Rename functional impact fields

model/src/main/java/org/cbioportal/genome_nexus/model/MutationAssessor.java

@@ -1,5 +1,6 @@
 package org.cbioportal.genome_nexus.model;
 import org.springframework.data.mongodb.core.mapping.Document;
+import org.springframework.data.mongodb.core.mapping.Field;
 
 @Document(collection = "mutation_assessor.annotation")
 public class MutationAssessor
@@ -34,24 +35,26 @@ public void setHgvspShort(String hgvspShort) {
         this.hgvspShort = hgvspShort;
     }
 
-    private Double f_score;
+    @Field("f_score")
+    private Double functionalImpactScore;
 
-    public Double getF_score() {
-        return f_score;
+    public Double getFunctionalImpactScore() {
+        return functionalImpactScore;
     }
 
-    public void setF_score(Double f_score) {
-        this.f_score = f_score;
+    public void setFunctionalImpactScore(Double functionalImpactScore) {
+        this.functionalImpactScore = functionalImpactScore;
     }
+
+    @Field("f_impact")
+    private String functionalImpactPrediction;
 
-    private String f_impact;
-
-    public String getF_impact() {
-        return f_impact;
+    public String getFunctionalImpactPrediction() {
+        return functionalImpactPrediction;
     }
 
-    public void setF_impact(String f_impact) {
-        this.f_impact = f_impact;
+    public void setFunctionalImpactPrediction(String functionalImpactPrediction) {
+        this.functionalImpactPrediction = functionalImpactPrediction;
     }
 
     private String msa;

service/src/test/java/org/cbioportal/genome_nexus/service/internal/MutationAssessorServiceTest.java

@@ -53,12 +53,12 @@ public void getMutationAssessorByMutationAssessorVariant()
         VariantAnnotation variantAnnotation1 = new VariantAnnotation();
         variantAnnotation1.setVariant("7:g.140453136A>T");
         MutationAssessor mutationAssessor1 = service.getMutationAssessorByMutationAssessorVariant("P15056,p.V600E", variantAnnotation1);
-        assertEquals(mutationAssessor1.getF_impact(), mockData.get("P15056,p.V600E").getF_impact());
+        assertEquals(mutationAssessor1.getFunctionalImpactPrediction(), mockData.get("P15056,p.V600E").getFunctionalImpactPrediction());
 
         VariantAnnotation variantAnnotation2 = new VariantAnnotation();
         variantAnnotation2.setVariant("12:g.25398285C>A");
         MutationAssessor mutationAssessor2 = service.getMutationAssessorByMutationAssessorVariant("P01116,p.G12C", variantAnnotation2);
-        assertEquals(mutationAssessor2.getF_impact(), mockData.get("P01116,p.G12C").getF_impact());
+        assertEquals(mutationAssessor2.getFunctionalImpactPrediction(), mockData.get("P01116,p.G12C").getFunctionalImpactPrediction());
 
         VariantAnnotation invalidVariantAnnotation = new VariantAnnotation();
         invalidVariantAnnotation.setVariant("INVALID");
@@ -82,12 +82,12 @@ public void getMutationAssessorByVariantAnnotation()
         Mockito.when(ensemblService.getUniprotId("ENST00000288602")).thenReturn("P15056");
         Mockito.when(mutationAssessorRepository.findById("P15056,p.V600E")).thenReturn(Optional.of(maMockData.get("P15056,p.V600E")));
         MutationAssessor mutationAssessor1 = service.getMutationAssessor(variantMockData.get("7:g.140453136A>T"));
-        assertEquals(mutationAssessor1.getF_score(), maMockData.get("P15056,p.V600E").getF_score());
+        assertEquals(mutationAssessor1.getFunctionalImpactScore(), maMockData.get("P15056,p.V600E").getFunctionalImpactScore());
 
         Mockito.when(proteinChangeResolver.resolveHgvspShort(variantMockData.get("12:g.25398285C>A"))).thenReturn("p.G12C");
         Mockito.when(ensemblService.getUniprotId("ENST00000256078")).thenReturn("P01116");
         Mockito.when(mutationAssessorRepository.findById("P01116,p.G12C")).thenReturn(Optional.of(maMockData.get("P01116,p.G12C")));
         MutationAssessor mutationAssessor2 = service.getMutationAssessor(variantMockData.get("12:g.25398285C>A"));
-        assertEquals(mutationAssessor2.getF_score(), maMockData.get("P01116,p.G12C").getF_score());
+        assertEquals(mutationAssessor2.getFunctionalImpactScore(), maMockData.get("P01116,p.G12C").getFunctionalImpactScore());
     }
 }

service/src/test/java/org/cbioportal/genome_nexus/service/mock/MutationAssessorMockData.java

@@ -19,8 +19,8 @@ public Map<String, MutationAssessor> generateData()
         mutationAssessor = new MutationAssessor();
         mutationAssessor.setHgvspShort("p.V600E");
         mutationAssessor.setUniprotId("P15056");
-        mutationAssessor.setF_score(7.110925419276407);
-        mutationAssessor.setF_impact("high");
+        mutationAssessor.setFunctionalImpactScore(7.110925419276407);
+        mutationAssessor.setFunctionalImpactPrediction("high");
         mutationAssessor.setMsa("P15056.4_full_b0.6_rg0.3");
         mutationAssessor.setMav(4);
         mutationAssessor.setSv(4);
@@ -30,8 +30,8 @@ public Map<String, MutationAssessor> generateData()
         mutationAssessor = new MutationAssessor();
         mutationAssessor.setHgvspShort("p.G12C");
         mutationAssessor.setUniprotId("P01116");
-        mutationAssessor.setF_score(5.8627536904542215);
-        mutationAssessor.setF_impact("medium");
+        mutationAssessor.setFunctionalImpactScore(5.8627536904542215);
+        mutationAssessor.setFunctionalImpactPrediction("medium");
         mutationAssessor.setMsa("P01116.1_full_b1.0_rg0.3");
         mutationAssessor.setMav(4);
         mutationAssessor.setSv(1);
@@ -41,8 +41,8 @@ public Map<String, MutationAssessor> generateData()
         mutationAssessor = new MutationAssessor();
         mutationAssessor.setHgvspShort("p.L25V");
         mutationAssessor.setUniprotId("P00519");
-        mutationAssessor.setF_score(2.554887124363546);
-        mutationAssessor.setF_impact("neutral");
+        mutationAssessor.setFunctionalImpactScore(2.554887124363546);
+        mutationAssessor.setFunctionalImpactPrediction("neutral");
         mutationAssessor.setMsa("P00519.4_full_b0.6_rg0.3");
         mutationAssessor.setMav(4);
         mutationAssessor.setSv(4);
@@ -52,8 +52,8 @@ public Map<String, MutationAssessor> generateData()
         mutationAssessor = new MutationAssessor();
         mutationAssessor.setHgvspShort(null);
         mutationAssessor.setUniprotId(null);
-        mutationAssessor.setF_score(null);
-        mutationAssessor.setF_impact(null);
+        mutationAssessor.setFunctionalImpactScore(null);
+        mutationAssessor.setFunctionalImpactPrediction(null);
         mutationAssessor.setMsa(null);
         mutationAssessor.setMav(null);
         mutationAssessor.setSv(null);

web/src/main/resources/application.properties.EXAMPLE

@@ -1,6 +1,6 @@
 # VEP web API URL with additional parameters. Note that "VARIANT" field will be replaced with
 # the actual variant value before each VEP request.
-vep.url=http://grch37.rest.ensembl.org/vep/human/hgvs/VARIANT?content-type=application/json&xref_refseq=1&ccds=1&canonical=1&domains=1&hgvs=1&numbers=1&protein=1
+vep.url=http://grch37.rest.ensembl.org/vep/human/hgvs/VARIANT?content-type=application/json&xref_refseq=1&ccds=1&canonical=1&domains=1&hgvs=1&numbers=1&protein=1&AlphaMissense=1
 
 # 200 is the max page size allowed by the public VEP service, it might be possible to increase this for a private instance
 vep.max_page_size=200
@@ -24,12 +24,6 @@ vep.max_page_size=200
 # the gene external references URL
 genexrefs.url=http://grch37.rest.ensembl.org/xrefs/id/ACCESSION?content-type=application/json
 
-# Mutation Assessor web API URL
-#"VARIANT" will be replaced with actual variant upon each request.
-mutationAssessor.url=http://mutationassessor.org/r3/?cm=var&var=VARIANT&frm=json&fts=input,rgaa,rgvt,msa,pdb,F_impact,F_score,vc_score,vs_score,info,var,gene,uprot,rsprot,gaps,msa_height,chr,rs_pos,rs_res,up_pos,up_res,cnt_cosmic,cnt_snps
-# mutationAssessor url for GRCh38
-# mutationAssessor.url=http://mutationassessor.org/r3/?cm=var&var=hg38,VARIANT&frm=json&fts=input,rgaa,rgvt,msa,pdb,F_impact,F_score,vc_score,vs_score,info,var,gene,uprot,rsprot,gaps,msa_height,chr,rs_pos,rs_res,up_pos,up_res,cnt_cosmic,cnt_snps
-
 # my variant info web API URL
 #"VARIANT" will be replaced with actual variant upon each request.
 myvariantinfo.url=https://myvariant.info/v1/variant/VARIANT