forked from enviPath/enviPy
Liam Brydon
901de4640c
**This pull request will need a separate migration pull-request**
I have added an alert box in two places when the user tries to predict with stereo chemistry.
When a user predicts a pathway with stereo chemistry an alert box is shown in that node's hover.
To do this I added two new fields. Pathway now has a "predicted" BooleanField indicating whether it was predicted or not. It is set to True if the pathway mode for prediction is "predict" or "incremental" and False if it is "build". I think it is a flag that could be useful in the future, perhaps for analysing how many predicted pathways are in enviPath?
Node now has a `stereo_removed` BooleanField which is set to True if the Node's parent Pathways has "predicted" as true and the node SMILES has stereochemistry.
<img width="500" alt="{927AC9FF-DBC9-4A19-9E6E-0EDD3B08C7AC}.png" src="attachments/69ea29bc-c2d2-4cd2-8e98-aae5c5737f69">
When a user does a prediction on a model's page it shows at the top of the list. This did not require any new fields as the entered SMILES does not get saved anywhere.
<img width="500" alt="{BED66F12-5F07-419E-AAA6-FE1FE5B4F266}.png" src="attachments/5fcc3a9b-4d1a-4e48-acac-76b7571f6507">
I think the alert box is an alright solution but if you have a great idea for something that looks/fits better please change it or let me know.
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#250
Co-authored-by: Liam Brydon <lbry121@aucklanduni.ac.nz>
Co-committed-by: Liam Brydon <lbry121@aucklanduni.ac.nz>
393 lines
14 KiB
Python
393 lines
14 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 Reaction, 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 ReactionViewTest(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(ReactionViewTest, 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_reaction(self):
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response = self.client.post(
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reverse("reactions"),
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{
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"reaction-name": "Eawag BBD reaction r0001",
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"reaction-description": "Description for Eawag BBD reaction r0001",
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"reaction-smirks": "C(CCl)Cl>>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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reaction_url = response.url
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r = Reaction.objects.get(url=reaction_url)
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self.assertEqual(r.package, self.user1_default_package)
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self.assertEqual(r.name, "Eawag BBD reaction r0001")
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self.assertEqual(r.description, "Description for Eawag BBD reaction r0001")
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self.assertEqual(r.smirks(), "C(CCl)Cl>>C(CO)Cl")
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self.assertEqual(self.user1_default_package.reactions.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("reactions"),
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{
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"reaction-name": "Eawag BBD reaction r0001",
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"reaction-description": "Description for Eawag BBD reaction r0001",
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"reaction-smirks": "C(CCl)Cl>>C(CO)Cl",
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},
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)
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self.assertEqual(response.url, reaction_url)
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self.assertEqual(response.status_code, 302)
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self.assertEqual(self.user1_default_package.reactions.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 reaction list", kwargs={"package_uuid": self.package.uuid}),
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{
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"reaction-name": "Eawag BBD reaction r0001",
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"reaction-description": "Description for Eawag BBD reaction r0001",
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"reaction-smirks": "C(CCl)Cl>>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.assertNotEqual(reaction_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("reactions"),
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{
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"reaction-name": "Eawag BBD reaction r0002",
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"reaction-description": "Description for Eawag BBD reaction r0002",
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"reaction-smirks": "C(CO)Cl>>C(C=O)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.reactions.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("reactions"),
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{
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"reaction-name": "Eawag BBD reaction r0001",
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"reaction-description": "Description for Eawag BBD reaction r0001",
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"reaction-smirks": "C(CCl)Cl>>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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reaction_url = response.url
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r = Reaction.objects.get(url=reaction_url)
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response = self.client.post(
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reverse(
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"package reaction detail",
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kwargs={
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"package_uuid": str(self.user1_default_package.uuid),
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"reaction_uuid": str(r.uuid),
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},
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),
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{
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"reaction-name": "Test Reaction Adjusted",
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"reaction-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 = Reaction.objects.get(url=reaction_url)
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self.assertEqual(r.name, "Test Reaction Adjusted")
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self.assertEqual(r.description, "New Description")
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# Rest stays untouched
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self.assertEqual(r.smirks(), "C(CCl)Cl>>C(CO)Cl")
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self.assertEqual(self.user1_default_package.reactions.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("reactions"),
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{
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"reaction-name": "Eawag BBD reaction r0001",
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"reaction-description": "Description for Eawag BBD reaction r0001",
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"reaction-smirks": "C(CCl)Cl>>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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reaction_url = response.url
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r = Reaction.objects.get(url=reaction_url)
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response = self.client.post(
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reverse(
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"package reaction detail",
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kwargs={"package_uuid": str(r.package.uuid), "reaction_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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self.assertEqual(len(r.scenarios.all()), 2)
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response = self.client.post(
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reverse(
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"package reaction detail",
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kwargs={"package_uuid": str(r.package.uuid), "reaction_uuid": str(r.uuid)},
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),
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{"selected-scenarios": [s1.url]},
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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(
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"package reaction detail",
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kwargs={"package_uuid": str(r.package.uuid), "reaction_uuid": str(r.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(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("reactions"),
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{
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"reaction-name": "Eawag BBD reaction r0001",
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"reaction-description": "Description for Eawag BBD reaction r0001",
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"reaction-smirks": "C(CCl)Cl>>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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reaction_url = response.url
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r = Reaction.objects.get(url=reaction_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": r.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_reaction = Reaction.objects.get(url=copied_object_url)
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self.assertEqual(copied_reaction.name, r.name)
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self.assertEqual(copied_reaction.description, r.description)
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self.assertEqual(copied_reaction.smirks(), r.smirks())
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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(r.package.uuid),
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},
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),
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{"hidden": "copy", "object_to_copy": r.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 {reaction_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="KEGG Reaction",
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defaults={
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"full_name": "KEGG Reaction Database",
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"description": "Database of biochemical reactions",
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"base_url": "https://www.genome.jp",
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"url_pattern": "https://www.genome.jp/entry/{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="RHEA",
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defaults={
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"full_name": "RHEA Reaction Database",
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"description": "Comprehensive resource of biochemical reactions",
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"base_url": "https://www.rhea-db.org",
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"url_pattern": "https://www.rhea-db.org/rhea/{id}",
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},
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)
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response = self.client.post(
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reverse("reactions"),
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{
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"reaction-name": "Eawag BBD reaction r0001",
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"reaction-description": "Description for Eawag BBD reaction r0001",
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"reaction-smirks": "C(CCl)Cl>>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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reaction_url = response.url
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r = Reaction.objects.get(url=reaction_url)
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response = self.client.post(
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reverse(
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"package reaction detail",
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kwargs={
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"package_uuid": str(r.package.uuid),
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"reaction_uuid": str(r.uuid),
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},
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),
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{"selected-database": ext_db.pk, "identifier": "C12345"},
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)
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self.assertEqual(r.external_identifiers.count(), 1)
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self.assertEqual(r.external_identifiers.first().database, ext_db)
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self.assertEqual(r.external_identifiers.first().identifier_value, "C12345")
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# TODO Fixture contains old url template there the real test fails, use old value instead
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# self.assertEqual(r.external_identifiers.first().url, 'https://www.genome.jp/entry/C12345')
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self.assertEqual(
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r.external_identifiers.first().url, "https://www.genome.jp/entry/reaction+C12345"
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)
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response = self.client.post(
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reverse(
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"package reaction detail",
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kwargs={
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"package_uuid": str(r.package.uuid),
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"reaction_uuid": str(r.uuid),
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},
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),
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{"selected-database": ext_db2.pk, "identifier": "60116"},
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)
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self.assertEqual(r.external_identifiers.count(), 2)
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self.assertEqual(r.external_identifiers.last().database, ext_db2)
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self.assertEqual(r.external_identifiers.last().identifier_value, "60116")
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self.assertEqual(r.external_identifiers.last().url, "https://www.rhea-db.org/rhea/60116")
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def test_delete(self):
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response = self.client.post(
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reverse("reactions"),
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{
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"reaction-name": "Eawag BBD reaction r0001",
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"reaction-description": "Description for Eawag BBD reaction r0001",
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"reaction-smirks": "C(CCl)Cl>>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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reaction_url = response.url
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r = Reaction.objects.get(url=reaction_url)
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response = self.client.post(
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reverse(
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"package reaction detail",
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kwargs={"package_uuid": str(r.package.uuid), "reaction_uuid": str(r.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.reactions.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("reactions"),
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{
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"reaction-name": "Eawag BBD reaction r0001",
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"reaction-description": "Description for Eawag BBD reaction r0001",
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"reaction-smirks": "C(CCl)Cl>>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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reaction_url = response.url
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r = Reaction.objects.get(url=reaction_url)
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response = self.client.post(
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reverse(
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"package reaction detail",
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kwargs={"package_uuid": str(r.package.uuid), "reaction_uuid": str(r.uuid)},
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),
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{"aliases": [alias_1, alias_2]},
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)
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r = Reaction.objects.get(url=reaction_url)
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self.assertEqual(len(r.aliases), 2)
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response = self.client.post(
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reverse(
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"package reaction detail",
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kwargs={"package_uuid": str(r.package.uuid), "reaction_uuid": str(r.uuid)},
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),
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{"aliases": [alias_1]},
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)
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r = Reaction.objects.get(url=reaction_url)
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self.assertEqual(len(r.aliases), 1)
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response = self.client.post(
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reverse(
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"package reaction detail",
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kwargs={"package_uuid": str(r.package.uuid), "reaction_uuid": str(r.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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r = Reaction.objects.get(url=reaction_url)
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self.assertEqual(len(r.aliases), 0)
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