...

envipath/settings.py

@@ -52,28 +52,6 @@ INSTALLED_APPS = [
     "migration",
 ]
 
-
-# Add the TENANT providing implementations for
-# Required
-# - Package
-# - Compound (TODO)
-# - CompoundStructure (TODO)
-# Optional
-# - PackageManager (TODO)
-# - GroupManager (TODO)
-# - SettingManager (TODO)
-TENANT = os.environ.get("TENANT", "public")
-INSTALLED_APPS.append(TENANT)
-PACKAGE_IMPLEMENTATION = f"{TENANT}.Package"
-PACKAGE_MODULE_PATH = f"{TENANT}.models.Package"
-
-
-def GET_PACKAGE_MODEL():
-    from django.apps import apps
-
-    return apps.get_model(TENANT, "Package")
-
-
 AUTHENTICATION_BACKENDS = [
     "django.contrib.auth.backends.ModelBackend",
 ]

epdb/admin.py

@@ -1,11 +1,11 @@
 from django.contrib import admin
-from django.conf import settings as s
 
 from .models import (
     User,
     UserPackagePermission,
     Group,
     GroupPackagePermission,
+    Package,
     MLRelativeReasoning,
     EnviFormer,
     Compound,
@@ -24,9 +24,6 @@ from .models import (
 )
 
 
-Package = s.GET_PACKAGE_MODEL()
-
-
 class UserAdmin(admin.ModelAdmin):
     list_display = ["username", "email", "is_active"]
 

epdb/legacy_api.py

@@ -1,6 +1,5 @@
 from typing import List, Dict, Optional, Any
 
-from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.http import HttpResponse
 from django.shortcuts import redirect
@@ -11,6 +10,7 @@ from .logic import PackageManager, UserManager, SettingManager
 from .models import (
     Compound,
     CompoundStructure,
+    Package,
     User,
     UserPackagePermission,
     Rule,
@@ -23,9 +23,6 @@ from .models import (
 )
 
 
-Package = s.GET_PACKAGE_MODEL()
-
-
 def _anonymous_or_real(request):
     if request.user.is_authenticated and not request.user.is_anonymous:
         return request.user

epdb/logic.py

@@ -11,6 +11,7 @@ from pydantic import ValidationError
 
 from epdb.models import (
     User,
+    Package,
     UserPackagePermission,
     GroupPackagePermission,
     Permission,
@@ -32,8 +33,6 @@ from utilities.misc import PackageImporter, PackageExporter
 
 logger = logging.getLogger(__name__)
 
-Package = s.GET_PACKAGE_MODEL()
-
 
 class EPDBURLParser:
     UUID_PATTERN = r"[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}"

epdb/management/commands/create_ml_models.py

@@ -2,9 +2,7 @@ from django.conf import settings as s
 from django.core.management.base import BaseCommand
 from django.db import transaction
 
-from epdb.models import EnviFormer, MLRelativeReasoning
-
-Package = s.GET_PACKAGE_MODEL()
+from epdb.models import MLRelativeReasoning, EnviFormer, Package
 
 
 class Command(BaseCommand):
@@ -77,13 +75,11 @@ class Command(BaseCommand):
             return packages
 
         # Iteratively create models in options["model_names"]
-        print(
-            f"Creating models: {options['model_names']}\n"
+        print(f"Creating models: {options['model_names']}\n"
               f"Data packages: {options['data_packages']}\n"
               f"Rule Packages (only for MLRR): {options['rule_packages']}\n"
               f"Eval Packages: {options['eval_packages']}\n"
-            f"Threshold: {options['threshold']:.2f}"
-        )
+              f"Threshold: {options['threshold']:.2f}")
         data_packages = decode_packages(options["data_packages"])
         eval_packages = decode_packages(options["eval_packages"])
         rule_packages = decode_packages(options["rule_packages"])
@@ -94,7 +90,7 @@ class Command(BaseCommand):
                     pack,
                     data_packages=data_packages,
                     eval_packages=eval_packages,
-                    threshold=options["threshold"],
+                    threshold=options['threshold'],
                     name=f"EnviFormer - {', '.join(options['data_packages'])} - T{options['threshold']:.2f}",
                     description=f"EnviFormer transformer trained on {options['data_packages']} "
                                 f"evaluated on {options['eval_packages']}.",
@@ -105,7 +101,7 @@ class Command(BaseCommand):
                     rule_packages=rule_packages,
                     data_packages=data_packages,
                     eval_packages=eval_packages,
-                    threshold=options["threshold"],
+                    threshold=options['threshold'],
                     name=f"ECC - {', '.join(options['data_packages'])} - T{options['threshold']:.2f}",
                     description=f"ML Relative Reasoning trained on {options['data_packages']} with rules from "
                                 f"{options['rule_packages']} and evaluated on {options['eval_packages']}.",

epdb/management/commands/load_enviformer.py

@@ -8,9 +8,7 @@ from django.conf import settings as s
 from django.core.management.base import BaseCommand
 from django.db import transaction
 
-from epdb.models import EnviFormer
-
-Package = s.GET_PACKAGE_MODEL()
+from epdb.models import EnviFormer, Package
 
 
 class Command(BaseCommand):

epdb/management/commands/localize_urls.py

@@ -1,8 +1,8 @@
 from django.apps import apps
-from django.conf import settings as s
 from django.core.management.base import BaseCommand
-from django.db.models import F, JSONField, TextField, Value
-from django.db.models.functions import Cast, Replace
+
+from django.db.models import F, Value, TextField, JSONField
+from django.db.models.functions import Replace, Cast
 
 from epdb.models import EnviPathModel
 
@@ -23,13 +23,10 @@ class Command(BaseCommand):
         )
 
     def handle(self, *args, **options):
-        Package = s.GET_PACKAGE_MODEL()
-        print("Localizing urls for Package")
-        Package.objects.update(url=Replace(F("url"), Value(options["old"]), Value(options["new"])))
-
         MODELS = [
             "User",
             "Group",
+            "Package",
             "Compound",
             "CompoundStructure",
             "Pathway",

epdb/migrations/0010_alter_userpackagepermission_package_and_more.py

@@ -1,190 +0,0 @@
-# Generated by Django 5.2.7 on 2025-10-29 13:32
-
-import django.db.models.deletion
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0009_joblog"),
-        ("public", "0001_initial"),
-    ]
-
-    operations = [
-        migrations.AlterField(
-            model_name="userpackagepermission",
-            name="package",
-            field=models.ForeignKey(
-                on_delete=django.db.models.deletion.CASCADE,
-                to="public.package",
-                verbose_name="Permission on",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="grouppackagepermission",
-            name="package",
-            field=models.ForeignKey(
-                on_delete=django.db.models.deletion.CASCADE,
-                to="public.package",
-                verbose_name="Permission on",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="epmodel",
-            name="package",
-            field=models.ForeignKey(
-                on_delete=django.db.models.deletion.CASCADE,
-                to="public.package",
-                verbose_name="Package",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="rule",
-            name="package",
-            field=models.ForeignKey(
-                on_delete=django.db.models.deletion.CASCADE,
-                to="public.package",
-                verbose_name="Package",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compound",
-            name="package",
-            field=models.ForeignKey(
-                on_delete=django.db.models.deletion.CASCADE,
-                to="public.package",
-                verbose_name="Package",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="scenario",
-            name="package",
-            field=models.ForeignKey(
-                on_delete=django.db.models.deletion.CASCADE,
-                to="public.package",
-                verbose_name="Package",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="pathway",
-            name="package",
-            field=models.ForeignKey(
-                on_delete=django.db.models.deletion.CASCADE,
-                to="public.package",
-                verbose_name="Package",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="package",
-            field=models.ForeignKey(
-                on_delete=django.db.models.deletion.CASCADE,
-                to="public.package",
-                verbose_name="Package",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="user",
-            name="default_package",
-            field=models.ForeignKey(
-                null=True,
-                on_delete=django.db.models.deletion.SET_NULL,
-                to="public.package",
-                verbose_name="Default Package",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="enviformer",
-            name="data_packages",
-            field=models.ManyToManyField(
-                related_name="%(app_label)s_%(class)s_data_packages",
-                to="public.package",
-                verbose_name="Data Packages",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="enviformer",
-            name="eval_packages",
-            field=models.ManyToManyField(
-                related_name="%(app_label)s_%(class)s_eval_packages",
-                to="public.package",
-                verbose_name="Evaluation Packages",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="enviformer",
-            name="rule_packages",
-            field=models.ManyToManyField(
-                related_name="%(app_label)s_%(class)s_rule_packages",
-                to="public.package",
-                verbose_name="Rule Packages",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="mlrelativereasoning",
-            name="data_packages",
-            field=models.ManyToManyField(
-                related_name="%(app_label)s_%(class)s_data_packages",
-                to="public.package",
-                verbose_name="Data Packages",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="mlrelativereasoning",
-            name="eval_packages",
-            field=models.ManyToManyField(
-                related_name="%(app_label)s_%(class)s_eval_packages",
-                to="public.package",
-                verbose_name="Evaluation Packages",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="mlrelativereasoning",
-            name="rule_packages",
-            field=models.ManyToManyField(
-                related_name="%(app_label)s_%(class)s_rule_packages",
-                to="public.package",
-                verbose_name="Rule Packages",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="rulebasedrelativereasoning",
-            name="data_packages",
-            field=models.ManyToManyField(
-                related_name="%(app_label)s_%(class)s_data_packages",
-                to="public.package",
-                verbose_name="Data Packages",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="rulebasedrelativereasoning",
-            name="eval_packages",
-            field=models.ManyToManyField(
-                related_name="%(app_label)s_%(class)s_eval_packages",
-                to="public.package",
-                verbose_name="Evaluation Packages",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="rulebasedrelativereasoning",
-            name="rule_packages",
-            field=models.ManyToManyField(
-                related_name="%(app_label)s_%(class)s_rule_packages",
-                to="public.package",
-                verbose_name="Rule Packages",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="setting",
-            name="rule_packages",
-            field=models.ManyToManyField(
-                blank=True,
-                related_name="setting_rule_packages",
-                to="public.package",
-                verbose_name="Setting Rule Packages",
-            ),
-        ),
-        migrations.DeleteModel(
-            name="Package",
-        ),
-    ]

epdb/models.py

@@ -7,7 +7,7 @@ import secrets
 from abc import abstractmethod
 from collections import defaultdict
 from datetime import datetime
-from typing import Union, List, Optional, Dict, Tuple, Set, Any, TYPE_CHECKING
+from typing import Union, List, Optional, Dict, Tuple, Set, Any
 from uuid import uuid4
 import math
 import joblib
@@ -32,8 +32,6 @@ from utilities.ml import Dataset, ApplicabilityDomainPCA, EnsembleClassifierChai
 
 logger = logging.getLogger(__name__)
 
-if TYPE_CHECKING:
-    Package = s.GET_PACKAGE_MODEL()
 
 ##########################
 # User/Groups/Permission #
@@ -47,10 +45,7 @@ class User(AbstractUser):
     )
     url = models.TextField(blank=False, null=True, verbose_name="URL", unique=True)
     default_package = models.ForeignKey(
-        s.PACKAGE_IMPLEMENTATION,
-        verbose_name="Default Package",
-        null=True,
-        on_delete=models.SET_NULL,
+        "epdb.Package", verbose_name="Default Package", null=True, on_delete=models.SET_NULL
     )
     default_group = models.ForeignKey(
         "Group",
@@ -240,7 +235,7 @@ class UserPackagePermission(Permission):
     )
     user = models.ForeignKey("User", verbose_name="Permission to", on_delete=models.CASCADE)
     package = models.ForeignKey(
-        s.PACKAGE_IMPLEMENTATION, verbose_name="Permission on", on_delete=models.CASCADE
+        "epdb.Package", verbose_name="Permission on", on_delete=models.CASCADE
     )
 
     class Meta:
@@ -256,7 +251,7 @@ class GroupPackagePermission(Permission):
     )
     group = models.ForeignKey("Group", verbose_name="Permission to", on_delete=models.CASCADE)
     package = models.ForeignKey(
-        s.PACKAGE_IMPLEMENTATION, verbose_name="Permission on", on_delete=models.CASCADE
+        "epdb.Package", verbose_name="Permission on", on_delete=models.CASCADE
     )
 
     class Meta:
@@ -656,7 +651,7 @@ class License(models.Model):
     image_link = models.URLField(blank=False, null=False, verbose_name="Image link")
 
 
-class AbstractPackage(EnviPathModel):
+class Package(EnviPathModel):
     reviewed = models.BooleanField(verbose_name="Reviewstatus", default=False)
     license = models.ForeignKey(
         "epdb.License", on_delete=models.SET_NULL, blank=True, null=True, verbose_name="License"
@@ -724,13 +719,10 @@ class AbstractPackage(EnviPathModel):
         rules = sorted(rules, key=lambda x: x.url)
         return rules
 
-    class Meta:
-        abstract = True
-
 
 class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin):
     package = models.ForeignKey(
-        s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
     default_structure = models.ForeignKey(
         "CompoundStructure",
@@ -780,7 +772,7 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
     @staticmethod
     @transaction.atomic
     def create(
-        package: "Package", smiles: str, name: str = None, description: str = None, *args, **kwargs
+        package: Package, smiles: str, name: str = None, description: str = None, *args, **kwargs
     ) -> "Compound":
         if smiles is None or smiles.strip() == "":
             raise ValueError("SMILES is required")
@@ -1058,7 +1050,7 @@ class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
 
 class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
     package = models.ForeignKey(
-        s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
 
     # # https://github.com/django-polymorphic/django-polymorphic/issues/229
@@ -1164,7 +1156,7 @@ class SimpleAmbitRule(SimpleRule):
     @staticmethod
     @transaction.atomic
     def create(
-        package: "Package",
+        package: Package,
         name: str = None,
         description: str = None,
         smirks: str = None,
@@ -1230,7 +1222,6 @@ class SimpleAmbitRule(SimpleRule):
 
     @property
     def related_reactions(self):
-        Package = s.GET_PACKAGE_MODEL()
         qs = Package.objects.filter(reviewed=True)
         return self.reaction_rule.filter(package__in=qs).order_by("name")
 
@@ -1323,7 +1314,7 @@ class SequentialRuleOrdering(models.Model):
 
 class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin):
     package = models.ForeignKey(
-        s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
     educts = models.ManyToManyField(
         "epdb.CompoundStructure", verbose_name="Educts", related_name="reaction_educts"
@@ -1345,7 +1336,7 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
     @staticmethod
     @transaction.atomic
     def create(
-        package: "Package",
+        package: Package,
         name: str = None,
         description: str = None,
         educts: Union[List[str], List[CompoundStructure]] = None,
@@ -1505,7 +1496,7 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
 
 class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
     package = models.ForeignKey(
-        s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
     setting = models.ForeignKey(
         "epdb.Setting", verbose_name="Setting", on_delete=models.CASCADE, null=True, blank=True
@@ -1582,11 +1573,9 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
         while len(queue):
             current = queue.pop()
             processed.add(current)
-
             nodes.append(current.d3_json())
 
-            for e in self.edges:
-                if current in e.start_nodes.all():
+            for e in self.edges.filter(start_nodes=current).distinct():
                 for prod in e.end_nodes.all():
                     if prod not in queue and prod not in processed:
                         queue.append(prod)
@@ -2061,7 +2050,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
 
 class EPModel(PolymorphicModel, EnviPathModel):
     package = models.ForeignKey(
-        s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
 
     def _url(self):
@@ -2070,17 +2059,17 @@ class EPModel(PolymorphicModel, EnviPathModel):
 
 class PackageBasedModel(EPModel):
     rule_packages = models.ManyToManyField(
-        s.PACKAGE_IMPLEMENTATION,
+        "Package",
         verbose_name="Rule Packages",
         related_name="%(app_label)s_%(class)s_rule_packages",
     )
     data_packages = models.ManyToManyField(
-        s.PACKAGE_IMPLEMENTATION,
+        "Package",
         verbose_name="Data Packages",
         related_name="%(app_label)s_%(class)s_data_packages",
     )
     eval_packages = models.ManyToManyField(
-        s.PACKAGE_IMPLEMENTATION,
+        "Package",
         verbose_name="Evaluation Packages",
         related_name="%(app_label)s_%(class)s_eval_packages",
     )
@@ -3448,7 +3437,7 @@ class PluginModel(EPModel):
 
 class Scenario(EnviPathModel):
     package = models.ForeignKey(
-        s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
     scenario_date = models.CharField(max_length=256, null=False, blank=False, default="No date")
     scenario_type = models.CharField(
@@ -3599,7 +3588,7 @@ class Setting(EnviPathModel):
     )
 
     rule_packages = models.ManyToManyField(
-        s.PACKAGE_IMPLEMENTATION,
+        "Package",
         verbose_name="Setting Rule Packages",
         related_name="setting_rule_packages",
         blank=True,

epdb/tasks.py

@@ -7,12 +7,9 @@ from uuid import uuid4
 
 from celery import shared_task
 from celery.utils.functional import LRUCache
-from django.conf import settings as s
 
 from epdb.logic import SPathway
-from epdb.models import Edge, EPModel, JobLog, Node, Pathway, Rule, Setting, User
-
-Package = s.GET_PACKAGE_MODEL()
+from epdb.models import EPModel, JobLog, Node, Package, Pathway, Rule, Setting, User, Edge
 
 logger = logging.getLogger(__name__)
 ML_CACHE = LRUCache(3)  # Cache the three most recent ML models to reduce load times.
@@ -175,6 +172,7 @@ def predict(
 
     except Exception as e:
         pw.kv.update({"status": "failed"})
+        pw.kv.update(**{"error": str(e)})
         pw.save()
 
         if JobLog.objects.filter(task_id=self.request.id).exists():

epdb/views.py

@@ -1,11 +1,11 @@
 import json
 import logging
-from typing import Any, Dict, List
+from typing import List, Dict, Any
 
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
-from django.http import HttpResponse, HttpResponseBadRequest, HttpResponseNotAllowed, JsonResponse
-from django.shortcuts import redirect, render
+from django.http import JsonResponse, HttpResponse, HttpResponseNotAllowed, HttpResponseBadRequest
+from django.shortcuts import render, redirect
 from django.urls import reverse
 from django.views.decorators.csrf import csrf_exempt
 from envipy_additional_information import NAME_MAPPING
@@ -14,43 +14,42 @@ from oauth2_provider.decorators import protected_resource
 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
 from utilities.misc import HTMLGenerator
-
 from .logic import (
-    EPDBURLParser,
     GroupManager,
     PackageManager,
-    SearchManager,
-    SettingManager,
     UserManager,
+    SettingManager,
+    SearchManager,
+    EPDBURLParser,
 )
 from .models import (
-    APIToken,
-    Compound,
-    CompoundStructure,
-    Edge,
-    EnviFormer,
-    EnzymeLink,
-    EPModel,
-    ExternalDatabase,
-    ExternalIdentifier,
-    Group,
+    Package,
     GroupPackagePermission,
-    JobLog,
-    License,
-    MLRelativeReasoning,
-    Node,
-    Pathway,
-    Permission,
+    Group,
+    CompoundStructure,
+    Compound,
     Reaction,
     Rule,
+    Pathway,
+    Node,
+    EPModel,
+    EnviFormer,
+    MLRelativeReasoning,
     RuleBasedRelativeReasoning,
     Scenario,
     SimpleAmbitRule,
-    User,
+    APIToken,
     UserPackagePermission,
+    Permission,
+    License,
+    User,
+    Edge,
+    ExternalDatabase,
+    ExternalIdentifier,
+    EnzymeLink,
+    JobLog,
 )
 
-Package = s.GET_PACKAGE_MODEL()
 logger = logging.getLogger(__name__)
 
 
@@ -83,7 +82,8 @@ def login(request):
         return render(request, "static/login.html", context)
 
     elif request.method == "POST":
-        from django.contrib.auth import authenticate, login
+        from django.contrib.auth import authenticate
+        from django.contrib.auth import login
 
         username = request.POST.get("username")
         password = request.POST.get("password")
@@ -832,7 +832,7 @@ def package_models(request, package_uuid):
                 request, "Invalid model type.", f'Model type "{model_type}" is not supported."'
             )
 
-        from .tasks import build_model, dispatch
+        from .tasks import dispatch, build_model
 
         dispatch(current_user, build_model, mod.pk)
 
@@ -2325,9 +2325,9 @@ def package_scenarios(request, package_uuid):
         context["unreviewed_objects"] = unreviewed_scenario_qs
 
         from envipy_additional_information import (
-            SEDIMENT_ADDITIONAL_INFORMATION,
             SLUDGE_ADDITIONAL_INFORMATION,
             SOIL_ADDITIONAL_INFORMATION,
+            SEDIMENT_ADDITIONAL_INFORMATION,
         )
 
         context["scenario_types"] = {

migration/views.py

@@ -1,18 +1,21 @@
+import gzip
 import json
 import logging
 import os.path
+from datetime import datetime
 
 from django.conf import settings as s
 from django.http import HttpResponseNotAllowed
 from django.shortcuts import render
-from rdkit import Chem
-from rdkit.Chem.MolStandardize import rdMolStandardize
 
-from epdb.models import CompoundStructure, Rule, SimpleAmbitRule
-from epdb.views import get_base_context
+from epdb.logic import PackageManager
+from epdb.models import Rule, SimpleAmbitRule, Package, CompoundStructure
+from epdb.views import get_base_context, _anonymous_or_real
 from utilities.chem import FormatConverter
 
-Package = s.GET_PACKAGE_MODEL()
+
+from rdkit import Chem
+from rdkit.Chem.MolStandardize import rdMolStandardize
 
 logger = logging.getLogger(__name__)
 
@@ -56,7 +59,9 @@ def run_both_engines(SMILES, SMIRKS):
         set(
             [
                 normalize_smiles(str(x))
-                for x in FormatConverter.sanitize_smiles([str(s) for s in all_rdkit_prods])[0]
+                for x in FormatConverter.sanitize_smiles(
+                    [str(s) for s in all_rdkit_prods]
+                )[0]
             ]
         )
     )
@@ -80,7 +85,8 @@ def migration(request):
                 url="http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1"
             )
             ALL_SMILES = [
-                cs.smiles for cs in CompoundStructure.objects.filter(compound__package=BBD)
+                cs.smiles
+                for cs in CompoundStructure.objects.filter(compound__package=BBD)
             ]
             RULES = SimpleAmbitRule.objects.filter(package=BBD)
 
@@ -136,7 +142,9 @@ def migration(request):
             )
 
         for r in migration_status["results"]:
-            r["detail_url"] = r["detail_url"].replace("http://localhost:8000", s.SERVER_URL)
+            r["detail_url"] = r["detail_url"].replace(
+                "http://localhost:8000", s.SERVER_URL
+            )
 
         context.update(**migration_status)
 
@@ -144,6 +152,8 @@ def migration(request):
 
 
 def migration_detail(request, package_uuid, rule_uuid):
+    current_user = _anonymous_or_real(request)
+
     if request.method == "GET":
         context = get_base_context(request)
 
@@ -225,7 +235,9 @@ def compare(request):
         context["smirks"] = (
             "[#1,#6:6][#7;X3;!$(NC1CC1)!$([N][C]=O)!$([!#8]CNC=O):1]([#1,#6:7])[#6;A;X4:2][H:3]>>[#1,#6:6][#7;X3:1]([#1,#6:7])[H:3].[#6;A:2]=O"
         )
-        context["smiles"] = "C(CC(=O)N[C@@H](CS[Se-])C(=O)NCC(=O)[O-])[C@@H](C(=O)[O-])N"
+        context["smiles"] = (
+            "C(CC(=O)N[C@@H](CS[Se-])C(=O)NCC(=O)[O-])[C@@H](C(=O)[O-])N"
+        )
         return render(request, "compare.html", context)
 
     elif request.method == "POST":

public/admin.py

@@ -1 +0,0 @@
-# Register your models here.

public/apps.py

@@ -1,6 +0,0 @@
-from django.apps import AppConfig
-
-
-class PublicConfig(AppConfig):
-    default_auto_field = "django.db.models.BigAutoField"
-    name = "public"

public/migrations/0001_initial.py

@@ -1,56 +0,0 @@
-# Generated by Django 5.2.7 on 2025-10-29 13:32
-
-import django.utils.timezone
-import model_utils.fields
-import uuid
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    initial = True
-
-    dependencies = []
-
-    operations = [
-        migrations.CreateModel(
-            name="Package",
-            fields=[
-                (
-                    "id",
-                    models.BigAutoField(
-                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
-                    ),
-                ),
-                (
-                    "created",
-                    model_utils.fields.AutoCreatedField(
-                        default=django.utils.timezone.now, editable=False, verbose_name="created"
-                    ),
-                ),
-                (
-                    "modified",
-                    model_utils.fields.AutoLastModifiedField(
-                        default=django.utils.timezone.now, editable=False, verbose_name="modified"
-                    ),
-                ),
-                (
-                    "uuid",
-                    models.UUIDField(
-                        default=uuid.uuid4, unique=True, verbose_name="UUID of this object"
-                    ),
-                ),
-                ("name", models.TextField(default="no name", verbose_name="Name")),
-                (
-                    "description",
-                    models.TextField(default="no description", verbose_name="Descriptions"),
-                ),
-                ("url", models.TextField(null=True, unique=True, verbose_name="URL")),
-                ("kv", models.JSONField(blank=True, default=dict, null=True)),
-                ("reviewed", models.BooleanField(default=False, verbose_name="Reviewstatus")),
-            ],
-            options={
-                "db_table": "epdb_package",
-                "managed": False,
-            },
-        ),
-    ]

public/migrations/0002_alter_package_options.py

@@ -1,16 +0,0 @@
-# Generated by Django 5.2.7 on 2025-10-29 18:39
-
-from django.db import migrations
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("public", "0001_initial"),
-    ]
-
-    operations = [
-        migrations.AlterModelOptions(
-            name="package",
-            options={},
-        ),
-    ]

public/migrations/0003_package_license.py

@@ -1,25 +0,0 @@
-# Generated by Django 5.2.7 on 2025-10-29 18:40
-
-import django.db.models.deletion
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0010_alter_userpackagepermission_package_and_more"),
-        ("public", "0002_alter_package_options"),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name="package",
-            name="license",
-            field=models.ForeignKey(
-                blank=True,
-                null=True,
-                on_delete=django.db.models.deletion.SET_NULL,
-                to="epdb.license",
-                verbose_name="License",
-            ),
-        ),
-    ]

public/models.py

@@ -1,6 +0,0 @@
-from epdb.models import AbstractPackage
-
-
-class Package(AbstractPackage):
-    class Meta:
-        db_table = "epdb_package"

public/tests.py

@@ -1 +0,0 @@
-# Create your tests here.

public/views.py

@@ -1 +0,0 @@
-# Create your views here.

tests/test_enviformer.py

@@ -1,15 +1,10 @@
 from collections import defaultdict
 from datetime import datetime
 from tempfile import TemporaryDirectory
-
-from django.conf import settings as s
 from django.test import TestCase, tag
-
 from epdb.logic import PackageManager
-from epdb.models import EnviFormer, Setting, User
-from epdb.tasks import predict, predict_simple
-
-Package = s.GET_PACKAGE_MODEL()
+from epdb.models import User, EnviFormer, Package, Setting
+from epdb.tasks import predict_simple, predict
 
 
 def measure_predict(mod, pathway_pk=None):

tests/test_model.py

@@ -1,13 +1,10 @@
 from tempfile import TemporaryDirectory
 
 import numpy as np
-from django.conf import settings as s
 from django.test import TestCase
 
 from epdb.logic import PackageManager
-from epdb.models import MLRelativeReasoning, User
-
-Package = s.GET_PACKAGE_MODEL()
+from epdb.models import User, MLRelativeReasoning, Package
 
 
 class ModelTest(TestCase):

tests/test_multigen_eval.py

@@ -1,12 +1,8 @@
-from django.conf import settings as s
 from django.test import TestCase
 from networkx.utils.misc import graphs_equal
-
 from epdb.logic import PackageManager, SPathway
-from epdb.models import Pathway, User
-from utilities.ml import graph_from_pathway, multigen_eval, pathway_edit_eval
-
-Package = s.GET_PACKAGE_MODEL()
+from epdb.models import Pathway, User, Package
+from utilities.ml import multigen_eval, pathway_edit_eval, graph_from_pathway
 
 
 class MultiGenTest(TestCase):

tests/test_simpleambitrule.py

@@ -1,10 +1,9 @@
-from unittest.mock import MagicMock, PropertyMock, patch
+from unittest.mock import patch, MagicMock, PropertyMock
 
-from django.conf import settings as s
 from django.test import TestCase
 
 from epdb.logic import PackageManager
-from epdb.models import SimpleAmbitRule, User
+from epdb.models import User, SimpleAmbitRule
 
 
 class SimpleAmbitRuleTest(TestCase):
@@ -210,7 +209,7 @@ class SimpleAmbitRuleTest(TestCase):
 
         self.assertEqual(rule.products_smarts, expected_products)
 
-    @patch(f"{s.PACKAGE_MODULE_PATH}.objects")
+    @patch("epdb.models.Package.objects")
     def test_related_reactions_property(self, mock_package_objects):
         """Test related_reactions property returns correct queryset."""
         mock_qs = MagicMock()

tests/views/test_model_views.py

@@ -1,11 +1,9 @@
-from django.conf import settings as s
 from django.test import TestCase, override_settings
 from django.urls import reverse
+from django.conf import settings as s
 
 from epdb.logic import UserManager
-from epdb.models import User
-
-Package = s.GET_PACKAGE_MODEL()
+from epdb.models import Package, User
 
 
 @override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)

tests/views/test_package_views.py

@@ -4,9 +4,7 @@ from django.test import TestCase, tag
 from django.urls import reverse
 
 from epdb.logic import UserManager
-from epdb.models import Group, GroupPackagePermission, Permission, UserPackagePermission
-
-Package = s.GET_PACKAGE_MODEL()
+from epdb.models import Package, UserPackagePermission, Permission, GroupPackagePermission, Group
 
 
 class PackageViewTest(TestCase):

tests/views/test_pathway_views.py

@@ -1,11 +1,9 @@
-from django.conf import settings as s
 from django.test import TestCase, override_settings
 from django.urls import reverse
+from django.conf import settings as s
 
-from epdb.logic import PackageManager, UserManager
-from epdb.models import Edge, Pathway
-
-Package = s.GET_PACKAGE_MODEL()
+from epdb.logic import UserManager, PackageManager
+from epdb.models import Pathway, Edge
 
 
 @override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)

tests/views/test_reaction_views.py

@@ -1,12 +1,9 @@
-from django.conf import settings as s
 from django.test import TestCase
 from django.urls import reverse
-from envipy_additional_information import Interval, Temperature
+from envipy_additional_information import Temperature, Interval
 
-from epdb.logic import PackageManager, UserManager
-from epdb.models import ExternalDatabase, Reaction, Scenario
-
-Package = s.GET_PACKAGE_MODEL()
+from epdb.logic import UserManager, PackageManager
+from epdb.models import Reaction, Scenario, ExternalDatabase
 
 
 class ReactionViewTest(TestCase):

tests/views/test_user_views.py

@@ -1,11 +1,8 @@
-from django.conf import settings as s
 from django.test import TestCase
-from django.urls import reverse
 
 from epdb.logic import PackageManager
-from epdb.models import User
-
-Package = s.GET_PACKAGE_MODEL()
+from epdb.models import Package, User
+from django.urls import reverse
 
 
 class UserViewTest(TestCase):

utilities/chem.py

@@ -2,12 +2,13 @@ import logging
 import re
 from abc import ABC
 from collections import defaultdict
-from typing import List, Optional, Dict, TYPE_CHECKING
+from typing import List, Optional, Dict, TYPE_CHECKING, Union
 
 from indigo import Indigo, IndigoException, IndigoObject
 from indigo.renderer import IndigoRenderer
 from rdkit import Chem, rdBase
 from rdkit.Chem import MACCSkeys, Descriptors
+from rdkit.Chem import rdchem
 from rdkit.Chem import rdChemReactions
 from rdkit.Chem.Draw import rdMolDraw2D
 from rdkit.Chem.MolStandardize import rdMolStandardize
@@ -90,8 +91,15 @@ class FormatConverter(object):
         return Chem.MolToSmiles(mol, canonical=canonical)
 
     @staticmethod
-    def InChIKey(smiles):
-        return Chem.MolToInchiKey(FormatConverter.from_smiles(smiles))
+    def InChIKey(mol_or_smiles: Union[rdchem.Mol | str]):
+        if isinstance(mol_or_smiles, str):
+            mol_or_smiles = mol_or_smiles.replace("~", "")
+            mol_or_smiles = FormatConverter.from_smiles(mol_or_smiles)
+
+        if mol_or_smiles is None:
+            return None
+
+        return Chem.MolToInchiKey(mol_or_smiles)
 
     @staticmethod
     def InChI(smiles):
@@ -288,7 +296,8 @@ class FormatConverter(object):
                             product = GetMolFrags(product, asMols=True)
                             for p in product:
                                 p = FormatConverter.standardize(
-                                    Chem.MolToSmiles(p), remove_stereo=remove_stereo
+                                    Chem.MolToSmiles(p).replace("~", ""),
+                                    remove_stereo=remove_stereo,
                                 )
                                 prods.append(p)
 

utilities/decorators.py

@@ -1,12 +1,10 @@
 # decorators.py
 from functools import wraps
 
-from django.conf import settings as s
 from django.shortcuts import get_object_or_404
 
 from epdb.logic import PackageManager
-
-Package = s.GET_PACKAGE_MODEL()
+from epdb.models import Package
 
 # Map HTTP methods to required permissions
 DEFAULT_METHOD_PERMISSIONS = {

utilities/misc.py

@@ -11,7 +11,6 @@ from enum import Enum
 from types import NoneType
 from typing import Any, Dict, List
 
-from django.conf import settings as s
 from django.db import transaction
 from envipy_additional_information import NAME_MAPPING, EnviPyModel, Interval
 from pydantic import BaseModel, HttpUrl
@@ -27,6 +26,7 @@ from epdb.models import (
     License,
     MLRelativeReasoning,
     Node,
+    Package,
     ParallelRule,
     Pathway,
     PluginModel,
@@ -35,14 +35,13 @@ from epdb.models import (
     RuleBasedRelativeReasoning,
     Scenario,
     SequentialRule,
+    Setting,
     SimpleAmbitRule,
     SimpleRDKitRule,
     SimpleRule,
 )
 from utilities.chem import FormatConverter
 
-Package = s.GET_PACKAGE_MODEL()
-
 logger = logging.getLogger(__name__)
 
 
@@ -1260,3 +1259,46 @@ class PathwayUtils:
                 res[edge.url] = rule_chain
 
         return res
+
+    def _find_intermediates(self, data_pathway, pred_pathway):
+        pass
+
+    def engineer(self, setting: "Setting"):
+        from epdb.logic import SPathway
+
+        # get a fresh copy
+        pw = Pathway.objects.get(id=self.pathway.pk)
+
+        root_nodes = [n.default_node_label.smiles for n in pw.root_nodes]
+
+        if len(root_nodes) != 1:
+            logger.warning(f"Pathway {pw.name} has {len(root_nodes)} root nodes")
+            return
+
+        spw = SPathway(root_nodes[0], None, setting)
+
+        level = 0
+        while not spw.done:
+            spw.predict_step(from_depth=level)
+            level += 1
+
+        # Generate Node / SMILES mapping
+        node_mapping = {}
+        from utilities.chem import FormatConverter
+
+        for node in pw.nodes:
+            for snode in spw.smiles_to_node.values():
+                data_smiles = node.default_node_label.smiles
+                pred_smiles = snode.smiles
+
+                data_key = FormatConverter.InChIKey(data_smiles.replace("~", ""))
+                pred_key = FormatConverter.InChIKey(pred_smiles.replace("~", ""))
+
+                if data_key == pred_key:
+                    node_mapping[snode] = node
+
+        print(node_mapping)
+
+        return spw
+
+        pass