Merge pull request #706 from common-workflow-language/skip-validation

Add flag to skip validation.

Author: mr-c

cwltool/argparser.py

@@ -214,6 +214,9 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     parser.add_argument("--custom-net", type=Text,
                         help="Will be passed to `docker run` as the '--net' "
                              "parameter. Implies '--enable-net'.")
+    parser.add_argument("--disable-validate", dest="do_validate",
+                        action="store_false", default=True,
+                        help=argparse.SUPPRESS)
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--enable-ga4gh-tool-registry", action="store_true", help="Enable resolution using GA4GH tool registry API",

cwltool/load_tool.py

@@ -193,7 +193,8 @@ def validate_document(document_loader,  # type: Loader
                       fetcher_constructor=None,  # type: FetcherConstructorType
                       skip_schemas=None,  # type: bool
                       overrides=None,  # type: List[Dict]
-                      metadata=None  # type: Optional[Dict]
+                      metadata=None,  # type: Optional[Dict]
+                      do_validate=True
                       ):
     # type: (...) -> Tuple[Loader, Names, Union[Dict[Text, Any], List[Dict[Text, Any]]], Dict[Text, Any], Text]
     """Validate a CWL document."""
@@ -209,7 +210,7 @@ def validate_document(document_loader,  # type: Loader
     jobobj = None
     if "cwl:tool" in workflowobj:
         job_loader = default_loader(fetcher_constructor)  # type: ignore
-        jobobj, _ = job_loader.resolve_all(workflowobj, uri)
+        jobobj, _ = job_loader.resolve_all(workflowobj, uri, checklinks=do_validate)
         uri = urllib.parse.urljoin(uri, workflowobj["https://w3id.org/cwl/cwl#tool"])
         del cast(dict, jobobj)["https://w3id.org/cwl/cwl#tool"]
 
@@ -262,7 +263,7 @@ def validate_document(document_loader,  # type: Loader
     _add_blank_ids(workflowobj)
 
     workflowobj["id"] = fileuri
-    processobj, new_metadata = document_loader.resolve_all(workflowobj, fileuri)
+    processobj, new_metadata = document_loader.resolve_all(workflowobj, fileuri, checklinks=do_validate)
     if not isinstance(processobj, (CommentedMap, CommentedSeq)):
         raise ValidationException("Workflow must be a dict or list.")
 
@@ -277,7 +278,8 @@ def validate_document(document_loader,  # type: Loader
     if preprocess_only:
         return document_loader, avsc_names, processobj, new_metadata, uri
 
-    schema.validate_doc(avsc_names, processobj, document_loader, strict)
+    if do_validate:
+        schema.validate_doc(avsc_names, processobj, document_loader, strict)
 
     if new_metadata.get("cwlVersion") != update.LATEST:
         processobj = cast(CommentedMap, cmap(update.update(

cwltool/main.py

@@ -396,7 +396,8 @@ def main(argsl=None,  # type: List[str]
                      'ga4gh_tool_registries': [],
                      'find_default_container': None,
                                    'make_template': False,
-                                   'overrides': None
+                                   'overrides': None,
+                                   'do_validate': True
         }):
             if not hasattr(args, k):
                 setattr(args, k, v)
@@ -478,7 +479,8 @@ def main(argsl=None,  # type: List[str]
                                     preprocess_only=args.print_pre or args.pack,
                                     fetcher_constructor=fetcher_constructor,
                                     skip_schemas=args.skip_schemas,
-                                    overrides=overrides)
+                                    overrides=overrides,
+                                    do_validate=args.do_validate)
 
             if args.print_pre:
                 stdout.write(json.dumps(processobj, indent=4))
@@ -498,6 +500,7 @@ def main(argsl=None,  # type: List[str]
 
             make_tool_kwds["find_default_container"] = functools.partial(find_default_container, args)
             make_tool_kwds["overrides"] = overrides
+            make_tool_kwds["disable_js_validation"] = args.disable_js_validation or (not args.do_validate)
 
             tool = make_tool(document_loader, avsc_names, metadata, uri,
                              makeTool, make_tool_kwds)

cwltool/workflow.py

@@ -557,7 +557,8 @@ def __init__(self, toolpath_object, **kwargs):
             step_inputs.extend(step.tool["inputs"])
             step_outputs.extend(step.tool["outputs"])
 
-        static_checker(workflow_inputs, workflow_outputs, step_inputs, step_outputs)
+        if kwargs.get("do_validate", True):
+            static_checker(workflow_inputs, workflow_outputs, step_inputs, step_outputs)
 
 
     def job(self,