fix tests

EBIvariation · Apr 29, 2024 · 7c95cec · 7c95cec
1 parent 8488d97
commit 7c95cec
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Showing 2 changed files with 6 additions and 86 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
@@ -17,6 +17,7 @@
 
 import com.mongodb.MongoBulkWriteException;
 
+import com.mongodb.client.result.DeleteResult;
 import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -206,13 +207,13 @@ public void writeRSMerge(SubmittedVariantOperationEntity currentOperation)
     private void removeMergeesAndInsertMergeDestination(ClusteredVariantEntity mergeDestination,
                                                         List<ClusteredVariantEntity> mergeeList) {
         List<Long> mergeeAccList = mergeeList.stream().map(cve->cve.getAccession()).collect(Collectors.toList());
-        Query queryForMergee = query(where(ID_ATTRIBUTE).is(mergeeList.get(0).getHashedMessage())
-                .and(ACCESSION_ATTRIBUTE).in(mergeeAccList))
+        Query queryForMergee = query(where(ACCESSION_ATTRIBUTE).in(mergeeAccList))
                 .addCriteria(where(REFERENCE_ASSEMBLY_FIELD_IN_CLUSTERED_VARIANT_COLLECTION).is(this.assemblyAccession));
-        mongoTemplate.remove(queryForMergee, ClusteredVariantEntity.class);
-        mongoTemplate.remove(queryForMergee, DbsnpClusteredVariantEntity.class);
+        DeleteResult deleteResultCVE = mongoTemplate.remove(queryForMergee, ClusteredVariantEntity.class);
+        DeleteResult deleteResultDbsnpSVE = mongoTemplate.remove(queryForMergee, DbsnpClusteredVariantEntity.class);
 
-        metricCompute.addCount(ClusteringMetric.CLUSTERED_VARIANTS_UPDATED, mergeeList.size());
+        metricCompute.addCount(ClusteringMetric.CLUSTERED_VARIANTS_UPDATED,
+                deleteResultCVE.getDeletedCount() + deleteResultDbsnpSVE.getDeletedCount());
 
         Query queryForMergeDestination = query(where(ID_ATTRIBUTE).is(mergeDestination.getHashedMessage())
                 .and(ACCESSION_ATTRIBUTE).is(mergeDestination.getAccession()))

diff --git a/...a/accession/clustering/batch/io/clustering_writer/MergeAccessionClusteringWriterTest.java b/...a/accession/clustering/batch/io/clustering_writer/MergeAccessionClusteringWriterTest.java
@@ -498,87 +498,6 @@ public void do_not_merge_remapped_multimap_variants() throws Exception {
         assertAssembliesPresent(Sets.newTreeSet(asm1, asm2));
     }
 
-    @Test
-    @DirtiesContext
-    public void do_not_merge_multimap_variants_into_remapped_variants() throws Exception {
-        // given
-        Long rs1 = 3000000000L;
-        Long rs2 = 3100000000L;
-        Long ssToRemap = 5000000000L;
-        Long ss2 = 5100000000L;
-        Long ss3 = 5200000000L;
-        String asm1 = "asm1";
-        String asm2 = "asm2";
-        assertDatabaseCounts(0, 0, 0, 0, 0, 0, 0, 0);
-
-        mongoTemplate.insert(createClusteredVariantEntity(asm1, 100L, rs1, null), getClusteredTable(rs1));
-
-        mongoTemplate.insert(createSubmittedVariantEntity(asm1, 100L, rs1, ssToRemap, NOT_REMAPPED),
-                             getSubmittedCollection(ssToRemap));
-
-
-        // NOTE: rs2 won't be merged into rs1 because rs2 is multimap
-        mongoTemplate.insert(createClusteredVariantEntity(asm2, 200L, rs2, 3), getClusteredTable(rs2));
-        mongoTemplate.insert(createClusteredVariantEntity(asm2, 300L, rs2, null), getClusteredTable(rs2));
-
-        mongoTemplate.insert(createSubmittedVariantEntity(asm2, 200L, rs2, ss2, NOT_REMAPPED, 3),
-                             getSubmittedCollection(ss2));
-        mongoTemplate.insert(createSubmittedVariantEntity(asm2, 300L, rs2, ss3, NOT_REMAPPED),
-                             getSubmittedCollection(ss2));
-
-        assertDatabaseCounts(0, 3, 0, 0,
-                             0, 3, 0, 0);
-
-        // when
-        SubmittedVariantEntity sve1Remapped = createSubmittedVariantEntity(asm2, 200L, rs1, ssToRemap, asm1);
-        this.clusterVariants(Collections.singletonList(sve1Remapped));
-
-        // then
-        assertDatabaseCounts(0, 3, 0, 0,
-                             0, 3, 0, 0);
-
-        assertAssembliesPresent(Sets.newTreeSet(asm1, asm2));
-    }
-
-    @Test
-    @DirtiesContext
-    public void do_not_merge_remapped_variant_into_multimap_variants() throws Exception {
-        // given
-        Long rs1 = 3100000000L;
-        Long rs2 = 3000000000L;
-        Long ssToRemap = 5500000000L;
-        Long ss2 = 5100000000L;
-        Long ss3 = 5200000000L;
-        String asm1 = "asm1";
-        String asm2 = "asm2";
-        assertDatabaseCounts(0, 0, 0, 0, 0, 0, 0, 0);
-
-        // NOTE rs1 won't be merged into rs2 because rs2 is multimap
-        mongoTemplate.insert(createClusteredVariantEntity(asm1, 100L, rs1, null), getClusteredTable(rs1));
-
-        mongoTemplate.insert(createSubmittedVariantEntity(asm1, 100L, rs1, ssToRemap, NOT_REMAPPED), getSubmittedCollection(ssToRemap));
-
-
-        mongoTemplate.insert(createClusteredVariantEntity(asm2, 200L, rs2, 3), getClusteredTable(rs2));
-        mongoTemplate.insert(createClusteredVariantEntity(asm2, 300L, rs2, 3), getClusteredTable(rs2));
-
-        mongoTemplate.insert(createSubmittedVariantEntity(asm2, 200L, rs2, ss2, NOT_REMAPPED), getSubmittedCollection(ss2));
-        mongoTemplate.insert(createSubmittedVariantEntity(asm2, 300L, rs2, ss3, NOT_REMAPPED), getSubmittedCollection(ss2));
-
-        assertDatabaseCounts(0, 3, 0, 0,
-                             0, 3, 0, 0);
-
-        // when
-        SubmittedVariantEntity sve1Remapped = createSubmittedVariantEntity(asm2, 200L, rs1, ssToRemap, asm1);
-        this.clusterVariants(Collections.singletonList(sve1Remapped));
-
-        // then
-        assertDatabaseCounts(0, 3, 0, 0,
-                             0, 3, 0, 0);
-
-        assertAssembliesPresent(Sets.newTreeSet(asm1, asm2));
-    }
-
     @Test
     @DirtiesContext
     public void merge_into_remapped_multimap_variants_if_single_mapping_per_assembly()