Cb/VDA-1961-1962 Add Columns to Drug and Measurement Review (#1119)

* Adding columns to drug review table in sd * Adding columns to measurement review table in sd * Set up configs for local dev (verily configs) (#1120) * bump 0.0.713 * Adding columns to drug review table in sd * Adding columns to measurement review table in sd --------- Co-authored-by: Dexter Amundsen <[email protected]> Co-authored-by: bumptagbot <[email protected]>
DataBiosphere · Jan 10, 2025 · 1d3c117 · 1d3c117
1 parent e83c510
commit 1d3c117
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Showing 6 changed files with 105 additions and 11 deletions.
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
@@ -13,14 +13,25 @@ SELECT
   de.drug_source_concept_id,
   CAST(FLOOR(TIMESTAMP_DIFF(de.drug_exposure_start_datetime, p.birth_datetime, DAY) / 365.25) AS INT64) AS age_at_occurrence,
   de.visit_occurrence_id,
+  de.drug_type_concept_id,
+  tc.concept_name AS drug_type_concept_name,
   vo.visit_concept_id,
-  vc.concept_name AS visit_concept_name
+  vc.concept_name AS visit_concept_name,
+  de.route_source_value AS route,
+  x.x_drug_form AS drug_form,
+  x.x_strength AS drug_strength,
+  x.x_dose AS dose_amt,
+  x.x_frequency AS drug_freq,
+  x.x_doc_type AS source_table
 
 FROM `${omopDataset}.drug_exposure` AS de
 
 JOIN `${omopDataset}.person` AS p
     ON p.person_id = de.person_id
 
+JOIN `${omopDataset}.x_drug_exposure` AS x
+    ON de.drug_exposure_id = x.drug_exposure_id
+
 JOIN `${omopDataset}.concept` AS ic
     ON ic.concept_id = de.drug_concept_id
 
@@ -29,3 +40,6 @@ LEFT JOIN `${omopDataset}.visit_occurrence` AS vo
 
 LEFT JOIN `${omopDataset}.concept` AS vc
     ON vc.concept_id = vo.visit_concept_id
+
+LEFT JOIN `${omopDataset}.concept` AS tc
+    ON tc.concept_id = de.drug_type_concept_id
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
@@ -15,7 +15,14 @@
     { "name": "source_criteria_id", "dataType": "INT64", "valueFieldName": "drug_source_concept_id" },
     { "name": "age_at_occurrence", "dataType": "INT64", "isComputeDisplayHint": true, "displayHintRangeMin": 0, "displayHintRangeMax": 89 },
     { "name": "visit_occurrence_id", "dataType": "INT64" },
-    { "name": "visit_type", "dataType": "INT64", "valueFieldName": "visit_concept_id", "displayFieldName": "visit_concept_name", "isComputeDisplayHint": true }
+    { "name": "visit_type", "dataType": "INT64", "valueFieldName": "visit_concept_id", "displayFieldName": "visit_concept_name", "isComputeDisplayHint": 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"}
   ],
   "idAttribute": "id",
   "optimizeGroupByAttributes": [ "ingredient" ]

diff --git a/underlay/src/main/resources/config/datamapping/sd/entity/measurementOccurrence/all.sql b/underlay/src/main/resources/config/datamapping/sd/entity/measurementOccurrence/all.sql
@@ -15,7 +15,10 @@ SELECT DISTINCT
   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,
-  vc.concept_name AS visit_concept_name
+  vc.concept_name AS visit_concept_name,
+  mo.measurement_type_concept_id,
+  tc.concept_name AS measurement_type_concept_name
+
 
 FROM `${omopDataset}.measurement` AS mo
 
@@ -36,3 +39,6 @@ ON vo.visit_occurrence_id = mo.visit_occurrence_id
 
 LEFT JOIN `${omopDataset}.concept` AS vc
     ON vc.concept_id = vo.visit_concept_id
+
+LEFT JOIN `${omopDataset}.concept` AS tc
+    ON tc.concept_id = mo.measurement_type_concept_id
diff --git a/underlay/src/main/resources/config/datamapping/sd/entity/measurementOccurrence/entity.json b/underlay/src/main/resources/config/datamapping/sd/entity/measurementOccurrence/entity.json
@@ -14,7 +14,8 @@
     { "name": "source_criteria_id", "dataType": "INT64", "valueFieldName": "measurement_source_concept_id" },
     { "name": "age_at_occurrence", "dataType": "INT64", "isComputeDisplayHint": true, "displayHintRangeMin": 0, "displayHintRangeMax": 89 },
     { "name": "visit_occurrence_id", "dataType": "INT64" },
-    { "name": "visit_type", "dataType": "INT64", "valueFieldName": "visit_concept_id", "displayFieldName": "visit_concept_name", "isComputeDisplayHint": true }
+    { "name": "visit_type", "dataType": "INT64", "valueFieldName": "visit_concept_id", "displayFieldName": "visit_concept_name", "isComputeDisplayHint": true },
+    {"name":  "measurement_type", "dataType":  "INT64", "valueFieldName":  "measurement_type_concept_id", "displayFieldName":  "measurement_type_concept_name"}
   ],
   "idAttribute": "id",
   "optimizeGroupByAttributes": [ "measurement" ]

diff --git a/underlay/src/main/resources/config/datamapping/sd/entity/person/all.sql b/underlay/src/main/resources/config/datamapping/sd/entity/person/all.sql
@@ -19,7 +19,7 @@ SELECT
     EXISTS
         (SELECT 1 FROM `${omopDataset}.genotype_result` gr WHERE p.person_id = gr.person_id
                   AND gr.assay_name = 'agd whole genome sequencing'  ) AS has_agd_genotype_result,
-    CASE WHEN d.death_date is null THEN true ELSE false END AS is_deceased
+    CASE WHEN d.death_date is null THEN false ELSE true END AS is_deceased
 
 FROM `${omopDataset}.person` p
 

diff --git a/underlay/src/main/resources/config/underlay/sd/ui.json b/underlay/src/main/resources/config/underlay/sd/ui.json
@@ -154,15 +154,63 @@
             },
             {
               "key": "start_date",
-              "width": 200,
+              "width": 150,
               "title": "Start date",
               "sortable": true
             },
             {
               "key": "end_date",
-              "width": 200,
+              "width": 150,
               "title": "End date",
               "sortable": true
+            },
+            {
+              "key": "exposure_type",
+              "width": 250,
+              "title": "Exposure type",
+              "sortable": true
+            },
+            {
+              "key": "form",
+              "width": 130,
+              "title": "Form",
+              "sortable": true
+            },
+            {
+              "key": "strength",
+              "width": 150,
+              "title": "Strength",
+              "sortable": true
+            },
+            {
+              "key": "amount",
+              "width": 130,
+              "title": "Amount",
+              "sortable": true
+            },
+            {
+              "key": "route",
+              "width": 150,
+              "title": "Route",
+              "sortable": true
+            },
+            {
+              "key": "frequency",
+              "width": 150,
+              "title": "Frequency",
+              "sortable": true
+            },
+            {
+              "key": "source",
+              "width": 150,
+              "title": "Source",
+              "sortable": true
+            },
+            {
+              "key": "age_at_occurrence",
+              "width": 200,
+              "title": "Age At Event",
+              "sortable": true
             }
           ]
         }
@@ -181,22 +229,40 @@
               "sortable": true,
               "filterable": true
             },
-            { "key": "date", "width": 200, "title": "Date", "sortable": true },
+            { "key": "start_date", "width": 200, "title": "Date", "sortable": true },
             {
               "key": "value_enum",
-              "width": 160,
+              "width": 200,
               "title": "Categorical value",
               "sortable": true,
               "filterable": true
             },
             {
               "key": "value_numeric",
-              "width": 160,
+              "width": 200,
               "title": "Numeric value",
               "sortable": true,
               "filterable": true
             },
-            { "key": "unit", "width": 160, "title": "Unit", "sortable": true }
+            { "key": "unit", "width": 160, "title": "Unit", "sortable": true },
+            {
+              "key": "measurement_type",
+              "width": 250,
+              "title": "Measurement type",
+              "sortable": true
+            },
+            {
+              "key": "source_value",
+              "width": 200,
+              "title": "Source value",
+              "sortable": true
+            },
+            {
+              "key": "age_at_occurrence",
+              "width": 170,
+              "title": "Age at event",
+              "sortable": true
+            }
           ]
         }
       },