VDA-1886,1887 update criteria list headers labs drugs (#1096)

* Updated criteria selector and indexing for drug and lab * Changed indexed dataset * Changed indexed dataset for local deploy --------- Co-authored-by: Dexter Amundsen <dexamundsen@verily.com>
DataBiosphere · Dec 9, 2024 · 8133e3a · 8133e3a
1 parent d8a9039
commit 8133e3a
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Showing 8 changed files with 5 additions and 33 deletions.
diff --git a/underlay/src/main/resources/config/criteria/emerge/criteriaselector/drug/drug.json b/underlay/src/main/resources/config/criteria/emerge/criteriaselector/drug/drug.json
@@ -5,20 +5,10 @@
       "widthString": "100%",
       "title": "Label"
     },
-    {
-      "key": "id",
-      "widthDouble": 120,
-      "title": "Concept Id"
-    },
-    {
-      "key": "is_standard",
-      "widthDouble": 180,
-      "title": "Source/Standard"
-    },
     {
       "key": "concept_code",
       "widthDouble": 120,
-      "title": "Code"
+      "title": "RxNorm"
     },
     {
       "key": "t_item_count",

diff --git a/underlay/src/main/resources/config/criteria/emerge/criteriaselector/lab/lab.json b/underlay/src/main/resources/config/criteria/emerge/criteriaselector/lab/lab.json
@@ -5,16 +5,6 @@
       "widthString": "100%",
       "title": "Label"
     },
-    {
-      "key": "id",
-      "widthDouble": 120,
-      "title": "Concept Id"
-    },
-    {
-      "key": "is_standard",
-      "widthDouble": 180,
-      "title": "Source/Standard"
-    },
     {
       "key": "concept_code",
       "widthDouble": 120,

diff --git a/underlay/src/main/resources/config/datamapping/emerge/entity/drug/all.sql b/underlay/src/main/resources/config/datamapping/emerge/entity/drug/all.sql
@@ -1,10 +1,8 @@
 SELECT
     cast(parse_numeric(dc.criteria_meta_seq) as INT64) as id,
-    cast(parse_numeric(dc.criteria_meta_seq) as INT64) as concept_id,
     dc.name,
-    'Source' as is_standard,
     cast(d.drug_rxcui_code as STRING) as concept_code,
-    concat(cast(parse_numeric(dc.criteria_meta_seq) as STRING),' ',dc.name) as label,
+    dc.name as label,
 FROM `${omopDataset}.med_criteria` dc
 JOIN (SELECT distinct drug_name, drug_rxcui_code from `${omopDataset}.meds`) d
     ON lower(dc.name) = lower(d.drug_name)
diff --git a/underlay/src/main/resources/config/datamapping/emerge/entity/drug/entity.json b/underlay/src/main/resources/config/datamapping/emerge/entity/drug/entity.json
@@ -3,9 +3,7 @@
   "allInstancesSqlFile": "all.sql",
   "attributes": [
     { "name": "id", "dataType": "INT64" },
-    { "name": "concept_id", "dataType": "INT64" },
     { "name": "name", "dataType": "STRING" },
-    { "name": "is_standard", "dataType": "STRING", "isComputeDisplayHint": true },
     { "name": "concept_code", "dataType": "STRING" },
     { "name": "label", "dataType": "STRING" }
   ],

diff --git a/underlay/src/main/resources/config/datamapping/emerge/entity/lab/all.sql b/underlay/src/main/resources/config/datamapping/emerge/entity/lab/all.sql
@@ -3,10 +3,7 @@ SELECT
     l.lab_name as name,
     l.loinc_code as concept_code,
     'LAB' as type,
-    CASE WHEN l.loinc_code IS NULL THEN 'Custom'
-         ELSE 'Standard' END as is_standard,
-    CASE WHEN l.loinc_code IS NULL THEN l.lab_name
-         ELSE concat(l.loinc_code, ' ', l.lab_name) END as label,
+    l.lab_name as label,
     case WHEN l.loinc_code IS NULL THEN 'VUMC-Lab'
          ELSE 'LOINC' END as vocabulary_id
 FROM `${omopDataset}.labs` l

diff --git a/underlay/src/main/resources/config/datamapping/emerge/entity/lab/entity.json b/underlay/src/main/resources/config/datamapping/emerge/entity/lab/entity.json
@@ -7,7 +7,6 @@
     { "name": "type", "dataType": "STRING" },
     { "name": "concept_code", "dataType": "STRING" },
     { "name": "vocabulary_id", "dataType": "STRING" },
-    { "name": "is_standard", "dataType": "STRING", "isComputeDisplayHint": true },
     { "name": "label", "dataType": "STRING" }
   ],
   "idAttribute": "id",

diff --git a/underlay/src/main/resources/config/indexer/emerge/emerge_20240603.json b/underlay/src/main/resources/config/indexer/emerge/emerge_20240603.json
@@ -11,7 +11,7 @@
     },
     "indexData": {
       "projectId": "vumc-emerge-dev",
-      "datasetId": "indexed_emerge_20240603_labs"
+      "datasetId": "indexed_emerge_20240603_1886"
     },
     "queryProjectId": "vumc-emerge-dev",
     "dataLocation": "us-central1"

diff --git a/underlay/src/main/resources/config/service/emerge/emerge_local.json b/underlay/src/main/resources/config/service/emerge/emerge_local.json
@@ -11,7 +11,7 @@
     },
     "indexData": {
       "projectId": "vumc-emerge-dev",
-      "datasetId": "indexed_emerge_20240603_labs"
+      "datasetId": "indexed_emerge_20240603_1886"
     },
     "queryProjectId": "vumc-emerge-dev",
     "dataLocation": "us-central1"