_standard_num_children, p.t_standard_path AS t_standard_path, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.procedure AS p WHERE (p.id IN (SELECT p.descendant FROM `broad-tanagra-dev.cmssynpuf_index_072623`.procedure_standard_ancestorDescendant AS p WHERE p.ancestor = 4176720) OR p.id = 4176720) LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/procedure-textFilter.sql b/service/src/test/resources/sql/cmssynpuf/procedure-textFilter.sql index 765b27281..95628548c 100644 --- a/service/src/test/resources/sql/cmssynpuf/procedure-textFilter.sql +++ b/service/src/test/resources/sql/cmssynpuf/procedure-textFilter.sql @@ -1 +1 @@ -SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_071923`.procedure AS p WHERE CONTAINS_SUBSTR(p.text, 'mammogram') LIMIT 30 +SELECT p.concept_code AS concept_code, p.id AS id, p.name AS name, p.standard_concept AS standard_concept, p.t_display_standard_concept AS t_display_standard_concept, p.vocabulary AS vocabulary FROM `broad-tanagra-dev.cmssynpuf_index_072623`.procedure AS p WHERE CONTAINS_SUBSTR(p.text, 'mammogram') LIMIT 30 diff --git a/service/src/test/resources/sql/cmssynpuf/procedureoccurrence-mammogram.sql b/service/src/test/resources/sql/cmssynpuf/procedureoccurrence-mammogram.sql index b41a96122..adca73539 100644 --- a/service/src/test/resources/sql/cmssynpuf/procedureoccurrence-mammogram.sql +++ b/service/src/test/resources/sql/cmssynpuf/procedureoccurrence-mammogram.sql @@ -1 +1 @@ -SELECT p.age_at_occurrence AS age_at_occurrence, p.date AS date, p.id AS id, p.person_id AS person_id, p.procedure AS procedure, p.source_criteria_id AS source_criteria_id, p.source_value AS source_value, p.t_display_procedure AS t_display_procedure FROM `broad-tanagra-dev.cmssynpuf_index_071923`.procedure_occurrence AS p WHERE p.id IN (SELECT i.id_procedure_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_procedure_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_procedure_occurrence_person AS i WHERE i.id_procedure_occurrence IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.procedure_occurrence AS p WHERE p.id IN (SELECT i.id_procedure_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_071923`.idpairs_procedure_occurrence_procedure AS i WHERE i.id_procedure IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_071923`.procedure AS p WHERE p.id = 4324693)))))) LIMIT 30 +SELECT p.age_at_occurrence AS age_at_occurrence, p.date AS date, p.id AS id, p.person_id AS person_id, p.procedure AS procedure, p.source_criteria_id AS source_criteria_id, p.source_value AS source_value, p.t_display_procedure AS t_display_procedure FROM `broad-tanagra-dev.cmssynpuf_index_072623`.procedure_occurrence AS p WHERE p.id IN (SELECT i.id_procedure_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_procedure_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_procedure_occurrence_person AS i WHERE i.id_procedure_occurrence IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.procedure_occurrence AS p WHERE p.id IN (SELECT i.id_procedure_occurrence FROM `broad-tanagra-dev.cmssynpuf_index_072623`.idpairs_procedure_occurrence_procedure AS i WHERE i.id_procedure IN (SELECT p.id FROM `broad-tanagra-dev.cmssynpuf_index_072623`.procedure AS p WHERE p.id = 4324693)))))) LIMIT 30 diff --git a/service/src/test/resources/sql/sdd/genotyping-noFilter.sql b/service/src/test/resources/sql/sdd/genotyping-noFilter.sql index 90219f87a..86c41b4e7 100644 --- a/service/src/test/resources/sql/sdd/genotyping-noFilter.sql +++ b/service/src/test/resources/sql/sdd/genotyping-noFilter.sql @@ -1 +1 @@ -SELECT g.id AS id, g.name AS name FROM `verily-tanagra-dev.sdstatic_index_051623`.genotyping AS g LIMIT 30 +SELECT g.id AS id, g.name AS name FROM `verily-tanagra-dev.sdstatic_index_072623`.genotyping AS g LIMIT 30 diff --git a/service/src/test/resources/sql/sdd/genotyping-standard-gwasPlatforms-hierarchyParentFilter.sql b/service/src/test/resources/sql/sdd/genotyping-standard-gwasPlatforms-hierarchyParentFilter.sql index ac1d2fd78..d052b452c 100644 --- a/service/src/test/resources/sql/sdd/genotyping-standard-gwasPlatforms-hierarchyParentFilter.sql +++ b/service/src/test/resources/sql/sdd/genotyping-standard-gwasPlatforms-hierarchyParentFilter.sql @@ -1 +1 @@ -SELECT g.id AS id, g.name AS name, (g.t_standard_path IS NOT NULL) AS t_standard_is_member, (g.t_standard_path IS NOT NULL AND g.t_standard_path='') AS t_standard_is_root, g.t_standard_num_children AS t_standard_num_children, g.t_standard_path AS t_standard_path FROM `verily-tanagra-dev.sdstatic_index_051623`.genotyping AS g WHERE g.id IN (SELECT g.child FROM `verily-tanagra-dev.sdstatic_index_051623`.genotyping_standard_childParent AS g WHERE g.parent = 101) LIMIT 30 +SELECT g.id AS id, g.name AS name, (g.t_standard_path IS NOT NULL) AS t_standard_is_member, (g.t_standard_path IS NOT NULL AND g.t_standard_path='') AS t_standard_is_root, g.t_standard_num_children AS t_standard_num_children, g.t_standard_path AS t_standard_path FROM `verily-tanagra-dev.sdstatic_index_072623`.genotyping AS g WHERE g.id IN (SELECT g.child FROM `verily-tanagra-dev.sdstatic_index_072623`.genotyping_standard_childParent AS g WHERE g.parent = 101) LIMIT 30 diff --git a/service/src/test/resources/sql/sdd/genotyping-standard-hierarchyMemberFilter.sql b/service/src/test/resources/sql/sdd/genotyping-standard-hierarchyMemberFilter.sql index 80a2bebe3..6e951cb1b 100644 --- a/service/src/test/resources/sql/sdd/genotyping-standard-hierarchyMemberFilter.sql +++ b/service/src/test/resources/sql/sdd/genotyping-standard-hierarchyMemberFilter.sql @@ -1 +1 @@ -SELECT g.id AS id, g.name AS name, (g.t_standard_path IS NOT NULL) AS t_standard_is_member, (g.t_standard_path IS NOT NULL AND g.t_standard_path='') AS t_standard_is_root, g.t_standard_num_children AS t_standard_num_children, g.t_standard_path AS t_standard_path FROM `verily-tanagra-dev.sdstatic_index_051623`.genotyping AS g WHERE g.t_standard_path IS NOT NULL LIMIT 30 +SELECT g.id AS id, g.name AS name, (g.t_standard_path IS NOT NULL) AS t_standard_is_member, (g.t_standard_path IS NOT NULL AND g.t_standard_path='') AS t_standard_is_root, g.t_standard_num_children AS t_standard_num_children, g.t_standard_path AS t_standard_path FROM `verily-tanagra-dev.sdstatic_index_072623`.genotyping AS g WHERE g.t_standard_path IS NOT NULL LIMIT 30 diff --git a/service/src/test/resources/sql/sdd/genotyping-standard-hierarchyRootFilter.sql b/service/src/test/resources/sql/sdd/genotyping-standard-hierarchyRootFilter.sql index 2b2736b6e..e521d66d5 100644 --- a/service/src/test/resources/sql/sdd/genotyping-standard-hierarchyRootFilter.sql +++ b/service/src/test/resources/sql/sdd/genotyping-standard-hierarchyRootFilter.sql @@ -1 +1 @@ -SELECT g.id AS id, g.name AS name, (g.t_standard_path IS NOT NULL) AS t_standard_is_member, (g.t_standard_path IS NOT NULL AND g.t_standard_path='') AS t_standard_is_root, g.t_standard_num_children AS t_standard_num_children, g.t_standard_path AS t_standard_path FROM `verily-tanagra-dev.sdstatic_index_051623`.genotyping AS g WHERE g.t_standard_path = '' LIMIT 30 +SELECT g.id AS id, g.name AS name, (g.t_standard_path IS NOT NULL) AS t_standard_is_member, (g.t_standard_path IS NOT NULL AND g.t_standard_path='') AS t_standard_is_root, g.t_standard_num_children AS t_standard_num_children, g.t_standard_path AS t_standard_path FROM `verily-tanagra-dev.sdstatic_index_072623`.genotyping AS g WHERE g.t_standard_path = '' LIMIT 30 diff --git a/service/src/test/resources/sql/sdd/genotyping-textFilter.sql b/service/src/test/resources/sql/sdd/genotyping-textFilter.sql index 6ca3a9d7e..ab4df6c75 100644 --- a/service/src/test/resources/sql/sdd/genotyping-textFilter.sql +++ b/service/src/test/resources/sql/sdd/genotyping-textFilter.sql @@ -1 +1 @@ -SELECT g.id AS id, g.name AS name FROM `verily-tanagra-dev.sdstatic_index_051623`.genotyping AS g WHERE CONTAINS_SUBSTR(g.id, 'Illumina') LIMIT 30 +SELECT g.id AS id, g.name AS name FROM `verily-tanagra-dev.sdstatic_index_072623`.genotyping AS g WHERE CONTAINS_SUBSTR(g.id, 'Illumina') LIMIT 30 diff --git a/service/src/test/resources/sql/sdd/note-noFilter.sql b/service/src/test/resources/sql/sdd/note-noFilter.sql index a8f98e961..aec76eee9 100644 --- a/service/src/test/resources/sql/sdd/note-noFilter.sql +++ b/service/src/test/resources/sql/sdd/note-noFilter.sql @@ -1 +1 @@ -SELECT n.concept_code AS concept_code, n.id AS id, n.name AS name, n.vocabulary AS vocabulary FROM `verily-tanagra-dev.sdstatic_index_051623`.note AS n LIMIT 30 +SELECT n.concept_code AS concept_code, n.id AS id, n.name AS name, n.vocabulary AS vocabulary FROM `verily-tanagra-dev.sdstatic_index_072623`.note AS n LIMIT 30 diff --git a/service/src/test/resources/sql/sdd/note-textFilter.sql b/service/src/test/resources/sql/sdd/note-textFilter.sql index b76f7cfb3..c0a900b7a 100644 --- a/service/src/test/resources/sql/sdd/note-textFilter.sql +++ b/service/src/test/resources/sql/sdd/note-textFilter.sql @@ -1 +1 @@ -SELECT n.concept_code AS concept_code, n.id AS id, n.name AS name, n.vocabulary AS vocabulary FROM `verily-tanagra-dev.sdstatic_index_051623`.note AS n WHERE CONTAINS_SUBSTR(n.text, 'admis') LIMIT 30 +SELECT n.concept_code AS concept_code, n.id AS id, n.name AS name, n.vocabulary AS vocabulary FROM `verily-tanagra-dev.sdstatic_index_072623`.note AS n WHERE CONTAINS_SUBSTR(n.text, 'admis') LIMIT 30 diff --git a/service/src/test/resources/sql/sdd/noteoccurrence-outpatient.sql b/service/src/test/resources/sql/sdd/noteoccurrence-outpatient.sql index d3b307a29..a44d93333 100644 --- a/service/src/test/resources/sql/sdd/noteoccurrence-outpatient.sql +++ b/service/src/test/resources/sql/sdd/noteoccurrence-outpatient.sql @@ -1 +1 @@ -SELECT n.age_at_occurrence AS age_at_occurrence, n.date AS date, n.id AS id, n.note AS note, n.person_id AS person_id, n.source_value AS source_value, n.t_display_note AS t_display_note, n.t_display_visit_type AS t_display_visit_type, n.text AS text, n.title AS title, n.visit_occurrence_id AS visit_occurrence_id, n.visit_type AS visit_type FROM `verily-tanagra-dev.sdstatic_index_051623`.note_occurrence AS n WHERE n.id IN (SELECT i.id_note_occurrence FROM `verily-tanagra-dev.sdstatic_index_051623`.idpairs_note_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `verily-tanagra-dev.sdstatic_index_051623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `verily-tanagra-dev.sdstatic_index_051623`.idpairs_note_occurrence_person AS i WHERE i.id_note_occurrence IN (SELECT n.id FROM `verily-tanagra-dev.sdstatic_index_051623`.note_occurrence AS n WHERE n.id IN (SELECT i.id_note_occurrence FROM `verily-tanagra-dev.sdstatic_index_051623`.idpairs_note_occurrence_note AS i WHERE i.id_note IN (SELECT n.id FROM `verily-tanagra-dev.sdstatic_index_051623`.note AS n WHERE n.id = 44814638)))))) LIMIT 30 +SELECT n.age_at_occurrence AS age_at_occurrence, n.date AS date, n.id AS id, n.note AS note, n.person_id AS person_id, n.source_value AS source_value, n.t_display_note AS t_display_note, n.t_display_visit_type AS t_display_visit_type, n.text AS text, n.title AS title, n.visit_occurrence_id AS visit_occurrence_id, n.visit_type AS visit_type FROM `verily-tanagra-dev.sdstatic_index_072623`.note_occurrence AS n WHERE n.id IN (SELECT i.id_note_occurrence FROM `verily-tanagra-dev.sdstatic_index_072623`.idpairs_note_occurrence_person AS i WHERE i.id_person IN (SELECT p.id FROM `verily-tanagra-dev.sdstatic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `verily-tanagra-dev.sdstatic_index_072623`.idpairs_note_occurrence_person AS i WHERE i.id_note_occurrence IN (SELECT n.id FROM `verily-tanagra-dev.sdstatic_index_072623`.note_occurrence AS n WHERE n.id IN (SELECT i.id_note_occurrence FROM `verily-tanagra-dev.sdstatic_index_072623`.idpairs_note_occurrence_note AS i WHERE i.id_note IN (SELECT n.id FROM `verily-tanagra-dev.sdstatic_index_072623`.note AS n WHERE n.id = 44814638)))))) LIMIT 30 diff --git a/service/src/test/resources/sql/sdd/person-admissionNote-count.sql b/service/src/test/resources/sql/sdd/person-admissionNote-count.sql index c78f0662d..0550591b3 100644 --- a/service/src/test/resources/sql/sdd/person-admissionNote-count.sql +++ b/service/src/test/resources/sql/sdd/person-admissionNote-count.sql @@ -1 +1 @@ -SELECT p.gender AS gender, p.race AS race, COUNT(p.id) AS t_count, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race FROM `verily-tanagra-dev.sdstatic_index_051623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `verily-tanagra-dev.sdstatic_index_051623`.idpairs_note_occurrence_person AS i WHERE i.id_note_occurrence IN (SELECT n.id FROM `verily-tanagra-dev.sdstatic_index_051623`.note_occurrence AS n WHERE n.id IN (SELECT i.id_note_occurrence FROM `verily-tanagra-dev.sdstatic_index_051623`.idpairs_note_occurrence_note AS i WHERE i.id_note IN (SELECT n.id FROM `verily-tanagra-dev.sdstatic_index_051623`.note AS n WHERE n.id = 44814638)))) GROUP BY gender, t_display_gender, race, t_display_race ORDER BY gender ASC, t_display_gender ASC, race ASC, t_display_race ASC +SELECT p.gender AS gender, p.race AS race, COUNT(p.id) AS t_count, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race FROM `verily-tanagra-dev.sdstatic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `verily-tanagra-dev.sdstatic_index_072623`.idpairs_note_occurrence_person AS i WHERE i.id_note_occurrence IN (SELECT n.id FROM `verily-tanagra-dev.sdstatic_index_072623`.note_occurrence AS n WHERE n.id IN (SELECT i.id_note_occurrence FROM `verily-tanagra-dev.sdstatic_index_072623`.idpairs_note_occurrence_note AS i WHERE i.id_note IN (SELECT n.id FROM `verily-tanagra-dev.sdstatic_index_072623`.note AS n WHERE n.id = 44814638)))) GROUP BY gender, t_display_gender, race, t_display_race ORDER BY gender ASC, t_display_gender ASC, race ASC, t_display_race ASC diff --git a/service/src/test/resources/sql/sdd/person-admissionNote.sql b/service/src/test/resources/sql/sdd/person-admissionNote.sql index a98d7266e..77e14e0e9 100644 --- a/service/src/test/resources/sql/sdd/person-admissionNote.sql +++ b/service/src/test/resources/sql/sdd/person-admissionNote.sql @@ -1 +1 @@ -SELECT CAST(FLOOR(TIMESTAMP_DIFF(CURRENT_TIMESTAMP(), p.age, DAY) / 365.25) AS INT64) AS age, p.biovu_sample_dna_yield AS biovu_sample_dna_yield, p.biovu_sample_has_plasma AS biovu_sample_has_plasma, p.biovu_sample_is_compromised AS biovu_sample_is_compromised, p.biovu_sample_is_nonshippable AS biovu_sample_is_nonshippable, p.ethnicity AS ethnicity, p.gender AS gender, p.has_biovu_sample AS has_biovu_sample, p.id AS id, p.race AS race, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.year_of_birth AS year_of_birth FROM `verily-tanagra-dev.sdstatic_index_051623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `verily-tanagra-dev.sdstatic_index_051623`.idpairs_note_occurrence_person AS i WHERE i.id_note_occurrence IN (SELECT n.id FROM `verily-tanagra-dev.sdstatic_index_051623`.note_occurrence AS n WHERE n.id IN (SELECT i.id_note_occurrence FROM `verily-tanagra-dev.sdstatic_index_051623`.idpairs_note_occurrence_note AS i WHERE i.id_note IN (SELECT n.id FROM `verily-tanagra-dev.sdstatic_index_051623`.note AS n WHERE n.id = 44814638)))) LIMIT 30 +SELECT CAST(FLOOR(TIMESTAMP_DIFF(CURRENT_TIMESTAMP(), p.age, DAY) / 365.25) AS INT64) AS age, p.biovu_sample_dna_yield AS biovu_sample_dna_yield, p.biovu_sample_has_plasma AS biovu_sample_has_plasma, p.biovu_sample_is_compromised AS biovu_sample_is_compromised, p.biovu_sample_is_nonshippable AS biovu_sample_is_nonshippable, p.ethnicity AS ethnicity, p.gender AS gender, p.has_biovu_sample AS has_biovu_sample, p.id AS id, p.race AS race, p.t_display_ethnicity AS t_display_ethnicity, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race, p.year_of_birth AS year_of_birth FROM `verily-tanagra-dev.sdstatic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `verily-tanagra-dev.sdstatic_index_072623`.idpairs_note_occurrence_person AS i WHERE i.id_note_occurrence IN (SELECT n.id FROM `verily-tanagra-dev.sdstatic_index_072623`.note_occurrence AS n WHERE n.id IN (SELECT i.id_note_occurrence FROM `verily-tanagra-dev.sdstatic_index_072623`.idpairs_note_occurrence_note AS i WHERE i.id_note IN (SELECT n.id FROM `verily-tanagra-dev.sdstatic_index_072623`.note AS n WHERE n.id = 44814638)))) LIMIT 30 diff --git a/service/src/test/resources/sql/sdd/person-genotyping-count.sql b/service/src/test/resources/sql/sdd/person-genotyping-count.sql index a862f1d51..419702c93 100644 --- a/service/src/test/resources/sql/sdd/person-genotyping-count.sql +++ b/service/src/test/resources/sql/sdd/person-genotyping-count.sql @@ -1 +1 @@ -SELECT p.gender AS gender, p.race AS race, COUNT(p.id) AS t_count, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race FROM `verily-tanagra-dev.sdstatic_index_051623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `verily-tanagra-dev.sdstatic_index_051623`.idpairs_genotyping_person AS i WHERE i.id_genotyping IN (SELECT g.id FROM `verily-tanagra-dev.sdstatic_index_051623`.genotyping AS g WHERE g.name = 'Illumina 5M')) GROUP BY gender, t_display_gender, race, t_display_race ORDER BY gender ASC, t_display_gender ASC, race ASC, t_display_race ASC +SELECT p.gender AS gender, p.race AS race, COUNT(p.id) AS t_count, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race FROM `verily-tanagra-dev.sdstatic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `verily-tanagra-dev.sdstatic_index_072623`.idpairs_genotyping_person AS i WHERE i.id_genotyping IN (SELECT g.id FROM `verily-tanagra-dev.sdstatic_index_072623`.genotyping AS g WHERE g.name = 'Illumina 5M')) GROUP BY gender, t_display_gender, race, t_display_race ORDER BY gender ASC, t_display_gender ASC, race ASC, t_display_race ASC diff --git a/service/src/test/resources/sql/sdd/person-genotyping.sql b/service/src/test/resources/sql/sdd/person-genotyping.sql index 0c2e7ec5f..18f742b35 100644 --- a/service/src/test/resources/sql/sdd/person-genotyping.sql +++ b/service/src/test/resources/sql/sdd/person-genotyping.sql @@ -1 +1 @@ -SELECT p.id AS id FROM `verily-tanagra-dev.sdstatic_index_051623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `verily-tanagra-dev.sdstatic_index_051623`.idpairs_genotyping_person AS i WHERE i.id_genotyping IN (SELECT g.id FROM `verily-tanagra-dev.sdstatic_index_051623`.genotyping AS g WHERE g.name = 'Illumina 5M')) LIMIT 30 +SELECT p.id AS id FROM `verily-tanagra-dev.sdstatic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `verily-tanagra-dev.sdstatic_index_072623`.idpairs_genotyping_person AS i WHERE i.id_genotyping IN (SELECT g.id FROM `verily-tanagra-dev.sdstatic_index_072623`.genotyping AS g WHERE g.name = 'Illumina 5M')) LIMIT 30 diff --git a/service/src/test/resources/sql/sdd/person-snp-count.sql b/service/src/test/resources/sql/sdd/person-snp-count.sql index 939532f8b..e0b4e05e8 100644 --- a/service/src/test/resources/sql/sdd/person-snp-count.sql +++ b/service/src/test/resources/sql/sdd/person-snp-count.sql @@ -1 +1 @@ -SELECT p.gender AS gender, p.race AS race, COUNT(p.id) AS t_count, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race FROM `verily-tanagra-dev.sdstatic_index_051623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `verily-tanagra-dev.sdstatic_index_051623`.idpairs_snp_person AS i WHERE i.id_snp IN (SELECT s.id FROM `verily-tanagra-dev.sdstatic_index_051623`.snp AS s WHERE s.id = 'RS12925749')) GROUP BY gender, t_display_gender, race, t_display_race ORDER BY gender ASC, t_display_gender ASC, race ASC, t_display_race ASC +SELECT p.gender AS gender, p.race AS race, COUNT(p.id) AS t_count, p.t_display_gender AS t_display_gender, p.t_display_race AS t_display_race FROM `verily-tanagra-dev.sdstatic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `verily-tanagra-dev.sdstatic_index_072623`.idpairs_snp_person AS i WHERE i.id_snp IN (SELECT s.id FROM `verily-tanagra-dev.sdstatic_index_072623`.snp AS s WHERE s.id = 'RS12925749')) GROUP BY gender, t_display_gender, race, t_display_race ORDER BY gender ASC, t_display_gender ASC, race ASC, t_display_race ASC diff --git a/service/src/test/resources/sql/sdd/person-snp.sql b/service/src/test/resources/sql/sdd/person-snp.sql index a44a51357..cb52c6975 100644 --- a/service/src/test/resources/sql/sdd/person-snp.sql +++ b/service/src/test/resources/sql/sdd/person-snp.sql @@ -1 +1 @@ -SELECT p.id AS id FROM `verily-tanagra-dev.sdstatic_index_051623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `verily-tanagra-dev.sdstatic_index_051623`.idpairs_snp_person AS i WHERE i.id_snp IN (SELECT s.id FROM `verily-tanagra-dev.sdstatic_index_051623`.snp AS s WHERE s.id = 'RS12925749')) LIMIT 30 +SELECT p.id AS id FROM `verily-tanagra-dev.sdstatic_index_072623`.person AS p WHERE p.id IN (SELECT i.id_person FROM `verily-tanagra-dev.sdstatic_index_072623`.idpairs_snp_person AS i WHERE i.id_snp IN (SELECT s.id FROM `verily-tanagra-dev.sdstatic_index_072623`.snp AS s WHERE s.id = 'RS12925749')) LIMIT 30 diff --git a/service/src/test/resources/sql/sdd/snp-noFilter.sql b/service/src/test/resources/sql/sdd/snp-noFilter.sql index 9920b9842..f089dea37 100644 --- a/service/src/test/resources/sql/sdd/snp-noFilter.sql +++ b/service/src/test/resources/sql/sdd/snp-noFilter.sql @@ -1 +1 @@ -SELECT s.id AS id FROM `verily-tanagra-dev.sdstatic_index_051623`.snp AS s LIMIT 30 +SELECT s.id AS id FROM `verily-tanagra-dev.sdstatic_index_072623`.snp AS s LIMIT 30 diff --git a/service/src/test/resources/sql/sdd/snp-textFilter.sql b/service/src/test/resources/sql/sdd/snp-textFilter.sql index f18a2a125..b7b7cdd00 100644 --- a/service/src/test/resources/sql/sdd/snp-textFilter.sql +++ b/service/src/test/resources/sql/sdd/snp-textFilter.sql @@ -1 +1 @@ -SELECT s.id AS id FROM `verily-tanagra-dev.sdstatic_index_051623`.snp AS s WHERE CONTAINS_SUBSTR(s.id, 'RS1292') LIMIT 30 +SELECT s.id AS id FROM `verily-tanagra-dev.sdstatic_index_072623`.snp AS s WHERE CONTAINS_SUBSTR(s.id, 'RS1292') LIMIT 30 diff --git a/underlay/src/main/java/bio/terra/tanagra/query/bigquery/BigQueryRowResult.java b/underlay/src/main/java/bio/terra/tanagra/query/bigquery/BigQueryRowResult.java index 01cebfdc9..7ff0c81d6 100644 --- a/underlay/src/main/java/bio/terra/tanagra/query/bigquery/BigQueryRowResult.java +++ b/underlay/src/main/java/bio/terra/tanagra/query/bigquery/BigQueryRowResult.java @@ -2,6 +2,7 @@ import bio.terra.tanagra.query.CellValue; import bio.terra.tanagra.query.ColumnHeaderSchema; +import bio.terra.tanagra.query.ColumnSchema; import bio.terra.tanagra.query.RowResult; import com.google.api.client.util.Preconditions; import com.google.cloud.bigquery.FieldValueList; @@ -23,8 +24,8 @@ class BigQueryRowResult implements RowResult { @Override public CellValue get(int index) { - return new BigQueryCellValue( - fieldValues.get(index), columnHeaderSchema.getColumnSchemas().get(index)); + ColumnSchema columnSchema = columnHeaderSchema.getColumnSchemas().get(index); + return new BigQueryCellValue(fieldValues.get(columnSchema.getColumnName()), columnSchema); } @Override diff --git a/underlay/src/main/java/bio/terra/tanagra/serialization/UFAttribute.java b/underlay/src/main/java/bio/terra/tanagra/serialization/UFAttribute.java index af8703bd2..b26b34293 100644 --- a/underlay/src/main/java/bio/terra/tanagra/serialization/UFAttribute.java +++ b/underlay/src/main/java/bio/terra/tanagra/serialization/UFAttribute.java @@ -20,15 +20,12 @@ public class UFAttribute { private final Attribute.Type type; private final String name; private final Literal.DataType dataType; - private final UFDisplayHint displayHint; private final List displayHintTypes; public UFAttribute(Attribute attribute) { this.type = attribute.getType(); this.name = attribute.getName(); this.dataType = attribute.getDataType(); - this.displayHint = - attribute.getDisplayHint() == null ? null : attribute.getDisplayHint().serialize(); this.displayHintTypes = attribute.getDisplayHintTypes(); } @@ -36,7 +33,6 @@ protected UFAttribute(Builder builder) { this.type = builder.type; this.name = builder.name; this.dataType = builder.dataType; - this.displayHint = builder.displayHint; this.displayHintTypes = builder.displayHintTypes; } @@ -45,7 +41,6 @@ public static class Builder { private Attribute.Type type; private String name; private Literal.DataType dataType; - private UFDisplayHint displayHint; private List displayHintTypes = new ArrayList<>(); public Builder type(Attribute.Type type) { @@ -63,11 +58,6 @@ public Builder dataType(Literal.DataType dataType) { return this; } - public Builder displayHint(UFDisplayHint displayHint) { - this.displayHint = displayHint; - return this; - } - public Builder displayHintTypes(List displayHintTypes) { this.displayHintTypes = displayHintTypes; return this; @@ -91,10 +81,6 @@ public Literal.DataType getDataType() { return dataType; } - public UFDisplayHint getDisplayHint() { - return displayHint; - } - public List getDisplayHintTypes() { return displayHintTypes; } diff --git a/underlay/src/main/java/bio/terra/tanagra/serialization/UFEntityMapping.java b/underlay/src/main/java/bio/terra/tanagra/serialization/UFEntityMapping.java index b884f7db6..3831aa63c 100644 --- a/underlay/src/main/java/bio/terra/tanagra/serialization/UFEntityMapping.java +++ b/underlay/src/main/java/bio/terra/tanagra/serialization/UFEntityMapping.java @@ -17,6 +17,7 @@ public class UFEntityMapping { private final String dataPointer; private final UFTablePointer tablePointer; + private final UFTablePointer displayHintTablePointer; private final Map attributeMappings; private final UFTextSearchMapping textSearchMapping; private final Map hierarchyMappings; @@ -24,6 +25,7 @@ public class UFEntityMapping { public UFEntityMapping(EntityMapping entityMapping) { this.dataPointer = entityMapping.getTablePointer().getDataPointer().getName(); this.tablePointer = new UFTablePointer(entityMapping.getTablePointer()); + this.displayHintTablePointer = new UFTablePointer(entityMapping.getDisplayHintTablePointer()); Map attributeMappings = new HashMap<>(); entityMapping.getEntity().getAttributes().stream() @@ -58,6 +60,7 @@ public UFEntityMapping(EntityMapping entityMapping) { private UFEntityMapping(Builder builder) { this.dataPointer = builder.dataPointer; this.tablePointer = builder.tablePointer; + this.displayHintTablePointer = builder.displayHintTablePointer; this.attributeMappings = builder.attributeMappings; this.textSearchMapping = builder.textSearchMapping; this.hierarchyMappings = builder.hierarchyMappings; @@ -67,6 +70,7 @@ private UFEntityMapping(Builder builder) { public static class Builder { private String dataPointer; private UFTablePointer tablePointer; + private UFTablePointer displayHintTablePointer; private Map attributeMappings; private UFTextSearchMapping textSearchMapping; private Map hierarchyMappings; @@ -81,6 +85,11 @@ public Builder tablePointer(UFTablePointer tablePointer) { return this; } + public Builder displayHintTablePointer(UFTablePointer displayHintTablePointer) { + this.displayHintTablePointer = displayHintTablePointer; + return this; + } + public Builder attributeMappings(Map attributeMappings) { this.attributeMappings = attributeMappings; return this; @@ -110,6 +119,10 @@ public UFTablePointer getTablePointer() { return tablePointer; } + public UFTablePointer getDisplayHintTablePointer() { + return displayHintTablePointer; + } + public Map getAttributeMappings() { return attributeMappings; } diff --git a/underlay/src/main/java/bio/terra/tanagra/underlay/Attribute.java b/underlay/src/main/java/bio/terra/tanagra/underlay/Attribute.java index 2c8bb5bd8..ca0102e2d 100644 --- a/underlay/src/main/java/bio/terra/tanagra/underlay/Attribute.java +++ b/underlay/src/main/java/bio/terra/tanagra/underlay/Attribute.java @@ -19,21 +19,15 @@ public enum Type { private final String name; private final Type type; private Literal.DataType dataType; - private DisplayHint displayHint; private final List displayHintTypes; private AttributeMapping sourceMapping; private AttributeMapping indexMapping; public Attribute( - String name, - Type type, - Literal.DataType dataType, - DisplayHint displayHint, - List displayHintTypes) { + String name, Type type, Literal.DataType dataType, List displayHintTypes) { this.name = name; this.type = type; this.dataType = dataType; - this.displayHint = displayHint; this.displayHintTypes = displayHintTypes == null ? new ArrayList<>() : new ArrayList<>(displayHintTypes); } @@ -52,15 +46,10 @@ public static Attribute fromSerialized(UFAttribute serialized) { if (Strings.isNullOrEmpty(serialized.getName())) { throw new InvalidConfigException("Attribute name is undefined"); } - DisplayHint displayHint = - serialized.getDisplayHint() == null - ? null - : serialized.getDisplayHint().deserializeToInternal(); return new Attribute( serialized.getName(), serialized.getType(), serialized.getDataType(), - displayHint, serialized.getDisplayHintTypes()); } @@ -80,14 +69,6 @@ public void setDataType(Literal.DataType dataType) { this.dataType = dataType; } - public DisplayHint getDisplayHint() { - return displayHint; - } - - public void setDisplayHint(DisplayHint displayHint) { - this.displayHint = displayHint; - } - public List getDisplayHintTypes() { return Collections.unmodifiableList(displayHintTypes); } diff --git a/underlay/src/main/java/bio/terra/tanagra/underlay/Entity.java b/underlay/src/main/java/bio/terra/tanagra/underlay/Entity.java index 998a429e1..2e8eca234 100644 --- a/underlay/src/main/java/bio/terra/tanagra/underlay/Entity.java +++ b/underlay/src/main/java/bio/terra/tanagra/underlay/Entity.java @@ -1,6 +1,7 @@ package bio.terra.tanagra.underlay; import bio.terra.tanagra.exception.InvalidConfigException; +import bio.terra.tanagra.query.CellValue; import bio.terra.tanagra.serialization.UFEntity; import bio.terra.tanagra.serialization.UFHierarchyMapping; import bio.terra.tanagra.utils.FileIO; @@ -13,10 +14,25 @@ import java.util.List; import java.util.Map; import java.util.stream.Collectors; +import org.apache.commons.lang3.tuple.Pair; public final class Entity { public static final String ENTITY_DIRECTORY_NAME = "entity"; + public static final Map> DISPLAY_HINTS_TABLE_SCHEMA = + Map.of( + "attribute_name", + Pair.of(CellValue.SQLDataType.STRING, true), + "min", + Pair.of(CellValue.SQLDataType.FLOAT, false), + "max", + Pair.of(CellValue.SQLDataType.FLOAT, false), + "enum_value", + Pair.of(CellValue.SQLDataType.INT64, false), + "enum_display", + Pair.of(CellValue.SQLDataType.STRING, false), + "enum_count", + Pair.of(CellValue.SQLDataType.INT64, false)); private final String name; private final String idAttributeName; private final Map attributes; @@ -226,23 +242,6 @@ private static Map deserializeHierarchies( return hierarchies; } - public void scanSourceData() { - // lookup the data type and calculate a display hint for each attribute - attributes.values().stream() - .forEach( - attribute -> { - AttributeMapping attributeMapping = attribute.getMapping(Underlay.MappingType.SOURCE); - - // lookup the datatype - attribute.setDataType(attributeMapping.computeDataType()); - - // generate the display hint - if (!isIdAttribute(attribute) && !attribute.skipCalculateDisplayHint()) { - attribute.setDisplayHint(attributeMapping.computeDisplayHint()); - } - }); - } - public String getName() { return name; } diff --git a/underlay/src/main/java/bio/terra/tanagra/underlay/EntityMapping.java b/underlay/src/main/java/bio/terra/tanagra/underlay/EntityMapping.java index ccc6f52f7..abd7bbe38 100644 --- a/underlay/src/main/java/bio/terra/tanagra/underlay/EntityMapping.java +++ b/underlay/src/main/java/bio/terra/tanagra/underlay/EntityMapping.java @@ -11,12 +11,18 @@ import java.util.Map; public final class EntityMapping { + private static final String DISPLAY_HINT_TABLE_PREFIX = "eldh_"; // entity-level display hint private final TablePointer tablePointer; + private final TablePointer displayHintTablePointer; private Entity entity; private final Underlay.MappingType mappingType; - private EntityMapping(TablePointer tablePointer, Underlay.MappingType mappingType) { + private EntityMapping( + TablePointer tablePointer, + TablePointer displayHintTablePointer, + Underlay.MappingType mappingType) { this.tablePointer = tablePointer; + this.displayHintTablePointer = displayHintTablePointer; this.mappingType = mappingType; } @@ -44,7 +50,12 @@ public static EntityMapping fromSerialized( ? TablePointer.fromSerialized(serialized.getTablePointer(), dataPointer) : TablePointer.fromTableName(entityName, dataPointer); - return new EntityMapping(tablePointer, mappingType); + TablePointer displayHintTablePointer = + serialized.getDisplayHintTablePointer() != null + ? TablePointer.fromSerialized(serialized.getTablePointer(), dataPointer) + : TablePointer.fromTableName(DISPLAY_HINT_TABLE_PREFIX + entityName, dataPointer); + + return new EntityMapping(tablePointer, displayHintTablePointer, mappingType); } public Query queryIds(String alias) { @@ -83,6 +94,10 @@ public TablePointer getTablePointer() { return tablePointer; } + public TablePointer getDisplayHintTablePointer() { + return displayHintTablePointer; + } + public Entity getEntity() { return entity; } diff --git a/underlay/src/main/java/bio/terra/tanagra/underlay/ValueDisplay.java b/underlay/src/main/java/bio/terra/tanagra/underlay/ValueDisplay.java index d6abc6f13..ab99fe169 100644 --- a/underlay/src/main/java/bio/terra/tanagra/underlay/ValueDisplay.java +++ b/underlay/src/main/java/bio/terra/tanagra/underlay/ValueDisplay.java @@ -3,6 +3,7 @@ import bio.terra.tanagra.exception.InvalidConfigException; import bio.terra.tanagra.query.Literal; import bio.terra.tanagra.serialization.displayhint.UFValueDisplay; +import java.util.Objects; public class ValueDisplay { private final Literal value; @@ -37,4 +38,21 @@ public Literal getValue() { public String getDisplay() { return display; } + + @Override + public boolean equals(Object o) { + if (this == o) { + return true; + } + if (o == null || getClass() != o.getClass()) { + return false; + } + ValueDisplay that = (ValueDisplay) o; + return value.equals(that.value) && Objects.equals(display, that.display); + } + + @Override + public int hashCode() { + return Objects.hash(value, display); + } } diff --git a/underlay/src/main/java/bio/terra/tanagra/underlay/displayhint/EnumVal.java b/underlay/src/main/java/bio/terra/tanagra/underlay/displayhint/EnumVal.java index f46538784..48d2acb34 100644 --- a/underlay/src/main/java/bio/terra/tanagra/underlay/displayhint/EnumVal.java +++ b/underlay/src/main/java/bio/terra/tanagra/underlay/displayhint/EnumVal.java @@ -2,6 +2,7 @@ import bio.terra.tanagra.serialization.displayhint.UFEnumVal; import bio.terra.tanagra.underlay.ValueDisplay; +import java.util.Objects; public class EnumVal { private final ValueDisplay valueDisplay; @@ -23,4 +24,21 @@ public ValueDisplay getValueDisplay() { public long getCount() { return count; } + + @Override + public boolean equals(Object o) { + if (this == o) { + return true; + } + if (o == null || getClass() != o.getClass()) { + return false; + } + EnumVal enumVal = (EnumVal) o; + return count == enumVal.count && valueDisplay.equals(enumVal.valueDisplay); + } + + @Override + public int hashCode() { + return Objects.hash(valueDisplay, count); + } } diff --git a/underlay/src/main/java/bio/terra/tanagra/underlay/displayhint/EnumVals.java b/underlay/src/main/java/bio/terra/tanagra/underlay/displayhint/EnumVals.java index a7e91c0b2..8a5d03642 100644 --- a/underlay/src/main/java/bio/terra/tanagra/underlay/displayhint/EnumVals.java +++ b/underlay/src/main/java/bio/terra/tanagra/underlay/displayhint/EnumVals.java @@ -243,4 +243,21 @@ private static Query queryPossibleEnumVals(FieldPointer value) { .groupBy(List.of(nestedValueFieldVar)) .build(); } + + @Override + public boolean equals(Object o) { + if (this == o) { + return true; + } + if (o == null || getClass() != o.getClass()) { + return false; + } + EnumVals enumVals = (EnumVals) o; + return enumValsList.equals(enumVals.enumValsList); + } + + @Override + public int hashCode() { + return Objects.hash(enumValsList); + } } diff --git a/underlay/src/main/java/bio/terra/tanagra/underlay/displayhint/NumericRange.java b/underlay/src/main/java/bio/terra/tanagra/underlay/displayhint/NumericRange.java index 7e94778d3..07ec5d695 100644 --- a/underlay/src/main/java/bio/terra/tanagra/underlay/displayhint/NumericRange.java +++ b/underlay/src/main/java/bio/terra/tanagra/underlay/displayhint/NumericRange.java @@ -18,6 +18,7 @@ import bio.terra.tanagra.underlay.DisplayHint; import java.util.ArrayList; import java.util.List; +import java.util.Objects; public final class NumericRange extends DisplayHint { private final Double minVal; @@ -110,4 +111,21 @@ public static NumericRange computeForField(FieldPointer value) { rowResult.get(minValAlias).getDouble().getAsDouble(), rowResult.get(maxValAlias).getDouble().getAsDouble()); } + + @Override + public boolean equals(Object o) { + if (this == o) { + return true; + } + if (o == null || getClass() != o.getClass()) { + return false; + } + NumericRange that = (NumericRange) o; + return minVal.equals(that.minVal) && maxVal.equals(that.maxVal); + } + + @Override + public int hashCode() { + return Objects.hash(minVal, maxVal); + } } diff --git a/underlay/src/main/java/bio/terra/tanagra/utils/BigQueryStorageWriteApi.java b/underlay/src/main/java/bio/terra/tanagra/utils/BigQueryStorageWriteApi.java new file mode 100644 index 000000000..774acf093 --- /dev/null +++ b/underlay/src/main/java/bio/terra/tanagra/utils/BigQueryStorageWriteApi.java @@ -0,0 +1,277 @@ +package bio.terra.tanagra.utils; + +import bio.terra.tanagra.exception.SystemException; +import com.google.api.core.ApiFuture; +import com.google.api.core.ApiFutureCallback; +import com.google.api.core.ApiFutures; +import com.google.api.gax.core.CredentialsProvider; +import com.google.api.gax.core.FixedExecutorProvider; +import com.google.cloud.bigquery.storage.v1.*; +import com.google.common.collect.ImmutableList; +import com.google.common.util.concurrent.MoreExecutors; +import com.google.protobuf.Descriptors; +import io.grpc.Status; +import io.grpc.Status.Code; +import java.io.IOException; +import java.util.List; +import java.util.Map; +import java.util.concurrent.Executors; +import java.util.concurrent.Phaser; +import java.util.concurrent.TimeUnit; +import java.util.concurrent.atomic.AtomicInteger; +import javax.annotation.concurrent.GuardedBy; +import org.json.JSONArray; +import org.json.JSONObject; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.threeten.bp.Duration; + +/** + * Utility class for using the BigQuery Storage Write API. Example code from: + * https://cloud.google.com/bigquery/docs/write-api-streaming#at-least-once + */ +public final class BigQueryStorageWriteApi { + private static final Logger LOGGER = LoggerFactory.getLogger(BigQueryStorageWriteApi.class); + + private static final int BATCH_SIZE = 1000; + private static final int MAX_BATCHES = 100; + + private BigQueryStorageWriteApi() {} + + public static void insertWithStorageWriteApi( + CredentialsProvider credentialsProvider, + TableName destinationTableName, + List records) + throws Descriptors.DescriptorValidationException, IOException, InterruptedException { + DataWriter writer = new DataWriter(); + + // One time initialization for the worker. + writer.initialize(credentialsProvider, destinationTableName); + + // Write one batch of data to the stream for each 1000 rows. + // Data may be batched up to the maximum request size: + // https://cloud.google.com/bigquery/quotas#write-api-limits + int batchNum = 0; + while (batchNum < MAX_BATCHES) { + int startIndex = batchNum * BATCH_SIZE; + if (records.size() <= startIndex) { + break; + } + + JSONArray jsonArr = new JSONArray(); + for (int j = 0; j < BATCH_SIZE; j++) { + if (records.size() == startIndex + j) { + break; + } + jsonArr.put(records.get(startIndex + j)); + } + writer.append(new AppendContext(jsonArr, 0)); + batchNum++; + } + LOGGER.info("BQ Storage Write API: numRecords={}, numBatches={}", records.size(), batchNum); + + try { + TimeUnit.SECONDS.sleep(5); + } catch (InterruptedException e) { + throw new SystemException("Error calling BQ Storage Write API", e); + } + + // Final cleanup for the stream during worker teardown. + writer.cleanup(); + } + + private static class AppendContext { + + private final JSONArray data; + private int retryCount; + + AppendContext(JSONArray data, int retryCount) { + this.data = data; + this.retryCount = retryCount; + } + + public JSONArray getData() { + return data; + } + + public int getRetryCount() { + return retryCount; + } + + public void incrementRetryCount() { + retryCount++; + } + } + + private static class DataWriter { + + private static final int MAX_RETRY_COUNT = 3; + private static final int MAX_RECREATE_COUNT = 3; + private static final ImmutableList RETRIABLE_ERROR_CODES = + ImmutableList.of( + Code.INTERNAL, + Code.ABORTED, + Code.CANCELLED, + Code.FAILED_PRECONDITION, + Code.DEADLINE_EXCEEDED, + Code.UNAVAILABLE); + + // Track the number of in-flight requests to wait for all responses before shutting down. + private final Phaser inflightRequestCount = new Phaser(1); + private final Object lock = new Object(); + private JsonStreamWriter streamWriter; + + @GuardedBy("lock") + private RuntimeException error; + + private final AtomicInteger recreateCount = new AtomicInteger(0); + + public void initialize(CredentialsProvider credentialsProvider, TableName parentTable) + throws Descriptors.DescriptorValidationException, IOException, InterruptedException { + // Use the JSON stream writer to send records in JSON format. Specify the table name to write + // to the default stream. + // For more information about JsonStreamWriter, see: + // https://googleapis.dev/java/google-cloud-bigquerystorage/latest/com/google/cloud/bigquery/storage/v1/JsonStreamWriter.html + streamWriter = + JsonStreamWriter.newBuilder(parentTable.toString(), BigQueryWriteClient.create()) + .setCredentialsProvider(credentialsProvider) + .setExecutorProvider( + FixedExecutorProvider.create(Executors.newScheduledThreadPool(100))) + .setChannelProvider( + BigQueryWriteSettings.defaultGrpcTransportProviderBuilder() + .setKeepAliveTime(Duration.ofMinutes(1)) + .setKeepAliveTimeout(Duration.ofMinutes(1)) + .setKeepAliveWithoutCalls(true) + .setChannelsPerCpu(2) + .build()) + .setEnableConnectionPool(true) + .build(); + } + + public void append(AppendContext appendContext) + throws Descriptors.DescriptorValidationException, IOException, InterruptedException { + synchronized (this.lock) { + if (!streamWriter.isUserClosed() + && streamWriter.isClosed() + && recreateCount.getAndIncrement() < MAX_RECREATE_COUNT) { + streamWriter = + JsonStreamWriter.newBuilder( + streamWriter.getStreamName(), BigQueryWriteClient.create()) + .build(); + this.error = null; + } + // If earlier appends have failed, we need to reset before continuing. + if (this.error != null) { + throw this.error; + } + } + // Append asynchronously for increased throughput. + ApiFuture future = streamWriter.append(appendContext.data); + ApiFutures.addCallback( + future, new AppendCompleteCallback(this, appendContext), MoreExecutors.directExecutor()); + + // Increase the count of in-flight requests. + inflightRequestCount.register(); + } + + public void cleanup() { + // Wait for all in-flight requests to complete. + inflightRequestCount.arriveAndAwaitAdvance(); + + // Close the connection to the server. + streamWriter.close(); + + // Verify that no error occurred in the stream. + synchronized (this.lock) { + if (this.error != null) { + throw this.error; + } + } + } + + static class AppendCompleteCallback implements ApiFutureCallback { + + private final DataWriter parent; + private final AppendContext appendContext; + + AppendCompleteCallback(DataWriter parent, AppendContext appendContext) { + this.parent = parent; + this.appendContext = appendContext; + } + + @Override + public void onSuccess(AppendRowsResponse response) { + System.out.format("Append success%n"); + this.parent.recreateCount.set(0); + done(); + } + + @Override + public void onFailure(Throwable throwable) { + // If the wrapped exception is a StatusRuntimeException, check the state of the operation. + // If the state is INTERNAL, CANCELLED, or ABORTED, you can retry. For more information, + // see: https://grpc.github.io/grpc-java/javadoc/io/grpc/StatusRuntimeException.html + Status status = Status.fromThrowable(throwable); + if (appendContext.retryCount < MAX_RETRY_COUNT + && RETRIABLE_ERROR_CODES.contains(status.getCode())) { + appendContext.retryCount++; + try { + // Since default stream appends are not ordered, we can simply retry the appends. + // Retrying with exclusive streams requires more careful consideration. + this.parent.append(appendContext); + // Mark the existing attempt as done since it's being retried. + done(); + return; + } catch (Exception e) { + // Fall through to return error. + System.out.format("Failed to retry append: %s%n", e); + } + } + + if (throwable instanceof Exceptions.AppendSerializationError) { + Exceptions.AppendSerializationError ase = (Exceptions.AppendSerializationError) throwable; + Map rowIndexToErrorMessage = ase.getRowIndexToErrorMessage(); + if (!rowIndexToErrorMessage.isEmpty()) { + // Omit the faulty rows + JSONArray dataNew = new JSONArray(); + for (int i = 0; i < appendContext.data.length(); i++) { + if (!rowIndexToErrorMessage.containsKey(i)) { + dataNew.put(appendContext.data.get(i)); + } // else {} // process faulty rows by placing them on a dead-letter-queue, for + // instance + } + + // Retry the remaining valid rows, but using a separate thread to + // avoid potentially blocking while we are in a callback. + if (dataNew.length() > 0) { + try { + this.parent.append(new AppendContext(dataNew, 0)); + } catch (Descriptors.DescriptorValidationException + | IOException + | InterruptedException e) { + throw new SystemException("Error calling BQ Storage Write API", e); + } + } + // Mark the existing attempt as done since we got a response for it + done(); + return; + } + } + + synchronized (this.parent.lock) { + if (this.parent.error == null) { + Exceptions.StorageException storageException = Exceptions.toStorageException(throwable); + this.parent.error = + (storageException != null) ? storageException : new RuntimeException(throwable); + } + } + done(); + } + + private void done() { + // Reduce the count of in-flight requests. + this.parent.inflightRequestCount.arriveAndDeregister(); + } + } + } +} diff --git a/underlay/src/main/java/bio/terra/tanagra/utils/GoogleBigQuery.java b/underlay/src/main/java/bio/terra/tanagra/utils/GoogleBigQuery.java index e6c3e4dfa..feeae2623 100644 --- a/underlay/src/main/java/bio/terra/tanagra/utils/GoogleBigQuery.java +++ b/underlay/src/main/java/bio/terra/tanagra/utils/GoogleBigQuery.java @@ -1,23 +1,12 @@ package bio.terra.tanagra.utils; import bio.terra.tanagra.exception.SystemException; +import com.google.api.gax.core.FixedCredentialsProvider; import com.google.api.gax.retrying.RetrySettings; import com.google.auth.oauth2.GoogleCredentials; -import com.google.cloud.bigquery.BigQuery; -import com.google.cloud.bigquery.BigQueryException; -import com.google.cloud.bigquery.BigQueryOptions; -import com.google.cloud.bigquery.Dataset; -import com.google.cloud.bigquery.DatasetId; -import com.google.cloud.bigquery.Job; -import com.google.cloud.bigquery.JobInfo; -import com.google.cloud.bigquery.JobStatistics; -import com.google.cloud.bigquery.QueryJobConfiguration; -import com.google.cloud.bigquery.Schema; -import com.google.cloud.bigquery.StandardTableDefinition; -import com.google.cloud.bigquery.Table; -import com.google.cloud.bigquery.TableId; -import com.google.cloud.bigquery.TableInfo; -import com.google.cloud.bigquery.TableResult; +import com.google.cloud.bigquery.*; +import com.google.cloud.bigquery.storage.v1.TableName; +import com.google.protobuf.Descriptors; import java.io.IOException; import java.net.SocketTimeoutException; import java.time.Duration; @@ -27,6 +16,7 @@ import java.util.concurrent.ConcurrentHashMap; import javax.annotation.Nullable; import org.apache.http.HttpStatus; +import org.json.JSONObject; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -44,11 +34,13 @@ public final class GoogleBigQuery { private static final org.threeten.bp.Duration MAX_BQ_CLIENT_TIMEOUT = org.threeten.bp.Duration.ofMinutes(5); + private final GoogleCredentials credentials; private final BigQuery bigQuery; private final ConcurrentHashMap tableSchemasCache; private final ConcurrentHashMap querySchemasCache; public GoogleBigQuery(GoogleCredentials credentials, String projectId) { + this.credentials = credentials; this.bigQuery = BigQueryOptions.newBuilder() .setCredentials(credentials) @@ -239,6 +231,29 @@ public void deleteTable(String projectId, String datasetId, String tableId) { } } + /** Append rows to a table using the Storage Write API. */ + public void insertWithStorageWriteApi( + String projectId, String datasetId, String tableId, List records) { + try { + BigQueryStorageWriteApi.insertWithStorageWriteApi( + FixedCredentialsProvider.create(credentials), + TableName.of(projectId, datasetId, tableId), + records); + } catch (IOException | InterruptedException | Descriptors.DescriptorValidationException ex) { + throw new SystemException("Error inserting rows with Storage Write API", ex); + } + } + + public int getNumRows(String projectId, String datasetId, String tableId) { + String queryRowCount = + "SELECT COUNT(*) FROM `" + projectId + "." + datasetId + "." + tableId + "`"; + QueryJobConfiguration queryConfig = QueryJobConfiguration.newBuilder(queryRowCount).build(); + TableResult results = + callWithRetries( + () -> bigQuery.query(queryConfig), "Error counting rows in BigQuery table: " + tableId); + return Integer.parseInt(results.getValues().iterator().next().get("f0_").getStringValue()); + } + /** * Utility method that checks if an exception thrown by the BQ client is retryable. * diff --git a/underlay/src/test/java/bio/terra/tanagra/query/bigquery/BigQueryRowResultTest.java b/underlay/src/test/java/bio/terra/tanagra/query/bigquery/BigQueryRowResultTest.java index 29ca5602b..fe0206c17 100644 --- a/underlay/src/test/java/bio/terra/tanagra/query/bigquery/BigQueryRowResultTest.java +++ b/underlay/src/test/java/bio/terra/tanagra/query/bigquery/BigQueryRowResultTest.java @@ -6,8 +6,7 @@ import bio.terra.tanagra.query.CellValue; import bio.terra.tanagra.query.ColumnHeaderSchema; import bio.terra.tanagra.query.ColumnSchema; -import com.google.cloud.bigquery.FieldValue; -import com.google.cloud.bigquery.FieldValueList; +import com.google.cloud.bigquery.*; import com.google.common.collect.ImmutableList; import java.util.Optional; import java.util.OptionalLong; @@ -21,7 +20,10 @@ void rowResult() { FieldValueList.of( ImmutableList.of( FieldValue.of(FieldValue.Attribute.PRIMITIVE, "foo"), - FieldValue.of(FieldValue.Attribute.PRIMITIVE, "42"))), + FieldValue.of(FieldValue.Attribute.PRIMITIVE, "42")), + FieldList.of( + Field.of("a", LegacySQLTypeName.STRING), + Field.of("b", LegacySQLTypeName.INTEGER))), new ColumnHeaderSchema( ImmutableList.of( new ColumnSchema("a", CellValue.SQLDataType.STRING),