Merge pull request #15 from common-workflow-language/cleaner_wf_conv

improve workflow conversion

Author: mr-c

cwlupgrader/main.py

@@ -2,21 +2,21 @@
 
 from __future__ import print_function
 import ruamel.yaml
-from typing import Any, Dict, List, Union
+from typing import Any, Dict, List, Text, Union
 from collections import Mapping, MutableMapping, Sequence
 import sys
 import copy
 
 def main():  # type: () -> int
     for path in sys.argv[1:]:
         with open(path) as entry:
-            document = ruamel.yaml.round_trip_load(entry)
+            document = ruamel.yaml.load(entry)
             if ('cwlVersion' in document
                     and document['cwlVersion'] == 'cwl:draft-3'):
                     draft3_to_v1_0(document)
             else:
                 print("Skipping non draft-3 CWL document", file=sys.stderr)
-            print(ruamel.yaml.round_trip_dump(document))
+            print(ruamel.yaml.dump(document))
     return 0
 
 def draft3_to_v1_0(document):  # type: (Dict[str, Any]) -> None
@@ -30,15 +30,23 @@ def _draft3_to_v1_0(document):
             inputOutputClean(document)
             for out in document["outputs"]:
                 out["outputSource"] = out.pop("source").lstrip('#')
+            new_steps = {}
             for step in document["steps"]:
-                step["out"] = step.pop("outputs")
+                new_step = {}  # type: Dict[Text, Any]
+                new_step["out"] = [ outp["id"][len(step["id"])+1:] for outp in
+                    step["outputs"] ]
+                ins = {}
                 for inp in step["inputs"]:
-                    inp["id"] = inp["id"][len(step["id"])+1:]  # remove step id prefix
+                    ident = inp["id"][len(step["id"])+1:]  # remove step id prefix
                     inp["source"] = inp["source"].lstrip('#')
-                step["in"] = step.pop("inputs")
+                    del inp["id"]
+                    ins[ident] = inp
+                new_step["in"] = ins
                 if "scatter" in step:
-                    step["scatter"] = step["scatter"][  # remove step prefix
+                    new_step["scatter"] = step["scatter"][  # remove step prefix
                         len(step["id"])*2+3:]
+                new_steps[step["id"].lstrip('#')] = new_step
+            document["steps"] = new_steps
         elif document["class"] == "File":
             document["location"] = document.pop("path")
         elif document["class"] == "CreateFileRequirement":