fix a bug with default parameters

src/jflow/workflow.py

@@ -220,14 +220,16 @@ class Workflow(threading.Thread):
     def _set_parameters(self, args):
         parameters = self.get_parameters()
         for param in parameters:
-            if args[param.name]:
-                try: args[param.name] = args[param.name].encode('ascii','ignore')
-                except: pass
-                if param.__class__ ==  Parameter:
-                    new_param = Parameter(param.name, param.help, default=args[param.name], type=param.type, choices=param.choices, 
-                                          required=param.required, flag=param.flag, group=param.group, display_name=param.display_name)
-                    self.__setattr__(param.name, new_param)
-                elif param.__class__ == InputFile:
+            try: args[param.name] = args[param.name].encode('ascii','ignore')
+            except: pass
+            if param.__class__ ==  Parameter:
+                if args[param.name]: default = args[param.name]
+                else: default = param.default
+                new_param = Parameter(param.name, param.help, default=default, type=param.type, choices=param.choices, 
+                                      required=param.required, flag=param.flag, group=param.group, display_name=param.display_name)
+                self.__setattr__(param.name, new_param)
+            elif param.__class__ == InputFile:
+                if args[param.name]:
                     # handle url inputs
                     default, is_uri = self._download_urlfile(args[param.name])
                     # handle upload inputs
@@ -235,11 +237,14 @@ class Workflow(threading.Thread):
                     except: is_local = False
                     if not is_uri and not is_local and param.type.__name__ == "inputfile" or param.type.__name__ == "browsefile":
                         default = os.path.join(self.jflow_config_reader.get_tmp_directory(), (args[param.name]))
-                    new_param = InputFile(param.name, param.help, file_format=param.file_format, default=default, type=param.type, 
-                                          choices=param.choices, required=param.required, flag=param.flag, 
-                                          group=param.group, display_name=param.display_name)
-                    self.__setattr__(param.name, new_param)
-                elif param.__class__ == InputFileList:
+                else: 
+                    default = param.default
+                new_param = InputFile(param.name, param.help, file_format=param.file_format, default=default, type=param.type, 
+                                      choices=param.choices, required=param.required, flag=param.flag, 
+                                      group=param.group, display_name=param.display_name)
+                self.__setattr__(param.name, new_param)
+            elif param.__class__ == InputFileList:
+                if args[param.name]:
                     path2test = args[param.name]
                     if not path2test.__class__.__name__ == "list":
                         path2test = [path2test]
@@ -260,28 +265,29 @@ class Workflow(threading.Thread):
                         for path in path2test:
                             default_vals.append(os.path.join(self.jflow_config_reader.get_tmp_directory(), (path)))
                     self.__getattribute__(param.name).extend(default_vals)
-                elif param.__class__ ==  ParameterList:
+            elif param.__class__ ==  ParameterList:
+                if args[param.name]:
                     self.__getattribute__(param.name).extend(args[param.name])
-                elif param.__class__ == MultiParameter:
-                    sub_args = {}
-                    for sarg in args[param.name]:
+            elif param.__class__ == MultiParameter:
+                sub_args = {}
+                for sarg in args[param.name]:
+                    sub_args[sarg[0]] = sarg[1]
+                for sub_param in param.sub_parameters:
+                    if sub_args.has_key(sub_param.flag):
+                        self.__getattribute__(param.name)[sub_param.name] = sub_args[sub_param.flag]
+                    else:
+                        self.__getattribute__(param.name)[sub_param.name] = sub_param.default
+            elif param.__class__ == MultiParameterList:
+                for sargs in args[param.name]:
+                    sub_args, final_sub_args = {}, {}
+                    for sarg in sargs:
                         sub_args[sarg[0]] = sarg[1]
                     for sub_param in param.sub_parameters:
                         if sub_args.has_key(sub_param.flag):
-                            self.__getattribute__(param.name)[sub_param.name] = sub_args[sub_param.flag]
+                            final_sub_args[sub_param.name] = sub_args[sub_param.flag]
                         else:
-                            self.__getattribute__(param.name)[sub_param.name] = sub_param.default
-                elif param.__class__ == MultiParameterList:
-                    for sargs in args[param.name]:
-                        sub_args, final_sub_args = {}, {}
-                        for sarg in sargs:
-                            sub_args[sarg[0]] = sarg[1]
-                        for sub_param in param.sub_parameters:
-                            if sub_args.has_key(sub_param.flag):
-                                final_sub_args[sub_param.name] = sub_args[sub_param.flag]
-                            else:
-                                final_sub_args[sub_param.name] = sub_param.default
-                        self.__getattribute__(param.name).append(final_sub_args)
+                            final_sub_args[sub_param.name] = sub_param.default
+                    self.__getattribute__(param.name).append(final_sub_args)
     
     def get_execution_graph(self):
         graph = Graph()