Add default command line arguments for cwltool as Factory

Author: Anton Khodak

cwltool/argparser.py

@@ -217,6 +217,16 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     return parser
 
 
+def get_default_args():
+    # type: () -> Dict[str, Any]
+    """
+    Get default values of cwltool's command line options
+    """
+    ap = arg_parser()
+    args = ap.parse_args()
+    return vars(args)
+
+
 class FSAction(argparse.Action):
     objclass = None  # type: Text
 

cwltool/factory.py

@@ -4,6 +4,7 @@
 from typing import Any, Dict, Text, Tuple, Union
 
 from . import load_tool, main, workflow
+from .argparser import get_default_args
 from .process import Process
 
 
@@ -41,7 +42,13 @@ def __init__(self,
         # type: (...) -> None
         self.makeTool = makeTool
         self.executor = executor
-        self.execkwargs = execkwargs
+
+        kwargs = get_default_args()
+        kwargs.pop("job_order")
+        kwargs.pop("workflow")
+        kwargs.pop("outdir")
+        kwargs.update(execkwargs)
+        self.execkwargs = kwargs
 
     def make(self, cwl):
         """Instantiate a CWL object from a CWl document."""

tests/test_examples.py

@@ -136,6 +136,16 @@ def test_factory(self):
         echo = f.make(get_data("tests/echo.cwl"))
         self.assertEqual(echo(inp="foo"), {"out": "foo\n"})
 
+    def test_default_args(self):
+        f = cwltool.factory.Factory()
+        assert f.execkwargs["use_container"] is True
+        assert f.execkwargs["on_error"] == "stop"
+
+    def test_redefined_args(self):
+        f = cwltool.factory.Factory(use_container=False, on_error="continue")
+        assert f.execkwargs["use_container"] is False
+        assert f.execkwargs["on_error"] == "continue"
+
     def test_partial_scatter(self):
         f = cwltool.factory.Factory(on_error="continue")
         fail = f.make(get_data("tests/wf/scatterfail.cwl"))