from python2 to python3 > ok from command line

src/jflow/workflow.py

@@ -30,7 +30,7 @@ import datetime
 import logging
 import traceback
 
-from ConfigParser import ConfigParser, NoOptionError
+from configparser import ConfigParser, NoOptionError
 from inspect import getcallargs
 from datetime import date as ddate
 
@@ -150,15 +150,15 @@ class Workflow(threading.Thread):
         if self.id is not None:
             self.directory = self.manager.get_workflow_directory(self.name, self.id)
             if not os.path.isdir(self.directory):
-                os.makedirs(self.directory, 0751)
+                os.makedirs(self.directory, 0o751)
             if self.stderr is None:
                 self.stderr = self._set_stderr()
             self._serialize()
             
         self.internal_components = self._import_internal_components()
         self.external_components = self._import_external_components()
-        
-    
+
+            
     def add_input_directory(self, name, help, default=None, required=False, flag=None, 
                             group="default", display_name=None, get_files_fn=None, add_to=None):
         new_param = InputDirectory(name, help, flag=flag, default=default, required=required, 
@@ -227,7 +227,7 @@ class Workflow(threading.Thread):
         new_param = MultiParameterList(name, help, flag=flag, required=required, group=group, display_name=display_name)
         self.__setattr__(name, new_param)
     
-    def add_parameter(self, name, help, default=None, type=types.StringType, choices=None, 
+    def add_parameter(self, name, help, default=None, type=str, choices=None, 
                       required=False, flag=None, group="default", display_name=None, add_to=None):
         new_param = ParameterFactory.factory(name, help, flag=flag, default=default, type=type, choices=choices, 
                               required=required, group=group, display_name=display_name)
@@ -241,7 +241,7 @@ class Workflow(threading.Thread):
             self.params_order.append(name)
             self.__setattr__(name, new_param)
     
-    def add_parameter_list(self, name, help, default=None, type=types.StringType, choices=None, 
+    def add_parameter_list(self, name, help, default=None, type=str, choices=None, 
                            required=False, flag=None, group="default", display_name=None, add_to=None):
         if default == None: default = []
         new_param = ParameterList(name, help, flag=flag, default=default, type=type, choices=choices, 
@@ -290,7 +290,7 @@ class Workflow(threading.Thread):
     def _prepare_parameter(self, args, parameter, key="name"):
         new_param = None
         # Retrieve value
-        if args.has_key(parameter.__getattribute__(key)):
+        if parameter.__getattribute__(key) in args:
             value = args[parameter.__getattribute__(key)]
         elif parameter.default != None:
             value = parameter.default
@@ -342,7 +342,7 @@ class Workflow(threading.Thread):
             if param.__class__ == MultiParameter:
                 new_param = MultiParameter(param.name, param.help, required=param.required, flag=param.flag, group=param.group, display_name=param.display_name)
                 new_param.sub_parameters = param.sub_parameters
-                if args.has_key(param.name):
+                if param.name in args:
                     sub_args = {}
                     for sarg in args[param.name]:
                         sub_args[sarg[0]] = sarg[1]
@@ -352,7 +352,7 @@ class Workflow(threading.Thread):
             elif param.__class__ == MultiParameterList:
                 new_param = MultiParameterList(param.name, param.help, required=param.required, flag=param.flag, group=param.group, display_name=param.display_name)
                 new_param.sub_parameters = param.sub_parameters
-                if args.has_key(param.name):
+                if param.name in args:
                     for idx, sargs in enumerate(args[param.name]):
                         new_multi_param = MultiParameter(param.name + '_' + str(idx), '', required=False, flag=None, group="default", display_name=None)
                         sub_args = {}
@@ -370,7 +370,7 @@ class Workflow(threading.Thread):
         gr = digraph()
         # build a all_nodes table to store all nodes
         all_nodes = {}
-        for ioparameter in self.__dict__.values():
+        for ioparameter in list(self.__dict__.values()):
             if issubclass(ioparameter.__class__, InputFile):
                 gr.add_node(ioparameter.name)
                 gr.add_node_attribute(ioparameter.name, self.INPUTFILE_GRAPH_LABEL)
@@ -412,7 +412,7 @@ class Workflow(threading.Thread):
             gr.add_node_attribute(cpt.get_nameid(), cpt.get_nameid())
             all_nodes[cpt.get_nameid()] = None
         for cpt in self.components:
-            for ioparameter in cpt.__dict__.values():
+            for ioparameter in list(cpt.__dict__.values()):
                 if issubclass( ioparameter.__class__, InputFile ) or issubclass( ioparameter.__class__, InputFileList) or issubclass( ioparameter.__class__, InputDirectory):
                     for parent in ioparameter.parent_linkTrace_nameid:
                         try: gr.add_edge((parent, ioparameter.linkTrace_nameid))
@@ -423,12 +423,12 @@ class Workflow(threading.Thread):
                         except: pass
         # check if all nodes are connected
         for edge in gr.edges():
-            if all_nodes.has_key(edge[0]):
+            if edge[0] in all_nodes:
                 del all_nodes[edge[0]]
-            if all_nodes.has_key(edge[1]):
+            if edge[1] in all_nodes:
                 del all_nodes[edge[1]]
         # then remove all unconnected nodes: to delete inputs not defined by the user
-        for orphan_node in all_nodes.keys():
+        for orphan_node in list(all_nodes.keys()):
             gr.del_node(orphan_node)
         return gr
 
@@ -593,10 +593,10 @@ class Workflow(threading.Thread):
         Threading uses Lock Object, do not consider these objects when serializing a workflow
         """
         odict = self.__dict__.copy()
-        del odict['_Thread__started']
-        del odict['_Thread__block']
-        del odict['_Thread__stderr']
-        if odict.has_key('external_components') :
+        del odict['_started']
+        del odict['_block']
+        del odict['_stderr']
+        if 'external_components' in odict:
             del odict['external_components']
         return odict
     
@@ -666,7 +666,7 @@ class Workflow(threading.Thread):
         pgparameters, parameters_order = {}, []
         for param in parameters:
             if param.group not in parameters_order: parameters_order.append(param.group)
-            if pgparameters.has_key(param.group):
+            if param.group in pgparameters:
                 pgparameters[param.group].append(param)
             else:
                 pgparameters[param.group] = [param]
@@ -675,7 +675,7 @@ class Workflow(threading.Thread):
     def get_parameters(self):
         params = []
         for param in self.params_order:
-            for attribute_value in self.__dict__.values():
+            for attribute_value in list(self.__dict__.values()):
                 if (issubclass(attribute_value.__class__, AbstractParameter)) and param == attribute_value.name:
                     params.append(attribute_value)
         return params
@@ -696,9 +696,9 @@ class Workflow(threading.Thread):
     
     def add_component(self, component_name, args=[], kwargs={}, component_prefix="default"):
         # first build and check if this component is OK
-        if self.internal_components.has_key(component_name) or self.external_components.has_key(component_name):
+        if component_name in self.internal_components or component_name in self.external_components:
             
-            if self.internal_components.has_key(component_name) :
+            if component_name in self.internal_components:
                 my_pckge = __import__(self.internal_components[component_name], globals(), locals(), [component_name], -1)
                 # build the object and define required field
                 cmpt_object = getattr(my_pckge, component_name)()
@@ -753,7 +753,7 @@ class Workflow(threading.Thread):
             return cmpt_object
         else:
             raise ImportError(component_name + " component cannot be loaded, available components are: {0}".format(
-                                           ", ".join(self.internal_components.keys() + self.external_components.keys())))
+                                           ", ".join(list(self.internal_components.keys()) + list(self.external_components.keys()))))
     
     def pre_process(self):
         pass
@@ -793,7 +793,7 @@ class Workflow(threading.Thread):
         return os.path.join(self.directory, component_name + "_" + component_prefix)
     
     def get_components_nameid(self):
-        return self.component_nameids.keys()
+        return list(self.component_nameids.keys())
     
     def wf_execution_wrapper(self):
         getattr(self, self.function)()
@@ -824,7 +824,7 @@ class Workflow(threading.Thread):
                     self.components = []
                     self.status = self.STATUS_STARTED
                     self.wf_execution_wrapper()
-                except SystemExit, e: 
+                except SystemExit: 
                     self.status = self.STATUS_FAILED
                     self.end_time = time.time()
                     self._serialize()
@@ -844,7 +844,7 @@ class Workflow(threading.Thread):
                     self.components = []
                     self.status = self.STATUS_STARTED
                     self.wf_execution_wrapper()
-                except SystemExit, e: 
+                except SystemExit: 
                     self.status = self.STATUS_FAILED
                     self.end_time = time.time()
                     self._serialize()
@@ -1049,7 +1049,7 @@ class Workflow(threading.Thread):
         workflow_dump.close()
 
     def _component_is_duplicated(self, component):
-        if component.get_nameid() in self.component_nameids.keys():
+        if component.get_nameid() in list(self.component_nameids.keys()):
             return True
         return False