Merge pull request #2418 from opencb/TASK-5877

TASK-5877 - Accept non-normalized variant ID filtering by variant
opencb · Apr 24, 2024 · 33dd860 · 33dd860
2 parents e7983a1 + 92492ec
commit 33dd860
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Showing 5 changed files with 64 additions and 5 deletions.
diff --git a/...rage-core/src/main/java/org/opencb/opencga/storage/core/variant/VariantStorageEngine.java b/...rage-core/src/main/java/org/opencb/opencga/storage/core/variant/VariantStorageEngine.java
@@ -1200,7 +1200,7 @@ public DataResult<Variant> getSampleData(String variantStr, String study, QueryO
     public Variant getVariant(String variantStr) {
         final Variant variant;
         if (VariantQueryUtils.isVariantId(variantStr)) {
-            variant = new Variant(variantStr);
+            variant = VariantQueryUtils.toVariant(variantStr, true);
         } else if (VariantQueryUtils.isVariantAccession(variantStr)) {
             VariantQueryResult<Variant> result = get(new Query(VariantQueryParam.ANNOT_XREF.key(), variantStr),
                     new QueryOptions(QueryOptions.INCLUDE, VariantField.ID).append(QueryOptions.LIMIT, 1).append(QueryOptions.COUNT, true));

diff --git a/...-core/src/main/java/org/opencb/opencga/storage/core/variant/query/VariantQueryParser.java b/...-core/src/main/java/org/opencb/opencga/storage/core/variant/query/VariantQueryParser.java
@@ -8,7 +8,9 @@
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.avro.ClinicalSignificance;
 import org.opencb.biodata.models.variant.avro.VariantType;
+import org.opencb.biodata.models.variant.exceptions.NonStandardCompliantSampleField;
 import org.opencb.biodata.models.variant.metadata.VariantFileHeaderComplexLine;
+import org.opencb.biodata.tools.variant.VariantNormalizer;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.commons.datastore.core.QueryParam;
@@ -862,8 +864,17 @@ public static ParsedVariantQuery.VariantQueryXref parseXrefs(Query query) {
                     }
                 }
             }
+        }
 
+        if (!xrefs.getVariants().isEmpty()) {
+            List<Variant> normalizedVariants = normalizeVariants(xrefs.getVariants());
+            for (Variant normalizedVariant : normalizedVariants) {
+                if (!xrefs.getVariants().contains(normalizedVariant)) {
+                    xrefs.getVariants().add(normalizedVariant);
+                }
+            }
         }
+
         if (isValidParam(query, ANNOT_GENE_ROLE_IN_CANER_GENES)) {
             List<String> thisGenes = query.getAsStringList(ANNOT_GENE_ROLE_IN_CANER_GENES.key());
             if (thisGenes.size() != 1 || !thisGenes.get(0).equals(NONE)) {
@@ -890,6 +901,21 @@ public static ParsedVariantQuery.VariantQueryXref parseXrefs(Query query) {
         return xrefs;
     }
 
+    public static Variant normalizeVariant(Variant variant) {
+        return normalizeVariants(Collections.singletonList(variant)).get(0);
+    }
+
+    public static List<Variant> normalizeVariants(List<Variant> variants) {
+        VariantNormalizer variantNormalizer = new VariantNormalizer();
+        List<Variant> normalizedVariants;
+        try {
+            normalizedVariants = variantNormalizer.normalize(variants, false);
+        } catch (NonStandardCompliantSampleField e) {
+            throw VariantQueryException.internalException(e);
+        }
+        return normalizedVariants;
+    }
+
     public static ParsedQuery<KeyOpValue<String, Float>> parseFreqFilter(Query query, QueryParam queryParam) {
         return VariantQueryUtils.splitValue(query, queryParam)
                 .map(VariantQueryUtils::parseKeyOpValue)

diff --git a/...e-core/src/main/java/org/opencb/opencga/storage/core/variant/query/VariantQueryUtils.java b/...e-core/src/main/java/org/opencb/opencga/storage/core/variant/query/VariantQueryUtils.java
@@ -578,6 +578,14 @@ public static Variant toVariant(String value) {
         return variant;
     }
 
+    public static Variant toVariant(String variantStr, boolean normalize) {
+        Variant variant = toVariant(variantStr);
+        if (normalize && variant != null) {
+            return VariantQueryParser.normalizeVariant(variant);
+        }
+        return variant;
+    }
+
     public static String[] splitStudyResource(String value) {
         int idx = value.lastIndexOf(STUDY_RESOURCE_SEPARATOR);
         if (idx <= 0 || idx == value.length() - 1) {

diff --git a/.../java/org/opencb/opencga/storage/core/variant/adaptors/VariantDBAdaptorMultiFileTest.java b/.../java/org/opencb/opencga/storage/core/variant/adaptors/VariantDBAdaptorMultiFileTest.java
@@ -1333,6 +1333,16 @@ public void testSampleData() throws Exception {
         assertEquals(0, variant.getStudies().get(0).getFiles().size());
     }
 
+    @Test
+    public void testSampleDataUnnormalized() throws Exception {
+        // Check unnormalized queries
+        Variant variant = variantStorageEngine.getSampleData("1:10352:T:TA", study1, new QueryOptions()).first();
+        assertEquals("1:10353:-:A", variant.toString());
+        System.out.println("variant = " + variant.toJson());
+        assertNotNull(variant.getStudies().get(0).getStats(DEFAULT_COHORT));
+        assertEquals(4, variant.getStudies().get(0).getSamples().size());
+        assertEquals(4, variant.getStudies().get(0).getFiles().size());
+    }
 
     @Test
     public void testCount() throws StorageEngineException {

diff --git a/.../src/test/java/org/opencb/opencga/storage/core/variant/adaptors/VariantDBAdaptorTest.java b/.../src/test/java/org/opencb/opencga/storage/core/variant/adaptors/VariantDBAdaptorTest.java
@@ -529,11 +529,14 @@ public long filterPopulation(DataResult<Variant> queryResult, Predicate<Variant>
     public void testGetAllVariants_variantId() {
         int i = 0;
         List<Variant> variants = new ArrayList<>();
+        Map<String, String> normalizedVariants = new HashMap<>();
         for (Variant variant : allVariants.getResults()) {
-            if (i++ % 10 == 0) {
-                if (!variant.isSymbolic()) {
-                    variants.add(variant);
-                }
+            if ((i++ % 10) == 0) {
+                variants.add(variant);
+            }
+            OriginalCall call = variant.getStudies().get(0).getFiles().get(0).getCall();
+            if (call != null) {
+                normalizedVariants.put(variant.toString(), call.getVariantId());
             }
         }
         List<Variant> result = query(new Query(ID.key(), variants), new QueryOptions()).getResults();
@@ -552,6 +555,18 @@ public void testGetAllVariants_variantId() {
             }
         }
         assertEquals(expectedList, actualList);
+
+        normalizedVariants.forEach((key, value) -> {
+            System.out.println(key + " = " + value);
+        });
+        List<Variant> resultNormalized = query(new Query(ID.key(), normalizedVariants.values()).append(INCLUDE_FILE.key(), ALL), new QueryOptions()).getResults();
+        assertEquals(normalizedVariants.size(), resultNormalized.size());
+        assertTrue(!resultNormalized.isEmpty());
+        for (Variant variant : resultNormalized) {
+            String expected = normalizedVariants.get(variant.toString());
+            String actual = variant.getStudies().get(0).getFiles().get(0).getCall().getVariantId();
+            assertEquals(expected, actual);
+        }
     }
 
     @Test