Show Pack Classification

Dockerfile

@@ -6,23 +6,18 @@ ENV PYTHONDONTWRITEBYTECODE=1 \
 
 WORKDIR /app
 
-
 RUN apt-get update && apt-get install -y --no-install-recommends \
     build-essential \
     libpq-dev \
     curl \
     openssh-client \
     git \
-    ca-certificates \
+    nodejs \
+    npm \
     && rm -rf /var/lib/apt/lists/*
 
-# Install Node 22 + pnpm
+# Install pnpm
-RUN curl -fsSL https://deb.nodesource.com/setup_22.x | bash - \
+RUN npm install -g pnpm
-    && apt-get update \
-    && apt-get install -y --no-install-recommends nodejs \
-    && corepack enable \
-    && corepack prepare pnpm@latest --activate \
-    && rm -rf /var/lib/apt/lists/*
 
 RUN curl -LsSf https://astral.sh/uv/install.sh | sh
 ENV PATH="/root/.local/bin:${PATH}"
@@ -37,17 +32,15 @@ RUN mkdir -p -m 0700 /root/.ssh \
 # We'll need access to private repos, let docker make use of host ssh agent and use it like:
 # docker build --ssh default -t envipath/envipy:1.0 .
 RUN --mount=type=ssh \
-    uv sync --locked --extra pepper-plugin
+    uv sync --locked --extra ms-login --extra pepper-plugin
 
 # Now copy source and do a final sync to install the project itself
 # Ensure .dockerignore is reasonable
-COPY biotransformer biotransformer
 COPY bridge bridge
 COPY envipath envipath
 COPY epapi epapi
 COPY epauth epauth
 COPY epdb epdb
-COPY epiuclid epiuclid
 COPY fixtures fixtures
 COPY migration migration
 COPY pepper pepper

bayer/admin.py

@@ -0,0 +1,3 @@
+from django.contrib import admin
+
+# Register your models here.

bayer/apps.py

@@ -0,0 +1,6 @@
+from django.apps import AppConfig
+
+
+class BayerConfig(AppConfig):
+    default_auto_field = 'django.db.models.BigAutoField'
+    name = 'bayer'

bayer/migrations/0001_initial.py

@@ -0,0 +1,35 @@
+# Generated by Django 5.2.7 on 2026-03-06 10:51
+
+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')),
+                ('classification_level', models.IntegerField(choices=[(0, 'Internal'), (10, 'Restricted'), (20, 'Secret')], default=10)),
+            ],
+            options={
+                'db_table': 'epdb_package',
+            },
+        ),
+    ]

bayer/migrations/0002_initial.py

@@ -0,0 +1,22 @@
+# Generated by Django 5.2.7 on 2026-03-06 10:51
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+        ('bayer', '0001_initial'),
+        ('epdb', '0019_remove_scenario_additional_information_and_more'),
+    ]
+
+    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'),
+        ),
+    ]

bayer/models.py

@@ -0,0 +1,95 @@
+from typing import List
+
+from django.conf import settings as s
+from django.db import models
+from django.db.models import QuerySet
+
+from epdb.models import (
+    EnviPathModel,
+    ParallelRule,
+    SequentialRule,
+    SimpleAmbitRule,
+    SimpleRDKitRule,
+)
+
+
+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"
+    )
+
+    class Classification(models.IntegerChoices):
+        INTERNAL = 0, "Internal"
+        RESTRICTED = 10 , "Restricted"
+        SECRET = 20, "Secret"
+
+    classification_level = models.IntegerField(
+        choices=Classification,
+        default=Classification.RESTRICTED,
+    )
+
+    def delete(self, *args, **kwargs):
+        # explicitly handle related Rules
+        for r in self.rules.all():
+            r.delete()
+        super().delete(*args, **kwargs)
+
+    def __str__(self):
+        return f"{self.name} (pk={self.pk})"
+
+    @property
+    def compounds(self) -> QuerySet:
+        return self.compound_set.all()
+
+    @property
+    def rules(self) -> QuerySet:
+        return self.rule_set.all()
+
+    @property
+    def reactions(self) -> QuerySet:
+        return self.reaction_set.all()
+
+    @property
+    def pathways(self) -> QuerySet:
+        return self.pathway_set.all()
+
+    @property
+    def scenarios(self) -> QuerySet:
+        return self.scenario_set.all()
+
+    @property
+    def models(self) -> QuerySet:
+        return self.epmodel_set.all()
+
+    def _url(self):
+        return "{}/package/{}".format(s.SERVER_URL, self.uuid)
+
+    def get_applicable_rules(self) -> List["Rule"]:
+        """
+        Returns a ordered set of rules where the following applies:
+        1. All Composite will be added to result
+        2. All SimpleRules will be added if theres no CompositeRule present using the SimpleRule
+        Ordering is based on "url" field.
+        """
+        rules = []
+        rule_qs = self.rules
+
+        reflected_simple_rules = set()
+
+        for r in rule_qs:
+            if isinstance(r, ParallelRule) or isinstance(r, SequentialRule):
+                rules.append(r)
+                for sr in r.simple_rules.all():
+                    reflected_simple_rules.add(sr)
+
+        for r in rule_qs:
+            if isinstance(r, SimpleAmbitRule) or isinstance(r, SimpleRDKitRule):
+                if r not in reflected_simple_rules:
+                    rules.append(r)
+
+        rules = sorted(rules, key=lambda x: x.url)
+        return rules
+
+    class Meta:
+        db_table = "epdb_package"

bayer/templates/objects/package.html

@@ -0,0 +1,97 @@
+{% extends "framework_modern.html" %}
+
+{% block content %}
+
+  {% block action_modals %}
+    {% include "modals/objects/edit_package_modal.html" %}
+    {% include "modals/objects/edit_package_permissions_modal.html" %}
+    {% include "modals/objects/publish_package_modal.html" %}
+    {% include "modals/objects/set_license_modal.html" %}
+    {% include "modals/objects/export_package_modal.html" %}
+    {% include "modals/objects/generic_delete_modal.html" %}
+  {% endblock action_modals %}
+
+  <div class="space-y-2 p-4">
+    <!-- Header Section -->
+    <div class="card bg-base-100">
+      <div class="card-body">
+        <div class="flex items-center justify-between">
+          <h2 class="card-title text-2xl">{{ package.name }} - ({{ package.get_classification_level_display }})</h2>
+          <div id="actionsButton" class="dropdown dropdown-e nd hidden">
+            <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
+              <svg
+                xmlns="http://www.w3.org/2000/svg"
+                width="16"
+                height="16"
+                viewBox="0 0 24 24"
+                fill="none"
+                stroke="currentColor"
+                stroke-width="2"
+                stroke-linecap="round"
+                stroke-linejoin="round"
+                class="lucide lucide-wrench"
+              >
+                <path
+                  d="M14.7 6.3a1 1 0 0 0 0 1.4l1.6 1.6a1 1 0 0 0 1.4 0l3.77-3.77a6 6 0 0 1-7.94 7.94l-6.91 6.91a2.12 2.12 0 0 1-3-3l6.91-6.91a6 6 0 0 1 7.94-7.94l-3.76 3.76z"
+                />
+              </svg>
+              Actions
+            </div>
+            <ul
+              tabindex="-1"
+              class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
+            >
+              {% block actions %}
+                {% include "actions/objects/package.html" %}
+              {% endblock %}
+            </ul>
+          </div>
+        </div>
+        <p class="mt-2">{{ package.description|safe }}</p>
+        <ul class="menu bg-base-200 rounded-box mt-4 w-full">
+          <li>
+            <a href="{{ package.url }}/pathway" class="hover:bg-base-300"
+              >Pathways ({{ package.pathways.count }})</a
+            >
+          </li>
+          <li>
+            <a href="{{ package.url }}/rule" class="hover:bg-base-300"
+              >Rules ({{ package.rules.count }})</a
+            >
+          </li>
+          <li>
+            <a href="{{ package.url }}/compound" class="hover:bg-base-300"
+              >Compounds ({{ package.compounds.count }})</a
+            >
+          </li>
+          <li>
+            <a href="{{ package.url }}/reaction" class="hover:bg-base-300"
+              >Reactions ({{ package.reactions.count }})</a
+            >
+          </li>
+          <li>
+            <a href="{{ package.url }}/model" class="hover:bg-base-300"
+              >Models ({{ package.models.count }})</a
+            >
+          </li>
+          <li>
+            <a href="{{ package.url }}/scenario" class="hover:bg-base-300"
+              >Scenarios ({{ package.scenarios.count }})</a
+            >
+          </li>
+        </ul>
+      </div>
+    </div>
+  </div>
+
+  <script>
+    // Show actions button if there are actions
+    document.addEventListener("DOMContentLoaded", function () {
+      const actionsButton = document.getElementById("actionsButton");
+      const actionsList = actionsButton?.querySelector("ul");
+      if (actionsList && actionsList.children.length > 0) {
+        actionsButton?.classList.remove("hidden");
+      }
+    });
+  </script>
+{% endblock content %}

bayer/tests.py

@@ -0,0 +1,3 @@
+from django.test import TestCase
+
+# Create your tests here.

bayer/views.py

@@ -0,0 +1,3 @@
+from django.shortcuts import render
+
+# Create your views here.

bridge/contracts.py

@@ -254,14 +254,7 @@ class Classifier(Plugin):
     def parse_config(cls, data: dict | None = None) -> EnviPyModel | None:
         if cls.Config is None:
             return None
-
+        return cls.Config(**(data or {}))
-        # remove empty strings a.k.a unset params to not overwrite defaults
-        cpy = {}
-        if data is not None:
-            for k, v in data.items():
-                if v != "":
-                    cpy[k] = v
-        return cls.Config(**cpy)
 
     @classmethod
     def create(cls, data: dict | None = None):

envipath/urls.py

@@ -40,9 +40,6 @@ if "migration" in s.INSTALLED_APPS:
 if s.MS_ENTRA_ENABLED:
     urlpatterns.append(path(f"{PATH_PREFIX}", include("epauth.urls")))
 
-if s.TENANT != "public":
-    urlpatterns.append(path(f"{PATH_PREFIX}", include(f"{s.TENANT}.urls")))
-
 # Custom error handlers
 handler400 = "epdb.views.handler400"
 handler403 = "epdb.views.handler403"

epapi/v1/endpoints/groups.py

@@ -1,23 +0,0 @@
-from django.conf import settings as s
-from ninja import Router
-from ninja_extra.pagination import paginate
-
-from epdb.logic import GroupManager
-
-from ..pagination import EnhancedPageNumberPagination
-from ..schemas import GroupOutSchema
-
-router = Router()
-
-
-@router.get("/groups/", response=EnhancedPageNumberPagination.Output[GroupOutSchema])
-@paginate(
-    EnhancedPageNumberPagination,
-    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
-)
-def list_all_groups(request):
-    """
-    List all groups the user has access to.
-    """
-    user = request.user
-    return GroupManager.get_groups(user)

epapi/v1/endpoints/joblogs.py

@@ -1,26 +0,0 @@
-from django.conf import settings as s
-from ninja import Router
-from ninja_extra.pagination import paginate
-
-from epdb.models import JobLog
-from ..pagination import EnhancedPageNumberPagination
-from ..schemas import JobLogOutSchema
-
-router = Router()
-
-
-@router.get("/joblog/", response=EnhancedPageNumberPagination.Output[JobLogOutSchema])
-@paginate(
-    EnhancedPageNumberPagination,
-    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
-)
-def list_all_joblogs(request):
-    """
-    List all JobLogs from reviewed packages.
-    """
-    current_user = request.user
-
-    if current_user.is_superuser:
-        return JobLog.objects.all().order_by("-created")
-    else:
-        return JobLog.objects.filter(user=current_user).order_by("-created")

epapi/v1/endpoints/settings.py

@@ -15,9 +15,9 @@ router = Router()
     EnhancedPageNumberPagination,
     page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
 )
-def list_all_settings(request):
+def list_all_pathways(request):
     """
-    List all settings the user has access to.
+    List all pathways from reviewed packages.
     """
     user = request.user
     return SettingManager.get_all_settings(user)

epapi/v1/router.py

@@ -1,7 +1,6 @@
 from ninja import Router
 from ninja.security import SessionAuth
 
-from envipath import settings as s
 from .auth import BearerTokenAuth
 from .endpoints import (
     packages,
@@ -14,9 +13,8 @@ from .endpoints import (
     structure,
     additional_information,
     settings,
-    groups,
-    joblogs,
 )
+from envipath import settings as s
 
 # Main router with authentication
 router = Router(
@@ -37,8 +35,6 @@ router.add_router("", models.router)
 router.add_router("", structure.router)
 router.add_router("", additional_information.router)
 router.add_router("", settings.router)
-router.add_router("", groups.router)
-router.add_router("", joblogs.router)
 
 if s.IUCLID_EXPORT_ENABLED:
     from epiuclid.api import router as iuclid_router

epapi/v1/schemas.py

@@ -1,10 +1,7 @@
-from datetime import datetime
+from ninja import FilterSchema, FilterLookup, Schema
 from typing import Annotated, Optional, List, Dict, Any
 from uuid import UUID
 
-from django.urls import reverse
-from ninja import Field, FilterSchema, FilterLookup, Schema
-
 
 # Filter schema for query parameters
 class ReviewStatusFilter(FilterSchema):
@@ -129,30 +126,3 @@ class SettingOutSchema(Schema):
     url: str = ""
     name: str
     description: str
-
-
-class GroupOutSchema(Schema):
-    uuid: UUID
-    url: str = ""
-    name: str
-    description: str
-
-
-class SimpleUserOutSchema(Schema):
-    uuid: UUID
-    url: str
-    name: str = Field(alias="username")
-
-
-class JobLogOutSchema(Schema):
-    user: SimpleUserOutSchema
-    id: UUID = Field(alias="task_id")
-    url: str
-    name: str = Field(alias="job_name")
-    created: datetime = Field(alias="created")
-    status: str = Field(alias="status")
-    done: Optional[datetime] = Field(None, alias="done_at")
-
-    @staticmethod
-    def resolve_url(obj):
-        return reverse("job detail", kwargs={"job_uuid": obj.task_id})

epauth/views.py

@@ -1,32 +1,12 @@
 import msal
 from django.conf import settings as s
-from django.contrib.auth import get_user_model
 from django.contrib.auth import login
 from django.shortcuts import redirect
+from django.contrib.auth import get_user_model
 
 from epdb.logic import UserManager
 
 
-def get_msal_app_with_cache(request):
-    """
-    Create MSAL app with session-based token cache.
-    """
-    cache = msal.SerializableTokenCache()
-
-    # Load cache from session if it exists
-    if request.session.get("msal_token_cache"):
-        cache.deserialize(request.session["msal_token_cache"])
-
-    msal_app = msal.ConfidentialClientApplication(
-        client_id=s.MS_ENTRA_CLIENT_ID,
-        client_credential=s.MS_ENTRA_CLIENT_SECRET,
-        authority=s.MS_ENTRA_AUTHORITY,
-        token_cache=cache,
-    )
-
-    return msal_app, cache
-
-
 def entra_login(request):
     msal_app = msal.ConfidentialClientApplication(
         client_id=s.MS_ENTRA_CLIENT_ID,
@@ -43,7 +23,11 @@ def entra_login(request):
 
 
 def entra_callback(request):
-    msal_app, cache = get_msal_app_with_cache(request)
+    msal_app = msal.ConfidentialClientApplication(
+        client_id=s.MS_ENTRA_CLIENT_ID,
+        client_credential=s.MS_ENTRA_CLIENT_SECRET,
+        authority=s.MS_ENTRA_AUTHORITY,
+    )
 
     flow = request.session.pop("msal_auth_flow", None)
     if not flow:
@@ -52,18 +36,11 @@ def entra_callback(request):
     # Acquire token using the flow and callback request
     result = msal_app.acquire_token_by_auth_code_flow(flow, request.GET)
 
-    # Save the token cache to session
-    if cache.has_state_changed:
-        request.session["msal_token_cache"] = cache.serialize()
-
     claims = result["id_token_claims"]
 
-    user_name = claims.get("name")
+    user_name = claims["name"]
-    user_email = claims.get("emailaddress", claims.get("email"))
+    user_email = claims["emailaddress"]
-    user_oid = claims.get("oid")
+    user_oid = claims["oid"]
-
-    if not all([user_name, user_email, user_oid]):
-        raise ValueError("Missing required claims in ID token")
 
     # Get implementing class
     User = get_user_model()
@@ -80,51 +57,4 @@ def entra_callback(request):
 
     login(request, u)
 
-    return redirect(s.SERVER_URL)  # Handle errors
+    return redirect("/")  # Handle errors
-
-
-def get_access_token_from_request(request, scopes=None):
-    """
-    Get an access token from the request using MSAL token cache.
-    """
-    if scopes is None:
-        scopes = s.MS_ENTRA_SCOPES
-
-    # Get user from request (must be authenticated)
-    if not request.user.is_authenticated:
-        return None
-
-    # Create MSAL app with persistent cache
-    msal_app, cache = get_msal_app_with_cache(request)
-
-    # Try to get accounts from cache
-    accounts = msal_app.get_accounts()
-
-    if not accounts:
-        return None
-
-    # Find the account that matches the current user
-    user_account = None
-    for account in accounts:
-        if account.get("local_account_id") == str(request.user.uuid):
-            user_account = account
-            break
-
-    # If no matching account found, use the first available account
-    if not user_account and accounts:
-        user_account = accounts[0]
-
-    if not user_account:
-        return None
-
-    # Try to acquire token silently from cache
-    result = msal_app.acquire_token_silent(scopes=scopes, account=user_account)
-
-    # Save cache changes back to session
-    if cache.has_state_changed:
-        request.session["msal_token_cache"] = cache.serialize()
-
-    if result and "access_token" in result:
-        return result
-
-    return None

epdb/admin.py

@@ -1,8 +1,5 @@
-import logging
-
 from django.conf import settings as s
 from django.contrib import admin
-from django.contrib import messages
 
 from .models import (
     AdditionalInformation,
@@ -32,8 +29,6 @@ from .models import (
 
 Package = s.GET_PACKAGE_MODEL()
 
-logger = logging.getLogger(__name__)
-
 
 class AdditionalInformationAdmin(admin.ModelAdmin):
     pass
@@ -50,113 +45,6 @@ class UserAdmin(admin.ModelAdmin):
         "date_joined",
     ]
 
-    actions = ["send_welcome_mail", "send_affiliation_mail"]
-
-    @admin.action(description="Send welcome mail")
-    def send_welcome_mail(self, request, queryset):
-        from django.core.mail import EmailMultiAlternatives
-
-        tpl = """Hello {username},
-
-Your account has been successfully activated.
-
-To log in, please visit
-https://envipath.org/password_reset/
-and request a new password.
-
-If you have any questions or feedback, feel free to visit our community forum at
-https://community.envipath.org/.
-You do not need to register again for the forum - you can log in using your enviPath account by clicking "Log In" and then "Log in with enviPath."
-
-Best regards,
-
-The enviPath Team"""
-
-        users = []
-
-        for user in queryset:
-            if user.is_active:
-                logger.info(f"{user.username} already active - not sending mail again")
-                continue
-            try:
-                msg = EmailMultiAlternatives(
-                    "Your enviPath Account Is Now Active",
-                    tpl.format(username=user.username),
-                    "admin@envipath.org",
-                    [user.email],
-                    bcc=["admin@envipath.org"],
-                )
-
-                msg.send(fail_silently=False)
-
-                user.is_active = True
-                user.password = "ASDF"
-                user.save()
-
-                users.append(user)
-                logger.info(f"{user.username} -> {user.email} mail sent")
-            except Exception as e:
-                logger.info(f"Error sending mail to {user.username}: {e}")
-
-        self.message_user(
-            request, f"Sent welcome mail to {[u.email for u in users]}", messages.SUCCESS
-        )
-
-    @admin.action(description="Send affiliation mail")
-    def send_affiliation_mail(self, request, queryset):
-        from django.core.mail import EmailMultiAlternatives
-
-        tpl = """Dear {username},
-
-Thank you for your interest in enviPath!
-
-Please note that the public enviPath system is intended for non-commercial use only.
-We see that you registered using the email address {email}.
-If possible, we kindly ask you to register using an official email address that reflects your affiliation (e.g., a university, NGO, or research organization).
-
-If you would like us to update your account, simply reply to this email and let us know which address we should use.
-We will then change it in our system, and you will receive a password reset email at the new address.
-
-If you are registering with a company email address and are interested in commercial use, you are very welcome to book a meeting with us so we can discuss how we can best support you.
-To book a meeting, please visit https://envipath.com/book
-
-If changing to an affiliation email address is not possible, please contact us at registration@envipath.org
-
-Best regards,
-
-enviPath team"""
-
-        users = []
-
-        for user in queryset:
-            if user.is_active or user.contacted:
-                logger.info(
-                    f"{user.username} already active or already contacted - not sending mail again"
-                )
-                continue
-            try:
-                msg = EmailMultiAlternatives(
-                    "Regarding your enviPath registration",
-                    tpl.format(username=user.username, email=user.email),
-                    "admin@envipath.org",
-                    [user.email],
-                    bcc=["admin@envipath.org"],
-                )
-
-                msg.send(fail_silently=False)
-
-                user.contacted = True
-                user.save()
-
-                users.append(user)
-                logger.info(f"{user.username} -> {user.email} affiliation mail sent")
-            except Exception as e:
-                logger.info(f"Error sending mail to {user.username}: {e}")
-
-        self.message_user(
-            request, f"Sent affiliation mail to {[u.email for u in users]}", messages.SUCCESS
-        )
-
 
 class UserPackagePermissionAdmin(admin.ModelAdmin):
     pass

epdb/exceptions.py

@@ -1,2 +0,0 @@
-class InvalidSMILESException(Exception):
-    pass

epdb/legacy_api.py

@@ -386,50 +386,23 @@ class PackageSchema(Schema):
 
     @staticmethod
     def resolve_readers(obj: Package):
-        readers = []
+        users = User.objects.filter(
+            id__in=UserPackagePermission.objects.filter(
+                package=obj, permission=UserPackagePermission.READ[0]
+            ).values_list("user", flat=True)
+        ).distinct()
 
-        user_ids = UserPackagePermission.objects.filter(package=obj).values_list("user", flat=True)
+        return [{u.id: u.get_name()} for u in users]
-
-        users = User.objects.filter(id__in=user_ids).distinct()
-
-        for u in users:
-            readers.append({"id": str(u.url), "identifier": "user", "name": u.get_name()})
-
-        group_ids = GroupPackagePermission.objects.filter(package=obj).values_list(
-            "group", flat=True
-        )
-
-        groups = Group.objects.filter(id__in=group_ids).distinct()
-
-        for g in groups:
-            readers.append({"id": str(g.url), "identifier": "group", "name": g.get_name()})
-
-        return readers
 
     @staticmethod
     def resolve_writers(obj: Package):
-        writers = []
+        users = User.objects.filter(
+            id__in=UserPackagePermission.objects.filter(
+                package=obj, permission=UserPackagePermission.WRITE[0]
+            ).values_list("user", flat=True)
+        ).distinct()
 
-        user_ids = UserPackagePermission.objects.filter(
+        return [{u.id: u.get_name()} for u in users]
-            package=obj,
-            permission__in=[UserPackagePermission.WRITE[0], UserPackagePermission.ALL[0]],
-        ).values_list("user", flat=True)
-
-        users = User.objects.filter(id__in=user_ids).distinct()
-
-        for u in users:
-            writers.append({"id": str(u.url), "identifier": "user", "name": u.get_name()})
-
-        group_ids = GroupPackagePermission.objects.filter(
-            package=obj, permission=[UserPackagePermission.WRITE[0], UserPackagePermission.ALL[0]]
-        ).values_list("group", flat=True)
-
-        groups = Group.objects.filter(id__in=group_ids).distinct()
-
-        for g in groups:
-            writers.append({"id": str(g.url), "identifier": "group", "name": g.get_name()})
-
-        return writers
 
     @staticmethod
     def resolve_review_comment(obj):
@@ -826,27 +799,6 @@ def delete_compound(request, package_uuid, compound_uuid):
         }
 
 
-class CreateCompoundStructure(Schema):
-    smiles: str
-    name: str | None = None
-    description: str | None = None
-    inchi: str | None = None
-    molfile: str | None = None
-
-
-@router.post("/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure")
-def create_package_compound_structure(
-    request, package_uuid, compound_uuid, structure: Form[CreateCompoundStructure]
-):
-    try:
-        p = get_package_for_write(request.user, package_uuid)
-        c = Compound.objects.get(package=p, uuid=compound_uuid)
-        cs = CompoundStructure.create(c, structure.smiles, structure.name, structure.description)
-        return redirect(cs.url)
-    except ValueError as e:
-        return 400, {"message": str(e)}
-
-
 @router.delete(
     "/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure/{uuid:structure_uuid}"
 )
@@ -1373,7 +1325,6 @@ class ScenarioSchema(Schema):
     aliases: List[str] = Field([], alias="aliases")
     collection: Dict["str", List[Dict[str, Any]]] = Field([], alias="collection")
     collectionID: Optional[str] = None
-    date: str = Field(None, alias="scenario_date")
     description: str = Field(None, alias="description")
     id: str = Field(None, alias="url")
     identifier: str = "scenario"
@@ -1517,56 +1468,28 @@ def create_package_additional_information(request, package_uuid):
         scen = request.POST.get("scenario")
         scenario = Scenario.objects.get(package=p, url=scen)
 
-        if request.POST.get("adInfoTypes[]"):
+        url_parser = EPDBURLParser(request.POST.get("attach_obj"))
-            url_parser = EPDBURLParser(request.POST.get("attach_obj"))
+        attach_obj = url_parser.get_object()
-            attach_obj = url_parser.get_object()
 
-            if not hasattr(attach_obj, "additional_information"):
+        if not hasattr(attach_obj, "additional_information"):
-                raise ValueError("Can't attach additional information to this object!")
+            raise ValueError("Can't attach additional information to this object!")
 
-            if not attach_obj.url.startswith(p.url):
+        if not attach_obj.url.startswith(p.url):
-                raise ValueError(
+            raise ValueError(
-                    "Additional Information can only be set to objects stored in the same package!"
+                "Additional Information can only be set to objects stored in the same package!"
-                )
+            )
 
-            types = request.POST.get("adInfoTypes[]", "").split(",")
+        types = request.POST.get("adInfoTypes[]", "").split(",")
 
-            for t in types:
+        for t in types:
-                ai = build_additional_information_from_request(request, t)
+            ai = build_additional_information_from_request(request, t)
 
-                AdditionalInformation.create(
+            AdditionalInformation.create(
-                    p,
+                p,
-                    ai,
+                ai,
-                    scenario=scenario,
+                scenario=scenario,
-                    content_object=attach_obj,
+                content_object=attach_obj,
-                )
+            )
-
-        elif request.POST.get("ais"):
-            import json
-
-            parsed_ais = json.loads(request.POST.get("ais"))
-
-            for ai_type, ais in parsed_ais.items():
-                for ai in ais:
-                    attach_obj = None
-                    if ai.get("related"):
-                        url_parser = EPDBURLParser(ai.get("related").get("url"))
-                        attach_obj = url_parser.get_object()
-
-                        if not hasattr(attach_obj, "additional_information"):
-                            raise ValueError("Can't attach additional information to this object!")
-
-                        if not attach_obj.url.startswith(p.url):
-                            raise ValueError(
-                                "Additional Information can only be set to objects stored in the same package!"
-                            )
-
-                    AdditionalInformation.create(
-                        p,
-                        AdditionalInformation.from_dict(ai_type, ai),
-                        scenario=scenario,
-                        content_object=attach_obj,
-                    )
 
         # TODO implement additional information endpoint ?
         return redirect(f"{scenario.url}")
@@ -1610,14 +1533,13 @@ class PathwayNode(Schema):
     dt50s: List[Dict[str, str]] = Field([], alias="dt50s")
     engineeredIntermediate: bool = Field(None, alias="engineered_intermediate")
     id: str = Field(None, alias="url")
-    idcomp: str = Field(None, alias="node_label_id")
+    idcomp: str = Field(None, alias="default_node_label.url")
-    idreact: str = Field(None, alias="node_label_id")
+    idreact: str = Field(None, alias="default_node_label.url")
     image: str = Field(None, alias="image")
     imageSize: int = Field(None, alias="image_size")
     name: str = Field(None, alias="name")
     proposed: List[Dict[str, str]] = Field([], alias="proposed_intermediate")
-    smiles: str = Field(None, alias="smiles")
+    smiles: str = Field(None, alias="default_node_label.smiles")
-    pseudo: bool = Field(False, alias="pseudo")
 
     @staticmethod
     def resolve_atom_count(obj: Node):
@@ -1771,29 +1693,6 @@ def create_package_pathway(
         return 403, {"message": str(e)}
 
 
-@router.post("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}")
-def update_pathway(request, package_uuid, pathway_uuid):
-    try:
-        p = get_package_for_write(request.user, package_uuid)
-
-        if request.POST.get("scenario"):
-            pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
-            scen = Scenario.objects.get(package=p, url=request.POST.get("scenario"))
-
-            pw.scenarios.add(scen)
-            pw.save()
-
-            return redirect(f"{pw.url}")
-
-        else:
-            return 400, {"message": "No scenario specified!"}
-
-    except ValueError:
-        return 403, {
-            "message": f"Deleting Pathway with id {pathway_uuid} failed due to insufficient rights!"
-        }
-
-
 @router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}")
 def delete_pathway(request, package_uuid, pathway_uuid):
     try:
@@ -1914,7 +1813,7 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
 
         if n.nodeDepth is not None and n.nodeDepth.strip() != "":
-            node_depth = int(float(n.nodeDepth))
+            node_depth = int(n.nodeDepth)
         else:
             node_depth = -1
 
@@ -2059,10 +1958,6 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             for pr in e.products.split(","):
                 products.append(Node.objects.get(pathway=pw, url=pr.strip()))
 
-        multi_step = False
-        if e.multistep and e.multistep.strip() == "true":
-            multi_step = True
-
         new_e = Edge.create(
             pathway=pw,
             start_nodes=educts,
@@ -2070,15 +1965,11 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             rule=None,
             name=None,
             description=e.edgeReason,
-            multi_step=multi_step,
         )
 
-        # Update depths as sideeffect of above operation
-        pw.update_depths()
-
         return redirect(new_e.url)
     except ValueError:
-        return 403, {"message": "Adding Edge failed!"}
+        return 403, {"message": "Adding node failed!"}
 
 
 @router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/edge/{uuid:edge_uuid}")

epdb/logic.py

@@ -264,12 +264,8 @@ class GroupManager(object):
         return bool(re.findall(GroupManager.group_pattern, url))
 
     @staticmethod
-    def create_group(current_user, name, description, *args, **kwargs):
+    def create_group(current_user, name, description):
         g = Group()
-
-        if "uuid" in kwargs:
-            g.uuid = kwargs["uuid"]
-
         # Clean for potential XSS
         g.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
         g.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -345,17 +341,52 @@ class PackageManager(object):
 
     @staticmethod
     def readable(user, package):
-        return (
+        if (
-            PackageManager.has_package_permission(user, package, "read") | package.reviewed is True
+            UserPackagePermission.objects.filter(package=package, user=user).exists()
-        )
+            or GroupPackagePermission.objects.filter(
+                package=package, group__in=GroupManager.get_groups(user)
+            )
+            or package.reviewed is True
+            or user.is_superuser
+        ):
+            return True
+
+        return False
 
     @staticmethod
     def writable(user, package):
-        return PackageManager.has_package_permission(user, package, "write")
+        if (
+            UserPackagePermission.objects.filter(
+                package=package, user=user, permission=Permission.WRITE[0]
+            ).exists()
+            or GroupPackagePermission.objects.filter(
+                package=package,
+                group__in=GroupManager.get_groups(user),
+                permission=Permission.WRITE[0],
+            ).exists()
+            or UserPackagePermission.objects.filter(
+                package=package, user=user, permission=Permission.ALL[0]
+            ).exists()
+            or user.is_superuser
+        ):
+            return True
+        return False
 
     @staticmethod
     def administrable(user, package):
-        return PackageManager.has_package_permission(user, package, "all")
+        if (
+            UserPackagePermission.objects.filter(
+                package=package, user=user, permission=Permission.ALL[0]
+            ).exists()
+            or GroupPackagePermission.objects.filter(
+                package=package,
+                group__in=GroupManager.get_groups(user),
+                permission=Permission.ALL[0],
+            ).exists()
+            or user.is_superuser
+        ):
+            return True
+        return False
 
     @staticmethod
     def has_package_permission(user: "User", package: Union[str, UUID, "Package"], permission: str):
@@ -439,9 +470,7 @@ class PackageManager(object):
             # remove package if user is owner and package is reviewed e.g. admin
             qs = qs.filter(reviewed=False)
 
-        qs = qs.distinct()
+        return qs.distinct()
-
-        return qs
 
     @staticmethod
     def get_all_writeable_packages(user):
@@ -485,9 +514,7 @@ class PackageManager(object):
 
         qs = qs.filter(reviewed=False)
 
-        qs = qs.distinct()
+        return qs.distinct()
-
-        return qs
 
     @staticmethod
     def get_packages():
@@ -689,10 +716,6 @@ class PackageManager(object):
                 struc.description = structure["description"]
                 struc.aliases = structure.get("aliases", [])
                 struc.smiles = structure["smiles"]
-
-                if structure.get("molfile"):
-                    struc.molfile = structure["molfile"]
-
                 struc.save()
 
                 for scen in structure["scenarios"]:
@@ -995,9 +1018,52 @@ class PackageManager(object):
 
         print("Fixing Node depths...")
         total_pws = Pathway.objects.filter(package=pack).count()
-
         for p, pw in enumerate(Pathway.objects.filter(package=pack)):
-            pw.update_depths()
+            in_count = defaultdict(lambda: 0)
+            out_count = defaultdict(lambda: 0)
+
+            for e in pw.edges:
+                # TODO check if this will remain
+                for react in e.start_nodes.all():
+                    out_count[str(react.uuid)] += 1
+
+                for prod in e.end_nodes.all():
+                    in_count[str(prod.uuid)] += 1
+
+            root_nodes = []
+            for n in pw.nodes:
+                num_parents = in_count[str(n.uuid)]
+                if num_parents == 0:
+                    # must be a root node or unconnected node
+                    if n.depth != 0:
+                        n.depth = 0
+                        n.save()
+
+                    # Only root node may have children
+                    if out_count[str(n.uuid)] > 0:
+                        root_nodes.append(n)
+
+            levels = [root_nodes]
+            seen = set()
+            # Do a bfs to determine depths starting with level 0 a.k.a. root nodes
+            for i, level_nodes in enumerate(levels):
+                new_level = []
+                for n in level_nodes:
+                    for e in n.out_edges.all():
+                        for prod in e.end_nodes.all():
+                            if str(prod.uuid) not in seen:
+                                old_depth = prod.depth
+                                if old_depth != i + 1:
+                                    prod.depth = i + 1
+                                    prod.save()
+
+                                new_level.append(prod)
+
+                    seen.add(str(n.uuid))
+
+                if new_level:
+                    levels.append(new_level)
+
             print(f"{p + 1}/{total_pws} fixed.", end="\r")
 
         return pack

epdb/management/commands/bootstrap.py

@@ -99,15 +99,11 @@ class Command(BaseCommand):
                 new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
                 new_license.save()
 
-    def import_package(self, data, owner, all_envipath_user_group):
+    def import_package(self, data, owner):
-        p = PackageManager.import_legacy_package(
+        return PackageManager.import_legacy_package(
             data, owner, keep_ids=True, add_import_timestamp=False, trust_reviewed=True
         )
 
-        PackageManager.grant_read(owner, p, all_envipath_user_group)
-
-        return p
-
     def create_default_setting(self, owner, packages):
         s = SettingManager.create_setting(
             owner,
@@ -202,7 +198,7 @@ class Command(BaseCommand):
                     s.BASE_DIR / "fixtures" / "packages" / "2025-07-18" / p, encoding="utf-8"
                 ).read()
             )
-            imported_package = self.import_package(package_data, admin, g)
+            imported_package = self.import_package(package_data, admin)
             mapping[p.replace(".json", "")] = imported_package
 
         setting = self.create_default_setting(admin, [mapping["EAWAG-BBD"]])

epdb/migrations/0001_initial.py

@@ -1,594 +0,0 @@
-# Generated by Django 5.2.1 on 2025-07-22 20:58
-
-import datetime
-import django.contrib.auth.models
-import django.contrib.auth.validators
-import django.contrib.postgres.fields
-import django.db.models.deletion
-import django.utils.timezone
-import model_utils.fields
-import uuid
-from django.conf import settings
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    initial = True
-
-    dependencies = [
-        ('auth', '0012_alter_user_first_name_max_length'),
-        ('contenttypes', '0002_remove_content_type_name'),
-    ]
-
-    operations = [
-        migrations.CreateModel(
-            name='Compound',
-            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')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-            ],
-        ),
-        migrations.CreateModel(
-            name='EPModel',
-            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')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-        ),
-        migrations.CreateModel(
-            name='Permission',
-            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')),
-                ('permission', models.CharField(choices=[('read', 'Read'), ('write', 'Write'), ('all', 'All')], max_length=32)),
-            ],
-        ),
-        migrations.CreateModel(
-            name='License',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('link', models.URLField(verbose_name='link')),
-                ('image_link', models.URLField(verbose_name='Image link')),
-            ],
-        ),
-        migrations.CreateModel(
-            name='Rule',
-            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')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-        ),
-        migrations.CreateModel(
-            name='User',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('password', models.CharField(max_length=128, verbose_name='password')),
-                ('last_login', models.DateTimeField(blank=True, null=True, verbose_name='last login')),
-                ('is_superuser', models.BooleanField(default=False, help_text='Designates that this user has all permissions without explicitly assigning them.', verbose_name='superuser status')),
-                ('username', models.CharField(error_messages={'unique': 'A user with that username already exists.'}, help_text='Required. 150 characters or fewer. Letters, digits and @/./+/-/_ only.', max_length=150, unique=True, validators=[django.contrib.auth.validators.UnicodeUsernameValidator()], verbose_name='username')),
-                ('first_name', models.CharField(blank=True, max_length=150, verbose_name='first name')),
-                ('last_name', models.CharField(blank=True, max_length=150, verbose_name='last name')),
-                ('is_staff', models.BooleanField(default=False, help_text='Designates whether the user can log into this admin site.', verbose_name='staff status')),
-                ('is_active', models.BooleanField(default=True, help_text='Designates whether this user should be treated as active. Unselect this instead of deleting accounts.', verbose_name='active')),
-                ('date_joined', models.DateTimeField(default=django.utils.timezone.now, verbose_name='date joined')),
-                ('email', models.EmailField(max_length=254, unique=True)),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('groups', models.ManyToManyField(blank=True, help_text='The groups this user belongs to. A user will get all permissions granted to each of their groups.', related_name='user_set', related_query_name='user', to='auth.group', verbose_name='groups')),
-                ('user_permissions', models.ManyToManyField(blank=True, help_text='Specific permissions for this user.', related_name='user_set', related_query_name='user', to='auth.permission', verbose_name='user permissions')),
-            ],
-            options={
-                'verbose_name': 'user',
-                'verbose_name_plural': 'users',
-                'abstract': False,
-            },
-            managers=[
-                ('objects', django.contrib.auth.models.UserManager()),
-            ],
-        ),
-        migrations.CreateModel(
-            name='APIToken',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('hashed_key', models.CharField(max_length=128, unique=True)),
-                ('created', models.DateTimeField(auto_now_add=True)),
-                ('expires_at', models.DateTimeField(blank=True, default=datetime.datetime(2025, 10, 20, 20, 58, 48, 351675, tzinfo=datetime.timezone.utc), null=True)),
-                ('name', models.CharField(blank=True, help_text='Optional name for the token', max_length=100)),
-                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
-            ],
-        ),
-        migrations.CreateModel(
-            name='CompoundStructure',
-            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')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('smiles', models.TextField(verbose_name='SMILES')),
-                ('canonical_smiles', models.TextField(verbose_name='Canonical SMILES')),
-                ('inchikey', models.TextField(max_length=27, verbose_name='InChIKey')),
-                ('normalized_structure', models.BooleanField(default=False)),
-                ('compound', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.compound')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='compound',
-            name='default_structure',
-            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='compound_default_structure', to='epdb.compoundstructure', verbose_name='Default Structure'),
-        ),
-        migrations.CreateModel(
-            name='Edge',
-            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')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-        ),
-        migrations.CreateModel(
-            name='EnviFormer',
-            fields=[
-                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
-                ('threshold', models.FloatField(default=0.5)),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.epmodel',),
-        ),
-        migrations.CreateModel(
-            name='PluginModel',
-            fields=[
-                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.epmodel',),
-        ),
-        migrations.CreateModel(
-            name='RuleBaseRelativeReasoning',
-            fields=[
-                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.epmodel',),
-        ),
-        migrations.CreateModel(
-            name='Group',
-            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(verbose_name='Group name')),
-                ('public', models.BooleanField(default=False, verbose_name='Public Group')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('group_member', models.ManyToManyField(related_name='groups_in_group', to='epdb.group', verbose_name='Group member')),
-                ('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Group Owner')),
-                ('user_member', models.ManyToManyField(related_name='users_in_group', to=settings.AUTH_USER_MODEL, verbose_name='User members')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='user',
-            name='default_group',
-            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='default_group', to='epdb.group', verbose_name='Default Group'),
-        ),
-        migrations.CreateModel(
-            name='Node',
-            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')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('depth', models.IntegerField(verbose_name='Node depth')),
-                ('default_node_label', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='default_node_structure', to='epdb.compoundstructure', verbose_name='Default Node Label')),
-                ('node_labels', models.ManyToManyField(related_name='node_structures', to='epdb.compoundstructure', verbose_name='All Node Labels')),
-                ('out_edges', models.ManyToManyField(to='epdb.edge', verbose_name='Outgoing Edges')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='edge',
-            name='end_nodes',
-            field=models.ManyToManyField(related_name='edge_products', to='epdb.node', verbose_name='End Nodes'),
-        ),
-        migrations.AddField(
-            model_name='edge',
-            name='start_nodes',
-            field=models.ManyToManyField(related_name='edge_educts', to='epdb.node', verbose_name='Start Nodes'),
-        ),
-        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')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('reviewed', models.BooleanField(default=False, verbose_name='Reviewstatus')),
-                ('license', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.license', verbose_name='License')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='epmodel',
-            name='package',
-            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package'),
-        ),
-        migrations.AddField(
-            model_name='compound',
-            name='package',
-            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package'),
-        ),
-        migrations.AddField(
-            model_name='user',
-            name='default_package',
-            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.package', verbose_name='Default Package'),
-        ),
-        migrations.CreateModel(
-            name='SequentialRule',
-            fields=[
-                ('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.rule',),
-        ),
-        migrations.CreateModel(
-            name='SimpleRule',
-            fields=[
-                ('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.rule',),
-        ),
-        migrations.AddField(
-            model_name='rule',
-            name='package',
-            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package'),
-        ),
-        migrations.AddField(
-            model_name='rule',
-            name='polymorphic_ctype',
-            field=models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype'),
-        ),
-        migrations.CreateModel(
-            name='Pathway',
-            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')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='node',
-            name='pathway',
-            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
-        ),
-        migrations.AddField(
-            model_name='edge',
-            name='pathway',
-            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
-        ),
-        migrations.CreateModel(
-            name='Reaction',
-            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')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('multi_step', models.BooleanField(verbose_name='Multistep Reaction')),
-                ('medline_references', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), null=True, size=None, verbose_name='Medline References')),
-                ('educts', models.ManyToManyField(related_name='reaction_educts', to='epdb.compoundstructure', verbose_name='Educts')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
-                ('products', models.ManyToManyField(related_name='reaction_products', to='epdb.compoundstructure', verbose_name='Products')),
-                ('rules', models.ManyToManyField(related_name='reaction_rule', to='epdb.rule', verbose_name='Rule')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='edge',
-            name='edge_label',
-            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.reaction', verbose_name='Edge label'),
-        ),
-        migrations.CreateModel(
-            name='Scenario',
-            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')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('scenario_date', models.CharField(default='No date', max_length=256)),
-                ('scenario_type', models.CharField(default='Not specified', max_length=256)),
-                ('additional_information', models.JSONField(verbose_name='Additional Information')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
-                ('parent', models.ForeignKey(default=None, null=True, on_delete=django.db.models.deletion.CASCADE, to='epdb.scenario')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='rule',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.AddField(
-            model_name='reaction',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.AddField(
-            model_name='pathway',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.AddField(
-            model_name='node',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.AddField(
-            model_name='edge',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.AddField(
-            model_name='compoundstructure',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.AddField(
-            model_name='compound',
-            name='scenarios',
-            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
-        ),
-        migrations.CreateModel(
-            name='Setting',
-            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')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('public', models.BooleanField(default=False)),
-                ('global_default', models.BooleanField(default=False)),
-                ('max_depth', models.IntegerField(default=5, verbose_name='Setting Max Depth')),
-                ('max_nodes', models.IntegerField(default=30, verbose_name='Setting Max Number of Nodes')),
-                ('model_threshold', models.FloatField(blank=True, default=0.25, null=True, verbose_name='Setting Model Threshold')),
-                ('model', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.epmodel', verbose_name='Setting EPModel')),
-                ('rule_packages', models.ManyToManyField(blank=True, related_name='setting_rule_packages', to='epdb.package', verbose_name='Setting Rule Packages')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='pathway',
-            name='setting',
-            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Setting'),
-        ),
-        migrations.AddField(
-            model_name='user',
-            name='default_setting',
-            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.setting', verbose_name='The users default settings'),
-        ),
-        migrations.CreateModel(
-            name='MLRelativeReasoning',
-            fields=[
-                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
-                ('threshold', models.FloatField(default=0.5)),
-                ('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
-                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
-                ('data_packages', models.ManyToManyField(related_name='data_packages', to='epdb.package', verbose_name='Data Packages')),
-                ('eval_packages', models.ManyToManyField(related_name='eval_packages', to='epdb.package', verbose_name='Evaluation Packages')),
-                ('rule_packages', models.ManyToManyField(related_name='rule_packages', to='epdb.package', verbose_name='Rule Packages')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.epmodel',),
-        ),
-        migrations.CreateModel(
-            name='ApplicabilityDomain',
-            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')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('num_neighbours', models.FloatField(default=5)),
-                ('reliability_threshold', models.FloatField(default=0.5)),
-                ('local_compatibilty_threshold', models.FloatField(default=0.5)),
-                ('model', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.mlrelativereasoning')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.CreateModel(
-            name='SimpleAmbitRule',
-            fields=[
-                ('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
-                ('smirks', models.TextField(verbose_name='SMIRKS')),
-                ('reactant_filter_smarts', models.TextField(null=True, verbose_name='Reactant Filter SMARTS')),
-                ('product_filter_smarts', models.TextField(null=True, verbose_name='Product Filter SMARTS')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.simplerule',),
-        ),
-        migrations.CreateModel(
-            name='SimpleRDKitRule',
-            fields=[
-                ('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
-                ('reaction_smarts', models.TextField(verbose_name='SMIRKS')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.simplerule',),
-        ),
-        migrations.CreateModel(
-            name='SequentialRuleOrdering',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('order_index', models.IntegerField()),
-                ('sequential_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.sequentialrule')),
-                ('simple_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.simplerule')),
-            ],
-        ),
-        migrations.AddField(
-            model_name='sequentialrule',
-            name='simple_rules',
-            field=models.ManyToManyField(through='epdb.SequentialRuleOrdering', to='epdb.simplerule', verbose_name='Simple rules'),
-        ),
-        migrations.CreateModel(
-            name='ParallelRule',
-            fields=[
-                ('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
-                ('simple_rules', models.ManyToManyField(to='epdb.simplerule', verbose_name='Simple rules')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.rule',),
-        ),
-        migrations.AlterUniqueTogether(
-            name='compound',
-            unique_together={('uuid', 'package')},
-        ),
-        migrations.CreateModel(
-            name='GroupPackagePermission',
-            fields=[
-                ('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
-                ('group', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.group', verbose_name='Permission to')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Permission on')),
-            ],
-            options={
-                'unique_together': {('package', 'group')},
-            },
-            bases=('epdb.permission',),
-        ),
-        migrations.CreateModel(
-            name='UserPackagePermission',
-            fields=[
-                ('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Permission on')),
-                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
-            ],
-            options={
-                'unique_together': {('package', 'user')},
-            },
-            bases=('epdb.permission',),
-        ),
-        migrations.CreateModel(
-            name='UserSettingPermission',
-            fields=[
-                ('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
-                ('setting', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Permission on')),
-                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
-            ],
-            options={
-                'unique_together': {('setting', 'user')},
-            },
-            bases=('epdb.permission',),
-        ),
-    ]

epdb/migrations/0002_externaldatabase_alter_apitoken_options_and_more.py

@@ -1,128 +0,0 @@
-# Generated by Django 5.2.1 on 2025-08-25 18:07
-
-import django.db.models.deletion
-import django.utils.timezone
-import model_utils.fields
-import uuid
-from django.conf import settings
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('contenttypes', '0002_remove_content_type_name'),
-        ('epdb', '0001_initial'),
-    ]
-
-    operations = [
-        migrations.CreateModel(
-            name='ExternalDatabase',
-            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, editable=False, unique=True)),
-                ('name', models.CharField(max_length=100, unique=True, verbose_name='Database Name')),
-                ('full_name', models.CharField(blank=True, max_length=255, verbose_name='Full Database Name')),
-                ('description', models.TextField(blank=True, verbose_name='Description')),
-                ('base_url', models.URLField(blank=True, null=True, verbose_name='Base URL')),
-                ('url_pattern', models.CharField(blank=True, help_text="URL pattern with {id} placeholder, e.g., 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'", max_length=500, verbose_name='URL Pattern')),
-                ('is_active', models.BooleanField(default=True, verbose_name='Is Active')),
-            ],
-            options={
-                'verbose_name': 'External Database',
-                'verbose_name_plural': 'External Databases',
-                'db_table': 'epdb_external_database',
-                'ordering': ['name'],
-            },
-        ),
-        migrations.AlterModelOptions(
-            name='apitoken',
-            options={'ordering': ['-created'], 'verbose_name': 'API Token', 'verbose_name_plural': 'API Tokens'},
-        ),
-        migrations.AlterModelOptions(
-            name='edge',
-            options={},
-        ),
-        migrations.RemoveField(
-            model_name='edge',
-            name='polymorphic_ctype',
-        ),
-        migrations.AddField(
-            model_name='apitoken',
-            name='is_active',
-            field=models.BooleanField(default=True, help_text='Whether this token is active'),
-        ),
-        migrations.AddField(
-            model_name='apitoken',
-            name='modified',
-            field=model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified'),
-        ),
-        migrations.AddField(
-            model_name='applicabilitydomain',
-            name='functional_groups',
-            field=models.JSONField(blank=True, default=dict, null=True),
-        ),
-        migrations.AddField(
-            model_name='mlrelativereasoning',
-            name='app_domain',
-            field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain'),
-        ),
-        migrations.AlterField(
-            model_name='apitoken',
-            name='created',
-            field=model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created'),
-        ),
-        migrations.AlterField(
-            model_name='apitoken',
-            name='expires_at',
-            field=models.DateTimeField(blank=True, help_text='Token expiration time (null for no expiration)', null=True),
-        ),
-        migrations.AlterField(
-            model_name='apitoken',
-            name='hashed_key',
-            field=models.CharField(help_text='SHA-256 hash of the token key', max_length=128, unique=True),
-        ),
-        migrations.AlterField(
-            model_name='apitoken',
-            name='name',
-            field=models.CharField(help_text='Descriptive name for this token', max_length=100),
-        ),
-        migrations.AlterField(
-            model_name='apitoken',
-            name='user',
-            field=models.ForeignKey(help_text='User who owns this token', on_delete=django.db.models.deletion.CASCADE, related_name='api_tokens', to=settings.AUTH_USER_MODEL),
-        ),
-        migrations.AlterField(
-            model_name='applicabilitydomain',
-            name='num_neighbours',
-            field=models.IntegerField(default=5),
-        ),
-        migrations.AlterModelTable(
-            name='apitoken',
-            table='epdb_api_token',
-        ),
-        migrations.CreateModel(
-            name='ExternalIdentifier',
-            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, editable=False, unique=True)),
-                ('object_id', models.IntegerField()),
-                ('identifier_value', models.CharField(max_length=255, verbose_name='Identifier Value')),
-                ('url', models.URLField(blank=True, null=True, verbose_name='Direct URL')),
-                ('is_primary', models.BooleanField(default=False, help_text='Mark this as the primary identifier for this database', verbose_name='Is Primary')),
-                ('content_type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
-                ('database', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.externaldatabase', verbose_name='External Database')),
-            ],
-            options={
-                'verbose_name': 'External Identifier',
-                'verbose_name_plural': 'External Identifiers',
-                'db_table': 'epdb_external_identifier',
-                'indexes': [models.Index(fields=['content_type', 'object_id'], name='epdb_extern_content_b76813_idx'), models.Index(fields=['database', 'identifier_value'], name='epdb_extern_databas_486422_idx')],
-                'unique_together': {('content_type', 'object_id', 'database', 'identifier_value')},
-            },
-        ),
-    ]

epdb/migrations/0003_applicabilitydomain_url_compound_url_and_more.py

@@ -1,228 +0,0 @@
-# Generated by Django 5.2.1 on 2025-08-26 17:05
-
-from django.db import migrations, models
-
-
-def populate_url(apps, schema_editor):
-    MODELS = [
-        'User',
-        'Group',
-        'Package',
-        'Compound',
-        'CompoundStructure',
-        'Pathway',
-        'Edge',
-        'Node',
-        'Reaction',
-        'SimpleAmbitRule',
-        'SimpleRDKitRule',
-        'ParallelRule',
-        'SequentialRule',
-        'Scenario',
-        'Setting',
-        'MLRelativeReasoning',
-        'EnviFormer',
-        'ApplicabilityDomain',
-    ]
-    for model in MODELS:
-        obj_cls = apps.get_model("epdb", model)
-        for obj in obj_cls.objects.all():
-            obj.url = assemble_url(obj)
-            if obj.url is None:
-                raise ValueError(f"Could not assemble url for {obj}")
-            obj.save()
-
-
-def assemble_url(obj):
-    from django.conf import settings as s
-    match obj.__class__.__name__:
-        case 'User':
-            return '{}/user/{}'.format(s.SERVER_URL, obj.uuid)
-        case 'Group':
-            return '{}/group/{}'.format(s.SERVER_URL, obj.uuid)
-        case 'Package':
-            return '{}/package/{}'.format(s.SERVER_URL, obj.uuid)
-        case 'Compound':
-            return '{}/compound/{}'.format(obj.package.url, obj.uuid)
-        case 'CompoundStructure':
-            return '{}/structure/{}'.format(obj.compound.url, obj.uuid)
-        case 'SimpleAmbitRule':
-            return '{}/simple-ambit-rule/{}'.format(obj.package.url, obj.uuid)
-        case 'SimpleRDKitRule':
-            return '{}/simple-rdkit-rule/{}'.format(obj.package.url, obj.uuid)
-        case 'ParallelRule':
-            return '{}/parallel-rule/{}'.format(obj.package.url, obj.uuid)
-        case 'SequentialRule':
-            return '{}/sequential-rule/{}'.format(obj.compound.url, obj.uuid)
-        case 'Reaction':
-            return '{}/reaction/{}'.format(obj.package.url, obj.uuid)
-        case 'Pathway':
-            return '{}/pathway/{}'.format(obj.package.url, obj.uuid)
-        case 'Node':
-            return '{}/node/{}'.format(obj.pathway.url, obj.uuid)
-        case 'Edge':
-            return '{}/edge/{}'.format(obj.pathway.url, obj.uuid)
-        case 'MLRelativeReasoning':
-            return '{}/model/{}'.format(obj.package.url, obj.uuid)
-        case 'EnviFormer':
-            return '{}/model/{}'.format(obj.package.url, obj.uuid)
-        case 'ApplicabilityDomain':
-            return '{}/model/{}/applicability-domain/{}'.format(obj.model.package.url, obj.model.uuid, obj.uuid)
-        case 'Scenario':
-            return '{}/scenario/{}'.format(obj.package.url, obj.uuid)
-        case 'Setting':
-            return '{}/setting/{}'.format(s.SERVER_URL, obj.uuid)
-        case _:
-            raise ValueError(f"Unknown model {obj.__class__.__name__}")
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ('epdb', '0002_externaldatabase_alter_apitoken_options_and_more'),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name='applicabilitydomain',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='compound',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='compoundstructure',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='edge',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='epmodel',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='group',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='node',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='package',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='pathway',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='reaction',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='rule',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='scenario',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='setting',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='user',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-
-        migrations.RunPython(populate_url, reverse_code=migrations.RunPython.noop),
-
-        migrations.AlterField(
-            model_name='applicabilitydomain',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='compound',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='compoundstructure',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='edge',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='epmodel',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='group',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='node',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='package',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='pathway',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='reaction',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='rule',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='scenario',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='setting',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='user',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-    ]

epdb/migrations/0004_alter_mlrelativereasoning_options_and_more.py

@@ -1,55 +0,0 @@
-# Generated by Django 5.2.1 on 2025-09-09 09:21
-
-import django.db.models.deletion
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('epdb', '0001_squashed_0003_applicabilitydomain_url_compound_url_and_more'),
-    ]
-
-    operations = [
-        migrations.AlterModelOptions(
-            name='mlrelativereasoning',
-            options={},
-        ),
-        migrations.AlterField(
-            model_name='mlrelativereasoning',
-            name='data_packages',
-            field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to='epdb.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='epdb.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='epdb.package', verbose_name='Rule Packages'),
-        ),
-        migrations.CreateModel(
-            name='RuleBasedRelativeReasoning',
-            fields=[
-                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
-                ('threshold', models.FloatField(default=0.5)),
-                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
-                ('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
-                ('min_count', models.IntegerField(default=10)),
-                ('max_count', models.IntegerField(default=0)),
-                ('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
-                ('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to='epdb.package', verbose_name='Data Packages')),
-                ('eval_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to='epdb.package', verbose_name='Evaluation Packages')),
-                ('rule_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to='epdb.package', verbose_name='Rule Packages')),
-            ],
-            options={
-                'abstract': False,
-            },
-            bases=('epdb.epmodel',),
-        ),
-        migrations.DeleteModel(
-            name='RuleBaseRelativeReasoning',
-        ),
-    ]

epdb/migrations/0005_alter_group_group_member.py

@@ -1,18 +0,0 @@
-# Generated by Django 5.2.1 on 2025-09-11 06:21
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('epdb', '0004_alter_mlrelativereasoning_options_and_more'),
-    ]
-
-    operations = [
-        migrations.AlterField(
-            model_name='group',
-            name='group_member',
-            field=models.ManyToManyField(blank=True, related_name='groups_in_group', to='epdb.group', verbose_name='Group member'),
-        ),
-    ]

epdb/migrations/0006_mlrelativereasoning_multigen_eval_and_more.py

@@ -1,23 +0,0 @@
-# Generated by Django 5.2.1 on 2025-09-18 06:42
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('epdb', '0005_alter_group_group_member'),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name='mlrelativereasoning',
-            name='multigen_eval',
-            field=models.BooleanField(default=False),
-        ),
-        migrations.AddField(
-            model_name='rulebasedrelativereasoning',
-            name='multigen_eval',
-            field=models.BooleanField(default=False),
-        ),
-    ]

epdb/migrations/0007_alter_enviformer_options_enviformer_app_domain_and_more.py

@@ -1,53 +0,0 @@
-# Generated by Django 5.2.1 on 2025-10-07 08:19
-
-import django.db.models.deletion
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('epdb', '0006_mlrelativereasoning_multigen_eval_and_more'),
-    ]
-
-    operations = [
-        migrations.AlterModelOptions(
-            name='enviformer',
-            options={},
-        ),
-        migrations.AddField(
-            model_name='enviformer',
-            name='app_domain',
-            field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain'),
-        ),
-        migrations.AddField(
-            model_name='enviformer',
-            name='data_packages',
-            field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to='epdb.package', verbose_name='Data Packages'),
-        ),
-        migrations.AddField(
-            model_name='enviformer',
-            name='eval_packages',
-            field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to='epdb.package', verbose_name='Evaluation Packages'),
-        ),
-        migrations.AddField(
-            model_name='enviformer',
-            name='eval_results',
-            field=models.JSONField(blank=True, default=dict, null=True),
-        ),
-        migrations.AddField(
-            model_name='enviformer',
-            name='model_status',
-            field=models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL'),
-        ),
-        migrations.AddField(
-            model_name='enviformer',
-            name='multigen_eval',
-            field=models.BooleanField(default=False),
-        ),
-        migrations.AddField(
-            model_name='enviformer',
-            name='rule_packages',
-            field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to='epdb.package', verbose_name='Rule Packages'),
-        ),
-    ]

epdb/migrations/0008_enzymelink.py

@@ -1,64 +0,0 @@
-# Generated by Django 5.2.7 on 2025-10-10 06:58
-
-import django.db.models.deletion
-import django.utils.timezone
-import model_utils.fields
-import uuid
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0007_alter_enviformer_options_enviformer_app_domain_and_more"),
-    ]
-
-    operations = [
-        migrations.CreateModel(
-            name="EnzymeLink",
-            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)),
-                ("ec_number", models.TextField(verbose_name="EC Number")),
-                ("classification_level", models.IntegerField(verbose_name="Classification Level")),
-                ("linking_method", models.TextField(verbose_name="Linking Method")),
-                ("edge_evidence", models.ManyToManyField(to="epdb.edge")),
-                ("reaction_evidence", models.ManyToManyField(to="epdb.reaction")),
-                (
-                    "rule",
-                    models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to="epdb.rule"),
-                ),
-            ],
-            options={
-                "abstract": False,
-            },
-        ),
-    ]

epdb/migrations/0009_joblog.py

@@ -1,66 +0,0 @@
-# Generated by Django 5.2.7 on 2025-10-27 09:39
-
-import django.db.models.deletion
-import django.utils.timezone
-import model_utils.fields
-from django.conf import settings
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0008_enzymelink"),
-    ]
-
-    operations = [
-        migrations.CreateModel(
-            name="JobLog",
-            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"
-                    ),
-                ),
-                ("task_id", models.UUIDField(unique=True)),
-                ("job_name", models.TextField()),
-                (
-                    "status",
-                    models.CharField(
-                        choices=[
-                            ("INITIAL", "Initial"),
-                            ("SUCCESS", "Success"),
-                            ("FAILURE", "Failure"),
-                            ("REVOKED", "Revoked"),
-                            ("IGNORED", "Ignored"),
-                        ],
-                        default="INITIAL",
-                        max_length=20,
-                    ),
-                ),
-                ("done_at", models.DateTimeField(blank=True, default=None, null=True)),
-                ("task_result", models.TextField(blank=True, default=None, null=True)),
-                (
-                    "user",
-                    models.ForeignKey(
-                        on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL
-                    ),
-                ),
-            ],
-            options={
-                "abstract": False,
-            },
-        ),
-    ]

epdb/migrations/0010_license_cc_string.py

@@ -1,18 +0,0 @@
-# Generated by Django 5.2.7 on 2025-11-11 14:11
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0009_joblog"),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name="license",
-            name="cc_string",
-            field=models.TextField(default="by-nc-sa", verbose_name="CC string"),
-            preserve_default=False,
-        ),
-    ]

epdb/migrations/0011_auto_20251111_1413.py

@@ -1,59 +0,0 @@
-# Generated by Django 5.2.7 on 2025-11-11 14:13
-
-import re
-
-from django.contrib.postgres.aggregates import ArrayAgg
-from django.db import migrations
-from django.db.models import Min
-
-
-def set_cc(apps, schema_editor):
-    License = apps.get_model("epdb", "License")
-
-    # For all existing licenses extract cc_string from link
-    for license in License.objects.all():
-        pattern = r"/licenses/([^/]+)/4\.0"
-        match = re.search(pattern, license.link)
-        if match:
-            license.cc_string = match.group(1)
-            license.save()
-        else:
-            raise ValueError(f"Could not find license for {license.link}")
-
-    # Ensure we have all licenses
-    cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
-    for cc_string in cc_strings:
-        if not License.objects.filter(cc_string=cc_string).exists():
-            new_license = License()
-            new_license.cc_string = cc_string
-            new_license.link = f"https://creativecommons.org/licenses/{cc_string}/4.0/"
-            new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
-            new_license.save()
-
-    # As we might have existing Licenses representing the same License,
-    # get min pk and all pks as a list
-    license_lookup_qs = License.objects.values("cc_string").annotate(
-        lowest_pk=Min("id"), all_pks=ArrayAgg("id", order_by=("id",))
-    )
-
-    license_lookup = {
-        row["cc_string"]: (row["lowest_pk"], row["all_pks"]) for row in license_lookup_qs
-    }
-
-    Packages = apps.get_model("epdb", "Package")
-
-    for k, v in license_lookup.items():
-        # Set min pk to all packages pointing to any of the duplicates
-        Packages.objects.filter(pk__in=v[1]).update(license_id=v[0])
-        # remove the min pk from "other" pks as we use them for deletion
-        v[1].remove(v[0])
-        # Delete redundant License objects
-        License.objects.filter(pk__in=v[1]).delete()
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0010_license_cc_string"),
-    ]
-
-    operations = [migrations.RunPython(set_cc)]

epdb/migrations/0012_node_stereo_removed_pathway_predicted.py

@@ -1,22 +0,0 @@
-# Generated by Django 5.2.7 on 2025-12-02 13:09
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0011_auto_20251111_1413"),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name="node",
-            name="stereo_removed",
-            field=models.BooleanField(default=False),
-        ),
-        migrations.AddField(
-            model_name="pathway",
-            name="predicted",
-            field=models.BooleanField(default=False),
-        ),
-    ]

epdb/migrations/0013_setting_expansion_schema.py

@@ -1,25 +0,0 @@
-# Generated by Django 5.2.7 on 2025-12-14 11:30
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0012_node_stereo_removed_pathway_predicted"),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name="setting",
-            name="expansion_schema",
-            field=models.CharField(
-                choices=[
-                    ("BFS", "Breadth First Search"),
-                    ("DFS", "Depth First Search"),
-                    ("GREEDY", "Greedy"),
-                ],
-                default="BFS",
-                max_length=20,
-            ),
-        ),
-    ]

epdb/migrations/0014_rename_expansion_schema_setting_expansion_scheme.py

@@ -1,17 +0,0 @@
-# Generated by Django 5.2.7 on 2025-12-14 16:02
-
-from django.db import migrations
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0013_setting_expansion_schema"),
-    ]
-
-    operations = [
-        migrations.RenameField(
-            model_name="setting",
-            old_name="expansion_schema",
-            new_name="expansion_scheme",
-        ),
-    ]

epdb/migrations/0015_user_is_reviewer.py

@@ -1,17 +0,0 @@
-# Generated by Django 5.2.7 on 2026-01-19 19:26
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0014_rename_expansion_schema_setting_expansion_scheme"),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name="user",
-            name="is_reviewer",
-            field=models.BooleanField(default=False),
-        ),
-    ]

epdb/migrations/0016_remove_enviformer_model_status_and_more.py

@@ -1,179 +0,0 @@
-# Generated by Django 5.2.7 on 2026-02-12 09:38
-
-import django.db.models.deletion
-from django.conf import settings
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0015_user_is_reviewer"),
-    ]
-
-    operations = [
-        migrations.RemoveField(
-            model_name="enviformer",
-            name="model_status",
-        ),
-        migrations.RemoveField(
-            model_name="mlrelativereasoning",
-            name="model_status",
-        ),
-        migrations.RemoveField(
-            model_name="rulebasedrelativereasoning",
-            name="model_status",
-        ),
-        migrations.AddField(
-            model_name="epmodel",
-            name="model_status",
-            field=models.CharField(
-                choices=[
-                    ("INITIAL", "Initial"),
-                    ("INITIALIZING", "Model is initializing."),
-                    ("BUILDING", "Model is building."),
-                    (
-                        "BUILT_NOT_EVALUATED",
-                        "Model is built and can be used for predictions, Model is not evaluated yet.",
-                    ),
-                    ("EVALUATING", "Model is evaluating"),
-                    ("FINISHED", "Model has finished building and evaluation."),
-                    ("ERROR", "Model has failed."),
-                ],
-                default="INITIAL",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="enviformer",
-            name="eval_packages",
-            field=models.ManyToManyField(
-                blank=True,
-                related_name="%(app_label)s_%(class)s_eval_packages",
-                to=settings.EPDB_PACKAGE_MODEL,
-                verbose_name="Evaluation Packages",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="enviformer",
-            name="rule_packages",
-            field=models.ManyToManyField(
-                blank=True,
-                related_name="%(app_label)s_%(class)s_rule_packages",
-                to=settings.EPDB_PACKAGE_MODEL,
-                verbose_name="Rule Packages",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="mlrelativereasoning",
-            name="eval_packages",
-            field=models.ManyToManyField(
-                blank=True,
-                related_name="%(app_label)s_%(class)s_eval_packages",
-                to=settings.EPDB_PACKAGE_MODEL,
-                verbose_name="Evaluation Packages",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="mlrelativereasoning",
-            name="rule_packages",
-            field=models.ManyToManyField(
-                blank=True,
-                related_name="%(app_label)s_%(class)s_rule_packages",
-                to=settings.EPDB_PACKAGE_MODEL,
-                verbose_name="Rule Packages",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="rulebasedrelativereasoning",
-            name="eval_packages",
-            field=models.ManyToManyField(
-                blank=True,
-                related_name="%(app_label)s_%(class)s_eval_packages",
-                to=settings.EPDB_PACKAGE_MODEL,
-                verbose_name="Evaluation Packages",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="rulebasedrelativereasoning",
-            name="rule_packages",
-            field=models.ManyToManyField(
-                blank=True,
-                related_name="%(app_label)s_%(class)s_rule_packages",
-                to=settings.EPDB_PACKAGE_MODEL,
-                verbose_name="Rule Packages",
-            ),
-        ),
-        migrations.CreateModel(
-            name="PropertyPluginModel",
-            fields=[
-                (
-                    "epmodel_ptr",
-                    models.OneToOneField(
-                        auto_created=True,
-                        on_delete=django.db.models.deletion.CASCADE,
-                        parent_link=True,
-                        primary_key=True,
-                        serialize=False,
-                        to="epdb.epmodel",
-                    ),
-                ),
-                ("threshold", models.FloatField(default=0.5)),
-                ("eval_results", models.JSONField(blank=True, default=dict, null=True)),
-                ("multigen_eval", models.BooleanField(default=False)),
-                ("plugin_identifier", models.CharField(max_length=255)),
-                (
-                    "app_domain",
-                    models.ForeignKey(
-                        blank=True,
-                        default=None,
-                        null=True,
-                        on_delete=django.db.models.deletion.SET_NULL,
-                        to="epdb.applicabilitydomain",
-                    ),
-                ),
-                (
-                    "data_packages",
-                    models.ManyToManyField(
-                        blank=True,
-                        related_name="%(app_label)s_%(class)s_data_packages",
-                        to=settings.EPDB_PACKAGE_MODEL,
-                        verbose_name="Data Packages",
-                    ),
-                ),
-                (
-                    "eval_packages",
-                    models.ManyToManyField(
-                        blank=True,
-                        related_name="%(app_label)s_%(class)s_eval_packages",
-                        to=settings.EPDB_PACKAGE_MODEL,
-                        verbose_name="Evaluation Packages",
-                    ),
-                ),
-                (
-                    "rule_packages",
-                    models.ManyToManyField(
-                        blank=True,
-                        related_name="%(app_label)s_%(class)s_rule_packages",
-                        to=settings.EPDB_PACKAGE_MODEL,
-                        verbose_name="Rule Packages",
-                    ),
-                ),
-            ],
-            options={
-                "abstract": False,
-            },
-            bases=("epdb.epmodel",),
-        ),
-        migrations.AddField(
-            model_name="setting",
-            name="property_models",
-            field=models.ManyToManyField(
-                blank=True,
-                related_name="settings",
-                to="epdb.propertypluginmodel",
-                verbose_name="Setting Property Models",
-            ),
-        ),
-        migrations.DeleteModel(
-            name="PluginModel",
-        ),
-    ]

epdb/migrations/0017_additionalinformation.py

@@ -1,93 +0,0 @@
-# Generated by Django 5.2.7 on 2026-02-20 12:02
-
-import django.db.models.deletion
-import uuid
-from django.conf import settings
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("contenttypes", "0002_remove_content_type_name"),
-        ("epdb", "0016_remove_enviformer_model_status_and_more"),
-    ]
-
-    operations = [
-        migrations.CreateModel(
-            name="AdditionalInformation",
-            fields=[
-                (
-                    "id",
-                    models.BigAutoField(
-                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
-                    ),
-                ),
-                ("uuid", models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
-                ("url", models.TextField(null=True, unique=True, verbose_name="URL")),
-                ("kv", models.JSONField(blank=True, default=dict, null=True)),
-                ("type", models.TextField(verbose_name="Additional Information Type")),
-                ("data", models.JSONField(blank=True, default=dict, null=True)),
-                ("object_id", models.PositiveBigIntegerField(blank=True, null=True)),
-                (
-                    "content_type",
-                    models.ForeignKey(
-                        blank=True,
-                        null=True,
-                        on_delete=django.db.models.deletion.CASCADE,
-                        to="contenttypes.contenttype",
-                    ),
-                ),
-                (
-                    "package",
-                    models.ForeignKey(
-                        on_delete=django.db.models.deletion.CASCADE,
-                        to=settings.EPDB_PACKAGE_MODEL,
-                        verbose_name="Package",
-                    ),
-                ),
-                (
-                    "scenario",
-                    models.ForeignKey(
-                        blank=True,
-                        null=True,
-                        on_delete=django.db.models.deletion.CASCADE,
-                        related_name="scenario_additional_information",
-                        to="epdb.scenario",
-                    ),
-                ),
-            ],
-            options={
-                "indexes": [
-                    models.Index(fields=["type"], name="epdb_additi_type_394349_idx"),
-                    models.Index(
-                        fields=["scenario", "type"], name="epdb_additi_scenari_a59edf_idx"
-                    ),
-                    models.Index(
-                        fields=["content_type", "object_id"], name="epdb_additi_content_44d4b4_idx"
-                    ),
-                    models.Index(
-                        fields=["scenario", "content_type", "object_id"],
-                        name="epdb_additi_scenari_ef2bf5_idx",
-                    ),
-                ],
-                "constraints": [
-                    models.CheckConstraint(
-                        condition=models.Q(
-                            models.Q(("content_type__isnull", True), ("object_id__isnull", True)),
-                            models.Q(("content_type__isnull", False), ("object_id__isnull", False)),
-                            _connector="OR",
-                        ),
-                        name="ck_addinfo_gfk_pair",
-                    ),
-                    models.CheckConstraint(
-                        condition=models.Q(
-                            ("scenario__isnull", False),
-                            ("content_type__isnull", False),
-                            _connector="OR",
-                        ),
-                        name="ck_addinfo_not_both_null",
-                    ),
-                ],
-            },
-        ),
-    ]

epdb/migrations/0018_auto_20260220_1203.py

@@ -1,132 +0,0 @@
-# Generated by Django 5.2.7 on 2026-02-20 12:03
-
-from django.db import migrations
-
-
-def get_additional_information(scenario):
-    from envipy_additional_information import registry
-    from envipy_additional_information.parsers import TypeOfAerationParser
-
-    for k, vals in scenario.additional_information.items():
-        if k == "enzyme":
-            continue
-
-        if k == "SpikeConentration":
-            k = "SpikeConcentration"
-
-        if k == "AerationType":
-            k = "TypeOfAeration"
-
-        for v in vals:
-            # Per default additional fields are ignored
-            MAPPING = {c.__name__: c for c in registry.list_models().values()}
-            try:
-                inst = MAPPING[k](**v)
-            except Exception:
-                if k == "TypeOfAeration":
-                    toa = TypeOfAerationParser()
-                    inst = toa.from_string(v["type"])
-
-            # Add uuid to uniquely identify objects for manipulation
-            if "uuid" in v:
-                inst.__dict__["uuid"] = v["uuid"]
-
-            yield inst
-
-
-def forward_func(apps, schema_editor):
-    Scenario = apps.get_model("epdb", "Scenario")
-    ContentType = apps.get_model("contenttypes", "ContentType")
-    AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
-
-    bulk = []
-    related = []
-    ctype = {o.model: o for o in ContentType.objects.all()}
-    parents = Scenario.objects.prefetch_related(
-        "compound_set",
-        "compoundstructure_set",
-        "reaction_set",
-        "rule_set",
-        "pathway_set",
-        "node_set",
-        "edge_set",
-    ).filter(parent__isnull=True)
-
-    for i, scenario in enumerate(parents):
-        print(f"{i + 1}/{len(parents)}", end="\r")
-        if scenario.parent is not None:
-            related.append(scenario.parent)
-            continue
-
-        for ai in get_additional_information(scenario):
-            bulk.append(
-                AdditionalInformation(
-                    package=scenario.package,
-                    scenario=scenario,
-                    type=ai.__class__.__name__,
-                    data=ai.model_dump(mode="json"),
-                )
-            )
-
-    print("\n", len(bulk))
-
-    related = Scenario.objects.prefetch_related(
-        "compound_set",
-        "compoundstructure_set",
-        "reaction_set",
-        "rule_set",
-        "pathway_set",
-        "node_set",
-        "edge_set",
-    ).filter(parent__isnull=False)
-
-    for i, scenario in enumerate(related):
-        print(f"{i + 1}/{len(related)}", end="\r")
-        parent = scenario.parent
-        # Check to which objects this scenario is attached to
-        for ai in get_additional_information(scenario):
-            rel_objs = [
-                "compound",
-                "compoundstructure",
-                "reaction",
-                "rule",
-                "pathway",
-                "node",
-                "edge",
-            ]
-            for rel_obj in rel_objs:
-                for o in getattr(scenario, f"{rel_obj}_set").all():
-                    bulk.append(
-                        AdditionalInformation(
-                            package=scenario.package,
-                            scenario=parent,
-                            type=ai.__class__.__name__,
-                            data=ai.model_dump(mode="json"),
-                            content_type=ctype[rel_obj],
-                            object_id=o.pk,
-                        )
-                    )
-
-    print("Start creating additional information objects...")
-    AdditionalInformation.objects.bulk_create(bulk)
-    print("Done!")
-    print(len(bulk))
-
-    Scenario.objects.filter(parent__isnull=False).delete()
-    # Call ai save to fix urls
-    ais = AdditionalInformation.objects.all()
-    total = ais.count()
-
-    for i, ai in enumerate(ais):
-        print(f"{i + 1}/{total}", end="\r")
-        ai.save()
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0017_additionalinformation"),
-    ]
-
-    operations = [
-        migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
-    ]

epdb/migrations/0019_remove_scenario_additional_information_and_more.py

@@ -1,20 +1,741 @@
-# Generated by Django 5.2.7 on 2026-02-23 08:45
+# Generated by Django 5.2.7 on 2026-03-06 10:51
 
-from django.db import migrations
+import django.contrib.auth.models
+import django.contrib.auth.validators
+import django.contrib.postgres.fields
+import django.db.models.deletion
+import django.utils.timezone
+import model_utils.fields
+import uuid
+from django.conf import settings
+from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
+
+    initial = True
+
     dependencies = [
-        ("epdb", "0018_auto_20260220_1203"),
+        ('auth', '0012_alter_user_first_name_max_length'),
+        ('contenttypes', '0002_remove_content_type_name'),
+        migrations.swappable_dependency(settings.EPDB_PACKAGE_MODEL),
     ]
 
     operations = [
-        migrations.RemoveField(
+        migrations.CreateModel(
-            model_name="scenario",
+            name='ApplicabilityDomain',
-            name="additional_information",
+            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)),
+                ('num_neighbours', models.IntegerField(default=5)),
+                ('reliability_threshold', models.FloatField(default=0.5)),
+                ('local_compatibilty_threshold', models.FloatField(default=0.5)),
+                ('functional_groups', models.JSONField(blank=True, default=dict, null=True)),
+            ],
+            options={
+                'abstract': False,
+            },
         ),
-        migrations.RemoveField(
+        migrations.CreateModel(
-            model_name="scenario",
+            name='Edge',
-            name="parent",
+            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)),
+                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.CreateModel(
+            name='EPModel',
+            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)),
+                ('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
+                ('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+        ),
+        migrations.CreateModel(
+            name='ExternalDatabase',
+            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, editable=False, unique=True)),
+                ('name', models.CharField(max_length=100, unique=True, verbose_name='Database Name')),
+                ('full_name', models.CharField(blank=True, max_length=255, verbose_name='Full Database Name')),
+                ('description', models.TextField(blank=True, verbose_name='Description')),
+                ('base_url', models.URLField(blank=True, null=True, verbose_name='Base URL')),
+                ('url_pattern', models.CharField(blank=True, help_text="URL pattern with {id} placeholder, e.g., 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'", max_length=500, verbose_name='URL Pattern')),
+                ('is_active', models.BooleanField(default=True, verbose_name='Is Active')),
+            ],
+            options={
+                'verbose_name': 'External Database',
+                'verbose_name_plural': 'External Databases',
+                'db_table': 'epdb_external_database',
+                'ordering': ['name'],
+            },
+        ),
+        migrations.CreateModel(
+            name='Permission',
+            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')),
+                ('permission', models.CharField(choices=[('read', 'Read'), ('write', 'Write'), ('all', 'All')], max_length=32)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='License',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('cc_string', models.TextField(verbose_name='CC string')),
+                ('link', models.URLField(verbose_name='link')),
+                ('image_link', models.URLField(verbose_name='Image link')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='Rule',
+            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)),
+                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
+                ('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+        ),
+        migrations.CreateModel(
+            name='User',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('password', models.CharField(max_length=128, verbose_name='password')),
+                ('last_login', models.DateTimeField(blank=True, null=True, verbose_name='last login')),
+                ('is_superuser', models.BooleanField(default=False, help_text='Designates that this user has all permissions without explicitly assigning them.', verbose_name='superuser status')),
+                ('username', models.CharField(error_messages={'unique': 'A user with that username already exists.'}, help_text='Required. 150 characters or fewer. Letters, digits and @/./+/-/_ only.', max_length=150, unique=True, validators=[django.contrib.auth.validators.UnicodeUsernameValidator()], verbose_name='username')),
+                ('first_name', models.CharField(blank=True, max_length=150, verbose_name='first name')),
+                ('last_name', models.CharField(blank=True, max_length=150, verbose_name='last name')),
+                ('is_staff', models.BooleanField(default=False, help_text='Designates whether the user can log into this admin site.', verbose_name='staff status')),
+                ('is_active', models.BooleanField(default=True, help_text='Designates whether this user should be treated as active. Unselect this instead of deleting accounts.', verbose_name='active')),
+                ('date_joined', models.DateTimeField(default=django.utils.timezone.now, verbose_name='date joined')),
+                ('email', models.EmailField(max_length=254, unique=True)),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
+                ('is_reviewer', models.BooleanField(default=False)),
+                ('default_package', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Default Package')),
+                ('groups', models.ManyToManyField(blank=True, help_text='The groups this user belongs to. A user will get all permissions granted to each of their groups.', related_name='user_set', related_query_name='user', to='auth.group', verbose_name='groups')),
+                ('user_permissions', models.ManyToManyField(blank=True, help_text='Specific permissions for this user.', related_name='user_set', related_query_name='user', to='auth.permission', verbose_name='user permissions')),
+            ],
+            options={
+                'verbose_name': 'user',
+                'verbose_name_plural': 'users',
+                'abstract': False,
+            },
+            managers=[
+                ('objects', django.contrib.auth.models.UserManager()),
+            ],
+        ),
+        migrations.CreateModel(
+            name='APIToken',
+            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')),
+                ('hashed_key', models.CharField(help_text='SHA-256 hash of the token key', max_length=128, unique=True)),
+                ('expires_at', models.DateTimeField(blank=True, help_text='Token expiration time (null for no expiration)', null=True)),
+                ('name', models.CharField(help_text='Descriptive name for this token', max_length=100)),
+                ('is_active', models.BooleanField(default=True, help_text='Whether this token is active')),
+                ('user', models.ForeignKey(help_text='User who owns this token', on_delete=django.db.models.deletion.CASCADE, related_name='api_tokens', to=settings.AUTH_USER_MODEL)),
+            ],
+            options={
+                'verbose_name': 'API Token',
+                'verbose_name_plural': 'API Tokens',
+                'db_table': 'epdb_api_token',
+                'ordering': ['-created'],
+            },
+        ),
+        migrations.CreateModel(
+            name='Compound',
+            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)),
+                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='CompoundStructure',
+            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)),
+                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
+                ('smiles', models.TextField(verbose_name='SMILES')),
+                ('canonical_smiles', models.TextField(verbose_name='Canonical SMILES')),
+                ('inchikey', models.TextField(max_length=27, verbose_name='InChIKey')),
+                ('normalized_structure', models.BooleanField(default=False)),
+                ('compound', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.compound')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.AddField(
+            model_name='compound',
+            name='default_structure',
+            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='compound_default_structure', to='epdb.compoundstructure', verbose_name='Default Structure'),
+        ),
+        migrations.CreateModel(
+            name='PropertyPluginModel',
+            fields=[
+                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
+                ('threshold', models.FloatField(default=0.5)),
+                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
+                ('multigen_eval', models.BooleanField(default=False)),
+                ('plugin_identifier', models.CharField(max_length=255)),
+            ],
+            options={
+                'abstract': False,
+            },
+            bases=('epdb.epmodel',),
+        ),
+        migrations.CreateModel(
+            name='Group',
+            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')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
+                ('name', models.TextField(verbose_name='Group name')),
+                ('public', models.BooleanField(default=False, verbose_name='Public Group')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('group_member', models.ManyToManyField(blank=True, related_name='groups_in_group', to='epdb.group', verbose_name='Group member')),
+                ('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Group Owner')),
+                ('user_member', models.ManyToManyField(related_name='users_in_group', to=settings.AUTH_USER_MODEL, verbose_name='User members')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.AddField(
+            model_name='user',
+            name='default_group',
+            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='default_group', to='epdb.group', verbose_name='Default Group'),
+        ),
+        migrations.CreateModel(
+            name='JobLog',
+            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')),
+                ('task_id', models.UUIDField(unique=True)),
+                ('job_name', models.TextField()),
+                ('status', models.CharField(choices=[('INITIAL', 'Initial'), ('SUCCESS', 'Success'), ('FAILURE', 'Failure'), ('REVOKED', 'Revoked'), ('IGNORED', 'Ignored')], default='INITIAL', max_length=20)),
+                ('done_at', models.DateTimeField(blank=True, default=None, null=True)),
+                ('task_result', models.TextField(blank=True, default=None, null=True)),
+                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        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')),
+                ('license', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.license', verbose_name='License')),
+            ],
+            options={
+                'swappable': 'EPDB_PACKAGE_MODEL',
+            },
+        ),
+        migrations.CreateModel(
+            name='Node',
+            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)),
+                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
+                ('depth', models.IntegerField(verbose_name='Node depth')),
+                ('stereo_removed', models.BooleanField(default=False)),
+                ('default_node_label', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='default_node_structure', to='epdb.compoundstructure', verbose_name='Default Node Label')),
+                ('node_labels', models.ManyToManyField(related_name='node_structures', to='epdb.compoundstructure', verbose_name='All Node Labels')),
+                ('out_edges', models.ManyToManyField(to='epdb.edge', verbose_name='Outgoing Edges')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.AddField(
+            model_name='edge',
+            name='end_nodes',
+            field=models.ManyToManyField(related_name='edge_products', to='epdb.node', verbose_name='End Nodes'),
+        ),
+        migrations.AddField(
+            model_name='edge',
+            name='start_nodes',
+            field=models.ManyToManyField(related_name='edge_educts', to='epdb.node', verbose_name='Start Nodes'),
+        ),
+        migrations.CreateModel(
+            name='SequentialRule',
+            fields=[
+                ('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+            bases=('epdb.rule',),
+        ),
+        migrations.CreateModel(
+            name='SimpleRule',
+            fields=[
+                ('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+            bases=('epdb.rule',),
+        ),
+        migrations.CreateModel(
+            name='Pathway',
+            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)),
+                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
+                ('predicted', models.BooleanField(default=False)),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.AddField(
+            model_name='node',
+            name='pathway',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
+        ),
+        migrations.AddField(
+            model_name='edge',
+            name='pathway',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.pathway', verbose_name='belongs to'),
+        ),
+        migrations.CreateModel(
+            name='Reaction',
+            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)),
+                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
+                ('multi_step', models.BooleanField(verbose_name='Multistep Reaction')),
+                ('medline_references', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), null=True, size=None, verbose_name='Medline References')),
+                ('educts', models.ManyToManyField(related_name='reaction_educts', to='epdb.compoundstructure', verbose_name='Educts')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
+                ('products', models.ManyToManyField(related_name='reaction_products', to='epdb.compoundstructure', verbose_name='Products')),
+                ('rules', models.ManyToManyField(related_name='reaction_rule', to='epdb.rule', verbose_name='Rule')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.CreateModel(
+            name='EnzymeLink',
+            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)),
+                ('ec_number', models.TextField(verbose_name='EC Number')),
+                ('classification_level', models.IntegerField(verbose_name='Classification Level')),
+                ('linking_method', models.TextField(verbose_name='Linking Method')),
+                ('edge_evidence', models.ManyToManyField(to='epdb.edge')),
+                ('rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.rule')),
+                ('reaction_evidence', models.ManyToManyField(to='epdb.reaction')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.AddField(
+            model_name='edge',
+            name='edge_label',
+            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.reaction', verbose_name='Edge label'),
+        ),
+        migrations.CreateModel(
+            name='Scenario',
+            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)),
+                ('scenario_date', models.CharField(default='No date', max_length=256)),
+                ('scenario_type', models.CharField(default='Not specified', max_length=256)),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.AddField(
+            model_name='rule',
+            name='scenarios',
+            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
+        ),
+        migrations.AddField(
+            model_name='reaction',
+            name='scenarios',
+            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
+        ),
+        migrations.AddField(
+            model_name='pathway',
+            name='scenarios',
+            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
+        ),
+        migrations.AddField(
+            model_name='node',
+            name='scenarios',
+            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
+        ),
+        migrations.AddField(
+            model_name='edge',
+            name='scenarios',
+            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
+        ),
+        migrations.AddField(
+            model_name='compoundstructure',
+            name='scenarios',
+            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
+        ),
+        migrations.AddField(
+            model_name='compound',
+            name='scenarios',
+            field=models.ManyToManyField(to='epdb.scenario', verbose_name='Attached Scenarios'),
+        ),
+        migrations.CreateModel(
+            name='Setting',
+            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)),
+                ('public', models.BooleanField(default=False)),
+                ('global_default', models.BooleanField(default=False)),
+                ('max_depth', models.IntegerField(default=5, verbose_name='Setting Max Depth')),
+                ('max_nodes', models.IntegerField(default=30, verbose_name='Setting Max Number of Nodes')),
+                ('model_threshold', models.FloatField(blank=True, default=0.25, null=True, verbose_name='Setting Model Threshold')),
+                ('expansion_scheme', models.CharField(choices=[('BFS', 'Breadth First Search'), ('DFS', 'Depth First Search'), ('GREEDY', 'Greedy')], default='BFS', max_length=20)),
+                ('model', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.epmodel', verbose_name='Setting EPModel')),
+                ('rule_packages', models.ManyToManyField(blank=True, related_name='setting_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Setting Rule Packages')),
+                ('property_models', models.ManyToManyField(blank=True, related_name='settings', to='epdb.propertypluginmodel', verbose_name='Setting Property Models')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.AddField(
+            model_name='pathway',
+            name='setting',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Setting'),
+        ),
+        migrations.AddField(
+            model_name='user',
+            name='default_setting',
+            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.setting', verbose_name='The users default settings'),
+        ),
+        migrations.CreateModel(
+            name='EnviFormer',
+            fields=[
+                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
+                ('threshold', models.FloatField(default=0.5)),
+                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
+                ('multigen_eval', models.BooleanField(default=False)),
+                ('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
+                ('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
+                ('eval_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
+                ('rule_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
+            ],
+            options={
+                'abstract': False,
+            },
+            bases=('epdb.epmodel',),
+        ),
+        migrations.CreateModel(
+            name='MLRelativeReasoning',
+            fields=[
+                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
+                ('threshold', models.FloatField(default=0.5)),
+                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
+                ('multigen_eval', models.BooleanField(default=False)),
+                ('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
+                ('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
+                ('eval_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
+                ('rule_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
+            ],
+            options={
+                'abstract': False,
+            },
+            bases=('epdb.epmodel',),
+        ),
+        migrations.AddField(
+            model_name='applicabilitydomain',
+            name='model',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.mlrelativereasoning'),
+        ),
+        migrations.AddField(
+            model_name='propertypluginmodel',
+            name='app_domain',
+            field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain'),
+        ),
+        migrations.AddField(
+            model_name='propertypluginmodel',
+            name='data_packages',
+            field=models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages'),
+        ),
+        migrations.AddField(
+            model_name='propertypluginmodel',
+            name='eval_packages',
+            field=models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages'),
+        ),
+        migrations.AddField(
+            model_name='propertypluginmodel',
+            name='rule_packages',
+            field=models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages'),
+        ),
+        migrations.CreateModel(
+            name='RuleBasedRelativeReasoning',
+            fields=[
+                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
+                ('threshold', models.FloatField(default=0.5)),
+                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
+                ('multigen_eval', models.BooleanField(default=False)),
+                ('min_count', models.IntegerField(default=10)),
+                ('max_count', models.IntegerField(default=0)),
+                ('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
+                ('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
+                ('eval_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
+                ('rule_packages', models.ManyToManyField(blank=True, related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
+            ],
+            options={
+                'abstract': False,
+            },
+            bases=('epdb.epmodel',),
+        ),
+        migrations.CreateModel(
+            name='ExternalIdentifier',
+            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, editable=False, unique=True)),
+                ('object_id', models.IntegerField()),
+                ('identifier_value', models.CharField(max_length=255, verbose_name='Identifier Value')),
+                ('url', models.URLField(blank=True, null=True, verbose_name='Direct URL')),
+                ('is_primary', models.BooleanField(default=False, help_text='Mark this as the primary identifier for this database', verbose_name='Is Primary')),
+                ('content_type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
+                ('database', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.externaldatabase', verbose_name='External Database')),
+            ],
+            options={
+                'verbose_name': 'External Identifier',
+                'verbose_name_plural': 'External Identifiers',
+                'db_table': 'epdb_external_identifier',
+                'indexes': [models.Index(fields=['content_type', 'object_id'], name='epdb_extern_content_b76813_idx'), models.Index(fields=['database', 'identifier_value'], name='epdb_extern_databas_486422_idx')],
+                'unique_together': {('content_type', 'object_id', 'database', 'identifier_value')},
+            },
+        ),
+        migrations.CreateModel(
+            name='SimpleAmbitRule',
+            fields=[
+                ('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
+                ('smirks', models.TextField(verbose_name='SMIRKS')),
+                ('reactant_filter_smarts', models.TextField(null=True, verbose_name='Reactant Filter SMARTS')),
+                ('product_filter_smarts', models.TextField(null=True, verbose_name='Product Filter SMARTS')),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+            bases=('epdb.simplerule',),
+        ),
+        migrations.CreateModel(
+            name='SimpleRDKitRule',
+            fields=[
+                ('simplerule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.simplerule')),
+                ('reaction_smarts', models.TextField(verbose_name='SMIRKS')),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+            bases=('epdb.simplerule',),
+        ),
+        migrations.CreateModel(
+            name='SequentialRuleOrdering',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('order_index', models.IntegerField()),
+                ('sequential_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.sequentialrule')),
+                ('simple_rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.simplerule')),
+            ],
+        ),
+        migrations.AddField(
+            model_name='sequentialrule',
+            name='simple_rules',
+            field=models.ManyToManyField(through='epdb.SequentialRuleOrdering', to='epdb.simplerule', verbose_name='Simple rules'),
+        ),
+        migrations.CreateModel(
+            name='ParallelRule',
+            fields=[
+                ('rule_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.rule')),
+                ('simple_rules', models.ManyToManyField(to='epdb.simplerule', verbose_name='Simple rules')),
+            ],
+            options={
+                'abstract': False,
+                'base_manager_name': 'objects',
+            },
+            bases=('epdb.rule',),
+        ),
+        migrations.AlterUniqueTogether(
+            name='compound',
+            unique_together={('uuid', 'package')},
+        ),
+        migrations.CreateModel(
+            name='AdditionalInformation',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
+                ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('type', models.TextField(verbose_name='Additional Information Type')),
+                ('data', models.JSONField(blank=True, default=dict, null=True)),
+                ('object_id', models.PositiveBigIntegerField(blank=True, null=True)),
+                ('content_type', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
+                ('scenario', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='scenario_additional_information', to='epdb.scenario')),
+            ],
+            options={
+                'indexes': [models.Index(fields=['type'], name='epdb_additi_type_394349_idx'), models.Index(fields=['scenario', 'type'], name='epdb_additi_scenari_a59edf_idx'), models.Index(fields=['content_type', 'object_id'], name='epdb_additi_content_44d4b4_idx'), models.Index(fields=['scenario', 'content_type', 'object_id'], name='epdb_additi_scenari_ef2bf5_idx')],
+                'constraints': [models.CheckConstraint(condition=models.Q(models.Q(('content_type__isnull', True), ('object_id__isnull', True)), models.Q(('content_type__isnull', False), ('object_id__isnull', False)), _connector='OR'), name='ck_addinfo_gfk_pair'), models.CheckConstraint(condition=models.Q(('scenario__isnull', False), ('content_type__isnull', False), _connector='OR'), name='ck_addinfo_not_both_null')],
+            },
+        ),
+        migrations.CreateModel(
+            name='GroupPackagePermission',
+            fields=[
+                ('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
+                ('group', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.group', verbose_name='Permission to')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Permission on')),
+            ],
+            options={
+                'unique_together': {('package', 'group')},
+            },
+            bases=('epdb.permission',),
+        ),
+        migrations.CreateModel(
+            name='UserPackagePermission',
+            fields=[
+                ('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Permission on')),
+                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
+            ],
+            options={
+                'unique_together': {('package', 'user')},
+            },
+            bases=('epdb.permission',),
+        ),
+        migrations.CreateModel(
+            name='UserSettingPermission',
+            fields=[
+                ('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
+                ('setting', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.setting', verbose_name='Permission on')),
+                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
+            ],
+            options={
+                'unique_together': {('setting', 'user')},
+            },
+            bases=('epdb.permission',),
         ),
     ]

epdb/migrations/0023_alter_compoundstructure_options_and_more.py

@@ -1,49 +0,0 @@
-# Generated by Django 6.0.3 on 2026-04-21 11:43
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0022_alter_classifierpluginmodel_data_packages_and_more"),
-    ]
-
-    operations = [
-        migrations.AlterModelOptions(
-            name="compoundstructure",
-            options={},
-        ),
-        migrations.AlterModelOptions(
-            name="epmodel",
-            options={},
-        ),
-        migrations.AlterModelOptions(
-            name="parallelrule",
-            options={},
-        ),
-        migrations.AlterModelOptions(
-            name="rule",
-            options={},
-        ),
-        migrations.AlterModelOptions(
-            name="sequentialrule",
-            options={},
-        ),
-        migrations.AlterModelOptions(
-            name="simpleambitrule",
-            options={},
-        ),
-        migrations.AlterModelOptions(
-            name="simplerdkitrule",
-            options={},
-        ),
-        migrations.AlterModelOptions(
-            name="simplerule",
-            options={},
-        ),
-        migrations.AddField(
-            model_name="compoundstructure",
-            name="molfile",
-            field=models.TextField(blank=True, null=True, verbose_name="Molfile"),
-        ),
-    ]

epdb/migrations/0024_user_contacted.py

@@ -1,17 +0,0 @@
-# Generated by Django 6.0.3 on 2026-04-21 19:56
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0023_alter_compoundstructure_options_and_more"),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name="user",
-            name="contacted",
-            field=models.BooleanField(blank=True, null=True),
-        ),
-    ]

epdb/migrations/0025_auto_20260511_2025.py

@@ -1,56 +0,0 @@
-# Generated by Django 6.0.3 on 2026-05-11 20:25
-
-from django.db import migrations
-from envipy_additional_information import HalfLife, HalfLifeModel, HalfLifeWS
-
-MAPPING = {
-    "": HalfLifeModel.OTHER,
-    "HS-SFO": HalfLifeModel.HS_SFO,
-    "FOMC": HalfLifeModel.FOMC,
-    "FOTC": HalfLifeModel.DFOP,
-    "FMOC": HalfLifeModel.FOMC,
-    "DFOP": HalfLifeModel.DFOP,
-    "SFO + SFO": HalfLifeModel.SFO_SFO,
-    "FOMC-SFO": HalfLifeModel.FOMC_SFO,
-    "first order kinetics": HalfLifeModel.SFO,
-    "SFO²": HalfLifeModel.SFO,
-    "HS": HalfLifeModel.HS,
-    "top down": HalfLifeModel.OTHER,
-    "SFO": HalfLifeModel.SFO,
-    "First Order": HalfLifeModel.SFO,
-    "SFO/SFO": HalfLifeModel.SFO_SFO,
-    "FOMC + SFO": HalfLifeModel.FOMC_SFO,
-    "true": HalfLifeModel.SFO,
-    "SFO-SFO": HalfLifeModel.SFO_SFO,
-    "DFOP-SFO": HalfLifeModel.DFOP_SFO,
-}
-
-
-def forward_func(apps, schema_editor):
-    AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
-
-    hls = AdditionalInformation.objects.filter(type="HalfLife")
-
-    for hl in hls:
-        data = hl.data
-        data["model"] = MAPPING[data["model"]].value
-        hl.data = HalfLife(**data).model_dump(mode="json")
-        hl.save()
-
-    hlws = AdditionalInformation.objects.filter(type="HalfLifeWS")
-
-    for hl in hlws:
-        data = hl.data
-        data["model"] = MAPPING[data["model"]].value
-        hl.data = HalfLifeWS(**data).model_dump(mode="json")
-        hl.save()
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0024_user_contacted"),
-    ]
-
-    operations = [
-        migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
-    ]

epdb/migrations/0026_auto_20260602_1718.py

@@ -1,48 +0,0 @@
-# Generated by Django 6.0.3 on 2026-06-02 17:18
-
-from django.db import migrations
-from envipy_additional_information import DOI
-
-
-def forward_func(apps, schema_editor):
-    AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
-
-    refs = AdditionalInformation.objects.filter(type="Reference")
-
-    remaining = []
-
-    for ref in refs:
-        r = ref.data["reference"]
-        try:
-            # PubMed IDs are plain ints, try parsing
-            _ = int(r)
-            # Nothing to do
-        except ValueError:
-            DOMAINS = [
-                "http://dx.doi.org/",
-                "https://dx.doi.org/",
-                "http://doi.org/",
-                "https://doi.org/",
-            ]
-            for d in DOMAINS:
-                r = r.replace(d, "")
-
-            if r.startswith("10."):
-                ref.type = DOI.__name__
-                ref.data = {"doi": r}
-                ref.save()
-            else:
-                remaining.append(ref)
-
-    if len(remaining) > 0:
-        raise ValueError(f"Could not parse {len(remaining)} references")
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0025_auto_20260511_2025"),
-    ]
-
-    operations = [
-        migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
-    ]

epdb/migrations/0027_alter_compound_aliases_and_more.py

@@ -1,150 +0,0 @@
-# Generated by Django 6.0.3 on 2026-07-01 20:59
-
-import django.contrib.postgres.fields
-import django.db.models.deletion
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0026_auto_20260602_1718"),
-    ]
-
-    operations = [
-        migrations.AlterField(
-            model_name="compound",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compound",
-            name="default_structure",
-            field=models.ForeignKey(
-                null=True,
-                on_delete=django.db.models.deletion.SET_NULL,
-                related_name="compound_default_structure",
-                to="epdb.compoundstructure",
-                verbose_name="Default Structure",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compound",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compoundstructure",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compoundstructure",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="edge",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="edge",
-            name="edge_label",
-            field=models.ForeignKey(
-                null=True,
-                on_delete=django.db.models.deletion.CASCADE,
-                to="epdb.reaction",
-                verbose_name="Edge label",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="edge",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="node",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="node",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="pathway",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="pathway",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="medline_references",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(),
-                blank=True,
-                null=True,
-                verbose_name="Medline References",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="rules",
-            field=models.ManyToManyField(
-                blank=True, related_name="reaction_rule", to="epdb.rule", verbose_name="Rule"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="rule",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="rule",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-    ]

epdb/models.py

@@ -31,7 +31,6 @@ from sklearn.model_selection import ShuffleSplit
 
 from bridge.contracts import Property
 from bridge.dto import RunResult, PropertyPrediction
-from epdb.exceptions import InvalidSMILESException
 from utilities.chem import FormatConverter, IndigoUtils, PredictionResult, ProductSet
 from utilities.ml import (
     ApplicabilityDomainPCA,
@@ -76,7 +75,6 @@ class User(AbstractUser):
         blank=False,
     )
     is_reviewer = models.BooleanField(default=False)
-    contacted = models.BooleanField(null=True, blank=True)
 
     USERNAME_FIELD = "email"
     REQUIRED_FIELDS = ["username"]
@@ -632,7 +630,7 @@ class EnviPathModel(TimeStampedModel):
 
 class AliasMixin(models.Model):
     aliases = ArrayField(
-        models.TextField(blank=False, null=False), verbose_name="Aliases", default=list, blank=True
+        models.TextField(blank=False, null=False), verbose_name="Aliases", default=list
     )
 
     @transaction.atomic
@@ -655,9 +653,7 @@ class AliasMixin(models.Model):
 
 
 class ScenarioMixin(models.Model):
-    scenarios = models.ManyToManyField(
+    scenarios = models.ManyToManyField("epdb.Scenario", verbose_name="Attached Scenarios")
-        "epdb.Scenario", verbose_name="Attached Scenarios", blank=True
-    )
 
     @transaction.atomic
     def set_scenarios(self, scenarios: List["Scenario"]):
@@ -783,7 +779,7 @@ class Compound(
         "CompoundStructure",
         verbose_name="Default Structure",
         related_name="compound_default_structure",
-        on_delete=models.SET_NULL,
+        on_delete=models.CASCADE,
         null=True,
     )
 
@@ -860,13 +856,13 @@ class Compound(
         package: "Package", smiles: str, name: str = None, description: str = None, *args, **kwargs
     ) -> "Compound":
         if smiles is None or smiles.strip() == "":
-            raise InvalidSMILESException("SMILES is required")
+            raise ValueError("SMILES is required")
 
         smiles = smiles.strip()
 
         parsed = FormatConverter.from_smiles(smiles)
         if parsed is None:
-            raise InvalidSMILESException("Given SMILES is invalid")
+            raise ValueError("Given SMILES is invalid")
 
         standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
 
@@ -1116,7 +1112,6 @@ class CompoundStructure(
     canonical_smiles = models.TextField(blank=False, null=False, verbose_name="Canonical SMILES")
     inchikey = models.TextField(max_length=27, blank=False, null=False, verbose_name="InChIKey")
     normalized_structure = models.BooleanField(null=False, blank=False, default=False)
-    molfile = models.TextField(blank=True, null=True, verbose_name="Molfile")
 
     external_identifiers = GenericRelation("ExternalIdentifier")
 
@@ -1177,8 +1172,6 @@ class CompoundStructure(
 
     @property
     def as_svg(self, width: int = 800, height: int = 400):
-        if self.molfile is not None and self.molfile.strip() != "":
-            return IndigoUtils.mol_to_svg(self.molfile, width=width, height=height)
         return IndigoUtils.mol_to_svg(self.smiles, width=width, height=height)
 
     @property
@@ -1215,9 +1208,6 @@ class CompoundStructure(
 
         return dict(hls)
 
-    def d3_json(self):
-        return {}
-
 
 class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
     rule = models.ForeignKey("Rule", on_delete=models.CASCADE, db_index=True)
@@ -1615,15 +1605,10 @@ class Reaction(
     products = models.ManyToManyField(
         "epdb.CompoundStructure", verbose_name="Products", related_name="reaction_products"
     )
-    rules = models.ManyToManyField(
+    rules = models.ManyToManyField("epdb.Rule", verbose_name="Rule", related_name="reaction_rule")
-        "epdb.Rule", verbose_name="Rule", related_name="reaction_rule", blank=True
-    )
     multi_step = models.BooleanField(verbose_name="Multistep Reaction")
     medline_references = ArrayField(
-        models.TextField(blank=False, null=False),
+        models.TextField(blank=False, null=False), null=True, verbose_name="Medline References"
-        null=True,
-        verbose_name="Medline References",
-        blank=True,
     )
 
     external_identifiers = GenericRelation("ExternalIdentifier")
@@ -1640,7 +1625,7 @@ class Reaction(
         educts: Union[List[str], List[CompoundStructure]] = None,
         products: Union[List[str], List[CompoundStructure]] = None,
         rules: Union[Rule | List[Rule]] = None,
-        multi_step: bool = False,
+        multi_step: bool = True,
     ):
         _educts = []
         _products = []
@@ -1705,7 +1690,7 @@ class Reaction(
         if name is not None and name.strip() != "":
             r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
-        if description is not None and description.strip() != "":
+        if description is not None and name.strip() != "":
             r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         r.multi_step = multi_step
@@ -1783,7 +1768,7 @@ class Reaction(
         return new_reaction
 
     def smirks(self):
-        return f"{'.'.join([cs.smiles for cs in self.educts.all().order_by('-pk')])}>>{'.'.join([cs.smiles for cs in self.products.all().order_by('-pk')])}"
+        return f"{'.'.join([cs.smiles for cs in self.educts.all()])}>>{'.'.join([cs.smiles for cs in self.products.all()])}"
 
     @property
     def as_svg(self):
@@ -1896,9 +1881,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 if n not in queue:
                     queue.append(n)
 
-        for i in queue:
-            processed.add(i)
-
         while len(queue):
             current = queue.pop()
             processed.add(current)
@@ -2176,7 +2158,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
         smiles: str,
         name: Optional[str] = None,
         description: Optional[str] = None,
-        depth: Optional[int] = -1,
+        depth: Optional[int] = 0,
     ):
         return Node.create(self, smiles, depth, name=name, description=description)
 
@@ -2191,68 +2173,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
     ):
         return Edge.create(self, start_nodes, end_nodes, rule, name=name, description=description)
 
-    def update_depths(self):
-        # Collect number of in and out links per node
-        in_count = defaultdict(lambda: 0)
-        out_count = defaultdict(lambda: 0)
-
-        for e in self.edges:
-            for react in e.start_nodes.all():
-                out_count[str(react.uuid)] += 1
-
-            for prod in e.end_nodes.all():
-                in_count[str(prod.uuid)] += 1
-
-        depth_map = {}
-        depth_map[0] = list()
-        processed = set()
-
-        data_driven_root_nodes = (
-            self.node_set.all()
-            .annotate(prod_cnt=Count("edge_products"), educt_cnt=Count("edge_educts"))
-            .filter(prod_cnt=0, educt_cnt__gt=0)
-            .distinct()
-        )
-
-        # Eval QuerySet
-        root_nodes_by_depth = list(self.root_nodes)
-
-        data_driven_root_nodes.update(depth=0)
-        root_nodes = [n for n in data_driven_root_nodes]
-
-        for n in root_nodes_by_depth:
-            if n not in root_nodes:
-                if len(n.edge_products.all()) == 0:
-                    root_nodes.append(n)
-
-        for n in root_nodes:
-            depth_map[0].append(n)
-
-        # At most depth len(nodes) is possible
-        for i in range(self.nodes.count()):
-            level_nodes = depth_map.get(i, [])
-
-            if len(level_nodes) == 0:
-                break
-
-            unique_next_level = set()
-            for n in level_nodes:
-                processed.add(n)
-                for e in self.edges:
-                    if n in e.start_nodes.all():
-                        for p in e.end_nodes.all():
-                            if p not in processed:
-                                unique_next_level.add(p)
-
-            if len(unique_next_level) > 0:
-                depth_map[i + 1] = list(unique_next_level)
-
-        for depth, nodes in depth_map.items():
-            for n in nodes:
-                if n.depth != depth and depth != 0:
-                    n.depth = depth
-                    n.save()
-
 
 class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
     pathway = models.ForeignKey(
@@ -2294,25 +2214,15 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             if isinstance(ai.get(), PropertyPrediction):
                 predicted_properties[ai.get().__class__.__name__].append(ai.data)
 
-        # If we have Subclasses of a CompoundStructure we can overwrite keys (e.g. images)
+        return {
-        # by overwriting keys
-        structure_data = self.default_node_label.d3_json()
-
-        res = {
             "depth": self.depth,
             "stereo_removed": self.stereo_removed,
             "url": self.url,
             "node_label_id": self.default_node_label.url,
             "image": f"{self.url}?image=svg",
             "image_svg": IndigoUtils.mol_to_svg(
-                self.default_node_label.molfile
+                self.default_node_label.smiles, width=40, height=40
-                if self.default_node_label.molfile is not None
-                and self.default_node_label.molfile.strip()
-                else self.default_node_label.smiles,
-                width=40,
-                height=40,
             ),
-            "image_type": "svg",
             "name": self.get_name(),
             "smiles": self.default_node_label.smiles,
             "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
@@ -2325,11 +2235,8 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "predicted_properties": predicted_properties,
             "is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
             "timeseries": self.get_timeseries_data(),
-            **structure_data,
         }
 
-        return res
-
     @staticmethod
     @transaction.atomic
     def create(
@@ -2364,17 +2271,12 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
     @property
     def as_svg(self):
-        if (
-            self.default_node_label.molfile is not None
-            and self.default_node_label.molfile.strip() != ""
-        ):
-            return IndigoUtils.mol_to_svg(self.default_node_label.molfile)
         return IndigoUtils.mol_to_svg(self.default_node_label.smiles)
 
     def get_timeseries_data(self):
         for ai in self.additional_information.all():
-            if ai.type == "OECD301FTimeSeries":
+            if ai.__class__.__name__ == "OECD301FTimeSeries":
-                return ai.get().model_dump(mode="json")
+                return ai.model_dump(mode="json")
 
         return None
 
@@ -2411,7 +2313,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
         "epdb.Pathway", verbose_name="belongs to", on_delete=models.CASCADE, db_index=True
     )
     edge_label = models.ForeignKey(
-        "epdb.Reaction", verbose_name="Edge label", null=True, on_delete=models.CASCADE
+        "epdb.Reaction", verbose_name="Edge label", null=True, on_delete=models.SET_NULL
     )
     start_nodes = models.ManyToManyField(
         "epdb.Node", verbose_name="Start Nodes", related_name="edge_educts"
@@ -2490,8 +2392,6 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
         rule: Optional[Rule] = None,
         name: Optional[str] = None,
         description: Optional[str] = None,
-        *args,
-        **kwargs,
     ):
         e = Edge()
         e.pathway = pathway
@@ -2521,7 +2421,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             educts=[n.default_node_label for n in e.start_nodes.all()],
             products=[n.default_node_label for n in e.end_nodes.all()],
             rules=rule,
-            multi_step=kwargs.get("multi_step", False),
+            multi_step=False,
         )
 
         e.edge_label = r
@@ -4529,22 +4429,18 @@ class AdditionalInformation(models.Model):
 
         return f"{self.scenario.url}/additional-information/{self.uuid}"
 
-    @staticmethod
+    def get(self) -> "EnviPyModel":
-    def from_dict(ai_type: str, ai_data: Dict[str, Any]):
         from envipy_additional_information import registry
 
         MAPPING = {c.__name__: c for c in registry.list_models().values()}
         try:
-            inst = MAPPING[ai_type](**ai_data)
+            inst = MAPPING[self.type](**self.data)
         except Exception as e:
-            print(f"Error loading {ai_type}: {e}")
+            print(f"Error loading {self.type}: {e}")
             raise e
 
-        return inst
-
-    def get(self) -> "EnviPyModel":
-        inst = AdditionalInformation.from_dict(self.type, self.data)
         inst.__dict__["uuid"] = str(self.uuid)
+
         return inst
 
     def __str__(self) -> str:

epdb/views.py

@@ -19,7 +19,6 @@ from sentry_sdk import capture_exception
 
 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
-from .exceptions import InvalidSMILESException
 
 from .logic import (
     EPDBURLParser,
@@ -755,11 +754,6 @@ def models(request):
             {"Model": s.SERVER_URL + "/model"},
         ]
 
-        context["entity_type"] = "model"
-        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/models/"
-        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
-        context["list_title"] = "models"
-
         # Keep model_types for potential modal/action use
         context["model_types"] = {
             "ML Relative Reasoning": {
@@ -772,26 +766,19 @@ def models(request):
                 "requires_rule_packages": True,
                 "requires_data_packages": True,
             },
+            "EnviFormer": {
+                "type": "enviformer",
+                "requires_rule_packages": False,
+                "requires_data_packages": True,
+            },
         }
 
-        if s.ENVIFORMER_PRESENT:
-            context["model_types"]["EnviFormer"] = (
-                {
-                    "type": "enviformer",
-                    "requires_rule_packages": False,
-                    "requires_data_packages": True,
-                },
-            )
-
         if s.FLAGS.get("PLUGINS", False):
             for k, v in s.CLASSIFIER_PLUGINS.items():
                 context["model_types"][v.display()] = {
                     "type": k,
                     "requires_rule_packages": v.requires_rule_packages(),
                     "requires_data_packages": v.requires_data_packages(),
-                    "additional_parameters": v.Config.__name__.lower()
-                    if v.Config.__name__ != ""
-                    else None,
                 }
             for k, v in s.PROPERTY_PLUGINS.items():
                 context["model_types"][v.display()] = {
@@ -800,6 +787,12 @@ def models(request):
                     "requires_data_packages": v.requires_data_packages(),
                 }
 
+        # Context for paginated template
+        context["entity_type"] = "model"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/models/"
+        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
+        context["list_title"] = "models"
+
         return render(request, "collections/models_paginated.html", context)
 
     elif request.method == "POST":
@@ -913,13 +906,12 @@ def package_models(request, package_uuid):
                 "requires_rule_packages": True,
                 "requires_data_packages": True,
             },
-        }
+            "EnviFormer": {
-        if s.ENVIFORMER_PRESENT:
-            context["model_types"]["EnviFormer"] = {
                 "type": "enviformer",
                 "requires_rule_packages": False,
                 "requires_data_packages": True,
-            }
+            },
+        }
 
         if s.FLAGS.get("PLUGINS", False):
             for k, v in s.CLASSIFIER_PLUGINS.items():
@@ -1095,11 +1087,6 @@ def package_model(request, package_uuid, model_uuid):
                             }
                         )
 
-                        # Sort data by prob desc
-                        res["pred"] = sorted(
-                            res["pred"], key=lambda x: x["probability"], reverse=True
-                        )
-
                 return JsonResponse(res, safe=False)
 
             elif half_life:
@@ -1203,7 +1190,9 @@ def package(request, package_uuid):
     if request.method == "GET":
         if request.GET.get("export", False) == "true":
             filename = f"{current_package.get_name().replace(' ', '_')}_{current_package.uuid}.json"
-            pack_json = PackageManager.export_package(current_package)
+            pack_json = PackageManager.export_package(
+                current_package, include_models=False, include_external_identifiers=False
+            )
             response = JsonResponse(pack_json, content_type="application/json")
             response["Content-Disposition"] = f'attachment; filename="{filename}"'
 
@@ -2339,13 +2328,7 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
         node_description = request.POST.get("node-description")
 
         node_smiles = request.POST.get("node-smiles").strip()
-
+        current_pathway.add_node(node_smiles, name=node_name, description=node_description)
-        try:
-            current_pathway.add_node(node_smiles, name=node_name, description=node_description)
-        except InvalidSMILESException:
-            return error(
-                request, "Node creation failed!", f"Given SMILES ({node_smiles}) is invalid"
-            )
 
         return redirect(current_pathway.url)
 
@@ -2523,9 +2506,6 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
             substrate_nodes, product_nodes, name=edge_name, description=edge_description
         )
 
-        # Update depths as sideeffect of above operation
-        current_pathway.update_depths()
-
         return redirect(current_pathway.url)
 
     else:
@@ -2866,15 +2846,9 @@ def groups(request):
             {"Group": s.SERVER_URL + "/group"},
         ]
 
-        # Context for paginated template
+        context["objects"] = Group.objects.all()
-        context["entity_type"] = "group"
-        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/groups/"
-        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
-        context["list_title"] = "groups"
-        context["list_mode"] = "combined"
-
-        return render(request, "collections/groups_paginated.html", context)
 
+        return render(request, "collections/objects_list.html", context)
     elif request.method == "POST":
         group_name = request.POST.get("group-name")
         group_description = request.POST.get("group-description", s.DEFAULT_VALUES["description"])
@@ -3097,21 +3071,12 @@ def jobs(request):
             {"Home": s.SERVER_URL},
             {"Jobs": s.SERVER_URL + "/jobs"},
         ]
-        # if current_user.is_superuser:
+        if current_user.is_superuser:
-        #     context["jobs"] = JobLog.objects.all().order_by("-created")
+            context["jobs"] = JobLog.objects.all().order_by("-created")
-        # else:
+        else:
-        #     context["jobs"] = JobLog.objects.filter(user=current_user).order_by("-created")
+            context["jobs"] = JobLog.objects.filter(user=current_user).order_by("-created")
 
-        # Context for paginated template
+        return render(request, "collections/joblog.html", context)
-        context["entity_type"] = "joblog"
-        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/joblog/"
-        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
-        context["list_title"] = "joblog"
-        context["list_mode"] = "combined"
-
-        return render(request, "collections/joblog_paginated.html", context)
-
-        # return render(request, "collections/joblog.html", context)
 
     elif request.method == "POST":
         job_name = request.POST.get("job-name")

migration/views.py

@@ -65,25 +65,6 @@ def run_both_engines(SMILES, SMIRKS):
 
 
 def migration(request):
-    accepted_diffs = [
-        "bt0055-3469.1",
-        "bt0056-2685",
-        "bt0193-4263",
-        "bt0231-1871.1",
-        "bt0242-3803",
-        "bt0254-4224.1",
-        "bt0254-4224.2",
-        "bt0291-1129",
-        "bt0337-3543",
-        "bt0391-4285",
-        "bt0402-3576",
-        "bt0404-3928",
-        "bt0416-4269",
-        "bt0432-4254",
-        "bt0337-4117",
-        "bt0322-3393",
-    ]
-
     if request.method == "GET":
         context = get_base_context(request)
 
@@ -128,11 +109,11 @@ def migration(request):
                         ),
                         "id": str(r.uuid),
                         "url": r.url,
-                        "status": res or r.name in accepted_diffs,
+                        "status": res,
                     }
                 )
 
-                if res or r.name in accepted_diffs:
+                if res:
                     success += 1
                 else:
                     error += 1
@@ -154,16 +135,7 @@ def migration(request):
 
         for r in migration_status["results"]:
             r["detail_url"] = r["detail_url"].replace("http://localhost:8000", s.SERVER_URL)
-            if r["name"] in accepted_diffs:
-                r["status"] = True
 
-        migration_status["results"] = sorted(
-            migration_status["results"], key=lambda x: (x["status"], x["name"])
-        )
-
-        num_success = sum([int(x["status"]) for x in migration_status["results"]])
-        migration_status["success"] = num_success
-        migration_status["error"] = migration_status["total"] - num_success
         context.update(**migration_status)
 
         return render(request, "migration.html", context)

package.json

@@ -21,11 +21,5 @@
     "django",
     "tailwindcss",
     "daisyui"
-  ],
+  ]
-  "pnpm": {
-    "onlyBuiltDependencies": [
-      "@parcel/watcher",
-      "@tailwindcss/oxide"
-    ]
-  }
 }

pepper/__init__.py

@@ -46,7 +46,7 @@ class PepperPrediction(PropertyPrediction):
 
         import matplotlib.patches as mpatches
         import numpy as np
-        from matplotlib.figure import Figure
+        from matplotlib import pyplot as plt
         from scipy import stats
 
         """
@@ -101,8 +101,7 @@ class PepperPrediction(PropertyPrediction):
         mask_red = x > vp
 
         # Plot
-        fig = Figure(figsize=(9, 5.5))
+        fig, ax = plt.subplots(figsize=(9, 5.5))
-        ax = fig.subplots()
         ax.plot(x, y, color="#1f4e79", lw=2, label="Lognormal PDF")
 
         if np.any(mask_green):
@@ -147,12 +146,13 @@ class PepperPrediction(PropertyPrediction):
         ]
         ax.legend(handles=patches, frameon=True)
 
-        fig.tight_layout()
+        plt.tight_layout()
 
         # --- Export to SVG string ---
         buf = io.StringIO()
         fig.savefig(buf, format="svg", bbox_inches="tight")
         svg = buf.getvalue()
+        plt.close(fig)
         buf.close()
 
         return svg

pepper/impl/pepper.py

@@ -187,9 +187,8 @@ class Pepper:
         groups = [group for group in dataset.group_by("structure_id")]
 
         # Unless explicitly set compute everything serial
-        n_threads = int(os.environ.get("N_PEPPER_THREADS", 1))
+        if os.environ.get("N_PEPPER_THREADS", 1) > 1:
-        if n_threads > 1:
+            results = Parallel(n_jobs=os.environ["N_PEPPER_THREADS"])(
-            results = Parallel(n_jobs=n_threads)(
                 delayed(compute_bayes_per_group)(group[1])
                 for group in dataset.group_by("structure_id")
             )

pnpm-workspace.yaml

@@ -1,5 +1,3 @@
-allowBuilds:
-  '@parcel/watcher': true
 onlyBuiltDependencies:
   - '@parcel/watcher'
   - '@tailwindcss/oxide'

static/css/input.css

@@ -34,8 +34,3 @@
 }
 
 @import "./daisyui-theme.css";
-
-select.select[multiple] {
-  display: block;
-  white-space: normal;
-}

static/js/alpine/components/widgets.js

@@ -59,9 +59,6 @@ document.addEventListener("alpine:init", () => {
     get isEditMode() {
       return this.mode === "edit";
     },
-    get isRequired() {
-      return (this.schema.required || []).indexOf(this.fieldName) > -1
-    }
   });
 
   // Text widget
@@ -296,34 +293,6 @@ document.addEventListener("alpine:init", () => {
     }),
   );
 
-    // PubMed link widget
-  Alpine.data(
-    "doiWidget",
-    (fieldName, data, schema, uiSchema, mode, debugErrors, context = null) => ({
-      ...baseWidget(
-        fieldName,
-        data,
-        schema,
-        uiSchema,
-        mode,
-        debugErrors,
-        context,
-      ),
-
-      get value() {
-        return this.data[this.fieldName] || "";
-      },
-      set value(v) {
-        this.data[this.fieldName] = v;
-      },
-      get doiUrl() {
-        return this.value
-          ? `https://dx.doi.org/${this.value}`
-          : null;
-      },
-    }),
-  );
-
   // Compound link widget
   Alpine.data(
     "compoundWidget",

static/js/pw.js

@@ -1,37 +1,5 @@
 console.log("loaded pw.js")
 
-function findPaths(source_idx, links) {
-    const resultLinks = new Set();
-    const visited = new Set();
-    // Helper function for depth-first search
-    function dfs(current) {
-
-        if (visited.has(current)) {
-            return;
-        }
-
-        if (links.filter(link => link.target.id === current).length === 0) {
-            return;
-        }
-
-        visited.add(current);
-        links.forEach(link => {
-            if (
-                link.target.id === current &&
-                !visited.has(link.source.id) &&
-                link.source.id !== link.target.id // Avoid self-loops
-            ) {
-                resultLinks.add(link); // Add link to result
-                dfs(link.source.id);
-            }
-        });
-        visited.delete(current);
-    }
-    // Start DFS
-    dfs(source_idx);
-    return Array.from(resultLinks);
-}
-
 function predictFromNode(url) {
     fetch("", {
         method: "POST",
@@ -55,7 +23,6 @@ function predictFromNode(url) {
 // elem = 'vizdiv'
 function draw(pathway, elem) {
 
-    const initialzoom = 2.5
     const nodeRadius = 20;
     const linkDistance = 100;
     const chargeStrength = -200;
@@ -96,7 +63,7 @@ function draw(pathway, elem) {
                 node.fx = width / 2 + depthMap.get(node.depth) * horizontalSpacing - ((nodesInLevel - 1) * horizontalSpacing) / 2;
             }
 
-            node.fy = (node.depth + initialzoom + 0.5) * levelSpacing + 50;
+            node.fy = node.depth * levelSpacing + 50;
             depthMap.set(node.depth, depthMap.get(node.depth) + 1);
         });
     }
@@ -134,24 +101,10 @@ function draw(pathway, elem) {
         // Update pseudo node positions first
         updatePseudoNodePositions();
 
-        link.attr("d", d => {
+        link.attr("x1", d => d.source.x)
-            // Check if it's a self-loop (source equals target)
+            .attr("y1", d => d.source.y)
-            if (d.source.id === d.target.id) {
+            .attr("x2", d => d.target.x)
-                // Create a bezier curve for self-loops
+            .attr("y2", d => d.target.y);
-                const x = d.source.x;
-                const y = d.source.y;
-                const loopRadius = nodeRadius * 2; // Adjust size of the loop
-
-                // Create a circular path to the left of the node
-                return `M ${x},${y - nodeRadius}
-                        C ${x - loopRadius},${y - nodeRadius - loopRadius}
-                          ${x - loopRadius},${y + nodeRadius + loopRadius}
-                          ${x},${y + nodeRadius}`;
-            } else {
-                // Regular straight line for normal edges
-                return `M ${d.source.x},${d.source.y} L ${d.target.x},${d.target.y}`;
-            }
-        });
 
         node.attr("transform", d => `translate(${d.x},${d.y})`);
     }
@@ -510,7 +463,7 @@ function draw(pathway, elem) {
                     // TODO needs to be generic once we store it as AddInf
                     for (var s of n.predicted_properties["PepperPrediction"]) {
                         if (s["mean"] != null) {
-                            tempContent += "<b>DT50 predicted via Pepper:</b> " + s["mean"].toFixed(2) + " days<br>"
+                            tempContent += "<b>DT50 predicted via Pepper:</b> " + s["mean"].toFixed(2) + "<br>"
                         }
                     }
                 }
@@ -610,8 +563,6 @@ function draw(pathway, elem) {
     // Apply zoom to the SVG element - this enables wheel zoom
     svg.call(zoom);
 
-    svg.call(zoom.scaleBy, initialzoom);
-
     // Also apply zoom to container to catch events that might not reach SVG
     // This ensures drag-to-pan works even when clicking on empty space
     container.call(zoom);
@@ -630,11 +581,11 @@ function draw(pathway, elem) {
         for (idx in parents) {
             p = nodes[parents[idx]]
             // console.log(p.depth)
-            // if (p.depth >= n.depth) {
+            if (p.depth >= n.depth) {
-            //     // keep the .5 steps for pseudo nodes
+                // keep the .5 steps for pseudo nodes
-            //     n.depth = n.pseudo ? p.depth + 1 : Math.floor(p.depth + 1);
+                n.depth = n.pseudo ? p.depth + 1 : Math.floor(p.depth + 1);
-            //     // console.log("Adjusting", orig_depth, Math.floor(p.depth + 1));
+                // console.log("Adjusting", orig_depth, Math.floor(p.depth + 1));
-            // }
+            }
         }
     });
 
@@ -648,45 +599,13 @@ function draw(pathway, elem) {
 
     // Kanten zeichnen
     const link = zoomable.append("g")
-        .selectAll("path")
+        .selectAll("line")
         .data(links)
-        .enter().append("path")
+        .enter().append("line")
         // Check if target is pseudo and draw marker only if not pseudo
         .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
-        .attr("marker-end", d => {
+        .attr("marker-end", d => d.target.pseudo ? '' : d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)')
-            if (d.target.pseudo) return '';
-            if (d.source.id === d.target.id) return 'url(#curve-arrow)'; // Use curve arrow for self-loops
-            return d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)';
-        })
-        .attr("fill", "none")
-        .on("click", function(event, d) {
-          const wasHighlighted = d3.select(this).classed("highlighted");
-	      d3.selectAll("path").classed("highlighted", false);
-          if (!wasHighlighted) {
-            const toHighlight = [];
-            toHighlight.push(d.el);
 
-            if (d.source.pseudo || d.target.pseudo) {
-              if (d.target.pseudo) {
-                d3.selectAll("path").each(e => {
-                  if (e !== undefined && e.source.id === d.target.id) {
-                    toHighlight.push(e.el);
-                  }
-                });
-              } else {
-                d3.selectAll("path").each(e => {
-                  if (e !== undefined && (e.target.id === d.source.id || e.source.id === d.source.id)) {
-                    toHighlight.push(e.el);
-                  }
-                });
-              }
-            }
-
-            for (const e of toHighlight) {
-              d3.select(e).classed("highlighted", true);
-            }
-          }
-        });
 
     // add element to links array
     link.each(function (d) {
@@ -703,41 +622,10 @@ function draw(pathway, elem) {
         .call(d3.drag()
             .on("start", dragstarted)
             .on("drag", dragged)
-            .on("end", dragended)
+            .on("end", dragended))
-        )
         .on("click", function (event, d) {
-          const wasHighlighted = d3.select(this).select("circle").classed("highlighted");
-          d3.selectAll('circle.highlighted').classed('highlighted', false);
-          d3.selectAll("path").classed("inedge", false);
-          d3.selectAll("path").classed("outedge", false);
-
-          if (!wasHighlighted) {
             d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
-            const inEdges = findPaths(d.id, links);
+        })
-            const outEdges = []
-            // Colorize out edges green
-            for (const l of links) {
-              if (l.source.id === d.id) {
-                outEdges.push(l);
-                if (l.target.pseudo) {
-                  for (const l2 of links) {
-                    if (l.target.id === l2.source.id) {
-                      outEdges.push(l2);
-                    }
-                  }
-                }
-              }
-            }
-
-            for (const e of inEdges) {
-              d3.select(e.el).classed("inedge", true);
-            }
-
-            for (const e of outEdges) {
-              d3.select(e.el).classed("outedge", true);
-            }
-          }
-        });
 
     // Kreise für die Knoten hinzufügen
     node.append("circle")
@@ -749,56 +637,44 @@ function draw(pathway, elem) {
     node.filter(d => !d.pseudo).each(function (d, i) {
         const g = d3.select(this);
 
-        if (d.image_type === "svg") {
+        // Parse the SVG string
-            // Parse the SVG string
+        const parser = new DOMParser();
-            const parser = new DOMParser();
+        const svgDoc = parser.parseFromString(d.image_svg, "image/svg+xml");
-            const svgDoc = parser.parseFromString(d.image_svg, "image/svg+xml");
+        const svgElem = svgDoc.documentElement;
-            const svgElem = svgDoc.documentElement;
 
-            // Create a unique prefix per node
+        // Create a unique prefix per node
-            const prefix = `node-${i}-`;
+        const prefix = `node-${i}-`;
 
-            // Rename all IDs and fix <use> references
+        // Rename all IDs and fix <use> references
-            svgElem.querySelectorAll("[id]").forEach(el => {
+        svgElem.querySelectorAll('[id]').forEach(el => {
-                const oldId = el.id;
+            const oldId = el.id;
-                const newId = prefix + oldId;
+            const newId = prefix + oldId;
-                el.id = newId;
+            el.id = newId;
 
-                const XLINK_NS = "http://www.w3.org/1999/xlink";
+            const XLINK_NS = "http://www.w3.org/1999/xlink";
-                // Update <use> elements that reference this old ID
+            // Update <use> elements that reference this old ID
-                const uses = Array.from(svgElem.querySelectorAll("use")).filter(
+            const uses = Array.from(svgElem.querySelectorAll('use')).filter(
-                    u => u.getAttributeNS(XLINK_NS, "href") === `#${oldId}`
+                u => u.getAttributeNS(XLINK_NS, 'href') === `#${oldId}`
-                );
+            );
 
-                uses.forEach(u => {
+            uses.forEach(u => {
-                    u.setAttributeNS(XLINK_NS, "href", `#${newId}`);
+                u.setAttributeNS(XLINK_NS, 'href', `#${newId}`);
-                });
             });
+        });
 
-            g.node().appendChild(svgElem);
+        g.node().appendChild(svgElem);
 
-            const vb = svgElem.viewBox.baseVal;
+        const vb = svgElem.viewBox.baseVal;
-            const svgWidth = vb.width || 40;
+        const svgWidth = vb.width || 40;
-            const svgHeight = vb.height || 40;
+        const svgHeight = vb.height || 40;
 
-            const scale = (nodeRadius * 2) / Math.max(svgWidth, svgHeight);
+        const scale = (nodeRadius * 2) / Math.max(svgWidth, svgHeight);
-
-            g.select("svg")
-                .attr("width", svgWidth * scale)
-                .attr("height", svgHeight * scale)
-                .attr("x", -svgWidth * scale / 2)
-                .attr("y", -svgHeight * scale / 2);
-        } else {
-            // We have a image type different than svg
-            // include it via img url
-            g.append("svg:image")
-                .attr("xlink:href", d.image)
-                .attr("width", 40)
-                .attr("height", 40)
-                .attr("x", -20)
-                .attr("y", -20);
-        }
 
+        g.select("svg")
+            .attr("width", svgWidth * scale)
+            .attr("height", svgHeight * scale)
+            .attr("x", -svgWidth * scale / 2)
+            .attr("y", -svgHeight * scale / 2);
     });
 
     // add element to nodes array
@@ -811,14 +687,14 @@ function draw(pathway, elem) {
 
 function serializeSVG(svgElement) {
 
-    svgElement.querySelectorAll("path.link").forEach(line => {
+    svgElement.querySelectorAll("line.link").forEach(line => {
         const style = getComputedStyle(line);
         line.setAttribute("stroke", style.stroke);
         line.setAttribute("stroke-width", style.strokeWidth);
         line.setAttribute("fill", style.fill);
     });
 
-    svgElement.querySelectorAll("path.link_no_arrow").forEach(line => {
+    svgElement.querySelectorAll("line.link_no_arrow").forEach(line => {
         const style = getComputedStyle(line);
         line.setAttribute("stroke", style.stroke);
         line.setAttribute("stroke-width", style.strokeWidth);

templates/actions/collections/group.html

@@ -0,0 +1,8 @@
+<li>
+  <a
+    role="button"
+    onclick="document.getElementById('new_group_modal').showModal(); return false;"
+  >
+    <span class="glyphicon glyphicon-plus"></span> New Group</a
+  >
+</li>

templates/actions/objects/pathway.html

@@ -1,5 +1,3 @@
-{% load envipytags %}
-
 {% if meta.can_edit %}
   <li>
     <a
@@ -17,12 +15,7 @@
       <i class="glyphicon glyphicon-plus"></i> Add Reaction</a
     >
   </li>
-  {% epdb_slot_templates "epdb.actions.objects.pathway.add" as action_button_templates %}
+  <li role="separator" class="divider"></li>
-
-  {% for tpl in action_button_templates %}
-    {% include tpl %}
-  {% endfor %}
-  <li role="separator" class="divider h-px"></li>
 {% endif %}
 <li>
   <a
@@ -74,7 +67,7 @@
       Rules</a
     >
   </li>
-  <li role="separator" class="divider h-px"></li>
+  <li role="separator" class="divider"></li>
   <li>
     <a
       class="button"
@@ -99,16 +92,11 @@
       <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
     >
   </li>
-  <li role="separator" class="divider h-px"></li>
+  <li role="separator" class="divider"></li>
   <li>
     <a
       class="button"
-      onclick="
+      onclick="document.getElementById('delete_pathway_node_modal').showModal(); return false;"
-      const modal = document.getElementById('delete_pathway_node_modal');
-      modal.showModal();
-      window.dispatchEvent(new Event('modal-opened'));
-      return false;
-      "
     >
       <i class="glyphicon glyphicon-trash"></i> Delete Compound</a
     >
@@ -116,12 +104,7 @@
   <li>
     <a
       class="button"
-      onclick="
+      onclick="document.getElementById('delete_pathway_edge_modal').showModal(); return false;"
-      const modal = document.getElementById('delete_pathway_edge_modal');
-      modal.showModal();
-      window.dispatchEvent(new Event('modal-opened'));
-      return false;
-      "
     >
       <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a
     >

templates/collections/_joblog_paginated_list_partial.html

@@ -1,102 +0,0 @@
-{# Partial for paginated list content - expects to be inside a remotePaginatedList Alpine.js context #}
-{# Variables: empty_text (string), show_review_badge (bool), always_show_badge (bool) #}
-{% load envipytags %}
-{# Loading state #}
-<div
-  x-show="isLoading"
-  class="mx-auto flex h-32 w-32 items-center justify-center"
->
-  {% include "components/loading-spinner.html" %}
-</div>
-
-{# Error state #}
-<div
-  x-show="!isLoading && error"
-  class="alert alert-error/50 text-sm"
-  x-text="error"
-></div>
-
-{# Content #}
-<template x-if="!isLoading && !error">
-  <div>
-    {# Empty state #}
-    <div
-      x-show="totalItems === 0"
-      class="text-base-content/70 py-8 text-center"
-    >
-      <p>No {{ empty_text|default:"items" }} found.</p>
-    </div>
-
-    {# Items list #}
-    <ul class="menu bg-base-100 rounded-box w-full" x-show="totalItems > 0">
-      <table class="table-zebra table">
-        <thead>
-          <tr>
-            <th>User</th>
-
-            <th>ID</th>
-            <th>Name</th>
-            <th>Status</th>
-            <th>Queued At</th>
-            <th>Done At</th>
-          </tr>
-        </thead>
-        <tbody>
-          <template x-for="obj in paginatedItems" :key="obj.url">
-            <tr>
-              <td>
-                <a :href="obj.user.url"><span x-text="obj.user.name"></span></a>
-              </td>
-
-              <td>
-                <a :href="obj.url"><span x-text="obj.id"></span></a>
-              </td>
-              <td><span x-text="obj.name"></span></td>
-              <td><span x-text="obj.status"></span></td>
-              <td><span x-text="obj.created"></span></td>
-              <td><span x-text="obj.done"></span></td>
-            </tr>
-          </template>
-        </tbody>
-      </table>
-    </ul>
-
-    {# Pagination controls #}
-    <div
-      x-show="totalPages > 1"
-      class="mt-4 flex items-center justify-between px-2"
-    >
-      <span class="text-base-content/70 text-sm">
-        Showing <span x-text="showingStart"></span>-<span
-          x-text="showingEnd"
-        ></span>
-        of <span x-text="totalItems"></span>
-      </span>
-      <div class="join">
-        <button
-          class="join-item btn btn-sm"
-          :disabled="currentPage === 1"
-          @click="prevPage()"
-        >
-          «
-        </button>
-        <template x-for="item in pageNumbers" :key="item.key">
-          <button
-            class="join-item btn btn-sm"
-            :class="{ 'btn-active': item.page === currentPage }"
-            :disabled="item.isEllipsis"
-            @click="!item.isEllipsis && goToPage(item.page)"
-            x-text="item.page"
-          ></button>
-        </template>
-        <button
-          class="join-item btn btn-sm"
-          :disabled="currentPage === totalPages"
-          @click="nextPage()"
-        >
-          »
-        </button>
-      </div>
-    </div>
-  </div>
-</template>

templates/collections/compounds_paginated.html

@@ -5,7 +5,7 @@
 
 {% block action_button %}
   <div class="flex items-center gap-2">
-    {% if meta.can_edit or not meta.url_contains_package %}
+    {% if meta.can_edit %}
       <button
         type="button"
         class="btn btn-primary btn-sm"

templates/collections/groups_paginated.html

@@ -1,21 +0,0 @@
-{% extends "collections/paginated_base.html" %}
-
-{% block page_title %}Groups{% endblock %}
-
-{% block action_button %}
-  <button
-    type="button"
-    class="btn btn-primary btn-sm"
-    onclick="document.getElementById('new_group_modal').showModal(); return false;"
-  >
-    New Group
-  </button>
-{% endblock action_button %}
-
-{% block action_modals %}
-  {% include "modals/collections/new_group_modal.html" %}
-{% endblock action_modals %}
-
-{% block description %}
-  <p>Users can team up in groups to share packages.</p>
-{% endblock description %}

templates/collections/joblog_paginated.html

@@ -1,13 +0,0 @@
-{% extends "collections/paginated_base.html" %}
-
-{% block page_title %}Jobs{% endblock %}
-
-{% block action_button %}
-{% endblock action_button %}
-
-{% block action_modals %}
-{% endblock action_modals %}
-
-{% block description %}
-  <p>List of Jobs submitted.</p>
-{% endblock description %}

templates/collections/models_paginated.html

@@ -3,16 +3,14 @@
 {% block page_title %}Models{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit or not meta.url_contains_package %}
+  {% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %}
-    {% if meta.enabled_features.MODEL_BUILDING %}
+    <button
-      <button
+      type="button"
-        type="button"
+      class="btn btn-primary btn-sm"
-        class="btn btn-primary btn-sm"
+      onclick="document.getElementById('new_model_modal').showModal(); return false;"
-        onclick="document.getElementById('new_model_modal').showModal(); return false;"
+    >
-      >
+      New Model
-        New Model
+    </button>
-      </button>
-    {% endif %}
   {% endif %}
 {% endblock action_button %}
 

templates/collections/packages_paginated.html

@@ -3,73 +3,75 @@
 {% block page_title %}Packages{% endblock %}
 
 {% block action_button %}
-  <div class="flex items-center gap-2">
+  {% if meta.can_edit %}
-    <button
+    <div class="flex items-center gap-2">
-      type="button"
+      <button
-      class="btn btn-primary btn-sm"
+        type="button"
-      id="new-package-button"
+        class="btn btn-primary btn-sm"
-      onclick="document.getElementById('new_package_modal').showModal(); return false;"
+        id="new-package-button"
-    >
+        onclick="document.getElementById('new_package_modal').showModal(); return false;"
-      <svg
-        xmlns="http://www.w3.org/2000/svg"
-        width="24"
-        height="24"
-        viewBox="0 0 24 24"
-        fill="none"
-        stroke="currentColor"
-        stroke-width="2"
-        stroke-linecap="round"
-        stroke-linejoin="round"
-        class="lucide lucide-folder-plus-icon lucide-folder-plus"
       >
-        <path d="M12 10v6" />
-        <path d="M9 13h6" />
-        <path
-          d="M20 20a2 2 0 0 0 2-2V8a2 2 0 0 0-2-2h-7.9a2 2 0 0 1-1.69-.9L9.6 3.9A2 2 0 0 0 7.93 3H4a2 2 0 0 0-2 2v13a2 2 0 0 0 2 2Z"
-        />
-      </svg>
-    </button>
-    <div class="dropdown dropdown-end">
-      <div tabindex="0" role="button" class="btn btn-sm">
-        Import
         <svg
           xmlns="http://www.w3.org/2000/svg"
-          width="16"
+          width="24"
-          height="16"
+          height="24"
           viewBox="0 0 24 24"
           fill="none"
           stroke="currentColor"
           stroke-width="2"
           stroke-linecap="round"
           stroke-linejoin="round"
-          class="lucide lucide-chevron-down ml-1"
+          class="lucide lucide-folder-plus-icon lucide-folder-plus"
         >
-          <path d="m6 9 6 6 6-6" />
+          <path d="M12 10v6" />
+          <path d="M9 13h6" />
+          <path
+            d="M20 20a2 2 0 0 0 2-2V8a2 2 0 0 0-2-2h-7.9a2 2 0 0 1-1.69-.9L9.6 3.9A2 2 0 0 0 7.93 3H4a2 2 0 0 0-2 2v13a2 2 0 0 0 2 2Z"
+          />
         </svg>
+      </button>
+      <div class="dropdown dropdown-end">
+        <div tabindex="0" role="button" class="btn btn-sm">
+          Import
+          <svg
+            xmlns="http://www.w3.org/2000/svg"
+            width="16"
+            height="16"
+            viewBox="0 0 24 24"
+            fill="none"
+            stroke="currentColor"
+            stroke-width="2"
+            stroke-linecap="round"
+            stroke-linejoin="round"
+            class="lucide lucide-chevron-down ml-1"
+          >
+            <path d="m6 9 6 6 6-6" />
+          </svg>
+        </div>
+        <ul
+          tabindex="-1"
+          class="dropdown-content menu bg-base-100 rounded-box z-50 w-56 p-2"
+        >
+          <li>
+            <a
+              role="button"
+              onclick="document.getElementById('import_package_modal').showModal(); return false;"
+            >
+              Import Package from JSON
+            </a>
+          </li>
+          <li>
+            <a
+              role="button"
+              onclick="document.getElementById('import_legacy_package_modal').showModal(); return false;"
+            >
+              Import Package from legacy JSON
+            </a>
+          </li>
+        </ul>
       </div>
-      <ul
-        tabindex="-1"
-        class="dropdown-content menu bg-base-100 rounded-box z-50 w-56 p-2"
-      >
-        <li>
-          <a
-            role="button"
-            onclick="document.getElementById('import_package_modal').showModal(); return false;"
-          >
-            Import Package from JSON
-          </a>
-        </li>
-        <li>
-          <a
-            role="button"
-            onclick="document.getElementById('import_legacy_package_modal').showModal(); return false;"
-          >
-            Import Package from legacy JSON
-          </a>
-        </li>
-      </ul>
     </div>
-  </div>
+  {% endif %}
 {% endblock action_button %}
 
 {% block action_modals %}

templates/collections/paginated_base.html

@@ -37,11 +37,7 @@
             perPage: {{ per_page|default:50 }}
           })"
       >
-        {% if entity_type == 'joblog' %}
+        {% include "collections/_paginated_list_partial.html" with empty_text=list_title|default:"items" show_review_badge=True %}
-          {% include "collections/_joblog_paginated_list_partial.html" with empty_text=list_title|default:"items" show_review_badge=True %}
-        {% else %}
-          {% include "collections/_paginated_list_partial.html" with empty_text=list_title|default:"items" show_review_badge=True %}
-        {% endif %}
       </div>
     {% else %}
       {# ===== TABBED MODE: Reviewed/Unreviewed tabs (default) ===== #}

templates/collections/pathways_paginated.html

@@ -3,7 +3,7 @@
 {% block page_title %}Pathways{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit or not meta.url_contains_package %}
+  {% if meta.can_edit %}
     <div class="flex items-center gap-2">
       <a
         class="btn btn-primary btn-sm"

templates/collections/reactions_paginated.html

@@ -3,7 +3,7 @@
 {% block page_title %}Reactions{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit or not meta.url_contains_package %}
+  {% if meta.can_edit %}
     <button
       type="button"
       class="btn btn-primary btn-sm"

templates/collections/rules_paginated.html

@@ -3,7 +3,7 @@
 {% block page_title %}Rules{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit or not meta.url_contains_package %}
+  {% if meta.can_edit %}
     <button
       type="button"
       class="btn btn-primary btn-sm"

templates/collections/scenarios_paginated.html

@@ -11,7 +11,7 @@
 {% endblock action_modals %}
 
 {% block action_button %}
-  {% if meta.can_edit or not meta.url_contains_package %}
+  {% if meta.can_edit %}
     <button
       type="button"
       class="btn btn-primary btn-sm"

templates/collections/structures_paginated.html

@@ -3,7 +3,7 @@
 {% block page_title %}{{ page_title|default:"Structures" }}{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit or not meta.url_contains_package %}
+  {% if meta.can_edit %}
     <button
       type="button"
       class="btn btn-primary btn-sm"

templates/components/schema_form.html

@@ -123,17 +123,6 @@
             </div>
           </template>
 
-          <!-- DOI link widget -->
-          <template
-            x-if="getWidget(fieldName, schema.properties[fieldName]) === 'doi-link'"
-          >
-            <div
-              x-data="doiWidget(fieldName, data, schema, uiSchema, mode, debugErrors, context)"
-            >
-              {% include "components/widgets/doi_link_widget.html" %}
-            </div>
-          </template>
-
           <!-- Compound link widget -->
           <template
             x-if="getWidget(fieldName, schema.properties[fieldName]) === 'compound-link'"

templates/components/widgets/doi_link_widget.html

@@ -1,69 +0,0 @@
-{# DOI link widget - pure HTML template #}
-<div class="form-control">
-  <div class="flex flex-col gap-2 sm:flex-row sm:items-baseline">
-    <!-- Label -->
-    <label class="label sm:w-48 sm:shrink-0">
-      <span
-        class="label-text"
-        :class="{
-              'text-error': $store.validationErrors.hasError(fieldName, context),
-              'text-sm text-base-content/60': isViewMode
-            }"
-        x-text="label"
-      ></span>
-    </label>
-
-    <!-- Input column -->
-    <div class="flex-1">
-      <!-- Help text -->
-      <template x-if="helpText">
-        <div class="label">
-          <span
-            class="label-text-alt text-base-content/60"
-            x-text="helpText"
-          ></span>
-        </div>
-      </template>
-
-      <!-- View mode: display as link -->
-      <template x-if="isViewMode">
-        <div class="mt-1">
-          <template x-if="value && doiUrl">
-            <a
-              :href="doiUrl"
-              class="link link-primary"
-              target="_blank"
-              x-text="value"
-            ></a>
-          </template>
-          <template x-if="!value">
-            <span class="text-base-content/50">—</span>
-          </template>
-        </div>
-      </template>
-
-      <!-- Edit mode -->
-      <template x-if="isEditMode">
-        <input
-          type="text"
-          class="input input-bordered w-full"
-          :class="{ 'input-error': $store.validationErrors.hasError(fieldName, context) }"
-          placeholder="DOI e.g. 10.1016/j.jhazmat.2016.08.036"
-          x-model="value"
-        />
-      </template>
-
-      <!-- Errors -->
-      <template x-if="$store.validationErrors.hasError(fieldName, context)">
-        <div class="label">
-          <template
-            x-for="errMsg in $store.validationErrors.getErrors(fieldName, context)"
-            :key="errMsg"
-          >
-            <span class="label-text-alt text-error" x-text="errMsg"></span>
-          </template>
-        </div>
-      </template>
-    </div>
-  </div>
-</div>

templates/components/widgets/select_widget.html

@@ -44,7 +44,6 @@
           :class="{ 'select-error': $store.validationErrors.hasError(fieldName, context) }"
           x-model="value"
           :multiple="multiple"
-          :required="isRequired"
         >
           <option value="" :selected="!value">Select...</option>
 

templates/modals/collections/new_model_modal.html

@@ -65,11 +65,11 @@
     },
 
     get showMlrr() {
-      return this.selectedType === 'ml-relative-reasoning';
+      return this.selectedType === 'mlrr';
     },
 
     get showRbrr() {
-      return this.selectedType === 'rule-based-relative-reasoning';
+      return this.selectedType === 'rbrr';
     },
 
     get showEnviformer() {

templates/modals/collections/new_prediction_setting_modal.html

@@ -203,11 +203,11 @@
               id="model-based-prediction-setting-threshold"
               name="model-based-prediction-setting-threshold"
               class="input input-bordered w-full"
-              value="0.25"
+              placeholder="0.25"
               type="number"
               min="0"
               max="1"
-              step="any"
+              step="0.05"
             />
           </div>
 

templates/modals/objects/delete_pathway_edge_modal.html

@@ -4,22 +4,6 @@
   id="delete_pathway_edge_modal"
   class="modal"
   x-data="modalForm({ state: { selectedEdge: '', imageUrl: '' } })"
-  @modal-opened.window="
-   const links = d3.selectAll('path.highlighted');
-   if (!links.empty()) {
-        const el = links.node();
-        const selectElement = document.getElementById('delete_pathway_edge_edges');
-        console.log(el);
-        console.log(el.__data__);
-        for (let option of selectElement.options) {
-            if (option.value === el.__data__.url) {
-                option.selected = true;
-                break;
-            }
-        }
-        selectElement.dispatchEvent(new Event('change'));
-   }
-  "
   @close="reset()"
 >
   <div class="modal-box">

templates/modals/objects/delete_pathway_node_modal.html

@@ -4,19 +4,6 @@
   id="delete_pathway_node_modal"
   class="modal"
   x-data="modalForm({ state: { selectedNode: '', imageUrl: '' } })"
-  @modal-opened.window="
-   const el = d3.select('circle.highlighted').node();
-   if (el !== null) {
-    const selectElement = document.getElementById('delete_pathway_node_nodes');
-    for (let option of selectElement.options) {
-        if (option.value === el.__data__.url) {
-            option.selected = true;
-            break;
-        }
-    }
-    selectElement.dispatchEvent(new Event('change'));
-   }
-  "
   @close="reset()"
 >
   <div class="modal-box">

templates/objects/compound.html

@@ -1,5 +1,4 @@
 {% extends "framework_modern.html" %}
-{% load envipytags %}
 
 {% block content %}
 
@@ -83,12 +82,6 @@
       <div class="collapse-content">{{ compound.description }}</div>
     </div>
 
-    <!-- Extension Slot for Viz -->
-    {% epdb_slot_templates "epdb.objects.compound.viz" as viz_templates %}
-    {% for tpl in viz_templates %}
-      {% include tpl %}
-    {% endfor %}
-
     <!-- Image Representation -->
     <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />

templates/objects/compound_structure.html

@@ -1,5 +1,4 @@
 {% extends "framework_modern.html" %}
-{% load envipytags %}
 
 {% block content %}
 
@@ -51,12 +50,6 @@
       </div>
     </div>
 
-    <!-- Extension Slot for Viz -->
-    {% epdb_slot_templates "epdb.objects.compound_structure.viz" as viz_templates %}
-    {% for tpl in viz_templates %}
-      {% include tpl %}
-    {% endfor %}
-
     <!-- Image Representation -->
     <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />

templates/objects/edge.html

@@ -92,7 +92,7 @@
         <div class="flex flex-wrap items-center justify-center gap-4">
           {% for educt in edge.start_nodes.all %}
             <a href="{{ educt.url }}" class="btn btn-outline btn-sm"
-              >{{ educt.get_name }}</a
+              >{{ educt.name }}</a
             >
           {% endfor %}
           <svg
@@ -112,7 +112,7 @@
           </svg>
           {% for product in edge.end_nodes.all %}
             <a href="{{ product.url }}" class="btn btn-outline btn-sm"
-              >{{ product.get_name }}</a
+              >{{ product.name }}</a
             >
           {% endfor %}
         </div>

templates/objects/group.html

@@ -56,9 +56,7 @@
         <ul class="menu bg-base-200 rounded-box">
           {% for um in group.user_member.all %}
             <li>
-              <a
+              <a href="{{ um.url }}" class="hover:bg-base-300"
-                href="{% if user.is_superuser %}{{ um.url }}{% else %}{{ "#" }}{% endif %}"
-                class="hover:bg-base-300"
                 >{{ um.username }}
                 {% if not um.is_active %}<i>(inactive)</i>{% endif %}</a
               >

templates/objects/node.html

@@ -1,5 +1,4 @@
 {% extends "framework_modern.html" %}
-{% load envipytags %}
 
 {% block content %}
 
@@ -55,12 +54,6 @@
       </div>
     </div>
 
-    {% epdb_slot_templates "epdb.objects.node.viz" as viz_templates %}
-
-    {% for tpl in viz_templates %}
-      {% include tpl %}
-    {% endfor %}
-
     <!-- Image Representation -->
     <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />

templates/objects/pathway.html

@@ -1,7 +1,5 @@
 {% extends "framework_modern.html" %}
 {% load static %}
-{% load envipytags %}
-
 {% block content %}
   <script src="https://d3js.org/d3.v7.min.js"></script>
   <style>
@@ -72,25 +70,12 @@
       stroke: red;
       stroke-width: 3px;
     }
-
-    .inedge {
-      stroke: red;
-      stroke-width: 3px;
-    }
-    .outedge {
-      stroke: green;
-      stroke-width: 3px;
-    }
   </style>
   <script src="{% static 'js/pw.js' %}"></script>
 
   {% block action_modals %}
     {% include "modals/objects/add_pathway_node_modal.html" %}
     {% include "modals/objects/add_pathway_edge_modal.html" %}
-    {% epdb_slot_templates "epdb.modals.objects.pathway.add" as add_templates %}
-    {% for tpl in add_templates %}
-      {% include tpl %}
-    {% endfor %}
     {% include "modals/objects/download_pathway_csv_modal.html" %}
     {% include "modals/objects/download_pathway_image_modal.html" %}
     {% include "modals/objects/identify_missing_rules_modal.html" %}
@@ -115,7 +100,7 @@
     </div>
 
     <!-- Graphical Representation -->
-    <div class="collapse-arrow bg-base-200 collapse overflow-y-auto">
+    <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />
       <div class="collapse-title text-xl font-medium">
         Graphical Representation
@@ -149,7 +134,7 @@
                 </div>
                 <ul
                   tabindex="0"
-                  class="dropdown-content menu bg-base-100 rounded-box z-50 w-96 p-2"
+                  class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
                 >
                   {% include "actions/objects/pathway.html" %}
                 </ul>
@@ -376,18 +361,6 @@
               >
                 <path d="M 0 0 L 10 5 L 0 10 z" fill="#999" />
               </marker>
-              <marker
-                id="curve-arrow"
-                viewBox="0 0 10 10"
-                refX="10"
-                refY="5"
-                markerWidth="6"
-                markerHeight="6"
-                orient="auto"
-                markerUnits="strokeWidth"
-              >
-                <path d="M 0 0 L 10 5 L 0 10 z" fill="#999" />
-              </marker>
               <marker
                 id="doublearrow"
                 viewBox="0 0 20 30"

templates/predict_pathway.html

@@ -105,7 +105,7 @@
         ></iframe>
       </div>
 
-      <label class="select mb-8 w-full" id="prediction-setting-label">
+      <label class="select mb-8 w-full">
         <span class="label">Predictor</span>
         <select id="prediction-setting" name="prediction-setting">
           <option disabled>Select a Setting</option>
@@ -148,21 +148,6 @@
   </div>
   {# prettier-ignore-start #}
   <script>
-    // Hide predictor selection and update button text if mode is "build"
-    function radioChange(event) {
-      if (event.target.value === "build") {
-        document.getElementById("prediction-setting-label").hidden = true;
-        document.getElementById("predict-submit-button").innerText = "Build";
-      } else {
-        document.getElementById("prediction-setting-label").hidden = false;
-        document.getElementById("predict-submit-button").innerText = "Predict";
-      }
-    }
-    const radioButtons = document.querySelectorAll('input[name="predict"]');
-    radioButtons.forEach(radio => {
-      radio.addEventListener('change', radioChange);
-    });
-
     // Helper function to safely get Ketcher instance from iframe
     function getKetcherInstance(iframeId) {
       const ketcherFrame = document.getElementById(iframeId);
@@ -212,13 +197,7 @@
         e.preventDefault();
         const button = this;
         button.disabled = true;
-
+        button.textContent = "Predicting...";
-        // Set text depending on mode
-        if (document.getElementById("predict-submit-button").innerText === "Build") {
-          button.textContent = "Building...";
-        } else {
-          button.textContent = "Predicting...";
-        }
 
         // Get SMILES from either input or Ketcher
         const smilesInput = document.getElementById("predict-smiles");

tests/test_compound_model.py

@@ -1,7 +1,5 @@
 from django.conf import settings as s
 from django.test import TestCase, override_settings
-
-from epdb.exceptions import InvalidSMILESException
 from epdb.logic import PackageManager
 from epdb.models import Compound, User, CompoundStructure
 
@@ -35,13 +33,13 @@ class CompoundTest(TestCase):
         self.assertEqual(c.description, "No Desc")
 
     def test_missing_smiles(self):
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Compound.create(self.package, smiles=None, name="Afoxolaner", description="No Desc")
 
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Compound.create(self.package, smiles="", name="Afoxolaner", description="No Desc")
 
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Compound.create(self.package, smiles="  ", name="Afoxolaner", description="No Desc")
 
     def test_smiles_are_trimmed(self):
@@ -98,7 +96,7 @@ class CompoundTest(TestCase):
         self.assertEqual(len(self.package.compounds), 1)
 
     def test_wrong_smiles(self):
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Compound.create(
                 self.package,
                 smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",

tests/test_reaction_model.py

@@ -1,7 +1,6 @@
 from django.conf import settings as s
 from django.test import TestCase, override_settings
 
-from epdb.exceptions import InvalidSMILESException
 from epdb.logic import PackageManager
 from epdb.models import Compound, User, Reaction, Rule
 
@@ -164,7 +163,7 @@ class ReactionTest(TestCase):
         self.assertEqual(len(self.package.reactions), 1)
 
     def test_wrong_smiles(self):
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Reaction.create(
                 package=self.package,
                 name="Eawag BBD reaction r0001",

tests/views/test_model_views.py

@@ -46,14 +46,6 @@ class ModelViewTest(TestCase):
         )
 
         expected = [
-            {
-                "products": [["CCN(CC)C(=O)C1=CC(C=O)=CC=C1"]],
-                "probability": 0.75,
-                "btrule": {
-                    "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/2f2e0c39-e109-4836-959f-2bda2524f022",
-                    "name": "bt0001-3568",
-                },
-            },
             {
                 "products": [["O=C(O)C1=CC(CO)=CC=C1", "CCNCC"]],
                 "probability": 0.25,
@@ -70,6 +62,14 @@ class ModelViewTest(TestCase):
                     "name": "bt0243-4301",
                 },
             },
+            {
+                "products": [["CCN(CC)C(=O)C1=CC(C=O)=CC=C1"]],
+                "probability": 0.75,
+                "btrule": {
+                    "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/2f2e0c39-e109-4836-959f-2bda2524f022",
+                    "name": "bt0001-3568",
+                },
+            },
         ]
 
         actual = response.json()["pred"]

utilities/chem.py

@@ -88,10 +88,6 @@ class FormatConverter(object):
     def from_smiles(smiles):
         return Chem.MolFromSmiles(smiles)
 
-    @staticmethod
-    def from_molfile(molfile: str):
-        return Chem.MolFromMolBlock(molfile)
-
     @staticmethod
     def to_smiles(mol, canonical=False):
         return Chem.MolToSmiles(mol, canonical=canonical)
@@ -175,17 +171,12 @@ class FormatConverter(object):
             try:
                 Chem.Kekulize(mol)
             except Exception:
-                mol = Chem.Mol(mol.ToBinary())
+                mc = Chem.Mol(mol.ToBinary())
 
-        if not mol.GetNumConformers():
+        if not mc.GetNumConformers():
-            Chem.rdDepictor.Compute2DCoords(mol)
+            Chem.rdDepictor.Compute2DCoords(mc)
 
-        drawer = rdMolDraw2D.MolDraw2DCairo(*mol_size)
+        pass
-        opts = drawer.drawOptions()
-        opts.clearBackground = False
-        drawer.DrawMolecule(mol)
-        drawer.FinishDrawing()
-        return drawer.GetDrawingText()
 
     @staticmethod
     def normalize(smiles):

utilities/legacy.py

@@ -64,7 +64,7 @@
 
 import logging
 
-from envipy_additional_information import HalfLife, HalfLifeWS, HalfLifeModel
+from envipy_additional_information import HalfLife, HalfLifeWS
 from envipy_additional_information.information import Interval
 from envipy_additional_information.parsers import (
     AcidityParser,
@@ -125,7 +125,6 @@ from envipy_additional_information.parsers import (
     LiquidMatrixSourceParser,
     OxygenUptakeRateParser,
     InitiatingOrganismParser,
-    PFASConfidenceParser,
 )
 
 logger = logging.getLogger(__name__)
@@ -142,7 +141,7 @@ def get_parameter(request, paramname):
     res = request.POST.get(paramname)
     if res is not None and res.strip() != "":
         return res
-    raise ValueError("Not all parameters are set!")
+    return ValueError("Not all parameters are set!")
 
 
 def get_parameter_or_empty_string(request, paramname):
@@ -474,12 +473,17 @@ def build_additional_information_from_request(request, type_):
 
             comment = get_parameter_or_empty_string(request, "comment")
             source = get_parameter_or_empty_string(request, "source")
-            # first_order = get_parameter_or_empty_string(request, "firstOrder")
+            first_order = get_parameter_or_empty_string(request, "firstOrder")
             model = get_parameter_or_empty_string(request, "model")
             fit = get_parameter_or_empty_string(request, "fit")
 
-            if model:
+            if first_order != "":
-                model = HalfLifeModel(model.upper())
+                if model != "":
+                    raise ValueError("not both, model and firstOrder can be set!")
+                if first_order == "true":
+                    model = "SFO"
+                else:
+                    logger.info("firstOrder is set to false which is not meaningful")
 
             return HalfLife(model=model, fit=fit, comment=comment, dt50=i, source=source)
 
@@ -504,10 +508,6 @@ def build_additional_information_from_request(request, type_):
             comment_ws = get_parameter_or_empty_string(request, "comment_ws")
             source_ws = get_parameter_or_empty_string(request, "source_ws")
             model_ws = get_parameter_or_empty_string(request, "model_ws")
-
-            if model_ws:
-                model_ws = HalfLifeModel(model_ws.upper())
-
             fit_ws = get_parameter_or_empty_string(request, "fit_ws")
 
             dt50_total = IntervalParser.from_string(hl_ws_total)
@@ -674,8 +674,7 @@ def build_additional_information_from_request(request, type_):
         elif type_ == "studywst":
             # study_wst_cond = get_parameter(request, "studywstcond")
             raise ValueError("studywstcond is not yet implemented")
-        elif type_ == "pfasconfidence":
+
-            return PFASConfidenceParser.from_string(get_parameter(request, "level"))
         else:
             raise ValueError(f"No corresponding AdditionalInformation for {type_} found!")
 

utilities/misc.py

@@ -6,15 +6,12 @@ import logging
 import uuid
 from collections import defaultdict
 from datetime import datetime
-from typing import Any, Dict, List, Optional, TYPE_CHECKING
+from typing import Any, Dict, List, TYPE_CHECKING
 
 from django.conf import settings as s
 from django.db import transaction
-from ninja import Schema
-from pydantic import HttpUrl
 
 from epdb.models import (
-    AdditionalInformation,
     Compound,
     CompoundStructure,
     Edge,
@@ -31,6 +28,7 @@ from epdb.models import (
     Rule,
     RuleBasedRelativeReasoning,
     Scenario,
+    SequentialRule,
     Setting,
     SimpleAmbitRule,
     SimpleRDKitRule,
@@ -45,235 +43,408 @@ if TYPE_CHECKING:
     from epdb.logic import SPathway
 
 
-class LicenseExportSchema(Schema):
-    cc_string: str
-    link: HttpUrl
-    image_link: HttpUrl
-
-
-##############
-# RefSchemas #
-##############
-class RefExportSchema(Schema):
-    uuid: str
-    url: str
-
-    @staticmethod
-    def resolve_uuid(obj):
-        value = obj.get("uuid") if isinstance(obj, dict) else obj.uuid
-        return str(value)
-
-
-class RefCompoundExportSchema(RefExportSchema): ...
-
-
-class RefCompoundStructureExportSchema(RefExportSchema): ...
-
-
-class RefReactionExportSchema(RefExportSchema): ...
-
-
-class RefRuleExportSchema(RefExportSchema): ...
-
-
-class RefNodeExportSchema(RefExportSchema): ...
-
-
-class RefEdgeExportSchema(RefExportSchema): ...
-
-
-class RefPathwayExportSchema(RefExportSchema): ...
-
-
-class RefScenarioExportSchema(RefExportSchema): ...
-
-
-############
-# Compound #
-############
-class CompoundExportSchema(RefCompoundExportSchema):
-    name: str
-    description: str
-    aliases: List[str]
-    default_structure: RefCompoundStructureExportSchema
-    structures: List["CompoundStructureExportSchema"]
-    scenarios: List[RefScenarioExportSchema]
-
-
-class CompoundStructureExportSchema(RefCompoundStructureExportSchema):
-    name: str
-    description: str
-    aliases: List[str]
-    smiles: str
-    molfile: Optional[str]
-    normalized_structure: bool
-    scenarios: List[RefScenarioExportSchema]
-
-
-############
-# Reaction #
-############
-class ReactionExportSchema(RefReactionExportSchema):
-    name: str
-    description: str
-    aliases: List[str]
-    educts: List[RefCompoundStructureExportSchema]
-    products: List[RefCompoundStructureExportSchema]
-    rules: List[RefRuleExportSchema]
-    multi_step: bool
-    medline_references: List[str] | None
-    scenarios: List[RefScenarioExportSchema]
-
-
-#########
-# Rules #
-#########
-class RuleExportSchema(RefRuleExportSchema):
-    name: str
-    description: str
-    aliases: List[str]
-    smirks: str
-    reactant_filter_smarts: Optional[str]
-    product_filter_smarts: Optional[str]
-    scenarios: List[RefScenarioExportSchema]
-
-
-class ParallelRuleExportSchema(RefRuleExportSchema):
-    name: str
-    description: str
-    aliases: List[str]
-    simple_rules: List[RefRuleExportSchema]
-    scenarios: List[RefScenarioExportSchema]
-
-
-###########################
-# Pathway / Nodes / Edges #
-###########################
-class NodeExportSchema(RefNodeExportSchema):
-    name: str
-    description: str
-    aliases: List[str]
-    default_node_label: RefCompoundStructureExportSchema
-    node_labels: List[RefCompoundStructureExportSchema]
-    depth: int
-    stereo_removed: bool
-    scenarios: List[RefScenarioExportSchema]
-
-
-class EdgeExportSchema(RefEdgeExportSchema):
-    name: str
-    description: str
-    aliases: List[str]
-    edge_label: RefReactionExportSchema
-    start_nodes: List[RefNodeExportSchema]
-    end_nodes: List[RefNodeExportSchema]
-    scenarios: List[RefScenarioExportSchema]
-
-
-class PathwayExportSchema(RefPathwayExportSchema):
-    name: str
-    description: str
-    aliases: List[str]
-    predicted: bool
-    nodes: List[NodeExportSchema]
-    edges: List[EdgeExportSchema]
-    scenarios: List[RefScenarioExportSchema]
-
-
-class ScenarioExportSchema(RefScenarioExportSchema):
-    name: str
-    description: str
-    scenario_date: str
-    scenario_type: str
-
-
-class AdditionalInformationExportSchema(RefExportSchema):
-    type: str
-    data: dict
-    scenario: RefScenarioExportSchema | None = None
-    attach_object: RefExportSchema | None = None
-
-    @staticmethod
-    def resolve_attach_object(obj):
-        if isinstance(obj, dict):
-            if obj.get("attach_object") is None:
-                return None
-            return RefExportSchema.model_validate(obj["attach_object"])
-        return obj.content_object
-
-
-###########
-# Package #
-###########
-class PackageExportSchema(Schema):
-    name: str
-    description: str
-    uuid: str
-    reviewed: bool
-    license: LicenseExportSchema | None
-    compounds: List[CompoundExportSchema]
-    reactions: List[ReactionExportSchema]
-    simple_rules: List[RuleExportSchema]
-    composite_rules: List[ParallelRuleExportSchema]
-    pathways: List[PathwayExportSchema]
-    scenarios: List[ScenarioExportSchema]
-    additional_information: List[AdditionalInformationExportSchema]
-
-    @staticmethod
-    def resolve_uuid(obj):
-        value = obj.get("uuid") if isinstance(obj, dict) else obj.uuid
-        return str(value)
-
-    @staticmethod
-    def resolve_simple_rules(obj):
-        if isinstance(obj, dict):
-            result = []
-            for r in obj.get("simple_rules", []):
-                result.append(RuleExportSchema.model_validate(r))
-            return result
-        return SimpleAmbitRule.objects.filter(package=obj)
-
-    @staticmethod
-    def resolve_composite_rules(obj):
-        if isinstance(obj, dict):
-            result = []
-            for r in obj.get("composite_rules", []):
-                result.append(ParallelRuleExportSchema.model_validate(r))
-            return result
-        return ParallelRule.objects.filter(package=obj)
-
-    @staticmethod
-    def resolve_additional_information(obj):
-        if isinstance(obj, dict):
-            result = []
-            for ai in obj.get("additional_information", []):
-                result.append(AdditionalInformationExportSchema.model_validate(ai))
-            return result
-        return AdditionalInformation.objects.filter(package=obj)
-
-
 class PackageExporter:
-    def __init__(self, package: Package):
+    def __init__(
+        self,
+        package: Package,
+        include_models: bool = False,
+        include_external_identifiers: bool = True,
+    ):
         self._raw_package = package
+        self.include_modes = include_models
+        self.include_external_identifiers = include_external_identifiers
 
     def do_export(self):
-        return PackageExporter._export_package_as_json(self._raw_package)
+        return PackageExporter._export_package_as_json(
+            self._raw_package, self.include_modes, self.include_external_identifiers
+        )
 
     @staticmethod
-    def _export_package_as_json(package: Package) -> Dict[str, Any]:
+    def _export_package_as_json(
+        package: Package, include_models: bool = False, include_external_identifiers: bool = True
+    ) -> Dict[str, Any]:
         """
         Dumps a Package and all its related objects as JSON.
 
         Args:
             package: The Package instance to dump
+            include_models: Whether to include EPModel objects
+            include_external_identifiers: Whether to include external identifiers
 
         Returns:
             Dict containing the complete package data as JSON-serializable structure
         """
 
-        data = PackageExportSchema.from_orm(package)
+        def serialize_base_object(
+            obj, include_aliases: bool = True, include_scenarios: bool = True
+        ) -> Dict[str, Any]:
+            """Serialize common EnviPathModel fields"""
+            base_dict = {
+                "uuid": str(obj.uuid),
+                "name": obj.name,
+                "description": obj.description,
+                "url": obj.url,
+                "kv": obj.kv,
+            }
 
-        return data.model_dump(mode="json")
+            # Add aliases if the object has them
+            if include_aliases and hasattr(obj, "aliases"):
+                base_dict["aliases"] = obj.aliases
+
+            # Add scenarios if the object has them
+            if include_scenarios and hasattr(obj, "scenarios"):
+                base_dict["scenarios"] = [
+                    {"uuid": str(s.uuid), "url": s.url} for s in obj.scenarios.all()
+                ]
+
+            return base_dict
+
+        def serialize_external_identifiers(obj) -> List[Dict[str, Any]]:
+            """Serialize external identifiers for an object"""
+            if not include_external_identifiers or not hasattr(obj, "external_identifiers"):
+                return []
+
+            identifiers = []
+            for ext_id in obj.external_identifiers.all():
+                identifier_dict = {
+                    "uuid": str(ext_id.uuid),
+                    "database": {
+                        "uuid": str(ext_id.database.uuid),
+                        "name": ext_id.database.name,
+                        "base_url": ext_id.database.base_url,
+                    },
+                    "identifier_value": ext_id.identifier_value,
+                    "url": ext_id.url,
+                    "is_primary": ext_id.is_primary,
+                }
+                identifiers.append(identifier_dict)
+            return identifiers
+
+        # Start with the package itself
+        result = serialize_base_object(package, include_aliases=True, include_scenarios=True)
+        result["reviewed"] = package.reviewed
+
+        # # Add license information
+        # if package.license:
+        #     result['license'] = {
+        #         'uuid': str(package.license.uuid),
+        #         'name': package.license.name,
+        #         'link': package.license.link,
+        #         'image_link': package.license.image_link
+        #     }
+        # else:
+        #     result['license'] = None
+
+        # Initialize collections
+        result.update(
+            {
+                "compounds": [],
+                "structures": [],
+                "rules": {"simple_rules": [], "parallel_rules": [], "sequential_rules": []},
+                "reactions": [],
+                "pathways": [],
+                "nodes": [],
+                "edges": [],
+                "scenarios": [],
+                "models": [],
+            }
+        )
+
+        print(f"Exporting package: {package.name}")
+
+        # Export compounds
+        print("Exporting compounds...")
+        for compound in package.compounds.prefetch_related("default_structure").order_by("url"):
+            compound_dict = serialize_base_object(
+                compound, include_aliases=True, include_scenarios=True
+            )
+
+            if compound.default_structure:
+                compound_dict["default_structure"] = {
+                    "uuid": str(compound.default_structure.uuid),
+                    "url": compound.default_structure.url,
+                }
+            else:
+                compound_dict["default_structure"] = None
+
+            compound_dict["external_identifiers"] = serialize_external_identifiers(compound)
+            result["compounds"].append(compound_dict)
+
+        # Export compound structures
+        print("Exporting compound structures...")
+        compound_structures = (
+            CompoundStructure.objects.filter(compound__package=package)
+            .select_related("compound")
+            .order_by("url")
+        )
+
+        for structure in compound_structures:
+            structure_dict = serialize_base_object(
+                structure, include_aliases=True, include_scenarios=True
+            )
+            structure_dict.update(
+                {
+                    "compound": {
+                        "uuid": str(structure.compound.uuid),
+                        "url": structure.compound.url,
+                    },
+                    "smiles": structure.smiles,
+                    "canonical_smiles": structure.canonical_smiles,
+                    "inchikey": structure.inchikey,
+                    "normalized_structure": structure.normalized_structure,
+                    "external_identifiers": serialize_external_identifiers(structure),
+                }
+            )
+            result["structures"].append(structure_dict)
+
+        # Export rules
+        print("Exporting rules...")
+
+        # Simple rules (including SimpleAmbitRule and SimpleRDKitRule)
+        for rule in SimpleRule.objects.filter(package=package).order_by("url"):
+            rule_dict = serialize_base_object(rule, include_aliases=True, include_scenarios=True)
+
+            # Add specific fields for SimpleAmbitRule
+            if isinstance(rule, SimpleAmbitRule):
+                rule_dict.update(
+                    {
+                        "rule_type": "SimpleAmbitRule",
+                        "smirks": rule.smirks,
+                        "reactant_filter_smarts": rule.reactant_filter_smarts or "",
+                        "product_filter_smarts": rule.product_filter_smarts or "",
+                    }
+                )
+            elif isinstance(rule, SimpleRDKitRule):
+                rule_dict.update(
+                    {"rule_type": "SimpleRDKitRule", "reaction_smarts": rule.reaction_smarts}
+                )
+            else:
+                rule_dict["rule_type"] = "SimpleRule"
+
+            result["rules"]["simple_rules"].append(rule_dict)
+
+        # Parallel rules
+        for rule in (
+            ParallelRule.objects.filter(package=package)
+            .prefetch_related("simple_rules")
+            .order_by("url")
+        ):
+            rule_dict = serialize_base_object(rule, include_aliases=True, include_scenarios=True)
+            rule_dict["rule_type"] = "ParallelRule"
+            rule_dict["simple_rules"] = [
+                {"uuid": str(sr.uuid), "url": sr.url} for sr in rule.simple_rules.all()
+            ]
+            result["rules"]["parallel_rules"].append(rule_dict)
+
+        # Sequential rules
+        for rule in (
+            SequentialRule.objects.filter(package=package)
+            .prefetch_related("simple_rules")
+            .order_by("url")
+        ):
+            rule_dict = serialize_base_object(rule, include_aliases=True, include_scenarios=True)
+            rule_dict["rule_type"] = "SequentialRule"
+            rule_dict["simple_rules"] = [
+                {
+                    "uuid": str(sr.uuid),
+                    "url": sr.url,
+                    "order_index": sr.sequentialruleordering_set.get(
+                        sequential_rule=rule
+                    ).order_index,
+                }
+                for sr in rule.simple_rules.all()
+            ]
+            result["rules"]["sequential_rules"].append(rule_dict)
+
+        # Export reactions
+        print("Exporting reactions...")
+        for reaction in package.reactions.prefetch_related("educts", "products", "rules").order_by(
+            "url"
+        ):
+            reaction_dict = serialize_base_object(
+                reaction, include_aliases=True, include_scenarios=True
+            )
+            reaction_dict.update(
+                {
+                    "educts": [{"uuid": str(e.uuid), "url": e.url} for e in reaction.educts.all()],
+                    "products": [
+                        {"uuid": str(p.uuid), "url": p.url} for p in reaction.products.all()
+                    ],
+                    "rules": [{"uuid": str(r.uuid), "url": r.url} for r in reaction.rules.all()],
+                    "multi_step": reaction.multi_step,
+                    "medline_references": reaction.medline_references,
+                    "external_identifiers": serialize_external_identifiers(reaction),
+                }
+            )
+            result["reactions"].append(reaction_dict)
+
+        # Export pathways
+        print("Exporting pathways...")
+        for pathway in package.pathways.order_by("url"):
+            pathway_dict = serialize_base_object(
+                pathway, include_aliases=True, include_scenarios=True
+            )
+
+            # Add setting reference if exists
+            if hasattr(pathway, "setting") and pathway.setting:
+                pathway_dict["setting"] = {
+                    "uuid": str(pathway.setting.uuid),
+                    "url": pathway.setting.url,
+                }
+            else:
+                pathway_dict["setting"] = None
+
+            result["pathways"].append(pathway_dict)
+
+        # Export nodes
+        print("Exporting nodes...")
+        pathway_nodes = (
+            Node.objects.filter(pathway__package=package)
+            .select_related("pathway", "default_node_label")
+            .prefetch_related("node_labels", "out_edges")
+            .order_by("url")
+        )
+
+        for node in pathway_nodes:
+            node_dict = serialize_base_object(node, include_aliases=True, include_scenarios=True)
+            node_dict.update(
+                {
+                    "pathway": {"uuid": str(node.pathway.uuid), "url": node.pathway.url},
+                    "default_node_label": {
+                        "uuid": str(node.default_node_label.uuid),
+                        "url": node.default_node_label.url,
+                    },
+                    "node_labels": [
+                        {"uuid": str(label.uuid), "url": label.url}
+                        for label in node.node_labels.all()
+                    ],
+                    "out_edges": [
+                        {"uuid": str(edge.uuid), "url": edge.url} for edge in node.out_edges.all()
+                    ],
+                    "depth": node.depth,
+                }
+            )
+            result["nodes"].append(node_dict)
+
+        # Export edges
+        print("Exporting edges...")
+        pathway_edges = (
+            Edge.objects.filter(pathway__package=package)
+            .select_related("pathway", "edge_label")
+            .prefetch_related("start_nodes", "end_nodes")
+            .order_by("url")
+        )
+
+        for edge in pathway_edges:
+            edge_dict = serialize_base_object(edge, include_aliases=True, include_scenarios=True)
+            edge_dict.update(
+                {
+                    "pathway": {"uuid": str(edge.pathway.uuid), "url": edge.pathway.url},
+                    "edge_label": {"uuid": str(edge.edge_label.uuid), "url": edge.edge_label.url},
+                    "start_nodes": [
+                        {"uuid": str(node.uuid), "url": node.url} for node in edge.start_nodes.all()
+                    ],
+                    "end_nodes": [
+                        {"uuid": str(node.uuid), "url": node.url} for node in edge.end_nodes.all()
+                    ],
+                }
+            )
+            result["edges"].append(edge_dict)
+
+        # Export scenarios
+        print("Exporting scenarios...")
+        for scenario in package.scenarios.order_by("url"):
+            scenario_dict = serialize_base_object(
+                scenario, include_aliases=False, include_scenarios=False
+            )
+            scenario_dict.update(
+                {
+                    "scenario_date": scenario.scenario_date,
+                    "scenario_type": scenario.scenario_type,
+                    "parent": {"uuid": str(scenario.parent.uuid), "url": scenario.parent.url}
+                    if scenario.parent
+                    else None,
+                    "additional_information": scenario.additional_information,
+                }
+            )
+            result["scenarios"].append(scenario_dict)
+
+        # Export models
+        if include_models:
+            print("Exporting models...")
+            package_models = (
+                package.models.select_related("app_domain")
+                .prefetch_related("rule_packages", "data_packages", "eval_packages")
+                .order_by("url")
+            )
+
+            for model in package_models:
+                model_dict = serialize_base_object(
+                    model, include_aliases=True, include_scenarios=False
+                )
+
+                # Common fields for PackageBasedModel
+                if hasattr(model, "rule_packages"):
+                    model_dict.update(
+                        {
+                            "rule_packages": [
+                                {"uuid": str(p.uuid), "url": p.url}
+                                for p in model.rule_packages.all()
+                            ],
+                            "data_packages": [
+                                {"uuid": str(p.uuid), "url": p.url}
+                                for p in model.data_packages.all()
+                            ],
+                            "eval_packages": [
+                                {"uuid": str(p.uuid), "url": p.url}
+                                for p in model.eval_packages.all()
+                            ],
+                            "threshold": model.threshold,
+                            "eval_results": model.eval_results,
+                            "model_status": model.model_status,
+                        }
+                    )
+
+                    if model.app_domain:
+                        model_dict["app_domain"] = {
+                            "uuid": str(model.app_domain.uuid),
+                            "url": model.app_domain.url,
+                        }
+                    else:
+                        model_dict["app_domain"] = None
+
+                # Specific fields for different model types
+                if isinstance(model, RuleBasedRelativeReasoning):
+                    model_dict.update(
+                        {
+                            "model_type": "RuleBasedRelativeReasoning",
+                            "min_count": model.min_count,
+                            "max_count": model.max_count,
+                        }
+                    )
+                elif isinstance(model, MLRelativeReasoning):
+                    model_dict["model_type"] = "MLRelativeReasoning"
+                elif isinstance(model, EnviFormer):
+                    model_dict["model_type"] = "EnviFormer"
+                else:
+                    model_dict["model_type"] = "EPModel"
+
+                result["models"].append(model_dict)
+
+        print(f"Export completed for package: {package.name}")
+        print(f"- Compounds: {len(result['compounds'])}")
+        print(f"- Structures: {len(result['structures'])}")
+        print(f"- Simple rules: {len(result['rules']['simple_rules'])}")
+        print(f"- Parallel rules: {len(result['rules']['parallel_rules'])}")
+        print(f"- Sequential rules: {len(result['rules']['sequential_rules'])}")
+        print(f"- Reactions: {len(result['reactions'])}")
+        print(f"- Pathways: {len(result['pathways'])}")
+        print(f"- Nodes: {len(result['nodes'])}")
+        print(f"- Edges: {len(result['edges'])}")
+        print(f"- Scenarios: {len(result['scenarios'])}")
+        print(f"- Models: {len(result['models'])}")
+
+        return result
 
 
 class PackageImporter:

uv.lock

@@ -17,7 +17,7 @@ wheels = [
 
 [[package]]
 name = "aiohttp"
-version = "3.13.5"
+version = "3.13.3"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "aiohappyeyeballs" },
@@ -28,76 +28,76 @@ dependencies = [
     { name = "propcache" },
     { name = "yarl" },
 ]
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