Configure source queries for new ingredient attributes in sd (#1149)

* configure source queries for new ingredient attributes * updated source queries to use INT64 for drug_exposure_id and for person_id --------- Co-authored-by: Chenchal Subraveti <[email protected]>
DataBiosphere · Jan 29, 2025 · 6bc2b90 · 6bc2b90
1 parent bf28064
commit 6bc2b90
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Showing 3 changed files with 45 additions and 9 deletions.
diff --git a/underlay/src/main/resources/config/datamapping/sd/entity/conditionOccurrence/entity.json b/underlay/src/main/resources/config/datamapping/sd/entity/conditionOccurrence/entity.json
@@ -4,7 +4,7 @@
   "attributes": [
     { "name": "id", "dataType": "INT64", "valueFieldName": "condition_occurrence_id", "isSuppressedForExport": true },
     { "name": "person_id", "dataType": "INT64" },
-    { "name": "GRID", "dataType": "STRING", "valueFieldName": "person_id", "displayFieldName": "person_source_value",
+    { "name": "GRID", "dataType": "INT64", "valueFieldName": "person_id", "displayFieldName": "person_source_value",
       "sourceQuery": {
         "displayFieldName": "person_source_value",
         "displayFieldTable": "${omopDataset}.person",

diff --git a/underlay/src/main/resources/config/datamapping/sd/entity/ingredientOccurrence/all.sql b/underlay/src/main/resources/config/datamapping/sd/entity/ingredientOccurrence/all.sql
@@ -17,7 +17,7 @@ SELECT
   tc.concept_name AS drug_type_concept_name,
   vo.visit_concept_id,
   vc.concept_name AS visit_concept_name,
-  de.route_source_value AS route,
+  de.route_source_value,
   x.x_drug_form AS drug_form,
   x.x_strength AS drug_strength,
   x.x_dose AS dose_amt,

diff --git a/underlay/src/main/resources/config/datamapping/sd/entity/ingredientOccurrence/entity.json b/underlay/src/main/resources/config/datamapping/sd/entity/ingredientOccurrence/entity.json
@@ -22,13 +22,49 @@
     { "name": "age_at_occurrence", "dataType": "INT64", "isComputeDisplayHint": true, "displayHintRangeMin": 0, "displayHintRangeMax": 89, "isSuppressedForExport": true },
     { "name": "visit_occurrence_id", "dataType": "INT64" },
     { "name": "visit_type", "dataType": "INT64", "valueFieldName": "visit_concept_id", "displayFieldName": "visit_concept_name", "isComputeDisplayHint": true, "isSuppressedForExport": true },
-    {"name":  "exposure_type", "dataType":  "INT64", "valueFieldName":  "drug_type_concept_id", "displayFieldName":  "drug_type_concept_name"},
-    {"name":  "form", "dataType":  "STRING", "valueFieldName":  "drug_form"},
-    {"name":  "strength", "dataType":  "STRING", "valueFieldName":  "drug_strength"},
-    {"name":  "amount", "dataType":  "STRING", "valueFieldName":  "dose_amt"},
-    {"name":  "route", "dataType":  "STRING", "valueFieldName":  "route"},
-    {"name":  "frequency", "dataType":  "STRING", "valueFieldName":  "drug_freq"},
-    {"name":  "source", "dataType":  "STRING", "valueFieldName":  "source_table"}
+    {"name":  "exposure_type", "dataType":  "INT64", "valueFieldName":  "drug_type_concept_id", "displayFieldName":  "drug_type_concept_name",
+      "sourceQuery": {
+        "displayFieldName": "concept_name",
+        "displayFieldTable": "${omopDataset}.concept",
+        "displayFieldTableJoinFieldName": "concept_id"
+      }
+    },
+    {"name":  "form", "dataType":  "INT64", "valueFieldName":  "drug_exposure_id", "displayFieldName":  "drug_form",
+      "sourceQuery": {
+        "displayFieldName": "x_drug_form",
+        "displayFieldTable": "${omopDataset}.x_drug_exposure",
+        "displayFieldTableJoinFieldName": "drug_exposure_id"
+      }
+    },
+    {"name":  "strength", "dataType":  "INT64", "valueFieldName":  "drug_exposure_id", "displayFieldName":  "drug_strength",
+      "sourceQuery": {
+        "displayFieldName": "x_strength",
+        "displayFieldTable": "${omopDataset}.x_drug_exposure",
+        "displayFieldTableJoinFieldName": "drug_exposure_id"
+      }
+    },
+    {"name":  "amount", "dataType":  "INT64", "valueFieldName":  "drug_exposure_id", "displayFieldName":  "dose_amt",
+      "sourceQuery": {
+        "displayFieldName": "x_dose",
+        "displayFieldTable": "${omopDataset}.x_drug_exposure",
+        "displayFieldTableJoinFieldName": "drug_exposure_id"
+      }
+    },
+    {"name":  "route", "dataType":  "STRING", "valueFieldName":  "route_source_value"},
+    {"name":  "frequency", "dataType":  "INT64", "valueFieldName":  "drug_exposure_id", "displayFieldName":  "drug_freq",
+      "sourceQuery": {
+        "displayFieldName": "x_frequency",
+        "displayFieldTable": "${omopDataset}.x_drug_exposure",
+        "displayFieldTableJoinFieldName": "drug_exposure_id"
+      }
+    },
+    {"name":  "source", "dataType":  "INT64", "valueFieldName":  "drug_exposure_id", "displayFieldName":  "source_table",
+      "sourceQuery": {
+        "displayFieldName": "x_doc_type",
+        "displayFieldTable": "${omopDataset}.x_drug_exposure",
+        "displayFieldTableJoinFieldName": "drug_exposure_id"
+      }
+    }
   ],
   "idAttribute": "id",
   "optimizeGroupByAttributes": [ "ingredient" ],