def test_qual_steady_state_with_extra_vars(self):
params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(
self.QUAL_FIXTURE_WITH_EXTRAS_PARAMS_VARS, ModelLanguage.SBML, UniformTimeCourseSimulation, 'KISAO_0000450',
include_compartment_sizes_in_simulation_variables=True,
include_model_parameters_in_simulation_variables=True,
validate=False,
native_ids=True, native_data_types=True)
param = next((param for param in params if param.target ==
"/sbml:sbml/sbml:model/qual:listOfQualitativeSpecies/qual:qualitativeSpecies[@qual:id='erk']/@qual:initialLevel"), None)
self.assertEqual(param.id, 'erk')
self.assertEqual(param.name, None)
self.assertEqual(param.target,
"/sbml:sbml/sbml:model/qual:listOfQualitativeSpecies/qual:qualitativeSpecies[@qual:id='erk']/@qual:initialLevel")
self.assertEqual(param.target_namespaces, {
'sbml': 'http://www.sbml.org/sbml/level3/version1/core',
'qual': 'http://www.sbml.org/sbml/level3/version1/qual/version1',
})
self.assertEqual(param.new_value, 1)
param = next((param for param in params if param.target ==
"/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='main']/@size"), None)
self.assertEqual(param, None)
variable = next((variable for variable in vars if variable.target ==
"/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='main']/@size"), None)
self.assertEqual(variable.id, 'main')
self.assertEqual(variable.name, None)
self.assertEqual(variable.target,
"/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='main']/@size")
self.assertEqual(variable.target_namespaces, {
'sbml': 'http://www.sbml.org/sbml/level3/version1/core',
})
def test_error_handling(self):
with self.assertRaises(FileNotFoundError):
get_parameters_variables_outputs_for_simulation('DOES-NOT-EXIST', ModelLanguage.SBML, UniformTimeCourseSimulation, None)
with self.assertRaises(ValueError):
get_parameters_variables_outputs_for_simulation(__file__, ModelLanguage.SBML, UniformTimeCourseSimulation, None)
with mock.patch.object(libsbml.Model, 'getNumPlugins', return_value=1):
with mock.patch.object(libsbml.Model, 'getPlugin', return_value=mock.Mock(getPackageName=lambda: 'other')):
with self.assertRaises(NotImplementedError):
get_parameters_variables_outputs_for_simulation(
self.CORE_FIXTURE, ModelLanguage.SBML, UniformTimeCourseSimulation, None)
with self.assertRaises(NotImplementedError):
get_parameters_variables_outputs_for_simulation(self.FBC_FIXTURE, ModelLanguage.SBML, None, None)
with self.assertRaises(NotImplementedError):
get_parameters_variables_outputs_for_simulation(self.FBC_FIXTURE, ModelLanguage.SBML, SteadyStateSimulation, 'KISAO_0000019')
def test_core_steady_state_with_more_params_and_vars_no_local_parameters(self):
params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(
self.CORE_FIXTURE_WITH_EXTRAS_PARAMS_VARS, ModelLanguage.SBML, SteadyStateSimulation, 'KISAO_0000019',
include_local_parameters_in_task_level_simulation_parameters=False,
include_compartment_sizes_in_simulation_variables=True,
include_model_parameters_in_simulation_variables=True,
validate=False)
self.assertEqual(next((param for param in params if param.id == 'value_parameter_local_param'), None), None)
def test_core_time_course_l3(self):
params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(
self.CORE_FIXTURE_L3, ModelLanguage.SBML, UniformTimeCourseSimulation, 'KISAO_0000019',
include_local_parameters_in_task_level_simulation_parameters=True)
param = next(param for param in params if param.id == 'value_parameter_k_PIP2hyd')
self.assertEqual(param.name, 'Value of parameter "k_PIP2hyd" of reaction "PIP2_hyd"')
self.assertEqual(param.new_value, '2.4')
self.assertEqual(param.target, ("/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='PIP2_hyd']/sbml:kineticLaw"
"/sbml:listOfLocalParameters/sbml:localParameter[@id='k_PIP2hyd']/@value"))
self.assertEqual(param.target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level3/version1/core'})
def test_core_steady_state_with_more_params_and_vars(self):
params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(
self.CORE_FIXTURE_WITH_EXTRAS_PARAMS_VARS, ModelLanguage.SBML, SteadyStateSimulation, 'KISAO_0000019',
include_local_parameters_in_task_level_simulation_parameters=True,
include_compartment_sizes_in_simulation_variables=True,
include_model_parameters_in_simulation_variables=True,
validate=False)
self.assertEqual(params[0].id, 'init_amount_species_Trim')
self.assertEqual(params[0].name, 'Initial amount of species "CDC28_Clb2_Sic1_Complex"')
self.assertEqual(params[0].new_value, '0.084410675')
self.assertEqual(params[0].target, "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Trim']/@initialAmount")
self.assertEqual(params[0].target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level2/version4'})
param = next((param for param in params if param.id == 'init_size_compartment_compartment'), None)
self.assertEqual(param, None)
param = next((param for param in params if param.id == 'value_parameter_local_param'), None)
self.assertEqual(param, None)
variable = next(variable for variable in vars if variable.id == 'size_compartment_compartment')
self.assertEqual(variable.name, 'Size of compartment "compartment"')
self.assertEqual(variable.symbol, None)
self.assertEqual(variable.target, "/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']/@size")
self.assertEqual(variable.target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level2/version4'})
variable = next(variable for variable in vars if variable.id == 'value_parameter_R1_local_param')
self.assertEqual(variable.name, 'Value of parameter "local_param" of reaction "Clb-Sic dissociation"')
self.assertEqual(variable.symbol, None)
self.assertEqual(variable.target, ("/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R1']/sbml:kineticLaw"
"/sbml:listOfParameters/sbml:parameter[@id='local_param']/@value"))
self.assertEqual(variable.target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level2/version4'})
params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(
self.CORE_FIXTURE_WITH_EXTRAS_PARAMS_VARS, ModelLanguage.SBML, SteadyStateSimulation, 'KISAO_0000019',
include_compartment_sizes_in_simulation_variables=False,
include_model_parameters_in_simulation_variables=False,
validate=False)
self.assertEqual(next((param for param in params if param.id == 'init_size_compartment_compartment'), None), None)
self.assertEqual(next((variable for variable in vars if variable.id == 'size_compartment_compartment'), None), None)
self.assertEqual(next((variable for variable in vars if variable.id == 'value_parameter_local_param'), None), None)
def test_qual_steady_state(self):
params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(
self.QUAL_FIXTURE, ModelLanguage.SBML, SteadyStateSimulation, 'KISAO_0000659')
self.assertEqual(vars[0].id, 'level_species_erk')
self.assertEqual(vars[0].name, 'Level of species "erk"')
self.assertEqual(vars[0].symbol, None)
self.assertEqual(vars[0].target, "/sbml:sbml/sbml:model/qual:listOfQualitativeSpecies/qual:qualitativeSpecies[@qual:id='erk']")
self.assertEqual(vars[0].target_namespaces, {
'sbml': 'http://www.sbml.org/sbml/level3/version1/core',
'qual': 'http://www.sbml.org/sbml/level3/version1/qual/version1',
})
def test_core_steady_state(self):
params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(
self.CORE_FIXTURE, ModelLanguage.SBML, SteadyStateSimulation, 'KISAO_0000019',
include_compartment_sizes_in_simulation_variables=True,
include_model_parameters_in_simulation_variables=True,
include_reaction_fluxes_in_kinetic_simulation_variables=True,
native_ids=True, native_data_types=True)
self.assertEqual(params[0].id, 'Trim')
self.assertEqual(params[0].name, 'CDC28_Clb2_Sic1_Complex')
self.assertEqual(params[0].new_value, 0.084410675)
self.assertEqual(params[0].target, "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Trim']/@initialConcentration")
self.assertEqual(params[0].target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level2/version4'})
self.assertEqual(params[-2].id, 'mu')
self.assertEqual(params[-2].new_value, 0.005)
self.assertEqual(params[-1].id, 'flag')
self.assertEqual(params[-1].name, None)
self.assertEqual(params[-1].new_value, 0)
self.assertEqual(params[-1].target, "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='flag']/@value")
self.assertEqual(params[-1].target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level2/version4'})
param = next(param for param in params if param.target ==
"/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']/@size")
self.assertEqual(param.name, None)
self.assertEqual(param.new_value, 1)
self.assertEqual(param.id, 'compartment')
self.assertEqual(param.target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level2/version4'})
self.assertNotEqual(vars[0].id, None)
variable = next((variable for variable in vars if variable.target ==
"/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='mass']"), None)
self.assertEqual(variable.name, 'mass')
self.assertEqual(variable.symbol, None)
self.assertEqual(variable.id, 'mass')
self.assertEqual(variable.target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level2/version4'})
variable = next(variable for variable in vars if variable.target ==
"/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='kswe']/@value")
self.assertEqual(variable.name, None)
self.assertEqual(variable.id, 'kswe')
self.assertEqual(variable.target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level2/version4'})
variable = next((variable for variable in vars if variable.id == 'kswe_prime'), None)
self.assertEqual(variable, None)
variable = next(variable for variable in vars if variable.target ==
"/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R1']")
self.assertEqual(variable.id, 'R1')
self.assertEqual(variable.name, "Clb-Sic dissociation")
self.assertEqual(variable.target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level2/version4'})
def test_fbc_steady_state_fva(self):
params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(self.FBC_FIXTURE, ModelLanguage.SBML, SteadyStateSimulation, 'KISAO_0000526',
native_ids=True, native_data_types=True)
self.assertEqual(vars[0].id, 'R_ACALD')
self.assertEqual(vars[0].name, 'acetaldehyde dehydrogenase (acetylating)')
self.assertEqual(vars[0].symbol, None)
self.assertEqual(vars[0].target, "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R_ACALD']/@minFlux")
self.assertEqual(vars[0].target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level3/version1/core'})
self.assertEqual(vars[-1].id, 'R_TPI')
self.assertEqual(vars[-1].name, 'triose-phosphate isomerase')
self.assertEqual(vars[-1].symbol, None)
self.assertEqual(vars[-1].target, "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R_TPI']/@maxFlux")
self.assertEqual(vars[-1].target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level3/version1/core'})
def test_core_time_course(self):
params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(
self.CORE_FIXTURE, ModelLanguage.SBML, UniformTimeCourseSimulation, 'KISAO_0000019')
self.assertEqual(vars[0].id, 'time')
self.assertEqual(vars[0].name, 'Time')
self.assertEqual(vars[0].symbol, Symbol.time)
self.assertEqual(vars[0].target, None)
self.assertEqual(vars[0].target_namespaces, {})
self.assertEqual(vars[-1].id, 'dynamics_species_mass')
self.assertEqual(vars[-1].name, 'Dynamics of species "mass"')
self.assertEqual(vars[-1].symbol, None)
self.assertEqual(vars[-1].target, "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='mass']")
self.assertEqual(vars[-1].target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level2/version4'})
def test_core_steady_state(self):
params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(
self.CORE_FIXTURE, ModelLanguage.SBML, SteadyStateSimulation, 'KISAO_0000019',
include_compartment_sizes_in_simulation_variables=True,
include_model_parameters_in_simulation_variables=True)
self.assertEqual(params[0].id, 'init_conc_species_Trim')
self.assertEqual(params[0].name, 'Initial concentration of species "CDC28_Clb2_Sic1_Complex"')
self.assertEqual(params[0].new_value, '0.084410675')
self.assertEqual(params[0].target, "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Trim']/@initialConcentration")
self.assertEqual(params[0].target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level2/version4'})
self.assertEqual(params[-2].id, 'value_parameter_mu')
self.assertEqual(params[-2].new_value, '0.005')
self.assertEqual(params[-1].id, 'value_parameter_flag')
self.assertEqual(params[-1].name, 'Value of parameter "flag"')
self.assertEqual(params[-1].new_value, '0')
self.assertEqual(params[-1].target, "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='flag']/@value")
self.assertEqual(params[-1].target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level2/version4'})
param = next(param for param in params if param.id == 'init_size_compartment_compartment')
self.assertEqual(param.name, 'Initial size of compartment "compartment"')
self.assertEqual(param.new_value, '1')
self.assertEqual(param.target, "/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']/@size")
self.assertEqual(param.target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level2/version4'})
self.assertNotEqual(vars[0].id, 'time')
variable = next((variable for variable in vars if variable.id == 'dynamics_species_mass'), None)
self.assertEqual(variable.name, 'Dynamics of species "mass"')
self.assertEqual(variable.symbol, None)
self.assertEqual(variable.target, "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='mass']")
self.assertEqual(variable.target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level2/version4'})
variable = next((variable for variable in vars if variable.id == 'compartment'), None)
self.assertEqual(variable, None)
variable = next(variable for variable in vars if variable.id == 'value_parameter_kswe')
self.assertEqual(variable.name, 'Value of parameter "kswe"')
self.assertEqual(variable.target, "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='kswe']/@value")
self.assertEqual(variable.target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level2/version4'})
variable = next((variable for variable in vars if variable.id == 'kswe_prime'), None)
self.assertEqual(variable, None)
def test_qual_time_course(self):
params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(
self.QUAL_FIXTURE, ModelLanguage.SBML, UniformTimeCourseSimulation, 'KISAO_0000450')
self.assertEqual(vars[0].id, 'time')
self.assertEqual(vars[0].name, 'Time')
self.assertEqual(vars[0].symbol, Symbol.time)
self.assertEqual(vars[0].target, None)
self.assertEqual(vars[0].target_namespaces, {})
self.assertEqual(vars[-1].id, 'level_species_nik')
self.assertEqual(vars[-1].name, 'Level of species "nik"')
self.assertEqual(vars[-1].symbol, None)
self.assertEqual(vars[-1].target, "/sbml:sbml/sbml:model/qual:listOfQualitativeSpecies/qual:qualitativeSpecies[@qual:id='nik']")
self.assertEqual(vars[-1].target_namespaces, {
'sbml': 'http://www.sbml.org/sbml/level3/version1/core',
'qual': 'http://www.sbml.org/sbml/level3/version1/qual/version1',
})
def test_qual_one_step(self):
params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(
self.QUAL_FIXTURE, ModelLanguage.SBML, OneStepSimulation, 'KISAO_0000450',
native_ids=True, native_data_types=True)
self.assertEqual(vars[0].id, None)
self.assertEqual(vars[0].name, None)
self.assertEqual(vars[0].symbol, Symbol.time)
self.assertEqual(vars[0].target, None)
self.assertEqual(vars[0].target_namespaces, {})
self.assertEqual(vars[-1].id, 'nik')
self.assertEqual(vars[-1].name, None)
self.assertEqual(vars[-1].symbol, None)
self.assertEqual(vars[-1].target, "/sbml:sbml/sbml:model/qual:listOfQualitativeSpecies/qual:qualitativeSpecies[@qual:id='nik']")
self.assertEqual(vars[-1].target_namespaces, {
'sbml': 'http://www.sbml.org/sbml/level3/version1/core',
'qual': 'http://www.sbml.org/sbml/level3/version1/qual/version1',
})
def test_fbc_steady_state_fba(self):
params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(
self.FBC_FIXTURE, ModelLanguage.SBML, SteadyStateSimulation, 'KISAO_0000437',
native_ids=True, native_data_types=True)
self.assertEqual(params[0].id, 'cobra_default_lb')
self.assertEqual(params[0].name, None)
self.assertEqual(params[0].target, "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='cobra_default_lb']/@value")
self.assertEqual(params[0].target_namespaces, {
'sbml': 'http://www.sbml.org/sbml/level3/version1/core',
})
self.assertEqual(params[0].new_value, -1000)
self.assertEqual(params[-1].id, 'R_EX_glc__D_e_lower_bound')
self.assertEqual(params[-1].name, None)
self.assertEqual(params[-1].target,
"/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='R_EX_glc__D_e_lower_bound']/@value")
self.assertEqual(params[-1].target_namespaces, {
'sbml': 'http://www.sbml.org/sbml/level3/version1/core',
})
self.assertEqual(params[-1].new_value, -10)
self.assertEqual(vars[0].id, 'obj')
self.assertEqual(vars[0].name, None)
self.assertEqual(vars[0].symbol, None)
self.assertEqual(vars[0].target, "/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='obj']/@value")
self.assertEqual(vars[0].target_namespaces, {
'sbml': 'http://www.sbml.org/sbml/level3/version1/core',
'fbc': 'http://www.sbml.org/sbml/level3/version1/fbc/version2',
})
self.assertEqual(vars[-1].id, 'R_TPI')
self.assertEqual(vars[-1].name, 'triose-phosphate isomerase')
self.assertEqual(vars[-1].symbol, None)
self.assertEqual(vars[-1].target, "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R_TPI']/@flux")
self.assertEqual(vars[-1].target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level3/version1/core'})
def test_core_time_course_l3(self):
params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(
self.CORE_FIXTURE_L3, ModelLanguage.SBML, UniformTimeCourseSimulation, 'KISAO_0000019',
)
def test_core_one_step(self):
params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(self.CORE_FIXTURE, ModelLanguage.SBML, OneStepSimulation, 'KISAO_0000019',
native_ids=True, native_data_types=True)
def test_fbc_steady_state_fba(self):
params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(
self.FBC_FIXTURE, ModelLanguage.SBML, SteadyStateSimulation, 'KISAO_0000437')
self.assertEqual(params[0].id, 'value_parameter_cobra_default_lb')
self.assertEqual(params[0].name, 'Value of parameter "cobra_default_lb"')
self.assertEqual(params[0].target, "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='cobra_default_lb']/@value")
self.assertEqual(params[0].target_namespaces, {
'sbml': 'http://www.sbml.org/sbml/level3/version1/core',
})
self.assertEqual(params[0].new_value, '-1000')
self.assertEqual(params[-1].id, 'value_parameter_R_EX_glc__D_e_lower_bound')
self.assertEqual(params[-1].name, 'Value of parameter "R_EX_glc__D_e_lower_bound"')
self.assertEqual(params[-1].target,
"/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='R_EX_glc__D_e_lower_bound']/@value")
self.assertEqual(params[-1].target_namespaces, {
'sbml': 'http://www.sbml.org/sbml/level3/version1/core',
})
self.assertEqual(params[-1].new_value, '-10')
self.assertEqual(vars[0].id, 'value_objective_obj')
self.assertEqual(vars[0].name, 'Value of objective "obj"')
self.assertEqual(vars[0].symbol, None)
self.assertEqual(vars[0].target, "/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='obj']/@value")
self.assertEqual(vars[0].target_namespaces, {
'sbml': 'http://www.sbml.org/sbml/level3/version1/core',
'fbc': 'http://www.sbml.org/sbml/level3/version1/fbc/version2',
})
self.assertEqual(vars[-1].id, 'flux_reaction_R_TPI')
self.assertEqual(vars[-1].name, 'Flux of reaction "triose-phosphate isomerase"')
self.assertEqual(vars[-1].symbol, None)
self.assertEqual(vars[-1].target, "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R_TPI']/@flux")
self.assertEqual(vars[-1].target_namespaces, {'sbml': 'http://www.sbml.org/sbml/level3/version1/core'})
params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(
self.FBC_FIXTURE, ModelLanguage.SBML, SteadyStateSimulation, 'KISAO_0000437',
change_level=Task,
native_ids=True, native_data_types=True)
self.assertNotIn('value_parameter_R_EX_glc__D_e_lower_bound', [param.id for param in params])
self.assertEqual(params[0].id, 'R_ACALD')
self.assertEqual(params[1].id, 'R_ACALD')
self.assertEqual(params[0].name, 'acetaldehyde dehydrogenase (acetylating)')
self.assertEqual(params[1].name, 'acetaldehyde dehydrogenase (acetylating)')
self.assertEqual(params[0].target, "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R_ACALD']/@fbc:lowerFluxBound")
self.assertEqual(params[1].target, "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R_ACALD']/@fbc:upperFluxBound")
target_namespaces = {
'sbml': 'http://www.sbml.org/sbml/level3/version1/core',
'fbc': 'http://www.sbml.org/sbml/level3/version1/fbc/version2',
}
self.assertEqual(params[0].target_namespaces, target_namespaces)
self.assertEqual(params[1].target_namespaces, target_namespaces)
self.assertEqual(params[0].new_value, -1000)
self.assertEqual(params[1].new_value, 1000)
params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(
self.FBC_FIXTURE, ModelLanguage.SBML, SteadyStateSimulation, 'KISAO_0000437',
change_level=Task,
native_ids=False, native_data_types=False)
self.assertNotIn('value_parameter_R_EX_glc__D_e_lower_bound', [param.id for param in params])
self.assertEqual(params[0].id, 'lower_bound_reaction_R_ACALD')
self.assertEqual(params[1].id, 'upper_bound_reaction_R_ACALD')
self.assertEqual(params[0].name, 'Lower bound of reaction "acetaldehyde dehydrogenase (acetylating)"')
self.assertEqual(params[1].name, 'Upper bound of reaction "acetaldehyde dehydrogenase (acetylating)"')
self.assertEqual(params[0].target, "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R_ACALD']/@fbc:lowerFluxBound")
self.assertEqual(params[1].target, "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R_ACALD']/@fbc:upperFluxBound")
target_namespaces = {
'sbml': 'http://www.sbml.org/sbml/level3/version1/core',
'fbc': 'http://www.sbml.org/sbml/level3/version1/fbc/version2',
}
self.assertEqual(params[0].target_namespaces, target_namespaces)
self.assertEqual(params[1].target_namespaces, target_namespaces)
self.assertEqual(params[0].new_value, '-1000.0')
self.assertEqual(params[1].new_value, '1000.0')
with self.assertRaisesRegex(NotImplementedError, 'can only made at the SED document or task level'):
get_parameters_variables_outputs_for_simulation(
self.FBC_FIXTURE, ModelLanguage.SBML, SteadyStateSimulation, 'KISAO_0000437',
change_level=None)
def test_fbc_time_course(self):
with self.assertRaises(NotImplementedError):
get_parameters_variables_outputs_for_simulation(self.FBC_FIXTURE, ModelLanguage.SBML, UniformTimeCourseSimulation, None)
def test_fbc_one_step(self):
with self.assertRaises(NotImplementedError):
get_parameters_variables_outputs_for_simulation(self.FBC_FIXTURE, ModelLanguage.SBML, OneStepSimulation, None)
