Upgrade to Cypress 13 (#1966)

* try cypress 13 upgrade

* update license

* fix mytools test's input failure

* see if experimentalMemoryManagement resolves crashes

* will the newest version help performance?

* try fixing organizations test (remove entry from collection)

* try fixing mytools (get buttons by data-cy)

* try intercepting tool's unpublish request

* try fixing checker flake (add visit, add visibility assertion)

* fix some flakes/errors
- mytools: scrollIntoView might help with typing in modals
- checkerWorkflowFromWorkflow: apply same visibility assertion as tool version

* fix goodTopic flake

* add assertions to fix searchTable flake

* try longer wait time in linkCheck

* fix link in download cli client
(handled in hotfix, but fix here to pass linkCheck)

* hopefully handle occasional flakes
- myworkflows: visibility assertion to fix typing
- starErrorMessage: assert starred state

* myworkflows fix didn't work - try scrollIntoView?

* try scrolling into modal

* mat-horizontal-stepper errored more

* add wait for redirect, observe decode

* try moving intercept to beforeEach

THIRD-PARTY-LICENSES.csv

@@ -207,7 +207,7 @@
 "[email protected]","Apache-2.0","https://github.com/mathjax/MathJax"
 "[email protected]","MIT","https://github.com/mermaid-js/mermaid"
 "[email protected]","ISC","https://github.com/isaacs/minimatch"
-"[email protected].6","MIT","https://github.com/substack/minimist"
+"[email protected].8","MIT","https://github.com/minimistjs/minimist"
 "[email protected]","ISC","https://github.com/isaacs/minipass"
 "[email protected]","MIT","https://github.com/isaacs/minizlib"
 "[email protected]","BSD-2-Clause","https://github.com/maxogden/mississippi"

cypress.config.ts

@@ -6,6 +6,7 @@ export default defineConfig({
   viewportWidth: 1440,
   defaultCommandTimeout: 30000,
   requestTimeout: 30000,
+  experimentalMemoryManagement: true,
   retries: {
     runMode: 3,
     openMode: 0,

cypress/e2e/group1/checkerWorkflowFromTools.ts

@@ -19,6 +19,7 @@ describe('Checker workflow test from my-tools', () => {
   resetDB();
   setTokenUserViewPort();
   beforeEach(() => {
+    cy.intercept('api/containers/*?include=validations').as('getTool');
     // Visit my-tools page
     cy.visit('/my-tools');
   });
@@ -34,7 +35,6 @@ describe('Checker workflow test from my-tools', () => {
 
   describe('Should be able to register and publish a checker workflow from a tool', () => {
     it('visit a tool and have the correct buttons and be able to register a checker workflow', () => {
-      cy.intercept('api/containers/*?include=validations').as('getTool');
       cy.wait('@getTool');
       goToB3();
 
@@ -43,9 +43,9 @@ describe('Checker workflow test from my-tools', () => {
       cy.get('#launchCheckerWorkflow').should('not.exist');
       cy.get('#addCheckerWorkflowButton').should('be.visible').click();
 
-      cy.get('#checkerWorkflowPath').type('/Dockstore.cwl');
+      cy.get('#checkerWorkflowPath').should('be.visible').type('/Dockstore.cwl');
 
-      cy.get('#checkerWorkflowTestParameterFilePath').type('/test.json');
+      cy.get('#checkerWorkflowTestParameterFilePath').should('be.visible').type('/test.json');
 
       cy.get('#submitButton').click();
 
@@ -89,12 +89,14 @@ describe('Checker workflow test from my-tools', () => {
     });
     it('visit the tool and have its publish/unpublish reflected in the checker workflow', () => {
       cy.intercept('api/containers/*?include=validations').as('getTool');
+      cy.intercept('api/containers/4/publish').as('unpublishTool');
       cy.wait('@getTool');
       goToB3();
       // In the parent tool right now
       // Didn't change the tool path upon entry or select
       // cy.url().should('eq','/my-tools/quay.io/A2/b3')
       cy.get('#publishToolButton').should('be.visible').should('contain', 'Unpublish').click();
+      cy.wait('@unpublishTool');
 
       goToTab('Versions');
       cy.contains('button', 'Actions').should('be.visible').click();

cypress/e2e/group1/checkerWorkflowFromWorkflow.ts

@@ -46,8 +46,8 @@ describe('Checker workflow test from my-workflows', () => {
       cy.get('#launchCheckerWorkflow').should('not.exist');
       goToTab('Info');
       cy.get('#addCheckerWorkflowButton').should('be.visible').click();
-      cy.get('#checkerWorkflowPath').type('/Dockstore.cwl');
-      cy.get('#checkerWorkflowTestParameterFilePath').type('/test.json');
+      cy.get('#checkerWorkflowPath').should('be.visible').type('/Dockstore.cwl');
+      cy.get('#checkerWorkflowTestParameterFilePath').should('be.visible').type('/test.json');
       cy.fixture('refreshedChecker').then((json) => {
         cy.intercept('GET', '/api/workflows/*/refresh', {
           body: json,

cypress/e2e/group2/myworkflows.ts

@@ -229,7 +229,7 @@ describe('Dockstore my workflows', () => {
       cy.contains('goodTopic').should('not.exist');
 
       cy.visit(privateEntryURI);
-      cy.get('.mat-radio-label').contains('Manual').click();
+      cy.contains('mat-radio-button', 'Manual').find('input').should('not.be.disabled').click({ force: true });
       cy.visit(privateEntryURI);
       cy.get('[data-cy=viewPublicWorkflowButton]').should('be.visible').click();
       cy.contains('goodTopic').should('exist');
@@ -529,9 +529,9 @@ describe('Dockstore my workflows part 3', () => {
       // Untouched form should not have errors but is disabled
       cy.get('#submitButton').should('be.disabled');
       notHaveAlert();
-      cy.get('#sourceCodeRepositoryInput').clear().type('beef/stew');
+      cy.get('#sourceCodeRepositoryInput').scrollIntoView().should('be.visible').clear().type('beef/stew');
       cy.get('#submitButton').should('be.disabled');
-      cy.get('#sourceCodeRepositoryWorkflowPathInput').clear().type('/Dockstore.cwl');
+      cy.get('#sourceCodeRepositoryWorkflowPathInput').scrollIntoView().should('be.visible').clear().type('/Dockstore.cwl');
       notHaveAlert();
       // Apparently the actual radio button inside Angular material buttons is hidden, so doing it this way
       cy.get('#descriptorTypeRadioButtons').contains(cwlDescriptorType).find('.mat-radio-container').click();

cypress/e2e/group2/organizations.ts

@@ -280,6 +280,7 @@ describe('Dockstore Organizations', () => {
       cy.url().should('include', url);
       cy.get('[data-cy=cancel-remove-entry-from-org]').click();
       cy.url().should('include', url);
+      cy.get('app-collection-entry-confirm-remove').should('not.exist');
       cy.get('#removeEntryButton').click();
       cy.url().should('include', url);
       cy.get('[data-cy=accept-remove-entry-from-org]').click();
@@ -293,7 +294,6 @@ describe('Dockstore Organizations', () => {
       cy.contains('This collection has no associated entries');
       cy.visit('/organizations/Potatoe');
       cy.contains('Members').should('be.visible');
-
       approvePotatoOrganization();
       for (const url of ['/organizations', '/organizations/Potatoe', '/organizations/Potatoe/collections/veryFakeCollectionName']) {
         cy.visit(url);

cypress/e2e/group3/mytools.ts

@@ -144,15 +144,15 @@ describe('Dockstore my tools', () => {
       selectTool('b1');
       cy.contains('Versions').click();
       cy.contains('button', 'Actions').should('be.visible').click();
-      cy.contains('button:visible', 'Edit').should('be.visible').click();
+      cy.get('[data-cy=editTagButton]').should('be.visible').click();
       // For some unknown reason, Cypress likes to type '/test.wdl.json' in the wrong place
       cy.wait(5000);
       cy.get('input[data-cy=addWDLField]').should('be.visible').should('have.value', '').type('/test.wdl.json');
       cy.get('input[data-cy=addCWLField]').should('be.visible').should('have.value', '').type('/test.cwl.json');
       cy.get('#saveVersionModal').click();
       cy.get('#saveVersionModal').should('not.exist');
       cy.contains('button', 'Actions').should('be.visible').click();
-      cy.contains('button:visible', 'Edit').should('be.visible').click();
+      cy.get('[data-cy=editTagButton]').should('be.visible').click();
       cy.get('#removeCWLTestParameterFileButton').click();
       cy.get('#removeWDLTestParameterFileButton').click();
       cy.get('#saveVersionModal').click();
@@ -278,7 +278,7 @@ describe('Dockstore my tools', () => {
       cy.contains('Create tool with descriptor(s) on remote sites').should('be.visible').click();
       cy.get('.modal-footer').contains('Next').first().click();
 
-      cy.get('#sourceCodeRepositoryInput').type('testnamespace/testname').wait(1000);
+      cy.get('#sourceCodeRepositoryInput').scrollIntoView().should('be.visible').click().type('testnamespace/testname');
 
       cy.get('[data-cy=imageRegistryProviderSelect]').click();
       cy.contains('Amazon ECR').click();
@@ -342,7 +342,7 @@ describe('Dockstore my tools', () => {
       cy.contains('Create tool with descriptor(s) on remote sites').should('be.visible').click();
       cy.get('.modal-footer').contains('Next').first().click();
 
-      cy.get('#sourceCodeRepositoryInput').type('testnamespace/testname').wait(1000);
+      cy.get('#sourceCodeRepositoryInput').scrollIntoView().should('be.visible').click().type('testnamespace/testname');
 
       cy.get('[data-cy=imageRegistryProviderSelect]').click();
       cy.contains('Amazon ECR').click();
@@ -448,7 +448,7 @@ describe('Dockstore my tools', () => {
       cy.contains('Create tool with descriptor(s) on remote sites').should('be.visible').click();
       cy.get('.modal-footer').contains('Next').first().click();
 
-      cy.get('#sourceCodeRepositoryInput').type('testnamespace/testname').wait(1000);
+      cy.get('#sourceCodeRepositoryInput').scrollIntoView().should('be.visible').click().type('testnamespace/testname');
 
       cy.get('[data-cy=imageRegistryProviderSelect]').click();
       cy.contains('mat-option', 'Seven Bridges').click();

cypress/e2e/group3/starErrorMessage.ts

@@ -39,6 +39,7 @@ describe('Tool and workflow starring error messages', () => {
     cy.visit(url);
 
     cy.get('#starringButtonIcon').click();
+    cy.get('#starCountButton').should('contain', 1);
 
     cy.intercept('PUT', routePath, {
       body: 'You cannot unstar the ' + type + ' ' + name + ' because you have not starred it.',

cypress/e2e/immutableDatabaseTests/linkCheck.ts

@@ -25,7 +25,7 @@ describe('Find broken anchor links', () => {
 
   function checkUrls(path: string) {
     let brokenUrls = [];
-    cy.visit(path).wait(500); // Temporary solution to ensure the page loads entirely
+    cy.visit(path).wait(1000); // Temporary solution to ensure the page loads entirely
     cy.get('a')
       .each((anchor) => {
         cy.get(anchor).then((anchor) => {
@@ -73,7 +73,7 @@ describe('Find broken image links', () => {
 
   function checkImages(path: string, selector: string) {
     let brokenImages = [];
-    cy.visit(path).wait(500);
+    cy.visit(path).wait(1000);
     cy.get('app-root').should('be.visible');
     cy.get('img')
       .each((image) => {

cypress/e2e/immutableDatabaseTests/searchTable.ts

@@ -394,28 +394,32 @@ describe('search table items per page', () => {
     cy.get('[data-cy=advanced-search]').click();
 
     cy.get('[data-cy=dropdown]').click();
-    cy.get('[data-cy=file_select').should('not.exist');
-    cy.get('[data-cy=desc_select').should('be.visible').click();
+    cy.get('[data-cy=file_select]').should('not.exist');
+    cy.get('[data-cy=desc_select]').should('be.visible').click();
 
     cy.get('[data-cy=NOTFilter]').click().type('garyluu');
     cy.get('[data-cy=confirm-search]').click();
+    // Check that the advanced search dialog box has been closed
+    cy.get('app-advancedsearch').should('not.exist');
 
     cy.get('[data-cy=advanced-search]').click();
     cy.get('[data-cy=clear-advanced-search]').click();
+    cy.get('app-advancedsearch').should('not.exist');
 
     cy.get('[data-cy=advanced-search]').click();
 
     cy.get('[data-cy=dropdown]').click();
-    cy.get('[data-cy=desc_select').should('be.visible').click();
+    cy.get('[data-cy=desc_select]').should('be.visible').click();
 
     cy.get('[data-cy=dropdown]').click();
-    cy.get('[data-cy=desc_select').should('not.exist');
-    cy.get('[data-cy=file_select').should('be.visible').click();
+    cy.get('[data-cy=desc_select]').should('not.exist');
+    cy.get('[data-cy=file_select]').should('be.visible').click();
 
     cy.get('[data-cy=ANDNoSplitFilter]').click().type('gary');
     cy.get('[data-cy=ORFilter]').click().type('A2');
     cy.get('[data-cy=NOTFilter]').click().type('b3');
     cy.get('[data-cy=confirm-search]').click();
+    cy.get('app-advancedsearch').should('not.exist');
 
     cy.get('[data-cy=advanced-search]').click();
     cy.get('[data-cy=clear-advanced-search]').click();

cypress/e2e/immutableDatabaseTests/services.ts

@@ -27,21 +27,28 @@ import {
 describe('Dockstore Home', () => {
   describe('GitHub App Callback Routing', () => {
     setTokenUserViewPort();
+    beforeEach(() => {
+      cy.intercept('GET', '/api/metadata/entryTypeMetadataList').as('getMetadata');
+    });
     it('Redirects to my-tools', () => {
       cy.visit('/githubCallback?state=/my-tools/quay.io/A2/b1');
-      cy.url().should('contain', '/my-tools/quay.io/A2/b1');
+      cy.wait('@getMetadata');
+      cy.url().should('contain', '%2Fmy-tools%2Fquay.io%2FA2%2Fb1');
     });
     it('Redirects to my-workflows', () => {
       cy.visit('/githubCallback?state=/my-workflows/github.com/A/l');
-      cy.url().should('contain', '/my-workflows/github.com/A/l');
+      cy.wait('@getMetadata');
+      cy.url().should('contain', '%2Fmy-workflows%2Fgithub.com%2FA%2Fl');
     });
     it('Redirects to my-services', () => {
       cy.visit('/githubCallback?state=/services/github.com/garyluu/another-test-service');
-      cy.url().should('contain', '/services/github.com/garyluu/another-test-service');
+      cy.wait('@getMetadata');
+      cy.url().should('contain', '%2Fservices%2Fgithub.com%2Fgaryluu%2Fanother-test-service');
     });
     it('Redirects to dashboard', () => {
       cy.visit('githubCallback?state=/dashboard');
-      cy.url().should('contain', '/dashboard');
+      cy.wait('@getMetadata');
+      cy.url().should('contain', '%2Fdashboard');
     });
   });