Deepcopy imported workflows to avoid re-parsing conflict

Author: alexbarrera

cwltool/update.py

@@ -3,6 +3,7 @@
 import json
 import re
 import traceback
+from copy import deepcopy
 
 from schema_salad.ref_resolver import Loader
 import schema_salad.validate
@@ -326,9 +327,6 @@ def _draft3toDraft4dev1(doc, loader, baseuri):
     # type: (Any, Loader, str) -> 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: (str) -> str
                 doc, frg = urlparse.urldefrag(f)
@@ -351,8 +349,9 @@ def fixup(f):  # type: (str) -> str
                     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):
         doc = [_draft3toDraft4dev1(item, loader, baseuri) for item in doc]
@@ -368,15 +367,13 @@ def _draft4Dev1toDev2(doc, loader, baseuri):
     # type: (Any, Loader, str) -> 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):
         doc = [_draft4Dev1toDev2(item, loader, baseuri) for item in doc]