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>
114 lines
4.2 KiB
Python
114 lines
4.2 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 Rule, User
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@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
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class RuleTest(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(RuleTest, 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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r = Rule.create(
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rule_type="SimpleAmbitRule",
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package=self.package,
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name="bt0022-2833",
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description="Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative",
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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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)
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self.assertEqual(
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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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)
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self.assertEqual(r.name, "bt0022-2833")
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self.assertEqual(
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r.description,
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"Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative",
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)
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def test_smirks_are_trimmed(self):
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r = Rule.create(
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rule_type="SimpleAmbitRule",
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package=self.package,
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name="bt0022-2833",
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description="Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative",
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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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)
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self.assertEqual(
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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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)
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def test_name_and_description_optional(self):
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r = Rule.create(
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rule_type="SimpleAmbitRule",
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package=self.package,
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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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)
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self.assertRegex(r.name, "Rule \\d+")
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self.assertEqual(r.description, "no description")
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def test_empty_name_and_description_are_ignored(self):
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r = Rule.create(
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rule_type="SimpleAmbitRule",
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package=self.package,
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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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name="",
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description="",
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)
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self.assertRegex(r.name, "Rule \\d+")
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self.assertEqual(r.description, "no description")
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def test_deduplication(self):
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r1 = Rule.create(
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rule_type="SimpleAmbitRule",
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package=self.package,
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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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name="",
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description="",
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)
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r2 = Rule.create(
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rule_type="SimpleAmbitRule",
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package=self.package,
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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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name="",
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description="",
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)
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self.assertEqual(r1.pk, r2.pk)
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self.assertEqual(len(self.package.rules), 1)
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def test_valid_smirks(self):
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with self.assertRaises(ValueError):
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Rule.create(
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rule_type="SimpleAmbitRule",
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package=self.package,
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smirks="This is not a valid SMIRKS",
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name="",
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description="",
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)
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def test_delete(self):
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r = Rule.create(
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rule_type="SimpleAmbitRule",
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package=self.package,
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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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name="",
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description="",
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)
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r.delete()
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self.assertEqual(Rule.objects.filter(package=self.package).count(), 0)
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