Source code for cobra.test.test_manipulation.test_validate

"""Test functionalities of cobra component validation functions."""

import pytest

from cobra.core import Metabolite, Model, Reaction
from cobra.manipulation import check_mass_balance, check_metabolite_compartment_formula

[docs]def test_validate_mass_balance(model: Model) -> None: """Test reaction mass balance validation.""" assert len(check_mass_balance(model)) == 0 # if we remove the SBO term which marks the reaction as # mass balanced, then the reaction should be detected as # no longer mass balanced EX_rxn = model.reactions.query(lambda r: r.boundary)[0] EX_rxn.annotation.pop("sbo") balance = check_mass_balance(model) assert len(balance) == 1 assert EX_rxn in balance m1 = Metabolite("m1", formula="()") r1 = Reaction("r1") r1.add_metabolites({m1: 1}) with pytest.raises(ValueError), pytest.warns(UserWarning): r1.check_mass_balance()
[docs]def test_validate_formula_compartment(model: Model) -> None: """Test metabolite formulae validation.""" model.metabolites[1].formula = "(a*.bcde)" errors = check_metabolite_compartment_formula(model) assert len(errors) == 1