Add tests

leexgh · Jan 8, 2025 · 645f222 · 645f222
1 parent f6c9d04
commit 645f222
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Showing 4 changed files with 101 additions and 5 deletions.
diff --git a/...test/java/org/cbioportal/genome_nexus/service/enricher/IsoformAnnotationEnricherTest.java b/...test/java/org/cbioportal/genome_nexus/service/enricher/IsoformAnnotationEnricherTest.java
@@ -26,6 +26,7 @@ public class IsoformAnnotationEnricherTest
 {
     @Mock
     EnsemblService ensemblService;
+    @Mock
     OncokbService  oncokbService;
 
     private final VariantAnnotationMockData variantAnnotationMockData = new VariantAnnotationMockData();
@@ -69,9 +70,9 @@ public void enrichAnnotationWithNoOverride() throws IOException
     public void enrichAnnotationWithSingleOverride() throws IOException
     {
         Map<String, VariantAnnotation> variantMockData = this.variantAnnotationMockData.generateData();
-
+        this.mockOncokbServiceMethods();
         IsoformAnnotationEnricher enricher = new IsoformAnnotationEnricher(
-            "uniprot", "uniprot", this.ensemblService, null
+            "uniprot", "uniprot", this.ensemblService, this.oncokbService
         );
 
         // override canonical transcripts with just one matching transcript
@@ -105,7 +106,7 @@ public void enrichAnnotationWithSingleOverride() throws IOException
     public void enrichAnnotationWithMultipleOverride() throws IOException
     {
         Map<String, VariantAnnotation> variantMockData = this.variantAnnotationMockData.generateData();
-
+        this.mockOncokbServiceMethods();
         IsoformAnnotationEnricher enricher = new IsoformAnnotationEnricher(
             "mskcc", "mskcc", this.ensemblService, this.oncokbService
         );
@@ -148,4 +149,11 @@ public void enrichAnnotationWithMultipleOverride() throws IOException
             canonicalTranscripts.get(2).getTranscriptId()
         );
     }
+
+    private void mockOncokbServiceMethods()
+    {
+        Set<String> oncokbGeneSymbolList = new HashSet<>();
+        oncokbGeneSymbolList.add("TPRXL");
+        Mockito.when(this.oncokbService.getOncokbGeneSymbolList()).thenReturn(oncokbGeneSymbolList);
+    }
 }
diff --git a/.../test/java/org/cbioportal/genome_nexus/service/internal/VariantAnnotationServiceTest.java b/.../test/java/org/cbioportal/genome_nexus/service/internal/VariantAnnotationServiceTest.java
@@ -17,6 +17,7 @@
 import org.cbioportal.genome_nexus.service.EnsemblService;
 import org.cbioportal.genome_nexus.service.MutationAssessorService;
 import org.cbioportal.genome_nexus.service.MyVariantInfoService;
+import org.cbioportal.genome_nexus.service.OncokbService;
 import org.cbioportal.genome_nexus.component.annotation.HugoGeneSymbolResolver;
 import org.cbioportal.genome_nexus.component.annotation.NotationConverter;
 import org.cbioportal.genome_nexus.component.annotation.ProteinChangeResolver;
@@ -79,6 +80,9 @@ public class VariantAnnotationServiceTest
     @Mock
     private MyVariantInfoService myVariantInfoService;
 
+    @Mock
+    private OncokbService oncokbService;
+
     @Spy
     private NotationConverter notationConverter;
 
@@ -117,6 +121,10 @@ public void getAnnotationByVariantString()
         VariantAnnotation annotation5 = variantAnnotationService.getAnnotation("chr24:g.41242962_41242963insGA");
         assertEquals(variantMockData.get("Y:g.41242962_41242963insGA").getStart(), annotation5.getStart());
         assertEquals(variantMockData.get("Y:g.41242962_41242963insGA").getVariant(), annotation5.getVariant());
+
+        VariantAnnotation annotation6 = variantAnnotationService.getAnnotation("11:g.118392020_118392034delinsTTAC");
+        assertEquals(variantMockData.get("11:g.118392020_118392034delinsTTAC").getStart(), annotation6.getStart());
+        assertEquals(variantMockData.get("11:g.118392020_118392034delinsTTAC").getVariant(), annotation6.getVariant());
     }
 
     @Test
@@ -132,6 +140,7 @@ public void getAnnotationsByVariantString()
         variants.add("12:g.25398285C>A");
         variants.add("chr23:g.41242962_41242963insGA");
         variants.add("chr24:g.41242962_41242963insGA");
+        variants.add("11:g.118392020_118392034delinsTTAC");
 
         List<VariantAnnotation> annotations = variantAnnotationService.getAnnotations(variants);
         assertEquals(variantMockData.get("7:g.140453136A>T").getStart(), annotations.get(0).getStart());
@@ -142,6 +151,8 @@ public void getAnnotationsByVariantString()
         assertEquals(variantMockData.get("X:g.41242962_41242963insGA").getVariant(), annotations.get(2).getVariant());
         assertEquals(variantMockData.get("Y:g.41242962_41242963insGA").getStart(), annotations.get(3).getStart());
         assertEquals(variantMockData.get("Y:g.41242962_41242963insGA").getVariant(), annotations.get(3).getVariant());
+        assertEquals(variantMockData.get("11:g.118392020_118392034delinsTTAC").getStart(), annotations.get(4).getStart());
+        assertEquals(variantMockData.get("11:g.118392020_118392034delinsTTAC").getVariant(), annotations.get(4).getVariant());
     }
 
     @Test
@@ -265,6 +276,7 @@ public void getIsorformOverrideEnrichedAnnotationByVariantString()
 
         this.mockVariantFetcherMethods(variantMockData);
         this.mockEnsemblServiceMethods();
+        this.mockOncokbServiceMethods();
 
         VariantAnnotation annotation1 = variantAnnotationService.getAnnotation(
             "7:g.140453136A>T", "mskcc", null, null);
@@ -279,6 +291,13 @@ public void getIsorformOverrideEnrichedAnnotationByVariantString()
         // second transcript of this annotation should be marked as canonical, the first one should NOT be marked
         assertEquals(null, annotation2.getTranscriptConsequences().get(0).getCanonical());
         assertEquals("1", annotation2.getTranscriptConsequences().get(1).getCanonical());
+
+        // should choose canonical transcript based on oncokb gene symbol list
+        // choose the oncokb gene transcript as cannoical
+        VariantAnnotation annotation3 = variantAnnotationService.getAnnotation(
+            "11:g.118392020_118392034delinsTTAC", "mskcc", null, null);
+        assertEquals("1", annotation3.getTranscriptConsequences().get(0).getCanonical());
+        assertEquals(null, annotation3.getTranscriptConsequences().get(1).getCanonical());
     }
 
     private void mockVariantFetcherMethods(Map<String, VariantAnnotation> variantMockData)
@@ -289,19 +308,22 @@ private void mockVariantFetcherMethods(Map<String, VariantAnnotation> variantMoc
         Mockito.when(this.fetcher.fetchAndCache("12:g.25398285C>A")).thenReturn(variantMockData.get("12:g.25398285C>A"));
         Mockito.when(this.fetcher.fetchAndCache("X:g.41242962_41242963insGA")).thenReturn(variantMockData.get("X:g.41242962_41242963insGA"));
         Mockito.when(this.fetcher.fetchAndCache("Y:g.41242962_41242963insGA")).thenReturn(variantMockData.get("Y:g.41242962_41242963insGA"));
+        Mockito.when(this.fetcher.fetchAndCache("11:g.118392020_118392034delinsTTAC")).thenReturn(variantMockData.get("11:g.118392020_118392034delinsTTAC"));
         Mockito.doNothing().when(this.baseVariantAnnotationServiceImpl).saveToIndexDb(any(), any());
 
         List<String> variants = new ArrayList<>(4);
         variants.add("7:g.140453136A>T");
         variants.add("12:g.25398285C>A");
         variants.add("X:g.41242962_41242963insGA");
         variants.add("Y:g.41242962_41242963insGA");
+        variants.add("11:g.118392020_118392034delinsTTAC");
 
         List<VariantAnnotation> returnValue = new ArrayList<>(3);
         returnValue.add(variantMockData.get("7:g.140453136A>T"));
         returnValue.add(variantMockData.get("12:g.25398285C>A"));
         returnValue.add(variantMockData.get("X:g.41242962_41242963insGA"));
         returnValue.add(variantMockData.get("Y:g.41242962_41242963insGA"));
+        returnValue.add(variantMockData.get("11:g.118392020_118392034delinsTTAC"));
 
         Mockito.when(this.fetcher.fetchAndCache(variants)).thenReturn(returnValue);
     }
@@ -358,14 +380,28 @@ private void mockPtmServiceMethods(Map<String, List<PostTranslationalModificatio
 
     private void mockEnsemblServiceMethods()
     {
-        // when called for "mskcc" override, set first transcript "ENST00000288602" as canonical
         Set<String> mskccOverrides = new HashSet<>();
+        // For variant 7:g.140453136A>T
+        // when called for "mskcc" override, set first transcript "ENST00000288602" as canonical
         mskccOverrides.add("ENST00000288602");
+
+        // For variant 11:g.118392020_118392034delinsTTAC, two transcripts need to be added
+        mskccOverrides.add("ENST00000534358");
+        mskccOverrides.add("ENST00000554407");
         Mockito.when(this.ensemblService.getCanonicalTranscriptIdsBySource("mskcc")).thenReturn(mskccOverrides);
 
-        // when called for "uniprot" override, set second transcript "ENST00000479537" as canonical
         Set<String> uniprotOverrides = new HashSet<>();
+        // For variant 7:g.140453136A>T
+        // when called for "uniprot" override, set second transcript "ENST00000479537" as canonical
         uniprotOverrides.add("ENST00000479537");
         Mockito.when(this.ensemblService.getCanonicalTranscriptIdsBySource("uniprot")).thenReturn(uniprotOverrides);
     }
+
+    private void mockOncokbServiceMethods()
+    {
+        Set<String> oncokbGeneSymbolList = new HashSet<>();
+        oncokbGeneSymbolList.add("BRAF");
+        oncokbGeneSymbolList.add("KMT2A");
+        Mockito.when(this.oncokbService.getOncokbGeneSymbolList()).thenReturn(oncokbGeneSymbolList);
+    }
 }
diff --git a/...ice/src/test/java/org/cbioportal/genome_nexus/service/mock/VariantAnnotationMockData.java b/...ice/src/test/java/org/cbioportal/genome_nexus/service/mock/VariantAnnotationMockData.java
@@ -79,6 +79,7 @@ public Map<String, VariantAnnotation> generateData() throws IOException
             this.objectMapper.readVariantAnnotation("13_g.48954120_48954122delinsAAA.json"));
         mockData.put("10:g.8100129_8100132delinsAACT",
             this.objectMapper.readVariantAnnotation("10_g.8100129_8100132delinsAACT.json"));
+        mockData.put("11:g.118392020_118392034delinsTTAC", this.objectMapper.readVariantAnnotation("11_g.118392020_118392034delinsTTAC.json"));
         return mockData;
     }
 }
diff --git a/service/src/test/resources/variant/11_g.118392020_118392034delinsTTAC.json b/service/src/test/resources/variant/11_g.118392020_118392034delinsTTAC.json
@@ -0,0 +1,51 @@
+{
+    "variant": "11:g.118392020_118392034delinsTTAC",
+    "originalVariantQuery": "11:g.118392020_118392034delinsTTAC",
+    "hgvsg": "11:g.118392020_118392034delinsTTAC",
+    "id": "11:g.118392020_118392034delinsTTAC",
+    "assembly_name": "GRCh37",
+    "seq_region_name": "11",
+    "start": 118392020,
+    "end": 118392034,
+    "allele_string": "GGGGTCTTTTCTGTA/TTAC",
+    "strand": 1,
+    "most_severe_consequence": "splice_acceptor_variant",
+    "transcript_consequences": [
+      {
+        "exon": "35/36",
+        "transcript_id": "ENST00000534358",
+        "hgvsp": "ENSP00000436786.1:p.Arg3844LeufsTer6",
+        "hgvsc": "ENST00000534358.1:c.11531_11545delinsTTAC",
+        "variant_allele": "TTAC",
+        "codons": "cGGGGTCTTTTCTGTAag/cTTACag",
+        "protein_id": "ENSP00000436786",
+        "protein_start": 3844,
+        "protein_end": 3849,
+        "gene_symbol": "KMT2A",
+        "gene_id": "ENSG00000118058",
+        "amino_acids": "RGLFCK/LTX",
+        "hgnc_id": "7132",
+        "canonical": "1",
+        "refseq_transcript_ids": [
+          "NM_005933.3",
+          "NM_001197104.1"
+        ],
+        "consequence_terms": [
+          "frameshift_variant"
+        ]
+      },
+      {
+        "exon": "2/3",
+        "transcript_id": "ENST00000554407",
+        "hgvsc": "ENST00000554407.1:n.273-5_282delinsGTAA",
+        "variant_allele": "TTAC",
+        "gene_symbol": "RP11-770J1.3",
+        "gene_id": "ENSG00000255435",
+        "consequence_terms": [
+          "splice_acceptor_variant",
+          "non_coding_transcript_exon_variant",
+          "intron_variant"
+        ]
+      }
+    ]
+}