add tool making kwargs to Factory

Author: mr-c

cwltool/factory.py

@@ -38,25 +38,28 @@ def __init__(self,
                  makeTool=workflow.defaultMakeTool,  # type: tCallable[[Any], Process]
                  # should be tCallable[[Dict[Text, Any], Any], Process] ?
                  executor=None,  # type: tCallable[...,Tuple[Dict[Text,Any], Text]]
-                 **execkwargs  # type: Any
+                 makekwargs={},  # type: Dict[Any, Any]
+                 **execkwargs    # type: Dict[Any, Any]
                  ):
         # type: (...) -> None
         self.makeTool = makeTool
         if executor is None:
             executor = SingleJobExecutor()
         self.executor = executor
 
-        kwargs = get_default_args()
-        kwargs.pop("job_order")
-        kwargs.pop("workflow")
-        kwargs.pop("outdir")
-        kwargs.update(execkwargs)
-        self.execkwargs = kwargs
+        newExecKwargs = get_default_args()
+        newExecKwargs.pop("job_order")
+        newExecKwargs.pop("workflow")
+        newExecKwargs.pop("outdir")
+        newExecKwargs.update(execkwargs)
+        self.execkwargs = newExecKwargs
+        self.makekwargs = makekwargs
 
     def make(self, cwl):
         """Instantiate a CWL object from a CWl document."""
         load = load_tool.load_tool(cwl, self.makeTool,
-                                   strict=self.execkwargs.get("strict", True))
+                                   strict=self.execkwargs.get("strict", True),
+                                   kwargs=self.makekwargs)
         if isinstance(load, int):
             raise Exception("Error loading tool")
         return Callable(load, self)

tests/test_examples.py

@@ -29,9 +29,9 @@
 import cwltool.workflow
 import schema_salad.validate
 from cwltool.main import main
-from cwltool.utils import onWindows, windows_default_container_id
+from cwltool.utils import onWindows
 
-from .util import get_data, needs_docker
+from .util import get_data, needs_docker, get_windows_safe_factory
 
 sys.argv = ['']
 
@@ -136,20 +136,10 @@ def test_params(self):
         self.assertEqual(expr.interpolate("$(foo[\"b\\'ar\"].baz) $(foo[\"b\\'ar\"].baz)", inputs), "true true")
         self.assertEqual(expr.interpolate("$(foo['b\\\"ar'].baz) $(foo['b\\\"ar'].baz)", inputs), "null null")
 
-def _find_default_container(default_container_id, builder):
-   return default_container_id
-
-
 class TestFactory(unittest.TestCase):
 
     def test_factory(self):
-        if onWindows():
-            opts = {'find_default_container': functools.partial(
-                _find_default_container, windows_default_container_id),
-                    'use_container': True}
-        else:
-            opts = {}
-        f = cwltool.factory.Factory(**opts)
+        f = get_windows_safe_factory()
         echo = f.make(get_data("tests/echo.cwl"))
         self.assertEqual(echo(inp="foo"), {"out": "foo\n"})
 

tests/test_iwdr.py

@@ -2,7 +2,7 @@
 
 import cwltool
 import cwltool.factory
-from .util import get_data
+from .util import get_data, get_windows_safe_factory
 
 
 class TestInitialWorkDir(unittest.TestCase):
@@ -11,6 +11,6 @@ def test_newline_in_entry(self):
         """
         test that files in InitialWorkingDirectory are created with a newline character
         """
-        f = cwltool.factory.Factory()
+        f = get_windows_safe_factory()
         echo = f.make(get_data("tests/wf/iwdr-entry.cwl"))
         self.assertEqual(echo(message="hello"), {"out": "CONFIGVAR=hello\n"})

tests/test_js_sandbox.py

@@ -13,7 +13,7 @@
                                exec_js_process)
 import cwltool.sandboxjs
 from cwltool.utils import onWindows
-from .util import get_data
+from .util import get_data, get_windows_safe_factory
 import pytest
 
 
@@ -48,7 +48,7 @@ def test_is_javascript_installed(self):
 class TestValueFrom(unittest.TestCase):
 
     def test_value_from_two_concatenated_expressions(self):
-        f = cwltool.factory.Factory()
+        f = get_windows_safe_factory()
         echo = f.make(get_data("tests/wf/vf-concat.cwl"))
         self.assertEqual(echo(), {u"out": u"a sting\n"})
 

tests/test_parallel.py

@@ -7,7 +7,7 @@
 import cwltool.factory
 from cwltool.executors import MultithreadedJobExecutor
 from cwltool.utils import onWindows
-from .util import get_data
+from .util import get_data, get_windows_safe_factory
 
 
 class TestParallel(unittest.TestCase):
@@ -27,7 +27,7 @@ def test_sequential_workflow(self):
     def test_scattered_workflow(self):
         test_file = "tests/wf/scatter-wf4.cwl"
         job_file = "tests/wf/scatter-job2.json"
-        f = cwltool.factory.Factory(executor=MultithreadedJobExecutor())
+        f = get_windows_safe_factory(executor=MultithreadedJobExecutor())
         echo = f.make(get_data(test_file))
         with open(get_data(job_file)) as job:
             self.assertEqual(echo(**json.load(job)), {'out': ['foo one three', 'foo two four']})

tests/util.py

@@ -6,6 +6,22 @@
 import distutils.spawn
 import pytest
 
+from cwltool.utils import onWindows
+from cwltool.factory import Factory
+
+def get_windows_safe_factory(**execkwargs):
+    if onWindows():
+        opts = {'find_default_container': functools.partial(
+            force_default_container, windows_default_container_id),
+                'use_container': True,
+                'default_container': windows_default_container_id}
+    else:
+        opts = {}
+    return Factory(makekwargs=opts, **execkwargs)
+
+def force_default_container(default_container_id, builder):
+   return default_container_id
+
 def get_data(filename):
     filename = os.path.normpath(
         filename)  # normalizing path depending on OS or else it will cause problem when joining path