def test_rate_law_expressions_with_multiple_model_types(self):
fixture_filename = os.path.join(os.path.dirname(__file__), 'fixtures', 'example-model.xlsx')
model = Reader().run(fixture_filename)[Model][0]
rate_laws = model.get_rate_laws(id='AK_AMP-backward')
self.assertEqual(len(rate_laws), 1)
rate_law = rate_laws[0]
self.assertEqual(len(rate_law.expression.species), 1)
self.assertEqual(rate_law.expression.species[0].id, 'Adk_Protein[c]')
self.assertEqual(len(rate_law.expression.parameters), 1)
self.assertEqual(rate_law.expression.parameters[0].id, 'k_cat_rev_ak')
self.assertEqual(len(rate_law.expression.observables), 1)
self.assertEqual(rate_law.expression.observables[0].id, 'AXP_c')
self.assertEqual(len(rate_law.expression.functions), 1)
self.assertEqual(rate_law.expression.functions[0].id, 'func_1')
class TestInitialDynamicComponentsComprehensively(unittest.TestCase):
def setUp(self):
self.model_file = os.path.join(os.path.dirname(__file__), 'fixtures',
'test_dynamic_expressions.xlsx')
self.model = Reader().run(self.model_file)[Model][0]
de_simulation_config = SimulationConfig(time_max=10)
wc_sim_config = WCSimulationConfig(de_simulation_config)
multialgorithm_simulation = MultialgorithmSimulation(
self.model, wc_sim_config)
_, self.dynamic_model = multialgorithm_simulation.build_simulation()
def test(self):
# test all DynamicComponents that implement eval()
### Test DynamicExpressions ###
# each one is tested using each of the objects it uses in some instance in self.model_file
# DynamicFunction
for id, dynamic_function in self.dynamic_model.dynamic_functions.items(
):
expected_value = float(self.model.get_functions(id=id)[0].comments)
numpy.testing.assert_approx_equal(dynamic_function.eval(0),
expected_value)
# test eval_dynamic_functions()
for func_id, func_val in self.dynamic_model.eval_dynamic_functions(
0).items():
expected_value = float(
self.model.get_functions(id=func_id)[0].comments)
numpy.testing.assert_approx_equal(func_val, expected_value)
a_func_id = list(self.dynamic_model.dynamic_functions)[0]
for func_id, func_val in \
self.dynamic_model.eval_dynamic_functions(0, functions_to_eval=[a_func_id]).items():
expected_value = float(
self.model.get_functions(id=func_id)[0].comments)
numpy.testing.assert_approx_equal(func_val, expected_value)
# DynamicStopCondition
for id, dynamic_stop_condition in self.dynamic_model.dynamic_stop_conditions.items(
):
expected_val_in_comment = self.model.get_stop_conditions(
id=id)[0].comments
if expected_val_in_comment == 'True':
expected_value = True
elif expected_val_in_comment == 'False':
expected_value = False
self.assertEqual(expected_value, dynamic_stop_condition.eval(0))
# DynamicObservable
for id, dynamic_observable in self.dynamic_model.dynamic_observables.items(
):
expected_value = float(
self.model.get_observables(id=id)[0].comments)
numpy.testing.assert_approx_equal(dynamic_observable.eval(0),
expected_value)
# test eval_dynamic_observables()
for obs_id, obs_val in self.dynamic_model.eval_dynamic_observables(
0).items():
expected_value = float(
self.model.get_observables(id=obs_id)[0].comments)
numpy.testing.assert_approx_equal(obs_val, expected_value)
an_obs_id = list(self.dynamic_model.dynamic_observables)[0]
for obs_id, obs_val in \
self.dynamic_model.eval_dynamic_observables(0, observables_to_eval=[an_obs_id]).items():
expected_value = float(
self.model.get_observables(id=obs_id)[0].comments)
numpy.testing.assert_approx_equal(obs_val, expected_value)
# DynamicRateLaw
for id, dynamic_rate_law in self.dynamic_model.dynamic_rate_laws.items(
):
expected_value = float(self.model.get_rate_laws(id=id)[0].comments)
numpy.testing.assert_approx_equal(dynamic_rate_law.eval(0),
expected_value)
### Test DynamicComponents ###
# DynamicCompartment
for id, dynamic_compartment in self.dynamic_model.dynamic_compartments.items(
):
expected_value = float(
self.model.get_compartments(id=id)[0].comments)
numpy.testing.assert_approx_equal(dynamic_compartment.eval(0),
expected_value)
# DynamicParameter
for id, dynamic_parameter in self.dynamic_model.dynamic_parameters.items(
):
expected_value = float(
self.model.get_parameters(id=id)[0].comments)
numpy.testing.assert_approx_equal(dynamic_parameter.eval(0),
expected_value)
# DynamicSpecies
for id, dynamic_species in self.dynamic_model.dynamic_species.items():
expected_value = float(self.model.get_species(id=id)[0].comments)
numpy.testing.assert_approx_equal(dynamic_species.eval(0),
expected_value)
# FIX FOR DE-SIM CHANGES: need to make a few dynamic models to test all branches of get_stop_condition()
# a dynamic model with no stop concitions
# a dynamic model with stop condidtions that all evaluate false
# a dynamic model with at least one stop condidtions that evaluates true
def test_get_stop_condition(self):
all_stop_conditions = self.dynamic_model.get_stop_condition()
self.assertTrue(callable(all_stop_conditions))
self.assertTrue(all_stop_conditions(0))
