enviPy-bayer/tests/test_reaction_model.py

from django.test import TestCase

from epdb.logic import PackageManager
from epdb.models import Compound, User, Reaction, Rule


class ReactionTest(TestCase):
    fixtures = ["test_fixtures.jsonl.gz"]

    @classmethod
    def setUpClass(cls):
        super(ReactionTest, cls).setUpClass()
        cls.user = User.objects.get(username='anonymous')
        cls.package = PackageManager.create_package(cls.user, 'Anon Test Package', 'No Desc')

    def test_smoke(self):
        educt = Compound.create(
            self.package,
            smiles='C(CCl)Cl',
            name='1,2-Dichloroethane',
            description='Eawag BBD compound c0001'
        ).default_structure

        product = Compound.create(
            self.package,
            smiles='C(CO)Cl',
            name='2-Chloroethanol',
            description='Eawag BBD compound c0005'
        ).default_structure

        r = Reaction.create(
            package=self.package,
            name='Eawag BBD reaction r0001',
            educts=[educt],
            products=[product],
            multi_step=False
        )

        self.assertEqual(r.smirks(), 'C(CCl)Cl>>C(CO)Cl')
        self.assertEqual(r.name, 'Eawag BBD reaction r0001')
        self.assertEqual(r.description, 'no description')

    def test_string_educts_and_products(self):
        r = Reaction.create(
            package=self.package,
            name='Eawag BBD reaction r0001',
            educts=['C(CCl)Cl'],
            products=['C(CO)Cl'],
            multi_step=False
        )

        self.assertEqual(r.smirks(), 'C(CCl)Cl>>C(CO)Cl')

    def test_missing_smiles(self):
        educt = Compound.create(
            self.package,
            smiles='C(CCl)Cl',
            name='1,2-Dichloroethane',
            description='Eawag BBD compound c0001'
        ).default_structure

        product = Compound.create(
            self.package,
            smiles='C(CO)Cl',
            name='2-Chloroethanol',
            description='Eawag BBD compound c0005'
        ).default_structure

        with self.assertRaises(ValueError):
            _ = Reaction.create(
                package=self.package,
                name='Eawag BBD reaction r0001',
                educts=[educt],
                products=[],
                multi_step=False
            )

        with self.assertRaises(ValueError):
            _ = Reaction.create(
                package=self.package,
                name='Eawag BBD reaction r0001',
                educts=[],
                products=[product],
                multi_step=False
            )

        with self.assertRaises(ValueError):
            _ = Reaction.create(
                package=self.package,
                name='Eawag BBD reaction r0001',
                educts=[],
                products=[],
                multi_step=False
            )

    def test_empty_name_and_description_are_ignored(self):
        r = Reaction.create(
            package=self.package,
            name='',
            description='',
            educts=['C(CCl)Cl'],
            products=['C(CO)Cl'],
            multi_step=False,
        )

        self.assertEqual(r.name, 'no name')
        self.assertEqual(r.description, 'no description')

    def test_deduplication(self):
        rule = Rule.create(
            package=self.package,
            rule_type='SimpleAmbitRule',
            name='bt0022-2833',
            description='Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative',
            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]',
        )

        r1 = Reaction.create(
            package=self.package,
            name='Eawag BBD reaction r0001',
            educts=['C(CCl)Cl'],
            products=['C(CO)Cl'],
            rules=[rule],
            multi_step=False
        )

        r2 = Reaction.create(
            package=self.package,
            name='Eawag BBD reaction r0001',
            educts=['C(CCl)Cl'],
            products=['C(CO)Cl'],
            rules=[rule],
            multi_step=False
        )

        # Check if create detects that this Compound already exist
        # In this case the existing object should be returned
        self.assertEqual(r1.pk, r2.pk)
        self.assertEqual(len(self.package.reactions), 1)

    def test_deduplication_without_rules(self):
        r1 = Reaction.create(
            package=self.package,
            name='Eawag BBD reaction r0001',
            educts=['C(CCl)Cl'],
            products=['C(CO)Cl'],
            multi_step=False
        )

        r2 = Reaction.create(
            package=self.package,
            name='Eawag BBD reaction r0001',
            educts=['C(CCl)Cl'],
            products=['C(CO)Cl'],
            multi_step=False
        )

        # Check if create detects that this Compound already exist
        # In this case the existing object should be returned
        self.assertEqual(r1.pk, r2.pk)
        self.assertEqual(len(self.package.reactions), 1)

    def test_wrong_smiles(self):
        with self.assertRaises(ValueError):
            _ = Reaction.create(
                package=self.package,
                name='Eawag BBD reaction r0001',
                educts=['ASDF'],
                products=['C(CO)Cl'],
                multi_step=False
            )

    def test_delete(self):
        r = Reaction.create(
            package=self.package,
            name='Eawag BBD reaction r0001',
            educts=['C(CCl)Cl'],
            products=['C(CO)Cl'],
            multi_step=False
        )

        r.delete()

        self.assertEqual(Reaction.objects.filter(package=self.package).count(), 0)