Impl. heatmap tracks for treatment profiles and treatment selection menu

end-to-end-test/local/specs/treatment.screenshot.spec.js

@@ -0,0 +1,42 @@
+var assert = require('assert');
+var goToUrlAndSetLocalStorage = require('../../shared/specUtils').goToUrlAndSetLocalStorage;
+var assertScreenShotMatch = require('../../shared/lib/testUtils').assertScreenShotMatch;
+var waitForOncoprint = require('../../shared/specUtils').waitForOncoprint;
+var selectReactSelectOption =  require('../../shared/specUtils').selectReactSelectOption;
+var oncoprintTabUrl = require('./treatment.spec').oncoprintTabUrl;
+var openHeatmapMenu = require('./treatment.spec').openHeatmapMenu;
+
+describe('treatment feature', () => {
+
+    describe('oncoprint tab', () => {
+
+        beforeEach(()=>{
+            goToUrlAndSetLocalStorage(oncoprintTabUrl);
+            waitForOncoprint();
+        });
+
+            it('shows treatment profile heatmap track for treatment', () => {
+                openHeatmapMenu();
+                selectReactSelectOption( $('.oncoprint__controls__heatmap_menu'), 'IC50 values of compounds on cellular phenotype readout');
+                $('.oncoprint__controls__heatmap_menu textarea').setValue('17-AAG');
+                $('div.icon-area div.icon').waitForExist();
+                $('button=Add Treatments to Heatmap').click();
+                openHeatmapMenu();
+                waitForOncoprint();
+                var res = browser.checkElement('[id=oncoprintDiv]');
+                assertScreenShotMatch(res);
+            });
+
+            it('selects treatment in treatment select box when icon present', () => {
+                openHeatmapMenu();
+                selectReactSelectOption( $('.oncoprint__controls__heatmap_menu'), 'IC50 values of compounds on cellular phenotype readout');
+                $('.oncoprint__controls__heatmap_menu textarea').setValue('17-AAG');
+                $('div.icon-area div.icon').waitForExist();
+                $('.treatment-selector .Select-control').click();
+                var res = browser.checkElement('.Select-option*=17-AAG');
+                assertScreenShotMatch(res);
+            });
+
+    });
+
+});

end-to-end-test/local/specs/treatment.spec.js

@@ -0,0 +1,134 @@
+var assert = require('assert');
+var goToUrlAndSetLocalStorage = require('../../shared/specUtils').goToUrlAndSetLocalStorage;
+var waitForOncoprint = require('../../shared/specUtils').waitForOncoprint;
+var reactSelectOption =  require('../../shared/specUtils').reactSelectOption;
+var getReactSelectOptions =  require('../../shared/specUtils').getReactSelectOptions;
+var selectReactSelectOption =  require('../../shared/specUtils').selectReactSelectOption;
+var useExternalFrontend = require('../../shared/specUtils').useExternalFrontend;
+
+const CBIOPORTAL_URL = process.env.CBIOPORTAL_URL.replace(/\/$/, "");
+const oncoprintTabUrl = CBIOPORTAL_URL+'/results/oncoprint?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=study_es_0&case_set_id=study_es_0_all&clinicallist=NUM_SAMPLES_PER_PATIENT%2CPROFILED_IN_study_es_0_mutations%2CPROFILED_IN_study_es_0_gistic&data_priority=0&gene_list=CDKN2A%2520MDM2%2520MDM4%2520TP53&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=study_es_0_gistic&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=study_es_0_mutations&show_samples=false&tab_index=tab_visualize'
+
+describe('treatment feature', function() {
+
+    this.retries(2);
+
+    if (useExternalFrontend) {
+
+        describe('oncoprint tab', () => {
+
+            beforeEach(()=>{
+                goToUrlAndSetLocalStorage(oncoprintTabUrl);
+                waitForOncoprint();
+            });
+
+            it('shows treatment data type option in heatmap menu', () => {
+                openHeatmapMenu();
+                assert( reactSelectOption( $('.oncoprint__controls__heatmap_menu'), 'EC50 values of compounds on cellular phenotype readout') );
+                assert( reactSelectOption( $('.oncoprint__controls__heatmap_menu'), 'IC50 values of compounds on cellular phenotype readout') );
+            });
+
+            it('shows treatment text area box in heatmap menu when treatment data type is selected', () => {
+                openHeatmapMenu();
+                selectReactSelectOption( $('.oncoprint__controls__heatmap_menu'), 'IC50 values of compounds on cellular phenotype readout');
+                assert( $('.oncoprint__controls__heatmap_menu.text-icon-area') );
+            });
+
+            it('does not show genes of gene text area in treatment text area,and vice versa', () => {
+                openHeatmapMenu();
+                var geneText =  $('.oncoprint__controls__heatmap_menu textarea').getText();
+                selectReactSelectOption( $('.oncoprint__controls__heatmap_menu'), 'IC50 values of compounds on cellular phenotype readout');
+                var treatmentText =  $('.oncoprint__controls__heatmap_menu textarea').getText();
+                assert.notEqual(geneText, treatmentText);
+                selectReactSelectOption( $('.oncoprint__controls__heatmap_menu'), 'mRNA expression (microarray) Z-Score normalized');
+                assert.equal($('.oncoprint__controls__heatmap_menu textarea').getText(), geneText);
+            });
+
+            it('shows treatment selection box in heatmap menu when treatment data type is selected', () => {
+                openHeatmapMenu();
+                selectReactSelectOption( $('.oncoprint__controls__heatmap_menu'), 'IC50 values of compounds on cellular phenotype readout');
+                assert(  $('.oncoprint__controls__heatmap_menu.treatment-selector') );
+            });
+
+            it('adds icon when entering a valid treatment in treatment text area', () => {
+                openHeatmapMenu();
+                selectReactSelectOption( $('.oncoprint__controls__heatmap_menu'), 'IC50 values of compounds on cellular phenotype readout');
+                $('.oncoprint__controls__heatmap_menu textarea').setValue('17-AAG');
+                $('div.icon*=17-AAG').waitForExist();
+                assert( $('div.icon*=17-AAG') );
+            });
+
+            it('click of icon remove button removes icon', () => {
+                openHeatmapMenu();
+                selectReactSelectOption( $('.oncoprint__controls__heatmap_menu'), 'IC50 values of compounds on cellular phenotype readout');
+                $('.oncoprint__controls__heatmap_menu textarea').setValue('17-AAG');
+                $('div.icon-area div.icon').waitForExist();
+                var iconButton = $('div.icon-area div.icon-button');
+                iconButton.click();
+                $('div.icon-area div.icon').waitForExist(undefined, true);
+                assert( ! $('div.icon-area div.icon').isExisting() );
+            });
+
+            it('removes valid treatment from treatment text area when recognized', () => {
+                openHeatmapMenu();
+                selectReactSelectOption( $('.oncoprint__controls__heatmap_menu'), 'IC50 values of compounds on cellular phenotype readout');
+                $('.oncoprint__controls__heatmap_menu textarea').setValue('17-AAG');
+                $('div.icon-area div.icon').waitForExist();
+                assert( ! $('.oncoprint__controls__heatmap_menu textarea').getValue() );
+            });
+
+            it('shows all treatments in the treatment select box', () => {
+                openHeatmapMenu();
+                selectReactSelectOption( $('.oncoprint__controls__heatmap_menu'), 'IC50 values of compounds on cellular phenotype readout');
+                var treatments = getReactSelectOptions( $('.oncoprint__controls__heatmap_menu .treatment-selector') );
+                assert.equal(treatments.length, 10);
+            });
+
+            it('adds treatment to icons when selected in treatment select box', () => {
+                openHeatmapMenu();
+                selectReactSelectOption( $('.oncoprint__controls__heatmap_menu'), 'IC50 values of compounds on cellular phenotype readout');
+                var treatments = getReactSelectOptions( $('.oncoprint__controls__heatmap_menu .treatment-selector') );
+                var treatment = treatments[0];
+                var treatmentName = treatment.getText();
+                treatmentName = treatmentName.replace(/.*\((.*)\).*/, "$1")
+                treatment.click();
+                $('div.icon*='+treatmentName).waitForExist();
+                assert( $('div.icon*='+treatmentName) );
+            });
+
+            it('filters treatment select options when using search of treatment select box', () => {
+                openHeatmapMenu();
+                selectReactSelectOption( $('.oncoprint__controls__heatmap_menu'), 'IC50 values of compounds on cellular phenotype readout');
+                var searchBox = $('.oncoprint__controls__heatmap_menu .treatment-selector .Select-control input');
+                searchBox.setValue('17-AAG');
+                var treatments = getReactSelectOptions( $('.oncoprint__controls__heatmap_menu .treatment-selector') );
+                assert(treatments.length, 1);
+            });
+
+            it('sets `treatment_list` URL parameter', () => {
+                openHeatmapMenu();
+                selectReactSelectOption( $('.oncoprint__controls__heatmap_menu'), 'IC50 values of compounds on cellular phenotype readout');
+                $('.oncoprint__controls__heatmap_menu textarea').setValue('17-AAG');
+                $('div.icon-area div.icon').waitForExist();
+                $('button=Add Treatments to Heatmap').click();
+                waitForOncoprint();
+                var url = browser.url().value;
+                var regex = /treatment_list=17-AAG/;
+                assert(url.match(regex));
+            });
+
+        });
+
+    }
+
+});
+
+var openHeatmapMenu = () => {
+    var heatmapButton = browser.$('button[id=heatmapDropdown]');
+    heatmapButton.click();
+}
+
+module.exports = {
+    oncoprintTabUrl: oncoprintTabUrl,
+    openHeatmapMenu: openHeatmapMenu,
+};

src/pages/resultsView/ResultsViewPageStore.ts

@@ -80,8 +80,10 @@ import {MergedGeneQuery} from '../../shared/lib/oql/oql-parser';
 import GeneMolecularDataCache from "../../shared/cache/GeneMolecularDataCache";
 import GenesetMolecularDataCache from "../../shared/cache/GenesetMolecularDataCache";
 import GenesetCorrelatedGeneCache from "../../shared/cache/GenesetCorrelatedGeneCache";
+import TreatmentMolecularDataCache from "../../shared/cache/TreatmentMolecularDataCache";
 import GeneCache from "../../shared/cache/GeneCache";
 import GenesetCache from "../../shared/cache/GenesetCache";
+import TreatmentCache from "../../shared/cache/TreatmentCache";
 import {IOncoKbData} from "../../shared/model/OncoKB";
 import {generateQueryVariantId} from "../../public-lib/lib/OncoKbUtils";
 import {
@@ -90,7 +92,9 @@ import {
     ExpressionEnrichment,
     Geneset,
     GenesetDataFilterCriteria,
-    GenesetMolecularData
+    GenesetMolecularData,
+    Treatment,
+    TreatmentFilter
 } from "../../shared/api/generated/CBioPortalAPIInternal";
 import internalClient from "../../shared/api/cbioportalInternalClientInstance";
 import {CancerGene, IndicatorQueryResp} from "../../shared/api/generated/OncoKbAPI";
@@ -175,7 +179,8 @@ export const AlterationTypeConstants = {
     PROTEIN_LEVEL: 'PROTEIN_LEVEL',
     FUSION: 'FUSION',
     GENESET_SCORE: 'GENESET_SCORE',
-    METHYLATION: 'METHYLATION'
+    METHYLATION: 'METHYLATION',
+    GENERIC_ASSAY: 'GENERIC_ASSAY'
 };
 
 export const AlterationTypeDisplayConstants = {
@@ -884,7 +889,8 @@ export class ResultsViewPageStore {
             this.molecularProfilesInStudies,
             this.studyToDataQueryFilter,
             this.genes,
-            this.genesets
+            this.genesets,
+            this.treatmentsInStudies
         ],
         invoke:async()=>{
             const ret:MolecularProfile[] = [];
@@ -918,7 +924,9 @@ export class ResultsViewPageStore {
                             ret.push(profile);
                         }
                     }));
-                } else if (profile.molecularAlterationType === AlterationTypeConstants.GENESET_SCORE) {
+                } else if (profile.molecularAlterationType === AlterationTypeConstants.GENESET_SCORE
+                            || profile.molecularAlterationType === AlterationTypeConstants.GENERIC_ASSAY
+                    ) {
                     // geneset profile, we dont have the META projection for geneset data, so just add it
                     /*promises.push(internalClient.fetchGeneticDataItemsUsingPOST({
                         geneticProfileId: molecularProfileId,
@@ -2079,19 +2087,21 @@ export class ResultsViewPageStore {
             const MRNA_EXPRESSION = AlterationTypeConstants.MRNA_EXPRESSION;
             const PROTEIN_LEVEL = AlterationTypeConstants.PROTEIN_LEVEL;
             const METHYLATION = AlterationTypeConstants.METHYLATION;
+            const GENERIC_ASSAY = AlterationTypeConstants.GENERIC_ASSAY;
             const selectedMolecularProfileIds = stringListToSet(
                 this.selectedMolecularProfiles.result!.map((profile)=>profile.molecularProfileId)
             );
 
             const expressionHeatmaps = _.sortBy(
                 _.filter(this.molecularProfilesInStudies.result!, profile=>{
                     return ((profile.molecularAlterationType === MRNA_EXPRESSION ||
-                        profile.molecularAlterationType === PROTEIN_LEVEL) && profile.showProfileInAnalysisTab) ||
-                        profile.molecularAlterationType === METHYLATION;
+                        profile.molecularAlterationType === PROTEIN_LEVEL ||
+                        profile.molecularAlterationType === GENERIC_ASSAY) && profile.showProfileInAnalysisTab) ||
+                        profile.molecularAlterationType === METHYLATION
                     }
                 ),
                 profile=>{
-                    // Sort order: selected and [mrna, protein, methylation], unselected and [mrna, protein, meth]
+                    // Sort order: selected and [mrna, protein, methylation, treatment], unselected and [mrna, protein, meth, treatment]
                     if (profile.molecularProfileId in selectedMolecularProfileIds) {
                         switch (profile.molecularAlterationType) {
                             case MRNA_EXPRESSION:
@@ -2100,15 +2110,19 @@ export class ResultsViewPageStore {
                                 return 1;
                             case METHYLATION:
                                 return 2;
+                            case GENERIC_ASSAY:
+                                return 3;
                         }
                     } else {
                         switch(profile.molecularAlterationType) {
                             case MRNA_EXPRESSION:
-                                return 3;
-                            case PROTEIN_LEVEL:
                                 return 4;
-                            case METHYLATION:
+                            case PROTEIN_LEVEL:
                                 return 5;
+                            case METHYLATION:
+                                return 6;
+                            case GENERIC_ASSAY:
+                                return 7;
                         }
                     }
                 }
@@ -2280,6 +2294,27 @@ export class ResultsViewPageStore {
                     geneticEntityId: geneset.genesetId, cytoband: "-", geneticEntityData: geneset});
             }
             return Promise.resolve(res);
+
+        }
+    });
+
+    readonly treatmentsInStudies = remoteData<Treatment[]>({
+        await:()=>[this.studyIds],
+        invoke: async () => {
+            return internalClient.fetchTreatmentsUsingPOST({
+                treatmentFilter: { studyIds:this.studyIds.result! } as TreatmentFilter
+            })
+        },
+        onResult:(treatments:Treatment[])=>{
+            this.treatmentCache.addData(treatments);
+        }
+    });
+
+    readonly selectedTreatments = remoteData<Treatment[]>({
+        await: ()=>[this.treatmentsInStudies],
+        invoke: () => {
+            const treatmentIdFromUrl =  this.rvQuery.treatmentIds;
+            return Promise.resolve(_.filter(this.treatmentsInStudies.result!, (d:Treatment) => treatmentIdFromUrl.includes(d.treatmentId)));
         }
     });
 
@@ -2305,6 +2340,23 @@ export class ResultsViewPageStore {
         }
     });
 
+    readonly treatmentLinkMap = remoteData<{[treatmentId: string]: string}>({
+        invoke: async () => {
+            if (this.rvQuery.treatmentIds && this.rvQuery.treatmentIds.length) {
+                const treatments = await internalClient.fetchTreatmentsUsingPOST({
+                    treatmentFilter: { studyIds:this.studyIds.result! } as TreatmentFilter
+                });
+                const linkMap: {[treatmentId: string]: string} = {};
+                treatments.forEach(({treatmentId, refLink}) => {
+                    linkMap[treatmentId] = refLink;
+                });
+                return linkMap;
+            } else {
+                return {};
+            }
+        }
+    });
+
     readonly customDriverAnnotationReport = remoteData<{ hasBinary:boolean, tiers:string[] }>({
         await:()=>[
             this.mutations
@@ -3107,6 +3159,17 @@ export class ResultsViewPageStore {
         )
     });
 
+    readonly treatmentMolecularDataCache = remoteData({
+        await:() => [
+            this.molecularProfileIdToDataQueryFilter
+        ],
+        invoke: () => Promise.resolve(
+            new TreatmentMolecularDataCache(
+                this.molecularProfileIdToDataQueryFilter.result!
+            )
+        )
+    });
+
     @cached get geneCache() {
         return new GeneCache();
     }
@@ -3115,6 +3178,10 @@ export class ResultsViewPageStore {
         return new GenesetCache();
     }
 
+    @cached get treatmentCache() {
+        return new TreatmentCache();
+    }
+
     public numericGeneMolecularDataCache = new MobxPromiseCache<{entrezGeneId:number, molecularProfileId:string}, NumericGeneMolecularData[]>(
         q=>({
             await: ()=>[

src/pages/resultsView/ResultsViewPageStoreUtils.ts

@@ -398,7 +398,8 @@ export function getMolecularProfiles(query:any){
         query.genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION,
         query.genetic_profile_ids_PROFILE_MRNA_EXPRESSION,
         query.genetic_profile_ids_PROFILE_PROTEIN_EXPRESSION,
-        query.genetic_profile_ids_PROFILE_GENESET_SCORE
+        query.genetic_profile_ids_PROFILE_GENESET_SCORE,
+        query.genetic_profile_ids_GENERIC_ASSAY
     ].filter((profile:string|undefined)=>!!profile);
 
     // append 'genetic_profile_ids' which is sometimes in use

src/pages/resultsView/ResultsViewQuery.ts

@@ -15,6 +15,7 @@ export class ResultsViewQuery {
     @observable public _rppaScoreThreshold:number|undefined;
     @observable public _zScoreThreshold:number|undefined;
     @observable public genesetIds:string[] = [];
+    @observable public treatmentIds:string[] = [];
     @observable public cohortIdsList:string[] = [];//queried id(any combination of physical and virtual studies)
     @observable public oqlQuery:string = "";
 
@@ -103,6 +104,14 @@ export function updateResultsViewQuery(
         }
     }
 
+    if (urlQuery.treatment_list) {
+        // we have to trim because for some reason we get a single space from submission
+        const parsedTreatmentList = urlQuery.treatment_list.trim().length ? (urlQuery.treatment_list.trim().split(/;/)) : [];
+        if (!_.isEqual(parsedTreatmentList, rvQuery.treatmentIds)) {
+            rvQuery.treatmentIds = parsedTreatmentList;
+        }
+    }
+
     // cohortIdsList will contain virtual study ids (physicalstudies will contain the phsyical studies which comprise the virtual studies)
     // although resultsViewStore does
     if (!rvQuery.cohortIdsList || !_.isEqual(_.sortBy(rvQuery.cohortIdsList), _.sortBy(cancerStudyIds))) {