def test_add_mechanisms(self):
mixture = Mixture()
tx = SimpleTranscription()
tl = SimpleTranslation()
test_mech = {tx.mechanism_type: tx, tl.mechanism_type: tl}
# test that mixture has no mechanism
self.assertTrue(isinstance(mixture.mechanisms, dict) and len(mixture.mechanisms) == 0)
#test mechanism setter
mixture.mechanisms = test_mech
self.assertEqual(mixture.mechanisms.keys(), test_mech.keys())
#test mechanisms are copied
self.assertEqual(type(mixture.mechanisms[tx.mechanism_type]), type(test_mech[tx.mechanism_type]))
self.assertFalse(mixture.mechanisms[tx.mechanism_type] == test_mech[tx.mechanism_type])
#remove all mechanisms
mixture.mechanisms = {}
self.assertEqual(mixture.mechanisms, {})
#test add_mechanism
mixture.add_mechanism(tx, tx.mechanism_type)
mixture.add_mechanism(tl)
self.assertEqual(mixture.mechanisms.keys(), test_mech.keys())
#test add_mechanisms with list
mixture.mechanisms = {}
test_mech_list = list(test_mech.values())
mixture.add_mechanisms(test_mech_list)
self.assertEqual(mixture.mechanisms.keys(), test_mech.keys())
def test_update_mechanisms(self):
tx = SimpleTranscription()
tl = SimpleTranslation()
test_mech = {tx.mechanism_type: tx, tl.mechanism_type: tl}
# test that component has no mechanism
self.assertTrue(isinstance(self.component.mechanisms, dict) and len(self.component.mechanisms) == 0)
#test mechanism setter
self.component.mechanisms = test_mech
self.assertEqual(self.component.mechanisms.keys(), test_mech.keys())
#test mechanisms are copied
self.assertEqual(type(self.component.mechanisms[tx.mechanism_type]), type(test_mech[tx.mechanism_type]))
self.assertFalse(self.component.mechanisms[tx.mechanism_type] == test_mech[tx.mechanism_type])
#remove all mechanisms
self.component.mechanisms = {}
self.assertEqual(self.component.mechanisms, {})
#test add_mechanism
self.component.add_mechanism(tx, tx.mechanism_type)
self.component.add_mechanism(tl)
self.assertEqual(self.component.mechanisms.keys(), test_mech.keys())
#test add_mechanisms with list
self.component.mechanisms = {}
test_mech_list = list(test_mech.values())
self.component.add_mechanisms(test_mech_list)
self.assertEqual(self.component.mechanisms.keys(), test_mech.keys())
def test_get_parameter(self):
# testing an invalid parameter
with self.assertRaisesRegex(ValueError, 'No parameters can be found that match the'):
self.component.get_parameter(param_name='kb')
# Create Param Dict
kb, ku, ktx, ktl, kdeg, cooperativity = 100, 10, 3, 2, 1, 4
p_id = 'p10'
parameters = {"kb": kb, "kdeg":kdeg,
("transcription", None, "ktx"): ktx,
("transcription", p_id, 'ku'): ku,
(None, p_id, "ktl"): ktl }
# update the component parameters
self.component.update_parameters(parameters=parameters)
tx = SimpleTranscription()
# testing the different parameter definitions
self.assertEqual(self.component.get_parameter(param_name='kb').value, kb)
self.assertEqual(self.component.get_parameter(mechanism=tx, param_name='ktx').value, ktx)
self.assertEqual(self.component.get_parameter(part_id=p_id, param_name='ktl').value, ktl)
self.assertEqual(self.component.get_parameter(mechanism=tx, part_id=p_id, param_name='ku').value, ku)
# testing parameter with return_numerical = True
self.assertEqual(self.component.get_parameter(param_name='kb', return_numerical = True), kb)
one_param = {"kb": kb}
self.component.update_parameters(parameters=one_param)
# testing that one_param was registered
self.assertEqual(self.component.get_parameter(param_name="kb").value, one_param["kb"])
#testing a parameter which can't be found
with self.assertRaisesRegex(ValueError, "No parameters can be found"):
self.component.get_parameter("not a parameter")
def test_add_mechanism(self):
tx = SimpleTranscription()
tl = SimpleTranslation()
#test adding a single mechanism instead of a list still works
self.component.add_mechanisms(tx)
self.assertTrue(tx.mechanism_type in self.component.mechanisms)
#add a non-mechanism
with self.assertRaisesRegex(TypeError,
'mechanism must be a Mechanism.'):
self.component.add_mechanism(None)
with self.assertRaisesRegex(
ValueError, 'add_mechanisms expected a list of Mechanisms.'):
self.component.add_mechanisms(None)
#add same mechanism, new type
self.component.add_mechanism(tx, mech_type="new")
self.assertTrue("new" in self.component.mechanisms)
self.assertTrue(
type(self.component.mechanisms["new"]) == SimpleTranscription)
#Add invalid mech_type
with self.assertRaisesRegex(TypeError,
'mechanism keys must be strings.'):
self.component.add_mechanism(tx, mech_type=1234)
#add a mechanism already in the Component
with self.assertRaisesRegex(
ValueError,
f"mech_type {tx.mechanism_type} already in component"):
self.component.add_mechanism(tx)
#add mechanism with optional_mechanism - does not overwrite!
self.component.add_mechanism(tl,
mech_type=tx.mechanism_type,
optional_mechanism=True)
self.assertTrue(tx.mechanism_type in self.component.mechanisms)
self.assertTrue(
type(self.component.mechanisms[tx.mechanism_type]) ==
SimpleTranscription)
#add mechanism with overwrite
self.component.add_mechanism(tl,
mech_type=tx.mechanism_type,
overwrite=True)
self.assertTrue(tx.mechanism_type in self.component.mechanisms)
self.assertTrue(
type(self.component.mechanisms[tx.mechanism_type]) ==
SimpleTranslation)