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_write_sbml_file(self):
import libsbml
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)
document, _ = crn.generate_sbml_model()
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)
_file.assert_called_once_with(file_name, 'w')
_file().write.assert_called_once_with(sbml_string)
def test_bioscrape_import_simulate_via_sbml():
from biocrnpyler import ChemicalReactionNetwork, Species
try:
import numpy as np
X = Species("X")
CRN = ChemicalReactionNetwork(species=[X], reactions=[])
with pytest.warns(None) as record:
sim_result, bioscrape_model = CRN.simulate_with_bioscrape_via_sbml(
timepoints=np.linspace(0, 10, 100),
initial_condition_dict={str(X): 1},
return_model=True)
#In the case bioscrape is not imported
if sim_result is None and bioscrape_model is None:
# only one warning was triggered
assert len(record) == 1
# check the warning message
assert str(record[0].message
) == "bioscrape was not found, please install bioscrape"
#In the case bioscrape is imported
else:
assert str(X) in sim_result
assert bioscrape_model is not None
except ModuleNotFoundError:
print('test skipped')
def test_initial_condition_vector(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')
init_cond = {s1: 5, s3: 10}
x0 = crn.initial_condition_vector(init_cond_dict=init_cond)
not_in_the_list = False
for key, value in init_cond.items():
if value not in x0 and key == s3:
not_in_the_list = True
self.assertTrue(not_in_the_list)
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)])
def test_initial_condition_in_crn():
S = Species("S")
S2 = Species("S2")
S3 = Species("S3")
CRN = ChemicalReactionNetwork(species=[S, S2, S3], reactions=[])
#No Initial Concentration Dict
assert S not in CRN.initial_concentration_dict
#test setter
CRN.initial_concentration_dict = {S: 10, S2: 10}
assert S in CRN.initial_concentration_dict
assert CRN.initial_concentration_dict[S] == 10
#Test setter overwriting
CRN.initial_concentration_dict = {S: 11, S3: 10}
assert S2 in CRN.initial_concentration_dict
assert CRN.initial_concentration_dict[S] == 11
assert CRN.initial_concentration_dict[S2] == 10
assert CRN.initial_concentration_dict[S3] == 10
#Test setter reset
CRN.initial_concentration_dict = None
assert S not in CRN.initial_concentration_dict
assert S2 not in CRN.initial_concentration_dict
assert S3 not in CRN.initial_concentration_dict
def test_compile_crn(self):
from biocrnpyler import ChemicalReactionNetwork
from biocrnpyler import Species
from biocrnpyler import Reaction
from biocrnpyler import Mixture
a = Species(name='a')
b = Species(name='b')
species_list = [a, b]
def mock_update_reactions():
rxn = Reaction(inputs=[a], outputs=[b], k=0.1)
return [rxn]
rxn = Reaction(inputs=[a], outputs=[b], k=0.1)
CRN = ChemicalReactionNetwork(species_list, [rxn])
mixture = Mixture(species=species_list)
mixture.update_reactions = mock_update_reactions
crn_from_mixture = mixture.compile_crn()
self.assertEqual(CRN.species, crn_from_mixture.species)
self.assertEqual(CRN.reactions, crn_from_mixture.reactions)
def test_compile_crn(self):
a = Species(name='a')
b = Species(name='b')
species_list = [a, b]
rxn = Reaction.from_massaction(inputs=[a], outputs=[b], k_forward=0.1)
CRN = ChemicalReactionNetwork(species_list, [rxn])
# create a component
component = Component("comp")
# creating a mock update function to decouple the update process from the rest of the code
def mock_update_reactions():
rxn = Reaction.from_massaction(inputs=[a], outputs=[b], k_forward=0.1)
return [rxn]
def mock_update_species():
return [a, b]
component.update_species = mock_update_species
component.update_reactions = mock_update_reactions
mixture = Mixture(components=[component])
crn_from_mixture = mixture.compile_crn()
# test that the mixture has the same species as the manually build CRN object
self.assertEqual(set(CRN.species), set(crn_from_mixture.species))
# test that the mixture has the same reactions as the manually build CRN object
self.assertEqual(CRN.reactions, crn_from_mixture.reactions)
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_libroadrunner_import():
from biocrnpyler import ChemicalReactionNetwork
CRN = ChemicalReactionNetwork(species=[], reactions=[])
try:
import roadrunner
except ModuleNotFoundError:
# libroadrunner is not installed, let's check if it triggers a warning inside simulate_with_roadrunner()
with pytest.warns(UserWarning, match='libroadrunner was not found, please install libroadrunner'):
CRN.simulate_with_roadrunner(timepoints=list(range(0,10)))
else:
# no exception was triggered, we can simulate the CRN with roadrunner
sim_results = CRN.simulate_with_roadrunner(timepoints=list(range(0,10)))
assert sim_results is not None
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_compile_crn_directives(self):
a = Species(name='a')
b = Species(name='b')
species_list = [a, b]
rxn = Reaction.from_massaction(inputs=[a], outputs=[b], k_forward=0.1)
CRN = ChemicalReactionNetwork(species_list, [rxn])
# create a component
component = Component("comp")
# creating a mock update function to decouple the update process from the rest of the code
def mock_update_reactions():
rxn = Reaction.from_massaction(inputs=[a], outputs=[b], k_forward=0.1)
return [rxn]
def mock_update_species():
return [a, b]
component.update_species = mock_update_species
component.update_reactions = mock_update_reactions
mixture = Mixture(components=[component])
#All the directives used below should not change the CRN.
#They just remove some checks and safegaurds, but compilation should work the same in this simple case.
#directives are best used in specific cases to compile very large models where speed is essential
crn_from_mixture1 = mixture.compile_crn(copy_objects = False)
# test that the mixture has the same species as the manually build CRN object
self.assertEqual(set(CRN.species), set(crn_from_mixture1.species))
# test that the mixture has the same reactions as the manually build CRN object
self.assertEqual(CRN.reactions, crn_from_mixture1.reactions)
crn_from_mixture2 = mixture.compile_crn(add_reaction_species = False)
# test that the mixture has the same species as the manually build CRN object
self.assertEqual(set(CRN.species), set(crn_from_mixture2.species))
# test that the mixture has the same reactions as the manually build CRN object
self.assertEqual(CRN.reactions, crn_from_mixture2.reactions)
crn_from_mixture3 = mixture.compile_crn(initial_concentrations_at_end = True)
# test that the mixture has the same species as the manually build CRN object
self.assertEqual(set(CRN.species), set(crn_from_mixture3.species))
# test that the mixture has the same reactions as the manually build CRN object
self.assertEqual(CRN.reactions, crn_from_mixture3.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)
def test_generate_sbml_model(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)
document, model = crn.generate_sbml_model()
self.assertEqual(len(model.getListOfSpecies()), len(crn.species))
self.assertEqual(len(model.getListOfReactions()), len(crn.reactions))
def test_bioscrape_import_simulate():
from biocrnpyler import ChemicalReactionNetwork, Species
try:
import numpy as np
X = Species("X")
CRN = ChemicalReactionNetwork(species=[X],reactions=[])
with pytest.warns(None) as record:
sim_result = CRN.simulate_with_bioscrape(timepoints=np.linspace(0, 10, 100), initial_condition_dict = {str(X):1})
#In the case bioscrape is not imported
if sim_result is None:
# check the warning message
assert "simulate_with_bioscrape is depricated and will cease working in a future release." in str(record[0].message)
#In the case bioscrape is imported
else:
assert str(X) in sim_result
except ModuleNotFoundError:
print('test skipped')
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_libroadrunner_import():
from biocrnpyler import ChemicalReactionNetwork
try:
import numpy as np
CRN = ChemicalReactionNetwork(species=[], reactions=[])
with pytest.warns(None) as record:
sim_results = CRN.runsim_roadrunner(timepoints=np.linspace(
0, 10, 100),
filename=None)
assert sim_results is None
# only one warning was triggered
assert len(record) == 1
# check the warning message
assert str(
record[0].message
) == "libroadrunner was not found, please install libroadrunner"
except ModuleNotFoundError:
print('test skipped')
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_compile_crn(self):
a = Species(name='a')
b = Species(name='b')
species_list = [a, b]
# creating a mock update function to decouple the update process from the rest of the code
def mock_update_reactions():
rxn = Reaction(inputs=[a], outputs=[b], k=0.1)
return [rxn]
rxn = Reaction(inputs=[a], outputs=[b], k=0.1)
CRN = ChemicalReactionNetwork(species_list, [rxn])
mixture = Mixture(species=species_list)
mixture.update_reactions = mock_update_reactions
crn_from_mixture = mixture.compile_crn()
# test that the mixture has the same species as the manually build CRN object
self.assertEqual(CRN.species, crn_from_mixture.species)
# test that the mixture has the same reactions as the manually build CRN object
self.assertEqual(CRN.reactions, crn_from_mixture.reactions)
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