...

envipath/settings.py

@@ -52,6 +52,28 @@ 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,
@@ -24,6 +24,9 @@ from .models import (
 )
 
 
+Package = s.GET_PACKAGE_MODEL()
+
+
 class UserAdmin(admin.ModelAdmin):
     list_display = ["username", "email", "is_active"]
 

epdb/legacy_api.py

@@ -1,5 +1,6 @@
 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
@@ -10,7 +11,6 @@ from .logic import PackageManager, UserManager, SettingManager
 from .models import (
     Compound,
     CompoundStructure,
-    Package,
     User,
     UserPackagePermission,
     Rule,
@@ -23,6 +23,9 @@ 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

@@ -11,7 +11,6 @@ from pydantic import ValidationError
 
 from epdb.models import (
     User,
-    Package,
     UserPackagePermission,
     GroupPackagePermission,
     Permission,
@@ -33,6 +32,8 @@ 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

@@ -2,7 +2,9 @@ from django.conf import settings as s
 from django.core.management.base import BaseCommand
 from django.db import transaction
 
-from epdb.models import MLRelativeReasoning, EnviFormer, Package
+from epdb.models import EnviFormer, MLRelativeReasoning
+
+Package = s.GET_PACKAGE_MODEL()
 
 
 class Command(BaseCommand):
@@ -75,11 +77,13 @@ class Command(BaseCommand):
             return packages
 
         # Iteratively create models in options["model_names"]
-        print(f"Creating models: {options['model_names']}\n"
+        print(
-              f"Data packages: {options['data_packages']}\n"
+            f"Creating models: {options['model_names']}\n"
-              f"Rule Packages (only for MLRR): {options['rule_packages']}\n"
+            f"Data packages: {options['data_packages']}\n"
-              f"Eval Packages: {options['eval_packages']}\n"
+            f"Rule Packages (only for MLRR): {options['rule_packages']}\n"
-              f"Threshold: {options['threshold']:.2f}")
+            f"Eval Packages: {options['eval_packages']}\n"
+            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"])
@@ -90,10 +94,10 @@ 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']}.",
+                    f"evaluated on {options['eval_packages']}.",
                 )
             elif model_name == "mlrr":
                 model = MLRelativeReasoning.create(
@@ -101,10 +105,10 @@ 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']}.",
+                    f"{options['rule_packages']} and evaluated on {options['eval_packages']}.",
                 )
             else:
                 raise ValueError(f"Cannot create model of type {model_name}, unknown model type")

epdb/management/commands/load_enviformer.py

@@ -8,7 +8,9 @@ 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
+from epdb.models import EnviFormer
+
+Package = s.GET_PACKAGE_MODEL()
 
 
 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 import F, Value, TextField, JSONField
+from django.db.models.functions import Cast, Replace
-from django.db.models.functions import Replace, Cast
 
 from epdb.models import EnviPathModel
 
@@ -23,10 +23,13 @@ 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

@@ -0,0 +1,190 @@
+# 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
+from typing import Union, List, Optional, Dict, Tuple, Set, Any, TYPE_CHECKING
 from uuid import uuid4
 import math
 import joblib
@@ -32,6 +32,8 @@ from utilities.ml import Dataset, ApplicabilityDomainPCA, EnsembleClassifierChai
 
 logger = logging.getLogger(__name__)
 
+if TYPE_CHECKING:
+    Package = s.GET_PACKAGE_MODEL()
 
 ##########################
 # User/Groups/Permission #
@@ -45,7 +47,10 @@ class User(AbstractUser):
     )
     url = models.TextField(blank=False, null=True, verbose_name="URL", unique=True)
     default_package = models.ForeignKey(
-        "epdb.Package", verbose_name="Default Package", null=True, on_delete=models.SET_NULL
+        s.PACKAGE_IMPLEMENTATION,
+        verbose_name="Default Package",
+        null=True,
+        on_delete=models.SET_NULL,
     )
     default_group = models.ForeignKey(
         "Group",
@@ -235,7 +240,7 @@ class UserPackagePermission(Permission):
     )
     user = models.ForeignKey("User", verbose_name="Permission to", on_delete=models.CASCADE)
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Permission on", on_delete=models.CASCADE
+        s.PACKAGE_IMPLEMENTATION, verbose_name="Permission on", on_delete=models.CASCADE
     )
 
     class Meta:
@@ -251,7 +256,7 @@ class GroupPackagePermission(Permission):
     )
     group = models.ForeignKey("Group", verbose_name="Permission to", on_delete=models.CASCADE)
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Permission on", on_delete=models.CASCADE
+        s.PACKAGE_IMPLEMENTATION, verbose_name="Permission on", on_delete=models.CASCADE
     )
 
     class Meta:
@@ -651,7 +656,7 @@ class License(models.Model):
     image_link = models.URLField(blank=False, null=False, verbose_name="Image link")
 
 
-class Package(EnviPathModel):
+class AbstractPackage(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"
@@ -719,10 +724,13 @@ class Package(EnviPathModel):
         rules = sorted(rules, key=lambda x: x.url)
         return rules
 
+    class Meta:
+        abstract = True
+
 
 class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin):
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
     default_structure = models.ForeignKey(
         "CompoundStructure",
@@ -772,7 +780,7 @@ 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")
@@ -1050,7 +1058,7 @@ class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
 
 class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
 
     # # https://github.com/django-polymorphic/django-polymorphic/issues/229
@@ -1156,7 +1164,7 @@ class SimpleAmbitRule(SimpleRule):
     @staticmethod
     @transaction.atomic
     def create(
-        package: Package,
+        package: "Package",
         name: str = None,
         description: str = None,
         smirks: str = None,
@@ -1222,6 +1230,7 @@ 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")
 
@@ -1314,7 +1323,7 @@ class SequentialRuleOrdering(models.Model):
 
 class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin):
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
     educts = models.ManyToManyField(
         "epdb.CompoundStructure", verbose_name="Educts", related_name="reaction_educts"
@@ -1336,7 +1345,7 @@ 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,
@@ -1496,7 +1505,7 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
 
 class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        s.PACKAGE_IMPLEMENTATION, 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
@@ -1573,12 +1582,14 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
         while len(queue):
             current = queue.pop()
             processed.add(current)
+
             nodes.append(current.d3_json())
 
-            for e in self.edges.filter(start_nodes=current).distinct():
+            for e in self.edges:
-                for prod in e.end_nodes.all():
+                if current in e.start_nodes.all():
-                    if prod not in queue and prod not in processed:
+                    for prod in e.end_nodes.all():
-                        queue.append(prod)
+                        if prod not in queue and prod not in processed:
+                            queue.append(prod)
 
         # We shouldn't lose or make up nodes...
         assert len(nodes) == len(self.nodes)
@@ -2050,7 +2061,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin):
 
 class EPModel(PolymorphicModel, EnviPathModel):
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        s.PACKAGE_IMPLEMENTATION, verbose_name="Package", on_delete=models.CASCADE, db_index=True
     )
 
     def _url(self):
@@ -2059,17 +2070,17 @@ class EPModel(PolymorphicModel, EnviPathModel):
 
 class PackageBasedModel(EPModel):
     rule_packages = models.ManyToManyField(
-        "Package",
+        s.PACKAGE_IMPLEMENTATION,
         verbose_name="Rule Packages",
         related_name="%(app_label)s_%(class)s_rule_packages",
     )
     data_packages = models.ManyToManyField(
-        "Package",
+        s.PACKAGE_IMPLEMENTATION,
         verbose_name="Data Packages",
         related_name="%(app_label)s_%(class)s_data_packages",
     )
     eval_packages = models.ManyToManyField(
-        "Package",
+        s.PACKAGE_IMPLEMENTATION,
         verbose_name="Evaluation Packages",
         related_name="%(app_label)s_%(class)s_eval_packages",
     )
@@ -3437,7 +3448,7 @@ class PluginModel(EPModel):
 
 class Scenario(EnviPathModel):
     package = models.ForeignKey(
-        "epdb.Package", verbose_name="Package", on_delete=models.CASCADE, db_index=True
+        s.PACKAGE_IMPLEMENTATION, 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(
@@ -3588,7 +3599,7 @@ class Setting(EnviPathModel):
     )
 
     rule_packages = models.ManyToManyField(
-        "Package",
+        s.PACKAGE_IMPLEMENTATION,
         verbose_name="Setting Rule Packages",
         related_name="setting_rule_packages",
         blank=True,

epdb/tasks.py

@@ -7,9 +7,12 @@ 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 EPModel, JobLog, Node, Package, Pathway, Rule, Setting, User, Edge
+from epdb.models import Edge, EPModel, JobLog, Node, Pathway, Rule, Setting, User
+
+Package = s.GET_PACKAGE_MODEL()
 
 logger = logging.getLogger(__name__)
 ML_CACHE = LRUCache(3)  # Cache the three most recent ML models to reduce load times.
@@ -172,7 +175,6 @@ 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 List, Dict, Any
+from typing import Any, Dict, List
 
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
-from django.http import JsonResponse, HttpResponse, HttpResponseNotAllowed, HttpResponseBadRequest
+from django.http import HttpResponse, HttpResponseBadRequest, HttpResponseNotAllowed, JsonResponse
-from django.shortcuts import render, redirect
+from django.shortcuts import redirect, render
 from django.urls import reverse
 from django.views.decorators.csrf import csrf_exempt
 from envipy_additional_information import NAME_MAPPING
@@ -14,42 +14,43 @@ 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,
-    UserManager,
-    SettingManager,
     SearchManager,
-    EPDBURLParser,
+    SettingManager,
+    UserManager,
 )
 from .models import (
-    Package,
+    APIToken,
-    GroupPackagePermission,
-    Group,
-    CompoundStructure,
     Compound,
+    CompoundStructure,
+    Edge,
+    EnviFormer,
+    EnzymeLink,
+    EPModel,
+    ExternalDatabase,
+    ExternalIdentifier,
+    Group,
+    GroupPackagePermission,
+    JobLog,
+    License,
+    MLRelativeReasoning,
+    Node,
+    Pathway,
+    Permission,
     Reaction,
     Rule,
-    Pathway,
-    Node,
-    EPModel,
-    EnviFormer,
-    MLRelativeReasoning,
     RuleBasedRelativeReasoning,
     Scenario,
     SimpleAmbitRule,
-    APIToken,
-    UserPackagePermission,
-    Permission,
-    License,
     User,
-    Edge,
+    UserPackagePermission,
-    ExternalDatabase,
-    ExternalIdentifier,
-    EnzymeLink,
-    JobLog,
 )
 
+Package = s.GET_PACKAGE_MODEL()
 logger = logging.getLogger(__name__)
 
 
@@ -82,8 +83,7 @@ def login(request):
         return render(request, "static/login.html", context)
 
     elif request.method == "POST":
-        from django.contrib.auth import authenticate
+        from django.contrib.auth import authenticate, login
-        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 dispatch, build_model
+        from .tasks import build_model, dispatch
 
         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

@@ -1,22 +1,19 @@
-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 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
-
-
 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 utilities.chem import FormatConverter
+
+Package = s.GET_PACKAGE_MODEL()
+
 logger = logging.getLogger(__name__)
 
 
@@ -59,9 +56,7 @@ def run_both_engines(SMILES, SMIRKS):
         set(
             [
                 normalize_smiles(str(x))
-                for x in FormatConverter.sanitize_smiles(
+                for x in FormatConverter.sanitize_smiles([str(s) for s in all_rdkit_prods])[0]
-                    [str(s) for s in all_rdkit_prods]
-                )[0]
             ]
         )
     )
@@ -85,8 +80,7 @@ def migration(request):
                 url="http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1"
             )
             ALL_SMILES = [
-                cs.smiles
+                cs.smiles for cs in CompoundStructure.objects.filter(compound__package=BBD)
-                for cs in CompoundStructure.objects.filter(compound__package=BBD)
             ]
             RULES = SimpleAmbitRule.objects.filter(package=BBD)
 
@@ -142,9 +136,7 @@ def migration(request):
             )
 
         for r in migration_status["results"]:
-            r["detail_url"] = r["detail_url"].replace(
+            r["detail_url"] = r["detail_url"].replace("http://localhost:8000", s.SERVER_URL)
-                "http://localhost:8000", s.SERVER_URL
-            )
 
         context.update(**migration_status)
 
@@ -152,8 +144,6 @@ 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)
 
@@ -235,9 +225,7 @@ 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"] = (
+        context["smiles"] = "C(CC(=O)N[C@@H](CS[Se-])C(=O)NCC(=O)[O-])[C@@H](C(=O)[O-])N"
-            "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

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

public/apps.py

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

public/migrations/0001_initial.py

@@ -0,0 +1,56 @@
+# 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

@@ -0,0 +1,16 @@
+# 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

@@ -0,0 +1,25 @@
+# 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

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

public/tests.py

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

public/views.py

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

tests/test_enviformer.py

@@ -1,10 +1,15 @@
 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 User, EnviFormer, Package, Setting
+from epdb.models import EnviFormer, Setting, User
-from epdb.tasks import predict_simple, predict
+from epdb.tasks import predict, predict_simple
+
+Package = s.GET_PACKAGE_MODEL()
 
 
 def measure_predict(mod, pathway_pk=None):

tests/test_model.py

@@ -1,10 +1,13 @@
 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 User, MLRelativeReasoning, Package
+from epdb.models import MLRelativeReasoning, User
+
+Package = s.GET_PACKAGE_MODEL()
 
 
 class ModelTest(TestCase):

tests/test_multigen_eval.py

@@ -1,8 +1,12 @@
+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, Package
+from epdb.models import Pathway, User
-from utilities.ml import multigen_eval, pathway_edit_eval, graph_from_pathway
+from utilities.ml import graph_from_pathway, multigen_eval, pathway_edit_eval
+
+Package = s.GET_PACKAGE_MODEL()
 
 
 class MultiGenTest(TestCase):

tests/test_simpleambitrule.py

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

@@ -1,9 +1,11 @@
+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 Package, User
+from epdb.models import User
+
+Package = s.GET_PACKAGE_MODEL()
 
 
 @override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)

tests/views/test_package_views.py

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

tests/views/test_pathway_views.py

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

tests/views/test_reaction_views.py

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

tests/views/test_user_views.py

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

utilities/chem.py

@@ -2,13 +2,12 @@ import logging
 import re
 from abc import ABC
 from collections import defaultdict
-from typing import List, Optional, Dict, TYPE_CHECKING, Union
+from typing import List, Optional, Dict, TYPE_CHECKING
 
 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
@@ -91,15 +90,8 @@ class FormatConverter(object):
         return Chem.MolToSmiles(mol, canonical=canonical)
 
     @staticmethod
-    def InChIKey(mol_or_smiles: Union[rdchem.Mol | str]):
+    def InChIKey(smiles):
-        if isinstance(mol_or_smiles, str):
+        return Chem.MolToInchiKey(FormatConverter.from_smiles(smiles))
-            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):
@@ -296,8 +288,7 @@ class FormatConverter(object):
                             product = GetMolFrags(product, asMols=True)
                             for p in product:
                                 p = FormatConverter.standardize(
-                                    Chem.MolToSmiles(p).replace("~", ""),
+                                    Chem.MolToSmiles(p), remove_stereo=remove_stereo
-                                    remove_stereo=remove_stereo,
                                 )
                                 prods.append(p)
 

utilities/decorators.py

@@ -1,10 +1,12 @@
 # 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
-from epdb.models import Package
+
+Package = s.GET_PACKAGE_MODEL()
 
 # Map HTTP methods to required permissions
 DEFAULT_METHOD_PERMISSIONS = {

utilities/misc.py

@@ -11,6 +11,7 @@ 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
@@ -26,7 +27,6 @@ from epdb.models import (
     License,
     MLRelativeReasoning,
     Node,
-    Package,
     ParallelRule,
     Pathway,
     PluginModel,
@@ -35,13 +35,14 @@ 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__)
 
 
@@ -1259,46 +1260,3 @@ 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