Clean up lambda handling in SBML

gyorilab · Jul 11, 2023 · d5be529 · d5be529
1 parent 1ce2ce0
commit d5be529
Showing 1 changed file with 10 additions and 13 deletions.
diff --git a/mira/sources/sbml/processor.py b/mira/sources/sbml/processor.py
@@ -21,7 +21,6 @@
 
 from mira.metamodel import *
 from mira.resources import get_resource_file
-from .. import clean_formula
 
 
 class TqdmLoggingHandler(logging.Handler):
@@ -124,16 +123,15 @@ def _lookup_concepts_filtered(species_ids) -> List[Concept]:
  all_species = {species.id for species in self.sbml_model.species}
 
  all_parameters = {
- clean_formula(parameter.id): {
+ parameter.id: {
  'value': parameter.value,
  'description': parameter.name,
  'units': self.get_object_units(parameter)
  }
  for parameter in self.sbml_model.parameters
  }
  parameter_symbols = \
- {clean_formula(parameter.id):
- sympy.Symbol(clean_formula(parameter.id))
+ {parameter.id: sympy.Symbol(parameter.id)
  for parameter in self.sbml_model.parameters}
  compartment_symbols = {compartment.id: sympy.Symbol(compartment.id)
  for compartment in self.sbml_model.compartments}
@@ -149,8 +147,7 @@ def _lookup_concepts_filtered(species_ids) -> List[Concept]:
  args = [fun_def.getArgument(i).getName()
  for i in range(fun_def.getNumArguments())]
  arg_symbols = {
- clean_formula(arg):
- sympy.Symbol(clean_formula(arg)) for arg in args
+ arg: sympy.Symbol(arg) for arg in args
  }
 
  signature = tuple(arg_symbols.values())
@@ -172,10 +169,11 @@ def _lookup_concepts_filtered(species_ids) -> List[Concept]:
  for species in self.sbml_model.species
  }
 
- all_locals = {k: v for k, v in (list(parameter_symbols.items()) +
- list(compartment_symbols.items()) +
- list(function_lambdas.items()) +
- list(species_id_map.items()))}
+ all_locals = {get_parseable_expression(k): v
+ for k, v in (list(parameter_symbols.items()) +
+ list(compartment_symbols.items()) +
+ list(function_lambdas.items()) +
+ list(species_id_map.items()))}
 
  # Handle custom assignment rules in the model
  assignment_rules = {}
@@ -196,10 +194,9 @@ def _lookup_concepts_filtered(species_ids) -> List[Concept]:
  all_parameters[parameter.id] = {'value': parameter.value,
  'description': parameter.name if parameter.name else None,
  'units': self.get_object_units(parameter)}
- parameter_symbols[clean_formula(parameter.id)] = \
- sympy.Symbol(clean_formula(parameter.id))
+ parameter_symbols[parameter.id] = sympy.Symbol(parameter.id)
 
- rate_expr = sympy.parse_expr(clean_formula(rate_law.formula),
+ rate_expr = sympy.parse_expr(get_parseable_expression(rate_law.formula),
  local_dict=all_locals)
  # At this point we need to make sure we substitute the assignments
  rate_expr = rate_expr.subs(assignment_rules)