Customizable Dynamic Kaplan-Meier Plot for Survival Analysis

end-to-end-test/remote/specs/core/comparisonTab.screenshot.spec.js

@@ -422,7 +422,8 @@ describe('results view comparison tab screenshot tests', () => {
             await waitForElementDisplayed('b=RER1', { timeout: 10000 });
             await clickElement('b=RER1');
             await (await getElement('body')).moveTo({
-                x:0, y:0
+                x: 0,
+                y: 0,
             });
             const res = await browser.checkElement(
                 '.msk-tab:not(.hiddenByPosition)',

package.json

@@ -82,7 +82,6 @@
   "author": "",
   "license": "AGPL-3.0-or-later",
   "dependencies": {
-    "3dmol": "^1.3.7",
     "@babel/core": "7.4.4",
     "@babel/plugin-syntax-dynamic-import": "^7.8.3",
     "@babel/plugin-transform-modules-commonjs": "^7.4.4",
@@ -145,6 +144,7 @@
     "@types/seedrandom": "2.4.27",
     "@types/sinon": "^4.1.3",
     "@types/superagent": "^2.0.36",
+    "3dmol": "^1.3.7",
     "addthis-snippet": "^1.0.1",
     "autobind-decorator": "^2.1.0",
     "autoprefixer": "^6.7.0",
@@ -195,7 +195,6 @@
     "html-webpack-plugin": "^5.3.2",
     "igv": "^2.11.2",
     "imports-loader": "^0.8.0",
-    "jStat": "^1.7.0",
     "javascript-natural-sort": "^0.7.1",
     "jquery": "3.6.0",
     "jquery-migrate": "3.0.0",
@@ -204,6 +203,7 @@
     "json-fn": "^1.1.1",
     "jsonpath": "^1.1.1",
     "jspdf": "^1.3.3",
+    "jStat": "^1.7.0",
     "jstree": "^3.3.4",
     "jszip": "^3.7.1",
     "lerna": "3.19.0",

packages/cbioportal-ts-api-client/src/index.tsx

@@ -77,6 +77,9 @@ export {
     StructuralVariantFilter,
     StructuralVariantQuery,
     StructuralVariantGeneSubQuery,
+    ClinicalEventRequest,
+    ClinicalEventRequestIdentifier,
+    SurvivalRequest,
     StructuralVariantFilterQuery,
     GeneFilterQuery,
     AndedSampleTreatmentFilters,

src/config/IAppConfig.ts

@@ -172,6 +172,7 @@ export interface IServerConfig {
     skin_comparison_view_mutation_table_columns_show_on_init: string;
     skin_patient_view_copy_number_table_columns_show_on_init: string;
     skin_patient_view_structural_variant_table_columns_show_on_init: string;
+    skin_survival_plot_clinical_event_types_show_on_init: string;
     skin_results_view_tables_default_sort_column: string;
     skin_patient_view_tables_default_sort_column: string;
     skin_patient_view_custom_sample_type_colors_json: string;

src/config/serverConfigDefaults.ts

@@ -224,6 +224,8 @@ export const ServerConfigDefaults: Partial<IServerConfig> = {
 
     skin_patient_view_structural_variant_table_columns_show_on_init: '',
 
+    skin_survival_plot_clinical_event_types_show_on_init: '',
+
     skin_results_view_tables_default_sort_column: 'Annotation',
 
     skin_patient_view_tables_default_sort_column: 'Annotation',

src/pages/groupComparison/ClinicalData.tsx

@@ -1,7 +1,13 @@
-import * as React from 'react';
-import { observer, Observer } from 'mobx-react';
 import autobind from 'autobind-decorator';
-import LoadingIndicator from 'shared/components/loadingIndicator/LoadingIndicator';
+import {
+    DownloadControlOption,
+    DownloadControls,
+    remoteData,
+} from 'cbioportal-frontend-commons';
+import { Sample } from 'cbioportal-ts-api-client';
+import { getRemoteDataGroupStatus } from 'cbioportal-utils';
+import { getServerConfig } from 'config/config';
+import _ from 'lodash';
 import {
     action,
     autorun,
@@ -10,16 +16,22 @@ import {
     makeObservable,
     observable,
 } from 'mobx';
-import { SimpleGetterLazyMobXTableApplicationDataStore } from 'shared/lib/ILazyMobXTableApplicationDataStore';
-import ClinicalDataEnrichmentsTable from './ClinicalDataEnrichmentsTable';
-import _ from 'lodash';
+import { observer, Observer } from 'mobx-react';
+import { OncoprintJS } from 'oncoprintjs';
+import CategoryPlot, {
+    CategoryPlotType,
+} from 'pages/groupComparison/CategoryPlot';
 import {
-    DownloadControlOption,
-    DownloadControls,
-    remoteData,
-} from 'cbioportal-frontend-commons';
-import { getRemoteDataGroupStatus } from 'cbioportal-utils';
+    ClinicalNumericalDataVisualisation,
+    ClinicalNumericalVisualisationType,
+} from 'pages/groupComparison/ClinicalNumericalDataVisualisation';
+import { createSurvivalAttributeIdsDict } from 'pages/resultsView/survival/SurvivalUtil';
+import * as React from 'react';
+import ReactSelect from 'react-select1';
 import client from 'shared/api/cbioportalClientInstance';
+import LoadingIndicator from 'shared/components/loadingIndicator/LoadingIndicator';
+import { MakeMobxView } from 'shared/components/MobxView';
+import { IBoxScatterPlotData } from 'shared/components/plots/BoxScatterPlot';
 import {
     basicAppearance,
     boxPlotTooltip,
@@ -32,39 +44,27 @@ import {
     IStringAxisData,
     makeBoxScatterPlotData,
 } from 'shared/components/plots/PlotsTabUtils';
-import ScrollBar from 'shared/components/Scrollbar/ScrollBar';
-import { IBoxScatterPlotData } from 'shared/components/plots/BoxScatterPlot';
 import { scatterPlotSize } from 'shared/components/plots/PlotUtils';
-import {
-    CLINICAL_TAB_NOT_ENOUGH_GROUPS_MSG,
-    ClinicalDataEnrichmentWithQ,
-    GetStatisticalCautionInfo,
-} from './GroupComparisonUtils';
-import ReactSelect from 'react-select1';
-import { MakeMobxView } from 'shared/components/MobxView';
-import OverlapExclusionIndicator from './OverlapExclusionIndicator';
-import { RESERVED_CLINICAL_VALUE_COLORS } from '../../shared/lib/Colors';
-import ErrorMessage from '../../shared/components/ErrorMessage';
+import ScrollBar from 'shared/components/Scrollbar/ScrollBar';
 import ComplexKeyMap from 'shared/lib/complexKeyDataStructures/ComplexKeyMap';
-import { Sample } from 'cbioportal-ts-api-client';
+import { SimpleGetterLazyMobXTableApplicationDataStore } from 'shared/lib/ILazyMobXTableApplicationDataStore';
+import ErrorMessage from '../../shared/components/ErrorMessage';
+import { RESERVED_CLINICAL_VALUE_COLORS } from '../../shared/lib/Colors';
 import ComparisonStore, {
     OverlapStrategy,
 } from '../../shared/lib/comparison/ComparisonStore';
-import { createSurvivalAttributeIdsDict } from 'pages/resultsView/survival/SurvivalUtil';
+import ClinicalDataEnrichmentsTable from './ClinicalDataEnrichmentsTable';
 import {
     filterSampleList,
     getComparisonCategoricalNaValue,
 } from './ClinicalDataUtils';
 import {
-    ClinicalNumericalDataVisualisation,
-    ClinicalNumericalVisualisationType,
-} from 'pages/groupComparison/ClinicalNumericalDataVisualisation';
+    CLINICAL_TAB_NOT_ENOUGH_GROUPS_MSG,
+    ClinicalDataEnrichmentWithQ,
+    GetStatisticalCautionInfo,
+} from './GroupComparisonUtils';
+import OverlapExclusionIndicator from './OverlapExclusionIndicator';
 import { SummaryStatisticsTable } from './SummaryStatisticsTable';
-import CategoryPlot, {
-    CategoryPlotType,
-} from 'pages/groupComparison/CategoryPlot';
-import { OncoprintJS } from 'oncoprintjs';
-import { getServerConfig } from 'config/config';
 
 export interface IClinicalDataProps {
     store: ComparisonStore;
@@ -231,7 +231,8 @@ export default class ClinicalData extends React.Component<
             // There is no need to still keep them in clinical tab
             // So, exclude them from the data store
             const survivalAttributeIdsDict = createSurvivalAttributeIdsDict(
-                this.props.store.survivalClinicalAttributesPrefix.result || []
+                this.props.store.predefinedSurvivalClinicalAttributesPrefix
+                    .result || []
             );
             // In addition remove a few more attributes from the comparison page
             // for GENIE BPC related to years. In the future we might want to

src/pages/groupComparison/GroupComparisonPage.tsx

@@ -52,6 +52,7 @@ import GroupComparisonMutationsTab from './GroupComparisonMutationsTab';
 import GroupComparisonPathwayMapperUserSelectionStore from './pathwayMapper/GroupComparisonPathwayMapperUserSelectionStore';
 import { Tour } from 'tours';
 import GenericAssayEnrichmentCollections from './GenericAssayEnrichmentCollections';
+import 'react-toastify/dist/ReactToastify.css';
 
 export interface IGroupComparisonPageProps {
     routing: any;
@@ -75,7 +76,15 @@ export default class GroupComparisonPage extends React.Component<
         this.pathwayMapperUserSelectionStore = new GroupComparisonPathwayMapperUserSelectionStore();
         this.queryReaction = reaction(
             () => this.urlWrapper.query.comparisonId,
-            sessionId => {
+            (sessionId, previousSessionId) => {
+                // New session is created when a custom survival plot is added or deleted.
+                // In this case, we don't want to reload the page.
+                if (localStorage.getItem('preventPageReload') === 'true') {
+                    localStorage.removeItem('preventPageReload');
+                    if (previousSessionId !== undefined) {
+                        return;
+                    }
+                }
                 if (
                     !props.routing.location.pathname.includes('/comparison') ||
                     !sessionId
@@ -133,7 +142,8 @@ export default class GroupComparisonPage extends React.Component<
             this.store.mRNAEnrichmentProfiles,
             this.store.proteinEnrichmentProfiles,
             this.store.methylationEnrichmentProfiles,
-            this.store.survivalClinicalDataExists,
+            this.store.predefinedSurvivalClinicalDataExists,
+            this.store.clinicalEventOptions,
             this.store.genericAssayEnrichmentProfilesGroupedByGenericAssayType,
             this.store
                 .genericAssayBinaryEnrichmentProfilesGroupedByGenericAssayType,

src/pages/groupComparison/GroupComparisonStore.ts

@@ -1,54 +1,50 @@
-import {
-    ComparisonGroup,
-    defaultGroupOrder,
-    finalizeStudiesAttr,
-    getOrdinals,
-    getStudyIds,
-} from './GroupComparisonUtils';
+import autobind from 'autobind-decorator';
 import { remoteData, stringListToIndexSet } from 'cbioportal-frontend-commons';
 import {
-    SampleFilter,
     CancerStudy,
-    MutationMultipleStudyFilter,
+    Gene,
     GenePanelDataMultipleStudyFilter,
     Mutation,
-    Gene,
-    GenePanelData,
-    Sample,
-    MutationCountByPosition,
+    MutationMultipleStudyFilter,
+    SampleFilter,
 } from 'cbioportal-ts-api-client';
-import { action, observable, makeObservable, computed } from 'mobx';
-import client from '../../shared/api/cbioportalClientInstance';
-import comparisonClient from '../../shared/api/comparisonGroupClientInstance';
 import _ from 'lodash';
-import autobind from 'autobind-decorator';
+import { action, computed, makeObservable, observable } from 'mobx';
+import { fetchPatients } from 'pages/resultsView/ResultsViewPageStoreUtils';
+import { getSampleMolecularIdentifiers } from 'pages/studyView/StudyViewComparisonUtils';
 import { pickClinicalDataColors } from 'pages/studyView/StudyViewUtils';
-import { AppStore } from '../../AppStore';
-import { GACustomFieldsEnum, trackEvent } from 'shared/lib/tracking';
-import ifNotDefined from '../../shared/lib/ifNotDefined';
-import GroupComparisonURLWrapper from './GroupComparisonURLWrapper';
-import ComparisonStore, {
-    OverlapStrategy,
-} from '../../shared/lib/comparison/ComparisonStore';
+import { AxisScale, DataFilter } from 'react-mutation-mapper';
 import sessionServiceClient from 'shared/api//sessionServiceInstance';
-import { COLORS } from '../studyView/StudyViewUtils';
 import {
     ComparisonSession,
     SessionGroupData,
     VirtualStudy,
 } from 'shared/api/session-service/sessionServiceModels';
-import ComplexKeySet from 'shared/lib/complexKeyDataStructures/ComplexKeySet';
 import { REQUEST_ARG_ENUM } from 'shared/constants';
-import { AxisScale, DataFilter } from 'react-mutation-mapper';
-import { fetchGenes, getAllGenes } from 'shared/lib/StoreUtils';
+import { FeatureFlagEnum } from 'shared/featureFlags';
 import {
     CoverageInformation,
     getCoverageInformation,
 } from 'shared/lib/GenePanelUtils';
-import { fetchPatients } from 'pages/resultsView/ResultsViewPageStoreUtils';
+import { getAllGenes } from 'shared/lib/StoreUtils';
+import ComplexKeySet from 'shared/lib/complexKeyDataStructures/ComplexKeySet';
 import { isSampleProfiled } from 'shared/lib/isSampleProfiled';
-import { getSampleMolecularIdentifiers } from 'pages/studyView/StudyViewComparisonUtils';
-import { FeatureFlagEnum } from 'shared/featureFlags';
+import { AppStore } from '../../AppStore';
+import client from '../../shared/api/cbioportalClientInstance';
+import comparisonClient from '../../shared/api/comparisonGroupClientInstance';
+import ComparisonStore, {
+    OverlapStrategy,
+} from '../../shared/lib/comparison/ComparisonStore';
+import ifNotDefined from '../../shared/lib/ifNotDefined';
+import { COLORS } from '../studyView/StudyViewUtils';
+import GroupComparisonURLWrapper from './GroupComparisonURLWrapper';
+import {
+    ComparisonGroup,
+    defaultGroupOrder,
+    finalizeStudiesAttr,
+    getOrdinals,
+    getStudyIds,
+} from './GroupComparisonUtils';
 
 export default class GroupComparisonStore extends ComparisonStore {
     @observable private sessionId: string;
@@ -146,7 +142,7 @@ export default class GroupComparisonStore extends ComparisonStore {
     }
 
     @action
-    protected async saveAndGoToSession(newSession: ComparisonSession) {
+    public async saveAndGoToSession(newSession: ComparisonSession) {
         const { id } = await comparisonClient.addComparisonSession(newSession);
         this.urlWrapper.updateURL({ comparisonId: id });
     }
@@ -655,7 +651,7 @@ export default class GroupComparisonStore extends ComparisonStore {
     }
 
     // override parent method
-    protected get isLeftTruncationFeatureFlagEnabled() {
+    public get isLeftTruncationFeatureFlagEnabled() {
         return this.appStore.featureFlagStore.has(
             FeatureFlagEnum.LEFT_TRUNCATION_ADJUSTMENT
         );