def _parse_expressions(self):
expr_namespace = (self.model.parameters | self.model.expressions
| self.model.observables)
expr_symbols = {e.name: sympy.Symbol(e.name) for e in expr_namespace}
for e in self._x.iterfind(_ns('{0}ListOfFunctions/{0}Function')):
for arg in e.iterfind(_ns('{0}ListOfArguments/{0}Argument')):
tag_name = arg.get('id')
try:
self.model.tags[tag_name]
except KeyError:
tag = self.tag(tag_name)
expr_symbols[tag_name] = tag
expr_name = e.get('id')
expr_text = e.find(_ns('{0}Expression')).text
expr_val = 0
try:
expr_val = parse_bngl_expr(expr_text, local_dict=expr_symbols)
except Exception as ex:
self._warn_or_except('Could not parse expression %s: '
'%s\n\nError: %s' %
(expr_name, expr_text, str(ex)))
if isinstance(expr_val, numbers.Number):
self.parameter(expr_name, expr_val)
else:
self.expression(expr_name, expr_val)
def _eval_in_model_env(self, expression):
"""
Evaluates an expression string in the model environment
"""
components = dict((c.name, c) for c in self.model.all_components())
self._model_env.update(components)
# Quick security check on the expression
if re.match(r'^[\w\s()/+\-._*^]*$', expression):
return parse_bngl_expr(expression, local_dict=self._model_env)
else:
self._warn_or_except('Security check on expression "%s" failed' %
expression)
return None
def _parse_expressions(self):
expr_namespace = (self.model.parameters | self.model.expressions)
expr_symbols = {e.name: e for e in expr_namespace}
for e in self._x.iterfind(_ns('{0}ListOfFunctions/{0}Function')):
for arg in e.iterfind(_ns('{0}ListOfArguments/{0}Argument')):
tag_name = arg.get('id')
try:
self.model.tags[tag_name]
except KeyError:
tag = self.tag(tag_name)
expr_symbols[tag_name] = tag
expr_name = e.get('id')
expr_text = e.find(_ns('{0}Expression')).text
expr_val = 0
try:
expr_val = parse_bngl_expr(expr_text, local_dict=expr_symbols)
except Exception as ex:
self._warn_or_except('Could not parse expression %s: '
'%s\n\nError: %s' %
(expr_name, expr_text, str(ex)))
# Replace observables now, so they get expanded by .expand_expr()
# Doing this as part of expr_symbols breaks local functions!
observables = {
sympy.Symbol(o.name): o
for o in self.model.observables
}
# Add renamed observables
observables.update({
sympy.Symbol(obs_old): self.model.observables[obs_new]
for obs_old, obs_new in self._renamed_observables.items()
})
expr_val = expr_val.xreplace(observables)
if isinstance(expr_val, numbers.Number):
self.parameter(expr_name, expr_val)
else:
self.expression(expr_name, expr_val)