def test_species_concentration_units(self):
model = Model()
st_1 = model.species_types.create(id='st_1')
st_2 = model.species_types.create(id='st_2')
c_1 = model.compartments.create(id='c_1')
c_2 = model.compartments.create(id='c_2')
st_1_c_1 = model.species.create(species_type=st_1, compartment=c_1)
st_1_c_2 = model.species.create(species_type=st_1, compartment=c_2)
st_2_c_1 = model.species.create(species_type=st_2, compartment=c_1)
st_2_c_2 = model.species.create(species_type=st_2, compartment=c_2)
st_1_c_1.id = st_1_c_1.gen_id()
st_1_c_2.id = st_1_c_2.gen_id()
st_2_c_1.id = st_2_c_1.gen_id()
st_2_c_2.id = st_2_c_2.gen_id()
st_1_c_1.distribution_init_concentration = DistributionInitConcentration(units=unit_registry.parse_units('gram'))
st_1_c_2.distribution_init_concentration = DistributionInitConcentration(units=unit_registry.parse_units('hour'))
st_2_c_1.distribution_init_concentration = DistributionInitConcentration(units=unit_registry.parse_units('liter'))
st_2_c_2.distribution_init_concentration = DistributionInitConcentration(units=unit_registry.parse_units('second'))
st_1_c_1.distribution_init_concentration.id = st_1_c_1.distribution_init_concentration.gen_id()
st_1_c_2.distribution_init_concentration.id = st_1_c_2.distribution_init_concentration.gen_id()
st_2_c_1.distribution_init_concentration.id = st_2_c_1.distribution_init_concentration.gen_id()
st_2_c_2.distribution_init_concentration.id = st_2_c_2.distribution_init_concentration.gen_id()
ChangeValueTransform((('species', {'id': 'st_1[c_1]'}),
'distribution_init_concentration',
'units'), unit_registry.parse_units('meter')).run(model)
self.assertEqual(st_1_c_1.distribution_init_concentration.units, unit_registry.parse_units('meter'))
self.assertEqual(st_1_c_2.distribution_init_concentration.units, unit_registry.parse_units('hour'))
self.assertEqual(st_2_c_1.distribution_init_concentration.units, unit_registry.parse_units('liter'))
self.assertEqual(st_2_c_2.distribution_init_concentration.units, unit_registry.parse_units('second'))
def test_parameter_value(self):
model = Model()
p_1 = model.parameters.create(id='p_1', value=1)
p_2 = model.parameters.create(id='p_2', value=3)
ChangeValueTransform((('parameters', {'id': 'p_1'}), 'value'), 2).run(model)
self.assertEqual(p_1.value, 2)
self.assertEqual(p_2.value, 3)
def test_parameter_units(self):
model = Model()
p_1 = model.parameters.create(id='p_1', units=unit_registry.parse_units('M'))
p_2 = model.parameters.create(id='p_2', units=unit_registry.parse_units('l'))
ChangeValueTransform((('parameters', {'id': 'p_1'}), 'units'), unit_registry.parse_units('m^2')).run(model)
self.assertEqual(p_1.units, unit_registry.parse_units('m^2'))
self.assertEqual(p_2.units, unit_registry.parse_units('l'))
def test_function_expression(self):
model = Model()
f = model.functions.create(id='f', expression=FunctionExpression(expression='x'))
g = model.functions.create(id='g', expression=FunctionExpression(expression='y'))
ChangeValueTransform((('functions', {'id': 'g'}), 'expression', 'expression'), 'z').run(model)
self.assertEqual(f.expression.expression, 'x')
self.assertEqual(g.expression.expression, 'z')
def test_compartment_density(self):
model = Model()
c = model.compartments.create(id='c', init_volume=InitVolume(mean=1.))
e = model.compartments.create(id='e', init_volume=InitVolume(mean=1.))
ChangeValueTransform((('compartments', {'id': 'c'}), ('init_volume',), ('mean',)), 2.).run(model)
self.assertEqual(c.init_volume.mean, 2.)
self.assertEqual(e.init_volume.mean, 1.)
def test_reaction_expression(self):
model = Model()
s_1 = model.submodels.create(id='s_1')
r_1_1 = model.reactions.create(submodel=s_1, id='r_1_1')
rl_f = model.rate_laws.create(reaction=r_1_1, direction=RateLawDirection.forward, expression=RateLawExpression(expression='x'))
rl_b = model.rate_laws.create(reaction=r_1_1, direction=RateLawDirection.backward, expression=RateLawExpression(expression='y'))
ChangeValueTransform((('reactions', {'id': 'r_1_1'}),
('rate_laws', {'direction': RateLawDirection.forward}),
'expression',
'expression'), 'z').run(model)
self.assertEqual(rl_f.expression.expression, 'z')
self.assertEqual(rl_b.expression.expression, 'y')
def test_species_concentration_value(self):
model = Model()
st_1 = model.species_types.create(id='st_1')
st_2 = model.species_types.create(id='st_2')
c_1 = model.compartments.create(id='c_1')
c_2 = model.compartments.create(id='c_2')
st_1_c_1 = model.species.create(species_type=st_1, compartment=c_1)
st_1_c_2 = model.species.create(species_type=st_1, compartment=c_2)
st_2_c_1 = model.species.create(species_type=st_2, compartment=c_1)
st_2_c_2 = model.species.create(species_type=st_2, compartment=c_2)
st_1_c_1.id = st_1_c_1.gen_id()
st_1_c_2.id = st_1_c_2.gen_id()
st_2_c_1.id = st_2_c_1.gen_id()
st_2_c_2.id = st_2_c_2.gen_id()
st_1_c_1.distribution_init_concentration = DistributionInitConcentration(mean=1, std=2)
st_1_c_2.distribution_init_concentration = DistributionInitConcentration(mean=2, std=2)
st_2_c_1.distribution_init_concentration = DistributionInitConcentration(mean=3, std=2)
st_2_c_2.distribution_init_concentration = DistributionInitConcentration(mean=4, std=2)
st_1_c_1.distribution_init_concentration.id = st_1_c_1.distribution_init_concentration.gen_id()
st_1_c_2.distribution_init_concentration.id = st_1_c_2.distribution_init_concentration.gen_id()
st_2_c_1.distribution_init_concentration.id = st_2_c_1.distribution_init_concentration.gen_id()
st_2_c_2.distribution_init_concentration.id = st_2_c_2.distribution_init_concentration.gen_id()
ChangeValueTransform((('species', {'id': st_2_c_1.id}),
'distribution_init_concentration',
'mean'), 0).run(model)
self.assertEqual(st_1_c_1.distribution_init_concentration.mean, 1)
self.assertEqual(st_1_c_2.distribution_init_concentration.mean, 2)
self.assertEqual(st_2_c_1.distribution_init_concentration.mean, 0)
self.assertEqual(st_2_c_2.distribution_init_concentration.mean, 4)
ChangeValueTransform((('species', {'id': st_2_c_1.id}),
'distribution_init_concentration',
'std'), 0).run(model)
self.assertEqual(st_1_c_1.distribution_init_concentration.std, 2)
self.assertEqual(st_1_c_2.distribution_init_concentration.std, 2)
self.assertEqual(st_2_c_1.distribution_init_concentration.std, 0)
self.assertEqual(st_2_c_2.distribution_init_concentration.std, 2)
def test_reaction_flux_bounds_max(self):
model = Model()
s_1 = model.submodels.create(id='s_1')
s_2 = model.submodels.create(id='s_2')
r_1_1 = model.reactions.create(submodel=s_1, id='r_1_1', flux_bounds=FluxBounds(max=1))
r_1_2 = model.reactions.create(submodel=s_1, id='r_1_2', flux_bounds=FluxBounds(max=2))
r_2_1 = model.reactions.create(submodel=s_2, id='r_2_1', flux_bounds=FluxBounds(max=3))
r_2_2 = model.reactions.create(submodel=s_2, id='r_2_2', flux_bounds=FluxBounds(max=4))
ChangeValueTransform((('reactions', {'id': 'r_2_2'}), ('flux_bounds',), ('max',)), 0).run(model)
self.assertEqual(r_1_1.flux_bounds.max, 1)
self.assertEqual(r_1_2.flux_bounds.max, 2)
self.assertEqual(r_2_1.flux_bounds.max, 3)
self.assertEqual(r_2_2.flux_bounds.max, 0)
def test_reaction_flux_bounds_min(self):
model = Model()
s_1 = model.submodels.create(id='s_1')
s_2 = model.submodels.create(id='s_2')
r_1_1 = model.reactions.create(submodel=s_1, id='r_1_1', flux_bounds=FluxBounds(min=1, units=unit_registry.parse_units('M s^-1')))
r_1_2 = model.reactions.create(submodel=s_1, id='r_1_2', flux_bounds=FluxBounds(min=2, units=unit_registry.parse_units('M s^-1')))
r_2_1 = model.reactions.create(submodel=s_2, id='r_2_1', flux_bounds=FluxBounds(min=3, units=unit_registry.parse_units('M s^-1')))
r_2_2 = model.reactions.create(submodel=s_2, id='r_2_2', flux_bounds=FluxBounds(min=4, units=unit_registry.parse_units('M s^-1')))
ChangeValueTransform((('reactions', {'id': 'r_1_2'}), ('flux_bounds',), ('min',)), 0).run(model)
self.assertEqual(r_1_1.flux_bounds.min, 1)
self.assertEqual(r_1_2.flux_bounds.min, 0)
self.assertEqual(r_2_1.flux_bounds.min, 3)
self.assertEqual(r_2_2.flux_bounds.min, 4)
def test_reaction_reversible(self):
model = Model()
s_1 = model.submodels.create(id='s_1')
s_2 = model.submodels.create(id='s_2')
r_1_1 = model.reactions.create(submodel=s_1, id='r_1_1', reversible=False)
r_1_2 = model.reactions.create(submodel=s_1, id='r_1_2', reversible=False)
r_2_1 = model.reactions.create(submodel=s_2, id='r_2_1', reversible=True)
r_2_2 = model.reactions.create(submodel=s_2, id='r_2_2', reversible=True)
ChangeValueTransform((('reactions', {'id': 'r_2_1'}), 'reversible'), False).run(model)
self.assertEqual(r_1_1.reversible, False)
self.assertEqual(r_1_2.reversible, False)
self.assertEqual(r_2_1.reversible, False)
self.assertEqual(r_2_2.reversible, True)
def test_reaction_k_cat(self):
model = Model()
s_1 = model.submodels.create(id='s_1')
r_1_1 = model.reactions.create(submodel=s_1, id='r_1_1')
k_cat_f = model.parameters.create(id='k_cat_f', value=1)
k_cat_b = model.parameters.create(id='k_cat_b', value=2)
rl_f = model.rate_laws.create(reaction=r_1_1, direction=RateLawDirection.forward,
expression=RateLawExpression(
parameters=[k_cat_f]))
rl_b = model.rate_laws.create(reaction=r_1_1, direction=RateLawDirection.backward,
expression=RateLawExpression(
parameters=[k_cat_b]))
rl_f.id = rl_f.gen_id()
rl_b.id = rl_b.gen_id()
ChangeValueTransform((('parameters', {'id': 'k_cat_b'}), 'value'), 0).run(model)
self.assertEqual(k_cat_f.value, 1)
self.assertEqual(k_cat_b.value, 0)
def test___eq__(self):
t1 = ChangeValueTransform((('species', {'id': 'st_1[c_1]'}),
'distribution_init_concentration',
'std'), 0)
t2 = ChangeValueTransform((('species', {'id': 'st_1[c_1]'}),
'distribution_init_concentration',
'std'), 0)
self.assertEqual(t1, t2)
t2.value = 1.
self.assertNotEqual(t1, t2)
self.assertNotEqual(t1, 1.)
self.assertNotEqual(1., t1)
t1 = ChangeValueTransform((('species', {'id': 'st_1[c_1]'}),
'distribution_init_concentration',
'std'), 0)
t2 = ChangeValueTransform((('species', {'id': 'st_1[c_1]'}),
'distribution_init_concentration',
'mean'), 0)
self.assertNotEqual(t1, t2)
def test_attr_path_to_from_str(self):
t1 = ChangeValueTransform('species', 0)
t2 = ChangeValueTransform(None, 0)
t2.attr_path = ChangeValueTransform.attr_path_from_str(t1.attr_path_to_str())
self.assertEqual(t1.attr_path, t2.attr_path)
t1 = ChangeValueTransform(['species'], 0)
t2 = ChangeValueTransform(None, 0)
t2.attr_path = ChangeValueTransform.attr_path_from_str(t1.attr_path_to_str())
self.assertEqual(t1.attr_path, t2.attr_path)
t1 = ChangeValueTransform(['species', 'reactions'], 0)
t2 = ChangeValueTransform(None, 0)
t2.attr_path = ChangeValueTransform.attr_path_from_str(t1.attr_path_to_str())
self.assertEqual(t1.attr_path, t2.attr_path)
t1 = ChangeValueTransform([['species', {'id': 'st_1[c_1]'}],
'distribution_init_concentration',
'std'], 0)
t2 = ChangeValueTransform(None, 0)
t2.attr_path = ChangeValueTransform.attr_path_from_str(t1.attr_path_to_str())
self.assertEqual(t1.attr_path, t2.attr_path)
t1 = ChangeValueTransform(['rate_laws', {'direction': RateLawDirection.forward}], 0)
t2 = ChangeValueTransform(None, 0)
t2.attr_path = ChangeValueTransform.attr_path_from_str(t1.attr_path_to_str())
self.assertEqual(t1.attr_path, t2.attr_path)