fixe a bug when overloading get_config

bin/jflow_cli.py

@@ -30,14 +30,6 @@ import jflow.utils as utils
 from cctools.util import time_format
 
 
-# Overload the convert_arg_line_to_args to take config files as argument
-class ConfigArgumentParser (argparse.ArgumentParser):    
-    def convert_arg_line_to_args(self, arg_line):
-        for arg in arg_line.split():
-            if not arg.strip():
-                continue
-            yield arg
-
 def display_workflow_status(workflow, detailed=False):
     if workflow.start_time: start_time = time.asctime(time.localtime(workflow.start_time))
     else: start_time = "-"
@@ -89,7 +81,7 @@ if __name__ == '__main__':
     wfmanager = WorkflowsManager()
     
     # Create the top-level parser
-    parser = ConfigArgumentParser(fromfile_prefix_chars='@')
+    parser = argparse.ArgumentParser(fromfile_prefix_chars='@')
     subparsers = parser.add_subparsers(title='Available sub commands')
     
     # Add rerun workflow availability
@@ -116,9 +108,14 @@ if __name__ == '__main__':
         sub_parser = subparsers.add_parser(instance.name, help=instance.description)
         for param in instance.parameters:
             sub_parser.add_argument(param.flag, **param.export_to_argparse())
-        sub_parser.set_defaults(cmd_object=instance.__class__.__name__)
-    args = vars(parser.parse_args())
+        sub_parser.set_defaults(cmd_object=instance.__class__.__name__, cmd_class=instance.__class__)
 
+    args = vars(parser.parse_args())
+    if args.has_key("cmd_class"):
+        # re parse args with the right parser
+        parser.convert_arg_line_to_args = args["cmd_class"].config_parser
+        args = vars(parser.parse_args())
+        
     if args["cmd_object"] in wf_classes:
         wfmanager.run_workflow(args["cmd_object"], args)
     elif args["cmd_object"] == "rerun":