forked from enviPath/enviPy
Basic System (#31)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#31
This commit is contained in:
@ -5,7 +5,7 @@ from epdb.models import Compound, User, CompoundStructure
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class CompoundTest(TestCase):
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fixtures = ["test_fixture.json.gz"]
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fixtures = ["test_fixture.cleaned.json"]
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def setUp(self):
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pass
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@ -53,6 +53,14 @@ class CompoundTest(TestCase):
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description='No Desc'
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)
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with self.assertRaises(ValueError):
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_ = Compound.create(
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self.package,
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smiles=' ',
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name='Afoxolaner',
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description='No Desc'
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)
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def test_smiles_are_trimmed(self):
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c = Compound.create(
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self.package,
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196
tests/test_reaction_model.py
Normal file
196
tests/test_reaction_model.py
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@ -0,0 +1,196 @@
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from django.test import TestCase
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from epdb.logic import PackageManager
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from epdb.models import Compound, User, CompoundStructure, Reaction, Rule
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class ReactionTest(TestCase):
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fixtures = ["test_fixture.cleaned.json"]
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def setUp(self):
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pass
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@classmethod
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def setUpClass(cls):
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super(ReactionTest, cls).setUpClass()
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cls.user = User.objects.get(username='anonymous')
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cls.package = PackageManager.create_package(cls.user, 'Anon Test Package', 'No Desc')
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@classmethod
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def tearDownClass(cls):
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pass
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def tearDown(self):
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pass
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def test_smoke(self):
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educt = Compound.create(
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self.package,
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smiles='C(CCl)Cl',
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name='1,2-Dichloroethane',
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description='Eawag BBD compound c0001'
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).default_structure
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product = Compound.create(
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self.package,
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smiles='C(CO)Cl',
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name='2-Chloroethanol',
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description='Eawag BBD compound c0005'
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).default_structure
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r = Reaction.create(
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package=self.package,
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name='Eawag BBD reaction r0001',
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educts=[educt],
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products=[product],
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multi_step=False
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)
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self.assertEqual(r.smirks(), 'C(CCl)Cl>>C(CO)Cl')
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self.assertEqual(r.name, 'Eawag BBD reaction r0001')
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self.assertEqual(r.description, 'no description')
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def test_string_educts_and_products(self):
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r = Reaction.create(
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package=self.package,
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name='Eawag BBD reaction r0001',
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educts=['C(CCl)Cl'],
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products=['C(CO)Cl'],
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multi_step=False
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)
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self.assertEqual(r.smirks(), 'C(CCl)Cl>>C(CO)Cl')
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def test_missing_smiles(self):
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educt = Compound.create(
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self.package,
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smiles='C(CCl)Cl',
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name='1,2-Dichloroethane',
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description='Eawag BBD compound c0001'
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).default_structure
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product = Compound.create(
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self.package,
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smiles='C(CO)Cl',
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name='2-Chloroethanol',
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description='Eawag BBD compound c0005'
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).default_structure
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with self.assertRaises(ValueError):
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_ = Reaction.create(
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package=self.package,
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name='Eawag BBD reaction r0001',
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educts=[educt],
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products=[],
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multi_step=False
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)
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with self.assertRaises(ValueError):
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_ = Reaction.create(
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package=self.package,
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name='Eawag BBD reaction r0001',
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educts=[],
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products=[product],
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multi_step=False
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)
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with self.assertRaises(ValueError):
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_ = Reaction.create(
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package=self.package,
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name='Eawag BBD reaction r0001',
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educts=[],
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products=[],
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multi_step=False
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)
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def test_empty_name_and_description_are_ignored(self):
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r = Reaction.create(
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package=self.package,
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name='',
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description='',
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educts=['C(CCl)Cl'],
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products=['C(CO)Cl'],
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multi_step=False,
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)
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self.assertEqual(r.name, 'no name')
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self.assertEqual(r.description, 'no description')
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def test_deduplication(self):
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rule = Rule.create(
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package=self.package,
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rule_type='SimpleAmbitRule',
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name='bt0022-2833',
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description='Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative',
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smirks='[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]',
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)
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r1 = Reaction.create(
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package=self.package,
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name='Eawag BBD reaction r0001',
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educts=['C(CCl)Cl'],
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products=['C(CO)Cl'],
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rules=[rule],
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multi_step=False
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)
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r2 = Reaction.create(
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package=self.package,
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name='Eawag BBD reaction r0001',
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educts=['C(CCl)Cl'],
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products=['C(CO)Cl'],
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rules=[rule],
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multi_step=False
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)
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# Check if create detects that this Compound already exist
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# In this case the existing object should be returned
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self.assertEqual(r1.pk, r2.pk)
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self.assertEqual(len(self.package.reactions), 1)
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def test_deduplication_without_rules(self):
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r1 = Reaction.create(
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package=self.package,
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name='Eawag BBD reaction r0001',
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educts=['C(CCl)Cl'],
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products=['C(CO)Cl'],
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multi_step=False
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)
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r2 = Reaction.create(
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package=self.package,
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name='Eawag BBD reaction r0001',
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educts=['C(CCl)Cl'],
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products=['C(CO)Cl'],
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multi_step=False
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)
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# Check if create detects that this Compound already exist
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# In this case the existing object should be returned
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self.assertEqual(r1.pk, r2.pk)
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self.assertEqual(len(self.package.reactions), 1)
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def test_wrong_smiles(self):
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with self.assertRaises(ValueError):
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_ = Reaction.create(
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package=self.package,
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name='Eawag BBD reaction r0001',
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educts=['ASDF'],
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products=['C(CO)Cl'],
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multi_step=False
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)
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def test_delete(self):
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r = Reaction.create(
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package=self.package,
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name='Eawag BBD reaction r0001',
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educts=['C(CCl)Cl'],
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products=['C(CO)Cl'],
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multi_step=False
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)
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r.delete()
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self.assertEqual(Reaction.objects.filter(package=self.package).count(), 0)
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116
tests/test_rule_model.py
Normal file
116
tests/test_rule_model.py
Normal file
@ -0,0 +1,116 @@
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from django.test import TestCase
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from epdb.logic import PackageManager
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from epdb.models import Rule, User
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class RuleTest(TestCase):
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fixtures = ["test_fixture.cleaned.json"]
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def setUp(self):
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pass
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@classmethod
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def setUpClass(cls):
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super(RuleTest, cls).setUpClass()
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cls.user = User.objects.get(username='anonymous')
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cls.package = PackageManager.create_package(cls.user, 'Anon Test Package', 'No Desc')
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@classmethod
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def tearDownClass(cls):
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pass
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def tearDown(self):
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pass
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def test_smoke(self):
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r = Rule.create(
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rule_type='SimpleAmbitRule',
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package=self.package,
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name='bt0022-2833',
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description='Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative',
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smirks='[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]',
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)
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self.assertEqual(r.smirks,
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'[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]')
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self.assertEqual(r.name, 'bt0022-2833')
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self.assertEqual(r.description,
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'Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative')
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def test_smirks_are_trimmed(self):
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r = Rule.create(
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rule_type='SimpleAmbitRule',
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package=self.package,
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name='bt0022-2833',
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description='Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative',
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smirks=' [H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4] ',
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)
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self.assertEqual(r.smirks,
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'[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]')
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def test_name_and_description_optional(self):
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r = Rule.create(
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rule_type='SimpleAmbitRule',
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package=self.package,
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smirks='[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]',
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)
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self.assertRegex(r.name, 'Rule \\d+')
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self.assertEqual(r.description, 'no description')
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def test_empty_name_and_description_are_ignored(self):
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r = Rule.create(
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rule_type='SimpleAmbitRule',
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package=self.package,
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smirks='[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]',
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name='',
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description='',
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)
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self.assertRegex(r.name, 'Rule \\d+')
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self.assertEqual(r.description, 'no description')
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def test_deduplication(self):
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r1 = Rule.create(
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rule_type='SimpleAmbitRule',
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package=self.package,
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smirks='[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]',
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name='',
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description='',
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)
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r2 = Rule.create(
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rule_type='SimpleAmbitRule',
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package=self.package,
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smirks='[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]',
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name='',
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description='',
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)
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self.assertEqual(r1.pk, r2.pk)
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self.assertEqual(len(self.package.rules), 1)
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def test_valid_smirks(self):
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with self.assertRaises(ValueError):
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r = Rule.create(
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rule_type='SimpleAmbitRule',
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package=self.package,
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smirks='This is not a valid SMIRKS',
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name='',
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description='',
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)
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def test_delete(self):
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r = Rule.create(
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rule_type='SimpleAmbitRule',
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package=self.package,
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smirks='[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]',
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name='',
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description='',
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)
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r.delete()
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self.assertEqual(Rule.objects.filter(package=self.package).count(), 0)
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