enviPy-bayer/tests/views/test_pathway_views.py

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

from epdb.logic import PackageManager, UserManager
from epdb.models import Edge, Pathway

Package = s.GET_PACKAGE_MODEL()


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

    @classmethod
    def setUpClass(cls):
        super(PathwayViewTest, cls).setUpClass()
        cls.user1 = UserManager.create_user(
            "user1",
            "user1@envipath.com",
            "SuperSafe",
            set_setting=True,
            add_to_group=True,
            is_active=True,
        )
        cls.user1_default_package = cls.user1.default_package
        cls.package = PackageManager.create_package(cls.user1, "Test", "Test Pack")

    def setUp(self):
        self.client.force_login(self.user1)

    def test_predict_pathway(self):
        response = self.client.post(
            reverse("pathways"),
            {
                "name": "Test Pathway",
                "description": "Just a Description",
                "predict": "predict",
                "smiles": "CCN(CC)C(=O)C1=CC(=CC=C1)CO",
            },
        )
        self.assertEqual(response.status_code, 302)
        pathway_url = response.url

        pw = Pathway.objects.get(url=pathway_url)
        self.assertEqual(self.user1_default_package, pw.package)

        self.assertEqual(pw.name, "Test Pathway")
        self.assertEqual(pw.description, "Just a Description")
        self.assertEqual(len(pw.root_nodes), 1)
        self.assertEqual(
            pw.root_nodes.first().default_node_label.smiles, "CCN(CC)C(=O)C1=CC(CO)=CC=C1"
        )

        first_level_nodes = {
            # Edge 1
            "CCN(CC)C(=O)C1=CC(C=O)=CC=C1",
            # Edge 2
            "CCNC(=O)C1=CC(CO)=CC=C1",
            "CC=O",
            # Edge 3
            "CCNCC",
            "O=C(O)C1=CC(CO)=CC=C1",
        }

        predicted_nodes = set()
        edges = Edge.objects.filter(start_nodes__in=[pw.root_nodes.first()])

        for edge in edges:
            for n in edge.end_nodes.all():
                predicted_nodes.add(n.default_node_label.smiles)

        self.assertEqual(first_level_nodes, predicted_nodes)

    def test_predict_package_pathway(self):
        response = self.client.post(
            reverse("package pathway list", kwargs={"package_uuid": str(self.package.uuid)}),
            {
                "name": "Test Pathway",
                "description": "Just a Description",
                "predict": "predict",
                "smiles": "CCN(CC)C(=O)C1=CC(=CC=C1)CO",
            },
        )
        self.assertEqual(response.status_code, 302)
        pathway_url = response.url

        pw = Pathway.objects.get(url=pathway_url)
        self.assertEqual(self.package, pw.package)

        self.assertEqual(pw.name, "Test Pathway")
        self.assertEqual(pw.description, "Just a Description")
        self.assertEqual(len(pw.root_nodes), 1)
        self.assertEqual(
            pw.root_nodes.first().default_node_label.smiles, "CCN(CC)C(=O)C1=CC(CO)=CC=C1"
        )

        first_level_nodes = {
            # Edge 1
            "CCN(CC)C(=O)C1=CC(C=O)=CC=C1",
            # Edge 2
            "CCNC(=O)C1=CC(CO)=CC=C1",
            "CC=O",
            # Edge 3
            "CCNCC",
            "O=C(O)C1=CC(CO)=CC=C1",
        }

        predicted_nodes = set()
        edges = Edge.objects.filter(start_nodes__in=[pw.root_nodes.first()])

        for edge in edges:
            for n in edge.end_nodes.all():
                predicted_nodes.add(n.default_node_label.smiles)

        self.assertEqual(first_level_nodes, predicted_nodes)

    def test_set_aliases(self):
        alias_1 = "Alias 1"
        alias_2 = "Alias 2"

        response = self.client.post(
            reverse("package pathway list", kwargs={"package_uuid": str(self.package.uuid)}),
            {
                "name": "Test Pathway",
                "description": "Just a Description",
                "predict": "predict",
                "smiles": "CCN(CC)C(=O)C1=CC(=CC=C1)CO",
            },
        )

        self.assertEqual(response.status_code, 302)
        pathway_url = response.url
        pw = Pathway.objects.get(url=pathway_url)

        response = self.client.post(
            reverse(
                "package pathway detail",
                kwargs={"package_uuid": str(pw.package.uuid), "pathway_uuid": str(pw.uuid)},
            ),
            {"aliases": [alias_1, alias_2]},
        )

        pw = Pathway.objects.get(url=pathway_url)
        self.assertEqual(len(pw.aliases), 2)

        response = self.client.post(
            reverse(
                "package pathway detail",
                kwargs={"package_uuid": str(pw.package.uuid), "pathway_uuid": str(pw.uuid)},
            ),
            {"aliases": [alias_1]},
        )

        pw = Pathway.objects.get(url=pathway_url)
        self.assertEqual(len(pw.aliases), 1)

        response = self.client.post(
            reverse(
                "package pathway detail",
                kwargs={"package_uuid": str(pw.package.uuid), "pathway_uuid": str(pw.uuid)},
            ),
            {
                # We have to set an empty string to avoid that the parameter is removed
                "aliases": ""
            },
        )

        pw = Pathway.objects.get(url=pathway_url)
        self.assertEqual(len(pw.aliases), 0)