Made the transcript summary URL configurable in the mutations tab

package.json

@@ -192,7 +192,7 @@
     "react-markdown": "^3.4.1",
     "react-mfb": "^0.6.0",
     "react-motion": "^0.4.7",
-    "react-mutation-mapper": "^0.3.0",
+    "react-mutation-mapper": "^0.3.1",
     "react-overlays": "0.7.4",
     "react-portal": "^4.2.0",
     "react-rangeslider": "^2.1.0",

src/config/IAppConfig.ts

@@ -99,6 +99,7 @@ export interface IServerConfig {
     default_cross_cancer_study_session_id: string | null;
     study_view: StudyView;
     uniprot_id_url: string | null;
+    ensembl_transcript_url: string | null;
     studiesWithGermlineConsentedSamples: string[] | undefined;
     mdacc_heatmap_study_meta_url: string | null;
     mdacc_heatmap_study_url: string | null;

src/config/serverConfigDefaults.ts

@@ -152,6 +152,9 @@ const ServerConfigDefaults: Partial<IServerConfig> = {
     uniprot_id_url:
         'https://www.uniprot.org/uniprot/?query=accession:<%= swissProtAccession %>&format=tab&columns=entry+name',
 
+    ensembl_transcript_url:
+        'http://grch37.ensembl.org/homo_sapiens/Transcript/Summary?t=<%= transcriptId %>',
+
     query_product_limit: 1000000,
 
     skin_show_gsva: false,

src/pages/resultsView/mutation/Mutations.tsx

@@ -3,6 +3,7 @@ import {observer} from "mobx-react";
 import {MSKTabs, MSKTab} from "shared/components/MSKTabs/MSKTabs";
 import {ResultsViewPageStore} from "../ResultsViewPageStore";
 import ResultsViewMutationMapper from "./ResultsViewMutationMapper";
+import {convertToMutationMapperProps} from "shared/components/mutationMapper/MutationMapperConfig";
 import MutationMapperUserSelectionStore from "shared/components/mutationMapper/MutationMapperUserSelectionStore";
 import {observable} from "mobx";
 import AppConfig from 'appConfig';
@@ -108,6 +109,7 @@ export default class Mutations extends React.Component<IMutationsPageProps, {}>
                             />
                         </div>
                         <ResultsViewMutationMapper
+                            {...convertToMutationMapperProps(AppConfig.serverConfig)}
                             store={mutationMapperStore}
                             trackVisibility={this.userSelectionStore.trackVisibility}
                             discreteCNACache={this.props.store.discreteCNACache}
@@ -119,7 +121,6 @@ export default class Mutations extends React.Component<IMutationsPageProps, {}>
                             genomeNexusMyVariantInfoCache={this.props.store.genomeNexusMyVariantInfoCache}
                             pdbHeaderCache={this.props.store.pdbHeaderCache}
                             myCancerGenomeData={this.props.store.myCancerGenomeData}
-                            config={AppConfig.serverConfig}
                             userEmailAddress={this.props.appStore.userName!}
                         />
                     </MSKTab>

src/pages/resultsView/mutation/ResultsViewMutationMapper.tsx

@@ -105,11 +105,11 @@ export default class ResultsViewMutationMapper extends MutationMapper<IResultsVi
                 civicGenes={this.props.store.civicGenes}
                 civicVariants={this.props.store.civicVariants}
                 userEmailAddress={this.props.userEmailAddress}
-                enableOncoKb={this.props.config.show_oncokb}
-                enableFunctionalImpact={this.props.config.show_genomenexus}
-                enableHotspot={this.props.config.show_hotspot}
-                enableMyCancerGenome={this.props.config.mycancergenome_show}
-                enableCivic={this.props.config.show_civic}
+                enableOncoKb={this.props.enableOncoKb}
+                enableFunctionalImpact={this.props.enableGenomeNexus}
+                enableHotspot={this.props.enableHotspot}
+                enableMyCancerGenome={this.props.enableMyCancerGenome}
+                enableCivic={this.props.enableCivic}
                 totalNumberOfExons={this.totalExonNumber}
             />
         );

src/pages/staticPages/tools/mutationMapper/MutationMapperTool.tsx

@@ -1,22 +1,22 @@
 import * as React from 'react';
 import { inject, observer } from "mobx-react";
 import {action, computed, observable} from "mobx";
-import {bind} from "bind-decorator";
+import autobind from 'autobind-decorator';
 import {Collapse} from 'react-collapse';
 import {ControlLabel, FormControl, FormGroup} from "react-bootstrap";
 import {PageLayout} from "shared/components/PageLayout/PageLayout";
 import Helmet from "react-helmet";
 
 import Loader from "shared/components/loadingIndicator/LoadingIndicator";
 import {MSKTab, MSKTabs} from "shared/components/MSKTabs/MSKTabs";
+import {convertToMutationMapperProps} from "shared/components/mutationMapper/MutationMapperConfig";
 import MutationMapperUserSelectionStore from "shared/components/mutationMapper/MutationMapperUserSelectionStore";
 import {parseInput} from "shared/lib/MutationInputParser";
 
 import StandaloneMutationMapper from "./StandaloneMutationMapper";
 import MutationMapperToolStore from "./MutationMapperToolStore";
 
 import AppConfig from "appConfig";
-import autobind from 'autobind-decorator';
 
 interface IMutationMapperToolProps {
     routing: any;
@@ -374,6 +374,7 @@ export default class MutationMapperTool extends React.Component<IMutationMapperT
                 tabs.push(
                     <MSKTab key={gene} id={gene} linkText={gene}>
                         <StandaloneMutationMapper
+                            {...convertToMutationMapperProps(AppConfig.serverConfig)}
                             store={mutationMapperStore}
                             trackVisibility={this.userSelectionStore.trackVisibility}
                             downloadDataFetcher={this.store.downloadDataFetcher}
@@ -382,7 +383,6 @@ export default class MutationMapperTool extends React.Component<IMutationMapperT
                             pubMedCache={this.store.pubMedCache}
                             pdbHeaderCache={this.store.pdbHeaderCache}
                             myCancerGenomeData={this.store.myCancerGenomeData}
-                            config={AppConfig.serverConfig}
                             showTranscriptDropDown={true}
                             showOnlyAnnotatedTranscriptsInDropdown={!this.store.hasInputWithProteinChanges}
                         />
@@ -394,7 +394,7 @@ export default class MutationMapperTool extends React.Component<IMutationMapperT
         return tabs;
     }
 
-    @bind
+    @autobind
     @action
     protected handleFileSelect(e: any)
     {
@@ -411,7 +411,7 @@ export default class MutationMapperTool extends React.Component<IMutationMapperT
         }
     }
 
-    @bind
+    @autobind
     @action
     protected fileLoadEndHandler(e: any)
     {
@@ -424,14 +424,14 @@ export default class MutationMapperTool extends React.Component<IMutationMapperT
         }
     }
 
-    @bind
+    @autobind
     @action
     protected handleInputChange(e: any)
     {
         this.inputText = e.target.value;
     }
 
-    @bind
+    @autobind
     @action
     protected handleTabChange(id: string|undefined) {
         // update the hash if routing exits
@@ -444,7 +444,7 @@ export default class MutationMapperTool extends React.Component<IMutationMapperT
         }
     }
 
-    @bind
+    @autobind
     @action
     protected handleModifyInput()
     {
@@ -455,7 +455,7 @@ export default class MutationMapperTool extends React.Component<IMutationMapperT
         this.inputControlsVisible = true;
     }
 
-    @bind
+    @autobind
     @action
     protected handleVisualize()
     {
@@ -471,31 +471,31 @@ export default class MutationMapperTool extends React.Component<IMutationMapperT
         this.inputControlsVisible = false;
     }
 
-    @bind
+    @autobind
     @action
     protected handleDataFormatToggle()
     {
         this.dataFormatCollapsed = !this.dataFormatCollapsed;
     }
 
-    @bind
+    @autobind
     @action
     protected handleLoadExamplePartiallyAnnotated()
     {
         this.inputText = require('raw-loader!./resources/standaloneMutationDataExample.txt');
     }
 
-    @bind
+    @autobind
     @action
     protected handleLoadExampleGenomicCoordinates()
     {
         this.inputText = require('raw-loader!./resources/standaloneMutationDataExampleWithGenomicCoordinatesOnly.txt');
     }
 
-    @bind
+    @autobind
     @action
     protected handleLoadExampleGeneAndProteinChange()
     {
         this.inputText = require('raw-loader!./resources/standaloneMutationDataExampleWithGeneAndProteinChangeOnly.txt');
     }
-}
+}

src/pages/staticPages/tools/mutationMapper/StandaloneMutationMapper.tsx

@@ -34,10 +34,10 @@ export default class StandaloneMutationMapper extends MutationMapper<IStandalone
                 myCancerGenomeData={this.props.myCancerGenomeData}
                 hotspotData={this.props.store.indexedHotspotData}
                 oncoKbData={this.props.store.oncoKbData}
-                enableOncoKb={this.props.config.show_oncokb}
-                enableFunctionalImpact={this.props.config.show_genomenexus}
-                enableHotspot={this.props.config.show_hotspot}
-                enableMyCancerGenome={this.props.config.mycancergenome_show}
+                enableOncoKb={this.props.enableOncoKb}
+                enableFunctionalImpact={this.props.enableGenomeNexus}
+                enableHotspot={this.props.enableHotspot}
+                enableMyCancerGenome={this.props.enableMyCancerGenome}
                 enableCivic={false}
             />
         );

src/shared/components/mutationMapper/MutationMapper.tsx

@@ -35,19 +35,6 @@ import WindowStore from "../window/WindowStore";
 
 import styles from "./mutationMapper.module.scss";
 
-export interface IMutationMapperConfig {
-    show_oncokb?: boolean;
-    show_genomenexus?: boolean;
-    show_hotspot?: boolean;
-    mycancergenome_show?: boolean;
-    show_civic?: boolean;
-    isoformOverrideSource?: string;
-    mygene_info_url: string | null;
-    uniprot_id_url: string | null;
-    genomenexus_url: string | null;
-    oncokb_public_api_url: string | null;
-}
-
 export interface IMutationMapperProps {
     store: MutationMapperStore;
     trackVisibility?: TrackVisibility;
@@ -56,19 +43,28 @@ export interface IMutationMapperProps {
     showPlotDownloadControls?: boolean;
     mutationTable?: JSX.Element;
     pubMedCache?: PubMedCache;
-    genomeNexusUrl?: string;
     showTranscriptDropDown?: boolean;
     showOnlyAnnotatedTranscriptsInDropdown?: boolean;
     filterMutationsBySelectedTranscript?: boolean;
-    isoformOverrideSource?: string;
     mainLoadingIndicator?: JSX.Element;
     geneSummaryLoadingIndicator?: JSX.Element;
-    config: IMutationMapperConfig;
     studyId?: string;
     myCancerGenomeData?: IMyCancerGenomeData;
     pdbHeaderCache?: PdbHeaderCache;
     oncoKbEvidenceCache?:OncoKbEvidenceCache;
     genomeNexusCache?:GenomeNexusCache;
+    // server config properties
+    genomeNexusUrl?: string;
+    oncoKbPublicApiUrl?: string;
+    isoformOverrideSource?: string;
+    myGeneInfoUrlTemplate?: string;
+    uniprotIdUrlTemplate?: string;
+    transcriptSummaryUrlTemplate?: string;
+    enableOncoKb?: boolean;
+    enableGenomeNexus?: boolean;
+    enableHotspot?: boolean;
+    enableMyCancerGenome?: boolean;
+    enableCivic?: boolean;
 }
 
 @observer

src/shared/components/mutationMapper/MutationMapperConfig.ts

@@ -0,0 +1,33 @@
+import {IMutationMapperProps} from "./MutationMapper";
+
+// This is a subset of IServerConfig containing config values used only in Mutation Mapper
+export interface IMutationMapperConfig {
+    show_oncokb?: boolean;
+    show_genomenexus?: boolean;
+    show_hotspot?: boolean;
+    mycancergenome_show?: boolean;
+    show_civic?: boolean;
+    isoformOverrideSource?: string;
+    mygene_info_url: string | null;
+    uniprot_id_url: string | null;
+    ensembl_transcript_url: string | null;
+    genomenexus_url: string | null;
+    oncokb_public_api_url: string | null;
+}
+
+export function convertToMutationMapperProps(config: IMutationMapperConfig): Partial<IMutationMapperProps>
+{
+    return {
+        genomeNexusUrl: config.genomenexus_url || undefined,
+        oncoKbPublicApiUrl: config.oncokb_public_api_url || undefined,
+        isoformOverrideSource: config.isoformOverrideSource,
+        myGeneInfoUrlTemplate: config.mygene_info_url || undefined,
+        uniprotIdUrlTemplate: config.uniprot_id_url || undefined,
+        transcriptSummaryUrlTemplate: config.ensembl_transcript_url || undefined,
+        enableOncoKb: config.show_oncokb,
+        enableGenomeNexus: config.show_genomenexus,
+        enableHotspot: config.show_hotspot,
+        enableMyCancerGenome: config.mycancergenome_show,
+        enableCivic: config.show_civic
+    };
+}

src/shared/components/mutationMapper/MutationMapperStore.ts

@@ -41,7 +41,7 @@ import {
 } from "shared/lib/MutationUtils";
 import {defaultOncoKbIndicatorFilter} from "shared/lib/OncoKbUtils";
 
-import {IMutationMapperConfig} from "./MutationMapper";
+import {IMutationMapperConfig} from "./MutationMapperConfig";
 import autobind from "autobind-decorator";
 import {normalizeMutation, normalizeMutations} from "./MutationMapperUtils";
 

yarn.lock

@@ -12623,10 +12623,10 @@ react-motion@^0.5.2:
     prop-types "^15.5.8"
     raf "^3.1.0"
 
-react-mutation-mapper@^0.3.0:
-  version "0.3.0"
-  resolved "https://registry.yarnpkg.com/react-mutation-mapper/-/react-mutation-mapper-0.3.0.tgz#145db33bbfd29a112d36a7f425e565247c37e6d5"
-  integrity sha512-H1mX5awL9bS8/9x9ARxz7fHp8MxclexGq/I8Bimkn8+y1bv2mgi7ubLtNjcAqAMpqyMqm8Jw0lb0tyhvaK9LaQ==
+react-mutation-mapper@^0.3.1:
+  version "0.3.1"
+  resolved "https://registry.yarnpkg.com/react-mutation-mapper/-/react-mutation-mapper-0.3.1.tgz#a7cb97b5babd2f8001f74b927c3b986ff5f1085e"
+  integrity sha512-4eNNt7IPJTsbIzJrPiL471wIvGiG8xGG2lWqwld+TYOK8C7cqcit4BOjz7mkngPLix/CcanflPQQnnH/cCtDsg==
   dependencies:
     autobind-decorator "^2.4.0"
     cbioportal-frontend-commons "^0.0.23"