forked from enviPath/enviPy
507 lines
19 KiB
Python
507 lines
19 KiB
Python
from django.conf import settings as s
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from django.test import TestCase, override_settings
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from django.urls import reverse
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from envipy_additional_information import Temperature, Interval
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from epdb.logic import UserManager, PackageManager
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from epdb.models import Compound, Scenario, ExternalDatabase
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@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
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class CompoundViewTest(TestCase):
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fixtures = ["test_fixtures_incl_model.jsonl.gz"]
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# A valid V2000 molfile for 4-Nitrobenzoic acid (O=C(O)C1=CC=C([N+](=O)[O-])C=C1)
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VALID_MOLFILE = """\n Mrv2211 01012500002D\n\n 12 12 0 0 0 0 999 V2000\n 1.4289 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.7145 -2.0625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.4289 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.7145 1.2375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1.4289 0.8250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.7145 -2.8875 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0\n 0.0000 -3.3000 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0\n 1.4289 -3.3000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 2 0 0 0 0\n 2 3 1 0 0 0 0\n 3 4 2 0 0 0 0\n 4 5 1 0 0 0 0\n 5 6 2 0 0 0 0\n 6 1 1 0 0 0 0\n 2 7 1 0 0 0 0\n 7 8 2 0 0 0 0\n 7 9 1 0 0 0 0\n 5 10 1 0 0 0 0\n 10 11 1 0 0 0 0\n 10 12 2 0 0 0 0\nM CHG 2 10 1 11 -1\nM END\n"""
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@classmethod
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def setUpClass(cls):
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super(CompoundViewTest, cls).setUpClass()
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cls.user1 = UserManager.create_user(
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"user1",
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"user1@envipath.com",
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"SuperSafe",
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set_setting=False,
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add_to_group=True,
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is_active=True,
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)
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cls.user1_default_package = cls.user1.default_package
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cls.package = PackageManager.create_package(cls.user1, "Test", "Test Pack")
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def setUp(self):
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self.client.force_login(self.user1)
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def test_create_compound(self):
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response = self.client.post(
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reverse("compounds"),
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{
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"compound-name": "1,2-Dichloroethane",
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"compound-description": "Eawag BBD compound c0001",
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"compound-smiles": "C(CCl)Cl",
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},
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)
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self.assertEqual(response.status_code, 302)
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compound_url = response.url
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c = Compound.objects.get(url=compound_url)
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self.assertEqual(c.package, self.user1_default_package)
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self.assertEqual(c.name, "1,2-Dichloroethane")
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self.assertEqual(c.description, "Eawag BBD compound c0001")
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self.assertEqual(c.default_structure.smiles, "C(CCl)Cl")
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self.assertEqual(c.default_structure.canonical_smiles, "ClCCCl")
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self.assertEqual(c.structures.all().count(), 2)
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self.assertEqual(self.user1_default_package.compounds.count(), 1)
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# Adding the same rule again should return the existing one, hence not increasing the number of rules
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response = self.client.post(
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reverse("compounds"),
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{
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"compound-name": "1,2-Dichloroethane",
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"compound-description": "Eawag BBD compound c0001",
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"compound-smiles": "C(CCl)Cl",
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},
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)
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self.assertEqual(response.url, compound_url)
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self.assertEqual(response.status_code, 302)
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self.assertEqual(self.user1_default_package.compounds.count(), 1)
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# Adding the same rule in a different package should create a new rule
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response = self.client.post(
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reverse("package compound list", kwargs={"package_uuid": self.package.uuid}),
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{
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"compound-name": "1,2-Dichloroethane",
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"compound-description": "Eawag BBD compound c0001",
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"compound-smiles": "C(CCl)Cl",
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},
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)
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self.assertEqual(response.status_code, 302)
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self.assertNotEqual(compound_url, response.url)
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# adding another reaction should increase count
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response = self.client.post(
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reverse("compounds"),
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{
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"compound-name": "2-Chloroethanol",
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"compound-description": "Eawag BBD compound c0005",
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"compound-smiles": "C(CO)Cl",
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},
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)
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self.assertEqual(response.status_code, 302)
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self.assertEqual(self.user1_default_package.compounds.count(), 2)
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# Edit
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def test_edit_rule(self):
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response = self.client.post(
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reverse("compounds"),
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{
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"compound-name": "1,2-Dichloroethane",
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"compound-description": "Eawag BBD compound c0001",
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"compound-smiles": "C(CCl)Cl",
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},
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)
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self.assertEqual(response.status_code, 302)
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compound_url = response.url
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c = Compound.objects.get(url=compound_url)
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response = self.client.post(
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reverse(
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"package compound detail",
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kwargs={
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"package_uuid": str(self.user1_default_package.uuid),
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"compound_uuid": str(c.uuid),
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},
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),
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{
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"compound-name": "Test Compound Adjusted",
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"compound-description": "New Description",
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},
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)
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self.assertEqual(response.status_code, 302)
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c = Compound.objects.get(url=compound_url)
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self.assertEqual(c.name, "Test Compound Adjusted")
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self.assertEqual(c.description, "New Description")
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# Rest stays untouched
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self.assertEqual(c.default_structure.smiles, "C(CCl)Cl")
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self.assertEqual(self.user1_default_package.compounds.count(), 1)
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# Scenario
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def test_set_scenario(self):
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s1 = Scenario.create(
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self.user1_default_package,
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"Test Scen",
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"Test Desc",
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"2025-10",
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"soil",
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[Temperature(interval=Interval(start=20, end=30))],
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)
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s2 = Scenario.create(
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self.user1_default_package,
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"Test Scen2",
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"Test Desc2",
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"2025-10",
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"soil",
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[Temperature(interval=Interval(start=10, end=20))],
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)
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response = self.client.post(
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reverse("compounds"),
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{
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"compound-name": "1,2-Dichloroethane",
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"compound-description": "Eawag BBD compound c0001",
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"compound-smiles": "C(CCl)Cl",
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},
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)
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self.assertEqual(response.status_code, 302)
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compound_url = response.url
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c = Compound.objects.get(url=compound_url)
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response = self.client.post(
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reverse(
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"package compound detail",
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kwargs={"package_uuid": str(c.package.uuid), "compound_uuid": str(c.uuid)},
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),
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{"selected-scenarios": [s1.url, s2.url]},
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)
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self.assertEqual(len(c.scenarios.all()), 2)
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response = self.client.post(
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reverse(
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"package compound detail",
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kwargs={"package_uuid": str(c.package.uuid), "compound_uuid": str(c.uuid)},
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),
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{"selected-scenarios": [s1.url]},
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)
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self.assertEqual(len(c.scenarios.all()), 1)
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self.assertEqual(c.scenarios.first().url, s1.url)
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response = self.client.post(
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reverse(
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"package compound detail",
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kwargs={"package_uuid": str(c.package.uuid), "compound_uuid": str(c.uuid)},
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),
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{
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# We have to set an empty string to avoid that the parameter is removed
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"selected-scenarios": ""
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},
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)
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self.assertEqual(len(c.scenarios.all()), 0)
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#
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def test_copy(self):
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response = self.client.post(
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reverse("compounds"),
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{
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"compound-name": "1,2-Dichloroethane",
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"compound-description": "Eawag BBD compound c0001",
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"compound-smiles": "C(CCl)Cl",
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},
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)
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self.assertEqual(response.status_code, 302)
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compound_url = response.url
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c = Compound.objects.get(url=compound_url)
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response = self.client.post(
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reverse(
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"package detail",
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kwargs={
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"package_uuid": str(self.package.uuid),
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},
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),
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{"hidden": "copy", "object_to_copy": c.url},
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)
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self.assertEqual(response.status_code, 200)
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copied_object_url = response.json()["success"]
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copied_compound = Compound.objects.get(url=copied_object_url)
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self.assertEqual(copied_compound.name, c.name)
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self.assertEqual(copied_compound.description, c.description)
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self.assertEqual(copied_compound.default_structure.smiles, c.default_structure.smiles)
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# Copy to the same package should fail
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response = self.client.post(
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reverse(
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"package detail",
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kwargs={
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"package_uuid": str(c.package.uuid),
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},
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),
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{"hidden": "copy", "object_to_copy": c.url},
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)
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self.assertEqual(response.status_code, 400)
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self.assertEqual(
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response.json()["error"], f"Can't copy object {compound_url} to the same package!"
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)
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def test_references(self):
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ext_db, _ = ExternalDatabase.objects.get_or_create(
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name="PubChem Compound",
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defaults={
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"full_name": "PubChem Compound Database",
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"description": "Chemical database of small organic molecules",
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"base_url": "https://pubchem.ncbi.nlm.nih.gov",
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"url_pattern": "https://pubchem.ncbi.nlm.nih.gov/compound/{id}",
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},
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)
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ext_db2, _ = ExternalDatabase.objects.get_or_create(
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name="PubChem Substance",
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defaults={
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"full_name": "PubChem Substance Database",
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"description": "Database of chemical substances",
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"base_url": "https://pubchem.ncbi.nlm.nih.gov",
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"url_pattern": "https://pubchem.ncbi.nlm.nih.gov/substance/{id}",
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},
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)
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response = self.client.post(
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reverse("compounds"),
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{
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"compound-name": "1,2-Dichloroethane",
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"compound-description": "Eawag BBD compound c0001",
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"compound-smiles": "C(CCl)Cl",
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},
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)
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self.assertEqual(response.status_code, 302)
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compound_url = response.url
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c = Compound.objects.get(url=compound_url)
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response = self.client.post(
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reverse(
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"package compound detail",
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kwargs={
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"package_uuid": str(c.package.uuid),
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"compound_uuid": str(c.uuid),
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},
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),
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{"selected-database": ext_db.pk, "identifier": "25154249"},
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)
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self.assertEqual(c.external_identifiers.count(), 1)
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self.assertEqual(c.external_identifiers.first().database, ext_db)
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self.assertEqual(c.external_identifiers.first().identifier_value, "25154249")
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self.assertEqual(
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c.external_identifiers.first().url, "https://pubchem.ncbi.nlm.nih.gov/compound/25154249"
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)
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response = self.client.post(
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reverse(
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"package compound detail",
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kwargs={
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"package_uuid": str(c.package.uuid),
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"compound_uuid": str(c.uuid),
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},
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),
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{"selected-database": ext_db2.pk, "identifier": "25154249"},
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)
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self.assertEqual(c.external_identifiers.count(), 2)
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self.assertEqual(c.external_identifiers.last().database, ext_db2)
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self.assertEqual(c.external_identifiers.last().identifier_value, "25154249")
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self.assertEqual(
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c.external_identifiers.last().url, "https://pubchem.ncbi.nlm.nih.gov/substance/25154249"
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)
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def test_delete(self):
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response = self.client.post(
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reverse("compounds"),
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{
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"compound-name": "1,2-Dichloroethane",
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"compound-description": "Eawag BBD compound c0001",
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"compound-smiles": "C(CCl)Cl",
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},
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)
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self.assertEqual(response.status_code, 302)
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compound_url = response.url
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c = Compound.objects.get(url=compound_url)
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response = self.client.post(
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reverse(
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"package compound detail",
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kwargs={"package_uuid": str(c.package.uuid), "compound_uuid": str(c.uuid)},
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),
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{"hidden": "delete"},
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)
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self.assertEqual(self.user1_default_package.compounds.count(), 0)
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def test_set_aliases(self):
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alias_1 = "Alias 1"
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alias_2 = "Alias 2"
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response = self.client.post(
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reverse("compounds"),
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{
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"compound-name": "1,2-Dichloroethane",
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"compound-description": "Eawag BBD compound c0001",
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"compound-smiles": "C(CCl)Cl",
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},
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)
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self.assertEqual(response.status_code, 302)
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compound_url = response.url
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c = Compound.objects.get(url=compound_url)
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response = self.client.post(
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reverse(
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"package compound detail",
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kwargs={"package_uuid": str(c.package.uuid), "compound_uuid": str(c.uuid)},
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),
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{"aliases": [alias_1, alias_2]},
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)
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c = Compound.objects.get(url=compound_url)
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self.assertEqual(len(c.aliases), 2)
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response = self.client.post(
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reverse(
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"package compound detail",
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kwargs={"package_uuid": str(c.package.uuid), "compound_uuid": str(c.uuid)},
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),
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{"aliases": [alias_1]},
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)
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c = Compound.objects.get(url=compound_url)
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self.assertEqual(len(c.aliases), 1)
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response = self.client.post(
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reverse(
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"package compound detail",
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kwargs={"package_uuid": str(c.package.uuid), "compound_uuid": str(c.uuid)},
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),
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{
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# We have to set an empty string to avoid that the parameter is removed
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"aliases": ""
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},
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)
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c = Compound.objects.get(url=compound_url)
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self.assertEqual(len(c.aliases), 0)
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def test_create_compound_via_molfile(self):
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"""POSTing a valid molfile without a SMILES should create a compound successfully."""
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response = self.client.post(
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reverse("compounds"),
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{
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"compound-name": "4-Nitrobenzoic acid",
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"compound-description": "Created from molfile",
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"compound-molfile": self.VALID_MOLFILE,
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},
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)
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self.assertEqual(response.status_code, 302)
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compound_url = response.url
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c = Compound.objects.get(url=compound_url)
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self.assertEqual(c.name, "4-Nitrobenzoic acid")
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self.assertEqual(c.description, "Created from molfile")
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# SMILES should have been extracted from molfile, so it must be non-empty
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self.assertIsNotNone(c.default_structure.smiles)
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self.assertNotEqual(c.default_structure.smiles.strip(), "")
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def test_create_compound_molfile_takes_precedence_over_smiles(self):
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"""When both molfile and SMILES are submitted, the molfile should win."""
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response = self.client.post(
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reverse("compounds"),
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{
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"compound-name": "4-Nitrobenzoic acid",
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"compound-description": "Molfile precedence test",
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"compound-smiles": "C", # intentionally wrong/different
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"compound-molfile": self.VALID_MOLFILE,
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},
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)
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self.assertEqual(response.status_code, 302)
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compound_url = response.url
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c = Compound.objects.get(url=compound_url)
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# The resulting SMILES must NOT be the dummy "C" supplied via compound-smiles
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self.assertNotEqual(c.default_structure.smiles, "C")
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def test_create_compound_via_invalid_molfile_returns_error(self):
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"""POSTing an invalid molfile should not create a compound and should return an error response."""
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initial_count = self.user1_default_package.compounds.count()
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response = self.client.post(
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reverse("compounds"),
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{
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"compound-name": "Bad Molfile Compound",
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"compound-description": "Should fail",
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"compound-molfile": "this is not a molfile at all",
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},
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)
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# The view should signal an error (non-2xx or a redirect to an error page, not 302 to a new compound)
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self.assertNotEqual(response.status_code, 302)
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# No new compound should have been created
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self.assertEqual(self.user1_default_package.compounds.count(), initial_count)
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def test_create_compound_via_empty_molfile_falls_back_to_smiles(self):
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"""Submitting an empty molfile with a valid SMILES should fall back to SMILES."""
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response = self.client.post(
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reverse("compounds"),
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{
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"compound-name": "Fallback SMILES Compound",
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"compound-description": "Empty molfile fallback",
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"compound-smiles": "C(CCl)Cl",
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"compound-molfile": " ", # whitespace only
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},
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)
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self.assertEqual(response.status_code, 302)
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compound_url = response.url
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c = Compound.objects.get(url=compound_url)
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self.assertEqual(c.default_structure.smiles, "C(CCl)Cl")
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def test_create_compound_via_molfile_deduplication(self):
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"""Submitting the same molfile twice should return the existing compound."""
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response1 = self.client.post(
|
|
reverse("compounds"),
|
|
{
|
|
"compound-name": "4-Nitrobenzoic acid",
|
|
"compound-description": "Molfile dedup test",
|
|
"compound-molfile": self.VALID_MOLFILE,
|
|
},
|
|
)
|
|
|
|
self.assertEqual(response1.status_code, 302)
|
|
compound_url_1 = response1.url
|
|
|
|
response2 = self.client.post(
|
|
reverse("compounds"),
|
|
{
|
|
"compound-name": "4-Nitrobenzoic acid",
|
|
"compound-description": "Molfile dedup test",
|
|
"compound-molfile": self.VALID_MOLFILE,
|
|
},
|
|
)
|
|
|
|
self.assertEqual(response2.status_code, 302)
|
|
self.assertEqual(response2.url, compound_url_1)
|
|
self.assertEqual(self.user1_default_package.compounds.count(), 1)
|