convert inline Processes in workflow steps

Author: mr-c

cwlupgrader/main.py

@@ -109,15 +109,27 @@ def _v1_0_to_v1_1(document):
             if isinstance(steps, MutableSequence):
                 for entry in steps:
                     upgrade_v1_0_hints_and_reqs(entry)
+                    if 'run' in entry and isinstance(entry['run'], MutableMapping):
+                        process = entry['run']
+                        _v1_0_to_v1_1(process)
+                        if 'cwlVersion' in process:
+                            del process['cwlVersion']
             elif isinstance(steps, MutableMapping):
                 for step_name in steps:
-                    upgrade_v1_0_hints_and_reqs(steps[step_name])
+                    entry = steps[step_name]
+                    upgrade_v1_0_hints_and_reqs(entry)
+                    if 'run' in entry and isinstance(entry['run'], MutableMapping):
+                        process = entry['run']
+                        _v1_0_to_v1_1(process)
+                        if 'cwlVersion' in process:
+                            del process['cwlVersion']
         elif document['class'] == 'CommandLineTool':
             upgrade_v1_0_hints_and_reqs(document)
             move_up_loadcontents(document)
             network_access = has_hint_or_req(document, "NetworkAccess")
             listing = has_hint_or_req(document, "LoadListingRequirement")
             hints = document.get('hints', {})
+            # TODO: add comments to explain the extra hints
             if isinstance(hints, MutableSequence):
                 if not network_access:
                     hints.append({"class": "NetworkAcess", "networkAccess": True})

testing.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+git clone https://github.com/common-workflow-language/common-workflow-language.git cwl-v1.0
+cd cwl-v1.0/v1.0
+cp -r v1.0 v1.1
+rm v1.1/*.cwl
+for cwl in v1.0/*.cwl; do echo ${cwl}; cwl-upgrader ${cwl} > v1.1/${cwl##v1.0/}; done
+cp conformance_test_v1.0.yaml conformance_test_v1.0_to_v1_1.yaml
+sed -i 's=v1.0/=v1.1/=g' conformance_test_v1.0_to_v1_1.yaml
+cwltest --test conformance_test_v1.0_to_v1_1.yaml --tool cwltool -j$(nproc)
+if (find v1.1/ -type f | xargs grep cwlVersion | grep v1.0) ; then false; else true; fi
+