[Feature] Ketcher V3 (#427)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#427

.pre-commit-config.yaml

@@ -7,10 +7,10 @@ repos:
       - id: trailing-whitespace
         exclude: epiuclid/schemas/
       - id: end-of-file-fixer
-        exclude: epiuclid/schemas/
+        exclude: ^epiuclid/schemas/|^static/js/ketcher3/
       - id: check-yaml
       - id: check-added-large-files
-        exclude: ^static/images/|^epiuclid/schemas/|^fixtures/
+        exclude: ^static/images/|^epiuclid/schemas/|^fixtures/|^static/js/ketcher3/
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.13.3

Dockerfile

@@ -6,18 +6,23 @@ ENV PYTHONDONTWRITEBYTECODE=1 \
 
 WORKDIR /app
 
+
 RUN apt-get update && apt-get install -y --no-install-recommends \
     build-essential \
     libpq-dev \
     curl \
     openssh-client \
     git \
-    nodejs \
+    ca-certificates \
-    npm \
     && rm -rf /var/lib/apt/lists/*
 
-# Install pnpm
+# Install Node 22 + pnpm
-RUN npm install -g pnpm
+RUN curl -fsSL https://deb.nodesource.com/setup_22.x | bash - \
+    && 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}"
@@ -32,17 +37,17 @@ 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 ms-login --extra pepper-plugin
+    uv sync --locked --extra pepper-plugin
 
 # Now copy source and do a final sync to install the project itself
 # Ensure .dockerignore is reasonable
-COPY bayer bayer
-COPY bridge bridge
 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

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

bayer/apps.py

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

bayer/migrations/0001_initial.py

@@ -1,35 +0,0 @@
-# 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

@@ -1,22 +0,0 @@
-# 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/migrations/0003_package_data_pool.py

@@ -1,20 +0,0 @@
-# Generated by Django 6.0.3 on 2026-04-14 19:07
-
-import django.db.models.deletion
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('bayer', '0002_initial'),
-        ('epdb', '0023_alter_compoundstructure_options_and_more'),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name='package',
-            name='data_pool',
-            field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.group', verbose_name='Data pool'),
-        ),
-    ]

bayer/models.py

@@ -1,98 +0,0 @@
-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,
-    )
-
-    data_pool = models.ForeignKey("epdb.Group", on_delete=models.SET_NULL, blank=True, null=True,
-                                  verbose_name="Data pool", default=None)
-
-    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/modals/collections/new_package_modal.html

@@ -1,181 +0,0 @@
-{% load static %}
-
-<dialog
-  id="new_package_modal"
-  class="modal"
-  x-data="{
-    isSubmitting: false,
-    packageClassification: null,
-
-    reset() {
-      this.isSubmitting = false;
-      this.selectedType = '';
-      this.buildAppDomain = false;
-      this.requiresRulePackages = false;
-      this.requiresDataPackages = false;
-      this.additional_parameters = null;
-    },
-
-    setFormData(data) {
-      this.formData = data;
-    },
-
-    get isSecret() {
-      return this.packageClassification === '20';
-    },
-
-    submit(formId) {
-      const form = document.getElementById(formId);
-
-      // Remove previously injected inputs
-      form.querySelectorAll('.dynamic-param').forEach(el => el.remove());
-
-      // Add values from dynamic form into the html form
-      if (this.formData) {
-        Object.entries(this.formData).forEach(([key, value]) => {
-          const input = document.createElement('input');
-          input.type = 'hidden';
-          input.name = key;
-          input.value = value;
-          input.classList.add('dynamic-param');
-
-          form.appendChild(input);
-        });
-      }
-
-      if (form && form.checkValidity()) {
-        this.isSubmitting = true;
-        form.submit();
-      } else if (form) {
-        form.reportValidity();
-      }
-    }
-
-  }"
-  @close="reset()"
->
-  <div class="modal-box max-w-3xl">
-    <!-- Header -->
-    <h3 class="text-lg font-bold">New Package</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
-      </button>
-    </form>
-
-    <!-- Body -->
-    <div class="py-4">
-     <form
-        id="new_package_form"
-        accept-charset="UTF-8"
-        action=""
-        method="post"
-      >
-       {% csrf_token %}
-
-       <!-- Name -->
-        <div class="form-control mb-3">
-          <label class="label" for="package-name">
-            <span class="label-text">Name</span>
-          </label>
-          <input
-            id="package-name"
-            class="input input-bordered w-full"
-            name="package-name"
-            placeholder="Name"
-            required
-          />
-        </div>
-
-       <!-- Description -->
-        <div class="form-control mb-3">
-          <label class="label" for="package-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="package-description"
-            type="text"
-            class="input input-bordered w-full"
-            placeholder="Description..."
-            name="package-description"
-          />
-        </div>
-
-       <!-- Classification Level -->
-        <div class="form-control mb-3">
-          <label class="label" for="package-classification">
-            <span class="label-text">Package Classification</span>
-          </label>
-          <select
-            id="package-classification"
-            name="package-classification"
-            class="select select-bordered w-full"
-            x-model="packageClassification"
-            required
-          >
-            <option value="null" disabled selected>Select Classification</option>
-            <option value="0">Internal</option>
-            <option value="10">Restricted</option>
-            <option value="20">Secret</option>
-          </select>
-        </div>
-
-       <!-- Secret Groups -->
-        <div class="form-control mb-3" x-show="isSecret" x-cloak>
-          <label class="label" for="package-data-pool">
-            <span class="label-text">Data Pool for SECRET Package</span>
-          </label>
-          <p>Only users with this role can be granted access to this package</p>
-          <select
-            id="package-data-pool"
-            name="package-data-pool"
-            class="select select-bordered w-full"
-          >
-            <option value="" disabled selected>Select Data Pool</option>
-              {% for obj in meta.available_groups %}
-                {% if obj.secret %}
-                  <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
-                {% endif %}
-              {% endfor %}
-          </select>
-        </div>
-
-     </form>
-    </div>
-
-    <!-- Footer -->
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Cancel
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('new_package_form')"
-        :disabled="isSubmitting || !selectedType || loadingSchemas"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Creating...</span>
-      </button>
-    </div>
-  </div>
-
-  <!-- Backdrop -->
-  <form method="dialog" class="modal-backdrop">
-    <button :disabled="isSubmitting">close</button>
-  </form>
-</dialog>

bayer/templates/objects/package.html

@@ -1,97 +0,0 @@
-{% 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

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

bayer/views.py

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

bridge/contracts.py

@@ -254,7 +254,14 @@ 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):

docker-compose.dev.yml

@@ -1,15 +1,15 @@
 services:
   db:
     image: postgres:18
-    container_name: eppostgres
+    container_name: envipath-postgres
     environment:
-      POSTGRES_USER: ${POSTGRES_USER}
+      POSTGRES_USER: postgres
-      POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
+      POSTGRES_PASSWORD: postgres
-      POSTGRES_DB: ${POSTGRES_DB}
+      POSTGRES_DB: envipath
     ports:
       - "5432:5432"
     volumes:
-      - ep_bayer_postgres_data:/var/lib/postgresql
+      - postgres_data:/var/lib/postgresql
     healthcheck:
       test: ["CMD-SHELL", "pg_isready -U postgres"]
       interval: 5s
@@ -18,37 +18,9 @@ services:
 
   redis:
     image: redis:7-alpine
-    container_name: epredis
+    container_name: envipath-redis
     ports:
       - "6379:6379"
-    volumes:
-      - ep_bayer_redis_data:/data
-
-  biotransformer3:
-    image: envipath/biotransformer3:1.0
-    container_name: epbiotransformer3
-
-#  web:
-#    image: envipath/envipy-bayer:1.0
-#    container_name: epdjango
-#    ports:
-#      - "127.0.0.1:8000:8000"
-#    env_file:
-#      - .env
-#    command: gunicorn envipath.wsgi:application --bind 0.0.0.0:8000 --workers 3
-#    volumes:
-#      - ep_bayer_data:/opt/enviPy/
-
-  celery_worker:
-    image: envipath/envipy-bayer:1.0
-    container_name: epcelery
-    env_file:
-      - .env.dev
-    command: celery -A envipath worker --concurrency=6 -Q model,predict,background --pool threads
-    volumes:
-      - ep_bayer_data:/opt/enviPy/
 
 volumes:
-  ep_bayer_postgres_data:
+  postgres_data:
-  ep_bayer_redis_data:
-  ep_bayer_data:

docker-compose.yml

@@ -7,7 +7,7 @@ services:
       POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
       POSTGRES_DB: ${POSTGRES_DB}
     volumes:
-      - ep_bayer_postgres_data:/var/lib/postgresql
+      - ep_postgres_data:/var/lib/postgresql
     healthcheck:
       test: [ "CMD-SHELL", "pg_isready -U postgres" ]
       interval: 5s
@@ -18,14 +18,14 @@ services:
     image: redis:7-alpine
     container_name: epredis
     volumes:
-      - ep_bayer_redis_data:/data
+      - ep_redis_data:/data
 
   biotransformer3:
     image: envipath/biotransformer3:1.0
     container_name: epbiotransformer3
 
   web:
-    image: envipath/envipy-bayer:1.0
+    image: envipath/envipy:1.0
     container_name: epdjango
     ports:
       - "127.0.0.1:8000:8000"
@@ -33,18 +33,18 @@ services:
       - .env
     command: gunicorn envipath.wsgi:application --bind 0.0.0.0:8000 --workers 3
     volumes:
-      - ep_bayer_data:/opt/enviPy/
+      - ep_data:/opt/enviPy/
 
   celery_worker:
-    image: envipath/envipy-bayer:1.0
+    image: envipath/envipy:1.0
     container_name: epcelery
     env_file:
       - .env
     command: celery -A envipath worker --concurrency=6 -Q model,predict,background --pool threads
     volumes:
-      - ep_bayer_data:/opt/enviPy/
+      - ep_data:/opt/enviPy/
 
 volumes:
-  ep_bayer_postgres_data:
+  ep_postgres_data:
-  ep_bayer_redis_data:
+  ep_redis_data:
-  ep_bayer_data:
+  ep_data:

envipath/settings.py

@@ -9,7 +9,7 @@ https://docs.djangoproject.com/en/4.2/topics/settings/
 For the full list of settings and their values, see
 https://docs.djangoproject.com/en/4.2/ref/settings/
 """
-import json
+
 import os
 from pathlib import Path
 
@@ -20,7 +20,7 @@ from sklearn.tree import DecisionTreeClassifier
 # Build paths inside the project like this: BASE_DIR / 'subdir'.
 BASE_DIR = Path(__file__).resolve().parent.parent
 
-ENV_PATH = os.environ.get("ENV_PATH", BASE_DIR / ".env.dev")
+ENV_PATH = os.environ.get("ENV_PATH", BASE_DIR / ".env")
 print(f"Loading env from {ENV_PATH}")
 load_dotenv(ENV_PATH, override=False)
 
@@ -442,14 +442,3 @@ BIOTRANSFORMER_ENABLED = os.environ.get("BIOTRANSFORMER_ENABLED", "False") == "T
 FLAGS["BIOTRANSFORMER"] = BIOTRANSFORMER_ENABLED
 if BIOTRANSFORMER_ENABLED:
     BIOTRANSFORMER_URL = os.environ.get("BIOTRANSFORMER_URL", None)
-
-# PES
-PES_API_MAPPING = os.environ.get("PES_API_MAPPING", None)
-if PES_API_MAPPING:
-    import json
-    PES_API_MAPPING = json.loads(PES_API_MAPPING)
-else:
-    PES_API_MAPPING = {}
-
-# AD Group Mapping
-

envipath/urls.py

@@ -40,6 +40,9 @@ 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/tests/v1/test_api_permissions.py

@@ -117,25 +117,28 @@ class APIPermissionTestBase(TestCase):
 
         # Create test compounds in each package
         cls.reviewed_compound = Compound.create(
-            cls.reviewed_package, "C", "Reviewed Compound", "Test compound"
+            cls.reviewed_package, "C", name="Reviewed Compound", description="Test compound"
         )
         cls.owned_compound = Compound.create(
-            cls.unreviewed_package_owned, "CC", "Owned Compound", "Test compound"
+            cls.unreviewed_package_owned, "CC", name="Owned Compound", description="Test compound"
         )
         cls.read_compound = Compound.create(
-            cls.unreviewed_package_read, "CCC", "Read Compound", "Test compound"
+            cls.unreviewed_package_read, "CCC", name="Read Compound", description="Test compound"
         )
         cls.write_compound = Compound.create(
-            cls.unreviewed_package_write, "CCCC", "Write Compound", "Test compound"
+            cls.unreviewed_package_write, "CCCC", name="Write Compound", description="Test compound"
         )
         cls.all_compound = Compound.create(
-            cls.unreviewed_package_all, "CCCCC", "All Compound", "Test compound"
+            cls.unreviewed_package_all, "CCCCC", name="All Compound", description="Test compound"
         )
         cls.no_access_compound = Compound.create(
-            cls.unreviewed_package_no_access, "CCCCCC", "No Access Compound", "Test compound"
+            cls.unreviewed_package_no_access,
+            "CCCCCC",
+            name="No Access Compound",
+            description="Test compound",
         )
         cls.group_compound = Compound.create(
-            cls.group_package, "CCCCCCC", "Group Compound", "Test compound"
+            cls.group_package, "CCCCCCC", name="Group Compound", description="Test compound"
         )
 
 

epapi/tests/v1/test_contract_get_entities.py

@@ -294,8 +294,8 @@ class CompoundPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
         return Compound.create(
             package,
             smiles,
-            f"Reviewed Compound {idx:03d}",
+            name=f"Reviewed Compound {idx:03d}",
-            "Compound for pagination tests",
+            description="Compound for pagination tests",
         )
 
     @classmethod
@@ -305,8 +305,8 @@ class CompoundPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
         return Compound.create(
             package,
             smiles,
-            f"Draft Compound {idx:03d}",
+            name=f"Draft Compound {idx:03d}",
-            "Compound for pagination tests",
+            description="Compound for pagination tests",
         )
 
 

epapi/v1/endpoints/joblogs.py

@@ -0,0 +1,26 @@
+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/router.py

@@ -15,6 +15,7 @@ from .endpoints import (
     additional_information,
     settings,
     groups,
+    joblogs,
 )
 
 # Main router with authentication
@@ -37,6 +38,7 @@ 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

@@ -1,7 +1,10 @@
-from ninja import FilterSchema, FilterLookup, Schema
+from datetime import datetime
 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):
@@ -133,3 +136,23 @@ class GroupOutSchema(Schema):
     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

@@ -1,12 +1,32 @@
 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,
@@ -23,11 +43,7 @@ def entra_login(request):
 
 
 def entra_callback(request):
-    msal_app = msal.ConfidentialClientApplication(
+    msal_app, cache = get_msal_app_with_cache(request)
-        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:
@@ -36,11 +52,18 @@ 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["name"]
+    user_name = claims.get("name")
-    user_email = claims["emailaddress"]
+    user_email = claims.get("emailaddress", claims.get("email"))
-    user_oid = claims["oid"]
+    user_oid = claims.get("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()
@@ -57,4 +80,56 @@ def entra_callback(request):
 
     login(request, u)
 
-    return redirect("/")  # Handle errors
+    return redirect(s.SERVER_URL)  # Handle errors
+
+
+def get_access_token_from_request(request, scopes=None):
+    """
+    Get an access token from the request using MSAL token cache.
+    """
+
+    # Check if auth via Access Token
+    if request.headers.get("Authorization"):
+        return {"access_token": request.headers.get("Authorization").split(" ")[1]}
+
+    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

@@ -1,5 +1,8 @@
+import logging
+
 from django.conf import settings as s
 from django.contrib import admin
+from django.contrib import messages
 
 from .models import (
     AdditionalInformation,
@@ -29,6 +32,8 @@ from .models import (
 
 Package = s.GET_PACKAGE_MODEL()
 
+logger = logging.getLogger(__name__)
+
 
 class AdditionalInformationAdmin(admin.ModelAdmin):
     pass
@@ -45,6 +50,113 @@ 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

@@ -0,0 +1,10 @@
+class InvalidSMILESException(Exception):
+    pass
+
+
+class InvalidMolfileException(Exception):
+    pass
+
+
+class PackageImportException(Exception):
+    pass

epdb/legacy_api.py

@@ -386,23 +386,50 @@ class PackageSchema(Schema):
 
     @staticmethod
     def resolve_readers(obj: Package):
-        users = User.objects.filter(
+        readers = []
-            id__in=UserPackagePermission.objects.filter(
-                package=obj, permission=UserPackagePermission.READ[0]
-            ).values_list("user", flat=True)
-        ).distinct()
 
-        return [{u.id: u.get_name()} for u in users]
+        user_ids = UserPackagePermission.objects.filter(package=obj).values_list("user", flat=True)
+
+        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):
-        users = User.objects.filter(
+        writers = []
-            id__in=UserPackagePermission.objects.filter(
-                package=obj, permission=UserPackagePermission.WRITE[0]
-            ).values_list("user", flat=True)
-        ).distinct()
 
-        return [{u.id: u.get_name()} for u in users]
+        user_ids = UserPackagePermission.objects.filter(
+            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):
@@ -764,6 +791,7 @@ def get_package_compound_structure(request, package_uuid, compound_uuid, structu
 
 class CreateCompound(Schema):
     compoundSmiles: str
+    compoundMolFile: str | None = None
     compoundName: str | None = None
     compoundDescription: str | None = None
     inchi: str | None = None
@@ -777,9 +805,13 @@ def create_package_compound(
 ):
     try:
         p = get_package_for_write(request.user, package_uuid)
-        # inchi is not used atm
         c = Compound.create(
-            p, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
+            p,
+            c.compoundSmiles,
+            molfile=c.compoundMolFile,
+            name=c.compoundName,
+            description=c.compoundDescription,
+            inchi=c.inchi,
         )
         return redirect(c.url)
     except ValueError as e:
@@ -799,6 +831,27 @@ 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}"
 )
@@ -1325,6 +1378,7 @@ 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"
@@ -1468,6 +1522,7 @@ 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"))
             attach_obj = url_parser.get_object()
 
@@ -1491,6 +1546,33 @@ def create_package_additional_information(request, package_uuid):
                     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}")
     except ValueError:
@@ -1533,13 +1615,14 @@ 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="default_node_label.url")
+    idcomp: str = Field(None, alias="node_label_id")
-    idreact: str = Field(None, alias="default_node_label.url")
+    idreact: str = Field(None, alias="node_label_id")
     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")
+    proposed: List[Dict[str, str]] = []
-    smiles: str = Field(None, alias="default_node_label.smiles")
+    smiles: str = Field(None, alias="smiles")
+    pseudo: bool = Field(False, alias="pseudo")
 
     @staticmethod
     def resolve_atom_count(obj: Node):
@@ -1552,24 +1635,10 @@ class PathwayNode(Schema):
         # TODO
         return []
 
-    @staticmethod
-    def resolve_engineered_intermediate(obj: Node):
-        # TODO
-        return False
-
-    @staticmethod
-    def resolve_image(obj: Node):
-        return f"{obj.default_node_label.url}?image=svg"
-
     @staticmethod
     def resolve_image_size(obj: Node):
         return 400
 
-    @staticmethod
-    def resolve_proposed_intermediate(obj: Node):
-        # TODO
-        return []
-
 
 class PathwaySchema(Schema):
     aliases: List[str] = Field([], alias="aliases")
@@ -1693,6 +1762,29 @@ 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:
@@ -1798,6 +1890,7 @@ def get_package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
 class CreateNode(Schema):
     nodeAsSmiles: str
+    nodeAsMolFile: str | None = None
     nodeName: str | None = None
     nodeReason: str | None = None
     nodeDepth: str | None = None
@@ -1813,13 +1906,20 @@ 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(n.nodeDepth)
+            node_depth = int(float(n.nodeDepth))
         else:
             node_depth = -1
 
-        n = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
+        node = Node.create(
+            pw,
+            n.nodeAsSmiles,
+            node_depth,
+            molfile=n.nodeAsMolFile,
+            name=n.nodeName,
+            description=n.nodeReason,
+        )
 
-        return redirect(n.url)
+        return redirect(node.url)
     except ValueError:
         return 403, {"message": "Adding node failed!"}
 
@@ -1958,6 +2058,10 @@ 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,
@@ -1965,11 +2069,15 @@ 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 node failed!"}
+        return 403, {"message": "Adding Edge failed!"}
 
 
 @router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/edge/{uuid:edge_uuid}")
@@ -2160,3 +2268,26 @@ def get_setting(request, setting_uuid):
         return 403, {
             "message": f"Getting Setting with id {setting_uuid} failed due to insufficient rights!"
         }
+
+
+########
+# Util #
+########
+class NonPersistent(Schema):
+    smiles: str
+    setting_url: str = Field(..., alias="settingUri")
+
+
+@router.post("/util", response={200: Any, 403: Error})
+def predict(request, np: Form[NonPersistent]):
+    try:
+        from epdb.logic import SPathway
+
+        setting = SettingManager.get_setting_by_url(request.user, np.setting_url)
+        spw = SPathway(prediction_setting=setting, root_nodes=[np.smiles])
+        spw.predict()
+        return spw.to_json()
+    except ValueError:
+        return 403, {
+            "message": f"Getting Setting with id {np.setting_url} failed due to insufficient rights!"
+        }

epdb/logic.py

@@ -264,8 +264,12 @@ class GroupManager(object):
         return bool(re.findall(GroupManager.group_pattern, url))
 
     @staticmethod
-    def create_group(current_user, name, description):
+    def create_group(current_user, name, description, *args, **kwargs):
         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()
@@ -341,52 +345,17 @@ class PackageManager(object):
 
     @staticmethod
     def readable(user, package):
-        if (
+        return (
-            UserPackagePermission.objects.filter(package=package, user=user).exists()
+            PackageManager.has_package_permission(user, package, "read") | package.reviewed is True
-            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):
-        if (
+        return PackageManager.has_package_permission(user, package, "write")
-            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):
-        if (
+        return PackageManager.has_package_permission(user, package, "all")
-            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):
@@ -470,7 +439,9 @@ class PackageManager(object):
             # remove package if user is owner and package is reviewed e.g. admin
             qs = qs.filter(reviewed=False)
 
-        return qs.distinct()
+        qs = qs.distinct()
+
+        return qs
 
     @staticmethod
     def get_all_writeable_packages(user):
@@ -514,7 +485,9 @@ class PackageManager(object):
 
         qs = qs.filter(reviewed=False)
 
-        return qs.distinct()
+        qs = qs.distinct()
+
+        return qs
 
     @staticmethod
     def get_packages():
@@ -716,6 +689,10 @@ 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"]:
@@ -1018,52 +995,9 @@ 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)):
-            in_count = defaultdict(lambda: 0)
+            pw.update_depths()
-            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
@@ -1074,10 +1008,8 @@ class PackageManager(object):
         data: Dict[str, Any],
         owner: User,
         preserve_uuids=False,
-        add_import_timestamp=True,
-        trust_reviewed=False,
     ) -> Package:
-        importer = PackageImporter(data, preserve_uuids, add_import_timestamp, trust_reviewed)
+        importer = PackageImporter(data, preserve_uuids)
         imported_package = importer.do_import()
 
         up = UserPackagePermission()
@@ -1894,6 +1826,12 @@ class SPathway(object):
                 "to": to_indices,
             }
 
+            if edge.rule:
+                e["rule"] = edge.rule.simple_json()
+
+            if edge.probability:
+                e["probability"] = edge.probability
+
             edges.append(e)
 
         return {

epdb/management/commands/bootstrap.py

@@ -99,11 +99,15 @@ 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):
+    def import_package(self, data, owner, all_envipath_user_group):
-        return PackageManager.import_legacy_package(
+        p = 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,
@@ -198,7 +202,7 @@ class Command(BaseCommand):
                     s.BASE_DIR / "fixtures" / "packages" / "2025-07-18" / p, encoding="utf-8"
                 ).read()
             )
-            imported_package = self.import_package(package_data, admin)
+            imported_package = self.import_package(package_data, admin, g)
             mapping[p.replace(".json", "")] = imported_package
 
         setting = self.create_default_setting(admin, [mapping["EAWAG-BBD"]])

epdb/migrations/0001_initial.py

@@ -0,0 +1,594 @@
+# 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

@@ -0,0 +1,128 @@
+# 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

@@ -0,0 +1,228 @@
+# 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

@@ -0,0 +1,55 @@
+# 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

@@ -0,0 +1,18 @@
+# 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

@@ -0,0 +1,23 @@
+# 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

@@ -0,0 +1,53 @@
+# 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

@@ -0,0 +1,64 @@
+# 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

@@ -0,0 +1,66 @@
+# 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

@@ -0,0 +1,18 @@
+# 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

@@ -0,0 +1,59 @@
+# 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

@@ -0,0 +1,22 @@
+# 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

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

@@ -0,0 +1,17 @@
+# 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

@@ -0,0 +1,17 @@
+# 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

@@ -0,0 +1,179 @@
+# 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

@@ -0,0 +1,93 @@
+# 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

@@ -0,0 +1,132 @@
+# 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

@@ -1,741 +1,20 @@
-# Generated by Django 5.2.7 on 2026-03-06 10:51
+# Generated by Django 5.2.7 on 2026-02-23 08:45
 
-import django.contrib.auth.models
+from django.db import migrations
-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'),
+        ("epdb", "0018_auto_20260220_1203"),
-        ('contenttypes', '0002_remove_content_type_name'),
-        migrations.swappable_dependency(settings.EPDB_PACKAGE_MODEL),
     ]
 
     operations = [
-        migrations.CreateModel(
+        migrations.RemoveField(
-            name='ApplicabilityDomain',
+            model_name="scenario",
-            fields=[
+            name="additional_information",
-                ('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.CreateModel(
+        migrations.RemoveField(
-            name='Edge',
+            model_name="scenario",
-            fields=[
+            name="parent",
-                ('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

@@ -1,50 +1,49 @@
-# Generated by Django 6.0.3 on 2026-04-14 19:07
+# 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'),
+        ("epdb", "0022_alter_classifierpluginmodel_data_packages_and_more"),
     ]
 
     operations = [
         migrations.AlterModelOptions(
-            name='compoundstructure',
+            name="compoundstructure",
             options={},
         ),
         migrations.AlterModelOptions(
-            name='epmodel',
+            name="epmodel",
             options={},
         ),
         migrations.AlterModelOptions(
-            name='parallelrule',
+            name="parallelrule",
             options={},
         ),
         migrations.AlterModelOptions(
-            name='rule',
+            name="rule",
             options={},
         ),
         migrations.AlterModelOptions(
-            name='sequentialrule',
+            name="sequentialrule",
             options={},
         ),
         migrations.AlterModelOptions(
-            name='simpleambitrule',
+            name="simpleambitrule",
             options={},
         ),
         migrations.AlterModelOptions(
-            name='simplerdkitrule',
+            name="simplerdkitrule",
             options={},
         ),
         migrations.AlterModelOptions(
-            name='simplerule',
+            name="simplerule",
             options={},
         ),
         migrations.AddField(
-            model_name='group',
+            model_name="compoundstructure",
-            name='secret',
+            name="molfile",
-            field=models.BooleanField(default=False, verbose_name='Secret Group'),
+            field=models.TextField(blank=True, null=True, verbose_name="Molfile"),
         ),
     ]

epdb/migrations/0024_user_contacted.py

@@ -0,0 +1,17 @@
+# 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

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

@@ -0,0 +1,48 @@
+# 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

@@ -0,0 +1,150 @@
+# 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

@@ -31,6 +31,10 @@ from sklearn.model_selection import ShuffleSplit
 
 from bridge.contracts import Property
 from bridge.dto import RunResult, PropertyPrediction
+from epdb.exceptions import (
+    InvalidMolfileException,
+    InvalidSMILESException,
+)
 from utilities.chem import FormatConverter, IndigoUtils, PredictionResult, ProductSet
 from utilities.ml import (
     ApplicabilityDomainPCA,
@@ -75,6 +79,7 @@ class User(AbstractUser):
         blank=False,
     )
     is_reviewer = models.BooleanField(default=False)
+    contacted = models.BooleanField(null=True, blank=True)
 
     USERNAME_FIELD = "email"
     REQUIRED_FIELDS = ["username"]
@@ -203,7 +208,6 @@ class Group(TimeStampedModel):
     name = models.TextField(blank=False, null=False, verbose_name="Group name")
     owner = models.ForeignKey("User", verbose_name="Group Owner", on_delete=models.CASCADE)
     public = models.BooleanField(verbose_name="Public Group", default=False)
-    secret = models.BooleanField(verbose_name="Secret Group", default=False)
     description = models.TextField(
         blank=False, null=False, verbose_name="Descriptions", default="no description"
     )
@@ -631,7 +635,7 @@ class EnviPathModel(TimeStampedModel):
 
 class AliasMixin(models.Model):
     aliases = ArrayField(
-        models.TextField(blank=False, null=False), verbose_name="Aliases", default=list
+        models.TextField(blank=False, null=False), verbose_name="Aliases", default=list, blank=True
     )
 
     @transaction.atomic
@@ -654,7 +658,9 @@ class AliasMixin(models.Model):
 
 
 class ScenarioMixin(models.Model):
-    scenarios = models.ManyToManyField("epdb.Scenario", verbose_name="Attached Scenarios")
+    scenarios = models.ManyToManyField(
+        "epdb.Scenario", verbose_name="Attached Scenarios", blank=True
+    )
 
     @transaction.atomic
     def set_scenarios(self, scenarios: List["Scenario"]):
@@ -780,12 +786,19 @@ class Compound(
         "CompoundStructure",
         verbose_name="Default Structure",
         related_name="compound_default_structure",
-        on_delete=models.CASCADE,
+        on_delete=models.SET_NULL,
         null=True,
     )
 
     external_identifiers = GenericRelation("ExternalIdentifier")
 
+    def get_structure_by_smiles(self, smiles: str) -> "CompoundStructure":
+        for struct in self.structures.all():
+            if struct.smiles == smiles:
+                return struct
+
+        raise ValueError(f"No structure with SMILES {smiles} found for {self.get_name()}")
+
     @property
     def structures(self) -> QuerySet:
         return CompoundStructure.objects.filter(compound=self)
@@ -854,40 +867,73 @@ class Compound(
     @staticmethod
     @transaction.atomic
     def create(
-        package: "Package", smiles: str, name: str = None, description: str = None, *args, **kwargs
+        package: "Package",
+        smiles: str,
+        molfile: str | None = None,
+        name: str | None = None,
+        description: str | None = None,
+        *args,
+        **kwargs,
     ) -> "Compound":
+        # Molfile has precendence over SMILES
+        if molfile is not None and molfile.strip() != "":
+            mol = FormatConverter.from_molfile(molfile)
+
+            if mol is None:
+                raise InvalidMolfileException("Given molfile is invalid")
+            else:
+                # Overwrite SMILES from molfile
+                smiles = FormatConverter.to_smiles(mol)
+
         if smiles is None or smiles.strip() == "":
-            raise ValueError("SMILES is required")
+            raise InvalidSMILESException("SMILES is required")
 
         smiles = smiles.strip()
 
         parsed = FormatConverter.from_smiles(smiles)
         if parsed is None:
-            raise ValueError("Given SMILES is invalid")
+            raise InvalidSMILESException("Given SMILES is invalid")
-
-        standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
-
-        # Check if we find a direct match for a given SMILES
-        if CompoundStructure.objects.filter(smiles=smiles, compound__package=package).exists():
-            return CompoundStructure.objects.get(smiles=smiles, compound__package=package).compound
-
-        # Check if we can find the standardized one
-        if CompoundStructure.objects.filter(
-            smiles=standardized_smiles, compound__package=package
-        ).exists():
-            # TODO should we add a structure?
-            return CompoundStructure.objects.get(
-                smiles=standardized_smiles, compound__package=package
-            ).compound
-
-        # Generate Compound
-        c = Compound()
-        c.package = package
 
         if name is not None:
             # Clean for potential XSS
             name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
+        standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
+
+        qs = CompoundStructure.objects.filter(smiles=smiles, compound__package=package)
+
+        # Check if we find a direct match for a given SMILES
+        if qs.exists():
+            found_structure = qs.first()
+            found_compound = found_structure.compound
+
+            if name:
+                found_structure.add_alias(name)
+                found_compound.add_alias(name)
+
+            return found_compound
+
+        qs = CompoundStructure.objects.filter(smiles=standardized_smiles, compound__package=package)
+
+        # Check if we can find the standardized one
+        if qs.exists():
+            found_structure = qs.first()
+            found_compound = found_structure.compound
+
+            # We've only found the standardized one, create the very structure
+            _ = found_compound.add_structure(
+                smiles, molfile=molfile, name=name, description=description
+            )
+
+            if name:
+                found_compound.add_alias(name)
+
+            return found_compound
+
+        # Generate Compound
+        c = Compound()
+        c.package = package
+
         if name is None or name == "":
             name = f"Compound {Compound.objects.filter(package=package).count() + 1}"
 
@@ -911,7 +957,12 @@ class Compound(
             )
 
         cs = CompoundStructure.create(
-            c, smiles, name=name, description=description, normalized_structure=is_standardized
+            c,
+            smiles,
+            molfile=molfile,
+            name=name,
+            description=description,
+            normalized_structure=is_standardized,
         )
 
         c.default_structure = cs
@@ -924,11 +975,22 @@ class Compound(
         self,
         smiles: str,
         name: str = None,
+        molfile: str = None,
         description: str = None,
         default_structure: bool = False,
         *args,
         **kwargs,
     ) -> "CompoundStructure":
+        # Molfile has precendence over SMILES
+        if molfile is not None and molfile.strip() != "":
+            mol = FormatConverter.from_molfile(molfile)
+
+            if mol is None:
+                raise InvalidMolfileException("Given molfile is invalid")
+            else:
+                # Overwrite SMILES from molfile
+                smiles = FormatConverter.to_smiles(mol)
+
         if smiles is None or smiles == "":
             raise ValueError("SMILES is required")
 
@@ -948,16 +1010,28 @@ class Compound(
             )
 
         if is_standardized:
-            CompoundStructure.objects.get(smiles__in=smiles, compound__package=self.package)
+            CompoundStructure.objects.get(smiles=smiles, compound__package=self.package)
 
         # Check if we find a direct match for a given SMILES and/or its standardized SMILES
-        if CompoundStructure.objects.filter(
+        if CompoundStructure.objects.filter(smiles=smiles, compound__package=self.package).exists():
-            smiles__in=smiles, compound__package=self.package
+            found_cs = CompoundStructure.objects.get(smiles=smiles, compound__package=self.package)
-        ).exists():
+
-            return CompoundStructure.objects.get(smiles__in=smiles, compound__package=self.package)
+            if found_cs.molfile is None and (molfile is not None and molfile.strip() != ""):
+                logger.info(
+                    f"Setting molfile for found CompoundStructure(uuid={found_cs.uuid}) as it was empty"
+                )
+                found_cs.molfile = molfile
+                found_cs.save()
+
+            return found_cs
 
         cs = CompoundStructure.create(
-            self, smiles, name=name, description=description, normalized_structure=is_standardized
+            self,
+            smiles,
+            name=name,
+            molfile=molfile,
+            description=description,
+            normalized_structure=is_standardized,
         )
 
         if default_structure:
@@ -1113,6 +1187,7 @@ 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")
 
@@ -1137,10 +1212,42 @@ class CompoundStructure(
     @staticmethod
     @transaction.atomic
     def create(
-        compound: Compound, smiles: str, name: str = None, description: str = None, *args, **kwargs
+        compound: Compound,
+        smiles: str,
+        molfile: str = None,
+        name: str = None,
+        description: str = None,
+        *args,
+        **kwargs,
     ):
+        # Molfile has precendence over SMILES
+        if molfile is not None and molfile.strip() != "":
+            mol = FormatConverter.from_molfile(molfile)
+
+            if mol is None:
+                raise InvalidMolfileException("Given molfile is invalid")
+            else:
+                # Overwrite SMILES from molfile
+                smiles = FormatConverter.to_smiles(mol)
+
+        # Clean for potential XSS
+        if name is not None:
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         if CompoundStructure.objects.filter(compound=compound, smiles=smiles).exists():
-            return CompoundStructure.objects.get(compound=compound, smiles=smiles)
+            found_cs = CompoundStructure.objects.get(compound=compound, smiles=smiles)
+
+            if name:
+                found_cs.add_alias(name)
+
+            if found_cs.molfile is None and (molfile is not None and molfile.strip() != ""):
+                logger.info(
+                    f"Setting molfile for found CompoundStructure(uuid={found_cs.uuid}) as it was empty"
+                )
+                found_cs.molfile = molfile
+                found_cs.save()
+
+            return found_cs
 
         if compound.pk is None:
             raise ValueError("Unpersisted Compound! Persist compound first!")
@@ -1148,13 +1255,18 @@ class CompoundStructure(
         cs = CompoundStructure()
         # Clean for potential XSS
         if name is not None:
-            cs.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+            cs.name = name
 
-        if description is not None:
+        # We have a default here only set the value if it carries some payload
+        if description is not None and description.strip() != "":
             cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
-        cs.smiles = smiles
         cs.compound = compound
+        cs.smiles = smiles
+
+        # If molfile is not None, it hase to be a valid Molfile as we've survived the parsing check
+        if molfile is not None:
+            cs.molfile = molfile
 
         if "normalized_structure" in kwargs:
             cs.normalized_structure = kwargs["normalized_structure"]
@@ -1173,6 +1285,8 @@ 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
@@ -1209,6 +1323,9 @@ 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)
@@ -1367,6 +1484,9 @@ class SimpleAmbitRule(SimpleRule):
         if not FormatConverter.is_valid_smirks(smirks):
             raise ValueError(f'SMIRKS "{smirks}" is invalid!')
 
+        if name is not None:
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         query = SimpleAmbitRule.objects.filter(package=package, smirks=smirks)
 
         if reactant_filter_smarts is not None and reactant_filter_smarts.strip() != "":
@@ -1378,14 +1498,17 @@ class SimpleAmbitRule(SimpleRule):
         if query.exists():
             if query.count() > 1:
                 logger.error(f"More than one rule matched this one! {query}")
-            return query.first()
+
+            found_rule = query.first()
+
+            if name:
+                found_rule.add_alias(name)
+
+            return found_rule
 
         r = SimpleAmbitRule()
         r.package = package
 
-        if name is not None:
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         if name is None or name == "":
             name = f"Rule {Rule.objects.filter(package=package).count() + 1}"
 
@@ -1518,6 +1641,9 @@ class ParallelRule(Rule):
                     f"Simple rule {sr.uuid} does not belong to package {package.uuid}!"
                 )
 
+        if name is not None:
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         # Deduplication check
         query = ParallelRule.objects.annotate(
             srs_count=Count("simple_rules", filter=Q(simple_rules__in=simple_rules), distinct=True)
@@ -1529,15 +1655,19 @@ class ParallelRule(Rule):
 
         if existing_rule_qs.exists():
             if existing_rule_qs.count() > 1:
-                logger.error(f"Found more than one reaction for given input! {existing_rule_qs}")
+                logger.error(
-            return existing_rule_qs.first()
+                    f"Found more than one ParallelRule for given input! {existing_rule_qs}"
+                )
+
+            found_rule = existing_rule_qs.first()
+            if name:
+                found_rule.add_alias(name)
+
+            return found_rule
 
         r = ParallelRule()
         r.package = package
 
-        if name is not None:
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         if name is None or name == "":
             name = f"Rule {Rule.objects.filter(package=package).count() + 1}"
 
@@ -1606,10 +1736,15 @@ class Reaction(
     products = models.ManyToManyField(
         "epdb.CompoundStructure", verbose_name="Products", related_name="reaction_products"
     )
-    rules = models.ManyToManyField("epdb.Rule", verbose_name="Rule", related_name="reaction_rule")
+    rules = models.ManyToManyField(
+        "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), null=True, verbose_name="Medline References"
+        models.TextField(blank=False, null=False),
+        null=True,
+        verbose_name="Medline References",
+        blank=True,
     )
 
     external_identifiers = GenericRelation("ExternalIdentifier")
@@ -1626,8 +1761,12 @@ 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 = True,
+        multi_step: bool = False,
     ):
+        # Clean for potential XSS
+        if name is not None and name.strip() != "":
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         _educts = []
         _products = []
 
@@ -1682,16 +1821,23 @@ class Reaction(
                 logger.error(
                     f"Found more than one reaction for given input! {existing_reaction_qs}"
                 )
-            return existing_reaction_qs.first()
+
+            found_reaction = existing_reaction_qs.first()
+
+            if name:
+                found_reaction.add_alias(name)
+
+            return found_reaction
 
         r = Reaction()
         r.package = package
 
-        # Clean for potential XSS
+        if name is None or name == "":
-        if name is not None and name.strip() != "":
+            name = f"Reaction {Reaction.objects.filter(package=package).count() + 1}"
-            r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
-        if description is not None and name.strip() != "":
+        r.name = name
+
+        if description is not None and description.strip() != "":
             r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         r.multi_step = multi_step
@@ -1769,7 +1915,7 @@ class Reaction(
         return new_reaction
 
     def smirks(self):
-        return f"{'.'.join([cs.smiles for cs in self.educts.all()])}>>{'.'.join([cs.smiles for cs in self.products.all()])}"
+        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')])}"
 
     @property
     def as_svg(self):
@@ -1882,6 +2028,9 @@ 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)
@@ -1922,6 +2071,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 # add links start -> pseudo
                 new_link = {
                     "name": link["name"],
+                    "plain_name": link["plain_name"],
                     "id": link["id"],
                     "url": link["url"],
                     "image": link["image"],
@@ -1931,6 +2081,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                     "source": node_url_to_idx[link["start_node_urls"][0]],
                     "target": pseudo_idx,
                     "app_domain": link.get("app_domain", None),
+                    "to_pseudo": True,
                 }
                 adjusted_links.append(new_link)
 
@@ -1938,6 +2089,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 for target in link["end_node_urls"]:
                     new_link = {
                         "name": link["name"],
+                        "plain_name": link["plain_name"],
                         "id": link["id"],
                         "url": link["url"],
                         "image": link["image"],
@@ -1948,6 +2100,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                         "target": node_url_to_idx[target],
                         "app_domain": link.get("app_domain", None),
                         "multi_step": link["multi_step"],
+                        "from_pseudo": True,
                     }
                     adjusted_links.append(new_link)
 
@@ -2157,11 +2310,12 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
     def add_node(
         self,
         smiles: str,
-        name: Optional[str] = None,
+        molfile: str | None = None,
-        description: Optional[str] = None,
+        name: str | None = None,
-        depth: Optional[int] = 0,
+        description: str | None = None,
+        depth: int = -1,
     ):
-        return Node.create(self, smiles, depth, name=name, description=description)
+        return Node.create(self, smiles, depth, molfile=molfile, name=name, description=description)
 
     @transaction.atomic
     def add_edge(
@@ -2174,6 +2328,68 @@ 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(
@@ -2195,17 +2411,19 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
     def _url(self):
         return "{}/node/{}".format(self.pathway.url, self.uuid)
 
-    def get_name(self):
+    def get_name(self, include_suffix=True):
         non_generic_name = True
 
-        if self.name == "no name":
+        if self.name is None or self.name == "no name":
             non_generic_name = False
 
-        return (
+        if non_generic_name:
-            self.name
+            return self.name
-            if non_generic_name
+        else:
-            else f"{self.default_node_label.name} (taken from underlying structure)"
+            if include_suffix:
-        )
+                return f"{self.default_node_label.name} (taken from underlying structure)"
+            else:
+                return self.default_node_label.name
 
     def d3_json(self):
         app_domain_data = self.get_app_domain_assessment_data()
@@ -2215,16 +2433,27 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             if isinstance(ai.get(), PropertyPrediction):
                 predicted_properties[ai.get().__class__.__name__].append(ai.data)
 
-        return {
+        # If we have Subclasses of a CompoundStructure we can overwrite keys (e.g. images)
+        # 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.smiles, width=40, height=40
+                self.default_node_label.molfile
+                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(),
+            "plain_name": self.get_name(include_suffix=False),
             "smiles": self.default_node_label.smiles,
             "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
             "app_domain": {
@@ -2235,49 +2464,73 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             },
             "predicted_properties": predicted_properties,
             "is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
+            "proposed": self.get_proposed_info(),
             "timeseries": self.get_timeseries_data(),
+            **structure_data,
         }
 
+        return res
+
     @staticmethod
     @transaction.atomic
     def create(
         pathway: "Pathway",
         smiles: str,
         depth: int,
-        name: Optional[str] = None,
+        molfile: str | None = None,
-        description: Optional[str] = None,
+        name: str | None = None,
+        description: str | None = None,
     ):
+        # Molfile has precendence over SMILES
+        if molfile is not None and molfile.strip() != "":
+            mol = FormatConverter.from_molfile(molfile)
+
+            if mol is None:
+                raise InvalidMolfileException("Given molfile is invalid")
+            else:
+                # Overwrite SMILES from molfile
+                smiles = FormatConverter.to_smiles(mol)
+
         stereo_removed = False
         if pathway.predicted and FormatConverter.has_stereo(smiles):
             smiles = FormatConverter.standardize(smiles, remove_stereo=True)
             stereo_removed = True
 
-        c = Compound.create(pathway.package, smiles, name=name, description=description)
+        c = Compound.create(
+            pathway.package, smiles, molfile=molfile, name=name, description=description
+        )
 
-        if Node.objects.filter(pathway=pathway, default_node_label=c.default_structure).exists():
+        structure = c.get_structure_by_smiles(smiles)
-            return Node.objects.get(pathway=pathway, default_node_label=c.default_structure)
+
+        if Node.objects.filter(pathway=pathway, default_node_label=structure).exists():
+            return Node.objects.get(pathway=pathway, default_node_label=structure)
 
         n = Node()
         n.stereo_removed = stereo_removed
         n.pathway = pathway
         n.depth = depth
 
-        n.default_node_label = c.default_structure
+        n.default_node_label = structure
         n.save()
 
-        n.node_labels.add(c.default_structure)
+        n.node_labels.add(structure)
         n.save()
 
         return n
 
     @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.__class__.__name__ == "OECD301FTimeSeries":
+            if ai.type == "OECD301FTimeSeries":
-                return ai.model_dump(mode="json")
+                return ai.get().model_dump(mode="json")
 
         return None
 
@@ -2308,13 +2561,35 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return res
 
+    def get_proposed_info(self):
+        collected = defaultdict(dict)
+        for ai in self.additional_information.filter(
+            type__in=["ProposedIntermediate", "TransformationProductImportance", "Confidence"],
+            scenario__isnull=False,
+        ):
+            collected[str(ai.scenario.uuid)]["scenarioId"] = ai.scenario.url
+            collected[str(ai.scenario.uuid)]["scenarioName"] = ai.scenario.name
+
+            if ai.type == "ProposedIntermediate":
+                collected[str(ai.scenario.uuid)]["proposed"] = True
+
+            if ai.type == "Confidence":
+                collected[str(ai.scenario.uuid)]["Confidence"] = ai.get().level
+
+            if ai.type == "TransformationProductImportance":
+                collected[str(ai.scenario.uuid)]["Transformation product importance"] = (
+                    ai.get().importance.value
+                )
+
+        return list(collected.values())
+
 
 class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
     pathway = models.ForeignKey(
         "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.SET_NULL
+        "epdb.Reaction", verbose_name="Edge label", null=True, on_delete=models.CASCADE
     )
     start_nodes = models.ManyToManyField(
         "epdb.Node", verbose_name="Start Nodes", related_name="edge_educts"
@@ -2329,6 +2604,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
     def d3_json(self):
         edge_json = {
             "name": self.get_name(),
+            "plain_name": self.get_name(include_suffix=False),
             "id": self.url,
             "url": self.url,
             "image": self.url + "?image=svg",
@@ -2393,6 +2669,8 @@ 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
@@ -2422,7 +2700,7 @@ 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=False,
+            multi_step=kwargs.get("multi_step", False),
         )
 
         e.edge_label = r
@@ -2441,17 +2719,19 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return res
 
-    def get_name(self):
+    def get_name(self, include_suffix=True):
         non_generic_name = True
 
         if self.name == "no name":
             non_generic_name = False
 
-        return (
+        if non_generic_name:
-            self.name
+            return self.name
-            if non_generic_name
+        else:
-            else f"{self.edge_label.name} (taken from underlying reaction)"
+            if include_suffix:
-        )
+                return f"{self.edge_label.name} (taken from underlying reaction)"
+            else:
+                return self.edge_label.name
 
 
 class EPModel(PolymorphicModel, EnviPathModel, AdditionalInformationMixin):
@@ -4430,18 +4710,22 @@ class AdditionalInformation(models.Model):
 
         return f"{self.scenario.url}/additional-information/{self.uuid}"
 
-    def get(self) -> "EnviPyModel":
+    @staticmethod
+    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[self.type](**self.data)
+            inst = MAPPING[ai_type](**ai_data)
         except Exception as e:
-            print(f"Error loading {self.type}: {e}")
+            print(f"Error loading {ai_type}: {e}")
             raise e
 
-        inst.__dict__["uuid"] = str(self.uuid)
+        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

@@ -19,6 +19,7 @@ from sentry_sdk import capture_exception
 
 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
+from .exceptions import InvalidMolfileException, InvalidSMILESException
 
 from .logic import (
     EPDBURLParser,
@@ -587,38 +588,10 @@ def packages(request):
                 "package-description", s.DEFAULT_VALUES["description"]
             )
 
-            # EDIT START
-            data_pool = None
-            package_classification = request.POST.get("package-classification")
-            classification = Package.Classification(int(package_classification))
-            # For SECRET we'll need a data pool which will be an additional perm check later
-            if classification == Package.Classification.SECRET:
-                package_data_pool = request.POST.get("package-data-pool")
-
-                if package_data_pool is None:
-                    return error(request, "Invalid data pool.", "Data Pool is required!")
-
-                data_pool = GroupManager.get_group_by_url(current_user, package_data_pool)
-
-                if data_pool is None:
-                    return error(request, "Invalid data pool.", "Data Pool does not exist or no access!")
-
-                if not data_pool.secret:
-                    return error(request, "Invalid data pool.", "Data Pool is not a secret group!")
-
             created_package = PackageManager.create_package(
                 current_user, package_name, package_description
             )
 
-            created_package.classification_level = classification
-
-            # Set previously determined data pool
-            if classification == Package.Classification.SECRET:
-                created_package.data_pool = data_pool
-
-            created_package.save()
-            # EDIT END
-
             return redirect(created_package.url)
 
     elif request.method == "OPTIONS":
@@ -782,6 +755,11 @@ 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": {
@@ -794,11 +772,13 @@ def models(request):
                 "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):
@@ -807,6 +787,9 @@ def models(request):
                     "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()] = {
@@ -815,12 +798,6 @@ 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":
@@ -934,11 +911,12 @@ 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):
@@ -1115,6 +1093,11 @@ 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:
@@ -1218,9 +1201,7 @@ 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(
+            pack_json = PackageManager.export_package(current_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}"'
 
@@ -1403,12 +1384,18 @@ def package_compounds(request, package_uuid):
     elif request.method == "POST":
         compound_name = request.POST.get("compound-name")
         compound_smiles = request.POST.get("compound-smiles")
+        compound_molfile = request.POST.get("compound-molfile")
         compound_description = request.POST.get("compound-description")
+
         try:
             c = Compound.create(
-                current_package, compound_smiles, compound_name, compound_description
+                current_package,
+                compound_smiles,
+                molfile=compound_molfile,
+                name=compound_name,
+                description=compound_description,
             )
-        except ValueError as e:
+        except (InvalidSMILESException, InvalidMolfileException) as e:
             raise BadRequest(str(e))
 
         return redirect(c.url)
@@ -1534,11 +1521,15 @@ def package_compound_structures(request, package_uuid, compound_uuid):
     elif request.method == "POST":
         structure_name = request.POST.get("structure-name")
         structure_smiles = request.POST.get("structure-smiles")
+        structure_molfile = request.POST.get("structure-molfile")
         structure_description = request.POST.get("structure-description")
 
         try:
             cs = current_compound.add_structure(
-                structure_smiles, structure_name, structure_description
+                structure_smiles,
+                molfile=structure_molfile,
+                name=structure_name,
+                description=structure_description,
             )
         except ValueError:
             return error(
@@ -1926,9 +1917,9 @@ def package_reactions(request, package_uuid):
     elif request.method == "POST":
         reaction_name = request.POST.get("reaction-name")
         reaction_description = request.POST.get("reaction-description")
-        reactions_smirks = request.POST.get("reaction-smirks")
+        reaction_smiles = request.POST.get("reaction-smiles")
-        educts = reactions_smirks.split(">>")[0].split(".")
+        educts = reaction_smiles.split(">>")[0].split(".")
-        products = reactions_smirks.split(">>")[1].split(".")
+        products = reaction_smiles.split(">>")[1].split(".")
 
         r = Reaction.create(
             current_package,
@@ -2109,12 +2100,14 @@ def package_pathways(request, package_uuid):
         else:
             prediction_setting = current_user.prediction_settings()
 
+        is_predict_mode = pw_mode in {"predict", "incremental"}
+
         pw = Pathway.create(
             current_package,
-            stand_smiles,
+            stand_smiles if is_predict_mode else smiles,
             name=name,
             description=description,
-            predicted=pw_mode in {"predict", "incremental"},
+            predicted=is_predict_mode,
         )
 
         # set mode
@@ -2355,8 +2348,17 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
         node_name = request.POST.get("node-name")
         node_description = request.POST.get("node-description")
 
-        node_smiles = request.POST.get("node-smiles").strip()
+        node_smiles = request.POST.get("node-smiles")
-        current_pathway.add_node(node_smiles, name=node_name, description=node_description)
+        node_molfile = request.POST.get("node-molfile")
+
+        try:
+            current_pathway.add_node(
+                node_smiles, molfile=node_molfile, 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)
 
@@ -2464,7 +2466,26 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
             return JsonResponse({"success": current_node.url})
 
-        return HttpResponseBadRequest()
+        new_node_name = request.POST.get("node-name")
+        new_node_description = request.POST.get("node-description")
+
+        if any([new_node_name, new_node_description]):
+            if new_node_name is not None and new_node_name.strip() != "":
+                new_node_name = nh3.clean(new_node_name.strip(), tags=s.ALLOWED_HTML_TAGS).strip()
+                current_node.name = new_node_name
+
+            if new_node_description is not None and new_node_description.strip() != "":
+                new_node_description = nh3.clean(
+                    new_node_description.strip(), tags=s.ALLOWED_HTML_TAGS
+                ).strip()
+                current_node.description = new_node_description
+
+            current_node.save()
+
+            return redirect(current_node.url)
+
+        return error(request, "Node update failed!", "No changes were made to the node")
+
     else:
         return HttpResponseNotAllowed(["GET", "POST"])
 
@@ -2534,6 +2555,9 @@ 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:
@@ -3105,12 +3129,21 @@ 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")
 
-        return render(request, "collections/joblog.html", context)
+        # Context for paginated template
+        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

@@ -65,6 +65,25 @@ 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)
 
@@ -109,11 +128,11 @@ def migration(request):
                         ),
                         "id": str(r.uuid),
                         "url": r.url,
-                        "status": res,
+                        "status": res or r.name in accepted_diffs,
                     }
                 )
 
-                if res:
+                if res or r.name in accepted_diffs:
                     success += 1
                 else:
                     error += 1
@@ -135,7 +154,16 @@ 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

@@ -21,5 +21,11 @@
     "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 import pyplot as plt
+        from matplotlib.figure import Figure
         from scipy import stats
 
         """
@@ -101,7 +101,8 @@ class PepperPrediction(PropertyPrediction):
         mask_red = x > vp
 
         # Plot
-        fig, ax = plt.subplots(figsize=(9, 5.5))
+        fig = Figure(figsize=(9, 5.5))
+        ax = fig.subplots()
         ax.plot(x, y, color="#1f4e79", lw=2, label="Lognormal PDF")
 
         if np.any(mask_green):
@@ -146,13 +147,12 @@ class PepperPrediction(PropertyPrediction):
         ]
         ax.legend(handles=patches, frameon=True)
 
-        plt.tight_layout()
+        fig.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

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

pnpm-workspace.yaml

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

static/css/input.css

@@ -34,3 +34,12 @@
 }
 
 @import "./daisyui-theme.css";
+
+select.select[multiple] {
+  display: block;
+  white-space: normal;
+}
+
+p a {
+  @apply underline;
+}

static/js/alpine/components/widgets.js

@@ -59,6 +59,9 @@ document.addEventListener("alpine:init", () => {
     get isEditMode() {
       return this.mode === "edit";
     },
+    get isRequired() {
+      return (this.schema.required || []).indexOf(this.fieldName) > -1
+    }
   });
 
   // Text widget
@@ -293,6 +296,34 @@ 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/alpine/pagination.js

@@ -5,6 +5,126 @@
  */
 
 document.addEventListener('alpine:init', () => {
+
+  const basePagination = (
+    items,
+    currentPage,
+    totalPages,
+    totalItems,
+    perPage,
+    isReviewed,
+    instanceId
+  ) => ({
+    items,
+    currentPage,
+    totalPages,
+    totalItems,
+    perPage,
+    isReviewed,
+    instanceId,
+
+    get paginatedItems() {
+      return this.items;
+    },
+
+    get showingStart() {
+      if (this.totalItems === 0) return 0;
+      return (this.currentPage - 1) * this.perPage + 1;
+    },
+
+    get showingEnd() {
+      if (this.totalItems === 0) return 0;
+      return Math.min((this.currentPage - 1) * this.perPage + this.items.length, this.totalItems);
+    },
+
+    nextPage() {
+      if (this.currentPage < this.totalPages) {
+        this.fetchPage(this.currentPage + 1);
+      }
+    },
+
+    prevPage() {
+      if (this.currentPage > 1) {
+        this.fetchPage(this.currentPage - 1);
+      }
+    },
+
+    goToPage(page) {
+      if (page >= 1 && page <= this.totalPages) {
+        this.fetchPage(page);
+      }
+    },
+
+    get pageNumbers() {
+      const pages = [];
+      const total = this.totalPages;
+      const current = this.currentPage;
+
+      if (total === 0) {
+        return pages;
+      }
+
+      if (total <= 7) {
+        for (let i = 1; i <= total; i++) {
+          pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
+        }
+      } else {
+        pages.push({ page: 1, isEllipsis: false, key: `${this.instanceId}-page-1` });
+
+        let rangeStart;
+        let rangeEnd;
+
+        if (current <= 4) {
+          rangeStart = 2;
+          rangeEnd = 5;
+        } else if (current >= total - 3) {
+          rangeStart = total - 4;
+          rangeEnd = total - 1;
+        } else {
+          rangeStart = current - 1;
+          rangeEnd = current + 1;
+        }
+
+        if (rangeStart > 2) {
+          pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-start` });
+        }
+
+        for (let i = rangeStart; i <= rangeEnd; i++) {
+          pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
+        }
+
+        if (rangeEnd < total - 1) {
+          pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-end` });
+        }
+
+        pages.push({ page: total, isEllipsis: false, key: `${this.instanceId}-page-${total}` });
+      }
+
+      return pages;
+    }
+  });
+
+  Alpine.data('paginatedList',
+    (items, options = {}) => ({
+      ...basePagination(items,1, 0, 0, options.perPage || 50, options.isReviewed || false, options.instanceId || Math.random().toString(36).substring(2, 9),),
+
+      init() {
+        this.fetchPage(1);
+      },
+
+      async fetchPage(page) {
+        this.totalItems = this.items.length;
+        this.totalPages = Math.ceil(this.items.length / this.perPage);
+        this.currentPage = page
+
+        const start = page * this.perPage - this.perPage;
+        const end = page * this.perPage;
+        return this.items.slice(start, end);
+      }
+
+    })
+  );
+
   Alpine.data('remotePaginatedList', (options = {}) => ({
     items: [],
     currentPage: 1,

static/js/ketcher2/DEVNOTES.md

@@ -1,57 +0,0 @@
-## Prerequisites
-
-   Stable [Node.js](https://nodejs.org) version
-
-## Build instructions
-
-    npm install
-    npm start
-
-For production build:
-
-    npm run build
-   
-You could also build only the style with command
-
-    npm run style
-
-## Indigo Service
-
-Ketcher uses Indigo Service for server operations.
-You can use `--api-path` parameter to start with it:
-
-    npm start -- --api-path=<server-url>
-For production build:
-
-    npm run build -- --api-path=<server-url>
-
-You can find the instruction for service installation
-[here](http://lifescience.opensource.epam.com/indigo/service/index.html).
-
-## Tests instructions
-
-You can start tests for input/output `.mol`-files and render.
-
-    npm test
-
-Tests are started for all structures in `test/fixtures` directory.
-
-To start the tests separately:
-
-    npm run test-io
-    npm run test-render
-
-#### Parameters
-
-You can use following parameters to start the tests:
- - `--fixtures` - for the choice of a specific directory with molecules
- - `--headless` - for start of the browser in headless mode
-
-```
-npm run test-render -- --fixtures=fixtures/super --headless
-```
-
-If you have added new structures for testing to the `test/fixtures` directory 
-you have to generate `svg` from them for correct render-test with:
-
-    npm run generate-svg    

static/js/ketcher2/LICENSE

@@ -1,184 +0,0 @@
-                               Apache License
-                         Version 2.0, January 2004
-                      http://www.apache.org/licenses/
-
- TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
-
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-
- 5. Submission of Contributions. Unless You explicitly state otherwise,
-    any Contribution intentionally submitted for inclusion in the Work
-    by You to the Licensor shall be under the terms and conditions of
-    this License, without any additional terms or conditions.
-    Notwithstanding the above, nothing herein shall supersede or modify
-    the terms of any separate license agreement you may have executed
-    with Licensor regarding such Contributions.
-
- 6. Trademarks. This License does not grant permission to use the trade
-    names, trademarks, service marks, or product names of the Licensor,
-    except as required for reasonable and customary use in describing the
-    origin of the Work and reproducing the content of the NOTICE file.
-
- 7. Disclaimer of Warranty. Unless required by applicable law or
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-    Contributor provides its Contributions) on an "AS IS" BASIS,
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-    risks associated with Your exercise of permissions under this License.
-
- 8. Limitation of Liability. In no event and under no legal theory,
-    whether in tort (including negligence), contract, or otherwise,
-    unless required by applicable law (such as deliberate and grossly
-    negligent acts) or agreed to in writing, shall any Contributor be
-    liable to You for damages, including any direct, indirect, special,
-    incidental, or consequential damages of any character arising as a
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-    Work (including but not limited to damages for loss of goodwill,
-    work stoppage, computer failure or malfunction, or any and all
-    other commercial damages or losses), even if such Contributor
-    has been advised of the possibility of such damages.
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- 9. Accepting Warranty or Additional Liability. While redistributing
-    the Work or Derivative Works thereof, You may choose to offer,
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-    on Your own behalf and on Your sole responsibility, not on behalf
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- APPENDIX: How to apply the Apache License to your work.
-    To apply the Apache License to your work, attach the following
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- Copyright 2017 EPAM Systems
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- you may not use this file except in compliance with the License.
- You may obtain a copy of the License at
-
-     http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
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- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.

static/js/ketcher2/LICENSE-history

@@ -1,5 +0,0 @@
- Ketcher version 1 was released under GNU Affero General Public License v3.0
- Ketcher version 2 was re-licensed under Apache License, Version 2.
-
- Current version is distributed by the terms of the Apache License, Version 2.
- which is included in the file LICENSE, found at the root of the Ketcher source tree.

static/js/ketcher2/NOTICE

@@ -1,19 +0,0 @@
- Ketcher
- Copyright (C) 2017 EPAM Systems
- This product includes software developed at EPAM Systems, Inc.
-
- In addition, this product contains dependencies on files licensed under:
-
- The FreeBSD Documentation License https://www.freebsd.org/copyright/freebsd-doc-license.html
- The MIT License https://opensource.org/licenses/MIT
- X11 License http://www.xfree86.org/3.3.6/COPYRIGHT2.html
- Academic Free License https://opensource.org/licenses/AFL-3.0
- Apache License, Version 1.0 http://www.apache.org/licenses/LICENSE-1.0
- Apache License, Version 2.0 http://www.apache.org/licenses/LICENSE-2.0
- The 2-Clause BSD License https://opensource.org/licenses/BSD-2-Clause
- The 3-Clause BSD License https://opensource.org/licenses/BSD-3-Clause
- ISC License (ISC) https://opensource.org/licenses/ISC
- GNU Lesser General Public License version 2.1 https://opensource.org/licenses/LGPL-2.1
- The Mozilla Public License https://opensource.org/licenses/MPL-1.0
- Public Domain https://wiki.creativecommons.org/wiki/Public_domain
- Unlicense http://unlicense.org/

static/js/ketcher2/README.md

@@ -1,35 +0,0 @@
-# EPAM Ketcher projects
-Copyright (c) 2017 EPAM Systems, Inc
-
-Ketcher is an open-source web-based chemical structure editor incorporating high performance, good portability, light weight, and ability to easily integrate into a custom web-application. Ketcher is designed for chemists, laboratory scientists and technicians who draw structures and reactions.
-
-## KEY FEATURES
-* Fast 2D structure representation that satisfies common chemical drawing standards
-* 3D structure visualization
-* Draw and edit structures using major tools: Atom Tool, Bond Tool, and Template Tool
-* Template library (including custom and user's templates)
-* Add atom and bond basic properties and query features, add aliases and Generic groups
-* Select, modify, and erase connected and unconnected atoms and bonds using Selection Tool, or using Shift key
-* Simple Structure Clean up Tool (checks bonds length, angles and spatial arrangement of atoms) and Advanced Structure Clean up Tool (+ stereochemistry checking and structure layout) 
-* Aromatize/De-aromatize Tool
-* Calculate CIP Descriptors Tool
-* Structure Check Tool
-* MW and Structure Parameters Calculate Tool 
-* Stereochemistry support during editing, loading, and saving chemical structures
-* Storing history of actions, with the ability to rollback to previous state
-* Ability to load and save structures and reactions in MDL Molfile or RXN file format, InChI String, ChemAxon Extended SMILES, ChemAxon Extended CML file formats
-* Easy to use R-Group and S-Group tools (Generic, Multiple group, SRU polymer, peratom, Data S-Group) 
-* Reaction Tool (reaction generating, manual and automatic atom-to-atom mapping) 
-* Flip/Rotate Tool
-* Zoom in/out, hotkeys, cut/copy/paste
-* OCR - ability to recognize structures at pictures (image files) and reproduce them
-* Copy and paste between different chemical editors
-* Settings support (Rendering, Displaying, Debugging)
-* Use of SVG to achieve best quality in-browser chemical structure rendering
-* Languages: JavaScript with third-party libraries
-
-## Build instructions
-Please read [DEVNOTES.md](DEVNOTES.md) for details.
-
-## License
-Please read [LICENSE](LICENSE) and [NOTICE](NOTICE) for details.

static/js/ketcher2/doc/help.md

@@ -1,570 +0,0 @@
-**Ketcher** is a tool to draw molecular structures and chemical
-reactions.
-
-# Ketcher Overview
-
-**Ketcher** is a tool to draw molecular structures and chemical
-reactions. Ketcher operates in two modes, the Server mode with most
-functions available and the client mode with limited functions
-available.
-
-**Ketcher** consists of the following elements:
-
- ![](main.png "Main window")
-
-**Note** : Depending on the screen size, some tools on the _Tool
-palette_ can be displayed in expanded or collapsed forms.
-
-Using the _Tool palette_, you can
-
-  * draw and edit a molecule or reaction by clicking on and dragging
-  atoms, bonds, and other elements provided with the buttons on the
-  _Atoms_ toolbar and _Tool palette_;
-
-  * delete any element of the drawing (atom or bond) by clicking on it
-  with the Erase tool;
-
-  * delete the entire molecule or its fragment by a lasso,
-  rectangular, or fragment selection with the Erase tool;
-
-  * draw special structures (see the following sections);
-
-  * select the entire molecule or its fragment in one of the following
-  ways (click on the button to see the list of available options):
-
-    * in the expanded form
-
-      ![](expanded.png "Expanded tool")
-
-    * in the collapsed form
-
-      ![](collapsed.png "Collapsed tool")
-
-To select one atom or bond, click Lasso or Rectangle Selection tool,
-and then click the atom or bond.
-
-To select the entire structure:
-
-  * Select the Fragment Selection tool and then click the object.
-
-  * Select the Lasso or Rectangle Selection tool, and then drag the
-  mouse to select the object.
-
-  * `Ctrl-click` with the Lasso or Rectangle Selection tool.
-
-To select multiple atoms, bonds, structures, or other objects, do one
-of the following:
-
-  * `Shift-click` with the Lasso or Rectangle Selection tool selects
-  some (connected or not) atoms/bonds.
-
-  * With the Lasso or Rectangle Selection tool click and drag the
-  mouse around the atoms, bonds, or structures that you want to
-  select.
-
-**Note** : `Ctrl+Shift-click` with the Lasso or Rectangle Selection tool
-selects several structures.
-
-You can use the buttons of the _Main_ toolbar:
-
-
- ![](toolbar.png "Tolbar")
-
-  * **Clear Canvas** (1) button to start drawing a new molecule; this
-  command clears the drawing area;
-
-  * **Open…** (2) and **Save As…** (3) buttons to import a molecule
-  from a molecular file or save it to a supported molecular file
-  format;
-
-  * **Undo** / **Redo** (4), **Cut** (5), **Copy** (6), **Paste** (7),
-  **Zoom In** / **Out** (8), and **Scaling** (9) buttons to perform
-  the corresponding actions;
-
-  * **Layout** button (10) to change the position of the structure to
-  work with it with the most convenience;
-
-  * **Clean Up** button (11) to improve the appearance of the
-  structure by assigning them uniform bond lengths and angles.
-
-  * **Aromatize** / **Dearomatize** buttons (12) to mark aromatic
-  structures (to convert a structure to the Aromatic or Kekule
-  presentation);
-
-  * **Calculate CIP** button (13) to determine R/S and E/Z
-  configurations;
-
-  * **Check Structure** button (14) to check the following properties
-  of the structure:
-
-    ![](check.png "Structure Ckeck")
-
-  * **Calculated Values** button (15) to display some properties of
-  the structure:
-
-    ![](analyse.png "Calculated Values")
-
-  * **Recognize Molecule** button (16) to recognize a structure in the
-  image file and load it to the canvas;
-
-  * **3D Viewer** button (17) to open the structure in the
-  three-dimensional Viewer;
-
-  * **Settings** button (18) to make some settings for molecular
-    files:
-    
-    ![](settings.png "Settings")
-
-  * **Help** button (19) to view Help;
-    
-  * **About** button (20) to display version and copyright information
-  of the program.
-
-**Note** : **Layout,** **Clean Up,** **Aromatize** / **Dearomatize,**
-**Calculate CIP,** **Check Structure,** **Calculated Values,**
-**Recognize Molecule** and **3D View** buttons are active only in the
-Server mode.
-
-# 3D Viewer
-
-The structure appears in a modal window after clicking on the **3D
-Viewer** button:
-
- ![](miew.png "3D Viewer")
-
-You can perform the following actions:
-
-  * Rotate the structure holding the left mouse button;
-
-  * Zoom In/Out the structure;
-
-Ketcher Settings allow to change the appearance of the structure and background coloring.
-
-"Lines" drawing method, "Bright" atom name coloring
-method and "Light" background coloring are default.
-
-# Drawing Atoms
-
-To draw/edit atoms you can:
-
-  * select an atom in the Atoms toolbar and click inside the drawing
-  area;
-
-  * if the desired atom is absent in the toolbar, click on
-  the ![](periodic-table.png) button to invoke the Periodic Table and
-  click on the desired atom (available options: _Single_ – selection
-  of a single atom, _List_ – choose an atom from the list of selected
-  options (To allow one atom from a list of atoms of your choice at
-  that position), _Not List_ - exclude any atom on your list at that
-  position).
-
-    ![](periodic-dialog.png "Periodic Table")
-
-  * add an atom to the existing molecule by selecting an atom in the
-  _Atoms_ toolbar, clicking on an atom in the molecule, and dragging
-  the cursor; the atom will be added with a single bond; vacant
-  valences will be filled with the corresponding number of hydrogen
-  atoms;
-
-  * change an atom by selecting an atom in the _Atoms_ toolbar and
-  clicking on the atom to be changed; in the case a wrong valence thus
-  appears the atom will be underlined in red;
-
-  * change an atom by clicking on an existing atom with the
-  _Selection_ tool and waiting for a couple of seconds for the text
-  box to appear; type another atom symbol in the text box:
-
-    ![](inline-edit.png "Change Atom")
-
-  * change the charge of an atom by selecting the Charge Plus or
-  Charge Minus tool and clicking consecutively on an atom to
-  increase/decrease its charge
-
-    ![](charge.png "Ions")
-
-  * change an atom or its properties by double-clicking on the atom to
-  invoke the Atom Properties dialog (the dialog also provides atom
-  query features):
-
-    ![](atom-dialog.png "Atom Properties")
-
-  * click on the Periodic Table button, open the Extended table and
-  select a corresponding Generic group or Special Node:
-
-    ![](periodic-dialog-ext.png "Generic Groups")
-
-# Drawing Bonds
-
-To draw/edit bonds you can:
-
-  * Click an arrow on the Bond tool ![](bond.png) in the Tools palette
-  to open the drop-down list with the following bond types:
-
-    ![](bonds.png)
-
-    For the full screen format, the Bond tool from the Tools palette
-    splits into three: _Single Bond,__Single Up Bond,_ and _Any
-    Bond_,which include the corresponding bond types:
-
-    ![](bond-types.png)
-
-  * select a bond type from the drop down list and click inside the
-  drawing area; a bond of the selected type will be drawn;
-
-  * click on an atom in the molecule; a bond of the selected type will
-  be added to the atom at the angle of 120 degrees;
-
-  * add a bond to the existing molecule by clicking on an atom in the
-  molecule and dragging the cursor; in this case you can set the angle
-  manually;
-
-  * change the bond type by clicking on it;
-
-  * use the Chain Tool ![](chain.png) to draw consecutive single
-  bonds;
-
-  * change a bond or its properties by double-clicking on the bond to
-  invoke the Bond Properties dialog:
-
-    ![](bond-dialog.png "Bond Properties")
-
-  * clicking on a drawn stereo bond changes its direction.
-
-  * clicking with the Single Bond tool or Chain tool switches the bond type
-  cyclically: Single-Double-Triple-Single.
-
-# Drawing R-Groups
-
-Use the _R-Group_ toolbox ![](rgroup.png) to draw R-groups in Markush
-structures:
-
- ![](rgroup-types.png)
-
-Selecting the _R-Group_ _Label_ Tool and clicking on an atom in the
-structure invokes the dialog to select the R-Group label for a current
-atom position in the structure:
-
- ![](rgroup-dialog.png)
-
-Selecting the R-Group label and clicking **OK** converts the structure
-into a Markush structure with the selected R-Group label:
-
- ![](rgroup-example1.png)
-
-**Note** : You can choose several R-Group labels simultaneously:
-
- ![](rgroup-example2.png)
-
-Particular chemical fragments that may be substituted for a given
-R-Group form a set of R-Group members. R-Group members can be any
-structural fragment, including functional groups and single atoms or
-atom lists.
-
-To create a set of R-Group members:
-
-  1. Draw a structure to become an R-Group member.
-
-  2. Select the structure using the _R-Group Fragment Tool_ to invoke
-     the R-Group dialog; in this dialog select the label of the
-     R-Group to assign the fragment to.
-
-  3. Click on **OK** to convert the structure into an R-Group member.
-
-An R-Group attachment point is the atom in an R-Group member fragment
-that attaches the fragment to the initial Markush structure.
-
-Selecting the _Attachment Point Tool_ and clicking on an atom in the
-R-Group fragment converts this atom into an attachment point. If the
-R-Group contains more than one attachment point, you can specify one
-of them as primary and the other as secondary. You can select between
-either the primary or secondary attachment point using the dialog that
-appears after clicking on the atom:
-
- ![](attpoints-dialog.png)
-
-If there are two attachment points on an R-Group member, there must be
-two corresponding attachments (bonds) to the R-Group atom that has the
-same R-Group label. Clicking on **OK** in the above dialog creates the
-attachment point.
-
-Schematically, the entire process of the R-Group member creation can
-be presented as:
-
- ![](rgroup-example3.png)
-
- ![](rgroup-example4.png)
-
-# R-Group Logic
-
-**Ketcher** enables one to add logic when using R-Groups. To access
-the R-Group logic:
-
-  1. Create an R-Group member fragment as described above.
-
-  2. Move the cursor over the entire fragment for the green frame to
-     appear, then click inside the fragment. The following dialog
-     appears:
-
-     ![](rlogic-dialog.png)
-
-  3. Specify **Occurrence** to define how many of an R-Group
-     occurs. If an R-Group atom appears several times in the initial
-     structure, you will specify **Occurrence**">n", n
-     being the number of occurrences; if it appears once, you see
-     "R1 > 0".
-
-  4. Specify H at **unoccupied** R-Group sites ( **RestH** ): check or
-     clear the checkbox.
-
-  5. Specify the logical **Condition**. Use the R-Group condition **If
-     R(i) Then** to specify whether the presence of an R-Group is
-     dependent on the presence of another R-Group.
-
-
-# Marking S-Groups
-
-To mark S-Groups, use the _S-Group tool_ ![](sgroup.png) and the
-following dialog that appears after selecting a fragment with this
-tool:
-
- ![](sgroup-dialog.png "S-Group Dialog")
-
-Available S-Group types:
-
-_Generic_
-
-Generic is a pair of brackets without any labels.
-
-_Multiple group_
-
-A Multiple group indicates a number of replications of a fragment or a part of a
-structure in contracted form.
-
-_SRU Polymer_
-
-The Structural Repeating Unit (SRU) brackets enclose the structural
-repeating of a polymer. You have three available patterns:
-head-to-tail (the default), head-to-head, and either/unknown.
-
-_Superatom_
-
-An abbreviated structure (abbreviation) is all or part of a structure
-(molecule or reaction component) that has been abbreviated to a text
-label. Structures that you abbreviate keep their chemical
-significance, but their underlying structure is hidden. The current
-version can't display contracted structures but correctly
-saves/reads them into/from files.
-
-# Data S-Groups
-
-The _Data S-Groups Tool_ ![](sdata.png) is a separate tool for
-comfortable use with the accustomed set of descriptors (like Attached
-Data in **Marvin** Editor).
-
-You can attach data to an atom, a fragment, a single bond, or a
-group. The defined set of _Names_ and _Values_ is introduced for each
-type of selected elements:
-
- ![](sdata-dialog.png)
-
-  * Select the appropriate S-Group Field Name.
-
-  * Select or type the appropriate Field Value.
-
-  * Labels can be specified as Absolute, Relative or Attached.
-
-# Changing Structure Display
-
-Use the _Flip/Rotate_ tool ![](transform.png) to change the structure
-display:
-
- ![](transform-types.png)
-
-For the full screen format, the _Flip/Rotate_ tool is split into
-separate buttons:
-
- ![](rotate.png)
-
-_Rotate Tool_
-
-This tool allows rotating objects.
-  * If some objects are selected, the tool rotates the selected objects.
-  * If no objects are selected, or all objects are selected, the tool rotates the whole canvas
-  * The default rotation step is 15 degrees. 
-  * Press and hold the Ctrl key for more gradual continuous rotation with 1 degree rotation step
-
-Select any bond on the structure and click Alt+H to rotate the structure so that the selected bond is placed horizontally.
-Select any bond on the structure and click Alt+V to rotate the structure so that the selected bond is placed vertically.
-
-_Flip Tool_
-
-This tool flips the objects horizontally or vertically.
-  * If some objects are selected, the Horizontal Flip tool (or Alt+H) flips the selected objects horizontally
-  * If no objects are selected, or all objects are selected, the Horizontal Flip tool (or Alt+H) flips each structure horizontally
-  * If some objects are selected, the Vertical Flip tool (or Alt+V) flips the selected objects vertically
-  * If no objects are selected, or all objects are selected, the Vertical Flip tool (or Alt+V) flips each structure vertically
-
-# Drawing Reactions
-
-To draw/edit reactions you can
-
-  * draw reagents and products as described above;
-  * use options of the _Reaction Arrow Tool_ ![](reaction.png) to draw an
-  arrow and pluses in the reaction equation and map same atoms in
-  reagents and products.
-
-    ![](reaction-types.png)
-
-**Note** : Reaction Auto-Mapping Tool is available only in the Server
-mode.
-
-# Templates toolbar
-
-You can add templates (rings or other predefined structures) to the
-structure using the _Templates_ toolbar together with the _Custom
-Templates_ button located at the bottom:
-
- ![](template.png)
-
-To add a ring to the molecule, select a ring from the toolbar and
-click inside the drawing area, or click on an atom or a bond in the
-molecule.
-
-Rules of using templates:
-
-  * Selecting a template and clicking on an atom in the existing
-  structure adds the template to the structure connected with a single
-  bond:
-
-    ![](template-example1.png)
-
-  * Selecting a template and dragging the cursor from an atom in the
-  existing structure adds the template directly to this atom resulting
-  in the fused structure:
-
-    ![](template-example2.png)
-
-  * Dragging the cursor from an atom in the existing structure results
-  in the single bond attachment if the cursor is dragged to more than
-  the bond length; otherwise the fused structure is drawn.
-  * Selecting a template and clicking on a bond in the existing
-  structure created a bond-to-bond fused structure:
-
-    ![](template-example3.png)
-
-  * The bond in the initial structure is replaced with the bond in the
-  template.
-
-  * This procedure doesn't change the length of the bond in the
-  initial structure.
-
-  * Dragging the cursor relative to the initial bond applies the
-  template at the corresponding side of the bond.
-
-**Note** : The added template will be fused by the default attachment
-atom or bond preset in the program.
-
-**Note** : User is able to define the attachment atom and bond by clicking
-the Edit button for template structure.
-
-
-The _Custom Templates_ button ![](template-lib.png)invokes the scrolling
-list of templates available in the program; both built-in and created
-by user:
-
- ![](template-dialog.png)
-
-
-To create a user template:
-* draw a structure.
-* click the Save as button.
-* click the Save to Templates button.
-* enter a name and define the attachment atom and bond.
-
-# Working with Files
-
-Ketcher supports the following molecular formats that can be entered
-either manually or from files:
-
-  * MDL Molfile or RXN file;
-
-  * Daylight SMILES (Server mode only);
-
-  * Daylight SMARTS (Server mode only);
-
-  * InChi string (Server mode only);
-
-  * CML file (Server mode only).
-
-You can use the **Open…** and **Save As…** buttons of the _Main_
-toolbar to import a molecule from a molecular file or save it to a
-supported molecular file format. The _Open Structure_ dialog enables
-one to either browse for a file (Server mode) or manually input, e.g.,
-the Molfile ctable for the molecule to be imported:
-
- ![](open.png)
-
-The _Save Structure_ dialog enables one to save the molecular file:
-
- ![](save.png)
-
-**Note** : In the standalone version only mol/rxn are supported for
-Open and mol/rxn/SMILES for Save.
-
-
-# Hotkeys
-
-You can use keyboard hotkeys (including Numeric keypad) for some
-features/commands of the Editor. To display the hotkeys just place the
-cursor over a toolbar button. If a hotkey is available for the button,
-it will appear in brackets after the description of the button.
-
-| Key | Action |
-| --- | --- |
-| `Esc` | Switching between the Lasso/Rectangle/Fragment Selection tools |
-| `Del` | Delete the selected objects |
-| `0` | Draw Any bond. |
-| `1` | Single / Single Up / Single Down / Single Up/Down bond. Consecutive pressing switches between these types. |
-| `2` | Double / Double Cis/Trans bond |
-| `3` | Draw a triple bond. |
-| `4` | Draw an aromatic bond. |
-| `5` | Charge Plus/Charge Minus |
-| `A` | Draw any atom |
-| `H` | Draw a hydrogen |
-| `C` | Draw a carbon |
-| `N` | Draw a nitrogen |
-| `O` | Draw an oxygen |
-| `S` | Draw a sulfur |
-| `F` | Draw a fluorine |
-| `P` | Draw a phosphorus |
-| `I` | Draw an iodine |
-| `T` | Basic templates. Consecutive pressing switches between different templates |
-| `Shift+t` | Open template library |
-| `Alt+r` | Rotate tool |
-| `Alt+v` | Flip vertically |
-| `Alt+h` | Flip horizontally |
-| `Ctrl+g` | S-Group tool / Data S-Group tool |
-| `Ctrl+d` | Align and select all S-Group data
-| `Ctrl+r` | Switching between the R-Group Label Tool/R-Group Fragment Tool/Attachment Point Tool |
-| `Ctrl+Shift+r`  | R-Group Fragment Tool |
-| `Ctrl+Del` | Clear canvas |
-| `Ctrl+o` | Open |
-| `Ctrl+s` | Save As |
-| `Ctrl+z` | Undo |
-| `Ctrl+Shift+z` | Redo |
-| `Ctrl+x` | Cut selected objects |
-| `Ctrl+c` | Copy selected objects |
-| `Ctrl+v` | Paste selected objects |
-| `+` | Zoom In |
-| `-` | Zoom Out |
-| `Ctrl+l` | Layout |
-| `Ctrl+Shift+l` | Clean Up |
-| `Ctrl+p` | Calculate CIP |
-| `?` | Help |
-
-**Note** : Please, use `Ctrl+V` to paste the selected object in
-Google Chrome and Mozilla Firefox browsers.
-
-**Note 2** : Probably, you have forbidden access to the local storage.
-If you are using IE10 or IE11 and didn't forbid access to local storage 
-intentionally, you can pay attention here: https://stackoverflow.com/a/20848924