Merge master to rc

src/pages/patientView/PatientViewPage.tsx

@@ -382,7 +382,7 @@ export default class PatientViewPage extends React.Component<IPatientViewPagePro
                                         uniqueSampleKeyToTumorType={patientViewPageStore.uniqueSampleKeyToTumorType}
                                         molecularProfileIdToMolecularProfile={patientViewPageStore.molecularProfileIdToMolecularProfile.result}
                                         variantCountCache={patientViewPageStore.variantCountCache}
-                                        genomeNexusEnrichmentCache={patientViewPageStore.genomeNexusEnrichmentCache}
+                                        indexedVariantAnnotations={patientViewPageStore.indexedVariantAnnotations}
                                         discreteCNACache={patientViewPageStore.discreteCNACache}
                                         mrnaExprRankCache={patientViewPageStore.mrnaExprRankCache}
                                         oncoKbEvidenceCache={patientViewPageStore.oncoKbEvidenceCache}

src/pages/patientView/clinicalInformation/PatientViewPageStore.ts

@@ -18,7 +18,6 @@ import request from 'superagent';
 import DiscreteCNACache from "shared/cache/DiscreteCNACache";
 import {getTissueImageCheckUrl, getDarwinUrl} from "../../../shared/api/urls";
 import OncoKbEvidenceCache from "shared/cache/OncoKbEvidenceCache";
-import GenomeNexusEnrichmentCache from "shared/cache/GenomeNexusEnrichment";
 import PubMedCache from "shared/cache/PubMedCache";
 import {IOncoKbData} from "shared/model/OncoKB";
 import {IHotspotIndex} from "shared/model/CancerHotspots";
@@ -38,12 +37,14 @@ import {
     fetchMutSigData, findMrnaRankMolecularProfileId, mergeDiscreteCNAData, fetchSamplesForPatient, fetchClinicalData,
     fetchCopyNumberSegments, fetchClinicalDataForPatient, makeStudyToCancerTypeMap,
     fetchCivicGenes, fetchCnaCivicGenes, fetchCivicVariants, groupBySampleId, findSamplesWithoutCancerTypeClinicalData,
-    fetchStudiesForSamplesWithoutCancerTypeClinicalData, fetchOncoKbAnnotatedGenesSuppressErrors
+    fetchStudiesForSamplesWithoutCancerTypeClinicalData, fetchOncoKbAnnotatedGenesSuppressErrors, concatMutationData
 } from "shared/lib/StoreUtils";
 import {indexHotspotsData, fetchHotspotsData} from "shared/lib/CancerHotspotsUtils";
 import {stringListToSet} from "../../../shared/lib/StringUtils";
 import {Gene as OncoKbGene} from "../../../shared/api/generated/OncoKbAPI";
 import {MutationTableDownloadDataFetcher} from "shared/lib/MutationTableDownloadDataFetcher";
+import { VariantAnnotation } from 'shared/api/generated/GenomeNexusAPI';
+import { fetchVariantAnnotationsIndexedByGenomicLocation } from 'shared/lib/MutationAnnotator';
 
 type PageMode = 'patient' | 'sample';
 
@@ -267,6 +268,19 @@ export class PatientViewPageStore {
         invoke: async () => fetchMutSigData(this.studyId)
     });
 
+    // Mutation annotation
+    // genome nexus
+    readonly indexedVariantAnnotations = remoteData<{[genomicLocation: string]: VariantAnnotation} | undefined>({
+        await:()=>[
+            this.mutationData,
+            this.uncalledMutationData,
+        ],
+        invoke: async () => await fetchVariantAnnotationsIndexedByGenomicLocation(concatMutationData(this.mutationData, this.uncalledMutationData), ["annotation_summary", "hotspots"], AppConfig.isoformOverrideSource),
+        onError: (err: Error) => {
+            // fail silently, leave the error handling responsibility to the data consumer
+        }
+    }, undefined);
+
     readonly hotspotData = remoteData({
         await: ()=> [
             this.mutationData,
@@ -654,10 +668,6 @@ export class PatientViewPageStore {
         return new OncoKbEvidenceCache();
     }
 
-    @cached get genomeNexusEnrichmentCache() {
-        return new GenomeNexusEnrichmentCache();
-    }
-
     @cached get pubMedCache() {
         return new PubMedCache();
     }
@@ -675,7 +685,7 @@ export class PatientViewPageStore {
     }
 
     @cached get downloadDataFetcher() {
-        return new MutationTableDownloadDataFetcher(this.mutationData, () => this.genomeNexusEnrichmentCache);
+        return new MutationTableDownloadDataFetcher(this.mutationData);
     }
 
     @action setActiveTabId(id: string) {

src/pages/resultsView/ResultsViewPageStore.ts

@@ -15,7 +15,6 @@ import PubMedCache from "shared/cache/PubMedCache";
 import CancerTypeCache from "shared/cache/CancerTypeCache";
 import MutationCountCache from "shared/cache/MutationCountCache";
 import DiscreteCNACache from "shared/cache/DiscreteCNACache";
-import GenomeNexusEnrichmentCache from "shared/cache/GenomeNexusEnrichment";
 import PdbHeaderCache from "shared/cache/PdbHeaderCache";
 import {
     findMolecularProfileIdDiscrete, fetchMyCancerGenomeData,
@@ -83,6 +82,8 @@ import url from 'url';
 import OncoprintClinicalDataCache, {SpecialAttribute} from "../../shared/cache/OncoprintClinicalDataCache";
 import {getProteinPositionFromProteinChange} from "../../shared/lib/ProteinChangeUtils";
 import {isMutation} from "../../shared/lib/CBioPortalAPIUtils";
+import { fetchVariantAnnotationsIndexedByGenomicLocation } from "shared/lib/MutationAnnotator";
+import { VariantAnnotation } from "shared/api/generated/GenomeNexusAPI";
 
 type Optional<T> = (
     {isApplicable: true, value: T}
@@ -1205,14 +1206,14 @@ export class ResultsViewPageStore {
                         this.samples,
                         this.oncoKbAnnotatedGenes.result || {},
                         () => this.mutationsByGene[gene.hugoGeneSymbol],
-                        () => (this.genomeNexusEnrichmentCache),
                         () => (this.mutationCountCache),
                         this.studyIdToStudy,
                         this.molecularProfileIdToMolecularProfile,
                         this.clinicalDataForSamples,
                         this.studiesForSamplesWithoutCancerTypeClinicalData,
                         this.germlineConsentedSamples,
                         this.indexedHotspotData,
+                        this.indexedVariantAnnotations,
                         this.uniqueSampleKeyToTumorType.result!,
                         this.oncoKbData
                     );
@@ -1865,6 +1866,17 @@ export class ResultsViewPageStore {
     });
 
     // Mutation annotation
+    // genome nexus
+    readonly indexedVariantAnnotations = remoteData<{[genomicLocation: string]: VariantAnnotation} | undefined>({
+        await:()=>[
+            this.mutations
+        ],
+        invoke: async () => this.mutations.result? await fetchVariantAnnotationsIndexedByGenomicLocation(this.mutations.result, ["annotation_summary", "hotspots"], AppConfig.isoformOverrideSource) : undefined,
+        onError: (err: Error) => {
+            // fail silently, leave the error handling responsibility to the data consumer
+        }
+    }, undefined);
+
     // Hotspots
     readonly hotspotData = remoteData({
         await:()=>[
@@ -2324,10 +2336,6 @@ export class ResultsViewPageStore {
         return new DiscreteCNACache(this.studyToMolecularProfileDiscrete.result);
     }
 
-    @cached get genomeNexusEnrichmentCache() {
-        return new GenomeNexusEnrichmentCache();
-    }
-
     @cached get cancerTypeCache() {
         return new CancerTypeCache();
     }

src/pages/resultsView/coExpression/CoExpressionPlot.tsx

@@ -23,6 +23,7 @@ import Timer = NodeJS.Timer;
 import DownloadControls from "../../../shared/components/downloadControls/DownloadControls";
 import {axisLabel, isNotProfiled} from "./CoExpressionPlotUtils";
 import _ from "lodash";
+import {scatterPlotSize} from "../../../shared/components/plots/PlotUtils";
 
 type GeneId = { hugoGeneSymbol:string, entrezGeneId: number, cytoband:string};
 
@@ -219,6 +220,7 @@ export default class CoExpressionPlot extends React.Component<ICoExpressionPlotP
                 svgId={SVG_ID}
                 title={this.title}
                 data={this.data}
+                size={scatterPlotSize}
                 chartWidth={this.props.width}
                 chartHeight={this.props.height}
                 stroke={this.stroke}

src/pages/resultsView/expression/ExpressionWrapper.tsx

@@ -32,7 +32,7 @@ import {
     CNA_STROKE_WIDTH,
     getCnaQueries, IBoxScatterPlotPoint, INumberAxisData, IScatterPlotData, IScatterPlotSampleData, IStringAxisData,
     makeBoxScatterPlotData, makeScatterPlotPointAppearance,
-    mutationRenderPriority, MutationSummary, mutationSummaryToAppearance, scatterPlotLegendData, scatterPlotSize,
+    mutationRenderPriority, MutationSummary, mutationSummaryToAppearance, scatterPlotLegendData,
     scatterPlotTooltip, boxPlotTooltip, scatterPlotZIndexSortBy
 } from "../plots/PlotsTabUtils";
 import {getOncoprintMutationType} from "../../../shared/components/oncoprint/DataUtils";
@@ -48,6 +48,7 @@ import BoxScatterPlot from "../../../shared/components/plots/BoxScatterPlot";
 import {ViewType} from "../plots/PlotsTab";
 import DownloadControls from "../../../shared/components/downloadControls/DownloadControls";
 import {maxPage} from "../../../shared/components/lazyMobXTable/utils";
+import {scatterPlotSize} from "../../../shared/components/plots/PlotUtils";
 
 export interface ExpressionWrapperProps {
     store:ResultsViewPageStore;
@@ -276,7 +277,7 @@ export default class ExpressionWrapper extends React.Component<ExpressionWrapper
             } else {
                 return Promise.resolve(_.sortBy<any>(sortedData, d=>{
                     //Note: we have to use slice to convert Seamless immutable array to real array, otherwise jStat chokes
-                    return jStat.median(Array.prototype.slice((d.data.map((v:any)=>(v.value as number)))));
+                    return jStat.median(Array.prototype.slice.apply((d.data.map((v:any)=>(v.value as number)))));
                 }));
             }
         }

src/pages/resultsView/mutation/Mutations.tsx

@@ -81,7 +81,6 @@ export default class Mutations extends React.Component<IMutationsPageProps, {}>
                         <ResultsViewMutationMapper
                             store={mutationMapperStore}
                             discreteCNACache={this.props.store.discreteCNACache}
-                            genomeNexusEnrichmentCache={this.props.store.genomeNexusEnrichmentCache}
                             oncoKbEvidenceCache={this.props.store.oncoKbEvidenceCache}
                             pubMedCache={this.props.store.pubMedCache}
                             cancerTypeCache={this.props.store.cancerTypeCache}

src/pages/resultsView/mutation/ResultsViewMutationMapper.tsx

@@ -58,7 +58,6 @@ export default class ResultsViewMutationMapper extends MutationMapper<IResultsVi
                 oncoKbAnnotatedGenes={this.props.store.oncoKbAnnotatedGenes}
                 discreteCNACache={this.props.discreteCNACache}
                 studyIdToStudy={this.props.store.studyIdToStudy.result}
-                genomeNexusEnrichmentCache={this.props.genomeNexusEnrichmentCache}
                 molecularProfileIdToMolecularProfile={this.props.store.molecularProfileIdToMolecularProfile.result}
                 oncoKbEvidenceCache={this.props.oncoKbEvidenceCache}
                 pubMedCache={this.props.pubMedCache}
@@ -68,6 +67,7 @@ export default class ResultsViewMutationMapper extends MutationMapper<IResultsVi
                 downloadDataFetcher={this.props.store.downloadDataFetcher}
                 myCancerGenomeData={this.props.myCancerGenomeData}
                 hotspotData={this.props.store.indexedHotspotData}
+                indexedVariantAnnotations={this.props.store.indexedVariantAnnotations}
                 cosmicData={this.props.store.cosmicData.result}
                 oncoKbData={this.props.store.oncoKbData}
                 civicGenes={this.props.store.civicGenes}

src/pages/resultsView/mutation/ResultsViewMutationMapperStore.ts

@@ -10,10 +10,10 @@ import {
     fetchCosmicData, fetchCivicGenes, fetchCivicVariants
 } from "shared/lib/StoreUtils";
 import {IMutationMapperConfig} from "shared/components/mutationMapper/MutationMapper";
-import GenomeNexusEnrichmentCache from "shared/cache/GenomeNexusEnrichment";
 import MutationCountCache from "shared/cache/MutationCountCache";
 import {MutationTableDownloadDataFetcher} from "shared/lib/MutationTableDownloadDataFetcher";
 import MutationMapperStore from "shared/components/mutationMapper/MutationMapperStore";
+import { VariantAnnotation } from "shared/api/generated/GenomeNexusAPI";
 
 export default class ResultsViewMutationMapperStore extends MutationMapperStore
 {
@@ -29,14 +29,14 @@ export default class ResultsViewMutationMapperStore extends MutationMapperStore
                 // (which will be done in the getter thats passed in here) so that the cache itself is observable
                 // and we will react when it changes to a new object.
                 getMutations:()=>Mutation[],
-                protected genomeNexusEnrichmentCache: ()=>GenomeNexusEnrichmentCache,
                 private getMutationCountCache: ()=>MutationCountCache,
                 public studyIdToStudy:MobxPromise<{[studyId:string]:CancerStudy}>,
                 public molecularProfileIdToMolecularProfile:MobxPromise<{[molecularProfileId:string]:MolecularProfile}>,
                 public clinicalDataForSamples: MobxPromise<ClinicalData[]>,
                 public studiesForSamplesWithoutCancerTypeClinicalData: MobxPromise<CancerStudy[]>,
                 public germlineConsentedSamples:MobxPromise<SampleIdentifier[]>,
                 public indexedHotspotData:MobxPromise<IHotspotIndex|undefined>,
+                public indexedVariantAnnotations:MobxPromise<{[genomicLocation: string]: VariantAnnotation}|undefined>,
                 public uniqueSampleKeyToTumorType:{[uniqueSampleKey:string]:string},
                 public oncoKbData:IOncoKbDataWrapper)
     {
@@ -45,10 +45,10 @@ export default class ResultsViewMutationMapperStore extends MutationMapperStore
             gene,
             getMutations,
             indexedHotspotData,
+            indexedVariantAnnotations,
             oncoKbAnnotatedGenes,
             oncoKbData,
-            uniqueSampleKeyToTumorType,
-            genomeNexusEnrichmentCache,
+            uniqueSampleKeyToTumorType
         );
 
         labelMobxPromises(this);
@@ -91,6 +91,6 @@ export default class ResultsViewMutationMapperStore extends MutationMapperStore
     }, undefined);
 
     @cached get downloadDataFetcher(): MutationTableDownloadDataFetcher {
-        return new MutationTableDownloadDataFetcher(this.mutationData, this.genomeNexusEnrichmentCache, this.getMutationCountCache);
+        return new MutationTableDownloadDataFetcher(this.mutationData, this.getMutationCountCache);
     }
 }

src/pages/resultsView/plots/PlotsTab.tsx

@@ -15,7 +15,7 @@ import {
     makeBoxScatterPlotData, IScatterPlotSampleData, noMutationAppearance, IBoxScatterPlotPoint, boxPlotTooltip,
     getCnaQueries, getMutationQueries, getScatterPlotDownloadData, getBoxPlotDownloadData, getTablePlotDownloadData,
     mutationRenderPriority, mutationSummaryRenderPriority, MutationSummary, mutationSummaryToAppearance,
-    CNA_STROKE_WIDTH, scatterPlotSize, PLOT_SIDELENGTH, CLIN_ATTR_DATA_TYPE,
+    CNA_STROKE_WIDTH, PLOT_SIDELENGTH, CLIN_ATTR_DATA_TYPE,
     sortMolecularProfilesForDisplay, scatterPlotZIndexSortBy
 } from "./PlotsTabUtils";
 import {
@@ -40,6 +40,7 @@ import {logicalOr} from "../../../shared/lib/LogicUtils";
 import {SpecialAttribute} from "../../../shared/cache/OncoprintClinicalDataCache";
 import OqlStatusBanner from "../../../shared/components/oqlStatusBanner/OqlStatusBanner";
 import ScrollBar from "../../../shared/components/Scrollbar/ScrollBar";
+import {scatterPlotSize} from "../../../shared/components/plots/PlotUtils";
 
 enum EventKey {
     horz_logScale,

src/pages/resultsView/plots/PlotsTabUtils.tsx

@@ -184,20 +184,6 @@ export function scatterPlotZIndexSortBy<D extends Pick<IScatterPlotSampleData, "
     return sortBy;
 }
 
-export function scatterPlotSize(
-    d:IScatterPlotSampleData,
-    active:boolean,
-    isHighlighted:boolean
-) {
-    if (isHighlighted) {
-        return 8;
-    } else if (active) {
-        return 6;
-    } else {
-        return 4;
-    }
-}
-
 export function scatterPlotLegendData(
     data:IScatterPlotSampleData[],
     viewType:ViewType,

src/pages/tools/mutationMapper/MutationMapperTool.tsx

@@ -318,7 +318,6 @@ export default class MutationMapperTool extends React.Component<IMutationMapperT
                             oncoKbEvidenceCache={this.store.oncoKbEvidenceCache}
                             pubMedCache={this.store.pubMedCache}
                             pdbHeaderCache={this.store.pdbHeaderCache}
-                            genomeNexusEnrichmentCache={this.store.genomeNexusEnrichmentCache}
                             myCancerGenomeData={this.store.myCancerGenomeData}
                             config={AppConfig}
                         />

src/pages/tools/mutationMapper/MutationMapperToolStore.ts

@@ -20,7 +20,6 @@ import {fetchHotspotsData, indexHotspotsData} from "shared/lib/CancerHotspotsUti
 import {IHotspotIndex} from "shared/model/CancerHotspots";
 import OncoKbEvidenceCache from "shared/cache/OncoKbEvidenceCache";
 import PubMedCache from "shared/cache/PubMedCache";
-import GenomeNexusEnrichmentCache from "shared/cache/GenomeNexusEnrichment";
 import PdbHeaderCache from "shared/cache/PdbHeaderCache";
 import MutationMapperStore from "shared/components/mutationMapper/MutationMapperStore";
 import { VariantAnnotation, EnsemblTranscript } from "shared/api/generated/GenomeNexusAPI";
@@ -130,7 +129,7 @@ export default class MutationMapperToolStore
     }, []);
 
     readonly indexedVariantAnnotations = remoteData<{[genomicLocation: string]: VariantAnnotation} | undefined>({
-        invoke: async () => await fetchVariantAnnotationsIndexedByGenomicLocation(this.rawMutations, AppConfig.isoformOverrideSource),
+        invoke: async () => await fetchVariantAnnotationsIndexedByGenomicLocation(this.rawMutations, ["annotation_summary","hotspots"], AppConfig.isoformOverrideSource),
         onError: (err: Error) => {
             this.criticalErrors.push(err);
         }
@@ -182,10 +181,10 @@ export default class MutationMapperToolStore
                         gene,
                         getMutations,
                         this.indexedHotspotData,
+                        this.indexedVariantAnnotations,
                         this.oncoKbAnnotatedGenes.result || {},
                         this.oncoKbData,
                         this.uniqueSampleKeyToTumorType.result || {},
-                        () => (this.genomeNexusEnrichmentCache),
                     );
                     return map;
                 }, {}));
@@ -229,10 +228,6 @@ export default class MutationMapperToolStore
         return new PubMedCache();
     }
 
-    @cached get genomeNexusEnrichmentCache() {
-        return new GenomeNexusEnrichmentCache();
-    }
-
     @cached get pdbHeaderCache() {
         return new PdbHeaderCache();
     }

src/pages/tools/mutationMapper/StandaloneMutationMapper.tsx

@@ -19,7 +19,7 @@ export default class StandaloneMutationMapper extends MutationMapper<IMutationMa
             <StandaloneMutationTable
                 uniqueSampleKeyToTumorType={this.props.store.uniqueSampleKeyToTumorType}
                 oncoKbAnnotatedGenes={this.props.store.oncoKbAnnotatedGenes}
-                genomeNexusEnrichmentCache={this.props.genomeNexusEnrichmentCache}
+                indexedVariantAnnotations={this.props.store.indexedVariantAnnotations}
                 oncoKbEvidenceCache={this.props.oncoKbEvidenceCache}
                 pubMedCache={this.props.pubMedCache}
                 dataStore={this.props.store.dataStore}