Don't resolve format fields on initial load of job order object. (#1142)

Author: Peter Amstutz

cwltool/load_tool.py

@@ -40,7 +40,6 @@
     u"cwltool": "http://commonwl.org/cwltool#",
     u"path": {u"@type": u"@id"},
     u"location": {u"@type": u"@id"},
-    u"format": {u"@type": u"@id"},
     u"id": u"@id"
 }  # type: ContextType
 

cwltool/main.py

@@ -358,6 +358,7 @@ def path_to_loc(p):
             del p["path"]
 
     ns = {}  # type: Dict[Text, Union[Dict[Any, Any], Text, Iterable[Text]]]
+    ns.update(job_order_object.get("$namespaces", {}))
     ns.update(process.metadata.get("$namespaces", {}))
     ld = Loader(ns)