make sure input file, output file and parameter are correctly written down

src/jflow/workflow.py

@@ -63,7 +63,9 @@ class Workflow(threading.Thread):
     STATUS_COMPLETED = "completed"
     STATUS_FAILED = "failed"
     STATUS_ABORTED = "aborted"
-
+    INPUTFILE_TYPES = ["inputfile", "localfile", "urlfile", "browsefile"]
+    
+    
     def __init__(self, args={}, id=None, function= "process", parameters_section=None):
         """ 
         """
@@ -117,9 +119,11 @@ class Workflow(threading.Thread):
                 self.set_stderr()
             self._serialize()
     
-    def add_input_file(self, name, help, file_format="any", default=None, type=types.StringType, choices=None, 
+    def add_input_file(self, name, help, file_format="any", default=None, type="inputfile", choices=None, 
                        required=False, flag=None, group="default", display_name=None, is_list=False, add_to=None):
-        
+        if type not in self.INPUTFILE_TYPES:
+            raise ValueError("Workflow.add_input_file: wrong type provided: '"+type+"', this should be choosen between '" 
+                             + "', '".join(self.INPUTFILE_TYPES)+"'")
         if is_list:
             if default == None: default = []
             new_param = InputFileList(name, help, flag=flag, file_format=file_format, default=default, type=type, 
@@ -137,14 +141,14 @@ class Workflow(threading.Thread):
             self.params_order.append(name)
             self.__setattr__(name, new_param)
 
-    def add_output_file(self, name, help, file_format="any", default=None, type=types.StringType, choices=None, 
-                        required=False, flag=None, group="default", display_name=None, is_list=False, add_to=None):
+    def add_output_file(self, name, help, file_format="any", default=None, choices=None, required=False, 
+                        flag=None, group="default", display_name=None, is_list=False, add_to=None):
         if is_list:
             if default == None: default = []
-            new_param = OutputFileList(name, help, flag=flag, file_format=file_format, default=default, type=type, 
+            new_param = OutputFileList(name, help, flag=flag, file_format=file_format, default=default, type="localfile", 
                                        choices=choices, required=required, group=group, display_name=display_name)
         else:
-            new_param = OutputFile(name, help, flag=flag, file_format=file_format, default=default, type=type, 
+            new_param = OutputFile(name, help, flag=flag, file_format=file_format, default=default, type="localfile", 
                                    choices=choices, required=required, group=group, display_name=display_name)
         # if this input should be added to a particular parameter
         if add_to:
@@ -166,6 +170,9 @@ class Workflow(threading.Thread):
     
     def add_parameter(self, name, help, default=None, type=types.StringType, choices=None, required=False, 
                       flag=None, group="default", display_name=None, is_list=False, add_to=None):
+        if type in self.INPUTFILE_TYPES:
+            raise ValueError("Workflow.add_parameter: wrong type provided: '"+type+"', this should not be choosen between '" 
+                             + "', '".join(self.INPUTFILE_TYPES)+"'")
         if is_list:
             if default == None: default = []
             new_param = ParameterList(name, help, flag=flag, default=default, type=type, choices=choices, 
@@ -227,7 +234,12 @@ class Workflow(threading.Thread):
                                           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__ ==  ParameterList or param.__class__ ==  InputFileList:
+                elif param.__class__ == OutputFile:
+                    new_param = OutputFile(param.name, param.help, file_format=param.file_format, 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__ ==  ParameterList or param.__class__ ==  InputFileList or param.__class__ ==  OutputFileList:
                     self.__getattribute__(param.name).extend(args[param.name])
                 elif param.__class__ == MultiParameter:
                     sub_args = {}
@@ -238,6 +250,8 @@ class Workflow(threading.Thread):
                             self.__getattribute__(param.name)[sub_param.name] = sub_args[sub_param.flag]
                         else:
                             self.__getattribute__(param.name)[sub_param.name] = self.__getattribute__(param.name).default[sub_param.name]
+                elif param.__class__ == MultiParameterList:
+                    print args[param.name]
                             
     def _download_urlfile(self, input):
         try:

src/jflow/workflows_manager.py

@@ -70,8 +70,9 @@ class WorkflowsManager(object):
             for class_name, obj in inspect.getmembers(sys.modules[modname], inspect.isclass):
                 if issubclass(obj, jflow.workflow.Workflow) and obj.__name__ != jflow.workflow.Workflow.__name__:
                     # try to build the workflow
-                    try: wf_instances.append(obj(parameters_section=parameters_section))
-                    except: pass
+                    wf_instances.append(obj(parameters_section=parameters_section))
+                    #try: wf_instances.append(obj(parameters_section=parameters_section))
+                    #except: pass
         return wf_instances
     
     def rerun_workflow(self, workflow_id):