Preserve namespaces after packing

* fix #584

Author: Anton Khodak

cwltool/pack.py

@@ -149,6 +149,7 @@ def rewrite_id(r, mainuri):
 
     packed = {"$graph": [], "cwlVersion": metadata["cwlVersion"]
               }  # type: Dict[Text, Any]
+    namespaces = metadata.get('$namespaces')
 
     schemas = set()  # type: Set[Text]
     for r in sorted(runs):
@@ -185,5 +186,7 @@ def rewrite_id(r, mainuri):
         # duplicate 'cwlVersion' inside $graph when there is a single item
         # because we're printing contents inside '$graph' rather than whole dict
         packed["$graph"][0]["cwlVersion"] = packed["cwlVersion"]
+    if namespaces:
+        packed["$graph"][0]["$namespaces"] = dict(namespaces)
 
     return packed

tests/test_pack.py

@@ -116,3 +116,15 @@ def test_packed_workflow_execution(self):
                                stdout=normal_output), 0)
         self.assertEquals(json.loads(packed_output.getvalue()), json.loads(normal_output.getvalue()))
 
+    @pytest.mark.skipif(onWindows(),
+                        reason="Instance of cwltool is used, on Windows it invokes a default docker container"
+                               "which is not supported on AppVeyor")
+    def test_preserving_namespaces(self):
+        test_wf = "tests/wf/formattest.cwl"
+        document_loader, workflowobj, uri = fetch_document(
+            get_data(test_wf))
+        document_loader, avsc_names, processobj, metadata, uri = validate_document(
+            document_loader, workflowobj, uri)
+        packed = json.loads(print_pack(document_loader, processobj, uri, metadata))
+        assert "$namespaces" in packed
+

tests/wf/formattest.cwl

@@ -0,0 +1,20 @@
+$namespaces:
+  edam: "http://edamontology.org/"
+cwlVersion: v1.0
+class: CommandLineTool
+doc: "Reverse each line using the `rev` command"
+inputs:
+  input:
+    type: File
+    inputBinding: {}
+    format: edam:format_2330
+
+outputs:
+  output:
+    type: File
+    outputBinding:
+      glob: output.txt
+    format: edam:format_2330
+
+baseCommand: rev
+stdout: output.txt