def test_check_crn_validity(self):
from biocrnpyler import ChemicalReactionNetwork
from biocrnpyler import Species
from biocrnpyler import Reaction
s1 = Species(name='test_species1')
s2 = Species(name='test_species2')
species_list = [s1, s2]
rx1 = Reaction(inputs=[s1], outputs=[s2], k=0.1)
rxn_list = [rx1]
checked_species, checked_reactions = ChemicalReactionNetwork.check_crn_validity(
reactions=rxn_list, species=species_list)
self.assertEqual(species_list, checked_species)
self.assertEqual(rxn_list, checked_reactions)
species_list_with_none = species_list.copy()
species_list_with_none.append(None)
with self.assertRaises(ValueError):
ChemicalReactionNetwork.check_crn_validity(
reactions=rxn_list, species=species_list_with_none)
rxn_list_with_none = rxn_list.copy()
rxn_list_with_none.append(None)
with self.assertRaises(ValueError):
ChemicalReactionNetwork.check_crn_validity(
reactions=rxn_list_with_none, species=species_list)
s3 = Species(name='test_species3')
s4 = Species(name='test_species4')
rxn2 = Reaction(inputs=[s1], outputs=[s3], k=0.1)
with self.assertWarns(Warning):
ChemicalReactionNetwork.check_crn_validity(reactions=[rxn2],
species=species_list,
warnings=True)
rxn3 = Reaction(inputs=[s4], outputs=[s2], k=0.1)
with self.assertWarns(Warning):
ChemicalReactionNetwork.check_crn_validity(reactions=[rxn3],
species=species_list,
warnings=True)
def test_check_crn_validity(self):
checked_reactions, checked_species = ChemicalReactionNetwork.check_crn_validity(
reactions=self.rxn_list, species=self.species_list)
# test that the returned species list is the same as the species list supplied
self.assertEqual(self.species_list, checked_species)
# test that the returned reaction list is the same as the reaction list supplied
self.assertEqual(self.rxn_list, checked_reactions)
species_list_with_none = self.species_list.copy()
# injecting a None to the species list
species_list_with_none.append(None)
# test whether a non-species object is detected and Value error has been raised
# A non-species object was used as a species: [test_species1, test_species2, None]!"'
# A non-species object was used as a species: [test_species1, test_species2, None]!"
with self.assertRaisesRegex(
ValueError, "A non-species object was used as a species!"):
ChemicalReactionNetwork.check_crn_validity(
reactions=self.rxn_list, species=species_list_with_none)
rxn_list_with_none = self.rxn_list.copy()
# injecting a None to the reaction list
rxn_list_with_none.append(None)
# test whether a non-reaction object is detected and Value Error has been raised
with self.assertRaisesRegex(
ValueError, 'A non-reaction object was used as a reaction!'):
ChemicalReactionNetwork.check_crn_validity(
reactions=rxn_list_with_none, species=self.species_list)
rxn2 = Reaction.from_massaction(inputs=[self.s1],
outputs=[self.s3],
k_forward=0.1)
# test warning raised if a species (in the reaction outputs) is detected which is not part of the species list
with self.assertWarnsRegex(
Warning, f'are not part of any reactions in the CRN'):
ChemicalReactionNetwork.check_crn_validity(
reactions=[rxn2],
species=self.species_list,
show_warnings=True)
rxn3 = Reaction.from_massaction(inputs=[self.s4],
outputs=[self.s2],
k_forward=0.1)
# test warning raised if a species (in the reaction inputs) is detected which is not part of the species list
with self.assertWarnsRegex(
Warning, f'are not part of any reactions in the CRN'):
ChemicalReactionNetwork.check_crn_validity(
reactions=[rxn3],
species=self.species_list,
show_warnings=True)
# test warning if reaction has unlisted species
rxn4 = Reaction.from_massaction(inputs=[self.s4, self.s3],
outputs=[self.s2],
k_forward=0.1)
with self.assertWarnsRegex(
Warning,
f'are not listed in the Species list, but part of the reactions'
):
ChemicalReactionNetwork.check_crn_validity(
reactions=[rxn4],
species=[self.s4, self.s2],
show_warnings=True)
# test duplicate reactions are both added
rxn_list = [self.rx1, self.rx1]
CRN = ChemicalReactionNetwork(species=[self.s1, self.s2],
reactions=rxn_list)
self.assertTrue(CRN.reactions.count(self.rx1) == 2)
with self.assertWarnsRegex(Warning,
'may be duplicated in CRN definitions'):
ChemicalReactionNetwork.check_crn_validity(
reactions=rxn_list,
species=self.species_list,
show_warnings=True)
# test warning suppression
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
ChemicalReactionNetwork.check_crn_validity(
reactions=rxn_list,
species=self.species_list,
show_warnings=False)
assert not w
def test_check_crn_validity(self):
checked_species, checked_reactions = ChemicalReactionNetwork.check_crn_validity(
reactions=self.rxn_list, species=self.species_list)
# test that the returned species list is the same as the species list supplied
self.assertEqual(self.species_list, checked_species)
# test that the returned reaction list is the same as the reaction list supplied
self.assertEqual(self.rxn_list, checked_reactions)
species_list_with_none = self.species_list.copy()
# injecting a None to the species list
species_list_with_none.append(None)
# test whether a non-species object is detected and Value error has been raised
# A non-species object was used as a species: [test_species1, test_species2, None]!"'
# A non-species object was used as a species: [test_species1, test_species2, None]!"
with self.assertRaisesRegexp(
ValueError, "A non-species object was used as a species!"):
ChemicalReactionNetwork.check_crn_validity(
reactions=self.rxn_list, species=species_list_with_none)
rxn_list_with_none = self.rxn_list.copy()
# injecting a None to the reaction list
rxn_list_with_none.append(None)
# test whether a non-reaction object is detected and Value Error has been raised
with self.assertRaisesRegexp(
ValueError, 'A non-reaction object was used as a reaction!'):
ChemicalReactionNetwork.check_crn_validity(
reactions=rxn_list_with_none, species=self.species_list)
rxn2 = Reaction(inputs=[self.s1], outputs=[self.s3], k=0.1)
# test warning raised if a species (in the reaction outputs) is detected which is not part of the species list
with self.assertWarnsRegex(
Warning,
f'contains a species {self.s3.name} which is not in the CRN'):
ChemicalReactionNetwork.check_crn_validity(
reactions=[rxn2], species=self.species_list, warnings=True)
rxn3 = Reaction(inputs=[self.s4], outputs=[self.s2], k=0.1)
# test warning raised if a species (in the reaction inputs) is detected which is not part of the species list
with self.assertWarnsRegex(
Warning,
f'contains a species {self.s4.name} which is not in the CRN'):
ChemicalReactionNetwork.check_crn_validity(
reactions=[rxn3], species=self.species_list, warnings=True)
# test duplicate reactions
rxn_list = [self.rx1, self.rx1]
with self.assertWarnsRegex(Warning,
'may be duplicated in CRN definitions'):
ChemicalReactionNetwork.check_crn_validity(
reactions=rxn_list, species=self.species_list, warnings=True)