Fix serializing CWL requirements for certain features (#466)

We still have to refactor cwlts such that it never deletes any requirements. rabix/cwl-ts#112 Closes #466
rabix · Sep 17, 2020 · 62a7cac · 62a7cac
1 parent 7bc8047
commit 62a7cac
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Showing 4 changed files with 8 additions and 9 deletions.
diff --git a/package.json b/package.json
@@ -59,7 +59,7 @@
         "brace": "^0.11.0",
         "core-js": "^2.5.3",
         "cwl-svg": "2.0.1",
-        "cwlts": "1.15.29",
+        "cwlts": "^1.19.2",
         "font-awesome": "^4.7.0",
         "jquery": "^3.2.1",
         "js-yaml": "^3.10.0",
@@ -117,4 +117,4 @@
         "typescript": "~2.6.2",
         "webdriverio": "~4.10.2"
     }
-}
+}
diff --git a/src/app/editor-common/app-editor-base/app-editor-base.ts b/src/app/editor-common/app-editor-base/app-editor-base.ts
@@ -790,7 +790,7 @@ export abstract class AppEditorBase extends DirectiveBase implements StatusContr
 
                 const jobWithAbspaths = appIsLocal ? ensureAbsolutePaths(path.dirname(appID), job) : job;
 
-                return executor.execute(appID, this.dataModel, jobWithAbspaths, executorPath, executionParams).pipe(
+                return executor.execute(appID, appContent, this.dataModel, jobWithAbspaths, executorPath, executionParams).pipe(
                     finalize(() => this.fileRepository.reloadPath(executionParams.outDir.value))
                 );
             })

diff --git a/src/app/execution/services/executor/executor.service.ts b/src/app/execution/services/executor/executor.service.ts
@@ -83,9 +83,8 @@ export class ExecutorService2 {
 
     }
 
-    execute(appID: string, model: WorkflowModel | CommandLineToolModel, jobValue: Object = {}, executorPath: string = "", executionParams: Partial<CWLExecutionParamsConfig> = {}): Observable<any> {
+    execute(appID: string, appContent: string, model: WorkflowModel | CommandLineToolModel, jobValue: Object = {}, executorPath: string = "", executionParams: Partial<CWLExecutionParamsConfig> = {}): Observable<any> {
 
-        const appContent = serializeModel(model, true, false, true);
         const executor = new CWLExecutor({ executorPath: executorPath });
         const stepList = this.getStepList(model);
 

diff --git a/yarn.lock b/yarn.lock
@@ -3227,10 +3227,10 @@ [email protected]:
   dependencies:
     core-js "^2.5.1"
 
-cwlts@1.15.29:
-  version "1.15.29"
-  resolved "https://registry.yarnpkg.com/cwlts/-/cwlts-1.15.29.tgz#9000f26406f0af1506c5e123decd51122cc4f2d3"
-  integrity sha512-P690kLZZ1PRpT+qOgui2AnrCPbSp+t1QQW90O6egQhXCmeDfawczfoRMYPHKQtLfYQYVegKE2SPyM2g6SWapTA==
+cwlts@^1.19.2:
+  version "1.19.2"
+  resolved "https://registry.yarnpkg.com/cwlts/-/cwlts-1.19.2.tgz#a1fab0414ebbd1279d0dac4f95bcd45844b26999"
+  integrity sha512-ZXJ/O6x69oRgO+l+J5CEOgWl9+M7IA/TGxxCTMhoSb2/B330I858Ee6uSN6JcOYDy1o2Q5iHsLlmL0Z5BgTwwg==
   dependencies:
     ajv "^6.1.1"
     js-yaml "^3.10.0"