Use consistent job loader context between load_tool and load_job_order. (#425)

Author: tetron

cwltool/load_tool.py

@@ -24,6 +24,13 @@
 
 _logger = logging.getLogger("cwltool")
 
+jobloaderctx = {
+    u"cwl": "https://w3id.org/cwl/cwl#",
+    u"path": {u"@type": u"@id"},
+    u"location": {u"@type": u"@id"},
+    u"format": {u"@type": u"@id"},
+    u"id": u"@id"
+}
 
 def fetch_document(argsworkflow,  # type: Union[Text, dict[Text, Any]]
                    resolver=None,  # type: Callable[[Loader, Union[Text, dict[Text, Any]]], Text]
@@ -33,7 +40,7 @@ def fetch_document(argsworkflow,  # type: Union[Text, dict[Text, Any]]
     # type: (...) -> Tuple[Loader, CommentedMap, Text]
     """Retrieve a CWL document."""
 
-    document_loader = Loader({"cwl": "https://w3id.org/cwl/cwl#", "id": "@id"},
+    document_loader = Loader(jobloaderctx,
                              fetcher_constructor=fetcher_constructor)
 
     uri = None  # type: Text
@@ -143,6 +150,7 @@ def validate_document(document_loader,  # type: Loader
     jobobj = None
     if "cwl:tool" in workflowobj:
         jobobj, _ = document_loader.resolve_all(workflowobj, uri)
+        print "ZZZZZ", jobobj
         uri = urllib.parse.urljoin(uri, workflowobj["https://w3id.org/cwl/cwl#tool"])
         del cast(dict, jobobj)["https://w3id.org/cwl/cwl#tool"]
         workflowobj = fetch_document(uri, fetcher_constructor=fetcher_constructor)[1]

cwltool/main.py

@@ -22,7 +22,7 @@
 from . import draft2tool, workflow
 from .cwlrdf import printdot, printrdf
 from .errors import UnsupportedRequirement, WorkflowException
-from .load_tool import fetch_document, make_tool, validate_document
+from .load_tool import fetch_document, make_tool, validate_document, jobloaderctx
 from .mutation import MutationManager
 from .pack import pack
 from .pathmapper import (adjustDirObjs, adjustFileObjs, get_listing,
@@ -424,13 +424,9 @@ def load_job_order(args, t, stdin, print_input_deps=False, relative_deps=False,
 
     job_order_object = None
 
-    jobloaderctx = {
-        u"path": {u"@type": u"@id"},
-        u"location": {u"@type": u"@id"},
-        u"format": {u"@type": u"@id"},
-        u"id": u"@id"}
-    jobloaderctx.update(t.metadata.get("$namespaces", {}))
-    loader = Loader(jobloaderctx, fetcher_constructor=fetcher_constructor)
+    _jobloaderctx = jobloaderctx.copy()
+    _jobloaderctx.update(t.metadata.get("$namespaces", {}))
+    loader = Loader(_jobloaderctx, fetcher_constructor=fetcher_constructor)
 
     if len(args.job_order) == 1 and args.job_order[0][0] != "-":
         job_order_file = args.job_order[0]