def test_missing_flux_bounds2(data_directory): sbml_path = join(data_directory, "annotation.xml") with open(sbml_path, "r") as f_in: # missing flux bounds are set to [-INF, INF] model, errors = validate_sbml_model(f_in, set_missing_bounds=False) r1 = model.reactions.R1 assert r1.lower_bound == config.lower_bound assert r1.upper_bound == config.upper_bound
def test_validate(data_directory): """Test the validation code. """ sbml_path = join(data_directory, "mini_fbc2.xml") with open(sbml_path, "r") as f_in: model1, errors = validate_sbml_model(f_in, check_modeling_practice=True) assert model1 assert errors assert len(errors["SBML_WARNING"]) == 23
def test_validate(data_directory): """Test the validation code. """ sbml_path = join(data_directory, "mini_fbc2.xml") with open(sbml_path, "r") as f_in: model1, errors = validate_sbml_model(f_in, check_modeling_practice=True) assert model1 assert errors assert len(errors["SBML_WARNING"]) == 23
def test_missing_flux_bounds2(data_directory): sbml_path = join(data_directory, "annotation.xml") with open(sbml_path, "r") as f_in: # missing flux bounds are set to [-INF, INF] model, errors = validate_sbml_model(f_in, set_missing_bounds=False) r1 = model.reactions.R1 assert r1.lower_bound == -float("Inf") assert r1.upper_bound == float("Inf")
def test_missing_flux_bounds1(data_directory): sbml_path = join(data_directory, "annotation.xml") with open(sbml_path, "r") as f_in: # missing flux bounds are set to cobra.configuration.bounds model, errors = validate_sbml_model(f_in, set_missing_bounds=True) r1 = model.reactions.R1 assert r1.lower_bound == config.lower_bound assert r1.upper_bound == config.upper_bound
def test_validation_warnings(data_directory): """Test the validation warnings. """ sbml_path = join(data_directory, "validation.xml") with open(sbml_path, "r") as f_in: model1, errors = validate_sbml_model(f_in, check_modeling_practice=True) assert model1 assert errors assert len(errors["COBRA_WARNING"]) == 3 assert "No objective in listOfObjectives" in errors["COBRA_WARNING"]
def test_validation_warnings(data_directory): """Test the validation warnings. """ sbml_path = join(data_directory, "validation.xml") with open(sbml_path, "r") as f_in: model1, errors = validate_sbml_model(f_in, check_modeling_practice=True) assert model1 assert errors assert len(errors["COBRA_WARNING"]) == 3 assert "No objective in listOfObjectives" in errors["COBRA_WARNING"]