fix internal functions

Author: jan-janssen

python_workflow_definition/src/python_workflow_definition/cwl/__main__.py

@@ -5,13 +5,10 @@
 
 
 def load_function(file_name, funct):
-    if file_name.split("/")[-1] != "python_workflow_definition.py":
-        spec = importlib.util.spec_from_file_location("workflow", file_name)
-        module = importlib.util.module_from_spec(spec)
-        sys.modules["workflow"] = module
-        spec.loader.exec_module(module)
-    else:
-        module = importlib.import_module("python_workflow_definition.shared")
+    spec = importlib.util.spec_from_file_location("workflow", file_name)
+    module = importlib.util.module_from_spec(spec)
+    sys.modules["workflow"] = module
+    spec.loader.exec_module(module)
     return getattr(module, funct.split(".")[-1])
 
 
@@ -26,9 +23,13 @@ def convert_argument(arg):
 if __name__ == "__main__":
     # load input
     argument_lst = sys.argv[1:]
-    funct = [arg.split("=")[-1] for arg in argument_lst if "--function=" in arg][0]
-    file = [arg.split("=")[-1] for arg in argument_lst if "--workflowfile=" in arg][0]
-    workflow_function = load_function(file_name=file, funct=funct)
+    funct_lst = [arg.split("=")[-1] for arg in argument_lst if "--function=" in arg]
+    file_lst = [arg.split("=")[-1] for arg in argument_lst if "--workflowfile=" in arg]
+    if len(file_lst) > 0:
+        workflow_function = load_function(file_name=file_lst[0], funct=funct_lst[0])
+    else:
+        m, p = funct_lst[0].rsplit(".", 1)
+        workflow_function = importlib.import_module(m)
     kwargs = {
         arg.split("=")[0][6:]: convert_argument(arg=arg.split("=")[-1])
         for arg in argument_lst

python_workflow_definition/src/python_workflow_definition/cwl/export.py

@@ -108,9 +108,12 @@ def _write_function_cwl(workflow):
             "outputs": {},
         }
         file_name = function_nodes_dict[i].split(".")[-1] + "_" + str(i) + ".cwl"
-        template["inputs"]["workflowfile"]["default"]["location"] = (
-            function_nodes_dict[i].split(".")[0] + ".py"
-        )
+        if function_nodes_dict[i].split(".")[0] != "python_workflow_defintion":
+            template["inputs"]["workflowfile"]["default"]["location"] = (
+                function_nodes_dict[i].split(".")[0] + ".py"
+            )
+        else:
+            del template["inputs"]["workflowfile"]
         template["inputs"].update(
             _get_function_template(function_name=function_nodes_dict[i])
         )