Initial

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 2026-02-12 12:36
+
+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 2026-02-12 12:36
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+        ('bayer', '0001_initial'),
+        ('epdb', '0001_initial'),
+    ]
+
+    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 }} - <i>{{ package.get_classification_level_display }}</i></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.

envipath/settings.py

@@ -53,6 +53,7 @@ INSTALLED_APPS = [
     "epapi",  # API endpoints (v1, etc.)
     "epdb",
     "migration",
+    "bayer",
 ]
 
 TENANT = os.environ.get("TENANT", "public")
@@ -93,10 +94,15 @@ if os.environ.get("REGISTRATION_MANDATORY", False) == "True":
 
 ROOT_URLCONF = "envipath.urls"
 
+TEMPLATE_DIRS = [
+    os.path.join(BASE_DIR, "bayer", "templates"),
+    os.path.join(BASE_DIR, "templates"),
+]
+
 TEMPLATES = [
     {
         "BACKEND": "django.template.backends.django.DjangoTemplates",
-        "DIRS": (os.path.join(BASE_DIR, "templates"),),
+        "DIRS": TEMPLATE_DIRS,
         "APP_DIRS": True,
         "OPTIONS": {
             "context_processors": [

epdb/migrations/0001_initial.py

@@ -1,6 +1,5 @@
-# Generated by Django 5.2.1 on 2025-07-22 20:58
+# Generated by Django 5.2.7 on 2026-02-12 12:36
 
-import datetime
 import django.contrib.auth.models
 import django.contrib.auth.validators
 import django.contrib.postgres.fields
@@ -19,11 +18,12 @@ class Migration(migrations.Migration):
     dependencies = [
         ('auth', '0012_alter_user_first_name_max_length'),
         ('contenttypes', '0002_remove_content_type_name'),
+        migrations.swappable_dependency(settings.EPDB_PACKAGE_MODEL),
     ]
 
     operations = [
         migrations.CreateModel(
-            name='Compound',
+            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')),
@@ -31,9 +31,33 @@ class Migration(migrations.Migration):
                 ('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.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')),
+                ('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',
@@ -44,7 +68,9 @@ class Migration(migrations.Migration):
                 ('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)),
+                ('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={
@@ -52,6 +78,27 @@ class Migration(migrations.Migration):
                 '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=[
@@ -65,6 +112,7 @@ class Migration(migrations.Migration):
             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')),
             ],
@@ -78,8 +126,11 @@ class Migration(migrations.Migration):
                 ('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,
@@ -101,6 +152,9 @@ class Migration(migrations.Migration):
                 ('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')),
             ],
@@ -117,11 +171,34 @@ class Migration(migrations.Migration):
             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)),
+                ('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(
@@ -133,6 +210,7 @@ class Migration(migrations.Migration):
                 ('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')),
@@ -150,36 +228,6 @@ class Migration(migrations.Migration):
             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=[
@@ -191,17 +239,6 @@ class Migration(migrations.Migration):
             },
             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=[
@@ -209,10 +246,11 @@ class Migration(migrations.Migration):
                 ('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(related_name='groups_in_group', to='epdb.group', verbose_name='Group member')),
+                ('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')),
             ],
@@ -225,6 +263,41 @@ class Migration(migrations.Migration):
             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=[
@@ -234,9 +307,11 @@ class Migration(migrations.Migration):
                 ('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')),
@@ -255,38 +330,6 @@ class Migration(migrations.Migration):
             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=[
@@ -309,16 +352,6 @@ class Migration(migrations.Migration):
             },
             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=[
@@ -328,9 +361,11 @@ class Migration(migrations.Migration):
                 ('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='epdb.package', verbose_name='Package')),
+                ('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,
@@ -355,12 +390,13 @@ class Migration(migrations.Migration):
                 ('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='epdb.package', verbose_name='Package')),
+                ('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')),
             ],
@@ -368,6 +404,28 @@ class Migration(migrations.Migration):
                 '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',
@@ -382,11 +440,12 @@ class Migration(migrations.Migration):
                 ('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)),
                 ('additional_information', models.JSONField(verbose_name='Additional Information')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
                 ('parent', models.ForeignKey(default=None, null=True, on_delete=django.db.models.deletion.CASCADE, to='epdb.scenario')),
             ],
             options={
@@ -437,14 +496,16 @@ class Migration(migrations.Migration):
                 ('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='epdb.package', verbose_name='Setting Rule Packages')),
+                ('rule_packages', models.ManyToManyField(blank=True, related_name='setting_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Setting Rule Packages')),
             ],
             options={
                 'abstract': False,
@@ -461,39 +522,86 @@ class Migration(migrations.Migration):
             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',
+            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)),
-                ('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')),
+                ('multigen_eval', models.BooleanField(default=False)),
+                ('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')),
+                ('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(related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
+                ('rule_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
             ],
             options={
                 'abstract': False,
-                'base_manager_name': 'objects',
             },
             bases=('epdb.epmodel',),
         ),
         migrations.CreateModel(
-            name='ApplicabilityDomain',
+            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)),
+                ('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')),
+                ('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(related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
+                ('rule_packages', models.ManyToManyField(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.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)),
+                ('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=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
+                ('eval_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
+                ('rule_packages', models.ManyToManyField(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, 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')),
+                ('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={
-                'abstract': False,
+                '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(
@@ -558,7 +666,7 @@ class Migration(migrations.Migration):
                 ('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')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Permission on')),
             ],
             options={
                 'unique_together': {('package', 'group')},
@@ -570,7 +678,7 @@ class Migration(migrations.Migration):
             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')),
+                ('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={

epdb/migrations/0002_auto_20260212_1240.py

@@ -40,7 +40,7 @@ def set_cc(apps, schema_editor):
         row["cc_string"]: (row["lowest_pk"], row["all_pks"]) for row in license_lookup_qs
     }
 
-    Packages = apps.get_model("epdb", "Package")
+    Packages = apps.get_model("bayer", "Package")
 
     for k, v in license_lookup.items():
         # Set min pk to all packages pointing to any of the duplicates
@@ -53,7 +53,7 @@ def set_cc(apps, schema_editor):
 
 class Migration(migrations.Migration):
     dependencies = [
-        ("epdb", "0010_license_cc_string"),
+        ("epdb", "0001_initial"),
     ]
 
     operations = [migrations.RunPython(set_cc)]

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/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),
-        ),
-    ]