EVA-3434 Remove locus equality condition from DeprecatedVariantMongoR…

…eader (#430) * Remove locus equality condition from DeprecatedVariantMongoReader
EBIvariation · Feb 26, 2024 · 0c2c2f9 · 0c2c2f9
1 parent 0a608ec
commit 0c2c2f9
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Showing 2 changed files with 33 additions and 30 deletions.
diff --git a/...ava/uk/ac/ebi/eva/accession/release/batch/io/deprecated/DeprecatedVariantMongoReader.java b/...ava/uk/ac/ebi/eva/accession/release/batch/io/deprecated/DeprecatedVariantMongoReader.java
@@ -107,29 +107,19 @@ protected List<Variant> getVariants(Document deprecatedVariant) {
         Document inactiveEntity = inactiveObjects.iterator().next();
         String contig = inactiveEntity.getString(VariantMongoAggregationReader.CONTIG_FIELD);
         long start = inactiveEntity.getLong(VariantMongoAggregationReader.START_FIELD);
-        String type = inactiveEntity.getString(TYPE_FIELD);
-
-        for (Document submittedVariantOperation : submittedVariantOperations) {
-            Collection<Document> inactiveEntitySubmittedVariant = (Collection<Document>) submittedVariantOperation
-                    .get("inactiveObjects");
-            Document submittedVariant = inactiveEntitySubmittedVariant.iterator().next();
-            long submittedVariantStart = submittedVariant.getLong(START_FIELD);
-            String submittedVariantContig = submittedVariant.getString(CONTIG_FIELD);
-            String reference = submittedVariant.getString("ref");
-            String alternate = submittedVariant.getString("alt");
-
-            if (isSameLocation(contig, start, submittedVariantContig, submittedVariantStart, type)) {
-                // Since we only need evidence that at least one submitted variant agrees
-                // with the deprecated RS in locus, we just return one variant record per RS
-                Variant variantToReturn = new Variant(contig, start,
-                                                      start + Math.max(reference.length(), alternate.length()) - 1,
-                                                      reference, alternate);
-                variantToReturn.setMainId("rs" + deprecatedVariant.getLong("accession"));
-                return Arrays.asList(variantToReturn);
-            }
-        }
-
-        return new ArrayList<>();
+        // Since we only need evidence that at least one submitted variant agrees with the deprecated RS,
+        // we just return one variant record per RS
+        Collection<Document> inactiveEntitySubmittedVariant = (Collection<Document>) submittedVariantOperations
+                .iterator().next().get("inactiveObjects");
+        Document submittedVariant = inactiveEntitySubmittedVariant.iterator().next();
+        String reference = submittedVariant.getString("ref");
+        String alternate = submittedVariant.getString("alt");
+
+        Variant variantToReturn = new Variant(contig, start,
+                start + Math.max(reference.length(), alternate.length()) - 1,
+                reference, alternate);
+        variantToReturn.setMainId("rs" + deprecatedVariant.getLong("accession"));
+        return Arrays.asList(variantToReturn);
     }
 
     @Override

diff --git a/...uk/ac/ebi/eva/accession/release/batch/io/deprecated/DeprecatedVariantMongoReaderTest.java b/...uk/ac/ebi/eva/accession/release/batch/io/deprecated/DeprecatedVariantMongoReaderTest.java
@@ -76,6 +76,8 @@ public class DeprecatedVariantMongoReaderTest {
 
     private static final int TAXONOMY_2 = 3703;
 
+    private static final int TAXONOMY_3 = 3704;
+
     private static final int CHUNK_SIZE = 5;
 
     @Autowired
@@ -121,17 +123,20 @@ public void testOnlySpecifiedTaxVariantsRead() {
         DbsnpSubmittedVariantEntity ss1 = createSS(ASSEMBLY, TAXONOMY_1, 1L, 1L, 100L, "C", "A");
         DbsnpSubmittedVariantEntity ss2 = createSS(ASSEMBLY, TAXONOMY_2, 2L, 2L, 101L, "A", "T");
         DbsnpSubmittedVariantEntity ss3 = createSS(ASSEMBLY, TAXONOMY_2, 3L, 3L, 102L, "T", "G");
-        DbsnpClusteredVariantEntity rs1 = createRS(ss1, null);
-        DbsnpClusteredVariantEntity rs2 = createRS(ss2, null);
-        DbsnpClusteredVariantEntity rs3 = createRS(ss3, TAXONOMY_1);
-        this.mongoTemplate.insert(Stream.of(ss1, ss2, ss3).map(ss -> {
+        DbsnpSubmittedVariantEntity ss4 = createSS(ASSEMBLY, TAXONOMY_3, 4L, 4L, 103L, "A", "C");
+        DbsnpClusteredVariantEntity rs1 = createRS(ss1, null, null);
+        DbsnpClusteredVariantEntity rs2 = createRS(ss2, null, null);
+        DbsnpClusteredVariantEntity rs3 = createRS(ss3, TAXONOMY_1, null);
+        DbsnpClusteredVariantEntity rs4 = createRS(ss4, TAXONOMY_3, ss4.getStart() + 2);
+        // create RS
+        this.mongoTemplate.insert(Stream.of(ss1, ss2, ss3, ss4).map(ss -> {
             DbsnpSubmittedVariantOperationEntity dbsnpSvoeObj = new DbsnpSubmittedVariantOperationEntity();
             dbsnpSvoeObj.fill( EventType.UPDATED, ss.getAccession(),
                               "Declustered: None of the variant alleles match the reference allele.",
                               Arrays.asList(new DbsnpSubmittedVariantInactiveEntity(ss)));
             return dbsnpSvoeObj;
         }).collect(Collectors.toList()), DbsnpSubmittedVariantOperationEntity.class);
-        this.mongoTemplate.insert(Stream.of(rs1, rs2, rs3).map(rs -> {
+        this.mongoTemplate.insert(Stream.of(rs1, rs2, rs3, rs4).map(rs -> {
             DbsnpClusteredVariantOperationEntity dbsnpCvoeObj = new DbsnpClusteredVariantOperationEntity();
             dbsnpCvoeObj.fill( EventType.DEPRECATED, rs.getAccession(),
                                "Clustered variant completely declustered",
@@ -157,6 +162,13 @@ public void testOnlySpecifiedTaxVariantsRead() {
         assertEquals(2, deprecatedVariants.size());
         assertTrue(Arrays.asList("rs2", "rs3").contains(deprecatedVariants.get(0).getMainId()));
         assertTrue(Arrays.asList("rs2", "rs3").contains(deprecatedVariants.get(1).getMainId()));
+
+        this.reader = new DeprecatedVariantMongoReader(ASSEMBLY, TAXONOMY_3, mongoClient, TEST_DB, CHUNK_SIZE,
+                new DbsnpCollectionNames());
+        this.reader.open(new ExecutionContext());
+        deprecatedVariants = this.readIntoList();
+        assertEquals(1, deprecatedVariants.size());
+        assertEquals("rs4", deprecatedVariants.get(0).getMainId());
     }
 
     private DbsnpSubmittedVariantEntity createSS(String assembly, int taxonomy, Long ssAccession, Long rsAccession,
@@ -166,13 +178,14 @@ private DbsnpSubmittedVariantEntity createSS(String assembly, int taxonomy, Long
                                                false, false, 1);
     }
 
-    private DbsnpClusteredVariantEntity createRS(SubmittedVariantEntity sve, Integer alternateTaxonomy) {
+    private DbsnpClusteredVariantEntity createRS(SubmittedVariantEntity sve, Integer alternateTaxonomy, Long start) {
         Function<IClusteredVariant, String> hashingFunction =  new ClusteredVariantSummaryFunction().andThen(
                 new SHA1HashingFunction());
         int taxonomyToUse = Objects.isNull(alternateTaxonomy)? sve.getTaxonomyAccession(): alternateTaxonomy;
+        long startToUse = Objects.isNull(start) ? sve.getStart() : start;
         ClusteredVariant cv = new ClusteredVariant(sve.getReferenceSequenceAccession(), taxonomyToUse,
                                                    sve.getContig(),
-                                                   sve.getStart(),
+                                                   startToUse,
                                                    new Variant(sve.getContig(), sve.getStart(), sve.getStart(),
                                                                sve.getReferenceAllele(),
                                                                sve.getAlternateAllele()).getType(),