forked from enviPath/enviPy
jebus
762a6b7baf
Fixes #90 Fixes #91 Fixes #115 Fixes #104 Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#116
198 lines
6.7 KiB
Python
198 lines
6.7 KiB
Python
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
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class CompoundTest(TestCase):
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fixtures = ["test_fixtures.json.gz"]
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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(CompoundTest, 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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def test_smoke(self):
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c = Compound.create(
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self.package,
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smiles='C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F',
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name='Afoxolaner',
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description='No Desc'
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)
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self.assertEqual(c.default_structure.smiles,
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'C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F')
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self.assertEqual(c.name, 'Afoxolaner')
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self.assertEqual(c.description, 'No Desc')
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def test_missing_smiles(self):
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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=None,
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name='Afoxolaner',
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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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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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smiles=' C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F ',
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name='Afoxolaner',
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description='No Desc'
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)
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self.assertEqual(c.default_structure.smiles,
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'C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F')
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def test_name_and_description_optional(self):
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c = Compound.create(
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self.package,
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smiles='C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F',
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)
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self.assertEqual(c.name, 'Compound 1')
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self.assertEqual(c.description, 'no description')
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def test_empty_name_and_description_are_ignored(self):
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c = Compound.create(
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self.package,
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smiles='C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F',
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name='',
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description='',
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)
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self.assertEqual(c.name, 'Compound 1')
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self.assertEqual(c.description, 'no description')
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def test_deduplication(self):
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c1 = Compound.create(
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self.package,
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smiles='C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F',
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name='Afoxolaner',
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description='No Desc'
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)
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c2 = Compound.create(
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self.package,
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smiles='C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F',
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name='Afoxolaner',
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description='No Desc'
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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(c1.pk, c2.pk)
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self.assertEqual(len(self.package.compounds), 1)
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def test_wrong_smiles(self):
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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='C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F',
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name='Afoxolaner',
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description='No Desc'
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)
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def test_create_with_standardized_smiles(self):
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c = Compound.create(
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self.package,
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smiles='O=C(O)C1=CC=C([N+](=O)[O-])C=C1',
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name='Standardized SMILES',
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description='No Desc'
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)
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self.assertEqual(len(c.structures.all()), 1)
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cs = c.structures.all()[0]
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self.assertEqual(cs.normalized_structure, True)
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self.assertEqual(cs.smiles, 'O=C(O)C1=CC=C([N+](=O)[O-])C=C1')
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def test_create_with_non_standardized_smiles(self):
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c = Compound.create(
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self.package,
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smiles='[O-][N+](=O)c1ccc(C(=O)[O-])cc1',
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name='Non Standardized SMILES',
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description='No Desc'
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)
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self.assertEqual(len(c.structures.all()), 2)
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for cs in c.structures.all():
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if cs.normalized_structure:
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self.assertEqual(cs.smiles, 'O=C(O)C1=CC=C([N+](=O)[O-])C=C1')
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break
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else:
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# Loop finished without break, lets fail...
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self.assertEqual(1, 2)
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def test_add_structure_smoke(self):
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c = Compound.create(
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self.package,
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smiles='O=C(O)C1=CC=C([N+](=O)[O-])C=C1',
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name='Standardized SMILES',
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description='No Desc'
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)
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c.add_structure('[O-][N+](=O)c1ccc(C(=O)[O-])cc1', 'Non Standardized SMILES')
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self.assertEqual(len(c.structures.all()), 2)
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def test_add_structure_with_different_normalized_smiles(self):
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c = Compound.create(
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self.package,
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smiles='O=C(O)C1=CC=C([N+](=O)[O-])C=C1',
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name='Standardized SMILES',
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description='No Desc'
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)
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with self.assertRaises(ValueError):
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c.add_structure(
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'C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F',
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'Different Standardized SMILES')
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def test_delete(self):
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c = Compound.create(
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self.package,
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smiles='O=C(O)C1=CC=C([N+](=O)[O-])C=C1',
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name='Standardization Test',
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description='No Desc'
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)
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c.delete()
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self.assertEqual(Compound.objects.filter(package=self.package).count(), 0)
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self.assertEqual(CompoundStructure.objects.filter(compound__package=self.package).count(), 0)
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def test_set_as_default_structure(self):
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c1 = Compound.create(
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self.package,
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smiles='O=C(O)C1=CC=C([N+](=O)[O-])C=C1',
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name='Standardized SMILES',
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description='No Desc'
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)
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default_structure = c1.default_structure
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c2 = c1.add_structure('[O-][N+](=O)c1ccc(C(=O)[O-])cc1', 'Non Standardized SMILES')
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c1.set_default_structure(c2)
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self.assertNotEqual(default_structure, c2)
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