Beispiel #1
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    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)
Beispiel #2
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 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], [])
Beispiel #3
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 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])
Beispiel #4
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 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)
Beispiel #5
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 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)
Beispiel #6
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 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)
Beispiel #7
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 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)