Merge branch 'master' into feature-js-console-output

Author: tetron

README.rst

@@ -31,7 +31,7 @@ well)::
 
   pip install cwlref-runner
 
-If installling alongside another CWL implementation then::
+If installing alongside another CWL implementation then::
 
   pip install cwltool
 
@@ -77,7 +77,7 @@ the default cwl-runner use::
 Use with boot2docker
 --------------------
 boot2docker is running docker inside a virtual machine and it only mounts ``Users``
-on it. The default behavoir of CWL is to create temporary directories under e.g.
+on it. The default behavior of CWL is to create temporary directories under e.g.
 ``/Var`` which is not accessible to Docker containers.
 
 To run CWL successfully with boot2docker you need to set the ``--tmpdir-prefix``

cwltool/load_tool.py

@@ -133,7 +133,8 @@ def validate_document(document_loader,  # type: Loader
                       enable_dev=False,  # type: bool
                       strict=True,  # type: bool
                       preprocess_only=False,  # type: bool
-                      fetcher_constructor=None
+                      fetcher_constructor=None,
+                      skip_schemas=None
                       # type: Callable[[Dict[unicode, unicode], requests.sessions.Session], Fetcher]
                       ):
     # type: (...) -> Tuple[Loader, Names, Union[Dict[Text, Any], List[Dict[Text, Any]]], Dict[Text, Any], Text]
@@ -180,9 +181,10 @@ def validate_document(document_loader,  # type: Loader
         raise avsc_names
 
     processobj = None  # type: Union[CommentedMap, CommentedSeq, unicode]
+
     document_loader = Loader(sch_document_loader.ctx, schemagraph=sch_document_loader.graph,
                              idx=document_loader.idx, cache=sch_document_loader.cache,
-                             fetcher_constructor=fetcher_constructor)
+                             fetcher_constructor=fetcher_constructor, skip_schemas=skip_schemas)
 
     _add_blank_ids(workflowobj)
 

cwltool/main.py

@@ -141,6 +141,9 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     exgroup.add_argument("--non-strict", action="store_false", help="Lenient validation (ignore unrecognized fields)",
                          default=True, dest="strict")
 
+    parser.add_argument("--skip-schemas", action="store_true",
+            help="Skip loading of schemas", default=True, dest="skip_schemas")
+
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--verbose", action="store_true", help="Default logging")
     exgroup.add_argument("--quiet", action="store_true", help="Only print warnings and errors.")
@@ -637,6 +640,7 @@ def main(argsl=None,  # type: List[str]
                      'enable_dev': False,
                      'enable_ext': False,
                      'strict': True,
+                     'skip_schemas': False,
                      'rdf_serializer': None,
                      'basedir': None,
                      'tool_help': False,
@@ -704,7 +708,8 @@ def main(argsl=None,  # type: List[str]
                 = validate_document(document_loader, workflowobj, uri,
                                     enable_dev=args.enable_dev, strict=args.strict,
                                     preprocess_only=args.print_pre or args.pack,
-                                    fetcher_constructor=fetcher_constructor)
+                                    fetcher_constructor=fetcher_constructor,
+                                    skip_schemas=args.skip_schemas)
 
             if args.pack:
                 stdout.write(print_pack(document_loader, processobj, uri, metadata))

requirements.txt

@@ -3,5 +3,5 @@ ruamel.yaml==0.13.7
 rdflib==4.2.2
 rdflib-jsonld==0.4.0
 shellescape==3.4.1
-schema-salad>=2.4.20170308171942,<3
+schema-salad>=2.5.20170623152720,<3
 typing==3.5.2.2 ; python_version>="2.7"

setup.py

@@ -58,7 +58,7 @@
           'ruamel.yaml >= 0.12.4',
           'rdflib >= 4.2.2, < 4.3.0',
           'shellescape >= 3.4.1, < 3.5',
-          'schema-salad >= 2.4.20170308171942, < 3',
+          'schema-salad >= 2.5.20170623152720, < 3',
           'typing >= 3.5.2, < 3.6',
           'six >= 1.8.0',
       ],