Feat/support hgvsg (#530)

* normalize hgvsg using genome nexus

* address PR comments

* update pom

Author: bprize15

pom.xml

@@ -304,7 +304,7 @@
         <dependency>
             <groupId>com.github.genome-nexus</groupId>
             <artifactId>genome-nexus-java-api-client</artifactId>
-            <version>0709b8232b</version>
+            <version>c8ba14d555</version>
         </dependency>
         <dependency>
             <groupId>com.github.oncokb</groupId>

src/main/java/org/mskcc/oncokb/curation/service/MainService.java

@@ -127,17 +127,22 @@ public AlterationAnnotationStatus annotateAlteration(ReferenceGenome referenceGe
                     referenceGenome,
                     alterationWithEntityStatus.getEntity().getAlteration()
                 );
-                Optional<String> proteinChangeOptional = Optional.ofNullable(variantAnnotation)
-                    .map(VariantAnnotation::getAnnotationSummary)
-                    .map(VariantAnnotationSummary::getTranscriptConsequenceSummary)
-                    .map(TranscriptConsequenceSummary::getHgvspShort)
-                    .map(hgvsp -> hgvsp.replace("p.", ""));
-                if (proteinChangeOptional.isPresent()) {
-                    alterationWithEntityStatus.getEntity().setProteinChange(proteinChangeOptional.orElseThrow());
+
+                String hgvsg = variantAnnotation.getHgvsg();
+                if (StringUtils.isEmpty(hgvsg)) {
+                    throw new ApiException(variantAnnotation.getErrorMessage());
                 }
+                alterationWithEntityStatus.getEntity().setAlteration(hgvsg);
             } catch (ApiException e) {
-                alterationWithStatus.setMessage("Failed to be annotated by GenomeNexus.");
+                String message = "Failed to be annotated by GenomeNexus";
+                if (!e.getMessage().isEmpty()) {
+                    message += ": " + e.getMessage();
+                }
+                alterationWithStatus.setMessage(message);
+
+                alterationWithStatus.setEntity(alterationWithEntityStatus.getEntity());
                 alterationWithStatus.setType(EntityStatusType.WARNING);
+                return alterationWithStatus;
             }
         }
 

src/main/webapp/app/shared/modal/AddMutationModal.tsx

@@ -674,7 +674,8 @@ function AddMutationModal({
   }
 
   function getTabContent(alterationData: AlterationData, alterationIndex: number, excludingIndex?: number) {
-    const excludingSection = !_.isNil(excludingIndex) ? <></> : getExcludingSection(alterationData, alterationIndex);
+    const excludingSection =
+      !_.isNil(excludingIndex) || alterationData.type === 'GENOMIC_CHANGE' ? <></> : getExcludingSection(alterationData, alterationIndex);
 
     let content: JSX.Element;
     switch (alterationData.type) {
@@ -816,12 +817,6 @@ function AddMutationModal({
           placeholder="Input name"
           onChange={newValue => handleFieldChange(newValue, 'name', alterationIndex, excludingIndex)}
         />
-        <AddMutationModalField
-          label="Protein Change"
-          value={alterationData.proteinChange!}
-          placeholder="Input protein change"
-          onChange={newValue => handleFieldChange(newValue, 'proteinChange', alterationIndex, excludingIndex)}
-        />
       </div>
     );
   }