Add cohort review columns for procedure in SD (#1182)

* add review columns for procedure * add missing attributes for condition and observation * change dataset for indexing * revert change dataset for indexing
DataBiosphere · Feb 28, 2025 · 4343d45 · 4343d45
1 parent dc72d1d
commit 4343d45
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Showing 5 changed files with 56 additions and 2 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
@@ -25,6 +25,7 @@
         "displayFieldTableJoinFieldName": "concept_id"
       }
     },
+    { "name": "condition_concept_id", "dataType": "INT64" },
     { "name": "standard_concept", "dataType": "STRING",  "isSuppressedForExport": true },
     { "name": "start_date", "dataType": "TIMESTAMP", "valueFieldName": "condition_start_date" },
     { "name": "end_date", "dataType": "TIMESTAMP", "valueFieldName": "condition_end_date" },

diff --git a/underlay/src/main/resources/config/datamapping/sd/entity/observationOccurrence/entity.json b/underlay/src/main/resources/config/datamapping/sd/entity/observationOccurrence/entity.json
@@ -19,6 +19,7 @@
         "displayFieldTableJoinFieldName": "concept_id"
       }
     },
+    { "name": "observation_concept_id", "dataType": "INT64" },
     { "name": "standard_concept", "dataType": "STRING",  "isSuppressedForExport": true },
     { "name": "start_date", "dataType": "TIMESTAMP", "valueFieldName": "observation_date" },
     { "name": "value_as_string", "dataType": "STRING" },

diff --git a/underlay/src/main/resources/config/datamapping/sd/entity/procedureOccurrence/all.sql b/underlay/src/main/resources/config/datamapping/sd/entity/procedureOccurrence/all.sql
@@ -4,6 +4,8 @@ SELECT
   p.person_source_value,
   po.procedure_concept_id,
   pc.concept_name AS procedure_concept_name,
+  pc.concept_code AS procedure_concept_code,
+  (CASE WHEN pc.standard_concept IS NULL THEN 'Source' WHEN pc.standard_concept = 'S' THEN 'Standard' ELSE 'Unknown' END) AS standard_concept,
   po.procedure_date,
   po.procedure_source_value,
   po.procedure_source_concept_id,

diff --git a/underlay/src/main/resources/config/datamapping/sd/entity/procedureOccurrence/entity.json b/underlay/src/main/resources/config/datamapping/sd/entity/procedureOccurrence/entity.json
@@ -12,6 +12,15 @@
         "displayFieldTableJoinFieldName": "concept_id"
       }
     },
+    { "name": "procedure_concept_code", "dataType": "INT64", "valueFieldName": "procedure_concept_id", "displayFieldName": "procedure_concept_code",
+      "sourceQuery": {
+        "displayFieldName": "concept_code",
+        "displayFieldTable": "${omopDataset}.concept",
+        "displayFieldTableJoinFieldName": "concept_id"
+      }
+    },
+    { "name": "procedure_concept_id", "dataType": "INT64" },
+    { "name": "standard_concept", "dataType": "STRING",  "isSuppressedForExport": true },
     { "name": "start_date", "dataType": "TIMESTAMP", "valueFieldName": "procedure_date" },
     { "name": "source_value", "dataType": "STRING", "valueFieldName": "procedure_source_value" },
     { "name": "source_criteria_id", "dataType": "INT64", "valueFieldName": "procedure_source_concept_id" },

diff --git a/underlay/src/main/resources/config/underlay/sd/ui.json b/underlay/src/main/resources/config/underlay/sd/ui.json
@@ -111,12 +111,53 @@
           "columns": [
             {
               "key": "procedure",
-              "width": "100%",
+              "width": "20%",
               "title": "Procedure name",
               "sortable": true,
               "filterable": true
             },
-            { "key": "date", "width": 200, "title": "Date", "sortable": true }
+            {
+              "key": "procedure_concept_code",
+              "width": "15%",
+              "title": "Code",
+              "sortable": true,
+              "filterable": true
+            },
+            {
+              "key": "procedure_concept_id",
+              "width": "15%",
+              "title": "Concept ID",
+              "sortable": true,
+              "filterable": true
+            },
+            {
+              "key": "standard_concept",
+              "width": "15%",
+              "title": "Standard/source",
+              "sortable": true,
+              "filterable": true
+            },
+            {
+              "key": "start_date",
+              "width": "10%",
+              "title": "Date",
+              "sortable": true,
+              "filterable": true
+            },
+            {
+              "key": "age_at_occurrence",
+              "width": "10%",
+              "title": "Age at event",
+              "sortable": true,
+              "filterable": true
+            },
+            {
+              "key": "visit_type",
+              "width": "15%",
+              "title": "Visit type",
+              "sortable": true,
+              "filterable": true
+            }
           ]
         }
       },