Deepcopy imported workflows to avoid re-parsing conflict

Author: alexbarrera

cwltool/update.py

@@ -5,6 +5,7 @@
 import traceback
 from typing import (Any, Callable, Dict, Text,  # pylint: disable=unused-import
                     Tuple, Union)
+from copy import deepcopy
 
 import six
 from six.moves import urllib
@@ -349,9 +350,6 @@ def _draft3toDraft4dev1(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Any
     if isinstance(doc, dict):
         if "class" in doc and doc["class"] == "Workflow":
-            if 'parsed' in doc:
-                del doc['parsed']
-                return doc
 
             def fixup(f):  # type: (Text) -> Text
                 doc, frg = urllib.parse.urldefrag(f)
@@ -374,8 +372,9 @@ def fixup(f):  # type: (Text) -> Text
                     step["scatter"] = [fixup(s) for s in aslist(step["scatter"])]
             for out in doc["outputs"]:
                 out["source"] = fixup(out["source"])
-            doc['parsed']=True
         for key, value in doc.items():
+            if key == 'run':
+                value = deepcopy(value)
             doc[key] = _draft3toDraft4dev1(value, loader, baseuri)
     elif isinstance(doc, list):
         for i, a in enumerate(doc):
@@ -394,15 +393,13 @@ def _draft4Dev1toDev2(doc, loader, baseuri):
     # type: (Any, Loader, Text) -> Any
     if isinstance(doc, dict):
         if "class" in doc and doc["class"] == "Workflow":
-            if 'parsed' in doc:
-                del doc['parsed']
-                return doc
             for out in doc["outputs"]:
                 out["outputSource"] = out["source"]
                 del out["source"]
         for key, value in doc.items():
+            if key == 'run':
+                value = deepcopy(value)
             doc[key] = _draft4Dev1toDev2(value, loader, baseuri)
-        doc['parsed']=True
     elif isinstance(doc, list):
         for i, a in enumerate(doc):
             doc[i] = _draft4Dev1toDev2(a, loader, baseuri)