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

**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>

tests/test_compound_model.py

@@ -1,11 +1,12 @@
-from django.test import TestCase
-
+from django.conf import settings as s
+from django.test import TestCase, override_settings
 from epdb.logic import PackageManager
 from epdb.models import Compound, User, CompoundStructure
 
 
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
 class CompoundTest(TestCase):
-    fixtures = ["test_fixtures.jsonl.gz"]
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 
     def setUp(self):
         pass

tests/test_copy_objects.py

@@ -1,12 +1,14 @@
-from django.test import TestCase
+from django.conf import settings as s
+from django.test import TestCase, override_settings
 
 
 from epdb.logic import PackageManager
 from epdb.models import Compound, User, Reaction
 
 
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
 class CopyTest(TestCase):
-    fixtures = ["test_fixtures.jsonl.gz"]
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 
     @classmethod
     def setUpClass(cls):

tests/test_dataset.py

@@ -1,14 +1,16 @@
 import os.path
 from tempfile import TemporaryDirectory
-from django.test import TestCase
+from django.conf import settings as s
+from django.test import TestCase, override_settings
 from epdb.logic import PackageManager
 from epdb.models import Reaction, Compound, User, Rule, Package
 from utilities.chem import FormatConverter
 from utilities.ml import RuleBasedDataset, EnviFormerDataset
 
 
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
 class DatasetTest(TestCase):
-    fixtures = ["test_fixtures.jsonl.gz"]
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 
     def setUp(self):
         self.cs1 = Compound.create(
@@ -106,7 +108,9 @@ class DatasetTest(TestCase):
     def test_extra_features(self):
         reactions = [r for r in Reaction.objects.filter(package=self.BBD_SUBSET)]
         applicable_rules = [r for r in Rule.objects.filter(package=self.BBD_SUBSET)]
-        ds = RuleBasedDataset.generate_dataset(reactions, applicable_rules, feat_funcs=[FormatConverter.maccs, FormatConverter.morgan])
+        ds = RuleBasedDataset.generate_dataset(
+            reactions, applicable_rules, feat_funcs=[FormatConverter.maccs, FormatConverter.morgan]
+        )
         print(ds.shape)
 
     def test_to_arff(self):

tests/test_enviformer.py

@@ -3,7 +3,8 @@ from datetime import datetime
 from tempfile import TemporaryDirectory
 
 from django.conf import settings as s
-from django.test import TestCase, tag
+from django.test import TestCase, override_settings, tag
+
 
 from epdb.logic import PackageManager
 from epdb.models import EnviFormer, Setting, User
@@ -30,8 +31,9 @@ def measure_predict(mod, pathway_pk=None):
 
 
 @tag("slow")
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
 class EnviFormerTest(TestCase):
-    fixtures = ["test_fixtures.jsonl.gz"]
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 
     @classmethod
     def setUpClass(cls):

tests/test_model.py

@@ -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)),
                 }

tests/test_multigen_eval.py

@@ -1,5 +1,5 @@
 from django.conf import settings as s
-from django.test import TestCase
+from django.test import TestCase, override_settings
 from networkx.utils.misc import graphs_equal
 
 from epdb.logic import PackageManager, SPathway
@@ -9,8 +9,9 @@ from utilities.ml import graph_from_pathway, multigen_eval, pathway_edit_eval
 Package = s.GET_PACKAGE_MODEL()
 
 
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
 class MultiGenTest(TestCase):
-    fixtures = ["test_fixtures.jsonl.gz"]
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 
     @classmethod
     def setUpClass(cls):

tests/test_reaction_model.py

@@ -1,11 +1,13 @@
-from django.test import TestCase
+from django.conf import settings as s
+from django.test import TestCase, override_settings
 
 from epdb.logic import PackageManager
 from epdb.models import Compound, User, Reaction, Rule
 
 
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
 class ReactionTest(TestCase):
-    fixtures = ["test_fixtures.jsonl.gz"]
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 
     @classmethod
     def setUpClass(cls):

tests/test_rule_model.py

@@ -1,11 +1,12 @@
-from django.test import TestCase
-
+from django.conf import settings as s
+from django.test import TestCase, override_settings
 from epdb.logic import PackageManager
 from epdb.models import Rule, User
 
 
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
 class RuleTest(TestCase):
-    fixtures = ["test_fixtures.jsonl.gz"]
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 
     @classmethod
     def setUpClass(cls):

tests/test_simpleambitrule.py

@@ -1,15 +1,16 @@
 from unittest.mock import MagicMock, PropertyMock, patch
 
 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 SimpleAmbitRule, User
 from utilities.chem import FormatConverter
 
 
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
 class SimpleAmbitRuleTest(TestCase):
-    fixtures = ["test_fixtures.jsonl.gz"]
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 
     @classmethod
     def setUpClass(cls):

tests/views/test_compound_views.py

@@ -1,4 +1,5 @@
-from django.test import TestCase
+from django.conf import settings as s
+from django.test import TestCase, override_settings
 from django.urls import reverse
 from envipy_additional_information import Temperature, Interval
 
@@ -6,8 +7,9 @@ from epdb.logic import UserManager, PackageManager
 from epdb.models import Compound, Scenario, ExternalDatabase
 
 
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
 class CompoundViewTest(TestCase):
-    fixtures = ["test_fixtures.jsonl.gz"]
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 
     @classmethod
     def setUpClass(cls):

tests/views/test_model_views.py

@@ -9,12 +9,12 @@ Package = s.GET_PACKAGE_MODEL()
 
 
 @override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
-class PathwayViewTest(TestCase):
+class ModelViewTest(TestCase):
     fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 
     @classmethod
     def setUpClass(cls):
-        super(PathwayViewTest, cls).setUpClass()
+        super(ModelViewTest, cls).setUpClass()
         cls.user1 = UserManager.create_user(
             "user1",
             "user1@envipath.com",
@@ -72,7 +72,7 @@ class PathwayViewTest(TestCase):
             },
         ]
 
-        actual = response.json()
+        actual = response.json()["pred"]
         self.assertEqual(actual, expected)
 
         response = self.client.get(

tests/views/test_package_views.py

@@ -1,6 +1,6 @@
 from django.conf import settings as s
 from django.core.files.uploadedfile import SimpleUploadedFile
-from django.test import TestCase, tag
+from django.test import TestCase, override_settings, tag
 from django.urls import reverse
 
 from epdb.logic import UserManager
@@ -15,8 +15,9 @@ from epdb.models import (
 Package = s.GET_PACKAGE_MODEL()
 
 
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
 class PackageViewTest(TestCase):
-    fixtures = ["test_fixtures.jsonl.gz"]
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 
     @classmethod
     def setUpClass(cls):

tests/views/test_reaction_views.py

@@ -1,4 +1,5 @@
-from django.test import TestCase
+from django.conf import settings as s
+from django.test import TestCase, override_settings
 from django.urls import reverse
 from envipy_additional_information import Temperature, Interval
 
@@ -6,8 +7,9 @@ from epdb.logic import UserManager, PackageManager
 from epdb.models import Reaction, Scenario, ExternalDatabase
 
 
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
 class ReactionViewTest(TestCase):
-    fixtures = ["test_fixtures.jsonl.gz"]
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 
     @classmethod
     def setUpClass(cls):

tests/views/test_rule_views.py

@@ -1,4 +1,5 @@
-from django.test import TestCase
+from django.conf import settings as s
+from django.test import TestCase, override_settings
 from django.urls import reverse
 from envipy_additional_information import Temperature, Interval
 
@@ -6,8 +7,9 @@ from epdb.logic import UserManager, PackageManager
 from epdb.models import Rule, Scenario
 
 
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
 class RuleViewTest(TestCase):
-    fixtures = ["test_fixtures.jsonl.gz"]
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 
     @classmethod
     def setUpClass(cls):

tests/views/test_user_views.py

@@ -1,12 +1,14 @@
-from django.test import TestCase
+from django.conf import settings as s
+from django.test import TestCase, override_settings
+from django.urls import reverse
 
 from epdb.logic import PackageManager
 from epdb.models import Package, User
-from django.urls import reverse
 
 
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
 class UserViewTest(TestCase):
-    fixtures = ["test_fixtures.jsonl.gz"]
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 
     @classmethod
     def setUpClass(cls):
@@ -48,8 +50,9 @@ class UserViewTest(TestCase):
             },
         )
         self.assertEqual(response.status_code, 200)
-        # TODO currently fails as the fixture does not provide a global setting...
-        self.assertContains(response, "Registration failed!")
+        self.assertContains(
+            response, "Your account has been created! An admin will activate it soon!"
+        )
 
     def test_register_password_mismatch(self):
         response = self.client.post(