Merge pull request #4396 from alisman/pvTest

Add e2e test for patient view cohort navigation and annotation results

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

@@ -0,0 +1,34 @@
+var assert = require('assert');
+
+const {
+    goToUrlAndSetLocalStorage,
+    checkOncoprintElement,
+    waitForNetworkQuiet,
+} = require('../../../shared/specUtils');
+const { assertScreenShotMatch } = require('../../../shared/lib/testUtils');
+
+describe('Patient Cohort View Custom Tab Tests', () => {
+    const patientUrl = `https://www.cbioportal.org/patient?studyId=coadread_tcga_pub&caseId=TCGA-A6-2670#navCaseIds=coadread_tcga_pub:TCGA-A6-2670,coadread_tcga_pub:TCGA-A6-2672`;
+
+    it('Patient page valid after cohort navigation', function() {
+        goToUrlAndSetLocalStorage(patientUrl);
+
+        waitForNetworkQuiet();
+
+        $('.nextPageBtn').click();
+
+        waitForNetworkQuiet();
+
+        var res = browser.checkDocument();
+        assertScreenShotMatch(res);
+
+        // now reload so that we get to the patient via direct initial load (not cohort navigation)
+        browser.url(browser.getUrl());
+
+        waitForNetworkQuiet();
+
+        // check that it matches again
+        var res2 = browser.checkDocument();
+        assertScreenShotMatch(res2);
+    });
+});

src/config/IAppConfig.ts

@@ -152,7 +152,6 @@ export interface IServerConfig {
     oncokb_merge_icons_by_default: boolean;
     generic_assay_display_text: string; // this has a default
     saml_logout_local: boolean;
-    patient_view_use_legacy_timeline: boolean;
     installation_map_url: string;
     enable_request_body_gzip_compression: boolean;
     enable_treatment_groups: boolean;

src/config/serverConfigDefaults.ts

@@ -187,7 +187,7 @@ export const ServerConfigDefaults: Partial<IServerConfig> = {
         'TREATMENT_RESPONSE:Treatment Response,MUTATIONAL_SIGNATURE:Mutational Signature,ARMLEVEL_CNA:Arm-level CNA',
 
     saml_logout_local: false,
-    patient_view_use_legacy_timeline: false,
+
     enable_request_body_gzip_compression: false,
     enable_treatment_groups: false,
 

src/pages/patientView/PatientViewPage.tsx

@@ -2,38 +2,23 @@ import * as React from 'react';
 import _ from 'lodash';
 import {
     CancerStudy,
-    ClinicalData,
     DiscreteCopyNumberData,
     ResourceData,
 } from 'cbioportal-ts-api-client';
-import {
-    ClinicalDataBySampleId,
-    RequestStatus,
-} from 'cbioportal-ts-api-client';
 import { Else, If, Then } from 'react-if';
 import SampleManager from './SampleManager';
 import PatientHeader from './patientHeader/PatientHeader';
 import { PaginationControls } from '../../shared/components/paginationControls/PaginationControls';
 import { IColumnVisibilityDef } from 'shared/components/columnVisibilityControls/ColumnVisibilityControls';
 import { toggleColumnVisibility } from 'cbioportal-frontend-commons';
 import {
-    parseCohortIds,
     PatientViewPageStore,
     buildCohortIdsFromNavCaseIds,
 } from './clinicalInformation/PatientViewPageStore';
 import { inject, observer } from 'mobx-react';
-import {
-    action,
-    computed,
-    observable,
-    reaction,
-    makeObservable,
-    Reaction,
-    IReactionDisposer,
-} from 'mobx';
+import { action, computed, observable, makeObservable } from 'mobx';
 import { default as PatientViewMutationTable } from './mutation/PatientViewMutationTable';
 import { MSKTab } from '../../shared/components/MSKTabs/MSKTabs';
-import { validateParametersPatientView } from '../../shared/lib/validateParameters';
 import LoadingIndicator from 'shared/components/loadingIndicator/LoadingIndicator';
 import ValidationAlert from 'shared/components/ValidationAlert';
 import PatientViewMutationsDataStore from './mutation/PatientViewMutationsDataStore';
@@ -56,9 +41,7 @@ import { remoteData, getBrowserWindow } from 'cbioportal-frontend-commons';
 import 'cbioportal-frontend-commons/dist/styles.css';
 import 'react-mutation-mapper/dist/styles.css';
 import 'react-table/react-table.css';
-import { trackPatient } from 'shared/lib/tracking';
 import PatientViewUrlWrapper from './PatientViewUrlWrapper';
-import { PagePath } from 'shared/enums/PagePaths';
 import { GeneFilterOption } from './mutation/GeneFilterMenu';
 import { checkNonProfiledGenesExist } from './PatientViewPageUtils';
 import PatientViewGenePanelModal from './PatientViewGenePanelModal/PatientViewGenePanelModal';
@@ -158,14 +141,6 @@ export class PatientViewPageInner extends React.Component<
 
     public patientViewPageStore: PatientViewPageStore;
 
-    private disposers: IReactionDisposer[] = [];
-
-    componentWillUnmount() {
-        // this will destroy the reaction
-        // which will free parties for gc
-        this.disposers.forEach(d => d());
-    }
-
     constructor(props: IPatientViewPageProps) {
         super(props);
         makeObservable(this);