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Commit 572a0a4a authored by Frédéric Escudié's avatar Frédéric Escudié
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Keep parameters class in sub parameters fo MultipleParameter, MultipleParameterList. 

Keep ParameterList, InputFileList instead simple list.
Todo keep MultipleParameter instead dict and MultipleParameterList instead list of dict.
parent 981f9413
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src/jflow/workflow.py
View file @ 572a0a4a
......@@ -224,63 +224,62 @@ class Workflow(threading.Thread):
flags2exclude.append(paramsexclude.flag)
attribute_value.type.excludes[new_group] = flags2exclude
break
def _prepare_parameter(self, args, parameter):
new_param = None
# Retrieve value
if args.has_key(parameter.flag):
value = args[parameter.flag]
elif parameter != None:
value = parameter.default
else:
value = None
# Set new parameter
if parameter.__class__ == StrParameter or parameter.__class__ == IntParameter or parameter.__class__ == FloatParameter or parameter.__class__ == BoolParameter or parameter.__class__ == DateParameter:
new_param = ParameterFactory.factory( parameter.name, parameter.help, default=value, type=parameter.type, choices=parameter.choices,
required=parameter.required, flag=parameter.flag, group=parameter.group,
display_name=parameter.display_name )
elif parameter.__class__ == ParameterList:
new_param = ParameterList( parameter.name, parameter.help, default=value, type=parameter.type, choices=parameter.choices,
required=parameter.required, flag=parameter.flag, sub_parameters=parameter.sub_parameters,
group=parameter.group, display_name=parameter.display_name )
elif parameter.__class__ == InputFileList:
new_param = InputFileList( parameter.name, parameter.help, file_format=parameter.file_format, default=parameter.prepare_input_files(value),
type=parameter.type, choices=parameter.choices, required=parameter.required, flag=parameter.flag,
group=parameter.group, display_name=parameter.display_name, size_limit=parameter.size_limit )
elif parameter.__class__ == InputFile:
new_param = InputFile( parameter.name, parameter.help, file_format=parameter.file_format, default=parameter.prepare_input_file(value),
type=parameter.type, choices=parameter.choices, required=parameter.required, flag=parameter.flag,
group=parameter.group, display_name=parameter.display_name )
else:
raise Exception( "Unknown class '" + parameter.__class__.__name__ + "' for parameter.")
return new_param
def _set_parameters(self, args):
parameters = self.get_parameters()
for param in parameters:
try: args[param.name] = args[param.name].encode('ascii','ignore')
except: pass
if param.__class__ == StrParameter or param.__class__ == IntParameter or param.__class__ == FloatParameter or param.__class__ == BoolParameter or param.__class__ == DateParameter:
if args[param.name]: default = args[param.name]
else: default = param.default
new_param = ParameterFactory.factory(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]:
default = param.prepare_input_file(args[param.name])
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 and args[param.name]:
self.__setattr__(param.name, param.prepare_input_files(args[param.name]))
elif param.__class__ == ParameterList and args[param.name]:
self.__setattr__(param.name, args[param.name])
elif param.__class__ == MultiParameter:
if 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):
value = sub_args[sub_param.flag]
else:
value = sub_param.default
if sub_param.__class__ == InputFile:
value = sub_param.prepare_input_file(value)
elif sub_param.__class__ == InputFileList:
value = sub_param.prepare_input_files(value)
self.__getattribute__(param.name)[sub_param.name] = value
self.__getattribute__(param.name)[sub_param.name] = self._prepare_parameter( sub_args, sub_param )
elif param.__class__ == MultiParameterList:
final_vals = []
new_param = []
for sargs in args[param.name]:
sub_args, final_sub_args = {}, {}
new_multi_param = {}
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):
value = sub_args[sub_param.flag]
else:
value = sub_param.default
if sub_param.__class__ == InputFile:
value = sub_param.prepare_input_file(value)
elif sub_param.__class__ == InputFileList:
value = sub_param.prepare_input_files(value)
final_sub_args[sub_param.name] = value
final_vals.append(final_sub_args)
self.__setattr__(param.name, final_vals)
new_sub_param = self._prepare_parameter(sub_args, sub_param)
new_multi_param[new_sub_param.name] = new_sub_param
new_param.append(new_multi_param)
self.__setattr__(param.name, new_param)
else:
self.__setattr__(param.name, self._prepare_parameter(args, param ))
def get_execution_graph(self):
graph = Graph(graph_dict={})
......@@ -883,4 +882,4 @@ class Workflow(threading.Thread):
# Import symbols from module into global namespace, which we store as
# an attribute for later use (i.e. during compile)
for symbol in symbols:
self.globals[symbol] = getattr(m, symbol)
self.globals[symbol] = getattr(m, symbol)
\ No newline at end of file
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