storage: Fix NPE at SampleIndexOnlyVariantQueryExecutor for non multi…

…-file samples #TASK-4794
opencb · Jul 26, 2023 · 2943017 · 2943017
1 parent 4de465a
commit 2943017
Showing 1 changed file with 10 additions and 1 deletion.
diff --git a/.../org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java b/.../org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java
@@ -66,7 +66,7 @@ public class SampleIndexOnlyVariantQueryExecutor extends VariantQueryExecutor {
     private final VariantHadoopDBAdaptor dbAdaptor;
     private final VariantQueryParser variantQueryParser;
     private final VariantQueryProjectionParser variantQueryProjectionParser;
-    private Logger logger = LoggerFactory.getLogger(SampleIndexOnlyVariantQueryExecutor.class);
+    private static Logger logger = LoggerFactory.getLogger(SampleIndexOnlyVariantQueryExecutor.class);
 
     private static final ExecutorService THREAD_POOL = Executors.newCachedThreadPool(new BasicThreadFactory.Builder()
             .namingPattern("sample-index-async-count-%s")
@@ -373,6 +373,15 @@ enum FamilyRole {
                         for (Integer fileId : sampleFileIds) {
                             sampleFiles.add(metadataManager.getFileName(studyId, fileId));
                         }
+                    } else {
+                        List<Integer> fileIds = metadataManager.getFileIdsFromSampleId(studyId, sampleId, true);
+                        if (fileIds.isEmpty()) {
+                            logger.warn("Sample without indexed files!");
+                            sampleFiles = Collections.singletonList("sample_without_indexed_files.vcf");
+                        } else {
+                            String fileName = metadataManager.getFileName(studyId, fileIds.get(0));
+                            sampleFiles = Collections.singletonList(fileName);
+                        }
                     }
                     filterField = schema.getFileIndex()
                             .getCustomField(IndexFieldConfiguration.Source.FILE, StudyEntry.FILTER);