Updated indexing changes for cpt4, phewas for no-longer used columns (#…

…1070)
DataBiosphere · Nov 19, 2024 · 7315691 · 7315691
1 parent 8f068a5
commit 7315691
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Showing 5 changed files with 2 additions and 10 deletions.
diff --git a/underlay/src/main/resources/config/datamapping/emerge/entity/cpt4/all.sql b/underlay/src/main/resources/config/datamapping/emerge/entity/cpt4/all.sql
@@ -1,9 +1,7 @@
 SELECT
     pc.criteria_meta_seq as id,
-    pc.criteria_meta_seq as concept_id,
     regexp_replace(pc.name,concat(regexp_replace(pc.label, r'CPT Codes_Include_', ''),' '),'') as name,
     pc.type,
-    'Source' AS is_standard,
     regexp_replace(pc.label, r'CPT Codes_Include_', '') as concept_code,
     name as label
 FROM `${omopDataset}.cpt_criteria` pc
diff --git a/underlay/src/main/resources/config/datamapping/emerge/entity/cpt4/entity.json b/underlay/src/main/resources/config/datamapping/emerge/entity/cpt4/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/phewas/all.sql b/underlay/src/main/resources/config/datamapping/emerge/entity/phewas/all.sql
@@ -1,9 +1,7 @@
 SELECT
     pc.criteria_meta_seq AS id,
-    pc.criteria_meta_seq AS concept_id,
     REGEXP_EXTRACT(label, r'^PHEWAS_[0-9.]+-(.*)') AS name,
     pc.type,
-    'Source' AS is_standard,
     REGEXP_EXTRACT(label, r'^PHEWAS_([0-9.]+)-') AS concept_code,
     REGEXP_EXTRACT(label, r'^PHEWAS_(.*)') AS label
 FROM `${omopDataset}.phewas_criteria` pc
diff --git a/underlay/src/main/resources/config/datamapping/emerge/entity/phewas/entity.json b/underlay/src/main/resources/config/datamapping/emerge/entity/phewas/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/.../resources/config/datamapping/emerge/entitygroup/phewasPerson/occurrenceCriteria_icd9.sql b/.../resources/config/datamapping/emerge/entitygroup/phewasPerson/occurrenceCriteria_icd9.sql
@@ -3,7 +3,7 @@ FROM `${omopDataset}.icd_codes` AS io
          LEFT JOIN `${omopDataset}.phewas_criteria_icd` AS pci
                    ON pci.ICD9 = io.code
          LEFT JOIN (
-    SELECT criteria_meta_seq AS id, REGEXP_EXTRACT(label, r'^PHEWAS_([0-9.]+)-') AS code,*
-    FROM `${omopDataset}.phewas_criteria`
+           SELECT criteria_meta_seq AS id, REGEXP_EXTRACT(label, r'^PHEWAS_([0-9.]+)-') AS code
+           FROM `${omopDataset}.phewas_criteria`
 ) pc ON pc.code = pci.icd9
 WHERE pc.id IS NOT NULL