review comments incorporated

EBIvariation · Apr 26, 2024 · dab4e0f · dab4e0f
1 parent 2f29133
commit dab4e0f
Show file tree

Hide file tree

Showing 2 changed files with 15 additions and 12 deletions.
diff --git a/...n-clustering/src/main/java/uk/ac/ebi/eva/accession/clustering/batch/io/RSMergeWriter.java b/...n-clustering/src/main/java/uk/ac/ebi/eva/accession/clustering/batch/io/RSMergeWriter.java
@@ -192,20 +192,23 @@ public void writeRSMerge(SubmittedVariantOperationEntity currentOperation)
         ImmutablePair<ClusteredVariantEntity, List<ClusteredVariantEntity>> mergeDestinationAndMergees =
                 getMergeDestinationAndMergees(mergeCandidates);
         ClusteredVariantEntity mergeDestination = mergeDestinationAndMergees.getLeft();
+        List<ClusteredVariantEntity> mergees = mergeDestinationAndMergees.getRight();
 
-        // check if any variant with same hash as mergeDestination already exist in DB
-        ClusteredVariantEntity existingClusteredVariantEntity = getClusteredVariantEntityWithHash(mergeDestination);
-        if (existingClusteredVariantEntity != null && existingClusteredVariantEntity.getAccession()!=mergeDestination.getAccession()) {
-            if (mergeDestination.getAccession() == ClusteredVariantMergingPolicy.prioritise(mergeDestination.getAccession(),
-                    existingClusteredVariantEntity.getAccession()).accessionToKeep) {
-                merge(mergeDestination, existingClusteredVariantEntity, currentOperation);
-            } else {
-                merge(existingClusteredVariantEntity, mergeDestination, currentOperation);
-                mergeDestination = existingClusteredVariantEntity;
+        if (mergees.size() > 1) {
+            // check if any variant with same hash as mergeDestination already exist in DB
+            ClusteredVariantEntity existingClusteredVariantEntity = getClusteredVariantEntityWithHash(mergeDestination);
+            if (existingClusteredVariantEntity != null && existingClusteredVariantEntity.getAccession() != mergeDestination.getAccession()) {
+                if (mergeDestination.getAccession() == ClusteredVariantMergingPolicy.prioritise(mergeDestination.getAccession(),
+                        existingClusteredVariantEntity.getAccession()).accessionToKeep) {
+                    merge(mergeDestination, existingClusteredVariantEntity, currentOperation);
+                    mergees = mergees.stream()
+                            .filter(cve -> !(cve.equals(existingClusteredVariantEntity)
+                                    && cve.getAccession() == existingClusteredVariantEntity.getAccession()))
+                            .collect(Collectors.toList());
+                }
             }
         }
 
-        List<ClusteredVariantEntity> mergees = mergeDestinationAndMergees.getRight();
         for (ClusteredVariantEntity mergee: mergees) {
             logger.info("RS merge operation: Merging rs{} to rs{} due to hash collision...",
                         mergee.getAccession(), mergeDestination.getAccession());

diff --git a/...ustering/src/test/java/uk/ac/ebi/eva/accession/clustering/batch/io/RSMergeWriterTest.java b/...ustering/src/test/java/uk/ac/ebi/eva/accession/clustering/batch/io/RSMergeWriterTest.java
@@ -483,8 +483,8 @@ public void testRSWithSameHashAsMergeDestinationAlreadyExistsInDBWithLowerAccess
 
         SubmittedVariantOperationEntity mergeOperation1 = new SubmittedVariantOperationEntity();
         mergeOperation1.fill(RSMergeAndSplitCandidatesReaderConfiguration.MERGE_CANDIDATES_EVENT_TYPE,
-                ss2.getAccession(), null, "Different RS with matching loci",
-                Stream.of(ss2, ss3).map(SubmittedVariantInactiveEntity::new).collect(Collectors.toList()));
+                ss1.getAccession(), null, "Different RS with matching loci",
+                Stream.of(ss1, ss2, ss3).map(SubmittedVariantInactiveEntity::new).collect(Collectors.toList()));
         mergeOperation1.setId(ClusteringWriter.getMergeCandidateId(mergeOperation1));
         this.mongoTemplate.insert(Arrays.asList(mergeOperation1), SUBMITTED_VARIANT_OPERATION_COLLECTION);