class OracleTest(unittest.TestCase):
def setUp(self):
self.g1 = Gene('g1')
self.p1 = Protein('p1')
self.met1 = Metabolite('met1')
self.met2 = Metabolite('met2')
self.cplx1 = Complex('cplx1')
self.cytosol = Cytosol()
self.cond1 = PresentEntity(self.met1, self.cytosol)
self.cond2 = PresentEntity(self.met2, self.cytosol)
self.cond3 = PresentEntity(self.p1, self.cytosol)
self.cond4 = PresentEntity(self.cplx1, self.cytosol)
self.growth = Growth('growth', [self.cond2])
self.r1 = Reaction('r1', [self.cond1], [self.cond2])
self.r2 = Reaction('r2', [self.cond3], [self.cond4])
self.entities = [self.g1, self.p1, self.met1, self.met2, self.cplx1]
self.compartments = [self.cytosol]
self.activities = [self.growth, self.r1, self.r2]
self.setup_conds = [self.cond1, self.cond3]
self.mod1 = Model('m0', self.setup_conds, [self.growth, self.r1], [])
self.mod2 = Model('m1', self.setup_conds, [self.growth, self.r2], [])
self.oracle = Oracle(None, [], [], self.mod1, self.entities, self.compartments, self.activities)
def tearDown(self):
self.oracle = None
def test_in_vitro_basic(self):
met1 = Metabolite('met1')
met2 = Metabolite('met2')
cytosol = Cytosol()
cond1 = PresentEntity(met1, cytosol)
cond2 = PresentEntity(met2, cytosol)
r1 = Reaction('r1', [cond1], [cond2])
self.oracle = Oracle(None, [], [r1], None, [], [], [])
expD = ExperimentDescription(ReconstructionActivity('r1'), [])
out = self.oracle.execute_in_vitro_exp(expD)
self.assertEqual(out.outcome, True)
def test_in_vitro_enz(self):
met1 = Metabolite('met1')
met2 = Metabolite('met2')
cytosol = Cytosol()
cond1 = PresentEntity(met1, cytosol)
cond2 = PresentEntity(met2, cytosol)
cond_enz = PresentCatalyst(cytosol)
r1 = Reaction('r1', [cond1, cond_enz], [cond2])
enz = Protein('p1', properties=[Catalyses(r1)])
self.oracle = Oracle(None, [enz], [r1], None, [], [], [])
expD = ExperimentDescription(ReconstructionEnzReaction('r1', 'p1'), [])
out = self.oracle.execute_in_vitro_exp(expD)
self.assertEqual(out.outcome, True)
def test_in_vitro_transp(self):
met1 = Metabolite('met1')
met2 = Metabolite('met2')
cytosol = Cytosol()
cond1 = PresentEntity(met1, cytosol)
cond2 = PresentEntity(met2, cytosol)
cond_trp = PresentTransporter(cytosol)
r1 = Reaction('r1', [cond1, cond_trp], [cond2])
transp = Protein('p1', properties=[Transports(r1)])
self.oracle = Oracle(None, [transp], [r1], None, [], [], [])
expD = ExperimentDescription(ReconstructionTransporterRequired('r1', 'p1'), [])
out = self.oracle.execute_in_vitro_exp(expD)
self.assertEqual(out.outcome, True)
def test_in_vivo(self):
expD = ExperimentDescription(DetectionActivity('r1'), [])
res = self.oracle.execute_in_vivo(expD)
self.assertEqual(res.outcome, True)
def test_process_output_ent_detection_1(self):
expD = ExperimentDescription(DetectionEntity('met1'), [])
out = 'Answer: 1\nsynthesizable(met1,ver,c_05,m0)'
res = self.oracle.process_output(out, expD)
self.assertEqual(res.outcome, True)
def test_process_output_localisation_ent_1(self):
expD = ExperimentDescription(LocalisationEntity('met1', 'c_05'), [])
out = 'Answer: 1\nsynthesizable(met1,ver,c_05,m0)'
res = self.oracle.process_output(out, expD)
self.assertEqual(res.outcome, True)
def test_process_output_ent_detection_2(self):
expD = ExperimentDescription(DetectionEntity('met1'), [])
out = 'Answer: 1\ninitially_present(met1,ver,c_05,m0)'
res = self.oracle.process_output(out, expD)
self.assertEqual(res.outcome, True)
def test_process_output_localisation_ent_2(self):
expD = ExperimentDescription(LocalisationEntity('met1', 'c_05'), [])
out = 'Answer: 1\ninitially_present(met1,ver,c_05,m0)'
res = self.oracle.process_output(out, expD)
self.assertEqual(res.outcome, True)
def test_process_output_act_detection(self):
expD = ExperimentDescription(DetectionActivity('r1'), [])
out = 'Answer: 1\nactive(r1,m0)'
res = self.oracle.process_output(out, expD)
self.assertEqual(res.outcome, True)
def test_process_output_adam_two_factor(self):
expD = ExperimentDescription(AdamTwoFactorExperiment('g1', 'met1'), [])
out = 'Answer: 1\npredicts(m0,experiment(adam_two_factor_exp,g1,met1),true'
res = self.oracle.process_output(out, expD)
self.assertEqual(res.outcome, True)
