Merge branch 'master' into fix-10375

.circleci/config.yml

@@ -45,7 +45,7 @@ run_e2e_and_save_artifacts: &run_e2e_and_save_artifacts
                 sudo apt-get install build-essential libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev & \
                 yarn serveDist & \
                 cd end-to-end-test && \
-                yarn install --frozen-lockfile && \
+                yarn install --frozen-lockfile --ignore-engines && \
                 ../scripts/env_vars.sh && \
                 eval "$(../scripts/env_vars.sh)" && \
                 curl $CBIOPORTAL_URL > /dev/null && \
@@ -82,8 +82,8 @@ run_e2e_and_save_artifacts: &run_e2e_and_save_artifacts
               path: /tmp/repo/end-to-end-test/shared/imageCompare.html
               destination: /imageCompare.html
           - store_artifacts:
-              path: /tmp/repo/end-to-end-test/remote/junit/customReport.json
-              destination: /customReport.json
+              path: /tmp/repo/end-to-end-test/remote/junit/completeResults.json
+              destination: /completeResults.json
           - store_artifacts:
               path: /tmp/repo/end-to-end-test/remote/junit/errors
               destination: /errors
@@ -133,7 +133,7 @@ jobs:
             DISABLE_SOURCEMAP: true
             NO_PARALLEL: true
           no_output_timeout: 25m
-      - run: cd /tmp/repo/end-to-end-test && (ls node_modules || yarn install --frozen-lockfile)
+      - run: cd /tmp/repo/end-to-end-test && (ls node_modules || yarn install --frozen-lockfile --ignore-engines)
       - save_cache:
           paths:
             - node_modules
@@ -343,10 +343,10 @@ jobs:
                 path: /tmp/repo/end-to-end-test/shared/imageCompare.html
                 destination: /imageCompare.html
             - store_artifacts:
-                path: /tmp/repo/end-to-end-test/local/junit/customReport.json
-                destination: /customReport.json
+                path: /tmp/repo/end-to-end-test/local/junit/completeResults.json
+                destination: /completeResults.json
             - store_artifacts:
-                path: /tmp/repo/end-to-end-test/remote/junit/errors
+                path: /tmp/repo/end-to-end-test/local/junit/errors
                 destination: /errors
       - unless:
           condition: << pipeline.parameters.enable_localdb_e2e >>

README.md

@@ -159,7 +159,7 @@ Follow instructions to boot up frontend dev server. This is the frontend that wi
 cd end-to-end-test
 
 // install deps
-yarn 
+yarn --ignore-engines
 
 ```
 

end-to-end-test/local/specs/core/oncoprint.screenshot.spec.js

@@ -78,7 +78,7 @@ describe('oncoprint', function() {
     describe('generic assay categorical tracks', () => {
         it('shows binary and multiple category tracks', () => {
             goToUrlAndSetLocalStorage(genericArrayUrl, true);
-            waitForOncoprint(ONCOPRINT_TIMEOUT);
+            waitForOncoprint();
             const res = checkOncoprintElement();
             assertScreenShotMatch(res);
         });
@@ -95,7 +95,7 @@ describe('oncoprint', function() {
                     ),
                 }
             );
-            waitForOncoprint(ONCOPRINT_TIMEOUT);
+            waitForOncoprint();
         });
 
         it('initializes as configured by default', () => {
@@ -132,10 +132,8 @@ describe('oncoprint', function() {
             const urlWithUserConfig = createUrlWithSettingsQueryParam(
                 MANUAL_TRACK_CONFIG
             );
-            // go to home page first because navigating to same page with hash params doesn't cause change
-            goToUrlAndSetLocalStorage(CBIOPORTAL_URL, false);
             goToUrlAndSetLocalStorage(urlWithUserConfig, false);
-            waitForOncoprint(ONCOPRINT_TIMEOUT);
+            waitForOncoprint();
 
             const res = checkOncoprintElement();
             assertScreenShotMatch(res);
@@ -172,11 +170,9 @@ describe('oncoprint', function() {
             const urlWithUserConfig = createUrlWithSettingsQueryParam(
                 customConfig
             );
-            // go to home page first because navigating to same page with hash params doesn't cause change
-            goToUrlAndSetLocalStorage(CBIOPORTAL_URL, false);
-            browser.url(urlWithUserConfig);
+            goToUrlAndSetLocalStorage(urlWithUserConfig, false);
 
-            waitForOncoprint(ONCOPRINT_TIMEOUT);
+            waitForOncoprint();
 
             // Check save button enabled
             openTracksMenu();
@@ -187,7 +183,7 @@ describe('oncoprint', function() {
 
             // Click save button
             $saveSessionBtn.click();
-            waitForOncoprint(ONCOPRINT_TIMEOUT);
+            waitForOncoprint();
             // Check save button disabled
             classes = $saveSessionBtn.getAttribute('class').split(' ');
             const saveBtnIsDisabled = classes.includes('disabled');
@@ -249,7 +245,7 @@ describe('oncoprint', function() {
                     SERVER_CLINICAL_TRACK_CONFIG
                 ),
             });
-            waitForOncoprint(ONCOPRINT_TIMEOUT);
+            waitForOncoprint();
         });
 
         it('shows oql structural variant variations', function() {
@@ -269,7 +265,7 @@ function createUrlWithSettingsQueryParam(config) {
 function openTracksMenu() {
     const $tracksDropdown = $('#addTracksDropdown');
     $tracksDropdown.click();
-    waitForOncoprint(2000);
+    waitForOncoprint();
 }
 
 function changeNthTrack(track, menuOptionButtonText) {
@@ -279,7 +275,7 @@ function changeNthTrack(track, menuOptionButtonText) {
         timeout: 1000,
     });
     $(`li=${menuOptionButtonText}`).click();
-    waitForOncoprint(2000);
+    waitForOncoprint();
 }
 
 function getBookmarkUrl(browser) {
@@ -312,6 +308,6 @@ function createOncoprintFromLegacyFormat() {
     ).join(',');
     const legacyUrl = `${studyes0_oncoprintTabUrl}&clinicallist=${legacyFormatQueryParam}`;
     goToUrlAndSetLocalStorage(legacyUrl, false);
-    waitForOncoprint(ONCOPRINT_TIMEOUT);
+    waitForOncoprint();
     return legacyFormatQueryParam;
 }

end-to-end-test/local/specs/core/settings-menu.spec.js

@@ -80,6 +80,6 @@ describe('results view settings/annotation menu', function() {
 
 const openOncoprint = (url, property) => {
     goToUrlAndSetLocalStorageWithProperty(url, true, property);
-    waitForOncoprint(100000);
+    waitForOncoprint();
     setSettingsMenuOpen(true, 'GlobalSettingsButton');
 };

end-to-end-test/local/specs/custom-driver-annotations-in-result-view.spec.js

@@ -22,7 +22,7 @@ describe('custom driver annotations feature in result view', function() {
     describe('oncoprint tab - mutations', () => {
         beforeEach(() => {
             goToUrlAndSetLocalStorage(oncoprintTabUrl, true);
-            waitForOncoprint(100000);
+            waitForOncoprint();
             setSettingsMenuOpen(true, 'GlobalSettingsButton');
         });
 

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

@@ -54,7 +54,7 @@ describe('gsva feature', () => {
     describe('oncoprint tab', () => {
         beforeEach(() => {
             goToUrlAndSetLocalStorage(oncoprintTabUrl, true);
-            waitForOncoprint(20000);
+            waitForOncoprint();
         });
 
         it('shows GSVA heatmap track', () => {
@@ -76,7 +76,7 @@ describe('gsva feature', () => {
             ).waitForDisplayed();
             $(trackOptionsElts.dropdown_selector + ' li:nth-child(7)').click();
 
-            waitForOncoprint(20000);
+            waitForOncoprint();
             var res = checkOncoprintElement('.oncoprintContainer');
             assertScreenShotMatch(res);
         });

end-to-end-test/local/specs/hide-download-controls.spec.js

@@ -457,6 +457,7 @@ describe('hide download controls feature', function() {
                 'Clinical Data',
                 'CN Segments',
                 'Files & Links',
+                'Plots Beta!',
                 'Study Sponsors',
             ];
             before(() => {

end-to-end-test/local/specs/web-tour.spec.js

@@ -353,11 +353,17 @@ describe('Virtual Study Tour', () => {
     });
 });
 
-describe('Group Comparison Tour', () => {
+describe('Group Comparison Tour', function() {
     let step = -1;
 
+    this.retries(0);
+
     before(() => {
-        goToUrlAndSetLocalStorage(CBIOPORTAL_URL, false);
+        goToUrlAndSetLocalStorage(CBIOPORTAL_URL, true);
+    });
+
+    beforeEach(() => {
+        browser.setWindowSize(1600, 1200);
     });
 
     it('Initial step with -1.', () => {
@@ -473,6 +479,11 @@ describe('Group Comparison Tour', () => {
         !tourModal.$(SKIP_ALL_BTN).isDisplayed();
         !tourModal.$(NEXT_STEP_BTN).isDisplayed();
 
+        browser.setWindowSize(
+            browser.getWindowSize().width + 400,
+            browser.getWindowSize().height
+        );
+
         browser.pause(1000);
         // There should be the Mutated Genes table [data-tour="mutated-genes-table"]
         const mutatedGenesTable = $('[data-tour="mutated-genes-table"]').$(
@@ -482,6 +493,8 @@ describe('Group Comparison Tour', () => {
 
         // Select samples, IDH1 mutations, TP53 mutant and EGFR amplified samples
         mutatedGenesTable.$$('input')[0].waitForDisplayed();
+
+        //browser.debug();
         mutatedGenesTable.$$('input')[0].click();
         mutatedGenesTable.$$('input')[1].click();
 
@@ -633,7 +646,7 @@ describe('Group Comparison Tour', () => {
         step++;
     });
 
-    it('Step 8: Intro to the Survival tab, on the group comparison page.', () => {
+    it.skip('Step 8: Intro to the Survival tab, on the group comparison page.', () => {
         // The tour should be at step = 8
         assert.equal(step, 8);
 
@@ -657,7 +670,7 @@ describe('Group Comparison Tour', () => {
         step++;
     });
 
-    it('Step 9: Intro to the Clinical tab, on the group comparison page.', () => {
+    it.skip('Step 9: Intro to the Clinical tab, on the group comparison page.', () => {
         // The tour should be at step = 9
         assert.equal(step, 9);
 
@@ -681,7 +694,7 @@ describe('Group Comparison Tour', () => {
         step++;
     });
 
-    it('Step 10: Intro to the Genomic Alterations tab, on the group comparison page.', () => {
+    it.skip('Step 10: Intro to the Genomic Alterations tab, on the group comparison page.', () => {
         // The tour should be at step = 10
         assert.equal(step, 10);
 

end-to-end-test/package.json

@@ -4,7 +4,7 @@
   "description": "Dependencies for running tests with webdriverio and browserstack",
   "main": "index.js",
   "scripts": {
-    "test-webdriver-manager": "npx wdio ./shared/wdio/wdio.conf.js",
+    "test-webdriver-manager": "npx wdio  ./shared/wdio/wdio.conf.js",
     "test-webdriver-manager-local": "export TEST_TYPE=local && export MANAGER_MAX_INSTANCES=2 && yarn run test-webdriver-manager",
     "test-webdriver-manager-remote": "export TEST_TYPE=remote && yarn run test-webdriver-manager",
     "test-webdriver-manager-debug": "(DEBUG=true npx wdio ./shared/wdio/wdio.conf.js --inspect || bash shared/image-compare/upload_failed_screenshots.sh)",
@@ -15,8 +15,10 @@
   "author": "",
   "license": "AGPL-3.0-or-later",
   "dependencies": {
-    "@wdio/cli": "^6.10.5",
-    "@wdio/junit-reporter": "^6.11.0",
+    "@wdio/cli": "7.35",
+    "@wdio/codemod": "^0.12.0",
+    "@wdio/junit-reporter": "7",
+    "@wdio/sync": "^7.27.0",
     "browserstack-local": "1.3.0",
     "canvas": "^2.6.1",
     "clipboardy": "^2.0.0",
@@ -27,15 +29,15 @@
     "wdio-image-comparison-service": "^2.0.0",
     "wdio-junit-reporter": "^0.3.1",
     "wdio-novus-visual-regression-service": "^1.2.4",
-    "wdio-spec-reporter": "0.1.0"
+    "wdio-spec-reporter": "0.1.0",
+    "wdio-timeline-reporter": "^5.1.4"
   },
   "devDependencies": {
-    "@wdio/local-runner": "^6.10.5",
-    "@wdio/mocha-framework": "^6.10.4",
-    "@wdio/spec-reporter": "^6.8.1",
-    "@wdio/sync": "^6.10.4",
+    "@wdio/local-runner": "7",
+    "@wdio/mocha-framework": "7",
+    "@wdio/spec-reporter": "7",
     "chromedriver": "^87.0.1",
-    "wdio-chromedriver-service": "^6.0.4",
+    "wdio-chromedriver-service": "7",
     "wdio-json-reporter": "^2.0.0"
   }
 }

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

@@ -104,6 +104,8 @@ function runTests(pageName, url, tabLocation) {
 
             goToUrlWithCustomTabConfig(url, conf);
 
+            browser.setWindowSize(2000, browser.getWindowSize().height);
+
             $('.mainTabs').waitForDisplayed();
 
             assert.equal(
@@ -141,6 +143,8 @@ function runTests(pageName, url, tabLocation) {
 
             goToUrlWithCustomTabConfig(url, conf);
 
+            browser.setWindowSize(2000, browser.getWindowSize().height);
+
             $('.mainTabs').waitForDisplayed();
 
             assert.equal(
@@ -210,7 +214,7 @@ function runTests(pageName, url, tabLocation) {
             );
         });
 
-        it('Remounts tab only when tracked url param changes (part of hash in url wrapper)', () => {
+        it('Remounts tab only when tracked url param changes (part of hash in url wrapper)', function() {
             const conf = [
                 {
                     title: 'Async Tab',
@@ -229,12 +233,15 @@ function runTests(pageName, url, tabLocation) {
 
             goToUrlWithCustomTabConfig(url, conf);
 
+            browser.setWindowSize(1600, browser.getWindowSize().height);
+
             browser.execute(() => {
                 window.renderCustomTab1 = function(div, tab) {
                     $(div).append(`<div>First render</div>`);
                 };
             });
 
+            // offset to avoid overlapping elements
             $('=Async Tab').click();
 
             browser.pause(1000);

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

@@ -7,7 +7,7 @@ var checkElementWithMouseDisabled = require('../../../shared/specUtils')
     .checkElementWithMouseDisabled;
 var waitForNetworkQuiet = require('../../../shared/specUtils')
     .waitForNetworkQuiet;
-var { setCheckboxChecked } = require('../../../shared/specUtils');
+var { setCheckboxChecked, jsApiClick } = require('../../../shared/specUtils');
 var assertScreenShotMatch = require('../../../shared/lib/testUtils')
     .assertScreenShotMatch;
 var { jsApiHover } = require('../../../shared/specUtils');
@@ -74,17 +74,20 @@ describe('Patient View Genomic Evolution tab screenshot tests', function() {
 
     it('pvge only show highlighted in line chart', function() {
         setCheckboxChecked(false, 'input[data-test="VAFSequentialMode"]');
-        $('input[data-test="VAFOnlyHighlighted"]').click();
+        setCheckboxChecked(true, 'input[data-test="VAFOnlyHighlighted"]');
+
         const res = browser.checkElement('[data-test=VAFChartWrapper]');
         assertScreenShotMatch(res);
     });
     it('pvge line chart log scale', function() {
-        $('input[data-test="VAFLogScale"]').click();
+        jsApiClick('input[data-test="VAFLogScale"]');
+
         const res = browser.checkElement('[data-test=VAFChartWrapper]');
         assertScreenShotMatch(res);
     });
     it('pvge line chart with data range y axis', function() {
-        $('input[data-test="VAFDataRange"]').click();
+        jsApiClick('input[data-test="VAFDataRange"]');
+
         const res = browser.checkElement('[data-test=VAFChartWrapper]');
         assertScreenShotMatch(res);
     });