enviPy-bayer/tests/test_reaction_model.py

from django.conf import settings as s
from django.test import TestCase, override_settings

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


@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
class ReactionTest(TestCase):
    fixtures = ["test_fixtures_incl_model.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)