diff --git a/service/local-dev/run_server.sh b/service/local-dev/run_server.sh index f617f793b..9c475f26b 100755 --- a/service/local-dev/run_server.sh +++ b/service/local-dev/run_server.sh @@ -5,7 +5,7 @@ usage() { echo "$0 usage flags:" && grep " .)\ #" $0; } usage echo -while getopts ":avm" arg; do +while getopts ":avtm" arg; do case $arg in a) # Disable authentication. disableAuthChecks=1 @@ -13,6 +13,9 @@ while getopts ":avm" arg; do v) # Use Verily underlays. useVerilyUnderlays=1 ;; + t) # Use AoU test underlays + useAouUnderlays=1 + ;; m) # Use MariaDB. useMariaDB=1 ;; @@ -41,6 +44,11 @@ if [[ ${useVerilyUnderlays} ]]; then 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_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_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 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 index 67e62bdac..463967292 100644 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/SC2022Q4R6.json +++ b/service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/SC2022Q4R6.json @@ -3,7 +3,7 @@ "dataPointers" : [ { "type" : "BQ_DATASET", "name" : "index_dataset", - "projectId" : "all-of-us-ehr-dev", + "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", @@ -14,7 +14,7 @@ }, { "type" : "BQ_DATASET", "name" : "omop_dataset", - "projectId" : "all-of-us-ehr-dev", + "projectId" : "fc-aou-cdr-synth-test-2", "datasetId" : "SC2022Q4R6", "queryProjectId" : "fc-aou-cdr-synth-test-2", "dataflowRegion" : "us-central1", 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/original/ui/top_level.json index e364255aa..d9c8df81c 100644 --- a/service/src/main/resources/config/aou/test/SC2022Q4R6/original/ui/top_level.json +++ b/service/src/main/resources/config/aou/test/SC2022Q4R6/original/ui/top_level.json @@ -2,7 +2,7 @@ "dataConfig": { "primaryEntity": { "displayName": "Person", - "entity": "person", + "entity": "t_person", "key": "id", "classifications": [ ] @@ -11,13 +11,13 @@ { "id": "condition_occurrence", "displayName": "Condition Occurrences", - "entity": "condition_occurrence", + "entity": "t_condition_occurrence", "key": "id", "classifications": [ { "id": "condition", "attribute": "condition", - "entity": "condition", + "entity": "t_condition", "entityAttribute": "id", "hierarchy": "standard", "defaultSort": { @@ -30,13 +30,13 @@ { "id": "procedure_occurrence", "displayName": "Procedure Occurrences", - "entity": "procedure_occurrence", + "entity": "t_procedure_occurrence", "key": "id", "classifications": [ { "id": "procedure", "attribute": "procedure", - "entity": "procedure", + "entity": "t_procedure", "entityAttribute": "id", "hierarchy": "standard", "defaultSort": { @@ -49,13 +49,13 @@ { "id": "observation_occurrence", "displayName": "Observation Occurrence", - "entity": "observation_occurrence", + "entity": "t_observation_occurrence", "key": "id", "classifications": [ { "id": "observation", "attribute": "observation", - "entity": "observation", + "entity": "t_observation", "entityAttribute": "id", "defaultSort": { "attribute": "t_rollup_count", @@ -67,13 +67,13 @@ { "id": "ingredient_occurrence", "displayName": "Drug Occurrence", - "entity": "ingredient_occurrence", + "entity": "t_ingredient_occurrence", "key": "id", "classifications": [ { "id": "ingredient", "attribute": "id", - "entity": "ingredient", + "entity": "t_ingredient", "entityAttribute": "id", "hierarchy": "standard", "defaultSort": { @@ -83,7 +83,7 @@ "groupings": [ { "id": "brand", - "entity": "brand", + "entity": "t_brand", "defaultSort": { "attribute": "name", "direction": "ASC" @@ -97,13 +97,13 @@ { "id": "measurement_occurrence", "displayName": "Measurement Occurrence", - "entity": "measurement_occurrence", + "entity": "t_measurement_occurrence", "key": "id", "classifications": [ { "id": "measurement", "attribute": "measurement", - "entity": "measurement", + "entity": "t_measurement", "entityAttribute": "id", "hierarchy": "standard", "defaultSort": { 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 index 63fb10ed8..8b9f56610 100644 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/SR2022Q4R6.json +++ b/service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/SR2022Q4R6.json @@ -3,7 +3,7 @@ "dataPointers" : [ { "type" : "BQ_DATASET", "name" : "index_dataset", - "projectId" : "all-of-us-ehr-dev", + "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", @@ -14,7 +14,7 @@ }, { "type" : "BQ_DATASET", "name" : "omop_dataset", - "projectId" : "all-of-us-ehr-dev", + "projectId" : "fc-aou-cdr-synth-test", "datasetId" : "SR2022Q4R6", "queryProjectId" : "fc-aou-cdr-synth-test", "dataflowRegion" : "us-central1", 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/original/ui/top_level.json index e364255aa..d9c8df81c 100644 --- a/service/src/main/resources/config/aou/test/SR2022Q4R6/original/ui/top_level.json +++ b/service/src/main/resources/config/aou/test/SR2022Q4R6/original/ui/top_level.json @@ -2,7 +2,7 @@ "dataConfig": { "primaryEntity": { "displayName": "Person", - "entity": "person", + "entity": "t_person", "key": "id", "classifications": [ ] @@ -11,13 +11,13 @@ { "id": "condition_occurrence", "displayName": "Condition Occurrences", - "entity": "condition_occurrence", + "entity": "t_condition_occurrence", "key": "id", "classifications": [ { "id": "condition", "attribute": "condition", - "entity": "condition", + "entity": "t_condition", "entityAttribute": "id", "hierarchy": "standard", "defaultSort": { @@ -30,13 +30,13 @@ { "id": "procedure_occurrence", "displayName": "Procedure Occurrences", - "entity": "procedure_occurrence", + "entity": "t_procedure_occurrence", "key": "id", "classifications": [ { "id": "procedure", "attribute": "procedure", - "entity": "procedure", + "entity": "t_procedure", "entityAttribute": "id", "hierarchy": "standard", "defaultSort": { @@ -49,13 +49,13 @@ { "id": "observation_occurrence", "displayName": "Observation Occurrence", - "entity": "observation_occurrence", + "entity": "t_observation_occurrence", "key": "id", "classifications": [ { "id": "observation", "attribute": "observation", - "entity": "observation", + "entity": "t_observation", "entityAttribute": "id", "defaultSort": { "attribute": "t_rollup_count", @@ -67,13 +67,13 @@ { "id": "ingredient_occurrence", "displayName": "Drug Occurrence", - "entity": "ingredient_occurrence", + "entity": "t_ingredient_occurrence", "key": "id", "classifications": [ { "id": "ingredient", "attribute": "id", - "entity": "ingredient", + "entity": "t_ingredient", "entityAttribute": "id", "hierarchy": "standard", "defaultSort": { @@ -83,7 +83,7 @@ "groupings": [ { "id": "brand", - "entity": "brand", + "entity": "t_brand", "defaultSort": { "attribute": "name", "direction": "ASC" @@ -97,13 +97,13 @@ { "id": "measurement_occurrence", "displayName": "Measurement Occurrence", - "entity": "measurement_occurrence", + "entity": "t_measurement_occurrence", "key": "id", "classifications": [ { "id": "measurement", "attribute": "measurement", - "entity": "measurement", + "entity": "t_measurement", "entityAttribute": "id", "hierarchy": "standard", "defaultSort": {