Handle UnsupportedRequirement and return exit code 33. Add "pack" to internal set of configuration defaults.

Author: Peter Amstutz

cwltool/errors.py

@@ -1,2 +1,5 @@
 class WorkflowException(Exception):
     pass
+
+class UnsupportedRequirement(WorkflowException):
+    pass

cwltool/main.py

@@ -10,7 +10,7 @@
 import logging
 import copy
 from . import workflow
-from .errors import WorkflowException
+from .errors import WorkflowException, UnsupportedRequirement
 from . import process
 from .cwlrdf import printrdf, printdot
 from .process import shortname, Process
@@ -542,7 +542,8 @@ def main(argsl=None,
                     'basedir': None,
                     'tool_help': False,
                     'workflow': None,
-                    'job_order': None}.iteritems():
+                    'job_order': None,
+                    'pack': False}.iteritems():
             if not hasattr(args, k):
                 setattr(args, k, v)
 
@@ -662,6 +663,11 @@ def main(argsl=None,
                 u"Input object failed validation:\n%s", exc,
                 exc_info=(exc if args.debug else False))
             return 1
+        except UnsupportedRequirement as exc:
+            _logger.error(
+                u"Workflow or tool uses unsupported feature:\n%s", exc,
+                exc_info=(exc if args.debug else False))
+            return 33
         except WorkflowException as exc:
             _logger.error(
                 u"Workflow error, try again with --debug for more "

cwltool/process.py

@@ -18,7 +18,7 @@
 from .builder import Builder, adjustFileObjs
 import tempfile
 import glob
-from .errors import WorkflowException
+from .errors import WorkflowException, UnsupportedRequirement
 from .pathmapper import abspath
 from typing import Any, Callable, Generator, Union, IO, AnyStr, Tuple
 from collections import Iterable
@@ -120,10 +120,6 @@ def shortname(inputid):
     else:
         return d.path.split("/")[-1]
 
-
-class UnsupportedRequirement(Exception):
-    pass
-
 def checkRequirements(rec, supportedProcessRequirements):
     # type: (Any, Iterable[Any]) -> None
     if isinstance(rec, dict):