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src/jflow/parameter.py

@@ -757,16 +757,10 @@ class InputDirectory(StrParameter, LinkTraceback):
         StrParameter.__init__(self, name, help, flag=flag, default=default, type="inputdirectory", choices=choices, 
                            required=required, group=group, display_name=display_name, cmd_format=cmd_format, argpos=argpos)
 
-    def prepare_input_directory(self, input):
+    def prepare(self, input):
         if input == None:
             return None
-        try: is_local = os.path.isdir(input)
-        except: is_local = False
-        if not is_local :
-            jflow_config_reader = JFlowConfigReader()
-            new_path = os.path.join(jflow_config_reader.get_tmp_directory(), input)
-        if is_local: new_path = os.path.abspath(input)
-        return new_path
+        return os.path.abspath(input)
     
 class AbstractInputFile(AbstractIOFile):
     """
@@ -853,7 +847,7 @@ class InputFile(StrParameter, AbstractInputFile):
         else: ctype = self.get_type()
         return create_test_function(ctype)
 
-    def prepare_input_file(self, input):
+    def prepare(self, input):
         if input == None:
             return None
         # handle url inputs
@@ -951,7 +945,7 @@ class InputFileList(ParameterList, AbstractInputFile):
         else: ctype = self.get_type()
         return create_test_function(ctype)
 
-    def prepare_input_files(self, inputs):
+    def prepare(self, inputs):
         path2test = _copy.deepcopy(inputs)
         new_vals = list()
         if not path2test.__class__.__name__ == "list":

src/jflow/workflow.py

@@ -307,7 +307,7 @@ class Workflow(threading.Thread):
         elif parameter.__class__ == InputFileList:
             if value == "" : value = [] # from GUI
             iovalues = []
-            prepared_files = parameter.prepare_input_files(value)
+            prepared_files = parameter.prepare(value)
             for file in prepared_files:
                 iovalues.append(IOFile(file, parameter.file_format, parameter.linkTrace_nameid, None))
             new_param = InputFileList( parameter.name, parameter.help, file_format=parameter.file_format, default=iovalues,
@@ -316,14 +316,14 @@ class Workflow(threading.Thread):
             new_param.linkTrace_nameid = parameter.linkTrace_nameid            
         elif parameter.__class__ == InputFile:
             if value == "" : value = None # from GUI
-            prepared_file = parameter.prepare_input_file(value)
+            prepared_file = parameter.prepare(value)
             new_param = InputFile( parameter.name, parameter.help, file_format=parameter.file_format, default=prepared_file,
                                    type=parameter.type, choices=parameter.choices, required=parameter.required, flag=parameter.flag, 
                                    group=parameter.group, display_name=parameter.display_name )
             new_param.linkTrace_nameid = parameter.linkTrace_nameid
         elif parameter.__class__ == InputDirectory:
             if value == "" : value = None # from GUI
-            prepared_directory = parameter.prepare_input_directory(value)
+            prepared_directory = parameter.prepare(value)
             new_param = InputDirectory( parameter.name, parameter.help, default=prepared_directory, choices=parameter.choices, 
                                         required=parameter.required, flag=parameter.flag, group=parameter.group, 
                                         display_name=parameter.display_name )