Merge branch 'master' into rdf_python3_fix

Author: mr-c

cwltool/pack.py

@@ -157,4 +157,9 @@ def rewrite_id(r, mainuri):
 
     import_embed(packed, set())
 
+    if len(packed["$graph"]) == 1:
+        # duplicate 'cwlVersion' inside $graph when there is a single item
+        # because we're printing contents inside '$graph' rather than whole dict
+        packed["$graph"][0]["cwlVersion"] = packed["cwlVersion"]
+
     return packed

tests/test_pack.py

@@ -5,6 +5,7 @@
 from functools import partial
 
 import cwltool.pack
+from cwltool.main import print_pack as print_pack
 import cwltool.workflow
 from cwltool.load_tool import fetch_document, validate_document
 from cwltool.main import makeRelative
@@ -33,3 +34,29 @@ def test_pack(self):
         del expect_packed["$schemas"]
 
         self.assertEqual(expect_packed, packed)
+
+    def test_pack_missing_cwlVersion(self):
+        """Test to ensure the generated pack output is not missing
+        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 = json.loads(print_pack(document_loader, processobj, uri, metadata))
+
+        self.assertEqual('v1.0', packed["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 = json.loads(print_pack(document_loader, processobj, uri, metadata))
+
+        self.assertEqual('v1.0', packed["cwlVersion"])

tests/wf/hello-workflow.cwl

@@ -0,0 +1,38 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: Workflow
+
+label: "Hello World"
+doc: "Outputs a message using echo"
+
+inputs:
+  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_single_tool.cwl

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