pack.py: add 'cwlVersion' in pack dict, if only single item exists

test_pack.py: add test for single item workflow

test_pack.py: Use `single step` instead of `single item` in test function

Author: manu-chroma

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

@@ -33,3 +33,27 @@ def test_pack(self):
         del expect_packed["$schemas"]
 
         self.assertEqual(expect_packed, packed)
+
+    def test_pack_single_step(self):
+        """Test to ensure the generated pack output is not missing
+        the `cwlVersion` in case of single step workflow"""
+        # Since diff is longer than 3174 characters
+        self.maxDiff = None
+
+        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])

tests/wf/expect_packed_hello_workflow.cwl

@@ -0,0 +1,16 @@
+{
+    "class": "CommandLineTool",
+    "baseCommand": "echo",
+    "inputs": [
+        {
+            "type": "string",
+            "inputBinding": {
+                "position": 1
+            },
+            "id": "#main/message"
+        }
+    ],
+    "outputs": [],
+    "id": "#main",
+    "cwlVersion": "v1.0"
+}

tests/wf/hello-workflow.cwl

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