Merge pull request #3024 from alisman/separate-cache

Add separate genome nexus cache for mutation assessor Former-commit-id: e10f8e889b5bde02c5edd937a4c2870f0175f25e
cBioPortal · Jan 30, 2020 · 0a2245e · 0a2245e
2 parents d78b73a + a71b3fb
commit 0a2245e
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Showing 18 changed files with 409 additions and 206 deletions.
diff --git a/src/pages/patientView/PatientViewPage.tsx b/src/pages/patientView/PatientViewPage.tsx
@@ -958,6 +958,11 @@ export default class PatientViewPage extends React.Component<
                                                             .patientViewPageStore
                                                             .genomeNexusCache
                                                     }
+                                                    genomeNexusMutationAssessorCache={
+                                                        this
+                                                            .patientViewPageStore
+                                                            .genomeNexusMutationAssessorCache
+                                                    }
                                                     genomeNexusMyVariantInfoCache={
                                                         this
                                                             .patientViewPageStore

diff --git a/src/pages/patientView/clinicalInformation/PatientViewPageStore.ts b/src/pages/patientView/clinicalInformation/PatientViewPageStore.ts
@@ -31,6 +31,7 @@ import {
 import OncoKbEvidenceCache from 'shared/cache/OncoKbEvidenceCache';
 import PubMedCache from 'shared/cache/PubMedCache';
 import GenomeNexusCache from 'shared/cache/GenomeNexusCache';
+import GenomeNexusMutationAssessorCache from 'shared/cache/GenomeNexusMutationAssessorCache';
 import GenomeNexusMyVariantInfoCache from 'shared/cache/GenomeNexusMyVariantInfoCache';
 import { IOncoKbData } from 'shared/model/OncoKB';
 import { IHotspotIndex, indexHotspotsData } from 'react-mutation-mapper';
@@ -1391,6 +1392,10 @@ export class PatientViewPageStore {
         return new GenomeNexusMyVariantInfoCache();
     }
 
+    @cached get genomeNexusMutationAssessorCache() {
+        return new GenomeNexusMutationAssessorCache();
+    }
+
     @cached get pubMedCache() {
         return new PubMedCache();
     }

diff --git a/src/pages/resultsView/ResultsViewPageStore.ts b/src/pages/resultsView/ResultsViewPageStore.ts
@@ -42,6 +42,7 @@ import { cached, labelMobxPromises, MobxPromise } from 'mobxpromise';
 import OncoKbEvidenceCache from 'shared/cache/OncoKbEvidenceCache';
 import PubMedCache from 'shared/cache/PubMedCache';
 import GenomeNexusCache from 'shared/cache/GenomeNexusCache';
+import GenomeNexusMutationAssessorCache from 'shared/cache/GenomeNexusMutationAssessorCache';
 import GenomeNexusMyVariantInfoCache from 'shared/cache/GenomeNexusMyVariantInfoCache';
 import CancerTypeCache from 'shared/cache/CancerTypeCache';
 import MutationCountCache from 'shared/cache/MutationCountCache';
@@ -2958,6 +2959,7 @@ export class ResultsViewPageStore {
                                         ] || [],
                                     () => this.mutationCountCache,
                                     () => this.genomeNexusCache,
+                                    () => this.genomeNexusMutationAssessorCache,
                                     () => this.genomeNexusMyVariantInfoCache,
                                     () => this.discreteCNACache,
                                     this.studyToMolecularProfileDiscrete.result!,
@@ -4870,6 +4872,10 @@ export class ResultsViewPageStore {
         return new GenomeNexusCache();
     }
 
+    @cached get genomeNexusMutationAssessorCache() {
+        return new GenomeNexusMutationAssessorCache();
+    }
+
     @cached get genomeNexusMyVariantInfoCache() {
         return new GenomeNexusMyVariantInfoCache();
     }

diff --git a/src/pages/resultsView/mutation/Mutations.tsx b/src/pages/resultsView/mutation/Mutations.tsx
@@ -152,6 +152,10 @@ export default class Mutations extends React.Component<
                                 this.props.store.mutationCountCache
                             }
                             genomeNexusCache={this.props.store.genomeNexusCache}
+                            genomeNexusMutationAssessorCache={
+                                this.props.store
+                                    .genomeNexusMutationAssessorCache
+                            }
                             genomeNexusMyVariantInfoCache={
                                 this.props.store.genomeNexusMyVariantInfoCache
                             }

diff --git a/src/pages/resultsView/mutation/ResultsViewMutationMapper.tsx b/src/pages/resultsView/mutation/ResultsViewMutationMapper.tsx
@@ -113,6 +113,9 @@ export default class ResultsViewMutationMapper extends MutationMapper<
                 pubMedCache={this.props.pubMedCache}
                 mutationCountCache={this.props.mutationCountCache}
                 genomeNexusCache={this.props.genomeNexusCache}
+                genomeNexusMutationAssessorCache={
+                    this.props.genomeNexusMutationAssessorCache
+                }
                 genomeNexusMyVariantInfoCache={
                     this.props.genomeNexusMyVariantInfoCache
                 }

diff --git a/src/pages/resultsView/mutation/ResultsViewMutationMapperStore.ts b/src/pages/resultsView/mutation/ResultsViewMutationMapperStore.ts
@@ -23,6 +23,7 @@ import {
 import MutationCountCache from 'shared/cache/MutationCountCache';
 import DiscreteCNACache from 'shared/cache/DiscreteCNACache';
 import GenomeNexusCache from 'shared/cache/GenomeNexusCache';
+import GenomeNexusMutationAssessorCache from 'shared/cache/GenomeNexusMutationAssessorCache';
 import GenomeNexusMyVariantInfoCache from 'shared/cache/GenomeNexusMyVariantInfoCache';
 import { MutationTableDownloadDataFetcher } from 'shared/lib/MutationTableDownloadDataFetcher';
 import MutationMapperStore, {
@@ -47,6 +48,7 @@ export default class ResultsViewMutationMapperStore extends MutationMapperStore
         getMutations: () => Mutation[],
         private getMutationCountCache: () => MutationCountCache,
         private getGenomeNexusCache: () => GenomeNexusCache,
+        private getGenomeNexusMutationAssessorCache: () => GenomeNexusMutationAssessorCache,
         private getGenomeNexusMyVariantInfoCache: () => GenomeNexusMyVariantInfoCache,
         private getDiscreteCNACache: () => DiscreteCNACache,
         public studyToMolecularProfileDiscrete: {
@@ -132,6 +134,7 @@ export default class ResultsViewMutationMapperStore extends MutationMapperStore
             this.mutationData,
             this.studyToMolecularProfileDiscrete,
             this.getGenomeNexusCache,
+            this.getGenomeNexusMutationAssessorCache,
             this.getGenomeNexusMyVariantInfoCache,
             this.getMutationCountCache,
             this.getDiscreteCNACache

diff --git a/src/pages/staticPages/tools/mutationMapper/MutationMapperTool.tsx b/src/pages/staticPages/tools/mutationMapper/MutationMapperTool.tsx
@@ -469,6 +469,9 @@ export default class MutationMapperTool extends React.Component<
                             }
                             downloadDataFetcher={this.store.downloadDataFetcher}
                             genomeNexusCache={this.store.genomeNexusCache}
+                            genomeNexusMutationAssessorCache={
+                                this.store.genomeNexusMutationAssessorCache
+                            }
                             genomeNexusMyVariantInfoCache={
                                 this.store.genomeNexusMyVariantInfoCache
                             }

diff --git a/src/pages/staticPages/tools/mutationMapper/MutationMapperToolStore.ts b/src/pages/staticPages/tools/mutationMapper/MutationMapperToolStore.ts
@@ -42,6 +42,7 @@ import { fetchHotspotsData } from 'shared/lib/CancerHotspotsUtils';
 import OncoKbEvidenceCache from 'shared/cache/OncoKbEvidenceCache';
 import PubMedCache from 'shared/cache/PubMedCache';
 import GenomeNexusCache from 'shared/cache/GenomeNexusCache';
+import GenomeNexusMutationAssessorCache from 'shared/cache/GenomeNexusMutationAssessorCache';
 import GenomeNexusMyVariantInfoCache from 'shared/cache/GenomeNexusMyVariantInfoCache';
 import PdbHeaderCache from 'shared/cache/PdbHeaderCache';
 import MutationMapperStore from 'shared/components/mutationMapper/MutationMapperStore';
@@ -380,6 +381,10 @@ export default class MutationMapperToolStore {
         return new GenomeNexusCache();
     }
 
+    @cached get genomeNexusMutationAssessorCache() {
+        return new GenomeNexusMutationAssessorCache();
+    }
+
     @cached get genomeNexusMyVariantInfoCache() {
         return new GenomeNexusMyVariantInfoCache();
     }
@@ -397,6 +402,7 @@ export default class MutationMapperToolStore {
             this.mutations,
             undefined,
             () => this.genomeNexusCache,
+            () => this.genomeNexusMutationAssessorCache,
             () => this.genomeNexusMyVariantInfoCache
         );
     }

diff --git a/src/pages/staticPages/tools/mutationMapper/StandaloneMutationMapper.tsx b/src/pages/staticPages/tools/mutationMapper/StandaloneMutationMapper.tsx
@@ -30,6 +30,9 @@ export default class StandaloneMutationMapper extends MutationMapper<
                     this.props.store.indexedVariantAnnotations
                 }
                 genomeNexusCache={this.props.genomeNexusCache}
+                genomeNexusMutationAssessorCache={
+                    this.props.genomeNexusMutationAssessorCache
+                }
                 genomeNexusMyVariantInfoCache={
                     this.props.genomeNexusMyVariantInfoCache
                 }

diff --git a/src/shared/cache/GenomeNexusCache.ts b/src/shared/cache/GenomeNexusCache.ts
@@ -14,7 +14,7 @@ export function fetch(queries: Mutation[]): Promise<VariantAnnotation[]> {
     if (queries.length > 0) {
         return fetchVariantAnnotationsByMutation(
             queries,
-            ['annotation_summary', 'mutation_assessor'],
+            ['annotation_summary'],
             AppConfig.serverConfig.isoformOverrideSource
         );
     } else {

diff --git a/src/shared/cache/GenomeNexusMutationAssessorCache.ts b/src/shared/cache/GenomeNexusMutationAssessorCache.ts
@@ -0,0 +1,49 @@
+import * as _ from 'lodash';
+import { fetchVariantAnnotationsByMutation } from 'shared/lib/StoreUtils';
+import {
+    extractGenomicLocation,
+    genomicLocationString,
+} from 'shared/lib/MutationUtils';
+import { Mutation } from 'shared/api/generated/CBioPortalAPI';
+import LazyMobXCache, { CacheData } from 'shared/lib/LazyMobXCache';
+import AppConfig from 'appConfig';
+import { VariantAnnotation } from 'cbioportal-frontend-commons';
+
+export type GenomeNexusCacheDataType = CacheData<VariantAnnotation>;
+
+export function fetch(queries: Mutation[]): Promise<VariantAnnotation[]> {
+    if (queries.length > 0) {
+        return fetchVariantAnnotationsByMutation(
+            queries,
+            ['annotation_summary', 'mutation_assessor'],
+            AppConfig.serverConfig.isoformOverrideSource
+        );
+    } else {
+        return Promise.resolve([]);
+    }
+}
+
+export function queryToKey(m: Mutation) {
+    const genomicLocation = extractGenomicLocation(m);
+    if (genomicLocation) {
+        return genomicLocationString(genomicLocation);
+    } else {
+        // TODO: might be a better way to handle mutations w/o genomic location
+        // info. They should maybe not be fed to the cache in the first place
+        return '';
+    }
+}
+
+export default class GenomeNexusMutationAssessorCache extends LazyMobXCache<
+    VariantAnnotation,
+    Mutation
+> {
+    constructor() {
+        super(
+            (m: Mutation) => queryToKey(m), // queryToKey
+            (v: VariantAnnotation) =>
+                genomicLocationString(v.annotation_summary.genomicLocation), // dataToKey
+            fetch
+        );
+    }
+}