Merge branch 'cBioPortal:master' into pairwise_plots

.github/workflows/jitpack-build.yml

@@ -17,14 +17,29 @@ jobs:
 
       - name: Get release tag
         id: get_tag
-        run: echo "::set-output name=tag::${GITHUB_REF#refs/tags/}"
+        run: echo "tag=${GITHUB_REF#refs/tags/}" >> $GITHUB_OUTPUT
 
       - name: Trigger JitPack Build
         run: |
           TAG=${{ steps.get_tag.outputs.tag }}
           JITPACK_BUILD_URL="https://jitpack.io/com/github/cbioportal/cbioportal-frontend/$TAG/build.log"
-          echo "Triggering JitPack build for $TAG"
-          curl -I $JITPACK_BUILD_URL
-
-      - name: Notify success
-        run: echo "JitPack build triggered successfully."
+          
+          MAX_RETRIES=10
+          RETRY_DELAY=30
+          COUNTER=0
+          
+          while [ $COUNTER -lt $MAX_RETRIES ]; do
+            HTTP_STATUS=$(curl -s -o /dev/null -w "%{http_code}" -X POST "$JITPACK_BUILD_URL")
+          
+            if [ "$HTTP_STATUS" -eq 200 ]; then
+              echo "Build triggered successfully for version ${TAG}."
+              exit 0
+            else
+              echo "Attempt $((COUNTER+1)) failed with status $HTTP_STATUS: Tag not found yet. Retrying in $RETRY_DELAY seconds..."
+              ((COUNTER++))
+              sleep $RETRY_DELAY
+            fi
+          done
+          
+          echo "Failed to trigger JitPack build after $MAX_RETRIES attempts."
+          exit 1

package.json

@@ -1,7 +1,7 @@
 {
   "name": "cbioportal-frontend",
   "private": true,
-  "version": "3.3.288",
+  "version": "3.3.289",
   "workspaces": {
     "packages": [
       ".",

packages/react-variant-view/package.json

@@ -1,6 +1,6 @@
 {
   "name": "react-variant-view",
-  "version": "0.3.117",
+  "version": "0.3.118",
   "description": "cBioPortal Variant Viewer",
   "main": "dist/index.js",
   "module": "dist/index.es.js",

packages/react-variant-view/src/component/functionalPrediction/FunctionalPrediction.tsx

@@ -28,25 +28,21 @@ interface IFunctionalImpactData {
 @observer
 class FunctionalPrediction extends React.Component<IFunctionalPredictionProps> {
     public getData(
-        genomeNexusData: VariantAnnotation | undefined
+        genomeNexusData: VariantAnnotation | undefined,
+        selectedTranscriptId?: string
     ): IFunctionalImpactData {
         const mutationAssessor = genomeNexusData?.mutation_assessor;
-        const siftScore =
-            genomeNexusData &&
-            genomeNexusData.transcript_consequences &&
-            genomeNexusData.transcript_consequences[0].sift_score;
-        const siftPrediction =
-            genomeNexusData &&
-            genomeNexusData.transcript_consequences &&
-            genomeNexusData.transcript_consequences[0].sift_prediction;
-        const polyPhenScore =
-            genomeNexusData &&
-            genomeNexusData.transcript_consequences &&
-            genomeNexusData.transcript_consequences[0].polyphen_score;
-        const polyPhenPrediction =
-            genomeNexusData &&
-            genomeNexusData.transcript_consequences &&
-            genomeNexusData.transcript_consequences[0].polyphen_prediction;
+        const transcriptConsequence =
+            genomeNexusData && selectedTranscriptId
+                ? genomeNexusData.transcript_consequences.find(
+                      tc => tc.transcript_id === selectedTranscriptId
+                  )
+                : undefined;
+
+        const siftScore = transcriptConsequence?.sift_score;
+        const siftPrediction = transcriptConsequence?.sift_prediction;
+        const polyPhenScore = transcriptConsequence?.polyphen_score;
+        const polyPhenPrediction = transcriptConsequence?.polyphen_prediction;
 
         return {
             mutationAssessor,

src/pages/studyView/resources/FilesAndLinks.tsx

@@ -34,16 +34,19 @@ class FilesLinksTableComponent extends LazyMobXTable<{
 const RECORD_LIMIT = 500;
 
 function getResourceDataOfEntireStudy(studyIds: string[]) {
-    // Only handle the first studyId for now. Can be expanded to make a call per
-    // studyId.
-    const studyId = studyIds[0];
-    const allResources = internalClient.getAllStudyResourceDataInStudyPatientSampleUsingGET(
-        {
+    // Fetch resource data for each studyId, then return combined results
+    const allResources = studyIds.map(studyId =>
+        internalClient.getAllStudyResourceDataInStudyPatientSampleUsingGET({
             studyId: studyId,
             projection: 'DETAILED',
-        }
+        })
+    );
+
+    return Promise.all(allResources).then(allResources =>
+        _(allResources)
+            .flatMap()
+            .value()
     );
-    return allResources;
 }
 
 function getResourceDataOfPatients(studyClinicalData: {

src/shared/components/mutationTable/MutationTable.tsx

@@ -906,7 +906,8 @@ export default class MutationTable<
                     return FunctionalImpactColumnFormatter.renderFunction(
                         d,
                         this.props.genomeNexusCache,
-                        this.props.genomeNexusMutationAssessorCache
+                        this.props.genomeNexusMutationAssessorCache,
+                        this.props.selectedTranscriptId
                     );
                 } else {
                     return <span></span>;
@@ -917,7 +918,8 @@ export default class MutationTable<
                     d,
                     this.props.genomeNexusCache as GenomeNexusCache,
                     this.props
-                        .genomeNexusMutationAssessorCache as GenomeNexusMutationAssessorCache
+                        .genomeNexusMutationAssessorCache as GenomeNexusMutationAssessorCache,
+                    this.props.selectedTranscriptId
                 ),
             headerRender: FunctionalImpactColumnFormatter.headerRender,
             visible: false,

src/shared/components/mutationTable/column/FunctionalImpactColumnFormatter.tsx

@@ -457,7 +457,8 @@ export default class FunctionalImpactColumnFormatter {
     public static getData(
         data: Mutation[],
         siftPolyphenCache: GenomeNexusCache,
-        mutationAssessorCache: GenomeNexusMutationAssessorCache
+        mutationAssessorCache: GenomeNexusMutationAssessorCache,
+        selectedTranscriptId?: string
     ): FunctionalImpactData {
         const siftPolyphenCacheData = FunctionalImpactColumnFormatter.getDataFromCache(
             data,
@@ -471,10 +472,13 @@ export default class FunctionalImpactColumnFormatter {
             : null;
 
         const siftData = siftPolyphenCacheData
-            ? this.getSiftData(siftPolyphenCacheData.data)
+            ? this.getSiftData(siftPolyphenCacheData.data, selectedTranscriptId)
             : undefined;
         const polyphenData = siftPolyphenCacheData
-            ? this.getPolyphenData(siftPolyphenCacheData.data)
+            ? this.getPolyphenData(
+                  siftPolyphenCacheData.data,
+                  selectedTranscriptId
+              )
             : undefined;
         const mutationAssessor = mutationAssessorCacheData
             ? this.getMutationAssessorData(mutationAssessorCacheData.data)
@@ -496,17 +500,21 @@ export default class FunctionalImpactColumnFormatter {
         return functionalImpactData;
     }
 
-    public static getSiftData(siftDataCache: VariantAnnotation | null) {
+    public static getSiftData(
+        siftDataCache: VariantAnnotation | null,
+        selectedTranscriptId?: string
+    ) {
         let siftScore: number | undefined = undefined;
         let siftPrediction: string | undefined = undefined;
-
-        if (
-            siftDataCache &&
-            !_.isEmpty(siftDataCache.transcript_consequences)
-        ) {
-            siftScore = siftDataCache.transcript_consequences[0].sift_score;
-            siftPrediction =
-                siftDataCache.transcript_consequences[0].sift_prediction;
+        if (siftDataCache && selectedTranscriptId) {
+            // find transcript consequence that matches the selected transcript
+            const transcriptConsequence = siftDataCache.transcript_consequences.find(
+                tc => tc.transcript_id === selectedTranscriptId
+            );
+            if (transcriptConsequence) {
+                siftScore = transcriptConsequence.sift_score;
+                siftPrediction = transcriptConsequence.sift_prediction;
+            }
         }
 
         return {
@@ -515,19 +523,22 @@ export default class FunctionalImpactColumnFormatter {
         };
     }
 
-    public static getPolyphenData(polyphenDataCache: VariantAnnotation | null) {
+    public static getPolyphenData(
+        polyphenDataCache: VariantAnnotation | null,
+        selectedTranscriptId?: string
+    ) {
         let polyPhenScore: number | undefined = undefined;
         let polyPhenPrediction: string | undefined = undefined;
 
-        if (
-            polyphenDataCache &&
-            !_.isEmpty(polyphenDataCache.transcript_consequences)
-        ) {
-            polyPhenScore =
-                polyphenDataCache.transcript_consequences[0].polyphen_score;
-            polyPhenPrediction =
-                polyphenDataCache.transcript_consequences[0]
-                    .polyphen_prediction;
+        if (polyphenDataCache && selectedTranscriptId) {
+            // find transcript consequence that matches the selected transcript
+            const transcriptConsequence = polyphenDataCache.transcript_consequences.find(
+                tc => tc.transcript_id === selectedTranscriptId
+            );
+            if (transcriptConsequence) {
+                polyPhenScore = transcriptConsequence.polyphen_score;
+                polyPhenPrediction = transcriptConsequence.polyphen_prediction;
+            }
         }
 
         return {
@@ -545,7 +556,8 @@ export default class FunctionalImpactColumnFormatter {
     public static renderFunction(
         data: Mutation[],
         siftPolyphenCache: GenomeNexusCache | undefined,
-        mutationAssessorCache: GenomeNexusMutationAssessorCache | undefined
+        mutationAssessorCache: GenomeNexusMutationAssessorCache | undefined,
+        selectedTranscriptId?: string
     ) {
         const showMutationAssessor = shouldShowMutationAssessor();
 
@@ -568,11 +580,13 @@ export default class FunctionalImpactColumnFormatter {
                     )}
                 {FunctionalImpactColumnFormatter.makeFunctionalImpactViz(
                     siftPolyphenCacheData,
-                    FunctionalImpactColumnsName.SIFT
+                    FunctionalImpactColumnsName.SIFT,
+                    selectedTranscriptId
                 )}
                 {FunctionalImpactColumnFormatter.makeFunctionalImpactViz(
                     siftPolyphenCacheData,
-                    FunctionalImpactColumnsName.POLYPHEN2
+                    FunctionalImpactColumnsName.POLYPHEN2,
+                    selectedTranscriptId
                 )}
             </div>
         );
@@ -581,13 +595,15 @@ export default class FunctionalImpactColumnFormatter {
     public static download(
         data: Mutation[],
         siftPolyphenCache: GenomeNexusCache,
-        mutationAssessorCache: GenomeNexusMutationAssessorCache
+        mutationAssessorCache: GenomeNexusMutationAssessorCache,
+        selectedTranscriptId?: string
     ): string {
         if (siftPolyphenCache || mutationAssessorCache) {
             const functionalImpactData = FunctionalImpactColumnFormatter.getData(
                 data,
                 siftPolyphenCache,
-                mutationAssessorCache
+                mutationAssessorCache,
+                selectedTranscriptId
             );
             let downloadData = [];
             if (functionalImpactData) {
@@ -626,7 +642,8 @@ export default class FunctionalImpactColumnFormatter {
 
     private static makeFunctionalImpactViz(
         cacheData: GenomeNexusCacheDataType | null,
-        column: FunctionalImpactColumnsName
+        column: FunctionalImpactColumnsName,
+        selectedTranscriptId?: string
     ) {
         let status: TableCellStatus | null = null;
 
@@ -650,7 +667,8 @@ export default class FunctionalImpactColumnFormatter {
                     );
                 case FunctionalImpactColumnsName.SIFT:
                     functionalImpactData = FunctionalImpactColumnFormatter.getSiftData(
-                        cacheData.data
+                        cacheData.data,
+                        selectedTranscriptId
                     );
                     return (
                         <Sift
@@ -660,7 +678,8 @@ export default class FunctionalImpactColumnFormatter {
                     );
                 case FunctionalImpactColumnsName.POLYPHEN2:
                     functionalImpactData = FunctionalImpactColumnFormatter.getPolyphenData(
-                        cacheData.data
+                        cacheData.data,
+                        selectedTranscriptId
                     );
                     return (
                         <PolyPhen2