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[Misc] Performance improvements, SMIRKS Coverage, Minor Bugfixes (#132)

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Bump Python Version to 3.12
Make use of "epauth" optional
Cache `srs` property of rules to speed up apply
Adjust view names for use of `reverse()`
Fix Views for Scenario Attachments
Added Simply Compare View/Template to identify differences between rdkit and ambit
Make migrations consistent with tests + compare
Fixes #76
Set default year for Scenario Modal
Fix html tags for package description
Added Tests for Pathway / Rule
Added remove stereo for apply

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#132
This commit is contained in:
jebus
2025-09-26 19:33:03 +12:00
parent b5c759d74e
commit b757a07f91
23 changed files with 671 additions and 463 deletions
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tests/views/test_pathway_views.py Normal file
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from django.test import TestCase, override_settings
from django.urls import reverse
from django.conf import settings as s
from epdb.logic import UserManager, PackageManager
from epdb.models import Pathway, Edge
@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models")
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)