def test_calculate_max_number_activities(self):
# model with activities, archive with results that have add activity in interventions
a1 = mnm_repr.Activity('act1', None, ['a'], [])
a2 = mnm_repr.Activity('act1', None, ['b'], [])
a3 = mnm_repr.Activity('act1', None, ['c'], [])
a4 = mnm_repr.Activity('act1', None, ['d'], [])
base_model = mnm_repr.Model('m1', [], [a1], [])
des1 = exp_repr.ExperimentDescription(
None, [mnm_repr.Add(a2), mnm_repr.Add(a1)])
des2 = exp_repr.ExperimentDescription(None, [mnm_repr.Add(a3)])
des3 = exp_repr.ExperimentDescription(
None, [mnm_repr.Add(a4), mnm_repr.Add(a3)])
res1 = exp_repr.Result('r1', des1, None)
res2 = exp_repr.Result('r2', des2, None)
res3 = exp_repr.Result('r3', des3, None)
exp1 = exp_repr.Experiment('exp1', [res1])
exp2 = exp_repr.Experiment('exp2', [res2])
exp3 = exp_repr.Experiment('exp3', [res3])
arch = Archive()
arch.known_results = [exp1, exp2, exp3]
rev = RevisionModule(arch)
out = rev.calculate_max_number_activities(base_model)
self.assertEqual(out, 4)
def setUp(self):
self.con1 = mnm_repr.PresentEntity('ent1', 'comp1')
self.con2 = mnm_repr.PresentEntity('ent2', 'comp2')
self.con3 = mnm_repr.PresentEntity('ent3', 'comp3')
self.con4 = mnm_repr.PresentEntity('ent4', 'comp4')
self.act1 = mnm_repr.Activity('ID1', 'name1', [self.con1], [])
self.act2 = mnm_repr.Activity('ID2', 'name2', [self.con2], [])
def test_export_entities_properties(self):
# entity with properties to test the second part of the method
ent3 = mnm_repr.Protein(
'e3', 'none', 'none',
[mnm_repr.Catalyses(mnm_repr.Activity('a1', None, [], []))])
ent4 = mnm_repr.Complex(
'e4', 'none', 'none',
[mnm_repr.Transports(mnm_repr.Activity('a2', None, [], []))])
exported = exporter.export_entities([ent3, ent4])
self.assertEqual("\nprotein(e3,none).", exported[0])
self.assertEqual("\ncatalyses(e3,none,a1).", exported[1])
self.assertEqual("\ncomplex(e4,none).", exported[2])
self.assertEqual("\ntransports(e4,none,a2).", exported[3])
def test_export_force_new_model(self):
act1 = mnm_repr.Activity('act1', None, ['a'], [])
act2 = mnm_repr.Activity('act2', None, ['b'], [])
base_model = mnm_repr.Model('m1', [], [], [])
exm1 = mnm_repr.Model('m2', [], [act1], [])
exm2 = mnm_repr.Model('m3', [], [act2], [])
out = exporter.export_force_new_model(base_model, [exm1, exm2])
self.assertIn('\nexternal_model(m2).', out)
self.assertIn('\nexternal_model(m3).', out)
self.assertIn('\nin_model(act1,m2).', out)
self.assertIn('\nin_model(act2,m3).', out)
self.assertIn('\n#example different(m1, m2).', out)
self.assertIn('\n#example different(m1, m3).', out)
def test_export_activity(self):
# one substrate, one catalyst, one transporter; one product
cond_subst = mnm_repr.PresentEntity(mnm_repr.Metabolite('met1'),
mnm_repr.Medium())
cond_cat = mnm_repr.PresentCatalyst(mnm_repr.Medium())
cond_trp = mnm_repr.PresentTransporter(mnm_repr.Medium())
prod = mnm_repr.PresentEntity(mnm_repr.Metabolite('met2'),
mnm_repr.Medium())
act = mnm_repr.Activity('a1', 'none', [cond_subst, cond_cat, cond_trp],
[prod])
act.reversibility = True
exported = exporter.export_activity(act)
# forward
self.assertIn('\nsubstrate(met1,none,c_01,a1).', exported)
self.assertIn('\nenz_required(a1).', exported)
self.assertIn('\nenz_compartment(c_01,a1).', exported)
self.assertIn('\ntransp_required(a1).', exported)
self.assertIn('\ntransp_compartment(c_01,a1).', exported)
self.assertIn('\nproduct(met2,none,c_01,a1).', exported)
# reversed
self.assertIn('\nproduct(met1,none,c_01,a1_rev).', exported)
self.assertIn('\nenz_required(a1_rev).', exported)
self.assertIn('\nenz_compartment(c_01,a1_rev).', exported)
self.assertIn('\ntransp_required(a1_rev).', exported)
self.assertIn('\ntransp_compartment(c_01,a1_rev).', exported)
self.assertIn('\nsubstrate(met2,none,c_01,a1_rev).', exported)
def test_export_model_specification(self):
# 2 conds + 2 activ
cond_subst_1 = mnm_repr.PresentEntity(mnm_repr.Metabolite('met1'),
mnm_repr.Medium())
cond_subst_2 = mnm_repr.PresentEntity(mnm_repr.Metabolite('met2'),
mnm_repr.Medium())
act_1 = mnm_repr.Activity('a1', None, ['1'], [])
act_2 = mnm_repr.Activity('a2', None, ['2'], [])
m = mnm_repr.Model('m1', [cond_subst_1, cond_subst_2], [act_1, act_2],
[])
exported = exporter.export_model_specification(m)
self.assertIn('\nadded_to_model(setup_present(met1,none,c_01),m1).',
exported)
self.assertIn('\nadded_to_model(setup_present(met2,none,c_01),m1).',
exported)
self.assertIn('\nadded_to_model(a1,m1).', exported)
self.assertIn('\nadded_to_model(a2,m1).', exported)
def test_export_remove_activities(self):
a1 = mnm_repr.Activity('act1', None, ['a'], [])
a2 = mnm_repr.Activity('act2', None, ['b'], [])
out = exporter.export_remove_activities([a1, a2])
self.assertIn('\n#modeh remove(act1) =1 @1.', out)
self.assertIn('\n#modeh remove(act2) =1 @1.', out)