- No published tools. -
-- No published services. -
-- No published workflows. +
+ No published {{ pageEntryType === EntryType.AppTool ? 'tool' : pageEntryType }}s.
- No unpublished tools. -
-- No unpublished services. -
-- No unpublished workflows. +
+ No unpublished {{ pageEntryType === EntryType.AppTool ? 'tool' : pageEntryType }}s.
+
info This collection is part of an organization that is pending approval by a Dockstore curator.
@@ -101,18 +104,11 @@
diff --git a/src/app/starredentries/starredentries.component.scss b/src/app/starredentries/starredentries.component.scss
index 0ec205473b..af8054cb38 100644
--- a/src/app/starredentries/starredentries.component.scss
+++ b/src/app/starredentries/starredentries.component.scss
@@ -1,8 +1,3 @@
-.entryType-icons {
- align-self: center;
- justify-content: center;
-}
-
.starred-header {
margin-left: 30px;
margin-right: 30px;
diff --git a/src/app/test/openapi-mocked-objects.ts b/src/app/test/openapi-mocked-objects.ts
index 3e42f0ac38..2476ca5b86 100644
--- a/src/app/test/openapi-mocked-objects.ts
+++ b/src/app/test/openapi-mocked-objects.ts
@@ -1,4 +1,4 @@
-import { Workflow } from '../shared/openapi';
+import { Workflow, DockstoreTool, CollectionEntry } from '../shared/openapi';
export const sampleWorkflow1: Workflow = {
type: 'whatever',
@@ -13,4 +13,68 @@ export const sampleWorkflow1: Workflow = {
sourceControl: 'github.com',
source_control_provider: 'GITHUB',
full_workflow_path: 'github.com/updatedOrganization/updatedWorkflowPath',
+ entryTypeMetadata: {
+ searchEntryType: 'workflows',
+ searchSupported: true,
+ sitePath: 'workflows',
+ term: 'workflow',
+ termPlural: 'workflows',
+ trsPrefix: '#workflow/',
+ trsSupported: true,
+ type: 'WORKFLOW',
+ },
+};
+
+export const sampleTool1: DockstoreTool = {
+ id: 1,
+ default_cwl_path: 'sampleDefaultCWLPath',
+ default_dockerfile_path: 'sampleDefaultDockerfilePath',
+ default_wdl_path: 'sampleDefaultWDLPath',
+ gitUrl: 'sampleGitUrl',
+ mode: DockstoreTool.ModeEnum.MANUALIMAGEPATH,
+ name: 'sampleName',
+ namespace: 'sampleNamespace',
+ private_access: false,
+ registry_string: 'quay.io',
+ registry: DockstoreTool.RegistryEnum.QUAYIO,
+ toolname: 'sampleToolname',
+ defaultCWLTestParameterFile: 'sampleDefaultCWLTestParameterFile',
+ defaultWDLTestParameterFile: 'sampleDefaultWDLTestParameterFile',
+ tool_path: 'quay.io/sampleNamespace/sampleName',
+ entryTypeMetadata: {
+ searchEntryType: 'tools',
+ searchSupported: true,
+ sitePath: 'containers',
+ term: 'tool',
+ termPlural: 'tools',
+ trsPrefix: '',
+ trsSupported: true,
+ type: 'TOOL',
+ },
+};
+
+// Tool Collection entry
+export const sampleCollectionEntry1: CollectionEntry = {
+ categories: [],
+ dbUpdateDate: 1648777051404,
+ descriptorTypes: ['CWL'],
+ entryPath: 'quay.io/pancancer/pcawg-dkfz-workflow',
+ entryType: 'tool',
+ id: 188,
+ labels: ['variant-caller', 'pcawg'],
+ verified: true,
+ versionName: null,
+};
+
+// Notebook Collection entry with version
+export const sampleCollectionEntry2: CollectionEntry = {
+ categories: [],
+ dbUpdateDate: 1681400016194,
+ descriptorTypes: ['jupyter'],
+ entryPath: 'github.com/david4096/simple-notebook/simplers',
+ entryType: 'notebook',
+ id: 21113,
+ labels: ['book'],
+ verified: false,
+ versionName: 'version',
};
diff --git a/src/app/test/service-stubs.ts b/src/app/test/service-stubs.ts
index 4086eb8bdb..18b337c74a 100644
--- a/src/app/test/service-stubs.ts
+++ b/src/app/test/service-stubs.ts
@@ -14,6 +14,7 @@
* limitations under the License.
*/
import { EntryType } from 'app/shared/enum/entry-type';
+import { EntryType as newEntryType, EntryTypeMetadata } from 'app/shared/openapi';
import { BehaviorSubject, EMPTY, Observable, of as observableOf } from 'rxjs';
import { SearchFields } from '../search/state/search.service';
import { TagEditorMode } from '../shared/enum/tagEditorMode.enum';
@@ -915,3 +916,71 @@ export class VersionModalStubService {
export class OrgLogoStubService {
setDefault(img: any) {}
}
+
+export class EntryTypeMetadataStubService {
+ get(type: newEntryType): EntryTypeMetadata {
+ switch (type) {
+ case newEntryType.WORKFLOW: {
+ return {
+ searchEntryType: 'workflows',
+ searchSupported: true,
+ sitePath: 'workflows',
+ term: 'workflow',
+ termPlural: 'workflows',
+ trsPrefix: '#workflow/',
+ trsSupported: true,
+ type: 'WORKFLOW',
+ };
+ }
+ case newEntryType.TOOL: {
+ return {
+ searchEntryType: 'tools',
+ searchSupported: true,
+ sitePath: 'containers',
+ term: 'tool',
+ termPlural: 'tools',
+ trsPrefix: '',
+ trsSupported: true,
+ type: 'TOOL',
+ };
+ }
+ case newEntryType.SERVICE: {
+ return {
+ searchEntryType: '',
+ searchSupported: false,
+ sitePath: 'services',
+ term: 'service',
+ termPlural: 'services',
+ trsPrefix: '#service/',
+ trsSupported: true,
+ type: 'SERVICE',
+ };
+ }
+ case newEntryType.APPTOOL: {
+ return {
+ searchEntryType: 'tools',
+ searchSupported: true,
+ sitePath: 'containers',
+ term: 'tool',
+ termPlural: 'tools',
+ trsPrefix: '',
+ trsSupported: true,
+ type: 'APPTOOL',
+ };
+ }
+ case newEntryType.NOTEBOOK: {
+ return {
+ searchEntryType: '',
+ searchSupported: false,
+ sitePath: 'notebooks',
+ term: 'notebook',
+ termPlural: 'notebooks',
+ trsPrefix: '#notebook/',
+ trsSupported: true,
+ type: 'NOTEBOOK',
+ };
+ }
+ }
+ return null;
+ }
+}
diff --git a/src/app/workflow/register-workflow-modal/register-github-app-modal/register-github-app-modal.component.html b/src/app/workflow/register-workflow-modal/register-github-app-modal/register-github-app-modal.component.html
new file mode 100644
index 0000000000..b3efd1818f
--- /dev/null
+++ b/src/app/workflow/register-workflow-modal/register-github-app-modal/register-github-app-modal.component.html
@@ -0,0 +1,34 @@
+
+
Workflows, Notebooks, and ToolsWorkflows and Tools
-
-
+
+
+
-
+
@@ -176,10 +175,10 @@
- 
- 
+ 
;
diff --git a/src/app/organizations/collections.module.ts b/src/app/organizations/collections.module.ts
index d1df95a373..e15f113700 100644
--- a/src/app/organizations/collections.module.ts
+++ b/src/app/organizations/collections.module.ts
@@ -16,6 +16,7 @@ import { CollectionsComponent } from './collections/collections.component';
import { CreateCollectionModule } from './collections/create-collection.module';
import { RemoveCollectionDialogComponent } from './collections/remove-collection/remove-collection.component';
import { UpdateOrganizationDescriptionModule } from './organization/update-organization-description.module';
+import { PreviewWarningModule } from '../shared/modules/preview-warning.module';
@NgModule({
imports: [
@@ -32,6 +33,7 @@ import { UpdateOrganizationDescriptionModule } from './organization/update-organ
CategoryButtonModule,
ImgFallbackModule,
PipeModule,
+ PreviewWarningModule,
],
declarations: [CollectionsComponent, CollectionComponent, CollectionRemoveEntryDialogComponent, RemoveCollectionDialogComponent],
exports: [CollectionsComponent, CollectionComponent],
diff --git a/src/app/shared-workflow-services/shared-workflow-services.module.ts b/src/app/shared-workflow-services-notebooks/shared-workflow-services-notebooks.module.ts
similarity index 81%
rename from src/app/shared-workflow-services/shared-workflow-services.module.ts
rename to src/app/shared-workflow-services-notebooks/shared-workflow-services-notebooks.module.ts
index e7333c5d2d..6b30492880 100644
--- a/src/app/shared-workflow-services/shared-workflow-services.module.ts
+++ b/src/app/shared-workflow-services-notebooks/shared-workflow-services-notebooks.module.ts
@@ -18,8 +18,6 @@ import { CommonModule } from '@angular/common';
import { NgModule } from '@angular/core';
import { FormsModule } from '@angular/forms';
import { RouterModule } from '@angular/router';
-import { MyBioWorkflowsService } from 'app/myworkflows/my-bio-workflows.service';
-import { MyServicesService } from 'app/myworkflows/my-services.service';
import { MyWorkflowsService } from 'app/myworkflows/myworkflows.service';
import { EntryWizardModule } from 'app/shared/entry-wizard.module';
import { MyEntriesModule } from 'app/shared/modules/my-entries.module';
@@ -32,11 +30,14 @@ import { WorkflowModule } from '../shared/modules/workflow.module';
import { PipeModule } from '../shared/pipe/pipe.module';
import { RefreshWorkflowOrganizationComponent } from '../workflow/refresh-workflow-organization/refresh-workflow-organization.component';
import { RegisterWorkflowModalComponent } from '../workflow/register-workflow-modal/register-workflow-modal.component';
+import { RegisterGithubAppModalComponent } from 'app/workflow/register-workflow-modal/register-github-app-modal/register-github-app-modal.component';
+import { PreviewWarningModule } from 'app/shared/modules/preview-warning.module';
const DECLARATIONS: any[] = [
MyWorkflowComponent,
RefreshWorkflowOrganizationComponent,
RegisterWorkflowModalComponent,
+ RegisterGithubAppModalComponent,
SidebarAccordionComponent,
];
const IMPORTS = [
@@ -50,19 +51,20 @@ const IMPORTS = [
RouterModule,
MyEntriesModule,
EntryWizardModule,
+ PreviewWarningModule,
];
/**
- * This is a shared module between the My Workflows page and the My Services page.
+ * This is a shared module between the My Workflows page, My Services page, and My Notebooks page.
* It shares modules and components
*
* @export
- * @class SharedWorkflowServicesModule
+ * @class SharedWorkflowServicesNotebooksModule
*/
@NgModule({
declarations: DECLARATIONS,
imports: IMPORTS,
- providers: [MyWorkflowsService, MyBioWorkflowsService, MyServicesService],
+ providers: [MyWorkflowsService],
exports: [DECLARATIONS.concat(IMPORTS), SidebarAccordionComponent],
})
-export class SharedWorkflowServicesModule {}
+export class SharedWorkflowServicesNotebooksModule {}
diff --git a/src/app/shared/helpers.ts b/src/app/shared/helpers.ts
index 1d208acf5e..2d0a413e46 100644
--- a/src/app/shared/helpers.ts
+++ b/src/app/shared/helpers.ts
@@ -6,6 +6,7 @@ export function toExtendSite(url: string): boolean {
url.startsWith('/my-workflows') ||
url.startsWith('/my-tools') ||
url.startsWith('/my-services') ||
+ url.startsWith('/my-notebooks') ||
url.startsWith('/starred') ||
url.startsWith('/accounts') ||
url.startsWith('/dashboard')
diff --git a/src/app/shared/modules/my-sidebar.module.ts b/src/app/shared/modules/my-sidebar.module.ts
index a2ff6f4704..2f1bc4695c 100644
--- a/src/app/shared/modules/my-sidebar.module.ts
+++ b/src/app/shared/modules/my-sidebar.module.ts
@@ -15,13 +15,14 @@
*/
import { NgModule } from '@angular/core';
+import { CommonModule } from '@angular/common';
import { MySidebarComponent } from '../../my-sidebar/my-sidebar.component';
import { CustomMaterialModule } from 'app/shared/modules/material.module';
import { RouterModule } from '@angular/router';
@NgModule({
declarations: [MySidebarComponent],
- imports: [CustomMaterialModule, RouterModule],
+ imports: [CommonModule, CustomMaterialModule, RouterModule],
providers: [],
exports: [MySidebarComponent],
})
diff --git a/src/app/shared/user/user.query.ts b/src/app/shared/user/user.query.ts
index 986fd2f3b3..76f5d840ad 100644
--- a/src/app/shared/user/user.query.ts
+++ b/src/app/shared/user/user.query.ts
@@ -18,6 +18,7 @@ export class UserQuery extends Query {
canChangeUsername$: Observable = this.select((state) =>
state.extendedUserData ? state.extendedUserData.canChangeUsername : false
);
+ isUsernameChangeRequired$: Observable = this.select((state) => (state.user ? state.user.usernameChangeRequired : null));
username$: Observable = this.select((state) => (state.user ? state.user.username : null));
constructor(protected store: UserStore) {
super(store);
diff --git a/src/app/starredentries/starredentries.component.html b/src/app/starredentries/starredentries.component.html
index 85cd3a1ac9..0cbfeb5aff 100644
--- a/src/app/starredentries/starredentries.component.html
+++ b/src/app/starredentries/starredentries.component.html
@@ -113,13 +113,12 @@
-
-
+
{{ entry.entryPath + (entry.versionName ? ':' + entry.versionName : '') }}
diff --git a/src/app/organizations/collection/collection.component.ts b/src/app/organizations/collection/collection.component.ts index 8214be4a6e..b1fbfcbb21 100644 --- a/src/app/organizations/collection/collection.component.ts +++ b/src/app/organizations/collection/collection.component.ts @@ -17,6 +17,7 @@ import { UpdateOrganizationOrCollectionDescriptionComponent } from '../organizat import { CollectionsQuery } from '../state/collections.query'; import { CollectionsService } from '../state/collections.service'; import { OrganizationQuery } from '../state/organization.query'; +import { EntryType } from 'app/shared/enum/entry-type'; @Component({ selector: 'app-collection-entry-confirm-remove', @@ -50,6 +51,7 @@ export interface EntryDialogData { styleUrls: ['./collection.component.scss', '../organization/organization.component.scss'], }) export class CollectionComponent implements OnInit { + entryType = EntryType; WorkflowMode = Workflow.ModeEnum; DescriptorType = ToolDescriptor.TypeEnum; collection$: Observable
@@ -168,7 +167,7 @@
-
+
-
+
{{ tool?.namespace + '/' + tool?.name + (tool?.toolname ? '/' + tool?.toolname : '') }}
@@ -205,7 +204,7 @@ {{ tool?.namespace + '/' + tool?.name + (tool?.toolname ? '/' + tool?.toolna
-
+
-
+
-
+
@@ -205,7 +204,7 @@
-
+
+
{{ tool?.namespace + '/' + tool?.name + (tool?.toolname ? '/' + tool?.toolname : '') }}
{{ tool?.namespace + '/' + tool?.name + (tool?.toolname ? '/' + tool?.toolna
Register {{ entryType | titlecase }}
+
+
+
+ Navigate to GitHub to install our GitHub app on your repositories/organizations. See our
+
+ documentation
Register Workflow
Last update to this workflow version: {{ versionAgoMessage || 'n/a' }}Last update to this {{ entryType }} version: {{ versionAgoMessage || 'n/a' }}
Name
- {{
+ {{
workflow?.organization + '/' + workflow?.repository + (workflow?.workflowName ? '/' + workflow?.workflowName : '')
}}
diff --git a/src/assets/svg/my-nav/notebooks.svg b/src/assets/svg/my-nav/notebooks.svg
new file mode 100644
index 0000000000..4619172929
--- /dev/null
+++ b/src/assets/svg/my-nav/notebooks.svg
@@ -0,0 +1,3 @@
+
diff --git a/src/assets/svg/sub-nav/notebook.svg b/src/assets/svg/sub-nav/notebook.svg
index 1b591f25b3..4a183d249e 100644
--- a/src/assets/svg/sub-nav/notebook.svg
+++ b/src/assets/svg/sub-nav/notebook.svg
@@ -1 +1,10 @@
-
+
From 75066ec277b4eb0730f33c727ca86d97714853d2 Mon Sep 17 00:00:00 2001
From: Denis Yuen
Date: Thu, 27 Apr 2023 17:33:02 -0400
Subject: [PATCH 002/128] merge fix
---
cypress/e2e/group2/notebooks.ts | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/cypress/e2e/group2/notebooks.ts b/cypress/e2e/group2/notebooks.ts
index 845c737320..85887d66fa 100644
--- a/cypress/e2e/group2/notebooks.ts
+++ b/cypress/e2e/group2/notebooks.ts
@@ -99,7 +99,7 @@ describe('Dockstore notebooks', () => {
cy.visit('/my-notebooks/' + name);
// Check the labels on the tabs.
cy.get('.mat-tab-list').contains('Info');
- cy.get('.mat-tab-list').contains('Code');
+ cy.get('.mat-tab-list').contains('Preview');
cy.get('.mat-tab-list').contains('Versions');
cy.get('.mat-tab-list').contains('Files');
// Should initially display the Info tab.
From ccea277f4bf7cbecfc0624d8d3558e7751d8ba40 Mon Sep 17 00:00:00 2001
From: Kimberley Chong <97123241+KimberleyChong@users.noreply.github.com>
Date: Tue, 2 May 2023 10:20:08 -0400
Subject: [PATCH 003/128] fix some code smells (#1765)
---
cypress/e2e/group2/sharedWorkflows.ts | 1 -
src/app/container/container.component.html | 2 +-
.../list/published-tools.datasource.spec.ts | 4 ++--
.../collection-entry-confirm-remove.html | 2 +-
.../collection/collection.component.ts | 2 +-
.../remove-collection.component.html | 2 +-
.../state/extended-workflow.service.spec.ts | 9 +++++++--
.../source-file-tabs.component.ts | 2 +-
.../starredentries.component.ts | 4 +---
.../workflow/versions/versions.component.ts | 3 +--
src/styles.scss | 20 +++++++------------
11 files changed, 23 insertions(+), 28 deletions(-)
diff --git a/cypress/e2e/group2/sharedWorkflows.ts b/cypress/e2e/group2/sharedWorkflows.ts
index cdee10b1a1..66704964a2 100644
--- a/cypress/e2e/group2/sharedWorkflows.ts
+++ b/cypress/e2e/group2/sharedWorkflows.ts
@@ -15,7 +15,6 @@
*/
import {
cancelMatMenu,
- clickFirstActionsButtonPublic,
clickFirstActionsButtonPrivate,
goToTab,
goToUnexpandedSidebarEntry,
diff --git a/src/app/container/container.component.html b/src/app/container/container.component.html
index 6f181d6287..3dccd5cc85 100644
--- a/src/app/container/container.component.html
+++ b/src/app/container/container.component.html
@@ -399,7 +399,7 @@
diff --git a/src/app/containers/list/published-tools.datasource.spec.ts b/src/app/containers/list/published-tools.datasource.spec.ts
index 1a244c0fbc..f617b59ab4 100644
--- a/src/app/containers/list/published-tools.datasource.spec.ts
+++ b/src/app/containers/list/published-tools.datasource.spec.ts
@@ -19,8 +19,8 @@ import { HttpClientTestingModule } from '@angular/common/http/testing';
import { inject, TestBed } from '@angular/core/testing';
import { ImageProviderService } from '../../shared/image-provider.service';
import { ProviderService } from '../../shared/provider.service';
-import { ContainersService, MetadataService } from '../../shared/swagger';
-import { ContainersStubService, MetadataStubService } from './../../test/service-stubs';
+import { ContainersService } from '../../shared/swagger';
+import { ContainersStubService } from './../../test/service-stubs';
import { PublishedToolsDataSource } from './published-tools.datasource';
describe('Service: PublishedToolsDataSource', () => {
diff --git a/src/app/organizations/collection/collection-entry-confirm-remove.html b/src/app/organizations/collection/collection-entry-confirm-remove.html
index c011095aa4..343667a566 100644
--- a/src/app/organizations/collection/collection-entry-confirm-remove.html
+++ b/src/app/organizations/collection/collection-entry-confirm-remove.html
@@ -6,7 +6,7 @@ Remove Entry
{{data.collectionName}}?
+
-;
public noWorkflowHits$: Observable;
+ public noNotebookHits$: Observable;
public showWorkflowTagCloud$: Observable;
public showToolTagCloud$: Observable;
+ public showNotebookTagCloud$: Observable;
public selectedIndex$: Observable;
public selectedTab: number;
toolTagCloudData: Array;
workflowTagCloudData: Array;
+ notebookTagCloudData: Array;
options: CloudOptions = {
width: 500,
height: 200,
@@ -54,13 +57,16 @@ export class SearchResultsComponent extends Base implements OnInit {
super();
this.noWorkflowHits$ = this.searchQuery.noWorkflowHits$;
this.noToolHits$ = this.searchQuery.noToolHits$;
+ this.noNotebookHits$ = this.searchQuery.noNotebookHits$;
this.showToolTagCloud$ = this.searchQuery.showToolTagCloud$;
this.showWorkflowTagCloud$ = this.searchQuery.showWorkflowTagCloud$;
+ this.showNotebookTagCloud$ = this.searchQuery.showNotebookTagCloud$;
}
ngOnInit() {
this.createTagCloud('tool');
this.createTagCloud('workflow');
+ this.createTagCloud('notebook');
}
createTagCloud(type: string) {
@@ -68,7 +74,7 @@ export class SearchResultsComponent extends Base implements OnInit {
this.createToolTagCloud(toolQuery, type);
}
- clickTagCloudBtn(type: 'tool' | 'workflow') {
+ clickTagCloudBtn(type: 'tool' | 'workflow' | 'notebook') {
this.searchService.setShowTagCloud(type);
}
@@ -95,11 +101,16 @@ export class SearchResultsComponent extends Base implements OnInit {
this.toolTagCloudData = new Array();
}
this.toolTagCloudData.push(theTag);
- } else {
+ } else if (type === 'workflow') {
if (!this.workflowTagCloudData) {
this.workflowTagCloudData = new Array();
}
this.workflowTagCloudData.push(theTag);
+ } else {
+ if (!this.notebookTagCloudData) {
+ this.notebookTagCloudData = new Array();
+ }
+ this.notebookTagCloudData.push(theTag);
}
count--;
});
diff --git a/src/app/search/search.component.spec.ts b/src/app/search/search.component.spec.ts
index 2e053d9f8f..f58ad5f3cf 100644
--- a/src/app/search/search.component.spec.ts
+++ b/src/app/search/search.component.spec.ts
@@ -88,8 +88,10 @@ describe('SearchComponent', () => {
shortUrl: null,
workflowhit: null,
toolhit: null,
+ notebookhit: null,
showToolTagCloud: false,
showWorkflowTagCloud: false,
+ showNotebookTagCloud: false,
searchText: '',
filterKeys: [],
autocompleteTerms: [],
diff --git a/src/app/search/search.component.ts b/src/app/search/search.component.ts
index de538703ad..e5f59eaaa5 100644
--- a/src/app/search/search.component.ts
+++ b/src/app/search/search.component.ts
@@ -132,6 +132,7 @@ export class SearchComponent implements OnInit, OnDestroy {
public toolTips: Map;
private entryOrder: Map;
private expandedPanels: Map;
+ private exclusiveFilters: Array;
public basicSearchText$: Observable;
private advancedSearchOptions = ['ANDSplitFilter', 'ANDNoSplitFilter', 'ORFilter', 'NOTFilter', 'searchMode'];
public filterKeys$: Observable>;
@@ -161,16 +162,24 @@ export class SearchComponent implements OnInit, OnDestroy {
this.filterKeys$ = this.searchQuery.filterKeys$;
this.suggestTerm$ = this.searchQuery.suggestTerm$;
this.selectedIndex$ = this.searchQuery.savedTabIndex$;
- // Initialize mappings
- this.bucketStubs = this.searchService.initializeCommonBucketStubs();
- this.friendlyNames = this.searchService.initializeFriendlyNames();
- this.entryOrder = this.searchService.initializeEntryOrder();
- this.toolTips = this.searchService.initializeToolTips();
- this.expandedPanels = this.searchService.initializeExpandedPanels();
-
+ this.initializeMappings(0);
this.clearFacetSearches();
}
+ private tabIndex: number | null = null;
+
+ initializeMappings(newTabIndex: number) {
+ if (newTabIndex !== this.tabIndex) {
+ this.tabIndex = newTabIndex;
+ this.bucketStubs = this.searchService.initializeCommonBucketStubs(newTabIndex);
+ this.friendlyNames = this.searchService.initializeFriendlyNames(newTabIndex);
+ this.entryOrder = this.searchService.initializeEntryOrder(newTabIndex);
+ this.toolTips = this.searchService.initializeToolTips(newTabIndex);
+ this.expandedPanels = this.searchService.initializeExpandedPanels(newTabIndex);
+ this.exclusiveFilters = this.searchService.initializeExclusiveFilters(newTabIndex);
+ }
+ }
+
getKeys(bucketMap: Map): Array {
return Array.from(bucketMap.keys());
}
@@ -430,10 +439,11 @@ export class SearchComponent implements OnInit, OnDestroy {
* Update Functions
* ===============================================
*/
-
// Called from one place which is only when the URL has parsed and query non-result state has been set
updateQuery() {
- const tabIndex = SearchService.convertTabIndexToEntryType(this.searchQuery.getValue().currentTabIndex);
+ const tabIndex = this.searchQuery.getValue().currentTabIndex;
+ const entryType = SearchService.convertTabIndexToEntryType(tabIndex);
+ this.initializeMappings(tabIndex);
// Separating into 2 queries otherwise the queries interfere with each other (filter applied before aggregation)
// The first query handles the aggregation and is used to update the sidebar buckets
// The second query updates the result table
@@ -445,8 +455,9 @@ export class SearchComponent implements OnInit, OnDestroy {
this.searchTerm,
this.bucketStubs,
this.filters,
+ this.exclusiveFilters,
this.sortModeMap,
- tabIndex
+ entryType
);
const tableQuery = this.queryBuilderService.getResultQuery(
this.query_size,
@@ -454,7 +465,8 @@ export class SearchComponent implements OnInit, OnDestroy {
advancedSearchObject,
this.searchTerm,
this.filters,
- tabIndex
+ this.exclusiveFilters,
+ entryType
);
this.resetEntryOrder();
this.resetPageIndex();
@@ -487,9 +499,9 @@ export class SearchComponent implements OnInit, OnDestroy {
this.extendedGA4GHService.toolsIndexSearch(value).subscribe(
(hits: any) => {
this.hits = hits.hits.hits;
- const filteredHits: [Array, Array] = this.searchService.filterEntry(this.hits, this.query_size);
+ const filteredHits: [Array, Array, Array] = this.searchService.filterEntry(this.hits, this.query_size);
const searchText = this.searchQuery.getValue().searchText;
- this.searchService.setHits(filteredHits[0], filteredHits[1]);
+ this.searchService.setHits(filteredHits[0], filteredHits[1], filteredHits[2]);
if (searchText.length > 0 && hits) {
this.searchTerm = true;
}
@@ -520,8 +532,8 @@ export class SearchComponent implements OnInit, OnDestroy {
const toolHits = results[0].hits.hits;
const workflowHits = results[1].hits.hits;
this.hits = toolHits.concat(workflowHits);
- const filteredHits: [Array, Array] = this.searchService.filterEntry(this.hits, this.query_size);
- this.searchService.setHits(filteredHits[0], filteredHits[1]);
+ const filteredHits: [Array, Array, Array] = this.searchService.filterEntry(this.hits, this.query_size);
+ this.searchService.setHits(filteredHits[0], filteredHits[1], filteredHits[2]);
});
}
@@ -538,7 +550,7 @@ export class SearchComponent implements OnInit, OnDestroy {
resetEntryOrder() {
this.entryOrder.clear();
- this.entryOrder = this.searchService.initializeEntryOrder();
+ this.entryOrder = this.searchService.initializeEntryOrder(this.tabIndex);
this.orderedBuckets.clear();
}
@@ -548,7 +560,7 @@ export class SearchComponent implements OnInit, OnDestroy {
resetExpansionPanels() {
this.clearExpandedPanelsState();
- this.expandedPanels = this.searchService.initializeExpandedPanels();
+ this.expandedPanels = this.searchService.initializeExpandedPanels(this.tabIndex);
}
/**===============================================
diff --git a/src/app/search/search.module.ts b/src/app/search/search.module.ts
index 89e9c1a717..f9fe5406da 100644
--- a/src/app/search/search.module.ts
+++ b/src/app/search/search.module.ts
@@ -36,6 +36,7 @@ import { QueryBuilderService } from './query-builder.service';
import { SearchResultsComponent } from './search-results/search-results.component';
import { SearchToolTableComponent } from './search-tool-table/search-tool-table.component';
import { SearchWorkflowTableComponent } from './search-workflow-table/search-workflow-table.component';
+import { SearchNotebookTableComponent } from './search-notebook-table/search-notebook-table.component';
import { SearchComponent } from './search.component';
import { searchRouting } from './search.routing';
import { SearchService } from './state/search.service';
@@ -49,6 +50,7 @@ import { SearchAuthorsHtmlPipe } from './search-authors-html.pipe';
SearchResultsComponent,
SearchToolTableComponent,
SearchWorkflowTableComponent,
+ SearchNotebookTableComponent,
BasicSearchComponent,
IsAppToolPipe,
],
diff --git a/src/app/search/state/search.query.ts b/src/app/search/state/search.query.ts
index 1b2e2f631d..e46e4d1132 100644
--- a/src/app/search/state/search.query.ts
+++ b/src/app/search/state/search.query.ts
@@ -3,13 +3,14 @@ import { ActivatedRoute } from '@angular/router';
import { Query } from '@datorama/akita';
import { combineLatest, Observable } from 'rxjs';
import { map } from 'rxjs/operators';
-import { AppTool, DockstoreTool, Workflow } from '../../shared/swagger';
+import { AppTool, DockstoreTool, Workflow, Notebook } from '../../shared/swagger';
import { SearchState, SearchStore } from './search.store';
@Injectable({ providedIn: 'root' })
export class SearchQuery extends Query {
public workflowhit$: Observable = this.select((state) => state.workflowhit);
public toolhit$: Observable = this.select((state) => state.toolhit);
+ public notebookhit$: Observable = this.select((state) => state.notebookhit);
public shortUrl$: Observable = this.select((state) => state.shortUrl);
public workflows$: Observable> = this.workflowhit$.pipe(
map((elasticSearchResults: Array) =>
@@ -21,13 +22,20 @@ export class SearchQuery extends Query {
elasticSearchResults ? elasticSearchResults.map((elasticSearchResult) => elasticSearchResult._source) : null
)
);
+ public notebooks$: Observable> = this.notebookhit$.pipe(
+ map((elasticSearchResults: Array) =>
+ elasticSearchResults ? elasticSearchResults.map((elasticSearchResult) => elasticSearchResult._source) : null
+ )
+ );
public savedTabIndex$: Observable = this.select((state) => state.currentTabIndex);
public noToolHits$: Observable = this.tools$.pipe(map((tools: Array) => this.haveNoHits(tools)));
public noWorkflowHits$: Observable = this.workflows$.pipe(map((workflows: Array) => this.haveNoHits(workflows)));
+ public noNotebookHits$: Observable = this.notebooks$.pipe(map((notebooks: Array) => this.haveNoHits(notebooks)));
public searchText$: Observable = this.select((state) => state.searchText);
public basicSearchText$: Observable = this.searchText$.pipe(map((searchText) => this.joinComma(searchText)));
public showToolTagCloud$: Observable = this.select((state) => state.showToolTagCloud);
public showWorkflowTagCloud$: Observable = this.select((state) => state.showWorkflowTagCloud);
+ public showNotebookTagCloud$: Observable = this.select((state) => state.showNotebookTagCloud);
public filterKeys$: Observable> = this.select((state) => state.filterKeys);
public autoCompleteTerms$: Observable> = this.select((state) => state.autocompleteTerms);
public hasAutoCompleteTerms$: Observable = this.autoCompleteTerms$.pipe(map((terms) => terms.length > 0));
@@ -36,12 +44,17 @@ export class SearchQuery extends Query {
public suggestTerm$: Observable = this.select((state) => state.suggestTerm);
public pageSize$: Observable = this.select((state) => state.pageSize);
public pageIndex$: Observable = this.select((state) => state.pageIndex);
- public noBasicSearchHits$: Observable = combineLatest([this.noToolHits$, this.noWorkflowHits$, this.searchText$]).pipe(
- map(([noToolHits, noWorkflowHits, searchText]) => {
+ public noBasicSearchHits$: Observable = combineLatest([
+ this.noToolHits$,
+ this.noWorkflowHits$,
+ this.noNotebookHits$,
+ this.searchText$,
+ ]).pipe(
+ map(([noToolHits, noWorkflowHits, noNotebookHits, searchText]) => {
if (!searchText) {
return false;
} else {
- return noToolHits && noWorkflowHits;
+ return noToolHits && noWorkflowHits && noNotebookHits;
}
})
);
diff --git a/src/app/search/state/search.service.spec.ts b/src/app/search/state/search.service.spec.ts
index a6075bc819..29ecc8aa7f 100644
--- a/src/app/search/state/search.service.spec.ts
+++ b/src/app/search/state/search.service.spec.ts
@@ -109,7 +109,7 @@ describe('SearchService', () => {
url: null,
},
]);
- const filtered: [Array, Array] = service.filterEntry(elasticSearchResponse, 201);
+ const filtered: [Array, Array, Array] = service.filterEntry(elasticSearchResponse, 201);
const tools = filtered[0];
const workflows = filtered[1];
const toolsSource = tools[0]._source;
diff --git a/src/app/search/state/search.service.ts b/src/app/search/state/search.service.ts
index 63481273f1..f75e030407 100644
--- a/src/app/search/state/search.service.ts
+++ b/src/app/search/state/search.service.ts
@@ -83,80 +83,87 @@ export class SearchService {
* is displayed second, etc.
* @private
*/
- private orderedFacetInfos: Array = [
- { friendlyName: 'Category', esName: 'categories.name.keyword', initiallyExpanded: true },
- { friendlyName: 'Language', esName: 'descriptorType', initiallyExpanded: true },
- {
- friendlyName: 'Language Versions',
- esName: 'descriptor_type_versions.keyword',
- tooltip: 'Indicates that the tool or workflow contains at least one version that is written with the workflow language version',
- initiallyExpanded: false,
- },
- {
- friendlyName: 'Engine Versions',
- esName: 'engine_versions.keyword',
- tooltip: 'The workflow engine versions required to run a workflow or tool',
- initiallyExpanded: false,
- },
- { friendlyName: 'Author', esName: 'all_authors.name.keyword', initiallyExpanded: true },
- { friendlyName: 'Registry', esName: 'registry', initiallyExpanded: true },
- { friendlyName: 'Source Control', esName: 'source_control_provider.keyword', initiallyExpanded: true },
- { friendlyName: 'Namespace', esName: 'namespace', initiallyExpanded: true },
- { friendlyName: 'Organization', esName: 'organization', initiallyExpanded: true },
- { friendlyName: 'Labels', esName: 'labels.value.keyword', initiallyExpanded: false },
- {
- friendlyName: 'Private Access',
- esName: 'private_access',
- tooltip: "A private tool requires authentication to view on Docker's registry website and to pull the Docker image.",
- initiallyExpanded: false,
- exclusive: true,
- },
- {
- friendlyName: 'Verified Source',
- esName: SearchFields.VERIFIED_SOURCE,
- tooltip: 'Indicates which party performed the verification process on a tool or workflow.',
- initiallyExpanded: false,
- },
- {
- friendlyName: 'Verified Platforms',
- esName: 'verified_platforms.keyword',
- tooltip: 'Indicates which platform a tool or workflow (at least one version) was successfully run on.',
- initiallyExpanded: false,
- },
- { friendlyName: 'Input File Formats', esName: 'input_file_formats.value.keyword', initiallyExpanded: false },
- { friendlyName: 'Output File Formats', esName: 'output_file_formats.value.keyword', initiallyExpanded: false },
- {
- friendlyName: 'Verified',
- esName: 'verified',
- tooltip: 'Indicates that at least one version of a tool or workflow has been successfully run by our team or an outside party.',
- initiallyExpanded: true,
- exclusive: true,
- },
- {
- friendlyName: 'Has Checker Workflow',
- esName: 'has_checker',
- tooltip:
- 'Checker workflows are additional workflows you can associate with a tool or workflow to ensure ' +
- 'that, when given some inputs, it produces the expected outputs on a different platform other than the one it was developed on.',
- initiallyExpanded: false,
- exclusive: true,
- },
- {
- friendlyName: 'Open Data',
- esName: 'openData',
- tooltip:
- 'Indicates whether an entry can be run with no additional access permissions, potentially via an included test parameter file referencing open data.',
- initiallyExpanded: false,
- exclusive: true,
- },
- ];
- /**
- * These are the terms which use "must" filters
- * Example: Results returned can be private or public but never both
- * @memberof SearchService
- */
- public exclusiveFilters = this.orderedFacetInfos.filter((facetInfo) => facetInfo.exclusive).map((facetInfo) => facetInfo.esName);
+ private getOrderedFacetInfos(tabIndex: number): Array {
+ return [
+ { friendlyName: 'Category', esName: 'categories.name.keyword', initiallyExpanded: true },
+ {
+ friendlyName: tabIndex === SearchService.NOTEBOOKS_TAB_INDEX ? 'Format' : 'Language',
+ esName: 'descriptorType',
+ initiallyExpanded: true,
+ },
+ {
+ friendlyName: 'Language Versions',
+ esName: 'descriptor_type_versions.keyword',
+ tooltip: 'Indicates that the tool or workflow contains at least one version that is written with the workflow language version',
+ initiallyExpanded: false,
+ },
+ ...(tabIndex === SearchService.NOTEBOOKS_TAB_INDEX
+ ? [{ friendlyName: 'Language', esName: 'descriptorTypeSubclass', initiallyExpanded: true }]
+ : []),
+ {
+ friendlyName: 'Engine Versions',
+ esName: 'engine_versions.keyword',
+ tooltip: 'The workflow engine versions required to run a workflow or tool',
+ initiallyExpanded: false,
+ },
+ { friendlyName: 'Author', esName: 'all_authors.name.keyword', initiallyExpanded: true },
+ { friendlyName: 'Registry', esName: 'registry', initiallyExpanded: true },
+ { friendlyName: 'Source Control', esName: 'source_control_provider.keyword', initiallyExpanded: true },
+ { friendlyName: 'Namespace', esName: 'namespace', initiallyExpanded: true },
+ { friendlyName: 'Organization', esName: 'organization', initiallyExpanded: true },
+ { friendlyName: 'Labels', esName: 'labels.value.keyword', initiallyExpanded: false },
+ {
+ friendlyName: 'Private Access',
+ esName: 'private_access',
+ tooltip: "A private tool requires authentication to view on Docker's registry website and to pull the Docker image.",
+ initiallyExpanded: false,
+ exclusive: true,
+ },
+ {
+ friendlyName: 'Verified Source',
+ esName: SearchFields.VERIFIED_SOURCE,
+ tooltip: 'Indicates which party performed the verification process on a tool or workflow.',
+ initiallyExpanded: false,
+ },
+ {
+ friendlyName: 'Verified Platforms',
+ esName: 'verified_platforms.keyword',
+ tooltip: 'Indicates which platform a tool or workflow (at least one version) was successfully run on.',
+ initiallyExpanded: false,
+ },
+ { friendlyName: 'Input File Formats', esName: 'input_file_formats.value.keyword', initiallyExpanded: false },
+ { friendlyName: 'Output File Formats', esName: 'output_file_formats.value.keyword', initiallyExpanded: false },
+ {
+ friendlyName: 'Verified',
+ esName: 'verified',
+ tooltip: 'Indicates that at least one version of a tool or workflow has been successfully run by our team or an outside party.',
+ initiallyExpanded: true,
+ exclusive: true,
+ },
+ ...(tabIndex !== SearchService.NOTEBOOKS_TAB_INDEX
+ ? [
+ {
+ friendlyName: 'Has Checker Workflow',
+ esName: 'has_checker',
+ tooltip:
+ 'Checker workflows are additional workflows you can associate with a tool or workflow to ensure ' +
+ 'that, when given some inputs, it produces the expected outputs on a different platform other than the one it was developed on.',
+ initiallyExpanded: false,
+ exclusive: true,
+ },
+ ]
+ : []),
+ {
+ friendlyName: 'Open Data',
+ esName: 'openData',
+ tooltip:
+ 'Indicates whether an entry can be run with no additional access permissions, potentially via an included test parameter file referencing open data.',
+ initiallyExpanded: false,
+ exclusive: true,
+ },
+ ];
+ }
constructor(
private searchStore: SearchStore,
@@ -212,7 +219,7 @@ export class SearchService {
// For sorting workflows by name, sort full_workflow_path
if (entryType === 'tool' && attribute === 'name') {
attribute = 'tool_path';
- } else if (entryType === 'workflow' && attribute === 'name') {
+ } else if ((entryType === 'workflow' || entryType == 'notebook') && attribute === 'name') {
attribute = 'full_workflow_path';
}
let aVal = a[attribute];
@@ -296,7 +303,7 @@ export class SearchService {
this.setSearchText(suggestTerm);
}
- setShowTagCloud(entryType: 'tool' | 'workflow') {
+ setShowTagCloud(entryType: 'tool' | 'workflow' | 'notebook') {
if (entryType === 'tool') {
const showTagCloud: boolean = this.searchQuery.getValue().showToolTagCloud;
this.searchStore.update((state) => {
@@ -305,7 +312,7 @@ export class SearchService {
showToolTagCloud: !showTagCloud,
};
});
- } else {
+ } else if (entryType === 'workflow') {
const showTagCloud: boolean = this.searchQuery.getValue().showWorkflowTagCloud;
this.searchStore.update((state) => {
return {
@@ -313,6 +320,14 @@ export class SearchService {
showWorkflowTagCloud: !showTagCloud,
};
});
+ } else {
+ const showTagCloud: boolean = this.searchQuery.getValue().showNotebookTagCloud;
+ this.searchStore.update((state) => {
+ return {
+ ...state,
+ showNotebookTagCloud: !showTagCloud,
+ };
+ });
}
}
@@ -323,9 +338,10 @@ export class SearchService {
* @param {number} query_size
* @memberof SearchService
*/
- filterEntry(hits: Array, query_size: number): [Array, Array] {
+ filterEntry(hits: Array, query_size: number): [Array, Array, Array] {
const workflowHits = [];
const toolHits = [];
+ const notebookHits = [];
hits.forEach((hit) => {
hit['_source'] = this.providerService.setUpProvider(hit['_source']);
if (workflowHits.length + toolHits.length < query_size - 1) {
@@ -334,18 +350,21 @@ export class SearchService {
toolHits.push(hit);
} else if (hit['_index'] === 'workflows') {
workflowHits.push(hit);
+ } else if (hit['_index'] === 'notebooks') {
+ notebookHits.push(hit);
}
}
});
- return [toolHits, workflowHits];
+ return [toolHits, workflowHits, notebookHits];
}
- setHits(toolHits: Array, workflowHits: Array) {
+ setHits(toolHits: Array, workflowHits: Array, notebookHits: Array) {
this.searchStore.update((state) => {
return {
...state,
toolhit: toolHits,
workflowhit: workflowHits,
+ notebookhit: notebookHits,
};
});
}
@@ -600,33 +619,50 @@ export class SearchService {
}
// Initialization Functions
- initializeCommonBucketStubs() {
- return new Map(this.orderedFacetInfos.map((facetInfo) => [facetInfo.friendlyName, facetInfo.esName]));
+ initializeCommonBucketStubs(tabIndex: number) {
+ return new Map(this.getOrderedFacetInfos(tabIndex).map((facetInfo) => [facetInfo.friendlyName, facetInfo.esName]));
}
- initializeFriendlyNames() {
- return new Map(this.orderedFacetInfos.map((facetInfo) => [facetInfo.esName, facetInfo.friendlyName]));
+ initializeFriendlyNames(tabIndex: number) {
+ return new Map(this.getOrderedFacetInfos(tabIndex).map((facetInfo) => [facetInfo.esName, facetInfo.friendlyName]));
}
- initializeToolTips() {
+ initializeToolTips(tabIndex: number) {
return new Map(
- this.orderedFacetInfos.filter((facetInfo) => facetInfo.tooltip).map((facetInfo) => [facetInfo.esName, facetInfo.tooltip])
+ this.getOrderedFacetInfos(tabIndex)
+ .filter((facetInfo) => facetInfo.tooltip)
+ .map((facetInfo) => [facetInfo.esName, facetInfo.tooltip])
);
}
- initializeEntryOrder() {
- return new Map(this.orderedFacetInfos.map((facetInfo) => [facetInfo.esName, new SubBucket()]));
+ initializeEntryOrder(tabIndex: number) {
+ return new Map(this.getOrderedFacetInfos(tabIndex).map((facetInfo) => [facetInfo.esName, new SubBucket()]));
}
/**
* Initialize expanded panels to default state or restore previous state from local storage
*/
- initializeExpandedPanels() {
- if (localStorage.getItem(this.expandedPanelsStorageKey)) {
- return new Map(JSON.parse(localStorage.getItem(this.expandedPanelsStorageKey)));
- } else {
- return new Map(this.orderedFacetInfos.map((facetInfo) => [facetInfo.esName, facetInfo.initiallyExpanded]));
+ initializeExpandedPanels(tabIndex: number) {
+ // Use the "canned" facet information to determine which panels should be expanded
+ const expandedPanels = new Map(this.getOrderedFacetInfos(tabIndex).map((facetInfo) => [facetInfo.esName, facetInfo.initiallyExpanded]));
+ // Override with any stored values
+ const storedValue = localStorage.getItem(this.expandedPanelsStorageKey);
+ if (storedValue) {
+ const storedMap = new Map(JSON.parse(storedValue));
+ storedMap.forEach((expanded: boolean, key: string) => expandedPanels.set(key, expanded));
}
+ return expandedPanels;
+ }
+
+ /**
+ * Generate a list of terms which use "must" filters
+ * Example: Results returned can be private or public but never both
+ * @memberof SearchService
+ */
+ initializeExclusiveFilters(tabIndex: number): Array {
+ return this.getOrderedFacetInfos(tabIndex)
+ .filter((facetInfo) => facetInfo.exclusive)
+ .map((facetInfo) => facetInfo.esName);
}
// Functions called from HTML
diff --git a/src/app/search/state/search.store.ts b/src/app/search/state/search.store.ts
index 89b1c2ec2b..48894ff729 100644
--- a/src/app/search/state/search.store.ts
+++ b/src/app/search/state/search.store.ts
@@ -21,8 +21,10 @@ export interface SearchState {
shortUrl: string;
workflowhit: any;
toolhit: any;
+ notebookhit: any;
showToolTagCloud: boolean;
showWorkflowTagCloud: boolean;
+ showNotebookTagCloud: boolean;
searchText: string;
filterKeys: Array;
autocompleteTerms: Array;
@@ -39,8 +41,10 @@ export function createInitialState(): SearchState {
shortUrl: null,
workflowhit: null,
toolhit: null,
+ notebookhit: null,
showToolTagCloud: false,
showWorkflowTagCloud: false,
+ showNotebookTagCloud: false,
searchText: '',
filterKeys: [],
autocompleteTerms: [],
diff --git a/src/app/shared/tool-lister.ts b/src/app/shared/tool-lister.ts
index a152b54d70..b5eb20abde 100644
--- a/src/app/shared/tool-lister.ts
+++ b/src/app/shared/tool-lister.ts
@@ -49,7 +49,6 @@ export abstract class ToolLister implements AfterViewInit, OnDestroy {
}
abstract type: 'tool' | 'workflow';
- abstract displayedColumns: Array;
public dataSource: PublishedWorkflowsDataSource | PublishedToolsDataSource;
@ViewChild(MatPaginator, { static: true }) paginator: MatPaginator;
@ViewChild(MatSort, { static: true }) sort: MatSort;
diff --git a/src/app/test/service-stubs.ts b/src/app/test/service-stubs.ts
index 158055ca58..d724d1f1cb 100644
--- a/src/app/test/service-stubs.ts
+++ b/src/app/test/service-stubs.ts
@@ -311,6 +311,11 @@ export class SearchStubService {
],
]);
}
+
+ initializeExclusiveFilters() {
+ return new Map([]);
+ }
+
handleLink(linkArray: Array) {}
}
diff --git a/src/app/workflows/list/list.component.html b/src/app/workflows/list/list.component.html
index 1d1f1c8287..8576fc2263 100644
--- a/src/app/workflows/list/list.component.html
+++ b/src/app/workflows/list/list.component.html
@@ -57,6 +57,10 @@
Format
{{ workflow?.descriptorType | uppercase }}
+
+ Language
+ {{ workflow?.descriptorTypeSubclass }}
+
Links
@@ -65,8 +69,8 @@
-
Date: Fri, 12 May 2023 08:50:52 -0700
Subject: [PATCH 009/128] display Jupyter notebooks with nbformat < 4
https://ucsc-cgl.atlassian.net/browse/SEAB-5438
---
src/app/notebook/notebook.component.spec.ts | 8 +++++
src/app/notebook/notebook.component.ts | 33 +++++++++++++++++++--
2 files changed, 39 insertions(+), 2 deletions(-)
diff --git a/src/app/notebook/notebook.component.spec.ts b/src/app/notebook/notebook.component.spec.ts
index cf482d6312..20895ac358 100644
--- a/src/app/notebook/notebook.component.spec.ts
+++ b/src/app/notebook/notebook.component.spec.ts
@@ -184,4 +184,12 @@ describe('NotebookComponent', () => {
expect(element.querySelector('.output img').getAttribute('height')).toBe('480');
confirmSuccess();
});
+
+ it('should do a reasonable job of displaying a format 3 notebook', () => {
+ const cell = '{"cell_type": "code", "input": "some input", "outputs": [{"output_type": "display_data", "html": "
Date: Thu, 18 May 2023 13:56:33 -0700
Subject: [PATCH 010/128] improve Colab and add MyBinder notebook launch
https://ucsc-cgl.atlassian.net/browse/SEAB-5121
---
.circleci/config.yml | 2 +-
package.json | 6 +--
src/app/configuration.service.ts | 2 +
src/app/shared/dockstore.model.ts | 2 +
src/app/test/mocked-objects.ts | 1 +
.../launch-third-party.component.html | 53 ++++++++++++++++---
.../launch-third-party.component.ts | 45 +++++++++++++++-
7 files changed, 97 insertions(+), 14 deletions(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index ef7c52e0de..a91a813b39 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -578,7 +578,7 @@ commands:
name: Install java
command: |
sudo apt update -y
- sudo apt install openjdk-17-jdk -yq
+ sudo apt install openjdk-17-jre -yq
- run:
name: Install npm
command: |
diff --git a/package.json b/package.json
index e3894a74ef..30031d16d5 100644
--- a/package.json
+++ b/package.json
@@ -3,10 +3,10 @@
"version": "2.10.0",
"license": "Apache License 2.0",
"config": {
- "webservice_version": "1.13.0",
+ "webservice_version": "1.15.0",
"use_circle": true,
- "circle_ci_source": "https://app.circleci.com/pipelines/github/dockstore/dockstore/9739/workflows/67d0d5f8-1ba7-491d-9496-745b999b9e26/jobs/32375/artifacts",
- "circle_build_id": "32375",
+ "circle_ci_source": "https://app.circleci.com/pipelines/github/dockstore/dockstore/9891/workflows/f59191af-06ea-49ae-aefa-cdce0011cb7f/jobs/33457/artifacts",
+ "circle_build_id": "33457",
"base_branch": "develop"
},
"scripts": {
diff --git a/src/app/configuration.service.ts b/src/app/configuration.service.ts
index b9faeeaee9..590c86790e 100644
--- a/src/app/configuration.service.ts
+++ b/src/app/configuration.service.ts
@@ -45,6 +45,8 @@ export class ConfigurationService {
Dockstore.BD_CATALYST_SEVEN_BRIDGES_IMPORT_URL = config.bdCatalystSevenBridgesImportUrl;
Dockstore.BD_CATALYST_TERRA_IMPORT_URL = config.bdCatalystTerraImportUrl;
Dockstore.ELWAZI_IMPORT_URL = config.elwaziImportUrl;
+ Dockstore.COLAB_IMPORT_URL = config.colabImportUrl;
+ Dockstore.MYBINDER_IMPORT_URL = config.mybinderImportUrl;
Dockstore.GITHUB_CLIENT_ID = config.githubClientId;
Dockstore.GITHUB_AUTH_URL = config.gitHubAuthUrl;
diff --git a/src/app/shared/dockstore.model.ts b/src/app/shared/dockstore.model.ts
index da1f8d68cc..61ab8b5cd0 100644
--- a/src/app/shared/dockstore.model.ts
+++ b/src/app/shared/dockstore.model.ts
@@ -43,6 +43,8 @@ export class Dockstore {
static CAVATICA_IMPORT_URL = 'https://cavatica.sbgenomics.com/integration/trs/import';
static NEXTFLOW_TOWER_IMPORT_URL = 'https://tower.nf/launch';
static ELWAZI_IMPORT_URL = 'https://elwazi.terra.bio/#import-tool/dockstore';
+ static COLAB_IMPORT_URL = 'https://colab.research.google.com/github/';
+ static MYBINDER_IMPORT_URL = 'https://mybinder.org/v2/gh/';
static GITHUB_CLIENT_ID = 'will be filled in by configuration.service';
static GITHUB_AUTH_URL = 'https://github.com/login/oauth/authorize';
diff --git a/src/app/test/mocked-objects.ts b/src/app/test/mocked-objects.ts
index 8eb1573f12..8be00815a4 100644
--- a/src/app/test/mocked-objects.ts
+++ b/src/app/test/mocked-objects.ts
@@ -140,6 +140,7 @@ export const sampleWorkflowVersion: WorkflowVersion = {
id: 1,
reference: '',
name: 'master',
+ workflow_path: '/abc.wdl',
};
export const sampleToolVersion: Tag = {
diff --git a/src/app/workflow/launch-third-party/launch-third-party.component.html b/src/app/workflow/launch-third-party/launch-third-party.component.html
index fc5230ce20..cea59307a9 100644
--- a/src/app/workflow/launch-third-party/launch-third-party.component.html
+++ b/src/app/workflow/launch-third-party/launch-third-party.component.html
@@ -263,14 +263,51 @@
+
+
+
diff --git a/src/app/shared/state/extended-workflow.service.spec.ts b/src/app/shared/state/extended-workflow.service.spec.ts
index 4ae658f3de..16705aacf0 100644
--- a/src/app/shared/state/extended-workflow.service.spec.ts
+++ b/src/app/shared/state/extended-workflow.service.spec.ts
@@ -16,8 +16,13 @@
import { inject, TestBed } from '@angular/core/testing';
import { sampleWorkflow1 } from '../../test/mocked-objects';
-import { DateStubService, DockstoreStubService, ImageProviderStubService, ProviderStubService } from '../../test/service-stubs';
-import { WorkflowStubService } from '../../test/service-stubs';
+import {
+ DateStubService,
+ DockstoreStubService,
+ ImageProviderStubService,
+ ProviderStubService,
+ WorkflowStubService,
+} from '../../test/service-stubs';
import { DateService } from '../date.service';
import { DockstoreService } from '../dockstore.service';
import { ImageProviderService } from '../image-provider.service';
diff --git a/src/app/source-file-tabs/source-file-tabs.component.ts b/src/app/source-file-tabs/source-file-tabs.component.ts
index e3daf481d6..ae633b4d9e 100644
--- a/src/app/source-file-tabs/source-file-tabs.component.ts
+++ b/src/app/source-file-tabs/source-file-tabs.component.ts
@@ -10,7 +10,7 @@ import { SourceFile, ToolDescriptor, WorkflowVersion } from 'app/shared/openapi'
import { Observable } from 'rxjs';
import { finalize } from 'rxjs/operators';
import { WorkflowQuery } from '../shared/state/workflow.query';
-import { BioWorkflow, Notebook, Service, Tag } from '../shared/swagger';
+import { BioWorkflow, Notebook, Service } from '../shared/swagger';
import { SourceFileTabsService } from './source-file-tabs.service';
@Component({
diff --git a/src/app/starredentries/starredentries.component.ts b/src/app/starredentries/starredentries.component.ts
index 2ff8d4d768..cf73abcd17 100644
--- a/src/app/starredentries/starredentries.component.ts
+++ b/src/app/starredentries/starredentries.component.ts
@@ -9,10 +9,9 @@ import { MatTabChangeEvent } from '@angular/material/tabs';
import { UntypedFormControl } from '@angular/forms';
import { ExtendedDockstoreTool } from 'app/shared/models/ExtendedDockstoreTool';
import { ExtendedWorkflow } from 'app/shared/models/ExtendedWorkflow';
-// import { DockstoreService } from 'app/shared/dockstore.service';
import { OrgLogoService } from '../shared/org-logo.service';
import { EntryType } from '../shared/enum/entry-type';
-import { ActivatedRoute, Params } from '@angular/router';
+import { ActivatedRoute } from '@angular/router';
import { Location } from '@angular/common';
import { Dockstore } from 'app/shared/dockstore.model';
@@ -45,7 +44,6 @@ export class StarredEntriesComponent extends Base implements OnInit {
private imageProviderService: ImageProviderService,
private providerService: ProviderService,
private usersService: UsersService,
- // private dockstoreService: DockstoreService
private orgLogoService: OrgLogoService,
private activatedRoute: ActivatedRoute,
private location: Location
diff --git a/src/app/workflow/versions/versions.component.ts b/src/app/workflow/versions/versions.component.ts
index 8f66e8ee17..a7ae3e700c 100644
--- a/src/app/workflow/versions/versions.component.ts
+++ b/src/app/workflow/versions/versions.component.ts
@@ -22,9 +22,8 @@ import { AlertService } from '../../shared/alert/state/alert.service';
import { DateService } from '../../shared/date.service';
import { Dockstore } from '../../shared/dockstore.model';
import { DockstoreService } from '../../shared/dockstore.service';
-import { EntryType } from '../../shared/openapi';
+import { EntryType, VersionVerifiedPlatform } from '../../shared/openapi';
import { ExtendedWorkflow } from '../../shared/models/ExtendedWorkflow';
-import { VersionVerifiedPlatform } from '../../shared/openapi';
import { SessionQuery } from '../../shared/session/session.query';
import { ExtendedWorkflowQuery } from '../../shared/state/extended-workflow.query';
import { Workflow } from '../../shared/swagger/model/workflow';
diff --git a/src/styles.scss b/src/styles.scss
index efda1115b4..802036df83 100644
--- a/src/styles.scss
+++ b/src/styles.scss
@@ -474,9 +474,6 @@ table a {
table {
border-collapse: collapse;
-}
-
-table {
border: 1px solid mat.get-color-from-palette($dockstore-app-gray, 7);
}
@@ -700,6 +697,13 @@ div.tabs > div > div {
text-align: left;
padding: 25px;
line-height: 2;
+ background-color: #ffffff;
+ z-index: -2;
+ left: 0;
+ top: 30px;
+ bottom: 0;
+ right: 0;
+ overflow: auto;
}
div.tabs > div:not(:target) {
@@ -718,16 +722,6 @@ div.tabs > div:hover > a {
color: #fff;
}
-div.tabs > div > div {
- background-color: #ffffff;
- z-index: -2;
- left: 0;
- top: 30px;
- bottom: 0;
- right: 0;
- overflow: auto;
-}
-
div.tabs > div:not(:target) > div {
position: absolute;
}
From 06add5707f02874017102779c6d4b1982efb5f99 Mon Sep 17 00:00:00 2001
From: Steve Von Worley
Date: Thu, 4 May 2023 10:03:13 -0700
Subject: [PATCH 004/128] add notebooks support to search
https://ucsc-cgl.atlassian.net/browse/SEAB-5118
---
.../e2e/immutableDatabaseTests/notebooks.ts | 2 +
.../e2e/immutableDatabaseTests/searchTable.ts | 26 +++
cypress/fixtures/searchTableResponse.json | 64 +++++
src/app/search/query-builder.service.ts | 15 +-
src/app/search/search-entry-table.ts | 12 +-
.../search-notebook-table.component.html | 80 +++++++
.../search-notebook-table.component.scss | 11 +
.../search-notebook-table.component.spec.ts | 42 ++++
.../search-notebook-table.component.ts | 45 ++++
.../search-results.component.html | 34 +++
.../search-results.component.ts | 15 +-
src/app/search/search.component.spec.ts | 2 +
src/app/search/search.component.ts | 46 ++--
src/app/search/search.module.ts | 2 +
src/app/search/state/search.query.ts | 21 +-
src/app/search/state/search.service.spec.ts | 2 +-
src/app/search/state/search.service.ts | 220 ++++++++++--------
src/app/search/state/search.store.ts | 4 +
src/app/shared/tool-lister.ts | 1 -
src/app/test/service-stubs.ts | 5 +
src/app/workflows/list/list.component.html | 8 +-
src/app/workflows/list/list.component.ts | 9 +-
22 files changed, 534 insertions(+), 132 deletions(-)
create mode 100644 src/app/search/search-notebook-table/search-notebook-table.component.html
create mode 100644 src/app/search/search-notebook-table/search-notebook-table.component.scss
create mode 100644 src/app/search/search-notebook-table/search-notebook-table.component.spec.ts
create mode 100644 src/app/search/search-notebook-table/search-notebook-table.component.ts
diff --git a/cypress/e2e/immutableDatabaseTests/notebooks.ts b/cypress/e2e/immutableDatabaseTests/notebooks.ts
index 5e350cb2e0..58d5f6dc92 100644
--- a/cypress/e2e/immutableDatabaseTests/notebooks.ts
+++ b/cypress/e2e/immutableDatabaseTests/notebooks.ts
@@ -23,6 +23,8 @@ describe('Notebooks Pages', () => {
cy.url().should('contain', 'notebooks');
cy.get('[data-cy=header]').contains('h3', 'Notebooks');
cy.contains('Search notebooks');
+ cy.contains('Format');
+ cy.contains('Language');
});
it('should star notebook', () => {
diff --git a/cypress/e2e/immutableDatabaseTests/searchTable.ts b/cypress/e2e/immutableDatabaseTests/searchTable.ts
index 60c0242993..fa2e9a61ad 100644
--- a/cypress/e2e/immutableDatabaseTests/searchTable.ts
+++ b/cypress/e2e/immutableDatabaseTests/searchTable.ts
@@ -432,3 +432,29 @@ describe('search table items per page', () => {
cy.get('[data-cy=share_button').should('be.visible').click();
});
});
+
+// make sure that search table and tabs have been adjusted for notebooks
+describe('check search table and tabs for notebooks', () => {
+ setTokenUserViewPort();
+ beforeEach(() => {
+ cy.fixture('searchTableResponse').then((json) => {
+ cy.intercept('POST', '*' + ga4ghExtendedPath + '/tools/entry/_search', {
+ body: json,
+ });
+ });
+ });
+ it('should contain notebooks-related information', () => {
+ cy.visit('/search?notebooks');
+ // Check that Notebooks tab exists
+ cy.get('.mat-tab-label').contains('Notebooks');
+ // Select notebooks tab
+ goToTab('Notebooks');
+ cy.url().should('contain', 'notebooks');
+ // Check that the notebooks variations are in the table header
+ cy.get('.mat-header-cell').contains('Language');
+ cy.get('.mat-header-cell').contains('Format');
+ // Check that the notebooks variations are in the table body
+ cy.get('.mat-cell').contains('jupyter', { matchCase: false });
+ cy.get('.mat-cell').contains('python', { matchCase: false });
+ });
+});
diff --git a/cypress/fixtures/searchTableResponse.json b/cypress/fixtures/searchTableResponse.json
index 65d532ea3a..21c4f2975b 100644
--- a/cypress/fixtures/searchTableResponse.json
+++ b/cypress/fixtures/searchTableResponse.json
@@ -326,6 +326,70 @@
"defaultVersion": null,
"all_authors": [{"name": null, "email": null, "role": null, "affiliation": null}]
}
+ },
+ {
+ "_index": "notebooks",
+ "_type": "_doc",
+ "_id": "61",
+ "_score": 1.0,
+ "_source": {
+ "aliases": {},
+ "is_published": true,
+ "last_modified_date": null,
+ "isChecker": false,
+ "checker_id": null,
+ "repository": "n",
+ "source_control_provider": "GITHUB",
+ "descriptorType": "jupyter",
+ "descriptorTypeSubclass": "Python",
+ "full_workflow_path": "github.com/A/n",
+ "mode": "FULL",
+ "lastUpdated": 1520374057688,
+ "path": "github.com/A/n",
+ "starredUsers": [
+ {
+ "id": 5
+ }
+ ],
+ "workflowVersions": [
+ {
+ "doiURL": null,
+ "verifiedSource": null,
+ "versionEditor": null,
+ "verified": false,
+ "referenceType": "UNSET",
+ "commitID": null,
+ "id": 63,
+ "doiStatus": "NOT_REQUESTED"
+ },
+ {
+ "doiURL": null,
+ "verifiedSource": null,
+ "versionEditor": null,
+ "verified": false,
+ "referenceType": "UNSET",
+ "commitID": null,
+ "id": 64,
+ "doiStatus": "NOT_REQUESTED"
+ }
+ ],
+ "sourceControl": "github.com",
+ "has_checker": false,
+ "id": 11,
+ "last_modified": null,
+ "email": null,
+ "dbUpdateDate": null,
+ "author": null,
+ "defaultTestParameterFilePath": null,
+ "workflowName": null,
+ "workflow_path": "/notebook.ipynb",
+ "dbCreateDate": null,
+ "parent_id": null,
+ "organization": "A",
+ "gitUrl": "git@github.com:A/n.git",
+ "defaultVersion": null,
+ "all_authors": [{"name": null, "email": null, "role": null, "affiliation": null}]
+ }
}
]
}
diff --git a/src/app/search/query-builder.service.ts b/src/app/search/query-builder.service.ts
index 93a2a2ad28..3fcf95db50 100644
--- a/src/app/search/query-builder.service.ts
+++ b/src/app/search/query-builder.service.ts
@@ -49,6 +49,7 @@ export class QueryBuilderService {
searchTerm: boolean,
bucketStubs: any,
filters: any,
+ exclusiveFilters: any,
sortModeMap: any,
index: 'workflows' | 'tools' | 'notebooks'
): string {
@@ -58,7 +59,7 @@ export class QueryBuilderService {
sidebarBody = this.excludeContent(sidebarBody);
sidebarBody = sidebarBody.query('match', '_index', index);
sidebarBody = this.appendQuery(sidebarBody, values, advancedSearchObject, searchTerm);
- sidebarBody = this.appendAggregations(count, sidebarBody, bucketStubs, filters, sortModeMap);
+ sidebarBody = this.appendAggregations(count, sidebarBody, bucketStubs, filters, exclusiveFilters, sortModeMap);
const builtSideBarBody = sidebarBody.build();
const sideBarQuery = JSON.stringify(builtSideBarBody);
return sideBarQuery;
@@ -73,6 +74,7 @@ export class QueryBuilderService {
return body.rawOption('_source', [
'all_authors',
'descriptorType',
+ 'descriptorTypeSubclass',
'full_workflow_path',
'gitUrl',
'name',
@@ -104,13 +106,14 @@ export class QueryBuilderService {
advancedSearchObject: AdvancedSearchObject,
searchTerm: boolean,
filters: any,
+ exclusiveFilters: any,
index: 'tools' | 'workflows' | 'notebooks'
): string {
let tableBody = bodybuilder().size(query_size);
tableBody = this.sourceOptions(tableBody);
tableBody = tableBody.query('match', '_index', index);
tableBody = this.appendQuery(tableBody, values, advancedSearchObject, searchTerm);
- tableBody = this.appendFilter(tableBody, null, filters);
+ tableBody = this.appendFilter(tableBody, null, filters, exclusiveFilters);
// most popular results should be returned first
tableBody = tableBody.sort('stars_count', 'desc');
const builtTableBody = tableBody.build();
@@ -138,10 +141,10 @@ export class QueryBuilderService {
* @returns the new body builder object with filter applied
* @memberof SearchComponent
*/
- appendFilter(body: any, aggKey: string, filters: any): any {
+ appendFilter(body: any, aggKey: string, filters: any, exclusiveFilters: any): any {
filters.forEach((value: Set, key: string) => {
value.forEach((insideFilter) => {
- const isExclusiveFilter = this.searchService.exclusiveFilters.includes(key);
+ const isExclusiveFilter = exclusiveFilters.includes(key);
if (aggKey === key && !isExclusiveFilter) {
// Return some garbage filter because we've decided to append a filter, there's no turning back
// return body; // <--- this does not work
@@ -242,13 +245,13 @@ export class QueryBuilderService {
* @returns {*} the new body builder object
* @memberof SearchComponent
*/
- appendAggregations(count: number, body: any, bucketStubs: any, filters: any, sortModeMap: any): any {
+ appendAggregations(count: number, body: any, bucketStubs: any, filters: any, exclusiveFilters: any, sortModeMap: any): any {
// go through buckets
bucketStubs.forEach((key) => {
const order = this.searchService.parseOrderBy(key, sortModeMap);
if (count > 0) {
body = body.agg('filter', key, key, (a) => {
- return this.appendFilter(a, key, filters).aggregation('terms', key, key, { size: this.shard_size, order });
+ return this.appendFilter(a, key, filters, exclusiveFilters).aggregation('terms', key, key, { size: this.shard_size, order });
});
} else {
body = body.agg('terms', key, key, { size: this.shard_size, order });
diff --git a/src/app/search/search-entry-table.ts b/src/app/search/search-entry-table.ts
index 57b9142b1c..8a0836449e 100644
--- a/src/app/search/search-entry-table.ts
+++ b/src/app/search/search-entry-table.ts
@@ -21,7 +21,7 @@ import { combineLatest, Observable, Subject } from 'rxjs';
import { takeUntil } from 'rxjs/operators';
import { Base } from '../shared/base';
import { DateService } from '../shared/date.service';
-import { AppTool, DockstoreTool, Workflow } from '../shared/swagger';
+import { AppTool, DockstoreTool, Workflow, Notebook } from '../shared/swagger';
import { SearchQuery } from './state/search.query';
import { SearchService } from './state/search.service';
@@ -34,9 +34,9 @@ export abstract class SearchEntryTable extends Base implements OnInit {
protected ngUnsubscribe: Subject<{}> = new Subject();
public readonly displayedColumns = ['name', 'verified', 'all_authors', 'descriptorType', 'projectLinks', 'starredUsers'];
- abstract readonly entryType: 'tool' | 'workflow';
- abstract dataSource: MatTableDataSource;
- abstract privateNgOnInit(): Observable<(DockstoreTool | Workflow)[]>;
+ abstract readonly entryType: 'tool' | 'workflow' | 'notebook';
+ abstract dataSource: MatTableDataSource;
+ abstract privateNgOnInit(): Observable<(DockstoreTool | Workflow | Notebook)[]>;
constructor(protected dateService: DateService, protected searchQuery: SearchQuery, protected searchService: SearchService) {
super();
@@ -55,8 +55,8 @@ export abstract class SearchEntryTable extends Base implements OnInit {
// Must set data after paginator, just a material datatables thing.
this.dataSource.data = entries || [];
});
- this.dataSource.sortData = (data: DockstoreTool[] | AppTool[] | Workflow[], sort: MatSort) => {
- return data.slice().sort((a: Workflow | AppTool | DockstoreTool, b: Workflow | AppTool | DockstoreTool) => {
+ this.dataSource.sortData = (data: DockstoreTool[] | AppTool[] | Workflow[] | Notebook[], sort: MatSort) => {
+ return data.slice().sort((a: Workflow | AppTool | DockstoreTool | Notebook, b: Workflow | AppTool | DockstoreTool | Notebook) => {
return this.searchService.compareAttributes(a, b, sort.active, sort.direction, this.entryType);
});
};
diff --git a/src/app/search/search-notebook-table/search-notebook-table.component.html b/src/app/search/search-notebook-table/search-notebook-table.component.html
new file mode 100644
index 0000000000..c938baa0bc
--- /dev/null
+++ b/src/app/search/search-notebook-table/search-notebook-table.component.html
@@ -0,0 +1,80 @@
+;
+
+ beforeEach(
+ waitForAsync(() => {
+ TestBed.configureTestingModule({
+ declarations: [SearchNotebookTableComponent],
+ schemas: [NO_ERRORS_SCHEMA],
+ imports: [CustomMaterialModule, BrowserAnimationsModule, RouterTestingModule],
+ providers: [
+ { provide: DockstoreService, useClass: DockstoreStubService },
+ DateService,
+ { provide: SearchService, useClass: SearchStubService },
+ ],
+ }).compileComponents();
+ })
+ );
+
+ beforeEach(() => {
+ fixture = TestBed.createComponent(SearchNotebookTableComponent);
+ component = fixture.componentInstance;
+ fixture.detectChanges();
+ });
+
+ it('should create', () => {
+ expect(component).toBeTruthy();
+ });
+});
diff --git a/src/app/search/search-notebook-table/search-notebook-table.component.ts b/src/app/search/search-notebook-table/search-notebook-table.component.ts
new file mode 100644
index 0000000000..d9d7e995c1
--- /dev/null
+++ b/src/app/search/search-notebook-table/search-notebook-table.component.ts
@@ -0,0 +1,45 @@
+/*
+ * Copyright 2023 OICR, UCSC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import { Component, OnInit } from '@angular/core';
+import { MatTableDataSource } from '@angular/material/table';
+import { Observable } from 'rxjs';
+import { DateService } from '../../shared/date.service';
+import { Notebook } from '../../shared/swagger';
+import { SearchEntryTable } from '../search-entry-table';
+import { SearchQuery } from '../state/search.query';
+import { SearchService } from '../state/search.service';
+
+/**
+ * this component refers to search page not notebook listing search
+ */
+
+@Component({
+ selector: 'app-search-notebook-table',
+ templateUrl: './search-notebook-table.component.html',
+ styleUrls: ['../../shared/styles/entry-table.scss', './search-notebook-table.component.scss'],
+})
+export class SearchNotebookTableComponent extends SearchEntryTable implements OnInit {
+ public readonly displayedColumns = ['name', 'all_authors', 'descriptorType', 'descriptorTypeSubclass', 'projectLinks', 'starredUsers'];
+ readonly entryType = 'notebook';
+ public dataSource: MatTableDataSource;
+ constructor(dateService: DateService, searchQuery: SearchQuery, searchService: SearchService) {
+ super(dateService, searchQuery, searchService);
+ }
+
+ privateNgOnInit(): Observable> {
+ return this.searchQuery.notebooks$;
+ }
+}
diff --git a/src/app/search/search-results/search-results.component.html b/src/app/search/search-results/search-results.component.html
index bb00aded64..5c8d951e00 100644
--- a/src/app/search/search-results/search-results.component.html
+++ b/src/app/search/search-results/search-results.component.html
@@ -80,3 +80,37 @@
+
+
+ Name
+
+
+
+
+ Author
+
+
+ Format
+
+
+
+
+ Language
+
+
+
+
+ Links
+
+
+
+
+
+ Stars
+ {{ !notebook?.starredUsers || notebook?.starredUsers.length === 0 ? '' : notebook?.starredUsers?.length }}
+ star_rate
+
+
+
+
diff --git a/src/app/search/search-notebook-table/search-notebook-table.component.scss b/src/app/search/search-notebook-table/search-notebook-table.component.scss
new file mode 100644
index 0000000000..db11452167
--- /dev/null
+++ b/src/app/search/search-notebook-table/search-notebook-table.component.scss
@@ -0,0 +1,11 @@
+.mat-column-descriptorType {
+ max-width: 90px;
+}
+
+.mat-column-projectLinks {
+ max-width: 80px;
+}
+
+td.mat-cell {
+ border-bottom-style: none;
+}
diff --git a/src/app/search/search-notebook-table/search-notebook-table.component.spec.ts b/src/app/search/search-notebook-table/search-notebook-table.component.spec.ts
new file mode 100644
index 0000000000..8e3dbf3de7
--- /dev/null
+++ b/src/app/search/search-notebook-table/search-notebook-table.component.spec.ts
@@ -0,0 +1,42 @@
+/* eslint-disable no-unused-vars, @typescript-eslint/no-unused-vars */
+import { NO_ERRORS_SCHEMA } from '@angular/core';
+import { ComponentFixture, TestBed, waitForAsync } from '@angular/core/testing';
+
+import { BrowserAnimationsModule } from '@angular/platform-browser/animations';
+import { RouterTestingModule } from '@angular/router/testing';
+import { DateService } from '../../shared/date.service';
+import { DockstoreService } from '../../shared/dockstore.service';
+import { CustomMaterialModule } from '../../shared/modules/material.module';
+import { DockstoreStubService, SearchStubService } from '../../test/service-stubs';
+import { SearchService } from '../state/search.service';
+import { SearchNotebookTableComponent } from './search-notebook-table.component';
+
+describe('SearchNotebookTableComponent', () => {
+ let component: SearchNotebookTableComponent;
+ let fixture: ComponentFixture
+
+
+ {{
+ notebook?.organization + '/' + notebook?.repository + (notebook?.workflowName ? '/' + notebook?.workflowName : '')
+ }}
+
+
+ {{ notebook.topicAutomatic }}
+
+
+ {{ notebook?.descriptorType | descriptorLanguage }}
+
+
+ {{ notebook?.descriptorTypeSubclass }}
+
+
+
diff --git a/src/app/search/search-results/search-results.component.ts b/src/app/search/search-results/search-results.component.ts
index c320c28236..77cdbb7b3d 100644
--- a/src/app/search/search-results/search-results.component.ts
+++ b/src/app/search/search-results/search-results.component.ts
@@ -33,12 +33,15 @@ export class SearchResultsComponent extends Base implements OnInit {
faMinus = faMinus;
public noToolHits$: Observable
+
+
+
+
+
+
+ A Notebook is a document containing code and text that can be interactively edited and run
+ +
+
+
+
+
+
+
+
diff --git a/src/app/workflows/list/list.component.ts b/src/app/workflows/list/list.component.ts
index c7191b9b23..7fe788e223 100644
--- a/src/app/workflows/list/list.component.ts
+++ b/src/app/workflows/list/list.component.ts
@@ -35,7 +35,14 @@ import { PublishedWorkflowsDataSource } from './published-workflows.datasource';
export class ListWorkflowsComponent extends ToolLister implements OnInit {
@Input() previewMode: boolean;
- public displayedColumns = ['repository', 'verified', 'author', 'descriptorType', 'projectLinks', 'stars'];
+ public workflowColumns = ['repository', 'verified', 'author', 'descriptorType', 'projectLinks', 'stars'];
+ public notebookColumns = ['repository', 'author', 'descriptorType', 'descriptorTypeSubclass', 'projectLinks', 'stars'];
+ public typeToDisplayedColumns = {
+ workflow: this.workflowColumns,
+ service: this.workflowColumns,
+ appTool: this.workflowColumns,
+ notebook: this.notebookColumns,
+ };
public entryType$: Observable;
public entryTypeDisplayName$: Observable;
type: 'tool' | 'workflow' = 'workflow';
From 1eda8260679f0d78458c3a73a1547080836205c0 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 4 May 2023 13:53:35 -0400
Subject: [PATCH 005/128] Bump engine.io and socket.io (#1768)
* Bump engine.io and socket.io
Bumps [engine.io](https://github.com/socketio/engine.io) and [socket.io](https://github.com/socketio/socket.io). These dependencies needed to be updated together.
Updates `engine.io` from 6.2.1 to 6.4.2
- [Release notes](https://github.com/socketio/engine.io/releases)
- [Changelog](https://github.com/socketio/engine.io/blob/main/CHANGELOG.md)
- [Commits](https://github.com/socketio/engine.io/compare/6.2.1...6.4.2)
Updates `socket.io` from 4.5.4 to 4.6.1
- [Release notes](https://github.com/socketio/socket.io/releases)
- [Changelog](https://github.com/socketio/socket.io/blob/main/CHANGELOG.md)
- [Commits](https://github.com/socketio/socket.io/compare/4.5.4...4.6.1)
---
updated-dependencies:
- dependency-name: engine.io
dependency-type: indirect
- dependency-name: socket.io
dependency-type: indirect
...
Signed-off-by: dependabot[bot]
* Update license file
---------
Signed-off-by: dependabot[bot]
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
THIRD-PARTY-LICENSES.csv | 11 ++--
package-lock.json | 110 ++++++++++++++++-----------------------
2 files changed, 49 insertions(+), 72 deletions(-)
diff --git a/THIRD-PARTY-LICENSES.csv b/THIRD-PARTY-LICENSES.csv
index 4868a6186d..b39a25757d 100644
--- a/THIRD-PARTY-LICENSES.csv
+++ b/THIRD-PARTY-LICENSES.csv
@@ -529,8 +529,8 @@
"encodeurl@1.0.2","MIT","https://github.com/pillarjs/encodeurl"
"encoding@0.1.13","MIT","https://github.com/andris9/encoding"
"end-of-stream@1.4.4","MIT","https://github.com/mafintosh/end-of-stream"
-"engine.io-parser@5.0.4","MIT","https://github.com/socketio/engine.io-parser"
-"engine.io@6.2.1","MIT","https://github.com/socketio/engine.io"
+"engine.io-parser@5.0.6","MIT","https://github.com/socketio/engine.io-parser"
+"engine.io@6.4.2","MIT","https://github.com/socketio/engine.io"
"enhanced-resolve@5.10.0","MIT","https://github.com/webpack/enhanced-resolve"
"enquirer@2.3.6","MIT","https://github.com/enquirer/enquirer"
"ent@2.2.0","MIT","https://github.com/substack/node-ent"
@@ -1094,9 +1094,9 @@
"slice-ansi@4.0.0","MIT","https://github.com/chalk/slice-ansi"
"slide@1.1.6","ISC","https://github.com/isaacs/slide-flow-control"
"smart-buffer@4.2.0","MIT","https://github.com/JoshGlazebrook/smart-buffer"
-"socket.io-adapter@2.4.0","MIT","https://github.com/socketio/socket.io-adapter"
+"socket.io-adapter@2.5.2","MIT","https://github.com/socketio/socket.io-adapter"
"socket.io-parser@4.2.1","MIT","https://github.com/socketio/socket.io-parser"
-"socket.io@4.5.4","MIT","https://github.com/socketio/socket.io"
+"socket.io@4.6.1","MIT","https://github.com/socketio/socket.io"
"sockjs@0.3.24","MIT","https://github.com/sockjs/sockjs-node"
"socks-proxy-agent@4.0.2","MIT","https://github.com/TooTallNate/node-socks-proxy-agent"
"socks-proxy-agent@7.0.0","MIT","https://github.com/TooTallNate/node-socks-proxy-agent"
@@ -1231,8 +1231,7 @@
"wrap-ansi@7.0.0","MIT","https://github.com/chalk/wrap-ansi"
"wrappy@1.0.2","ISC","https://github.com/npm/wrappy"
"ws@7.5.9","MIT","https://github.com/websockets/ws"
-"ws@8.10.0","MIT","https://github.com/websockets/ws"
-"ws@8.2.3","MIT","https://github.com/websockets/ws"
+"ws@8.11.0","MIT","https://github.com/websockets/ws"
"xtend@4.0.2","MIT","https://github.com/Raynos/xtend"
"y18n@4.0.3","ISC","https://github.com/yargs/y18n"
"y18n@5.0.8","ISC","https://github.com/yargs/y18n"
diff --git a/package-lock.json b/package-lock.json
index d63a01e4ca..964fb6ebd2 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -8070,9 +8070,9 @@
}
},
"node_modules/engine.io": {
- "version": "6.2.1",
- "resolved": "https://registry.npmjs.org/engine.io/-/engine.io-6.2.1.tgz",
- "integrity": "sha512-ECceEFcAaNRybd3lsGQKas3ZlMVjN3cyWwMP25D2i0zWfyiytVbTpRPa34qrr+FHddtpBVOmq4H/DCv1O0lZRA==",
+ "version": "6.4.2",
+ "resolved": "https://registry.npmjs.org/engine.io/-/engine.io-6.4.2.tgz",
+ "integrity": "sha512-FKn/3oMiJjrOEOeUub2WCox6JhxBXq/Zn3fZOMCBxKnNYtsdKjxhl7yR3fZhM9PV+rdE75SU5SYMc+2PGzo+Tg==",
"dev": true,
"dependencies": {
"@types/cookie": "^0.4.1",
@@ -8084,16 +8084,16 @@
"cors": "~2.8.5",
"debug": "~4.3.1",
"engine.io-parser": "~5.0.3",
- "ws": "~8.2.3"
+ "ws": "~8.11.0"
},
"engines": {
"node": ">=10.0.0"
}
},
"node_modules/engine.io-parser": {
- "version": "5.0.4",
- "resolved": "https://registry.npmjs.org/engine.io-parser/-/engine.io-parser-5.0.4.tgz",
- "integrity": "sha512-+nVFp+5z1E3HcToEnO7ZIj3g+3k9389DvWtvJZz0T6/eOCPIyyxehFcedoYrZQrp0LgQbD9pPXhpMBKMd5QURg==",
+ "version": "5.0.6",
+ "resolved": "https://registry.npmjs.org/engine.io-parser/-/engine.io-parser-5.0.6.tgz",
+ "integrity": "sha512-tjuoZDMAdEhVnSFleYPCtdL2GXwVTGtNjoeJd9IhIG3C1xs9uwxqRNEu5WpnDZCaozwVlK/nuQhpodhXSIMaxw==",
"dev": true,
"engines": {
"node": ">=10.0.0"
@@ -15908,16 +15908,16 @@
}
},
"node_modules/socket.io": {
- "version": "4.5.4",
- "resolved": "https://registry.npmjs.org/socket.io/-/socket.io-4.5.4.tgz",
- "integrity": "sha512-m3GC94iK9MfIEeIBfbhJs5BqFibMtkRk8ZpKwG2QwxV0m/eEhPIV4ara6XCF1LWNAus7z58RodiZlAH71U3EhQ==",
+ "version": "4.6.1",
+ "resolved": "https://registry.npmjs.org/socket.io/-/socket.io-4.6.1.tgz",
+ "integrity": "sha512-KMcaAi4l/8+xEjkRICl6ak8ySoxsYG+gG6/XfRCPJPQ/haCRIJBTL4wIl8YCsmtaBovcAXGLOShyVWQ/FG8GZA==",
"dev": true,
"dependencies": {
"accepts": "~1.3.4",
"base64id": "~2.0.0",
"debug": "~4.3.2",
- "engine.io": "~6.2.1",
- "socket.io-adapter": "~2.4.0",
+ "engine.io": "~6.4.1",
+ "socket.io-adapter": "~2.5.2",
"socket.io-parser": "~4.2.1"
},
"engines": {
@@ -15925,10 +15925,13 @@
}
},
"node_modules/socket.io-adapter": {
- "version": "2.4.0",
- "resolved": "https://registry.npmjs.org/socket.io-adapter/-/socket.io-adapter-2.4.0.tgz",
- "integrity": "sha512-W4N+o69rkMEGVuk2D/cvca3uYsvGlMwsySWV447y99gUPghxq42BxqLNMndb+a1mm/5/7NeXVQS7RLa2XyXvYg==",
- "dev": true
+ "version": "2.5.2",
+ "resolved": "https://registry.npmjs.org/socket.io-adapter/-/socket.io-adapter-2.5.2.tgz",
+ "integrity": "sha512-87C3LO/NOMc+eMcpcxUBebGjkpMDkNBS9tf7KJqcDsmL936EChtVva71Dw2q4tQcuVC+hAUy4an2NO/sYXmwRA==",
+ "dev": true,
+ "dependencies": {
+ "ws": "~8.11.0"
+ }
},
"node_modules/socket.io-parser": {
"version": "4.2.1",
@@ -17384,27 +17387,6 @@
"url": "https://opencollective.com/webpack"
}
},
- "node_modules/webpack-dev-server/node_modules/ws": {
- "version": "8.10.0",
- "resolved": "https://registry.npmjs.org/ws/-/ws-8.10.0.tgz",
- "integrity": "sha512-+s49uSmZpvtAsd2h37vIPy1RBusaLawVe8of+GyEPsaJTCMpj/2v8NpeK1SHXjBlQ95lQTmQofOJnFiLoaN3yw==",
- "dev": true,
- "engines": {
- "node": ">=10.0.0"
- },
- "peerDependencies": {
- "bufferutil": "^4.0.1",
- "utf-8-validate": "^5.0.2"
- },
- "peerDependenciesMeta": {
- "bufferutil": {
- "optional": true
- },
- "utf-8-validate": {
- "optional": true
- }
- }
- },
"node_modules/webpack-merge": {
"version": "5.8.0",
"resolved": "https://registry.npmjs.org/webpack-merge/-/webpack-merge-5.8.0.tgz",
@@ -17600,9 +17582,9 @@
"integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8="
},
"node_modules/ws": {
- "version": "8.2.3",
- "resolved": "https://registry.npmjs.org/ws/-/ws-8.2.3.tgz",
- "integrity": "sha512-wBuoj1BDpC6ZQ1B7DWQBYVLphPWkm8i9Y0/3YdHjHKHiohOJ1ws+3OccDWtH+PoC9DZD5WOTrJvNbWvjS6JWaA==",
+ "version": "8.11.0",
+ "resolved": "https://registry.npmjs.org/ws/-/ws-8.11.0.tgz",
+ "integrity": "sha512-HPG3wQd9sNQoT9xHyNCXoDUa+Xw/VevmY9FoHyQ+g+rrMn4j6FB4np7Z0OhdTgjx6MgQLK7jwSy1YecU1+4Asg==",
"dev": true,
"engines": {
"node": ">=10.0.0"
@@ -23560,9 +23542,9 @@
}
},
"engine.io": {
- "version": "6.2.1",
- "resolved": "https://registry.npmjs.org/engine.io/-/engine.io-6.2.1.tgz",
- "integrity": "sha512-ECceEFcAaNRybd3lsGQKas3ZlMVjN3cyWwMP25D2i0zWfyiytVbTpRPa34qrr+FHddtpBVOmq4H/DCv1O0lZRA==",
+ "version": "6.4.2",
+ "resolved": "https://registry.npmjs.org/engine.io/-/engine.io-6.4.2.tgz",
+ "integrity": "sha512-FKn/3oMiJjrOEOeUub2WCox6JhxBXq/Zn3fZOMCBxKnNYtsdKjxhl7yR3fZhM9PV+rdE75SU5SYMc+2PGzo+Tg==",
"dev": true,
"requires": {
"@types/cookie": "^0.4.1",
@@ -23574,13 +23556,13 @@
"cors": "~2.8.5",
"debug": "~4.3.1",
"engine.io-parser": "~5.0.3",
- "ws": "~8.2.3"
+ "ws": "~8.11.0"
}
},
"engine.io-parser": {
- "version": "5.0.4",
- "resolved": "https://registry.npmjs.org/engine.io-parser/-/engine.io-parser-5.0.4.tgz",
- "integrity": "sha512-+nVFp+5z1E3HcToEnO7ZIj3g+3k9389DvWtvJZz0T6/eOCPIyyxehFcedoYrZQrp0LgQbD9pPXhpMBKMd5QURg==",
+ "version": "5.0.6",
+ "resolved": "https://registry.npmjs.org/engine.io-parser/-/engine.io-parser-5.0.6.tgz",
+ "integrity": "sha512-tjuoZDMAdEhVnSFleYPCtdL2GXwVTGtNjoeJd9IhIG3C1xs9uwxqRNEu5WpnDZCaozwVlK/nuQhpodhXSIMaxw==",
"dev": true
},
"enhanced-resolve": {
@@ -29367,24 +29349,27 @@
"integrity": "sha512-94hK0Hh8rPqQl2xXc3HsaBoOXKV20MToPkcXvwbISWLEs+64sBq5kFgn2kJDHb1Pry9yrP0dxrCI9RRci7RXKg=="
},
"socket.io": {
- "version": "4.5.4",
- "resolved": "https://registry.npmjs.org/socket.io/-/socket.io-4.5.4.tgz",
- "integrity": "sha512-m3GC94iK9MfIEeIBfbhJs5BqFibMtkRk8ZpKwG2QwxV0m/eEhPIV4ara6XCF1LWNAus7z58RodiZlAH71U3EhQ==",
+ "version": "4.6.1",
+ "resolved": "https://registry.npmjs.org/socket.io/-/socket.io-4.6.1.tgz",
+ "integrity": "sha512-KMcaAi4l/8+xEjkRICl6ak8ySoxsYG+gG6/XfRCPJPQ/haCRIJBTL4wIl8YCsmtaBovcAXGLOShyVWQ/FG8GZA==",
"dev": true,
"requires": {
"accepts": "~1.3.4",
"base64id": "~2.0.0",
"debug": "~4.3.2",
- "engine.io": "~6.2.1",
- "socket.io-adapter": "~2.4.0",
+ "engine.io": "~6.4.1",
+ "socket.io-adapter": "~2.5.2",
"socket.io-parser": "~4.2.1"
}
},
"socket.io-adapter": {
- "version": "2.4.0",
- "resolved": "https://registry.npmjs.org/socket.io-adapter/-/socket.io-adapter-2.4.0.tgz",
- "integrity": "sha512-W4N+o69rkMEGVuk2D/cvca3uYsvGlMwsySWV447y99gUPghxq42BxqLNMndb+a1mm/5/7NeXVQS7RLa2XyXvYg==",
- "dev": true
+ "version": "2.5.2",
+ "resolved": "https://registry.npmjs.org/socket.io-adapter/-/socket.io-adapter-2.5.2.tgz",
+ "integrity": "sha512-87C3LO/NOMc+eMcpcxUBebGjkpMDkNBS9tf7KJqcDsmL936EChtVva71Dw2q4tQcuVC+hAUy4an2NO/sYXmwRA==",
+ "dev": true,
+ "requires": {
+ "ws": "~8.11.0"
+ }
},
"socket.io-parser": {
"version": "4.2.1",
@@ -30496,13 +30481,6 @@
"ajv-formats": "^2.1.1",
"ajv-keywords": "^5.0.0"
}
- },
- "ws": {
- "version": "8.10.0",
- "resolved": "https://registry.npmjs.org/ws/-/ws-8.10.0.tgz",
- "integrity": "sha512-+s49uSmZpvtAsd2h37vIPy1RBusaLawVe8of+GyEPsaJTCMpj/2v8NpeK1SHXjBlQ95lQTmQofOJnFiLoaN3yw==",
- "dev": true,
- "requires": {}
}
}
},
@@ -30637,9 +30615,9 @@
"integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8="
},
"ws": {
- "version": "8.2.3",
- "resolved": "https://registry.npmjs.org/ws/-/ws-8.2.3.tgz",
- "integrity": "sha512-wBuoj1BDpC6ZQ1B7DWQBYVLphPWkm8i9Y0/3YdHjHKHiohOJ1ws+3OccDWtH+PoC9DZD5WOTrJvNbWvjS6JWaA==",
+ "version": "8.11.0",
+ "resolved": "https://registry.npmjs.org/ws/-/ws-8.11.0.tgz",
+ "integrity": "sha512-HPG3wQd9sNQoT9xHyNCXoDUa+Xw/VevmY9FoHyQ+g+rrMn4j6FB4np7Z0OhdTgjx6MgQLK7jwSy1YecU1+4Asg==",
"dev": true,
"requires": {}
},
From b551eb927f11a241dcfacfc36c1cf3bb7d6c6ab9 Mon Sep 17 00:00:00 2001
From: Steve Von Worley
Date: Thu, 4 May 2023 11:44:10 -0700
Subject: [PATCH 006/128] fix mathjax notebooks font url
https://ucsc-cgl.atlassian.net/browse/SEAB-5435
---
.circleci/config.yml | 2 +-
src/app/notebook/mathjax-config.js | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/.circleci/config.yml b/.circleci/config.yml
index ffab15c3c6..ef7c52e0de 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -386,7 +386,7 @@ jobs:
# TODO: https://gui.dockstore.org/${CIRCLE_TAG:-$CIRCLE_BRANCH}-$(echo $CIRCLE_SHA1 | cut -c -7) can probably be made into a bash/circle-ci variable.
- run:
name: Swap for CDN paths
- command: bash -i -c "find src \( -iname '*.html' -o -iname '*.ts' -o -iname '*.json' \) -exec sed -i 's~\(\.\./\)\+assets/~https://gui\.dockstore\.org/${CIRCLE_TAG:-$CIRCLE_BRANCH}-$(echo $CIRCLE_SHA1 | cut -c -7)/assets/~g' {} +"
+ command: bash -i -c "find src \( -iname '*.html' -o -iname '*.ts' -o -iname '*.js' -o -iname '*.json' \) -exec sed -i 's~\(\.\./\)\+assets/~https://gui\.dockstore\.org/${CIRCLE_TAG:-$CIRCLE_BRANCH}-$(echo $CIRCLE_SHA1 | cut -c -7)/assets/~g' {} +"
- run:
name: Build
command: NODE_OPTIONS="--max-old-space-size=1610" bash -i -c 'npm run build.prod -- --deploy-url https://gui.dockstore.org/${CIRCLE_TAG:-$CIRCLE_BRANCH}-$(echo $CIRCLE_SHA1 | cut -c -7)/'
diff --git a/src/app/notebook/mathjax-config.js b/src/app/notebook/mathjax-config.js
index 057e3d52be..85222171f3 100644
--- a/src/app/notebook/mathjax-config.js
+++ b/src/app/notebook/mathjax-config.js
@@ -8,7 +8,7 @@ window.MathJax = {
processEscapes: true,
},
chtml: {
- fontURL: '/assets/fonts/mathjax',
+ fontURL: '../../../../assets/fonts/mathjax',
},
options: {
// values adapted from https://docs.mathjax.org/en/latest/options/safe.html
From 148f4d4b67fd29528ab6ddf49f4e3f494510aa87 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 5 May 2023 13:49:27 -0400
Subject: [PATCH 007/128] Bump json5 from 2.2.1 to 2.2.3 (#1674)
* Bump json5 from 2.2.1 to 2.2.3
Bumps [json5](https://github.com/json5/json5) from 2.2.1 to 2.2.3.
- [Release notes](https://github.com/json5/json5/releases)
- [Changelog](https://github.com/json5/json5/blob/main/CHANGELOG.md)
- [Commits](https://github.com/json5/json5/compare/v2.2.1...v2.2.3)
---
updated-dependencies:
- dependency-name: json5
dependency-type: indirect
...
Signed-off-by: dependabot[bot]
* Update license file
---------
Signed-off-by: dependabot[bot]
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
THIRD-PARTY-LICENSES.csv | 2 +-
package-lock.json | 12 ++++++------
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/THIRD-PARTY-LICENSES.csv b/THIRD-PARTY-LICENSES.csv
index b39a25757d..6fbffe0bd9 100644
--- a/THIRD-PARTY-LICENSES.csv
+++ b/THIRD-PARTY-LICENSES.csv
@@ -754,7 +754,7 @@
"json-schema@0.4.0","(AFL-2.1 OR BSD-3-Clause)","https://github.com/kriszyp/json-schema"
"json-stable-stringify-without-jsonify@1.0.1","MIT","https://github.com/samn/json-stable-stringify"
"json-stringify-safe@5.0.1","ISC","https://github.com/isaacs/json-stringify-safe"
-"json5@2.2.1","MIT","https://github.com/json5/json5"
+"json5@2.2.3","MIT","https://github.com/json5/json5"
"jsonc-parser@3.1.0","MIT","https://github.com/microsoft/node-jsonc-parser"
"jsonfile@6.1.0","MIT","https://github.com/jprichardson/node-jsonfile"
"jsonparse@1.3.1","MIT","https://github.com/creationix/jsonparse"
diff --git a/package-lock.json b/package-lock.json
index 964fb6ebd2..12893943f3 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -11092,9 +11092,9 @@
"dev": true
},
"node_modules/json5": {
- "version": "2.2.1",
- "resolved": "https://registry.npmjs.org/json5/-/json5-2.2.1.tgz",
- "integrity": "sha512-1hqLFMSrGHRHxav9q9gNjJ5EXznIxGVO09xQRrwplcS8qs28pZ8s8hupZAmqDwZUmVZ2Qb2jnyPOWcDH8m8dlA==",
+ "version": "2.2.3",
+ "resolved": "https://registry.npmjs.org/json5/-/json5-2.2.3.tgz",
+ "integrity": "sha512-XmOWe7eyHYH14cLdVPoyg+GOH3rYX++KpzrylJwSW98t3Nk+U8XOl8FWKOgwtzdb8lXGf6zYwDUzeHMWfxasyg==",
"dev": true,
"bin": {
"json5": "lib/cli.js"
@@ -25760,9 +25760,9 @@
"dev": true
},
"json5": {
- "version": "2.2.1",
- "resolved": "https://registry.npmjs.org/json5/-/json5-2.2.1.tgz",
- "integrity": "sha512-1hqLFMSrGHRHxav9q9gNjJ5EXznIxGVO09xQRrwplcS8qs28pZ8s8hupZAmqDwZUmVZ2Qb2jnyPOWcDH8m8dlA==",
+ "version": "2.2.3",
+ "resolved": "https://registry.npmjs.org/json5/-/json5-2.2.3.tgz",
+ "integrity": "sha512-XmOWe7eyHYH14cLdVPoyg+GOH3rYX++KpzrylJwSW98t3Nk+U8XOl8FWKOgwtzdb8lXGf6zYwDUzeHMWfxasyg==",
"dev": true
},
"jsonc-parser": {
From 81008d575b7550ef03d1d00f704d468fbcb3d389 Mon Sep 17 00:00:00 2001
From: Steve Von Worley
Date: Fri, 12 May 2023 08:48:24 -0700
Subject: [PATCH 008/128] make all "launch with' tooltips appear to the left
https://ucsc-cgl.atlassian.net/browse/SEAB-5511
---
.../launch-third-party.component.html | 16 ++++++++++++++++
1 file changed, 16 insertions(+)
diff --git a/src/app/workflow/launch-third-party/launch-third-party.component.html b/src/app/workflow/launch-third-party/launch-third-party.component.html
index 50b0c0b408..fc5230ce20 100644
--- a/src/app/workflow/launch-third-party/launch-third-party.component.html
+++ b/src/app/workflow/launch-third-party/launch-third-party.component.html
@@ -37,11 +37,13 @@
[className]="'partner-launch'"
[disabled]="(hasContent$ | async) === false"
[matTooltip]="(hasContent$ | async) ? '' : 'The WDL workflow has no content.'"
+ matTooltipPosition="left"
>
@@ -226,6 +241,7 @@
mat-button
class="launch-with-button private-btn"
[matTooltip]="(hasContent$ | async) ? 'Export this workflow to Nextflow Tower' : 'The Nextflow workflow has no content.'"
+ matTooltipPosition="left"
target="_blank"
rel="noopener"
[attr.href]="
From 1ff633033c3be1fa552f7fe393579471d605ddd6 Mon Sep 17 00:00:00 2001
From: Steve Von Worley some html
"}]}'; + const notebook = `{"nbformat": 3, "worksheets": [{ "cells": [${cell}] }]}`; + format(notebook); + expect(element.querySelector('.source').textContent).toContain('some input'); + expect(element.querySelector('.output').textContent).toContain('some html'); + }); }); diff --git a/src/app/notebook/notebook.component.ts b/src/app/notebook/notebook.component.ts index 74f0652514..3525f91962 100644 --- a/src/app/notebook/notebook.component.ts +++ b/src/app/notebook/notebook.component.ts @@ -62,9 +62,11 @@ export class NotebookComponent implements OnChanges { try { // Parse the JSON content of the notebook file. const json = JSON.parse(sourceFile.content); + // Find the cells and, if necessary, convert them to a representation that approximates nbformat 4. + const cells = json?.nbformat < 4 ? this.cellsToNbformat4(json?.worksheets[0]?.cells) : json?.cells; // If the `cells` property is an array, filter spam and "pass" the cells to the template. - if (this.isArray(json?.cells)) { - this.cells = this.filterSpam(json.cells); + if (this.isArray(cells)) { + this.cells = this.filterSpam(cells); this.error = false; return; } @@ -101,4 +103,31 @@ export class NotebookComponent implements OnChanges { isArray(value: any): boolean { return Array.isArray(value); } + + cellsToNbformat4(cells: Cell[]): Cell[] { + if (this.isArray(cells)) { + cells.forEach((cell) => this.cellToNbFormat4(cell)); + } + return cells; + } + + cellToNbFormat4(cell: Cell): void { + if (cell.cell_type === 'code') { + // Handle some field name changes: 'input' -> 'source', 'prompt_number' -> 'execution_count' + cell.source ??= cell['input']; + cell.execution_count ??= cell['prompt_number']; + // Convert each output. + if (this.isArray(cell.outputs)) { + cell.outputs.forEach( + (output) => + // Map the old representation of rich outputs to a "mime bundle'. + (output.data ??= { + 'text/plain': output['text'], + 'text/html': output['html'], + 'image/png': output['png'], + }) + ); + } + } + } } From dbf206707d61ff2980967e6236d691b984c8f52d Mon Sep 17 00:00:00 2001 From: Steve Von Worley
- Google Colab
+
diff --git a/src/app/workflow/launch-third-party/launch-third-party.component.ts b/src/app/workflow/launch-third-party/launch-third-party.component.ts
index 83755cf570..7fc554c227 100644
--- a/src/app/workflow/launch-third-party/launch-third-party.component.ts
+++ b/src/app/workflow/launch-third-party/launch-third-party.component.ts
@@ -148,6 +148,27 @@ export class LaunchThirdPartyComponent extends Base implements OnChanges, OnInit
* The workflow path encoded for use as a query parameter value.
*/
workflowPathAsQueryValue: string;
+
+ /**
+ * The workflow organization, URL encoded.
+ */
+ workflowOrganizationAsQueryValue: string;
+
+ /**
+ * The workflow repository, URL encoded.
+ */
+ workflowRepositoryAsQueryValue: string;
+
+ /**
+ * The name of the selected version, URL encoded.
+ */
+ selectedVersionNameAsQueryValue: string;
+
+ /**
+ * The workflow path of the selected version, in absolute form, URL encoded.
+ */
+ selectedVersionWorkflowPathAsQueryValue: string;
+
partner = CloudInstance.PartnerEnum;
cloudInstances: Array
+ Google Colab
+ mybinder.org
+
{{ text }}
+ {{ text }}
Recent Activity
-
+
{{ entry.prettyPath }}
* Update license file
---------
Signed-off-by: dependabot[bot]
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
THIRD-PARTY-LICENSES.csv | 2 +-
package-lock.json | 12 ++++++------
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/THIRD-PARTY-LICENSES.csv b/THIRD-PARTY-LICENSES.csv
index 6fbffe0bd9..19165bdecf 100644
--- a/THIRD-PARTY-LICENSES.csv
+++ b/THIRD-PARTY-LICENSES.csv
@@ -1095,7 +1095,7 @@
"slide@1.1.6","ISC","https://github.com/isaacs/slide-flow-control"
"smart-buffer@4.2.0","MIT","https://github.com/JoshGlazebrook/smart-buffer"
"socket.io-adapter@2.5.2","MIT","https://github.com/socketio/socket.io-adapter"
-"socket.io-parser@4.2.1","MIT","https://github.com/socketio/socket.io-parser"
+"socket.io-parser@4.2.3","MIT","https://github.com/socketio/socket.io-parser"
"socket.io@4.6.1","MIT","https://github.com/socketio/socket.io"
"sockjs@0.3.24","MIT","https://github.com/sockjs/sockjs-node"
"socks-proxy-agent@4.0.2","MIT","https://github.com/TooTallNate/node-socks-proxy-agent"
diff --git a/package-lock.json b/package-lock.json
index 12893943f3..c8dcb0e47f 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -15934,9 +15934,9 @@
}
},
"node_modules/socket.io-parser": {
- "version": "4.2.1",
- "resolved": "https://registry.npmjs.org/socket.io-parser/-/socket.io-parser-4.2.1.tgz",
- "integrity": "sha512-V4GrkLy+HeF1F/en3SpUaM+7XxYXpuMUWLGde1kSSh5nQMN4hLrbPIkD+otwh6q9R6NOQBN4AMaOZ2zVjui82g==",
+ "version": "4.2.3",
+ "resolved": "https://registry.npmjs.org/socket.io-parser/-/socket.io-parser-4.2.3.tgz",
+ "integrity": "sha512-JMafRntWVO2DCJimKsRTh/wnqVvO4hrfwOqtO7f+uzwsQMuxO6VwImtYxaQ+ieoyshWOTJyV0fA21lccEXRPpQ==",
"dev": true,
"dependencies": {
"@socket.io/component-emitter": "~3.1.0",
@@ -29372,9 +29372,9 @@
}
},
"socket.io-parser": {
- "version": "4.2.1",
- "resolved": "https://registry.npmjs.org/socket.io-parser/-/socket.io-parser-4.2.1.tgz",
- "integrity": "sha512-V4GrkLy+HeF1F/en3SpUaM+7XxYXpuMUWLGde1kSSh5nQMN4hLrbPIkD+otwh6q9R6NOQBN4AMaOZ2zVjui82g==",
+ "version": "4.2.3",
+ "resolved": "https://registry.npmjs.org/socket.io-parser/-/socket.io-parser-4.2.3.tgz",
+ "integrity": "sha512-JMafRntWVO2DCJimKsRTh/wnqVvO4hrfwOqtO7f+uzwsQMuxO6VwImtYxaQ+ieoyshWOTJyV0fA21lccEXRPpQ==",
"dev": true,
"requires": {
"@socket.io/component-emitter": "~3.1.0",
From 7d361a548e7b3561c593541992966d884690b2f8 Mon Sep 17 00:00:00 2001
From: Steve Von Worley
Date: Thu, 25 May 2023 08:06:32 -0700
Subject: [PATCH 015/128] add rudimentary smoke tests for notebooks
https://ucsc-cgl.atlassian.net/browse/SEAB-5530
---
.../smokeTests/sharedTests/basic-enduser.ts | 102 ++++++++++++++++--
package.json | 4 +-
scripts/run-webservice-script.sh | 2 +-
3 files changed, 96 insertions(+), 12 deletions(-)
diff --git a/cypress/e2e/smokeTests/sharedTests/basic-enduser.ts b/cypress/e2e/smokeTests/sharedTests/basic-enduser.ts
index 0b8b6ee75f..20cc0ff29f 100644
--- a/cypress/e2e/smokeTests/sharedTests/basic-enduser.ts
+++ b/cypress/e2e/smokeTests/sharedTests/basic-enduser.ts
@@ -2,17 +2,30 @@ import { ga4ghPath } from '../../../../src/app/shared/constants';
import { goToTab } from '../../../support/commands';
import { ToolDescriptor } from '../../../../src/app/shared/swagger/model/toolDescriptor';
-// Test an entry, these should be ambiguous between tools and workflows.
+// Test an entry, these should be ambiguous between tools, workflows, and notebooks.
describe('run stochastic smoke test', () => {
testEntry('Tools');
testEntry('Workflows');
+ testEntry('Notebooks');
});
function testEntry(tab: string) {
- beforeEach('get random entry on first page', () => {
- cy.visit('/search');
+ function goToRandomEntry() {
+ // Notebooks search is not functional in staging or prod in 1.14.
+ // TODO after 1.15 release: remove the following code path
+ if (tab === 'Notebooks' && isStagingOrProd()) {
+ cy.visit('/notebooks');
+ cy.get('[data-cy=entry-link]')
+ .eq(0)
+ .then((el) => {
+ cy.log(el.prop('href')); // log the href in case a test fails
+ cy.visit(el.prop('href'));
+ });
+ return;
+ }
+ cy.visit('/search' + (tab === 'Notebooks' ? '?notebooks' : ''));
cy.get('[data-cy=workflowColumn] a');
goToTab(tab);
- const linkName = tab === 'Workflows' ? 'workflowColumn' : 'toolNames';
+ const linkName = getLinkName(tab);
// select a random entry on the first page and navigate to it
let chosen_index = 0;
cy.get('[data-cy=' + linkName + ']')
@@ -26,12 +39,12 @@ function testEntry(tab: string) {
cy.visit(el.prop('href'));
});
});
- });
+ }
it('check info tab', () => {
- // test export to zip button
+ goToRandomEntry();
goToTab('Info');
-
+ // test export to zip button
cy.get('[data-cy=downloadZip]').within(() => {
cy.get('a').then((el) => {
cy.request(el.prop('href')).its('status').should('eq', 200);
@@ -40,18 +53,38 @@ function testEntry(tab: string) {
});
it('check files tab', () => {
+ goToRandomEntry();
goToTab('Files');
cy.url().should('contain', '?tab=files');
- cy.contains('Descriptor Files');
+ cy.contains(tab === 'Notebooks' ? 'Notebook Files' : 'Descriptor Files');
});
it('check versions tab', () => {
+ goToRandomEntry();
goToTab('Versions');
cy.url().should('contain', '?tab=versions');
cy.get('[data-cy=versionRow]').should('have.length.of.at.least', 1);
});
}
+function getLinkName(tab: string): string {
+ switch (tab) {
+ case 'Tools':
+ return 'toolNames';
+ case 'Workflows':
+ return 'workflowColumn';
+ case 'Notebooks':
+ return 'notebookColumn';
+ default:
+ throw new Error('unknown tab');
+ }
+}
+
+function isStagingOrProd() {
+ const baseUrl = Cypress.config('baseUrl');
+ return baseUrl === 'https://staging.dockstore.org' || baseUrl === 'https://dockstore.org';
+}
+
const organizations = [['Broad Institute']];
describe('Check organizations page', () => {
it('has multiple organizations and org with content', () => {
@@ -179,11 +212,18 @@ const workflowVersionTuples = [
'Galaxy',
],
];
-// This test shouldn't be run for smoke tests as it depends on 'real' entries
+const notebookVersionTuples = [
+ // TODO when we add notebooks that will persist in the prod database, detail a few here
+];
+
+// These tests shouldn't be run for smoke tests as it depends on 'real' entries
if (Cypress.config('baseUrl') !== 'http://localhost:4200') {
describe('Monitor workflows', () => {
workflowVersionTuples.forEach((t) => testWorkflow(t[0], t[1], t[2], t[3], t[4]));
});
+ describe('Monitor notebooks', () => {
+ notebookVersionTuples.forEach((t) => testNotebook(t[0], t[1], t[2], t[3], t[4], t[5]));
+ });
}
function testWorkflow(url: string, version1: string, version2: string, trsUrl: string, type: string) {
@@ -282,6 +322,50 @@ function testWorkflow(url: string, version1: string, version2: string, trsUrl: s
});
}
+function testNotebook(url: string, version1: string, version2: string, trsUrl: string, path: string, type: string) {
+ it('notebook tabs work for ' + url, () => {
+ cy.visit('/notebooks/' + url + ':' + version1);
+
+ goToTab('Info');
+ cy.url().should('contain', '?tab=info');
+ cy.contains('mat-card-header', 'Notebook Information');
+
+ goToTab('Preview');
+ cy.url().should('contain', '?tab=preview');
+
+ goToTab('Versions');
+ cy.url().should('contain', '?tab=versions');
+
+ // check that clicking on a different version goes to that version's url
+ if (version1 !== version2) {
+ cy.contains('[data-cy=versionName]', version2).click();
+ cy.url().should('contain', url + ':' + version2);
+ }
+
+ goToTab('Files');
+ cy.url().should('contain', '?tab=files');
+
+ // Check the "Launch with" buttons.
+ // Notebooks "Launch with" is not fully functional in staging or prod in 1.14.
+ // TODO after 1.15 release: make the following code execute in all cases.
+ if (!isStagingOrProd()) {
+ let launchWithTuples: any[] = [];
+ if (type === 'Jupyter') {
+ launchWithTuples = [
+ ['colabLaunchWith', 'blob/' + version2 + path],
+ ['mybinderLaunchWith', version2 + '?labpath=' + path],
+ ];
+ }
+ launchWithTuples.forEach((t) => {
+ cy.get('[data-cy=' + t[0] + ']').should(($el) => {
+ // @ts-ignore
+ expect($el.attr('href')).to.contain(t[1]);
+ });
+ });
+ }
+ });
+}
+
// TODO: uncomment after tooltester logs are fixed
// describe('Test existence of Logs', () => {
// it('Find Logs in Workflows', () => {
diff --git a/package.json b/package.json
index ea409de2e6..be9ef54ae7 100644
--- a/package.json
+++ b/package.json
@@ -5,8 +5,8 @@
"config": {
"webservice_version": "1.15.0",
"use_circle": true,
- "circle_ci_source": "https://app.circleci.com/pipelines/github/dockstore/dockstore/9912/workflows/6645ef57-f01a-4d65-8b0e-36d3dbd95081/jobs/33626/artifacts",
- "circle_build_id": "33626",
+ "circle_ci_source": "https://app.circleci.com/pipelines/github/dockstore/dockstore/9918/workflows/b8714bc1-49a2-424d-8b14-527bc3d4a4e3/jobs/33676/artifacts",
+ "circle_build_id": "33676",
"base_branch": "develop"
},
"scripts": {
diff --git a/scripts/run-webservice-script.sh b/scripts/run-webservice-script.sh
index a587a55aee..bd93202ae5 100755
--- a/scripts/run-webservice-script.sh
+++ b/scripts/run-webservice-script.sh
@@ -16,4 +16,4 @@ psql -h localhost -c "create user dockstore with password 'dockstore' createdb;"
psql -h localhost -c "ALTER USER dockstore WITH superuser;" -U postgres
psql -h localhost -c 'create database webservice_test with owner = dockstore;' -U postgres
psql -h localhost -f test/${DB_DUMP:-db_dump.sql} webservice_test -U postgres
-java -jar dockstore-webservice.jar db migrate -i 1.5.0,1.6.0,1.7.0,add_service_1.7.0,1.8.0,1.9.0,1.10.0,alter_test_user_1.10.2,1.11.0,1.12.0,1.13.0,1.14.0 test/web.yml
+java -jar dockstore-webservice.jar db migrate -i 1.5.0,1.6.0,1.7.0,add_service_1.7.0,1.8.0,1.9.0,1.10.0,alter_test_user_1.10.2,1.11.0,1.12.0,1.13.0,1.14.0,add_notebook_1.14.0 test/web.yml
From dc77aa3f7b02c8002d5e9e6b4ff20446fcce9963 Mon Sep 17 00:00:00 2001
From: Ying Yang <68610185+y-ng@users.noreply.github.com>
Date: Thu, 25 May 2023 17:31:21 -0400
Subject: [PATCH 016/128] SEAB-5479: add period (#1779)
---
src/app/about/about.component.html | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/app/about/about.component.html b/src/app/about/about.component.html
index a18d70c400..6b84932254 100644
--- a/src/app/about/about.component.html
+++ b/src/app/about/about.component.html
@@ -108,7 +108,7 @@
You can use our hosted workflows service to store tools and workflows directly on dockstore.org in order to quickly get
From e208c633aadb0adc59c651703dba7b330ebc958a Mon Sep 17 00:00:00 2001
From: Steve Von Worley
Date: Fri, 26 May 2023 15:47:04 -0700
Subject: [PATCH 017/128] add colab and mybinder notebooks "launch with" icons
https://ucsc-cgl.atlassian.net/browse/SEAB-5545
---
.../launch-third-party.component.html | 4 ++--
src/assets/images/thirdparty/binder.svg | 13 +++++++++++++
src/assets/images/thirdparty/colab.svg | 7 +++++++
3 files changed, 22 insertions(+), 2 deletions(-)
create mode 100644 src/assets/images/thirdparty/binder.svg
create mode 100644 src/assets/images/thirdparty/colab.svg
diff --git a/src/app/workflow/launch-third-party/launch-third-party.component.html b/src/app/workflow/launch-third-party/launch-third-party.component.html
index cea59307a9..f97d7df95a 100644
--- a/src/app/workflow/launch-third-party/launch-third-party.component.html
+++ b/src/app/workflow/launch-third-party/launch-third-party.component.html
@@ -283,7 +283,7 @@
"
[disabled]="(hasContent$ | async) === false"
data-cy="colabLaunchWith"
- >Google Colab
Google Colab
mybinder.org
mybinder.org
{{ entry.lastUpdateDate | date: 'MMM d, yyyy' }}
diff --git a/src/app/home-page/widget/entry-box/entry-box.component.ts b/src/app/home-page/widget/entry-box/entry-box.component.ts
index 8612da79ca..d067d4ab65 100644
--- a/src/app/home-page/widget/entry-box/entry-box.component.ts
+++ b/src/app/home-page/widget/entry-box/entry-box.component.ts
@@ -83,14 +83,9 @@ export class EntryBoxComponent extends Base implements OnInit {
this.helpLink = Dockstore.DOCUMENTATION_URL + '/getting-started/notebooks/notebooks.html';
this.allEntriesLink = '/my-notebooks/';
this.entryTypeParam = 'NOTEBOOKS';
- // Not loading entries for Notebooks - remove when supported
- this.isLoading = false;
}
- // Do not get Notebook entries, unsupported - remove when suported
- if (this.entryType !== NewEntryType.NOTEBOOK) {
- this.getMyEntries();
- }
+ this.getMyEntries();
}
getMyEntries() {
diff --git a/src/materialColorScheme.scss b/src/materialColorScheme.scss
index dc085477b9..490626b68c 100644
--- a/src/materialColorScheme.scss
+++ b/src/materialColorScheme.scss
@@ -197,6 +197,8 @@ $workflow-selection-color: #d2fbf0;
$service-color: #ff6c44;
$service-selection-color: #ffdbcf;
+$notebook-selection-color: #dde1f2;
+
$org-selection-color: #dde1f2;
// Color used to indicate success in general (of an operation, verified badge, etc).
diff --git a/src/styles.scss b/src/styles.scss
index 802036df83..0be97462d4 100644
--- a/src/styles.scss
+++ b/src/styles.scss
@@ -894,6 +894,12 @@ app-workflow-sidebar-accordion
background: $workflow-selection-color !important;
}
+// Set the background to the color associated with notebooks (purple).
+// Used to set the background color in bubbles.
+.notebook-background {
+ background: $notebook-selection-color !important;
+}
+
// Set the background to the color associated with services (orange).
// Used to set the background color in bubbles.
.service-background {
From 246adc1c61184b7b0af0ee9dbbe6d244e16ba132 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 24 May 2023 11:42:49 -0400
Subject: [PATCH 014/128] Bump socket.io-parser from 4.2.1 to 4.2.3 (#1786)
* Bump socket.io-parser from 4.2.1 to 4.2.3
Bumps [socket.io-parser](https://github.com/socketio/socket.io-parser) from 4.2.1 to 4.2.3.
- [Release notes](https://github.com/socketio/socket.io-parser/releases)
- [Changelog](https://github.com/socketio/socket.io-parser/blob/main/CHANGELOG.md)
- [Commits](https://github.com/socketio/socket.io-parser/compare/4.2.1...4.2.3)
---
updated-dependencies:
- dependency-name: socket.io-parser
dependency-type: indirect
...
Signed-off-by: dependabot[bot] You can register your workflows and tools on Dockstore in three ways:
target="_blank" rel="noopener noreferrer" >github apps). You are responsible for ensuring that your descriptors point at valid Docker images + >). You are responsible for ensuring that your descriptors point at valid Docker images.Google Colab
mybinder.orgmybinder.org
diff --git a/src/app/stargazers/stargazers.component.ts b/src/app/stargazers/stargazers.component.ts
index 25f0cfbf8b..47eee4937e 100644
--- a/src/app/stargazers/stargazers.component.ts
+++ b/src/app/stargazers/stargazers.component.ts
@@ -19,6 +19,7 @@ import { takeUntil } from 'rxjs/operators';
import { Base } from '../shared/base';
import { altAvatarImg } from '../shared/constants';
import { StarentryService } from '../shared/starentry.service';
+import { User } from '../shared/swagger';
import { UserService } from '../shared/user/user.service';
import { StarringService } from '../starring/starring.service';
@@ -28,7 +29,7 @@ import { StarringService } from '../starring/starring.service';
styleUrls: ['./stargazers.component.css'],
})
export class StargazersComponent extends Base implements OnInit {
- starGazers: any;
+ starGazers: User[];
public altAvatarImg = altAvatarImg;
constructor(private starringService: StarringService, private userService: UserService, private starentryService: StarentryService) {
From d213713df4558b1bf5a707aa9c72e7f9fa8a0424 Mon Sep 17 00:00:00 2001
From: Nayeon Hyun <61166764+hyunnaye@users.noreply.github.com>
Date: Thu, 8 Jun 2023 10:30:20 -0400
Subject: [PATCH 021/128] SEAB-5387: added services integration and notebooks
count bubble in collections (#1776)
---
cypress/e2e/group2/organizations.ts | 21 +++++++++++++++++--
cypress/support/commands.ts | 10 +++++++++
package.json | 4 ++--
.../collection/collection.component.html | 11 ++++++----
.../collection/collection.component.ts | 19 +++++++++++++++++
.../collections/collections.component.html | 14 +++++++++++++
.../collections/collections.component.ts | 4 +++-
.../state/create-collection.service.ts | 3 ++-
src/app/organizations/organization.module.ts | 2 ++
.../organization/organization.component.html | 1 +
.../organization/organization.component.ts | 3 +++
.../organizations/state/collections.query.ts | 2 +-
.../state/collections.service.ts | 4 ++--
.../organizations/state/collections.store.ts | 2 +-
14 files changed, 86 insertions(+), 14 deletions(-)
diff --git a/cypress/e2e/group2/organizations.ts b/cypress/e2e/group2/organizations.ts
index 3daf9c6a14..45acfd9959 100644
--- a/cypress/e2e/group2/organizations.ts
+++ b/cypress/e2e/group2/organizations.ts
@@ -18,17 +18,17 @@ import {
approvePotatoOrganization,
createPotatoMembership,
rejectPotatoMembership,
- resetDB,
setTokenUserViewPort,
addToCollection,
insertNotebooks,
+ resetDBWithService,
} from '../../support/commands';
import { TokenUser } from '../../../src/app/shared/swagger';
import { TokenSource } from '../../../src/app/shared/enum/token-source.enum';
const imageURL = 'https://superduperfakepotatourl.com/potato.png';
describe('Dockstore Organizations', () => {
- resetDB();
+ resetDBWithService();
setTokenUserViewPort();
function typeInInput(fieldName: string, text: string) {
@@ -298,11 +298,24 @@ describe('Dockstore Organizations', () => {
cy.get('img[src*="default-org-logo"]').should('be.visible');
}
});
+ it('Should be able to add a service to collection', () => {
+ const servicePath = '/services/github.com/garyluu/another-test-service';
+ addToCollection(servicePath, 'Potatoe', 'veryFakeCollectionName');
+ cy.get('[data-cy=collectionLink]').should('contain', 'veryFakeCollectionName');
+ cy.visit('/organizations/Potatoe');
+ cy.get('[data-cy=collections-services-count-bubble]').should('be.visible');
+ cy.visit('/organizations/Potatoe/collections/veryFakeCollectionName');
+ cy.contains('github.com/garyluu/another-test-service');
+ });
insertNotebooks();
it('Should be able to add notebook to collection', () => {
const notebookPath = '/notebooks/github.com/dockstore-testing/simple-notebook';
addToCollection(notebookPath, 'Potatoe', 'veryFakeCollectionName');
cy.get('[data-cy=collectionLink]').should('contain', 'veryFakeCollectionName');
+ cy.visit('/organizations/Potatoe?notebooks');
+ cy.get('[data-cy=collections-notebooks-count-bubble]').should('be.visible');
+ cy.visit('/organizations/Potatoe/collections/veryFakeCollectionName?notebooks');
+ cy.contains('github.com/dockstore-testing/simple-notebook');
});
it('Should be able to remove collection', () => {
@@ -315,6 +328,10 @@ describe('Dockstore Organizations', () => {
cy.get('[data-cy=accept-remove-collection]').click();
cy.visit('/organizations/Potatoe/collections/veryFakeCollectionName');
cy.contains('veryFakeCollectionName').should('not.exist');
+ cy.visit('/organizations/Potatoe');
+ cy.get('[data-cy=collections-services-count-bubble]').should('not.exist');
+ cy.visit('/organizations/Potatoe?notebooks');
+ cy.get('[data-cy=collections-notebooks-count-bubble]').should('not.exist');
});
});
diff --git a/cypress/support/commands.ts b/cypress/support/commands.ts
index 8995a17e16..078ade7f48 100644
--- a/cypress/support/commands.ts
+++ b/cypress/support/commands.ts
@@ -66,6 +66,16 @@ export function resetDB() {
});
}
+export function resetDBWithService() {
+ before(() => {
+ cy.exec('java -jar dockstore-webservice.jar db drop-all --confirm-delete-everything test/web.yml');
+ cy.exec(psqlInvocation + ' -h localhost webservice_test -U dockstore < test/db_dump.sql');
+ cy.exec(
+ 'java -jar dockstore-webservice.jar db migrate -i 1.5.0,1.6.0,1.7.0,add_service_1.7.0,1.8.0,1.9.0,1.10.0,alter_test_user_1.10.2,1.11.0,1.12.0,1.13.0,1.14.0 test/web.yml'
+ );
+ });
+}
+
export function addBeforeSqlFromFile(fileName: string) {
before(() => {
cy.exec(psqlInvocation + ' -h localhost webservice_test -U dockstore < ' + fileName);
diff --git a/package.json b/package.json
index 3bf13818fc..2fe9fd19f7 100644
--- a/package.json
+++ b/package.json
@@ -5,8 +5,8 @@
"config": {
"webservice_version": "1.15.0",
"use_circle": true,
- "circle_ci_source": "https://app.circleci.com/pipelines/github/dockstore/dockstore/9918/workflows/b8714bc1-49a2-424d-8b14-527bc3d4a4e3/jobs/33676/artifacts",
- "circle_build_id": "33676"
+ "circle_ci_source": "https://app.circleci.com/pipelines/github/dockstore/dockstore/9967/workflows/e03b3b8b-aec8-4316-9918-995add989dd1/jobs/34030/artifacts",
+ "circle_build_id": "34030"
},
"scripts": {
"ng": "npx ng",
diff --git a/src/app/organizations/collection/collection.component.html b/src/app/organizations/collection/collection.component.html
index 124b1cdef7..73bcbbcb47 100644
--- a/src/app/organizations/collection/collection.component.html
+++ b/src/app/organizations/collection/collection.component.html
@@ -32,7 +32,7 @@
info This collection is part of an organization that is pending approval by a Dockstore curator.
@@ -93,15 +93,18 @@
-
+
info This collection has no associated entries. To add an entry, navigate to the public page of the tool or
workflow you want to add and select `Add to collection`
-
-
diff --git a/src/app/organizations/collection/collection.component.ts b/src/app/organizations/collection/collection.component.ts
index 3f7936059d..14e7daa8de 100644
--- a/src/app/organizations/collection/collection.component.ts
+++ b/src/app/organizations/collection/collection.component.ts
@@ -6,6 +6,7 @@ import { Dockstore } from '../../shared/dockstore.model';
import { TagEditorMode } from '../../shared/enum/tagEditorMode.enum';
import { OrgLogoService } from '../../shared/org-logo.service';
import { Collection, Organization } from '../../shared/swagger';
+import { Collection as OpenAPICollection, OrganizationsService } from '../../shared/openapi';
import { ToolDescriptor } from '../../shared/swagger/model/toolDescriptor';
import { Workflow } from '../../shared/swagger/model/workflow';
import { UserQuery } from '../../shared/user/user.query';
@@ -18,6 +19,8 @@ import { CollectionsQuery } from '../state/collections.query';
import { CollectionsService } from '../state/collections.service';
import { OrganizationQuery } from '../state/organization.query';
import { EntryType } from 'app/shared/enum/entry-type';
+import { HttpErrorResponse } from '@angular/common/http';
+import { AlertService } from '../../shared/alert/state/alert.service';
@Component({
selector: 'app-collection-entry-confirm-remove',
@@ -55,6 +58,7 @@ export class CollectionComponent implements OnInit {
WorkflowMode = Workflow.ModeEnum;
DescriptorType = ToolDescriptor.TypeEnum;
collection$: Observable;
+ openAPICollection: OpenAPICollection;
loadingCollection$: Observable;
organization$: Observable;
@@ -65,12 +69,15 @@ export class CollectionComponent implements OnInit {
isAdmin$: Observable;
isCurator$: Observable;
+
constructor(
private collectionsQuery: CollectionsQuery,
private organizationQuery: OrganizationQuery,
+ private organizationsService: OrganizationsService,
private collectionsService: CollectionsService,
public dialog: MatDialog,
private activatedRoute: ActivatedRoute,
+ private alertService: AlertService,
private userQuery: UserQuery,
public orgLogoService: OrgLogoService
) {}
@@ -87,6 +94,18 @@ export class CollectionComponent implements OnInit {
this.collectionsService.updateCollectionFromName(organizationName, collectionName);
this.isAdmin$ = this.userQuery.isAdmin$;
this.isCurator$ = this.userQuery.isCurator$;
+ this.organizationsService.getCollectionByName(organizationName, collectionName).subscribe(
+ (openAPICollection) => {
+ this.openAPICollection = openAPICollection;
+ },
+ (error: HttpErrorResponse) => {
+ this.alertService.detailedError(error);
+ }
+ );
+ }
+
+ checkHasOnlyNotebooks(collection: Collection): boolean {
+ return collection.entries.length === this.openAPICollection.notebooksLength;
}
/**
diff --git a/src/app/organizations/collections/collections.component.html b/src/app/organizations/collections/collections.component.html
index e6c97cf2b2..8571ae57d0 100644
--- a/src/app/organizations/collections/collections.component.html
+++ b/src/app/organizations/collections/collections.component.html
@@ -64,6 +64,20 @@ Tool
+
+ {{ collection.value.servicesLength }}
+ Services
+ Service
+
+
+ {{ collection.value.notebooksLength }}
+ Notebooks
+ Notebook
+