def load_translated_model(self):#, translated):
# if not translated:
# return
self._prism_model_str = ''
if self.model.PRISM_model != '':
try:
with read(self.model.PRISM_model_) as f:
self._prism_model_str = f.read()
# logger.debug(self._prism_model_str)
except IOError, e:
# logger.error(e)
pass
def object_temporal_formulas_changed(self, info):
if not os.path.isfile(info.object.temporal_formulas_):
return
with read(info.object.temporal_formulas_) as f:
lines = f.readlines()
if len(lines) == 0 or lines[0].strip() != 'Formulas:':
return
del self.temporal_formulas[:] # clear list
for line in lines[1:]:
line = line.strip()
# skip empty lines
if len(line) == 0:
continue
# extract formula
first = line.find('"')
second = line.find('"', first + 1)
formula = line[first + 1:second]
# extract parameters
parameters_start = line.find('{', second + 1)
parameters_end = line.find('}', parameters_start + 1)
parameters = []
for parameter in line[parameters_start + 1:parameters_end].split(','):
name_and_values = parameter.split('=')
name = name_and_values[0].strip()
values = name_and_values[1].split(':')
lower = values[0]
step = values[1]
upper = values[2]
# create parameter objects
parameters.append(TemporalFormulaParameter(name=name, lower=float(lower), step=float(step), upper=float(upper)))
# create formula object and add to list
temporal_formula = TemporalFormula(
formula=formula,
parameters=parameters,
params_handler=self,
)
self.temporal_formulas.append(temporal_formula)
def _directory_changed(self):
model_parameters_file = os.path.join(self.directory, "modelParameters.xml")
try:
with read(model_parameters_file) as f:
parser = sax.make_parser()
handler = ModelParametersXMLReader()
parser.setContentHandler(handler)
try:
parser.parse(f) # read parameters from file into dictionary
except sax._exceptions.SAXParseException, e:
print e
self.modelVariables = handler.modelVariables
self.ruleConstants = handler.ruleConstants
self.moleculeConstants = handler.moleculeConstants
self.rewardConstants = handler.rewardConstants
self.rewardConstant_descriptions = [
rewardConstant.description.replace("A", "a") for rewardConstant in handler.rewardConstants
]
self.rewardConstant = self.rewardConstant_descriptions[0]
except IOError, e:
# print e, 'ModelParameters._directory_changed()'
# raise e
pass
def load(self, file, force=False):
''' Reads parameters file,
resets traits,
sets traits to new parameters,
Returns True if a params file was successfully loaded.
'''
if self._dirty and not force:
if self._interaction_mode == 'terminal':
answer = raw_input('Save current parameters before continuing? [Y/n] ')
if len(answer.strip()) == 0 or answer.upper().startswith('Y'):
self.save() # will prompt for file name with self._params_file as default
elif self._interaction_mode == 'script':
logger.warn('Overwriting unsaved parameters: %s' % ','.join(['%s=%s' % (name, value) for name, value in self._dirty_parameters.items()]))
# open and parse params file with ParamsXMLReader
# reporting errors or responding to success
with read(file, 'rb') as fh:
parser = sax.make_parser()
parameters_dictionary = {} # keep reference to dictionary that will be filled by handler
handler = ParamsXMLReader(parameters_dictionary, self._parameter_set_name)
parser.setContentHandler(handler)
error = None
try:
# read parameters from file into dictionary
parser.parse(fh)
except sax._exceptions.SAXParseException:
error = "'%s' is not a well-formed XML file." % file
# check for other errors
if not hasattr(handler, 'parameter_set_name'):
error = "'%s' is not a parameters file." % file
# elif not handler.has_expected_parameter_set_name: # will also fail without changing anything, also good.
# error = "Incorrect parameter set: '%s' when '%s' expected." % (handler.parameter_set_name, handler.expected_parameter_set_name)
elif len(parameters_dictionary) == 0:
error = "No parameters in file '%s'." % file
if error is not None:
logger.error(error)
# auto_close_message(message=error) #TODO is this desirable when scripting?...might not happen, as with ProgressDialog
return False
# read parameters ok
# reset traits so we don't carry over parameters that are missing from
# the file we are loading
self._unresetable = self.reset(self.parameter_names()) #FIXME reverts to default values not preferences!
if len(self._unresetable) > 0:
logger.warn("Some parameters were not reset: %s", ', '.join(self._unresetable))
# change directory here so that relative paths don't trigger TraitError
if not os.path.isabs(file):
file = os.path.abspath(file) # prepends os.getcwd() to relative file names
self.directory = os.path.dirname(file)
# set parameters from dictionary, passing if values are not suitable
for name, value in parameters_dictionary.iteritems():
try:
set_trait_value_from_parameter_value(self, name, value)
except TraitError:
pass
# success!
# logger.debug("Loaded '%s'." % file)
self._params_file = file
self._dirty = False