Use appropriate genome-nexus url depending on study (#4787)

Use appropriate genome-nexus url depending on reference genome build
cBioPortal · Dec 5, 2023 · 5a8b09f · 5a8b09f
1 parent 4bcbe7e
commit 5a8b09f
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Showing 3 changed files with 43 additions and 21 deletions.
diff --git a/src/pages/groupComparison/GroupComparisonMutationMapperWrapper.tsx b/src/pages/groupComparison/GroupComparisonMutationMapperWrapper.tsx
@@ -22,7 +22,10 @@ import { LollipopTooltipCountInfo } from './LollipopTooltipCountInfo';
 import MutationMapperUserSelectionStore from 'shared/components/mutationMapper/MutationMapperUserSelectionStore';
 import styles from './styles.module.scss';
 import { saveOncoKbIconStyleToLocalStorage } from 'shared/lib/AnnotationColumnUtils';
-import { generateMutationIdByGeneAndProteinChange } from 'shared/lib/StoreUtils';
+import {
+    generateMutationIdByGeneAndProteinChange,
+    getGenomeBuildFromStudies,
+} from 'shared/lib/StoreUtils';
 
 interface IGroupComparisonMutationMapperWrapperProps {
     store: GroupComparisonStore;
@@ -45,6 +48,9 @@ export default class GroupComparisonMutationMapperWrapper extends React.Componen
     }
 
     @computed get mutationMapperToolStore() {
+        const genomeBuild = getGenomeBuildFromStudies(
+            this.props.store.studies.result
+        );
         const store = new MutationMapperToolStore(
             this.props.store.filteredAndAnnotatedMutations.result,
             {
@@ -56,8 +62,10 @@ export default class GroupComparisonMutationMapperWrapper extends React.Componen
                     .uniqueSampleKeyToTumorType.result,
                 uniqueSampleKeyToCancerType: this.props.store
                     .uniqueSampleKeyToCancerType.result,
+                genomeBuild: genomeBuild,
             }
         );
+
         return store;
     }
 

diff --git a/src/pages/staticPages/tools/mutationMapper/MutationMapperTool.tsx b/src/pages/staticPages/tools/mutationMapper/MutationMapperTool.tsx
@@ -59,7 +59,10 @@ export default class MutationMapperTool extends React.Component<
     @observable.ref lastParsedInputContent: string | undefined = undefined;
     @observable referenceGenomeSelection: string = REFERENCE_GENOME.grch37.NCBI;
 
-    private store: MutationMapperToolStore = new MutationMapperToolStore();
+    private store: MutationMapperToolStore = new MutationMapperToolStore(
+        undefined,
+        { genomeBuild: REFERENCE_GENOME.grch37.NCBI }
+    );
 
     constructor(props: IMutationMapperToolProps) {
         super(props);
@@ -73,9 +76,9 @@ export default class MutationMapperTool extends React.Component<
             getBrowserWindow().localStorage.getItem('referenceGenomeId') ===
                 REFERENCE_GENOME.grch38.NCBI
         ) {
-            this.store.setGenomeNexusUrl(
-                getServerConfig().genomenexus_url_grch38!
-            );
+            this.store = new MutationMapperToolStore(undefined, {
+                genomeBuild: REFERENCE_GENOME.grch38.UCSC,
+            });
             this.referenceGenomeSelection = REFERENCE_GENOME.grch38.NCBI;
         }
 

diff --git a/src/pages/staticPages/tools/mutationMapper/MutationMapperToolStore.ts b/src/pages/staticPages/tools/mutationMapper/MutationMapperToolStore.ts
@@ -60,8 +60,6 @@ import { SiteError } from 'shared/model/appMisc';
 export default class MutationMapperToolStore {
     @observable mutationData: Partial<MutationInput>[] | undefined;
     @observable criticalErrors: Error[] = [];
-    // if we use grch37(default), grch38GenomeNexusUrl will be undefined
-    @observable grch38GenomeNexusUrl: string | undefined = undefined;
 
     readonly genes = remoteData<Gene[]>(
         {
@@ -107,9 +105,15 @@ export default class MutationMapperToolStore {
     }
 
     @computed get genomeNexusClient() {
-        const client = this.grch38GenomeNexusUrl
-            ? new GenomeNexusAPI(this.grch38GenomeNexusUrl)
-            : defaultGenomeNexusClient;
+        let client = defaultGenomeNexusClient;
+        if (
+            this.mutationMapperStoreConfigOverride?.genomeBuild ===
+            REFERENCE_GENOME.grch38.UCSC
+        ) {
+            client = new GenomeNexusAPI(
+                getServerConfig().genomenexus_url_grch38!
+            );
+        }
 
         client.addErrorHandler(err => {
             eventBus.emit(
@@ -126,9 +130,15 @@ export default class MutationMapperToolStore {
     }
 
     @computed get genomeNexusInternalClient() {
-        const client = this.grch38GenomeNexusUrl
-            ? new GenomeNexusAPIInternal(this.grch38GenomeNexusUrl)
-            : defaultGenomeNexusInternalClient;
+        let client = defaultGenomeNexusInternalClient;
+        if (
+            this.mutationMapperStoreConfigOverride?.genomeBuild ===
+            REFERENCE_GENOME.grch38.UCSC
+        ) {
+            client = new GenomeNexusAPIInternal(
+                getServerConfig().genomenexus_url_grch38!
+            );
+        }
 
         client.addErrorHandler(err => {
             eventBus.emit(
@@ -349,9 +359,11 @@ export default class MutationMapperToolStore {
                                     {
                                         filterMutationsBySelectedTranscript: !this
                                             .hasInputWithProteinChanges,
-                                        genomeBuild: this.grch38GenomeNexusUrl
-                                            ? REFERENCE_GENOME.grch38.UCSC
-                                            : REFERENCE_GENOME.grch37.UCSC,
+                                        genomeBuild:
+                                            this
+                                                .mutationMapperStoreConfigOverride
+                                                ?.genomeBuild ||
+                                            REFERENCE_GENOME.grch37.UCSC,
                                         ...this
                                             .mutationMapperStoreConfigOverride,
                                     },
@@ -446,13 +458,12 @@ export default class MutationMapperToolStore {
         );
     }
 
-    public setGenomeNexusUrl(grch38GenomeNexusUrl: string | undefined) {
-        this.grch38GenomeNexusUrl = grch38GenomeNexusUrl;
-    }
-
     @autobind
     generateGenomeNexusHgvsgUrl(hgvsg: string) {
-        return getGenomeNexusHgvsgUrl(hgvsg, this.grch38GenomeNexusUrl);
+        return getGenomeNexusHgvsgUrl(
+            hgvsg,
+            this.genomeNexusClient.getDomain()
+        );
     }
 
     @cached @computed get pubMedCache() {