Merge branch 'hotfix/2.5.1'

package.json

@@ -3,7 +3,7 @@
   "version": "2.3.0",
   "license": "Apache License 2.0",
   "config": {
-    "webservice_version": "1.8.0-beta.9"
+    "webservice_version": "1.8.1-rc.0"
   },
   "scripts": {
     "ng": "npx ng",

src/app/configuration.service.ts

@@ -1,9 +1,9 @@
 import { Injectable } from '@angular/core';
-import { Config, MetadataService } from './shared/swagger';
-import { Dockstore } from './shared/dockstore.model';
 import { ConfigService } from 'ng2-ui-auth';
-import { AuthConfig } from './shared/auth.model';
 import { IOauth2Options } from 'ng2-ui-auth/lib/config-interfaces';
+import { AuthConfig } from './shared/auth.model';
+import { Dockstore } from './shared/dockstore.model';
+import { Config, MetadataService } from './shared/swagger';
 
 @Injectable({
   providedIn: 'root'
@@ -35,6 +35,8 @@ export class ConfigurationService {
     Dockstore.DNASTACK_IMPORT_URL = config.dnaStackImportUrl;
     Dockstore.DNANEXUS_IMPORT_URL = config.dnaNexusImportUrl;
     Dockstore.TERRA_IMPORT_URL = config.terraImportUrl;
+    Dockstore.BD_CATALYST_SEVEN_BRIDGES_IMPORT_URL = config.bdCatalystSevenBridgesImportUrl;
+    Dockstore.BD_CATALYST_TERRA_IMPORT_URL = config.bdCatalystTerraImportUrl;
 
     Dockstore.GITHUB_CLIENT_ID = config.githubClientId;
     Dockstore.GITHUB_AUTH_URL = config.gitHubAuthUrl;

src/app/home-page/home-logged-out/home.component.html

@@ -46,22 +46,26 @@ <h2 class="title caption">Docker Tools and Workflows for the Sciences</h2>
         </div>
       </div>
 
-      <div fxLayout="column wrap" fxLayoutAlign="center center" fxLayoutGap="5px">
-        <h3 class="search-title">New to Dockstore?</h3>
-        <div fxLayout="row wrap" fxLayoutAlign="center center" fxLayoutGap="20px" class="pb-5">
-          <a mat-raised-button href="#overview" class="button-link">Start here</a>
-        </div>
-
-        <!-- Left the boat and truck here in case we want them back -->
-        <!-- <div fxLayout="row wrap" fxLayoutAlign="center" fxLayoutGap="20px">
-          <img fxFlexAlign="end" src="../assets/images/dockstore/ship.png">
-          <img fxFlexAlign="end" src="../assets/images/dockstore/truck.png">
-        </div> -->
+      <div fxLayout="column wrap" fxLayoutAlign="center center" fxLayoutGap="5px" class="pb-3">
+        <h4 class="title caption text-center landing-message">
+          Dockstore, developed by the
+          <a class="white-link" href="https://www.cancercollaboratory.org/" target="_blank">Cancer Genome Collaboratory</a>, is an open
+          platform used by the <a class="white-link" href="https://genomicsandhealth.org/" target="_blank">GA4GH</a> for sharing
+          Docker-based tools described with either the
+          <a class="white-link" href="http://www.commonwl.org/" target="_blank">Common Workflow Language (CWL)</a>, the
+          <a class="white-link" href="https://software.broadinstitute.org/wdl/" target="_blank">Workflow Description Language (WDL)</a>, or
+          <a class="white-link" href="https://www.nextflow.io/" target="_blank">Nextflow</a>
+        </h4>
       </div>
     </div>
   </div>
 </div>
 
+<div class="header-lower boat-header" fxLayout="row wrap" fxLayoutAlign="end" fxLayoutGap="20px" fxShow fxHide.lt-md>
+  <img fxFlexAlign="end" src="../assets/images/dockstore/ship.png" />
+  <img fxFlexAlign="end" src="../assets/images/dockstore/truck.png" class="pr-2" />
+</div>
+
 <div class="header-lower" id="overview">
   <img class="blue-rectangle" src="../assets/images/dockstore/rectangle.png" alt="blue rectangle" />
 

src/app/home-page/home-logged-out/home.component.scss

@@ -113,22 +113,26 @@ span {
 }
 
 .top-section {
-  min-height: 800px;
-}
-
-.search-holder {
-  margin-top: 40px;
+  min-height: 500px;
 }
 
 .header-lower {
   min-height: 200px;
 }
 
+.boat-header {
+  background-color: #21335b;
+}
+
 .content-holder {
   padding: 40px 0px 40px 0px;
   min-height: 300px;
 }
 
+.landing-message {
+  max-width: 700px;
+}
+
 .stripe-holder {
   min-height: 175px;
   width: 100%;

src/app/search/search.component.ts

@@ -170,10 +170,6 @@ export class SearchComponent implements OnInit, OnDestroy {
     this.advancedSearchQuery.advancedSearch$.pipe(takeUntil(this.ngUnsubscribe)).subscribe(() => {
       this.updatePermalink();
     });
-    this.keyUp$.pipe(
-      debounceTime(formInputDebounceTime),
-      distinctUntilChanged(),
-      takeUntil(this.ngUnsubscribe)).subscribe(() => this.onKey());
   }
 
   /**
@@ -470,21 +466,6 @@ export class SearchComponent implements OnInit, OnDestroy {
     this.updatePermalink();
   }
 
-  /**
-   * Sets autocomplete terms based on the elasticsearch results
-   *
-   * @param {*} hits  Elasticsearch results
-   * @memberof SearchComponent
-   */
-  setAutocompleteTerms(hits: any): void {
-    try {
-      this.autocompleteTerms = hits.aggregations.autocomplete.buckets.map(term => term.key);
-    } catch (error) {
-      console.error('Could not retrieve autocomplete terms');
-      this.autocompleteTerms = [];
-    }
-  }
-
   searchSuggestTerm() {
     this.searchService.searchSuggestTerm();
   }

src/app/shared/dockstore.model.ts

@@ -34,6 +34,8 @@ export class Dockstore {
   static TERRA_IMPORT_URL = 'https://app.terra.bio/#import-tool/dockstore';
   static CGC_IMPORT_URL = 'https://cgc.sbgenomics.com/integration/trs/import';
   static ANVIL_IMPORT_URL = 'https://anvil.terra.bio/#import-tool/dockstore';
+  static BD_CATALYST_SEVEN_BRIDGES_IMPORT_URL = 'https://sb.biodatacatalyst.nhlbi.nih.gov/integration/trs/import';
+  static BD_CATALYST_TERRA_IMPORT_URL = 'https://terra.biodatacatalyst.nhlbi.nih.gov/#import-tool/dockstore';
 
   static GITHUB_CLIENT_ID = 'will be filled in by configuration.service';
   static GITHUB_AUTH_URL = 'https://github.com/login/oauth/authorize';

src/app/workflow/launch-third-party/launch-third-party.component.html

@@ -37,16 +37,10 @@ <h3>Launch with</h3>
           <div fxFlex="100%" *ngIf="workflow?.descriptorType === 'WDL'">
             <a
               mat-raised-button
-              [matTooltip]="
-                !(hasContent$ | async)
-                  ? 'The WDL has no content.  '
-                  : (hasFileImports$ | async)
-                  ? 'Terra does not support file-path imports in WDL. It only supports http(s) imports.'
-                  : ''
-              "
+              [matTooltip]="terraTooltip$ | async"
               target="_blank"
               rel="noopener"
-              [disabled]="!(hasContent$ | async) || (hasFileImports$ | async)"
+              [disabled]="disableTerraPlatform$ | async"
               [attr.href]="config.TERRA_IMPORT_URL + '/' + workflow?.full_workflow_path + ':' + selectedVersion?.name"
               color="primary"
               ><mat-icon svgIcon="terra"></mat-icon> Terra &raquo;</a
@@ -59,29 +53,47 @@ <h3>Launch with</h3>
               target="_blank"
               rel="noopener"
               [attr.href]="config.CGC_IMPORT_URL + '?trs=' + trsUrl"
-              [disabled]="!(hasContent$ | async) || (hasHttpImports$ | async)"
+              [disabled]="disableSevenBridgesPlatform$ | async"
               color="primary"
               ><img src="../assets/images/thirdparty/cgc.png" /> CGC
             </a>
           </div>
+          <div fxFlex="100%" *ngIf="workflow?.descriptorType === 'CWL'">
+            <a
+              mat-raised-button
+              [matTooltip]="bdCatalystSevenBridgesTooltip$ | async"
+              target="_blank"
+              rel="noopener"
+              [attr.href]="config.BD_CATALYST_SEVEN_BRIDGES_IMPORT_URL + '?trs=' + trsUrl"
+              [disabled]="disableSevenBridgesPlatform$ | async"
+              color="primary"
+              >NHLBI BioData Catalyst
+            </a>
+          </div>
           <div fxFlex="100%" *ngIf="workflow?.descriptorType === 'WDL'">
             <a
               mat-raised-button
-              [matTooltip]="
-                !(hasContent$ | async)
-                  ? 'The WDL has no content.  '
-                  : (hasFileImports$ | async)
-                  ? 'AnVIL does not support file-path imports in WDL. It only supports http(s) imports.'
-                  : ''
-              "
+              [matTooltip]="anvilTooltip$ | async"
               target="_blank"
               rel="noopener"
-              [disabled]="!(hasContent$ | async) || (hasFileImports$ | async)"
+              [disabled]="disableTerraPlatform$ | async"
               [attr.href]="config.ANVIL_IMPORT_URL + '/' + workflow?.full_workflow_path + ':' + selectedVersion?.name"
               color="primary"
               ><mat-icon class="anvil-icon" svgIcon="anvil"></mat-icon> AnVIL &raquo;</a
             >
           </div>
+          <div fxFlex="100%" *ngIf="workflow?.descriptorType === 'WDL'">
+            <a
+              mat-raised-button
+              [matTooltip]="bdCatalystTerraTooltip$ | async"
+              target="_blank"
+              rel="noopener"
+              [disabled]="disableTerraPlatform$ | async"
+              [attr.href]="config.BD_CATALYST_TERRA_IMPORT_URL + '/' + workflow?.full_workflow_path + ':' + selectedVersion?.name"
+              color="primary"
+              >NHLBI BioData Catalyst</a
+            >
+          </div>
         </div>
       </div>
     </div>

src/app/workflow/launch-third-party/launch-third-party.component.scss

@@ -1,6 +1,6 @@
 a {
-  margin-bottom: 10px;
-  width: 150px;
+  margin-bottom: 0.625rem;
+  width: 18.5rem;
   max-width: 98%;
   img {
     width: 24px;

src/app/workflow/launch-third-party/launch-third-party.component.ts

@@ -2,6 +2,7 @@ import { HttpUrlEncodingCodec } from '@angular/common/http';
 import { Component, Input, OnChanges, OnInit, SimpleChanges } from '@angular/core';
 import { MatIconRegistry } from '@angular/material/icon';
 import { DomSanitizer } from '@angular/platform-browser';
+import { combineLatest, Observable } from 'rxjs';
 import { map, share, takeUntil } from 'rxjs/operators';
 import { Base } from '../../shared/base';
 import { DescriptorTypeCompatService } from '../../shared/descriptor-type-compat.service';
@@ -13,7 +14,6 @@ import { SourceFile } from '../../shared/swagger/model/sourceFile';
 import { DescriptorsQuery } from './state/descriptors-query';
 import { DescriptorsStore } from './state/descriptors-store';
 import { DescriptorsService } from './state/descriptors.service';
-import { combineLatest, Observable } from 'rxjs';
 import FileTypeEnum = ToolFile.FileTypeEnum;
 
 // tslint:disable:max-line-length
@@ -147,18 +147,34 @@ export class LaunchThirdPartyComponent extends Base implements OnChanges, OnInit
   workflowPathAsQueryValue: string;
 
   // Note: intentionally not using this.hasContent$ in the next line, as that does not work
-  cgcTooltip$: Observable<string> = combineLatest(this.descriptorsQuery.hasContent$, this.hasHttpImports$).pipe(
-    map(([hasContent, hasHttpImports]) => {
-      if (!hasContent) {
-        return 'The CWL has no content.';
-      }
-      if (hasHttpImports) {
-        return (
-          'This version of the CWL has http(s) imports, which are not supported by the CGC. ' + 'Select a version without http(s) imports.'
-        );
-      }
-      return 'Export this workflow version to the CGC.';
-    })
+  cgcTooltip$: Observable<string> = combineLatest(this.hasContent$, this.hasHttpImports$).pipe(
+    map(([hasContent, hasHttpImports]) => this.sevenBridgesTooltip(hasContent, hasHttpImports, 'the CGC'))
+  );
+
+  disableSevenBridgesPlatform$: Observable<boolean> = combineLatest(this.hasContent$, this.hasHttpImports$).pipe(
+    map(([hasContent, hasHttpImports]) => !hasContent || hasHttpImports)
+  );
+
+  bdCatalystSevenBridgesTooltip$: Observable<string> = combineLatest(this.hasContent$, this.hasHttpImports$).pipe(
+    map(([hasContent, hasHttpImports]) =>
+      this.sevenBridgesTooltip(hasContent, hasHttpImports, 'NHLBI BioData Catalyst powered by Seven Bridges')
+    )
+  );
+
+  terraTooltip$: Observable<string> = combineLatest(this.hasContent$, this.hasFileImports$).pipe(
+    map(([hasContent, hasFileImports]) => this.terraTooltip(hasContent, hasFileImports, 'Terra'))
+  );
+
+  anvilTooltip$: Observable<string> = combineLatest(this.hasContent$, this.hasFileImports$).pipe(
+    map(([hasContent, hasFileImports]) => this.terraTooltip(hasContent, hasFileImports, 'AnVIL'))
+  );
+
+  bdCatalystTerraTooltip$: Observable<string> = combineLatest(this.hasContent$, this.hasFileImports$).pipe(
+    map(([hasContent, hasFileImports]) => this.terraTooltip(hasContent, hasFileImports, 'NHLBI BioData Catalyst powered by Terra'))
+  );
+
+  disableTerraPlatform$: Observable<boolean> = combineLatest(this.hasContent$, this.hasFileImports$).pipe(
+    map(([hasContent, hasFileImports]) => !hasContent || hasFileImports)
   );
 
   constructor(
@@ -210,4 +226,24 @@ export class LaunchThirdPartyComponent extends Base implements OnChanges, OnInit
       this.workflowPathAsQueryValue = new HttpUrlEncodingCodec().encodeValue(this.workflow.full_workflow_path);
     }
   }
+
+  private sevenBridgesTooltip(hasContent: boolean, hasHttpImports, platform: string): string {
+    if (!hasContent) {
+      return 'The CWL has no content.';
+    }
+    if (hasHttpImports) {
+      return `This version of the CWL has http(s) imports, which are not supported by ${platform}. Select a version without http(s) imports.`;
+    }
+    return `Export this workflow version to ${platform}.`;
+  }
+
+  private terraTooltip(hasContent: boolean, hasFileImports, platform: string): string {
+    if (!hasContent) {
+      return 'The WDL has no content.';
+    }
+    if (hasFileImports) {
+      return `${platform} does not support file-path imports in WDL. It only supports http(s) imports.`;
+    }
+    return `Export this workflow version to ${platform}.`;
+  }
 }