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>
191 lines
6.6 KiB
Python
191 lines
6.6 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 epdb.logic import PackageManager
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from epdb.models import Compound, User, CompoundStructure
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@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
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class CompoundTest(TestCase):
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fixtures = ["test_fixtures_incl_model.jsonl.gz"]
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def setUp(self):
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pass
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@classmethod
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def setUpClass(cls):
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super(CompoundTest, cls).setUpClass()
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cls.user = User.objects.get(username="anonymous")
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cls.package = PackageManager.create_package(cls.user, "Anon Test Package", "No Desc")
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def test_smoke(self):
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c = Compound.create(
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self.package,
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smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
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name="Afoxolaner",
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description="No Desc",
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)
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self.assertEqual(
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c.default_structure.smiles,
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"C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
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)
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self.assertEqual(c.name, "Afoxolaner")
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self.assertEqual(c.description, "No Desc")
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def test_missing_smiles(self):
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with self.assertRaises(ValueError):
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_ = Compound.create(self.package, smiles=None, name="Afoxolaner", description="No Desc")
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with self.assertRaises(ValueError):
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_ = Compound.create(self.package, smiles="", name="Afoxolaner", description="No Desc")
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with self.assertRaises(ValueError):
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_ = Compound.create(self.package, smiles=" ", name="Afoxolaner", description="No Desc")
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def test_smiles_are_trimmed(self):
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c = Compound.create(
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self.package,
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smiles=" C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F ",
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name="Afoxolaner",
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description="No Desc",
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)
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self.assertEqual(
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c.default_structure.smiles,
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"C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
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)
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def test_name_and_description_optional(self):
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c = Compound.create(
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self.package,
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smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
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)
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self.assertEqual(c.name, "Compound 1")
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self.assertEqual(c.description, "no description")
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def test_empty_name_and_description_are_ignored(self):
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c = Compound.create(
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self.package,
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smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
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name="",
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description="",
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)
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self.assertEqual(c.name, "Compound 1")
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self.assertEqual(c.description, "no description")
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def test_deduplication(self):
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c1 = Compound.create(
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self.package,
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smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
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name="Afoxolaner",
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description="No Desc",
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)
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c2 = Compound.create(
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self.package,
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smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
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name="Afoxolaner",
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description="No Desc",
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)
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# Check if create detects that this Compound already exist
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# In this case the existing object should be returned
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self.assertEqual(c1.pk, c2.pk)
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self.assertEqual(len(self.package.compounds), 1)
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def test_wrong_smiles(self):
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with self.assertRaises(ValueError):
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_ = Compound.create(
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self.package,
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smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
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name="Afoxolaner",
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description="No Desc",
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)
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def test_create_with_standardized_smiles(self):
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c = Compound.create(
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self.package,
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smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
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name="Standardized SMILES",
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description="No Desc",
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)
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self.assertEqual(len(c.structures.all()), 1)
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cs = c.structures.all()[0]
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self.assertEqual(cs.normalized_structure, True)
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self.assertEqual(cs.smiles, "O=C(O)C1=CC=C([N+](=O)[O-])C=C1")
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def test_create_with_non_standardized_smiles(self):
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c = Compound.create(
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self.package,
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smiles="[O-][N+](=O)c1ccc(C(=O)[O-])cc1",
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name="Non Standardized SMILES",
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description="No Desc",
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)
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self.assertEqual(len(c.structures.all()), 2)
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for cs in c.structures.all():
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if cs.normalized_structure:
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self.assertEqual(cs.smiles, "O=C(O)C1=CC=C([N+](=O)[O-])C=C1")
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break
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else:
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# Loop finished without break, lets fail...
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self.assertEqual(1, 2)
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def test_add_structure_smoke(self):
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c = Compound.create(
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self.package,
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smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
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name="Standardized SMILES",
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description="No Desc",
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)
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c.add_structure("[O-][N+](=O)c1ccc(C(=O)[O-])cc1", "Non Standardized SMILES")
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self.assertEqual(len(c.structures.all()), 2)
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def test_add_structure_with_different_normalized_smiles(self):
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c = Compound.create(
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self.package,
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smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
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name="Standardized SMILES",
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description="No Desc",
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)
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with self.assertRaises(ValueError):
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c.add_structure(
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"C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
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"Different Standardized SMILES",
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)
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def test_delete(self):
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c = Compound.create(
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self.package,
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smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
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name="Standardization Test",
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description="No Desc",
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)
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c.delete()
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self.assertEqual(Compound.objects.filter(package=self.package).count(), 0)
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self.assertEqual(
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CompoundStructure.objects.filter(compound__package=self.package).count(), 0
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)
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def test_set_as_default_structure(self):
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c1 = Compound.create(
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self.package,
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smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
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name="Standardized SMILES",
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description="No Desc",
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)
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default_structure = c1.default_structure
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c2 = c1.add_structure("[O-][N+](=O)c1ccc(C(=O)[O-])cc1", "Non Standardized SMILES")
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c1.set_default_structure(c2)
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self.assertNotEqual(default_structure, c2)
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