test_pack.py: Add tests to check cwlVersion in pack dict

Author: manu-chroma

tests/test_pack.py

@@ -34,26 +34,28 @@ def test_pack(self):
 
         self.assertEqual(expect_packed, packed)
 
-    def test_pack_single_step(self):
+    def test_pack_missing_cwlVersion(self):
         """Test to ensure the generated pack output is not missing
-        the `cwlVersion` in case of single step workflow"""
+        the `cwlVersion` in case of single tool workflow and single step workflow"""
         # Since diff is longer than 3174 characters
         self.maxDiff = None
 
+        # Testing single tool workflow
+        document_loader, workflowobj, uri = fetch_document(
+            get_data("tests/wf/hello_single_tool.cwl"))
+        document_loader, avsc_names, processobj, metadata, uri = validate_document(
+            document_loader, workflowobj, uri)
+        # generate pack output dict
+        packed = cwltool.pack.pack(document_loader, processobj, uri, metadata)
+
+        self.assertEqual('v1.0', packed["$graph"][0]["cwlVersion"])
+
+        # Testing single step workflow
         document_loader, workflowobj, uri = fetch_document(
             get_data("tests/wf/hello-workflow.cwl"))
         document_loader, avsc_names, processobj, metadata, uri = validate_document(
             document_loader, workflowobj, uri)
         # generate pack output dict
         packed = cwltool.pack.pack(document_loader, processobj, uri, metadata)
-        # open expect packed output
-        with open(get_data("tests/wf/expect_packed_hello_workflow.cwl")) as f:
-            expect_packed = json.load(f)
-            print(json.dumps(expect_packed))
-        adjustFileObjs(packed, partial(makeRelative,
-            os.path.abspath(get_data("tests/wf"))))
-        adjustDirObjs(packed, partial(makeRelative,
-            os.path.abspath(get_data("tests/wf"))))
 
-        print(json.dumps(packed["$graph"][0]))
-        self.assertEqual(expect_packed, packed["$graph"][0])
+        self.assertEqual('v1.0', packed["$graph"][0]["cwlVersion"])

tests/wf/expect_packed_hello_workflow.cwl

@@ -1,9 +1,38 @@
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: echo
+class: Workflow
+
+label: "Hello World"
+doc: "Outputs a message using echo"
+
 inputs:
-  message:
-    type: string
-    inputBinding:
-      position: 1
-outputs: []
+  usermessage: string
+
+outputs:
+  response:
+    outputSource: step0/response
+    type: File
+
+steps:
+  step0:
+    run:
+      class: CommandLineTool
+      inputs:
+        message:
+          type: string
+          doc: "The message to print"
+          default: "Hello World"
+          inputBinding:
+            position: 1
+      baseCommand: echo
+      arguments:
+         - "-n"
+         - "-e"
+      stdout: response.txt
+      outputs:
+        response:
+          type: stdout
+    in:
+      message: usermessage
+    out: [response]

tests/wf/hello-workflow.cwl

@@ -0,0 +1,9 @@
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: echo
+inputs:
+  message:
+    type: string
+    inputBinding:
+      position: 1
+outputs: []