forked from enviPath/enviPy
[Misc] Performance improvements, SMIRKS Coverage, Minor Bugfixes (#132)
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
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98
tests/views/test_pathway_views.py
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98
tests/views/test_pathway_views.py
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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 django.conf import settings as s
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from epdb.logic import UserManager, PackageManager
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from epdb.models import Pathway, Edge
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@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models")
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class PathwayViewTest(TestCase):
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fixtures = ["test_fixtures_incl_model.jsonl.gz"]
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@classmethod
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def setUpClass(cls):
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super(PathwayViewTest, cls).setUpClass()
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cls.user1 = UserManager.create_user("user1", "user1@envipath.com", "SuperSafe",
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set_setting=True, add_to_group=True, is_active=True)
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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_predict_pathway(self):
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response = self.client.post(reverse("pathways"), {
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'name': 'Test Pathway',
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'description': 'Just a Description',
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'predict': 'predict',
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'smiles': 'CCN(CC)C(=O)C1=CC(=CC=C1)CO',
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})
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self.assertEqual(response.status_code, 302)
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pathway_url = response.url
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pw = Pathway.objects.get(url=pathway_url)
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self.assertEqual(self.user1_default_package, pw.package)
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self.assertEqual(pw.name, 'Test Pathway')
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self.assertEqual(pw.description, 'Just a Description')
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self.assertEqual(len(pw.root_nodes), 1)
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self.assertEqual(pw.root_nodes.first().default_node_label.smiles, 'CCN(CC)C(=O)C1=CC(CO)=CC=C1')
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first_level_nodes = {
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# Edge 1
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'CCN(CC)C(=O)C1=CC(C=O)=CC=C1',
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# Edge 2
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'CCNC(=O)C1=CC(CO)=CC=C1',
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'CC=O',
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# Edge 3
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'CCNCC',
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'O=C(O)C1=CC(CO)=CC=C1',
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}
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predicted_nodes = set()
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edges = Edge.objects.filter(start_nodes__in=[pw.root_nodes.first()])
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for edge in edges:
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for n in edge.end_nodes.all():
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predicted_nodes.add(n.default_node_label.smiles)
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self.assertEqual(first_level_nodes, predicted_nodes)
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def test_predict_package_pathway(self):
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response = self.client.post(
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reverse("package pathway list", kwargs={'package_uuid': str(self.package.uuid)}), {
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'name': 'Test Pathway',
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'description': 'Just a Description',
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'predict': 'predict',
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'smiles': 'CCN(CC)C(=O)C1=CC(=CC=C1)CO',
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})
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self.assertEqual(response.status_code, 302)
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pathway_url = response.url
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pw = Pathway.objects.get(url=pathway_url)
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self.assertEqual(self.package, pw.package)
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self.assertEqual(pw.name, 'Test Pathway')
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self.assertEqual(pw.description, 'Just a Description')
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self.assertEqual(len(pw.root_nodes), 1)
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self.assertEqual(pw.root_nodes.first().default_node_label.smiles, 'CCN(CC)C(=O)C1=CC(CO)=CC=C1')
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first_level_nodes = {
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# Edge 1
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'CCN(CC)C(=O)C1=CC(C=O)=CC=C1',
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# Edge 2
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'CCNC(=O)C1=CC(CO)=CC=C1',
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'CC=O',
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# Edge 3
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'CCNCC',
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'O=C(O)C1=CC(CO)=CC=C1',
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}
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predicted_nodes = set()
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edges = Edge.objects.filter(start_nodes__in=[pw.root_nodes.first()])
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for edge in edges:
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for n in edge.end_nodes.all():
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predicted_nodes.add(n.default_node_label.smiles)
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self.assertEqual(first_level_nodes, predicted_nodes)
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225
tests/views/test_rule_views.py
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225
tests/views/test_rule_views.py
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from django.test import TestCase
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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 Rule, Scenario
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class RuleViewTest(TestCase):
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fixtures = ["test_fixtures.jsonl.gz"]
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@classmethod
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def setUpClass(cls):
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super(RuleViewTest, cls).setUpClass()
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cls.user1 = UserManager.create_user("user1", "user1@envipath.com", "SuperSafe",
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set_setting=False, add_to_group=True, is_active=True)
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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_rule(self):
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response = self.client.post(
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reverse("rules"), {
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"rule-name": "Test Rule",
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"rule-description": "Just a Description",
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"rule-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]",
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"rule-type": "SimpleAmbitRule",
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}
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)
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self.assertEqual(response.status_code, 302)
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rule_url = response.url
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r = Rule.objects.get(url=rule_url)
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self.assertEqual(r.package, self.user1_default_package)
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self.assertEqual(r.name, "Test Rule")
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self.assertEqual(r.description, "Just a Description")
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self.assertEqual(r.smirks,
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"[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]")
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self.assertEqual(self.user1_default_package.rules.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("rules"), {
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"rule-name": "Test Rule",
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"rule-description": "Just a Description",
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"rule-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]",
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"rule-type": "SimpleAmbitRule",
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}
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)
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self.assertEqual(response.url, rule_url)
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self.assertEqual(response.status_code, 302)
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self.assertEqual(self.user1_default_package.rules.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 rule list", kwargs={'package_uuid': self.package.uuid}), {
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"rule-name": "Test Rule",
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"rule-description": "Just a Description",
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"rule-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]",
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"rule-type": "SimpleAmbitRule",
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}
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)
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self.assertEqual(response.status_code, 302)
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self.assertNotEqual(rule_url, response.url)
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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("rules"), {
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"rule-name": "Test Rule",
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"rule-description": "Just a Description",
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"rule-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]",
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"rule-type": "SimpleAmbitRule",
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}
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)
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self.assertEqual(response.status_code, 302)
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rule_url = response.url
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r = Rule.objects.get(url=rule_url)
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response = self.client.post(
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reverse("package rule detail", kwargs={
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'package_uuid': str(self.user1_default_package.uuid),
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'rule_uuid': str(r.uuid)
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}), {
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"rule-name": "Test Rule Adjusted",
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"rule-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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r = Rule.objects.get(url=rule_url)
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self.assertEqual(r.name, "Test Rule Adjusted")
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self.assertEqual(r.description, "New Description")
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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("rules"), {
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"rule-name": "Test Rule",
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"rule-description": "Just a Description",
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"rule-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]",
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"rule-type": "SimpleAmbitRule",
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}
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)
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self.assertEqual(response.status_code, 302)
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rule_url = response.url
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r = Rule.objects.get(url=rule_url)
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response = self.client.post(
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reverse("package rule detail", kwargs={
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'package_uuid': str(r.package.uuid),
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'rule_uuid': str(r.uuid)
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}), {
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"selected-scenarios": [s1.url, s2.url]
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}
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)
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self.assertEqual(len(r.scenarios.all()), 2)
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response = self.client.post(
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reverse("package rule detail", kwargs={
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'package_uuid': str(r.package.uuid),
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'rule_uuid': str(r.uuid)
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}), {
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"selected-scenarios": [s1.url]
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}
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)
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self.assertEqual(len(r.scenarios.all()), 1)
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self.assertEqual(r.scenarios.first().url, s1.url)
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response = self.client.post(
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reverse("package rule detail", kwargs={
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'package_uuid': str(r.package.uuid),
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'rule_uuid': str(r.uuid)
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}), {
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"selected-scenarios": []
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}
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)
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self.assertEqual(len(r.scenarios.all()), 0)
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def test_copy(self):
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response = self.client.post(
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reverse("rules"), {
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"rule-name": "Test Rule",
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"rule-description": "Just a Description",
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"rule-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]",
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"rule-type": "SimpleAmbitRule",
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}
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)
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self.assertEqual(response.status_code, 302)
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rule_url = response.url
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r = Rule.objects.get(url=rule_url)
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response = self.client.post(
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reverse("package detail", kwargs={
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'package_uuid': str(r.package.uuid),
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}), {
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"hidden": "copy",
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"object_to_copy": r.url
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}
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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_rule = Rule.objects.get(url=copied_object_url)
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self.assertEqual(copied_rule.name, r.name)
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self.assertEqual(copied_rule.description, r.description)
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self.assertEqual(copied_rule.smirks, r.smirks)
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def test_delete(self):
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response = self.client.post(
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reverse("rules"), {
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"rule-name": "Test Rule",
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"rule-description": "Just a Description",
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"rule-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]",
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"rule-type": "SimpleAmbitRule",
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}
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)
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self.assertEqual(response.status_code, 302)
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rule_url = response.url
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r = Rule.objects.get(url=rule_url)
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response = self.client.post(
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reverse("package rule detail", kwargs={
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'package_uuid': str(r.package.uuid),
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'rule_uuid': str(r.uuid)
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}), {
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"hidden": "delete"
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}
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)
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self.assertEqual(self.user1_default_package.rules.count(), 0)
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