merge develop

cypress/e2e/group2/myworkflows.ts

@@ -545,9 +545,13 @@ 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').scrollIntoView().should('be.visible').clear().type('beef/stew');
+      cy.get('#sourceCodeRepositoryInput').scrollIntoView().should('be.visible');
+      cy.get('#sourceCodeRepositoryInput').clear();
+      cy.get('#sourceCodeRepositoryInput').type('beef/stew');
       cy.get('#submitButton').should('be.disabled');
-      cy.get('#sourceCodeRepositoryWorkflowPathInput').scrollIntoView().should('be.visible').clear().type('/Dockstore.cwl');
+      cy.get('#sourceCodeRepositoryWorkflowPathInput').scrollIntoView().should('be.visible');
+      cy.get('#sourceCodeRepositoryWorkflowPathInput').clear();
+      cy.get('#sourceCodeRepositoryWorkflowPathInput').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/group3/mytools.ts

@@ -278,7 +278,9 @@ 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').scrollIntoView().should('be.visible').click().type('testnamespace/testname');
+      cy.get('#sourceCodeRepositoryInput').scrollIntoView().should('be.visible');
+      cy.get('#sourceCodeRepositoryInput').click();
+      cy.get('#sourceCodeRepositoryInput').type('testnamespace/testname');
 
       cy.get('[data-cy=imageRegistryProviderSelect]').click();
       cy.contains('Amazon ECR').click();
@@ -342,7 +344,9 @@ 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').scrollIntoView().should('be.visible').click().type('testnamespace/testname');
+      cy.get('#sourceCodeRepositoryInput').scrollIntoView().should('be.visible');
+      cy.get('#sourceCodeRepositoryInput').click();
+      cy.get('#sourceCodeRepositoryInput').type('testnamespace/testname');
 
       cy.get('[data-cy=imageRegistryProviderSelect]').click();
       cy.contains('Amazon ECR').click();
@@ -448,7 +452,9 @@ 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').scrollIntoView().should('be.visible').click().type('testnamespace/testname');
+      cy.get('#sourceCodeRepositoryInput').scrollIntoView().should('be.visible');
+      cy.get('#sourceCodeRepositoryInput').click();
+      cy.get('#sourceCodeRepositoryInput').type('testnamespace/testname');
 
       cy.get('[data-cy=imageRegistryProviderSelect]').click();
       cy.contains('mat-option', 'Seven Bridges').click();
@@ -458,6 +464,7 @@ describe('Dockstore my tools', () => {
 
       cy.get('#imageRegistryInput').type('testnamespace/testname');
 
+      cy.get('#submitButton').scrollIntoView().should('be.enabled');
       cy.get('#submitButton').click();
 
       // TODO: This is temporarily disabled
@@ -532,7 +539,8 @@ describe('Dockstore my tools', () => {
       cy.visit('/containers/quay.io/A2/a');
       goToTab('Versions');
       cy.get('[data-cy=actionsButton]').should('be.visible').first().click();
-      cy.get('[data-cy=ok-dialog-close-button]').scrollIntoView().should('be.visible').click();
+      cy.get('[data-cy=ok-dialog-close-button]').scrollIntoView().should('be.visible');
+      cy.get('[data-cy=ok-dialog-close-button]').click();
     });
   });
 });

cypress/e2e/smokeTests/sharedTests/auth-tests.ts

@@ -179,7 +179,9 @@ function toggleHiddenToolVersion() {
 }
 
 function toggleHiddenWorkflowVersion() {
-  cy.get('[data-cy=versionRow]').last().scrollIntoView().contains('button', 'Actions').should('be.visible').click();
+  cy.get('[data-cy=versionRow]').last().scrollIntoView().contains('button', 'Actions').should('be.visible');
+  cy.get('[data-cy=versionRow]').last().contains('button', 'Actions').click();
+  cy.contains('button', 'Edit').scrollIntoView();
   cy.contains('button', 'Edit').click();
   // TODO: Use [data-cy=hiddenCheck] -- do after 1.14 deployed
   cy.contains('div', 'Hidden:').within(() => {
@@ -266,7 +268,9 @@ function testWorkflow(registry: string, repo: string, name: string) {
 
       goToTab('Info');
       cy.contains('button', 'Restub').click();
-      cy.contains('button', 'Publish').should('be.disabled');
+      // This fails because DOI is auto issued when published, and restub fails.
+      // See https://ucsc-gi.slack.com/archives/C05EZH3RVNY/p1718128426265779
+      // cy.contains('button', 'Publish').should('be.disabled');
 
       cy.get('[data-cy=refreshButton]').click();
       goToTab('Versions');

src/app/about/about.component.html

@@ -140,7 +140,7 @@ <h2>The Importance of Sharing</h2>
           <h3>Building a Community</h3>
           <p>
             Several large projects and organizations in the Biosciences, specifically cancer sequencing projects such as
-            <a target="_blank" rel="noopener noreferrer" href="https://dcc.icgc.org/pcawg">PCAWG</a>,
+            <a target="_blank" rel="noopener noreferrer" href="https://docs.icgc-argo.org/docs/data-access/icgc-25k-data">PCAWG</a>,
             <a target="_blank" rel="noopener noreferrer" href="https://precision.fda.gov/">PrecisionFDA</a>,
             <a target="_blank" rel="noopener noreferrer" href="https://www.broadinstitute.org/">the Broad Institute</a>,
             <a target="_blank" rel="noopener noreferrer" href="https://www.ucsc.edu/">the University of California Santa Cruz</a>, and

src/app/about/about.component.ts

@@ -6,12 +6,34 @@ import { map } from 'rxjs/operators';
 import { Funder, FundingComponent } from '../funding/funding.component';
 import { Dockstore } from '../shared/dockstore.model';
 import { Sponsor } from '../sponsors/sponsor.model';
+import { RouterLink } from '@angular/router';
+import { MatLegacyCardModule } from '@angular/material/legacy-card';
+import { MatLegacyTabsModule } from '@angular/material/legacy-tabs';
+import { ExtendedModule } from '@ngbracket/ngx-layout/extended';
+import { NgStyle, NgFor, AsyncPipe, SlicePipe } from '@angular/common';
+import { MatIconModule } from '@angular/material/icon';
+import { MatLegacyButtonModule } from '@angular/material/legacy-button';
+import { FlexModule } from '@ngbracket/ngx-layout/flex';
 
 @Component({
   selector: 'app-about',
   templateUrl: './about.component.html',
   styleUrls: ['./about.component.scss'],
   providers: [FundingComponent],
+  standalone: true,
+  imports: [
+    FlexModule,
+    MatLegacyButtonModule,
+    MatIconModule,
+    NgStyle,
+    ExtendedModule,
+    MatLegacyTabsModule,
+    MatLegacyCardModule,
+    RouterLink,
+    NgFor,
+    AsyncPipe,
+    SlicePipe,
+  ],
 })
 export class AboutComponent implements OnInit {
   Dockstore = Dockstore;
@@ -36,7 +58,7 @@ export class AboutComponent implements OnInit {
     new Sponsor('ucsc.png', new URL('https://ucscgenomics.soe.ucsc.edu/')),
     new Sponsor('broad.svg', new URL('https://www.broadinstitute.org/')),
     new Sponsor('ga4gh.svg', new URL('https://genomicsandhealth.org/')),
-    new Sponsor('pcawg.png', new URL('https://dcc.icgc.org/pcawg')),
+    new Sponsor('pcawg.png', new URL('https://docs.icgc-argo.org/docs/data-access/icgc-25k-data')),
     new Sponsor('precision.png', new URL('https://precision.fda.gov/')),
     new Sponsor('nf-core.png', new URL('https://nf-co.re/')),
   ];

src/app/aliases/aliases.component.ts

@@ -7,11 +7,18 @@ import { ActivatedRoute, Router } from '../test';
 import { AliasesQuery } from './state/aliases.query';
 import { AliasesService } from './state/aliases.service';
 import { EntryTypeMetadataService } from '../entry/type-metadata/entry-type-metadata.service';
+import { MatLegacyProgressBarModule } from '@angular/material/legacy-progress-bar';
+import { MatIconModule } from '@angular/material/icon';
+import { MatLegacyCardModule } from '@angular/material/legacy-card';
+import { NgIf, AsyncPipe } from '@angular/common';
+import { HeaderComponent } from '../header/header.component';
 
 @Component({
   selector: 'app-aliases',
   templateUrl: './aliases.component.html',
   styleUrls: ['./aliases.component.scss'],
+  standalone: true,
+  imports: [HeaderComponent, NgIf, MatLegacyCardModule, MatIconModule, MatLegacyProgressBarModule, AsyncPipe],
 })
 export class AliasesComponent extends Base implements OnInit {
   loading$: Observable<boolean>;

src/app/aliases/aliases.routing.ts

@@ -14,7 +14,7 @@
  *    limitations under the License.
  */
 
-import { RouterModule, Routes } from '@angular/router';
+import { Routes } from '@angular/router';
 import { AliasesComponent } from './aliases.component';
 
 const ALIASES_ROUTES: Routes = [
@@ -25,4 +25,4 @@ const ALIASES_ROUTES: Routes = [
   },
 ];
 
-export const AliasesRouting = RouterModule.forChild(ALIASES_ROUTES);
+export const AliasesRouting = ALIASES_ROUTES;

src/app/app.component.spec.ts

@@ -1,47 +1,118 @@
-import { TestBed, waitForAsync } from '@angular/core/testing';
-import { RouterTestingModule } from '@angular/router/testing';
-import { RouterLinkStubDirective, RouterOutletStubComponent } from './test/router-stubs';
+import { HttpClientTestingModule } from '@angular/common/http/testing';
 
 import { Component } from '@angular/core';
+import { TestBed, waitForAsync } from '@angular/core/testing';
+import { MatLegacyDialogModule } from '@angular/material/legacy-dialog';
 import { MatLegacySnackBarModule as MatSnackBarModule } from '@angular/material/legacy-snack-bar';
+import { RouterTestingModule } from '@angular/router/testing';
+import { AuthService } from 'ng2-ui-auth';
 import { AppComponent } from './app.component';
+import { MytoolsService } from './mytools/mytools.service';
+import { MyWorkflowsService } from './myworkflows/myworkflows.service';
+import { ServiceInfoService } from './service-info/service-info.service';
+import { ContainerService } from './shared/container.service';
+import { DateService } from './shared/date.service';
+import { DescriptorLanguageService } from './shared/entry/descriptor-language.service';
+import { LogoutService } from './shared/logout.service';
+import { Configuration, UsersService } from './shared/openapi';
+import { PagenumberService } from './shared/pagenumber.service';
+import { ProviderService } from './shared/provider.service';
+import { MyEntriesStateService } from './shared/state/my-entries.service';
+import { MyEntriesStore } from './shared/state/my-entries.store';
 import { TrackLoginService } from './shared/track-login.service';
-import { TosBannerStubService, TrackLoginStubService } from './test/service-stubs';
+import { UrlResolverService } from './shared/url-resolver.service';
+import { RouterLinkStubDirective, RouterOutletStubComponent } from './test/router-stubs';
+import {
+  AuthStubService,
+  ConfigurationStub,
+  ContainerStubService,
+  DateStubService,
+  DescriptorLanguageStubService,
+  GA4GHV20StubService,
+  LogoutStubService,
+  ProviderStubService,
+  TosBannerStubService,
+  TrackLoginStubService,
+  UrlResolverStubService,
+  UsersStubService,
+} from './test/service-stubs';
 import { TosBannerService } from './tosBanner/state/tos-banner.service';
 
-@Component({ selector: 'app-banner', template: '' })
+@Component({
+  selector: 'app-banner',
+  template: '',
+  standalone: true,
+  imports: [RouterTestingModule, MatSnackBarModule],
+})
 class BannerStubComponent {}
 
-@Component({ selector: 'app-navbar', template: '' })
+@Component({
+  selector: 'app-navbar',
+  template: '',
+  standalone: true,
+  imports: [RouterTestingModule, MatSnackBarModule],
+})
 class NavbarStubComponent {}
 
-@Component({ selector: 'app-footer', template: '' })
+@Component({
+  selector: 'app-footer',
+  template: '',
+  standalone: true,
+  imports: [RouterTestingModule, MatSnackBarModule],
+})
 class FooterStubComponent {}
 
-@Component({ selector: 'app-tos-banner', template: '' })
+@Component({
+  selector: 'app-tos-banner',
+  template: '',
+  standalone: true,
+  imports: [RouterTestingModule, MatSnackBarModule],
+})
 class TosBannerStubComponent {}
 
-@Component({ selector: 'app-sitewide-notifications', template: '' })
+@Component({
+  selector: 'app-sitewide-notifications',
+  template: '',
+  standalone: true,
+  imports: [RouterTestingModule, MatSnackBarModule],
+})
 class NotificationStubComponent {}
 
 describe('AppComponent', () => {
   beforeEach(
     waitForAsync(() => {
       TestBed.configureTestingModule({
-        declarations: [
-          AppComponent,
+        declarations: [RouterLinkStubDirective, RouterOutletStubComponent],
+        imports: [
+          RouterTestingModule,
+          MatLegacyDialogModule,
+          MatSnackBarModule,
+          HttpClientTestingModule,
           NavbarStubComponent,
           FooterStubComponent,
           BannerStubComponent,
-          RouterLinkStubDirective,
-          RouterOutletStubComponent,
           TosBannerStubComponent,
           NotificationStubComponent,
+          AppComponent,
         ],
-        imports: [RouterTestingModule, MatSnackBarModule],
         providers: [
           { provide: TrackLoginService, useClass: TrackLoginStubService },
           { provide: TosBannerService, useClass: TosBannerStubService },
+          { provide: AuthService, useClass: AuthStubService },
+          { provide: Configuration, useClass: ConfigurationStub },
+          { provide: ContainerService, useClass: ContainerStubService },
+          { provide: ServiceInfoService, useClass: GA4GHV20StubService },
+          { provide: DateService, useClass: DateStubService },
+          { provide: ProviderService, useClass: ProviderStubService },
+          { provide: DescriptorLanguageService, useClass: DescriptorLanguageStubService },
+          { provide: UrlResolverService, useClass: UrlResolverStubService },
+          { provide: UsersService, useClass: UsersStubService },
+          { provide: LogoutService, useClass: LogoutStubService },
+          MyEntriesStateService,
+          MyEntriesStore,
+          MytoolsService,
+          MyWorkflowsService,
+          PagenumberService,
         ],
       }).compileComponents();
     })

src/app/app.component.ts

@@ -1,21 +1,40 @@
+import { AsyncPipe, NgIf } from '@angular/common';
 import { Component, OnDestroy, OnInit } from '@angular/core';
 import { Title } from '@angular/platform-browser';
-import { ActivatedRoute, NavigationEnd, Router } from '@angular/router';
+import { ActivatedRoute, NavigationEnd, Router, RouterOutlet } from '@angular/router';
 import { Observable, Subject } from 'rxjs';
 import { filter, map, mergeMap, takeUntil } from 'rxjs/operators';
+import { BannerComponent } from './banner/banner.component';
+import { ChangeUsernameBannerComponent } from './changeUsernameBanner/changeUsernameBanner.component';
+import { FooterComponent } from './footer/footer.component';
+import { NavbarComponent } from './navbar/navbar.component';
+import { SitewideNotificationsComponent } from './notifications/sitewide-notifications.component';
 import { AlertService } from './shared/alert/state/alert.service';
 import { currentPrivacyPolicyVersion, currentTOSVersion } from './shared/constants';
 import { Dockstore } from './shared/dockstore.model';
 import { User } from './shared/openapi/model/user';
 import { TrackLoginService } from './shared/track-login.service';
-import { TosBannerQuery } from './tosBanner/state/tos-banner.query';
 import { UserQuery } from './shared/user/user.query';
+import { TosBannerQuery } from './tosBanner/state/tos-banner.query';
 import { TosBannerService } from './tosBanner/state/tos-banner.service';
+import { TosBannerComponent } from './tosBanner/tos-banner.component';
 
 @Component({
   selector: 'app-root',
   templateUrl: './app.component.html',
   styleUrls: ['./app.component.css'],
+  standalone: true,
+  imports: [
+    NgIf,
+    TosBannerComponent,
+    ChangeUsernameBannerComponent,
+    SitewideNotificationsComponent,
+    BannerComponent,
+    NavbarComponent,
+    RouterOutlet,
+    FooterComponent,
+    AsyncPipe,
+  ],
 })
 export class AppComponent implements OnInit, OnDestroy {
   public isLoggedIn$: Observable<boolean>;