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>
260 lines
8.7 KiB
Python
260 lines
8.7 KiB
Python
from django.conf import settings as s
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from django.core.files.uploadedfile import SimpleUploadedFile
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from django.test import TestCase, override_settings, tag
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from django.urls import reverse
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from epdb.logic import UserManager
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from epdb.models import (
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Group,
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GroupPackagePermission,
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License,
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Permission,
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UserPackagePermission,
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)
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Package = s.GET_PACKAGE_MODEL()
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@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
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class PackageViewTest(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(PackageViewTest, 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.user2 = UserManager.create_user(
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"user2",
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"user2@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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# Create the default license set.
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cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
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for cc_string in cc_strings:
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if not License.objects.filter(cc_string=cc_string).exists():
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new_license = License()
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new_license.cc_string = cc_string
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new_license.link = f"https://creativecommons.org/licenses/{cc_string}/4.0/"
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new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
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new_license.save()
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def setUp(self):
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self.client.force_login(self.user1)
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def test_create_package(self):
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response = self.client.post(
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reverse("packages"),
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{
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"package-name": "Test Package",
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"package-description": "Just a Description",
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},
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)
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self.assertEqual(response.status_code, 302)
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package_url = response.url
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p = Package.objects.get(url=package_url)
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self.assertEqual(p.name, "Test Package")
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self.assertEqual(p.description, "Just a Description")
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upp = UserPackagePermission.objects.get(package=p, user=self.user1)
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self.assertEqual(upp.permission, Permission.ALL[0])
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def test_import_package(self):
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file = SimpleUploadedFile(
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"Fixture_Package.json",
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open(s.FIXTURE_DIRS[0] / "Fixture_Package.json", "rb").read(),
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content_type="application/json",
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)
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response = self.client.post(
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reverse("packages"), {"file": file, "hidden": "import-package-json"}
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)
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self.assertEqual(response.status_code, 302)
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package_url = response.url
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p = Package.objects.get(url=package_url)
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self.assertEqual(p.pathways.count(), 22)
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self.assertEqual(p.rules.count(), 45)
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self.assertEqual(p.compounds.count(), 223)
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self.assertEqual(p.reactions.count(), 212)
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upp = UserPackagePermission.objects.get(package=p, user=self.user1)
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self.assertEqual(upp.permission, Permission.ALL[0])
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@tag("slow")
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def test_import_legacy_package(self):
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file = SimpleUploadedFile(
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"EAWAG-BBD.json",
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open(s.FIXTURE_DIRS[0] / "packages" / "2025-07-18" / "EAWAG-BBD.json", "rb").read(),
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content_type="application/json",
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)
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response = self.client.post(
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reverse("packages"), {"file": file, "hidden": "import-legacy-package-json"}
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)
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self.assertEqual(response.status_code, 302)
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package_url = response.url
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p = Package.objects.get(url=package_url)
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self.assertEqual(p.pathways.count(), 219)
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self.assertEqual(p.rules.count(), 498)
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self.assertEqual(p.compounds.count(), 1399)
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self.assertEqual(p.reactions.count(), 1480)
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self.assertEqual(p.scenarios.count(), 1914)
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upp = UserPackagePermission.objects.get(package=p, user=self.user1)
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self.assertEqual(upp.permission, Permission.ALL[0])
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def test_edit_package(self):
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response = self.client.post(
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reverse("packages"),
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{
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"package-name": "Test Package",
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"package-description": "Just a Description",
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},
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)
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self.assertEqual(response.status_code, 302)
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package_url = response.url
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self.client.post(
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package_url,
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{
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"package-name": "New Name",
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"package-description": "New Description",
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},
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)
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p = Package.objects.get(url=package_url)
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self.assertEqual(p.name, "New Name")
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self.assertEqual(p.description, "New Description")
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def test_edit_package_permissions(self):
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response = self.client.post(
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reverse("packages"),
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{
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"package-name": "Test Package",
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"package-description": "Just a Description",
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},
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)
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self.assertEqual(response.status_code, 302)
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package_url = response.url
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p = Package.objects.get(url=package_url)
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with self.assertRaises(UserPackagePermission.DoesNotExist):
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UserPackagePermission.objects.get(package=p, user=self.user2)
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self.client.post(
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package_url,
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{
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"grantee": self.user2.url,
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"read": "on",
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"write": "on",
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},
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)
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upp = UserPackagePermission.objects.get(package=p, user=self.user2)
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self.assertEqual(upp.permission, Permission.WRITE[0])
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def test_publish_package(self):
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response = self.client.post(
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reverse("packages"),
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{
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"package-name": "Test Package",
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"package-description": "Just a Description",
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},
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)
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self.assertEqual(response.status_code, 302)
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package_url = response.url
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p = Package.objects.get(url=package_url)
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self.client.post(package_url, {"hidden": "publish-package"})
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self.assertEqual(Group.objects.filter(public=True).count(), 1)
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g = Group.objects.get(public=True)
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gpp = GroupPackagePermission.objects.get(package=p, group=g)
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self.assertEqual(gpp.permission, Permission.READ[0])
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def test_set_package_license(self):
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response = self.client.post(
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reverse("packages"),
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{
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"package-name": "Test Package",
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"package-description": "Just a Description",
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},
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)
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package_url = response.url
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p = Package.objects.get(url=package_url)
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self.client.post(package_url, {"license": "no-license"})
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self.assertIsNone(p.license)
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# Test other possible licenses
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cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
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for cc_string in cc_strings:
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self.client.post(package_url, {"license": cc_string})
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# Without this, the instance of p doesn't have the license. However, the one retrieved with get does
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p = Package.objects.get(url=package_url)
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self.assertEqual(
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p.license.link, f"https://creativecommons.org/licenses/{cc_string}/4.0/"
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)
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# Test again to ensure that Licenses are reused
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cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
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for cc_string in cc_strings:
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self.client.post(package_url, {"license": cc_string})
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# Without this, the instance of p doesn't have the license. However, the one retrieved with get does
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p = Package.objects.get(url=package_url)
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self.assertEqual(
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p.license.link, f"https://creativecommons.org/licenses/{cc_string}/4.0/"
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)
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self.assertEqual(License.objects.count(), len(cc_strings))
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def test_delete_package(self):
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response = self.client.post(
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reverse("packages"),
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{
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"package-name": "Test Package",
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"package-description": "Just a Description",
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},
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)
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package_url = response.url
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p = Package.objects.get(url=package_url)
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p.delete()
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response = self.client.get(package_url)
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self.assertEqual(response.status_code, 404)
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def test_delete_default_package(self):
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self.client.force_login(self.user1)
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# Try to delete the default package
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response = self.client.post(self.user1.default_package.url, {"hidden": "delete"})
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self.assertEqual(response.status_code, 400)
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self.assertTrue(
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"You cannot delete the default package. "
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"If you want to delete this package you have to "
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"set another default package first" in response.content.decode()
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)
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