Generate the same document for a previously packed tool

Author: Anton Khodak

cwltool/pack.py

@@ -64,7 +64,12 @@ def replace_refs(d, rewrite, stem, newstem):
                 if v in rewrite:
                     d[s] = rewrite[v]
                 elif v.startswith(stem):
-                    d[s] = newstem + v[len(stem):]
+                    id_ = v[len(stem):]
+                    # prevent appending newstems if tool is already packed
+                    if id_.startswith(newstem.strip("#")):
+                        d[s] = "#" + id_
+                    else:
+                        d[s] = newstem + id_
             replace_refs(v, rewrite, stem, newstem)
 
 def import_embed(d, seen):

tests/test_pack.py

@@ -60,3 +60,25 @@ def test_pack_missing_cwlVersion(self):
         packed = json.loads(print_pack(document_loader, processobj, uri, metadata))
 
         self.assertEqual('v1.0', packed["cwlVersion"])
+
+    def test_pack_idempotence_tool(self):
+        """Test to ensure that pack produces exactly the same document for
+           an already packed document"""
+
+        # Testing single tool
+        self._pack_idempotently("tests/wf/null-expression1-tool.cwl")
+
+    def _pack_idempotently(self, document):
+        self.maxDiff = None
+        document_loader, workflowobj, uri = fetch_document(
+            get_data(document))
+        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))
+
+        document_loader, workflowobj, uri2 = fetch_document(packed)
+        document_loader, avsc_names, processobj, metadata, uri2 = validate_document(
+            document_loader, workflowobj, uri)
+        double_packed = json.loads(print_pack(document_loader, processobj, uri, metadata))
+        self.assertEqual(packed, double_packed)