def test_get_all_species_containing(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]
crn = ChemicalReactionNetwork(species=species_list, reactions=rxn_list)
s3 = Species(name='test_species3')
with self.assertRaises(ValueError):
crn.get_all_species_containing(species=species_list)
rtn_species_list = crn.get_all_species_containing(species=s3)
self.assertEqual(rtn_species_list, [])
rtn_species_list = crn.get_all_species_containing(species=s1)
self.assertEqual(rtn_species_list, [s1])
rtn_species_list = crn.get_all_species_containing(
species=s1, return_as_strings=True)
self.assertEqual(rtn_species_list, [repr(s1)])
class TestChemicalReactionNetwork(TestCase):
def setUp(self) -> None:
"""this method gets executed before every test"""
self.s1 = Species(name='test_species1')
self.s2 = Species(name='test_species2')
self.s3 = Species(name='test_species3')
self.s4 = Species(name='test_species4')
self.s_old = Species("s_old")
self.s_new = Species("s_new")
self.species_list = [self.s1, self.s2]
# creating a valid reaction two species
self.rx1 = Reaction.from_massaction(inputs=[self.s1],
outputs=[self.s2],
k_forward=0.1)
self.rxn_list = [self.rx1]
self.crn = ChemicalReactionNetwork(species=self.species_list,
reactions=self.rxn_list)
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_species_protection(self):
#tests that Species cannot be changed once they are in a CRN
S = Species("S")
S2 = Species("S2")
CRN = ChemicalReactionNetwork([S], [])
#Internal species copied correctly to return
assert S in CRN.species
#assert species are copied
assert not S is CRN._species[0]
#Returned list does not effect internal species
CRN.species[0] = S2
assert S2 not in CRN.species
#add species effects internal species list
CRN.add_species(S2)
assert S2 in CRN.species
#assert correct copying
assert S2 is not CRN._species[1]
with self.assertRaisesRegex(
AttributeError,
"The species in a CRN cannot be removed or modified*"):
CRN.species = []
#Test bypassing species protection
CRN = ChemicalReactionNetwork([], [])
CRN.add_species([S], copy_species=False)
assert S is CRN._species[0]
def test_reaction_protection(self):
#tests that Reactions cannot be changed once they are in a CRN
S = Species("S")
S2 = Species("S2")
R = Reaction.from_massaction([S], [S2], k_forward=1.0)
R2 = Reaction.from_massaction([S2], [S], k_forward=1.0)
CRN = ChemicalReactionNetwork([S, S2], [R])
#Internal reactions copied correctly to return
assert R in CRN.reactions
assert not R is CRN._reactions[0]
#Returned list does not effect internal reactions
CRN.reactions[0] = R2
assert R2 not in CRN.reactions
#add reactions effects internal reaction list
CRN.add_reactions(R2)
assert R2 in CRN.reactions
assert not R2 is CRN._reactions[1]
with self.assertRaisesRegex(
AttributeError,
"The reactions in a CRN cannot be removed or modified*"):
CRN.reactions = []
#test bypassing reaction protection
CRN = ChemicalReactionNetwork([], [])
CRN.add_reactions([R], copy_reactions=False)
assert R is CRN._reactions[0]
assert S in CRN.species
#test bypassing reaction protection
CRN = ChemicalReactionNetwork([], [])
CRN.add_reactions([R], add_species=False)
assert not S in CRN.species
def test_initial_condition_vector(self):
# no initial value is supplied for s2
init_cond = {self.s1: 5, self.s3: 10}
x0 = self.crn.initial_condition_vector(init_cond_dict=init_cond)
# test that value for s3 is not in the initial value list because s3 is not part of any reaction
not_in_the_list = False
for key, value in init_cond.items():
if value not in x0 and key == self.s3:
not_in_the_list = True
self.assertTrue(not_in_the_list)
def test_get_all_species_containing(self):
# test that the species arument must be Species object
with self.assertRaisesRegex(
ValueError,
'species argument must be an instance of Species!'):
self.crn.get_all_species_containing(species=self.species_list)
# s3 is not part of the CRN
rtn_species_list = self.crn.get_all_species_containing(species=self.s3)
# test that empty list is returned
self.assertEqual(rtn_species_list, [])
# test that s1 is returned only once
rtn_species_list = self.crn.get_all_species_containing(species=self.s1)
self.assertEqual(rtn_species_list, [self.s1])
# test that s1 is returned only once as a string
rtn_species_list = self.crn.get_all_species_containing(
species=self.s1, return_as_strings=True)
self.assertEqual(rtn_species_list, [repr(self.s1)])
def test_replace_species_in_Species(self):
#Test replace species in a Species
self.assertTrue(
self.s1.replace_species(self.s2, self.s_new) == self.s1)
self.assertTrue(
self.s_old.replace_species(self.s_old, self.s_new) == self.s_new)
def test_replace_Species_in_ComplexSpecies(self):
c1 = Complex([self.s1, self.s_old])
c2 = Complex([self.s1, c1])
self.assertTrue(c1.replace_species(self.s2, self.s_new) == c1)
self.assertTrue(
c1.replace_species(self.s_old, self.s_new) == Complex(
[self.s1, self.s_new]))
self.assertTrue(c2 == Complex([self.s1, c1]))
self.assertTrue(
c2.replace_species(self.s_new, self.s_old) == Complex(
[self.s1, Complex([self.s1, self.s_old])]))
def test_replace_Species_in_OrderedComplexSpecies(self):
oc1 = Complex([self.s1, self.s_old], ordered=True)
self.assertTrue(
oc1.replace_species(self.s_old, self.s_new) == Complex(
[self.s1, self.s_new], ordered=True))
def test_replace_species_in_Reaction(self):
c1 = Complex([self.s1, self.s_old])
c2 = Complex([self.s1, self.s_new])
r1 = Reaction.from_massaction([self.s1, self.s_old], [c1], k_forward=1)
self.assertTrue(
r1.replace_species(self.s_old, self.s_new) ==
Reaction.from_massaction([self.s1, self.s_new], [c2], k_forward=1))
def test_replace_species_with_a_non_massaction_reaction(self):
c1 = Complex([self.s1, self.s_old])
prop_hill_old = ProportionalHillPositive(k=1.,
s1=self.s1,
K=10,
d=self.s_old,
n=2)
r1 = Reaction([self.s1, self.s_old], [c1],
propensity_type=prop_hill_old)
prop_hill_new = ProportionalHillPositive(k=1.,
s1=self.s1,
K=10,
d=self.s_new,
n=2)
r1_new = Reaction([self.s1, self.s_new],
[c1.replace_species(self.s_old, self.s_new)],
propensity_type=prop_hill_new)
self.assertTrue(r1.replace_species(self.s_old, self.s_new) == r1_new)
def test_replace_in_a_chemical_reaction_network(self):
c1 = Complex([self.s1, self.s_old])
c2 = Complex([self.s1, c1])
species = [self.s1, self.s_old, c1, c2]
r1 = Reaction.from_massaction([self.s1, self.s_old], [c1], k_forward=1)
crn = ChemicalReactionNetwork(species=species, reactions=[r1])
new_crn = crn.replace_species(self.s_old, self.s_new)
self.assertTrue(self.s1 in new_crn.species)
self.assertFalse(self.s_old in new_crn.species)
self.assertTrue(self.s_new in new_crn.species)
self.assertFalse(c1 in new_crn.species)
self.assertFalse(c2 in new_crn.species)
c1_new = Complex([self.s1, self.s_new])
c2_new = Complex([self.s1, c1_new])
self.assertTrue(c1_new in new_crn.species)
self.assertTrue(c2_new in new_crn.species)
r1_new = Reaction.from_massaction([self.s1, self.s_new], [c1_new],
k_forward=1)
self.assertFalse(r1 in new_crn.reactions)
self.assertTrue(r1_new in new_crn.reactions)
def test_write_sbml_file(self):
s1, s2 = Species("S1"), Species("S2")
rx1 = Reaction.from_massaction(inputs=[s1],
outputs=[s2],
k_forward=0.1)
crn = ChemicalReactionNetwork(species=[s1, s2], reactions=[rx1])
model_id = 'test_model'
document, _ = crn.generate_sbml_model(model_id=model_id)
sbml_string = libsbml.writeSBMLToString(document)
file_name = 'test_sbml.xml'
with patch("builtins.open", new=mock_open()) as _file:
crn.write_sbml_file(file_name, model_id=model_id)
_file.assert_called_once_with(file_name, 'w')
_file().write.assert_called_once_with(sbml_string)
class TestChemicalReactionNetwork(TestCase):
def setUp(self) -> None:
"""this method gets executed before every test"""
self.s1 = Species(name='test_species1')
self.s2 = Species(name='test_species2')
self.s3 = Species(name='test_species3')
self.s4 = Species(name='test_species4')
self.species_list = [self.s1, self.s2]
# creating a valid reaction two species
self.rx1 = Reaction(inputs=[self.s1], outputs=[self.s2], k=0.1)
self.rxn_list = [self.rx1]
self.crn = ChemicalReactionNetwork(species=self.species_list,
reactions=self.rxn_list)
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)
def test_species_index(self):
# TODO add test if we actually use this function
pass
def test_initial_condition_vector(self):
# no initial value is supplied for s2
init_cond = {self.s1: 5, self.s3: 10}
x0 = self.crn.initial_condition_vector(init_cond_dict=init_cond)
# test that value for s3 is not in the initial value list because s3 is not part of any reaction
not_in_the_list = False
for key, value in init_cond.items():
if value not in x0 and key == self.s3:
not_in_the_list = True
self.assertTrue(not_in_the_list)
def test_get_all_species_containing(self):
# test that the species arument must be Species object
with self.assertRaisesRegexp(
ValueError,
'species argument must be an instance of Species!'):
self.crn.get_all_species_containing(species=self.species_list)
# s3 is not part of the CRN
rtn_species_list = self.crn.get_all_species_containing(species=self.s3)
# test that empty list is returned
self.assertEqual(rtn_species_list, [])
# test that s1 is returned only once
rtn_species_list = self.crn.get_all_species_containing(species=self.s1)
self.assertEqual(rtn_species_list, [self.s1])
# test that s1 is returned only once as a string
rtn_species_list = self.crn.get_all_species_containing(
species=self.s1, return_as_strings=True)
self.assertEqual(rtn_species_list, [repr(self.s1)])
def test_generate_sbml_model(self):
# generate an sbml model
document, model = self.crn.generate_sbml_model()
# all species from the CRN are accounted for
self.assertEqual(len(model.getListOfSpecies()), len(self.crn.species))
# all reactions from the CRN are accounted for
self.assertEqual(len(model.getListOfReactions()),
len(self.crn.reactions))
# test a reversible reaction
rx1 = Reaction(inputs=[self.s1], outputs=[self.s2], k=0.1, k_rev=0.1)
rxn_list = [rx1]
crn = ChemicalReactionNetwork(species=self.species_list,
reactions=rxn_list)
# generate an sbml model
document, model = crn.generate_sbml_model()
# all species from the CRN are accounted for
self.assertEqual(len(model.getListOfSpecies()), len(crn.species))
# all reactions from the CRN are accounted for
# the sbml represents a reverisble reaction with to separate reactions
self.assertEqual(len(model.getListOfReactions()),
2 * len(crn.reactions))
def test_write_sbml_file(self):
document, _ = self.crn.generate_sbml_model()
sbml_string = libsbml.writeSBMLToString(document)
file_name = 'test_sbml.xml'
with patch("builtins.open", new=mock_open()) as _file:
self.crn.write_sbml_file(file_name)
_file.assert_called_once_with(file_name, 'w')
_file().write.assert_called_once_with(sbml_string)