Make do_update optional to override updating behavior.

Sanity check tool has been updated to expected internal version before
executing.

Author: Peter Amstutz

cwltool/context.py

@@ -64,7 +64,7 @@ def __init__(self, kwargs=None):
         self.host_provenance = False       # type: bool
         self.user_provenance = False       # type: bool
         self.prov_obj = None               # type: Optional[ProvenanceProfile]
-        self.do_update = True              # type: bool
+        self.do_update = None              # type: Optional[bool]
         self.jobdefaults = None            # type: Optional[MutableMapping[Text, Any]]
 
         super(LoadingContext, self).__init__(kwargs)

cwltool/main.py

@@ -625,7 +625,8 @@ def formatTime(self, record, datefmt=None):
         loadingContext.construct_tool_object = getdefault(
             loadingContext.construct_tool_object, workflow.default_make_tool)
         loadingContext.resolver = getdefault(loadingContext.resolver, tool_resolver)
-        loadingContext.do_update = not (args.pack or args.print_subgraph)
+        if loadingContext.do_update is None:
+            loadingContext.do_update = not (args.pack or args.print_subgraph)
 
         uri, tool_file_uri = resolve_tool_uri(
             args.workflow, resolver=loadingContext.resolver,
@@ -654,7 +655,7 @@ def formatTime(self, record, datefmt=None):
                 = resolve_and_validate_document(loadingContext, workflowobj, uri,
                                     preprocess_only=(args.print_pre or args.pack),
                                     skip_schemas=args.skip_schemas)
-            
+
             if loadingContext.loader is None:
                 raise Exception("Impossible code path.")
             processobj, metadata = loadingContext.loader.resolve_ref(uri)

cwltool/process.py

@@ -46,6 +46,8 @@
 from .utils import (DEFAULT_TMP_PREFIX, aslist, cmp_like_py2,
                     copytree_with_merge, onWindows, random_outdir)
 from .validate_js import validate_js_expressions
+from .update import INTERNAL_VERSION
+
 try:
     from os import scandir  # type: ignore
 except ImportError:
@@ -586,6 +588,10 @@ def __init__(self,
     def _init_job(self, joborder, runtime_context):
         # type: (Mapping[Text, Text], RuntimeContext) -> Builder
 
+        if self.metadata.get("cwlVersion") != INTERNAL_VERSION:
+            raise WorkflowException("Process object loaded with version '%s', must update to '%s' in order to execute." % (
+                self.metadata.get("cwlVersion"), INTERNAL_VERSION))
+
         job = cast(Dict[Text, Union[Dict[Text, Any], List[Any], Text, None]],
                    copy.deepcopy(joborder))
 

cwltool/update.py

@@ -89,6 +89,8 @@ def fix_inputBinding(t):
 ALLUPDATES = UPDATES.copy()
 ALLUPDATES.update(DEVUPDATES)
 
+INTERNAL_VERSION = u"v1.1.0-dev1"
+
 def identity(doc, loader, baseuri):  # pylint: disable=unused-argument
     # type: (Any, Loader, Text) -> Tuple[Any, Union[Text, Text]]
     """The default, do-nothing, CWL document upgrade function."""