Closed jonrkarr closed 3 years ago
This example (BIOMD0000000297.xml.zip) executed with 1.5.7, but now fails with 1.5.9 and 1.5.10
Error
import gillespy2 gillespy2.import_SBML('tests/fixtures/BIOMD0000000297.edited/ex1/BIOMD0000000297.xml') --------------------------------------------------------------------------- ModelError Traceback (most recent call last) ~/.local/lib/python3.9/site-packages/gillespy2/core/model.py in add_assignment_rule(self, assignment_rules) 564 if problem is not None: --> 565 raise problem 566 if len(self.listOfRateRules) != 0: ModelError: Name "kswe" is unavailable. A species with that name exists. During handling of the above exception, another exception occurred: ParameterError Traceback (most recent call last) <ipython-input-2-38951b6d0dac> in <module> ----> 1 gillespy2.import_SBML('tests/fixtures/BIOMD0000000297.edited/ex1/BIOMD0000000297.xml') ~/.local/lib/python3.9/site-packages/gillespy2/core/model.py in import_SBML(filename, name, gillespy_model) 42 raise ImportError('SBML conversion not imported successfully') 43 ---> 44 return convert(filename, model_name=name, gillespy_model=gillespy_model) 45 46 ~/.local/lib/python3.9/site-packages/gillespy2/sbml/SBMLimport.py in convert(filename, model_name, gillespy_model) 364 __get_compartments(sbml_model, gillespy_model) 365 __get_reactions(sbml_model, gillespy_model, errors) --> 366 __get_rules(sbml_model, gillespy_model, errors) 367 __get_constraints(sbml_model, gillespy_model) 368 __get_events(sbml_model, gillespy_model) ~/.local/lib/python3.9/site-packages/gillespy2/sbml/SBMLimport.py in __get_rules(sbml_model, gillespy_model, errors) 232 gillespy_rule = gillespy2.AssignmentRule(name=rule_name, variable=rule_variable, 233 formula=rule_string) --> 234 gillespy_model.add_assignment_rule(gillespy_rule) 235 init_state[gillespy_rule.variable]=eval(gillespy_rule.formula, {**init_state, **eval_globals}) 236 ~/.local/lib/python3.9/site-packages/gillespy2/core/model.py in add_assignment_rule(self, assignment_rules) 582 self.listOfAssignmentRules[assignment_rules.name] = assignment_rules 583 except Exception as e: --> 584 raise ParameterError("Error using {} as a Assignment Rule. Reason given: ".format(assignment_rules, e)) 585 586 def timespan(self, time_span): ParameterError: Error using kswe: kswe_prime * Swe1 + kswe_doubleprime * Swe1M + kswe_tripleprime * PSwe1 as a Assignment Rule. Reason given:
Fixed in release v1.5.11
This example (BIOMD0000000297.xml.zip) executed with 1.5.7, but now fails with 1.5.9 and 1.5.10
Error