[no ticket][risk=no] Fix person id query for VCF extractions (#8971)

all-of-us · Nov 25, 2024 · 1b4a121 · 1b4a121
1 parent 040e500
commit 1b4a121
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Showing 2 changed files with 8 additions and 3 deletions.
diff --git a/api/src/main/java/org/pmiops/workbench/cohortbuilder/CohortQueryBuilder.java b/api/src/main/java/org/pmiops/workbench/cohortbuilder/CohortQueryBuilder.java
@@ -98,7 +98,12 @@ public QueryJobConfiguration buildUnionedParticipantIdQuery(
         .build();
   }
 
-  public QueryJobConfiguration buildPersonIdQuery(String personIdQuery) {
-    return QueryJobConfiguration.newBuilder(personIdQuery).setUseLegacySql(false).build();
+  // This method supports VCF extractions for Tanagra exports
+  public QueryJobConfiguration buildTanagraWGSPersonIdQuery(String personIdQuery) {
+    return QueryJobConfiguration.newBuilder(
+            personIdQuery
+                + " AND id IN (SELECT id FROM `${projectId}.${dataSetId}.T_ENT_person` WHERE has_whole_genome_variant = true)")
+        .setUseLegacySql(false)
+        .build();
   }
 }
diff --git a/api/src/main/java/org/pmiops/workbench/dataset/DataSetServiceImpl.java b/api/src/main/java/org/pmiops/workbench/dataset/DataSetServiceImpl.java
@@ -1430,7 +1430,7 @@ public List<String> getTanagraPersonIdsWithWholeGenome(
                 .get()
                 .describeExport(exportPreviewRequest, underlayName)
                 .getEntityIdSql();
-        participantIdQuery = cohortQueryBuilder.buildPersonIdQuery(cohortsQuery);
+        participantIdQuery = cohortQueryBuilder.buildTanagraWGSPersonIdQuery(cohortsQuery);
       } catch (ApiException e) {
         throw new BadRequestException("Bad Request: " + e.getMessage());
       }