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"]