Merge pull request #176 from fair-workflows/use-noodles-from-call

Use noodles.workflows.from_call for execute method

Author: svenvanderburg

fairworkflows/fairworkflow.py

@@ -379,37 +379,15 @@ def execute(self, *args, **kwargs):
         logger = logging.getLogger('noodles')
         logger.setLevel(logging.INFO)
         logger.handlers = [log_handler]
-        self.workflow_level_promise = self._replace_input_arguments(self.workflow_level_promise, args, kwargs)
+        self.workflow_level_promise = noodles.workflow.from_call(
+            noodles.get_workflow(self.workflow_level_promise).root_node.foo, args, kwargs, {})
         result = noodles.run_single(self.workflow_level_promise)
 
         # Generate the retrospective provenance as a (nano-) Publication object
         retroprov = self._generate_retrospective_prov_publication(log.getvalue())
 
         return result, retroprov
 
-    def _replace_input_arguments(self, promise: noodles.interface.PromisedObject, args, kwargs):
-        """
-        Replace the input arguments of the promise so we can run the workflow with the right
-        inputs. This goes into the guts of noodles, doing something noodles was not intended to be
-        used for.
-        TODO: find a better solution for this
-        """
-        workflow = noodles.get_workflow(promise)
-        signature = inspect.signature(workflow.root_node.foo)
-        arguments_dict = self._get_arguments_dict(args, kwargs, signature)
-        workflow.root_node.bound_args = inspect.BoundArguments(signature, arguments_dict)
-        return promise
-
-    @staticmethod
-    def _get_arguments_dict(args, kwargs, signature):
-        """
-        Create dictionary of keyword arguments from positional and keyword arguments and the
-        signature of the function.
-        """
-        arguments_dict = {key: arg for arg, key in zip(args, signature.parameters.keys())}
-        arguments_dict.update(kwargs)
-        return arguments_dict
-
     def _generate_retrospective_prov_publication(self, log:str) -> nanopub.Publication:
         """
         Utility method for generating a Publication object for the retrospective

tests/test_fairworkflow.py

@@ -373,16 +373,6 @@ def process_image(im: OtherType):
         assert result.message == obj.message
         assert isinstance(prov, Publication)
 
-    def test_get_arguments_dict(self):
-        args = (1, 2)
-        kwargs = {'c': 3, 'd': 4}
-
-        def func(a, b, c, d):
-            return
-
-        result = FairWorkflow._get_arguments_dict(args, kwargs, inspect.signature(func))
-        assert result == {'a': 1, 'b': 2, 'c': 3, 'd': 4}
-
     def test_workflow_non_decorated_step(self):
         def return_value(a: float) -> float:
             """Return the input value. NB: no is_fairstep decorator!"""