Merge pull request #4391 from alisman/nonprofiled

Add alerts on patient view alteration tables when one sample of many is not profiled

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

@@ -1,27 +1,31 @@
 var assert = require('assert');
-var goToUrlAndSetLocalStorage = require('../../../shared/specUtils')
-    .goToUrlAndSetLocalStorage;
+
+var {
+    goToUrlAndSetLocalStorage,
+    getElementByTestHandle,
+} = require('../../../shared/specUtils');
 
 const CBIOPORTAL_URL = process.env.CBIOPORTAL_URL.replace(/\/$/, '');
 
 describe('patient page', function() {
-    this.retries(2);
     before(() => {
         goToUrlAndSetLocalStorage(CBIOPORTAL_URL);
     });
 
-    it('should show all samples button for single sample view of multi sample patient', function() {
+    it('should show "all samples button" for single sample view of multi sample patient', function() {
         goToUrlAndSetLocalStorage(
             `${CBIOPORTAL_URL}/patient?studyId=lgg_ucsf_2014&tab=summaryTab&sampleId=P04_Pri`
         );
 
-        $('.//*[text()[contains(.,"Show all")]]').waitForExist();
+        $('button=Show all 4 samples').waitForExist();
+    });
 
-        assert.equal(
-            $('.//*[text()[contains(.,"Show all")]]')
-                .getText()
-                .toLowerCase(),
-            'show all 4 samples'.toLowerCase()
+    it('show appropriate messaging when a patient has only some profiled samples', () => {
+        goToUrlAndSetLocalStorage(
+            `${CBIOPORTAL_URL}/patient?studyId=mpcproject_broad_2021&caseId=MPCPROJECT_0013`
         );
+
+        // there is one partial profile message for CNA and sample 2
+        getElementByTestHandle('patientview-mutation-table').waitForDisplayed();
     });
 });

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

@@ -3,12 +3,15 @@ var assert = require('assert');
 const {
     goToUrlAndSetLocalStorage,
     checkOncoprintElement,
+    checkElementWithMouseDisabled,
     waitForNetworkQuiet,
 } = require('../../../shared/specUtils');
 const { assertScreenShotMatch } = require('../../../shared/lib/testUtils');
 
+const CBIOPORTAL_URL = process.env.CBIOPORTAL_URL.replace(/\/$/, '');
+
 describe('Patient Cohort View Custom Tab Tests', () => {
-    const patientUrl = `https://www.cbioportal.org/patient?studyId=coadread_tcga_pub&caseId=TCGA-A6-2670#navCaseIds=coadread_tcga_pub:TCGA-A6-2670,coadread_tcga_pub:TCGA-A6-2672`;
+    const patientUrl = `${CBIOPORTAL_URL}/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);
@@ -32,3 +35,17 @@ describe('Patient Cohort View Custom Tab Tests', () => {
         assertScreenShotMatch(res2);
     });
 });
+
+// describe('patient page', function() {
+//     before(() => {
+//         goToUrlAndSetLocalStorage(CBIOPORTAL_URL);
+//     });
+//
+//     it('should show all samples button for single sample view of multi sample patient', function() {
+//         goToUrlAndSetLocalStorage(
+//             `${CBIOPORTAL_URL}/patient?studyId=lgg_ucsf_2014&tab=summaryTab&sampleId=P04_Pri`
+//         );
+//
+//         checkElementWithMouseDisabled();
+//     });
+// });

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

@@ -375,7 +375,7 @@ describe('results page pathways tab with unprofiled genes', function() {
     });
 
     it(`results page pathwaymapper tab with unprofiled genes`, function() {
-        $('#cy').waitForDisplayed({ timeout: 15000 });
+        $('#cy').waitForDisplayed({ timeout: 30000 });
 
         waitForNetworkQuiet(15000);
 

end-to-end-test/shared/specUtils.js

@@ -102,6 +102,10 @@ function setSettingsMenuOpen(open, buttonId = 'GlobalSettingsButton') {
     );
 }
 
+function getElementByTestHandle(handle) {
+    return $(`[data-test=${handle}]`);
+}
+
 function setOncoprintMutationsMenuOpen(open) {
     const mutationColorMenuButton = '#mutationColorDropdown';
     const mutationColorMenuDropdown =
@@ -753,4 +757,5 @@ module.exports = {
     jq,
     setServerConfiguration,
     selectClinicalTabPlotType,
+    getElementByTestHandle,
 };

src/pages/patientView/PatientViewPageUtils.tsx

@@ -1,5 +1,9 @@
 import TumorColumnFormatter from './mutation/column/TumorColumnFormatter';
 import _ from 'lodash';
+import {
+    IGenePanelDataByProfileIdAndSample,
+    isSampleProfiledInProfile,
+} from 'shared/lib/isSampleProfiled';
 
 export function checkNonProfiledGenesExist(
     sampleIds: string[],
@@ -17,3 +21,33 @@ export function checkNonProfiledGenesExist(
         return _.values(profiledSamples).includes(false);
     });
 }
+
+export function getSamplesProfiledStatus(
+    sampleIds: string[],
+    genePanelData: IGenePanelDataByProfileIdAndSample,
+    profileId: string | undefined
+) {
+    const notProfiledIds: string[] = sampleIds.reduce(
+        (aggr: string[], sampleId: string) => {
+            const isProfiled = isSampleProfiledInProfile(
+                genePanelData,
+                profileId,
+                sampleId
+            );
+            if (!isProfiled) {
+                aggr.push(sampleId);
+            }
+            return aggr;
+        },
+        []
+    );
+
+    const noneProfiled = notProfiledIds.length === sampleIds.length;
+    const someProfiled = notProfiledIds.length < sampleIds.length;
+
+    return {
+        noneProfiled,
+        someProfiled,
+        notProfiledIds,
+    };
+}