Mark LoadListing as not in vocab so it must be fully qualified (#324)

* Mark LoadListing as not in vocab so it must be fully qualified and not a
keyword.

Author: tetron

cwltool/extensions.yml

@@ -7,6 +7,7 @@ $graph:
 - name: LoadListingRequirement
   type: record
   extends: cwl:ProcessRequirement
+  inVocab: false
   fields:
     class:
       type: string

cwltool/process.py

@@ -46,7 +46,7 @@
                                 "StepInputExpressionRequirement",
                                 "ResourceRequirement",
                                 "InitialWorkDirRequirement",
-                                "LoadListingRequirement"]
+                                "http://commonwl.org/cwltool#LoadListingRequirement"]
 
 cwl_files = (
     "Workflow.yml",
@@ -430,15 +430,15 @@ def __init__(self, toolpath_object, **kwargs):
                     self.outputs_record_schema["fields"].append(c)
 
         try:
-            self.inputs_record_schema = schema_salad.schema.make_valid_avro(self.inputs_record_schema, {}, set())
+            self.inputs_record_schema = cast(Dict[unicode, Any], schema_salad.schema.make_valid_avro(self.inputs_record_schema, {}, set()))
             avro.schema.make_avsc_object(self.inputs_record_schema, self.names)
         except avro.schema.SchemaParseException as e:
             raise validate.ValidationException(u"Got error `%s` while processing inputs of %s:\n%s" %
                                                (Text(e), self.tool["id"],
                                                 json.dumps(self.inputs_record_schema, indent=4)))
 
         try:
-            self.outputs_record_schema = schema_salad.schema.make_valid_avro(self.outputs_record_schema, {}, set())
+            self.outputs_record_schema = cast(Dict[unicode, Any], schema_salad.schema.make_valid_avro(self.outputs_record_schema, {}, set()))
             avro.schema.make_avsc_object(self.outputs_record_schema, self.names)
         except avro.schema.SchemaParseException as e:
             raise validate.ValidationException(u"Got error `%s` while processing outputs of %s:\n%s" %
@@ -494,7 +494,7 @@ def _init_job(self, joborder, **kwargs):
         builder.make_fs_access = kwargs.get("make_fs_access") or StdFsAccess
         builder.fs_access = builder.make_fs_access(kwargs["basedir"])
 
-        loadListingReq, _ = self.get_requirement("LoadListingRequirement")
+        loadListingReq, _ = self.get_requirement("http://commonwl.org/cwltool#LoadListingRequirement")
         if loadListingReq:
             builder.loadListing = loadListingReq.get("loadListing")
 

requirements.txt

@@ -3,5 +3,5 @@ ruamel.yaml==0.13.7
 rdflib==4.2.1
 rdflib-jsonld==0.4.0
 shellescape==3.4.1
-schema-salad>=2.3.20170302225134,<3
+schema-salad>=2.4.20170308171942,<3
 typing==3.5.2.2 ; python_version>="2.7"

setup.py

@@ -51,7 +51,7 @@
           'ruamel.yaml >= 0.12.4',
           'rdflib >= 4.2.2, < 4.3.0',
           'shellescape >= 3.4.1, < 3.5',
-          'schema-salad >= 2.3.20170302225134, < 3',
+          'schema-salad >= 2.4.20170308171942, < 3',
           'typing >= 3.5.2, < 3.6',
           'six >= 1.10.0',
 

tests/wf/listing_none.cwl

@@ -1,7 +1,9 @@
 class: CommandLineTool
 cwlVersion: v1.0
+$namespaces:
+  cwltool: http://commonwl.org/cwltool#
 requirements:
-  LoadListingRequirement:
+  cwltool:LoadListingRequirement:
     loadListing: null
 inputs:
   d: Directory

tests/wf/listing_shallow.cwl

@@ -1,7 +1,9 @@
 class: CommandLineTool
 cwlVersion: v1.0
+$namespaces:
+  cwltool: http://commonwl.org/cwltool#
 requirements:
-  LoadListingRequirement:
+  cwltool:LoadListingRequirement:
     loadListing: shallow
 inputs:
   d: Directory