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[Fix] Stereochemistry prediction handling (#228 and #238) (#250)

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**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>
This commit is contained in:
Liam Brydon
2025-12-03 10:19:34 +13:00
committed by jebus
parent 69df139256
commit 901de4640c
23 changed files with 126 additions and 49 deletions
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7
tests/test_model.py
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@ -2,7 +2,7 @@ from tempfile import TemporaryDirectory
import numpy as np
from django.conf import settings as s
from django.test import TestCase
from django.test import TestCase, override_settings
from epdb.logic import PackageManager
from epdb.models import MLRelativeReasoning, RuleBasedRelativeReasoning, User
@ -10,8 +10,9 @@ from epdb.models import MLRelativeReasoning, RuleBasedRelativeReasoning, User
Package = s.GET_PACKAGE_MODEL()
@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
class ModelTest(TestCase):
fixtures = ["test_fixtures.jsonl.gz"]
fixtures = ["test_fixtures_incl_model.jsonl.gz"]
@classmethod
def setUpClass(cls):
@ -52,7 +53,7 @@ class ModelTest(TestCase):
expected = {
("CC=O", "CCNC(=O)C1=CC(C)=CC=C1"): (
"bt0243-4301",
np.float64(0.33333333333333337),
np.float64(0.5),
),
("CC1=CC=CC(C(=O)O)=C1", "CCNCC"): ("bt0430-4011", np.float64(0.25)),
}