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TASK-5027 - NullPointerException executing JUnit tests SampleIndexOnlyVariantQueryExecutor #2340

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Sep 22, 2023
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TASK-5027 - NullPointerException executing JUnit tests SampleIndexOnlyVariantQueryExecutor #2340

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20 changes: 13 additions & 7 deletions .../org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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;
}
}
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