preserve_enviroment now defaults to $PATH. Updater now recognizes final.

Author: Peter Amstutz

cwltool/main.py

@@ -42,6 +42,7 @@ def arg_parser():
     parser.add_argument("--preserve-environment", type=str, nargs='+',
                         help="Preserve specified environment variables when running CommandLineTools",
                         metavar=("VAR1","VAR2"),
+                        default=("PATH",),
                         dest="preserve_environment")
 
     exgroup = parser.add_mutually_exclusive_group()
@@ -270,9 +271,9 @@ def load_tool(argsworkflow, updateonly, strict, makeTool, debug,
         fileuri, urifrag = urlparse.urldefrag(uri)
         workflowobj = document_loader.fetch(fileuri)
         if isinstance(workflowobj, list):
-            workflowobj = {"cwlVersion": "https://w3id.org/cwl/cwl#draft-2",
+            workflowobj = {"cwlVersion": "https://w3id.org/cwl/cwl#draft-3",
                            "id": fileuri,
-                           "@graph": workflowobj}
+                           "$graph": workflowobj}
 
         if "cwl:tool" in workflowobj:
             jobobj = workflowobj

cwltool/update.py

@@ -277,6 +277,9 @@ def _draftDraft3dev4toDev5(doc, loader, baseuri):
 def draftDraft3dev4toDev5(doc, loader, baseuri):
     return (_draftDraft3dev4toDev5(doc, loader, baseuri), "https://w3id.org/cwl/cwl#draft-3.dev5")
 
+def draftDraft3dev5toFinal(doc, loader, baseuri):
+    return (doc, "https://w3id.org/cwl/cwl#draft-3")
+
 
 def update(doc, loader, baseuri):
     updates = {
@@ -285,7 +288,7 @@ def update(doc, loader, baseuri):
         "https://w3id.org/cwl/cwl#draft-3.dev2": draftDraft3dev2toDev3,
         "https://w3id.org/cwl/cwl#draft-3.dev3": draftDraft3dev3toDev4,
         "https://w3id.org/cwl/cwl#draft-3.dev4": draftDraft3dev4toDev5,
-        "https://w3id.org/cwl/cwl#draft-3.dev5": None
+        "https://w3id.org/cwl/cwl#draft-3.dev5": draftDraft3dev5toFinal
     }
 
     def identity(doc, loader, baseuri):

setup.py

@@ -36,7 +36,7 @@
           'rdflib >= 4.2.0',
           'rdflib-jsonld >= 0.3.0',
           'shellescape',
-          'schema_salad == 1.6.20160202222448
+          'schema_salad == 1.6.20160202222448'
         ],
       test_suite='tests',
       tests_require=[],