Merge branch 'hotfix/2.1.5'

cypress/integration/checkerWorkflowFromWorkflows.js

@@ -33,7 +33,7 @@ describe('Checker workflow test from workflows', function() {
             cy.get('#viewCheckerWorkflowButton').should('visible').click()
 
             // In the checker workflow right now
-            cy.url().should('eq', String(global.baseUrl) + '/workflows/github.com/A/l/_cwl_checker:master?tab=info')
+            cy.url().should('eq', String(global.baseUrl) + '/workflows/github.com/A/l/_cwl_checker?tab=info')
             cy.get('#viewCheckerWorkflowButton').should('not.be.visible')
             cy.get('#addCheckerWorkflowButton').should('not.be.visible')
             cy.get('#launchCheckerWorkflow').should('not.be.visible')

src/app/container/container.component.ts

@@ -128,7 +128,7 @@ export class ContainerComponent extends Entry {
           if (this.tool.tags.length === 0) {
             this.selectedVersion = null;
           } else {
-            this.selectedVersion = this.selectVersion(this.tool.tags, this.urlVersion, this.tool.defaultVersion, this.selectedVersion);
+            this.selectedVersion = this.selectVersion(this.tool.tags, this.urlVersion, this.tool.defaultVersion);
           }
         }
         // Select version
@@ -171,7 +171,7 @@ export class ContainerComponent extends Entry {
       this.containersService.getPublishedContainerByToolPath(this.title)
         .subscribe(tool => {
           this.containerService.setTool(tool);
-          this.selectedVersion = this.selectVersion(this.tool.tags, this.urlVersion, this.tool.defaultVersion, this.selectedVersion);
+          this.selectedVersion = this.selectVersion(this.tool.tags, this.urlVersion, this.tool.defaultVersion);
 
           this.selectTab(this.validTabs.indexOf(this.currentTab));
           if (this.tool != null) {

src/app/shared/entry.ts

@@ -175,34 +175,37 @@ export abstract class Entry implements OnInit, OnDestroy, AfterViewInit {
     });
   }
 
-  public selectVersion(versions, urlVersion, defaultVersion, selectedVersion): any {
-    let useFirstTag = true;
-    let urlTagExists = false;
-    // Determine which tag to select
-    for (const item of versions) {
-      // If a tag is specified in the URL then use it
-      if (urlVersion !== null) {
-        if (item.name === urlVersion) {
-          selectedVersion = item;
-          useFirstTag = false;
-          urlTagExists = true;
-          break;
-        }
-      } else if (defaultVersion !== null && !urlTagExists) {
-        // If the tool has a default version then use it
-        if (item.name === defaultVersion) {
-          selectedVersion = item;
-          useFirstTag = false;
-          break;
-        }
+  /**
+   * Given an array of WorkflowVersions or Tag, decide which one to return (displayed to the user)
+   * 1. If the URL specifies a specific Tag or WorkflowVersion, choose to display that one.  Otherwise,
+   * 2. If the default version is specified, choose to display the default version.  Otherwise,
+   * 3. Choose the first version in the array (the last updated version?)
+   * @param {((Array<WorkflowVersion | Tag>))} versions    All versions of an entry.
+   * This is supposed to be (Array<WorkflowVersion> | Array<Tag>).
+   * No idea why errors appear when attempted to do so.
+   * @param {string} urlVersion  The version of the entry specified in the URL (possibly null or undefined)
+   * @param {string} defaultVersion  The default version of an entry (possibly null or undefined)
+   * @returns {((WorkflowVersion | Tag))}  The version to display to the user
+   * @memberof Entry
+   */
+  public selectVersion(versions: (Array<WorkflowVersion | Tag>), urlVersion: string, defaultVersion: string): (WorkflowVersion | Tag) {
+    if (!versions || versions.length === 0) {
+      return null;
+    }
+    let foundVersion: (WorkflowVersion | Tag);
+    if (urlVersion) {
+      foundVersion = versions.find((version: (WorkflowVersion | Tag)) => version.name === urlVersion);
+      if (foundVersion) {
+        return foundVersion;
       }
     }
-
-    // If no url tag or default version, select first element in the dropdown
-    if (useFirstTag && versions.length > 0) {
-      selectedVersion = versions[0];
+    if (defaultVersion) {
+      foundVersion = versions.find((version: (WorkflowVersion | Tag)) => version.name === defaultVersion);
+      if (foundVersion) {
+        return foundVersion;
+      }
     }
-    return selectedVersion;
+    return versions[0];
   }
 
   public getEntryPathFromURL(): string {
@@ -246,7 +249,7 @@ export abstract class Entry implements OnInit, OnDestroy, AfterViewInit {
          currentPath += ':' + this.selectedVersion.name;
        }
        currentPath += '?tab=' + this.currentTab;
-       this.location.go(currentPath);
+       this.location.replaceState(currentPath);
      }
    }
 
@@ -315,7 +318,7 @@ export abstract class Entry implements OnInit, OnDestroy, AfterViewInit {
     const url = decodeURIComponent(window.location.href);
     const containersIndex = this.getIndexInURL('/' + type);
     const newPath = url.substring(containersIndex);
-    this.location.go(newPath);
+    this.location.replaceState(newPath);
   }
 
   /**

src/app/shared/launch.service.ts

@@ -84,11 +84,27 @@ export abstract class LaunchService {
      * @param path The GA4GH Tool's path
      * @param versionName The ToolVersion's name
      */
-    getNxtTestJsonString(workflowPath: string, versionName: string) {
+    getTestJsonString(workflowPath: string, versionName: string, type: string) {
+      let urlType = 'PLAIN_NFL';
+      switch (type) {
+        case 'wdl':
+          urlType = 'PLAIN_WDL';
+          break;
+        case 'cwl':
+          urlType = 'PLAIN_CWL';
+          break;
+        case 'nextflow':
+          urlType = 'PLAIN_NFL';
+          break;
+        default:
+          console.log('Unknown descriptor type: ' + type);
+          return null;
+      }
+
       const prefix = `$ wget --header='Accept: text/plain`;
       const outputFile = `-O Dockstore.json`;
-      const encodedID = encodeURIComponent('#workflow/ ${ workflowPath) }');
-      const encodedVersion = encodeURIComponent('${ versionName }');
-      return `${prefix}'   ${ Dockstore.API_URI }${ga4ghPath}/tools/${ encodedID }/versions/${ encodedVersion }/NXT/tests ${outputFile}`;
+      const encodedID = encodeURIComponent(`#workflow/${ workflowPath }`);
+      const encodedVersion = encodeURIComponent(`${ versionName }`);
+      return `${prefix}' ${Dockstore.API_URI}${ga4ghPath}/tools/${encodedID}/versions/${encodedVersion}/${urlType}/tests ${outputFile}`;
     }
 }

src/app/workflow/launch/launch.component.ts

@@ -64,6 +64,6 @@ export class LaunchWorkflowComponent {
     this.checkEntryCommand = this.launchService.getCheckWorkflowString(workflowPath, versionName);
     this.consonance = this.launchService.getConsonanceString(workflowPath, versionName);
     this.nextflowNativeLaunchDescription = this.launchService.getNextflowNativeLaunchString(basePath, versionName);
-    this.wgetTestJsonDescription = this.launchService.getNxtTestJsonString(workflowPath, versionName);
+    this.wgetTestJsonDescription = this.launchService.getTestJsonString(workflowPath, versionName, this.currentDescriptor);
   }
 }

src/app/workflow/launch/workflow-launch.service.spec.ts

@@ -18,6 +18,7 @@ import { inject, TestBed } from '@angular/core/testing';
 import { WorkflowService } from './../../shared/workflow.service';
 import { WorkflowStubService } from './../../test/service-stubs';
 import { WorkflowLaunchService } from './workflow-launch.service';
+import { Dockstore } from '../../shared/dockstore.model';
 
 describe('WorkflowLaunchService', () => {
   beforeEach(() => {
@@ -60,4 +61,20 @@ describe('WorkflowLaunchService', () => {
     expect(service.getCheckWorkflowString('potato', 'stew')).toBe('$ dockstore checker launch --entry potato:stew checkparam.json');
     expect(service.getCheckWorkflowString(null, null)).toBe('');
   }));
+  it('should get the wget test parameter file command', inject([WorkflowLaunchService], (service: WorkflowLaunchService) => {
+    expect(service.getTestJsonString('github.com/garyluu/example_cwl_workflow', 'v1.0', 'cwl'))
+      .toBe(`$ wget --header='Accept: text/plain' ` +
+      `${Dockstore.API_URI}/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fgaryluu%2Fexample_cwl_workflow/versions/v1.0/PLAIN_CWL/tests ` +
+      `-O Dockstore.json`);
+    expect(service.getTestJsonString('github.com/garyluu/example_cwl_workflow', 'v1.0', 'wdl'))
+      .toBe(`$ wget --header='Accept: text/plain' ` +
+      `${Dockstore.API_URI}/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fgaryluu%2Fexample_cwl_workflow/versions/v1.0/PLAIN_WDL/tests ` +
+      `-O Dockstore.json`);
+    expect(service.getTestJsonString('github.com/garyluu/example_cwl_workflow', 'v1.0', 'nextflow'))
+      .toBe(`$ wget --header='Accept: text/plain' ` +
+      `${Dockstore.API_URI}/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fgaryluu%2Fexample_cwl_workflow/versions/v1.0/PLAIN_NFL/tests ` +
+      `-O Dockstore.json`);
+    expect(service.getTestJsonString('github.com/garyluu/example_cwl_workflow', 'v1.0', 'potato'))
+      .toBe(null);
+  }));
 });

src/app/workflow/workflow.component.css

@@ -34,3 +34,17 @@ pre {
 .button-wrap > .button:not(:last-child) {
   margin-bottom: 10px;
 }
+a.disabled {
+  color: gray;
+  cursor: not-allowed;
+}
+a.disabled > img {
+    filter: brightness(90%);
+}
+p.import-warning {
+  font-size: 11px;
+  font-style: italic;
+  text-align: left;
+  line-height: 1em;
+  margin-bottom: 4px;
+}

src/app/workflow/workflow.component.html

@@ -210,19 +210,20 @@ <h3>Source Repositories</h3>
         </div>
       </div>
     </div>
-    <div class="panel panel-default" *ngIf="workflow && (dnastackURL || fireCloudURL)">
+    <div class="panel panel-default" *ngIf="isWdl(workflow)">
       <div class="panel-heading">
         <h3>Launch with</h3>
       </div>
       <div class="panel-body">
         <div class="container-source-repos">
           <div class="container-launch-with">
             <div class="button-wrap">
+              <p *ngIf="dnastackURL && (wdlHasFileImports || wdlHasHttpImports)" class="import-warning" >Warning: this version of the WDL has imports, which are not supported by DNAstack. Make sure to select a version without imports in DNAstack.</p>
               <div *ngIf="dnastackURL" class="button">
                 <p><a href="{{dnastackURL}}"><img src="../../assets/images/thirdparty/dnastack.png"> DNAstack &raquo;</a></p>
               </div>
-              <div *ngIf="fireCloudURL" class="button">
-                <p><a href="{{fireCloudURL}}"><img src="../../assets/images/thirdparty/FireCloud-white-icon.svg"> FireCloud &raquo;</a></p>
+              <div *ngIf="enableLaunchWithFireCloud" class="button" [title]="wdlHasFileImports ? 'FireCloud does not support file-path imports in WDL. It only supports http(s) imports.' : ''">
+                <p><a [class.disabled]="wdlHasFileImports" (click)="gotoFirecloud()"><img src="../../assets/images/thirdparty/FireCloud-white-icon.svg"> FireCloud &raquo;</a></p>
               </div>
             </div>
           </div>

src/app/workflow/workflow.component.ts

@@ -38,6 +38,8 @@ import { Workflow } from './../shared/swagger/model/workflow';
 import { UrlResolverService } from './../shared/url-resolver.service';
 import { SourceFile } from '../shared/swagger/model/sourceFile';
 
+const importHttpRegEx: RegExp = new RegExp(/^\s*import\s+"https?/, 'm');
+
 @Component({
   selector: 'app-workflow',
   templateUrl: './workflow.component.html',
@@ -47,6 +49,9 @@ export class WorkflowComponent extends Entry {
   workflowEditData: any;
   dnastackURL: string;
   fireCloudURL: string;
+  public wdlHasHttpImports: boolean;
+  public wdlHasFileImports: boolean;
+  public enableLaunchWithFireCloud = Dockstore.FEATURES.enableLaunchWithFireCloud;
   public workflow;
   public missingWarning: boolean;
   public title: string;
@@ -110,18 +115,45 @@ export class WorkflowComponent extends Entry {
     }
   }
 
-  private isWdl(workflowRef: ExtendedWorkflow) {
-    return workflowRef.full_workflow_path && workflowRef.descriptorType === 'wdl';
+  public isWdl(workflowRef: ExtendedWorkflow) {
+    return workflowRef && workflowRef.full_workflow_path && workflowRef.descriptorType === 'wdl';
+  }
+
+  public gotoFirecloud() {
+    if (this.fireCloudURL) {
+      window.open(this.fireCloudURL);
+    }
   }
 
-  private setupFireCloudUrl(workflowRef: ExtendedWorkflow) {
-    if (Dockstore.FEATURES.enableLaunchWithFireCloud) {
-      this.fireCloudURL = null;
+  /**
+   * Checks WDL for import statements, setting wdlHasFileImports and wdlHasHttpImports properties
+   * accordingly. If the WDL has file imports, doesn't bother to check if there are http imports, to save
+   * an Ajax call.
+   *
+   * Also sets the fireCloudURL property if the WDL has no file imports.
+   *
+   * This can be done more cleanly, but since code has been moved and substantially changed in develop branch,
+   * leaving like this for hot fix.
+   *
+   * @param {ExtendedWorkflow} workflowRef
+   */
+  private checkWdlForImportsAndSetFirecloudUrl(workflowRef: ExtendedWorkflow) {
+    this.fireCloudURL = null;
+    this.wdlHasFileImports = false;
+    this.wdlHasHttpImports = false;
+    if (this.isWdl(workflowRef)) {
       const version: WorkflowVersion = this.selectedVersion;
-      if (version && this.isWdl(workflowRef)) {
+      if (version) {
         this.workflowsService.secondaryWdl(workflowRef.id, version.name).subscribe((sourceFiles: Array<SourceFile>) => {
           if (!sourceFiles || sourceFiles.length === 0) {
-            this.fireCloudURL =  `${Dockstore.FIRECLOUD_IMPORT_URL}/${workflowRef.full_workflow_path}:${version.name}`;
+            this.workflowsService.wdl(workflowRef.id, version.name).subscribe((sourceFile) => {
+              this.wdlHasHttpImports = importHttpRegEx.test(sourceFile.content);
+            });
+            if (this.enableLaunchWithFireCloud) {
+              this.fireCloudURL = `${Dockstore.FIRECLOUD_IMPORT_URL}/${workflowRef.full_workflow_path}:${version.name}`;
+            }
+          } else {
+            this.wdlHasFileImports = true;
           }
         });
       }
@@ -142,7 +174,7 @@ export class WorkflowComponent extends Entry {
       this.title = this.workflow.full_workflow_path;
       this.initTool();
       this.sortedVersions = this.getSortedVersions(this.workflow.workflowVersions, this.defaultVersion);
-      this.setupFireCloudUrl(this.workflow);
+      this.checkWdlForImportsAndSetFirecloudUrl(this.workflow);
     }
   }
 
@@ -153,7 +185,7 @@ export class WorkflowComponent extends Entry {
         if (workflow) {
           this.published = this.workflow.is_published;
           this.selectedVersion = this.selectVersion(this.workflow.workflowVersions, this.urlVersion,
-            this.workflow.defaultVersion, this.selectedVersion);
+            this.workflow.defaultVersion);
         }
         this.setUpWorkflow(workflow);
       }
@@ -173,7 +205,7 @@ export class WorkflowComponent extends Entry {
         .subscribe(workflow => {
           this.workflowService.setWorkflow(workflow);
           this.selectedVersion = this.selectVersion(this.workflow.workflowVersions, this.urlVersion,
-            this.workflow.defaultVersion, this.selectedVersion);
+            this.workflow.defaultVersion);
 
           this.selectTab(this.validTabs.indexOf(this.currentTab));
           if (this.workflow != null) {
@@ -297,7 +329,7 @@ export class WorkflowComponent extends Entry {
     if (this.workflow != null) {
       this.updateUrl(this.workflow.full_workflow_path, 'my-workflows', 'workflows');
     }
-    this.setupFireCloudUrl(this.workflow);
+    this.checkWdlForImportsAndSetFirecloudUrl(this.workflow);
   }
 
   setEntryTab(tabName: string): void {