Merge pull request #2340 from opencb/TASK-5027

TASK-5027 - NullPointerException executing JUnit tests SampleIndexOnlyVariantQueryExecutor
opencb · Sep 22, 2023 · 4a38bbd · 4a38bbd
2 parents b596f37 + 60b74ab
commit 4a38bbd
Showing 1 changed file with 13 additions and 7 deletions.
diff --git a/.../org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java b/.../org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java
@@ -248,11 +248,7 @@ private boolean isIncludeCovered(SampleIndexQuery sampleIndexQuery, Query inputQ
                 return false;
             }
 
-            List<String> sampleDataKeys = VariantQueryUtils.getIncludeSampleData(inputQuery);
-            if (sampleDataKeys == null) {
-                // Undefined, get default sampleDataKeys
-                sampleDataKeys = HBaseToVariantConverter.getFixedFormat(study.getStudyMetadata());
-            }
+            List<String> sampleDataKeys = getSampleDataKeys(inputQuery, study);
 
             if (sampleDataKeys.size() != 1) {
                 // One and only one sampledatakey
@@ -490,8 +486,9 @@ private class AddMissingDataTask implements Task<Variant, Variant> {
             for (Integer fileId : fileIds) {
                 filesFromSample.add(metadataManager.getFileName(studyId, fileId));
             }
-            List<String> includeSampleData = VariantQueryUtils.getIncludeSampleData(parsedQuery.getInputQuery());
-            gtIdx = includeSampleData.indexOf("GT");
+
+            List<String> sampleDataKeys = getSampleDataKeys(parsedQuery.getInputQuery(), parsedQuery.getProjection().getStudy(studyId));
+            gtIdx = sampleDataKeys.indexOf("GT");
         }
 
         @Override
@@ -657,4 +654,13 @@ private void mergeFileEntries(StudyEntry studyEntry, List<FileEntry> newFileEntr
             }
         }
     }
+
+    private List<String> getSampleDataKeys(Query parsedQuery, VariantQueryProjection.StudyVariantQueryProjection parsedQuery1) {
+        List<String> sampleDataKeys = VariantQueryUtils.getIncludeSampleData(parsedQuery);
+        if (sampleDataKeys == null) {
+            // Undefined, get default sampleDataKeys
+            sampleDataKeys = HBaseToVariantConverter.getFixedFormat(parsedQuery1.getStudyMetadata());
+        }
+        return sampleDataKeys;
+    }
 }