diff --git a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/brand.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/brand.json similarity index 69% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/brand.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entity/brand.json index 0403f94a4..b91b1f66a 100644 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/brand.json +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/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/vumc/sdd_refresh0323/original/entity/condition.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/condition.json similarity index 78% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/condition.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entity/condition.json index 8d7f876d9..e8701cc41 100644 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/condition.json +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/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/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/original/entity/device.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/device.json similarity index 75% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/device.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entity/device.json index 2e72d8d62..078cd332c 100644 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/device.json +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/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/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/vumc/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/vumc/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/vumc/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/original/entity/ingredient.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/ingredient.json similarity index 81% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/ingredient.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entity/ingredient.json index 0e7901ee5..59a4ddcc0 100644 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/ingredient.json +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/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/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/original/entity/measurement.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/measurement.json similarity index 90% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/measurement.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entity/measurement.json index 70324f369..f71f480d4 100644 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/measurement.json +++ b/service/src/main/resources/config/vumc/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_refresh0323/original/entity/measurement_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/measurement_occurrence.json similarity index 55% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/measurement_occurrence.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entity/measurement_occurrence.json index cc142dabb..2fcd3d557 100644 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/measurement_occurrence.json +++ b/service/src/main/resources/config/vumc/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_refresh0323/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/vumc/sdd_refresh0323/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/vumc/sdd_refresh0323/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/original/entity/observation.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/observation.json similarity index 79% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/observation.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entity/observation.json index 668afebce..92f45b426 100644 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/observation.json +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/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/vumc/sdd_refresh0323/original/entity/observation_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/observation_occurrence.json similarity index 55% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/observation_occurrence.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entity/observation_occurrence.json index c1709a63a..da8e8c476 100644 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/observation_occurrence.json +++ b/service/src/main/resources/config/vumc/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/vumc/sdd_refresh0323/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_refresh0323/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_refresh0323/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/original/entity/procedure.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/procedure.json similarity index 78% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/procedure.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entity/procedure.json index 5b26c710e..b45e3d76c 100644 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/procedure.json +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/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_refresh0323/original/entity/procedure_occurrence.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/procedure_occurrence.json similarity index 51% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/procedure_occurrence.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entity/procedure_occurrence.json index 6d1d61acc..fdc4cc913 100644 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/procedure_occurrence.json +++ b/service/src/main/resources/config/vumc/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/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/original/entity/visit.json b/service/src/main/resources/config/vumc/sdd_refresh0323/entity/visit.json similarity index 85% rename from service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/visit.json rename to service/src/main/resources/config/vumc/sdd_refresh0323/entity/visit.json index 0b9a91bde..68bcc9d58 100644 --- a/service/src/main/resources/config/vumc/sdd_refresh0323/original/entity/visit.json +++ b/service/src/main/resources/config/vumc/sdd_refresh0323/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/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 - } ] - }, - 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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" : 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}, - "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" : { - 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}, - "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" : { - 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"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" : { - 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}, - "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 0a0147f2f..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\": \"Program data\", \"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\": \"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\": \"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\": \"Program data\", \"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/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_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_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/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/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