[Fix] AppDomain Leftovers (#161)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#161

.env.local.example

@@ -0,0 +1,22 @@
+# Django settings
+SECRET_KEY='a-secure-secret-key-for-development'
+DEBUG=True
+ALLOWED_HOSTS=*
+
+# Database settings (using PostgreSQL for local development)
+POSTGRES_USER=postgres
+POSTGRES_PASSWORD=postgres
+POSTGRES_DB=envipath
+POSTGRES_SERVICE_NAME=localhost
+POSTGRES_PORT=5432
+
+# Celery settings
+CELERY_BROKER_URL='redis://localhost:6379/0'
+CELERY_RESULT_BACKEND='redis://localhost:6379/0'
+FLAG_CELERY_PRESENT=False
+
+# Other settings
+LOG_LEVEL='INFO'
+SERVER_URL='http://localhost:8000'
+PLUGINS_ENABLED=True
+EP_DATA_DIR='data'

.env.prod.example

@@ -0,0 +1,18 @@
+# settings.py
+EP_DATA_DIR=
+ALLOWED_HOSTS=
+DEBUG=
+LOG_LEVEL=
+ENVIFORMER_PRESENT=
+FLAG_CELERY_PRESENT=
+SERVER_URL=
+PLUGINS_ENABLED=
+# DB
+POSTGRES_SERVICE_NAME=
+POSTGRES_DB=
+POSTGRES_USER=
+POSTGRES_PASSWORD=
+POSTGRES_PORT=
+# MAIL
+EMAIL_HOST_USER=
+EMAIL_HOST_PASSWORD=

.gitignore

@@ -1,176 +1,12 @@
-# ---> Python
+*.pyc
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-cover/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
 db.sqlite3
-db.sqlite3-journal
+.idea/
-
+static/admin/
-# Flask stuff:
+static/django_extensions/
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-.pybuilder/
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# UV
-#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#uv.lock
-
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
-.pdm.toml
-.pdm-python
-.pdm-build/
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
 .env
-.venv
+debug.log
-env/
+scratches/
-venv/
-ENV/
-env.bak/
-venv.bak/
 
-# Spyder project settings
+data/
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-# pytype static type analyzer
-.pytype/
-
-# Cython debug symbols
-cython_debug/
-
-# PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
-
-# Ruff stuff:
-.ruff_cache/
-
-# PyPI configuration file
-.pypirc
 
+.DS_Store

.pre-commit-config.yaml

@@ -0,0 +1,30 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.13.3
+    hooks:
+      # Run the linter.
+      - id: ruff-check
+        types_or: [python, pyi]
+        args: [--fix]
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [python, pyi]
+
+  # - repo: local
+  #   hooks:
+  #     - id: django-check
+  #       name: Run Django Check
+  #       entry: uv run python manage.py check
+  #       language: system
+  #       pass_filenames: false
+  #       types: [python]

.python-version

@@ -0,0 +1 @@
+3.12

README.md

@@ -1,2 +1,91 @@
 # enviPy
 
+## Local Development Setup
+
+These instructions will guide you through setting up the project for local development.
+
+### Prerequisites
+
+- Python 3.11 or later
+- [uv](https://github.com/astral-sh/uv) - A fast Python package installer and resolver.
+- **Docker and Docker Compose** - Required for running the PostgreSQL database.
+- Git
+
+> **Note:** This application requires PostgreSQL, which uses `ArrayField`. Docker is the recommended way to run PostgreSQL locally.
+
+### 1. Install Dependencies
+
+This project uses `uv` to manage dependencies and `poe-the-poet` for task running. First, [install `uv` if you don't have it yet](https://docs.astral.sh/uv/guides/install-python/).
+
+Then, sync the project dependencies. This will create a virtual environment in `.venv` and install all necessary packages, including `poe-the-poet`.
+
+```bash
+uv sync --dev
+```
+
+> **Note on RDkit:** If you have a different version of rdkit installed globally, the dependency installation may fail. If this happens, please uninstall the global version and run `uv sync` again.
+
+### 2. Set Up Environment File
+
+Copy the example environment file for local setup:
+
+```bash
+cp .env.local.example .env
+```
+
+This file contains the necessary environment variables for local development.
+
+### 3. Quick Setup with Poe
+
+The easiest way to set up the development environment is by using the `poe` task runner, which is executed via `uv run`.
+
+```bash
+uv run poe setup
+```
+
+This single command will:
+1. Start the PostgreSQL database using Docker Compose.
+2. Run database migrations.
+3. Bootstrap initial data (anonymous user, default packages, models).
+
+After setup, start the development server:
+
+```bash
+uv run poe dev
+```
+
+The application will be available at `http://localhost:8000`.
+
+#### Other useful Poe commands:
+
+You can list all available commands by running `uv run poe --help`.
+
+```bash
+uv run poe db-up         # Start PostgreSQL only
+uv run poe db-down       # Stop PostgreSQL
+uv run poe migrate       # Run migrations only
+uv run poe bootstrap     # Bootstrap data only
+uv run poe shell         # Open the Django shell
+uv run poe clean         # Remove database volumes (WARNING: destroys all data)
+```
+
+### Troubleshooting
+
+*   **Docker Connection Error:** If you see an error like `open //./pipe/dockerDesktopLinuxEngine: The system cannot find the file specified` (on Windows), it likely means your Docker Desktop application is not running. Please start Docker Desktop and try the command again.
+
+*   **SSH Keys for Git Dependencies:** Some dependencies are installed from private git repositories and require SSH authentication. Ensure your SSH keys are configured correctly for Git.
+    *   For a general guide, see [GitHub's official documentation](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent).
+    *   **Windows Users:** If `uv sync` hangs while fetching git dependencies, you may need to explicitly configure Git to use the Windows OpenSSH client and use the `ssh-agent` to manage your key's passphrase.
+
+        1.  **Point Git to the correct SSH executable:**
+            ```powershell
+            git config --global core.sshCommand "C:/Windows/System32/OpenSSH/ssh.exe"
+            ```
+        2.  **Enable and use the SSH agent:**
+            ```powershell
+            # Run these commands in an administrator PowerShell
+            Get-Service ssh-agent | Set-Service -StartupType Automatic -PassThru | Start-Service
+
+            # Add your key to the agent. It will prompt for the passphrase once.
+            ssh-add
+            ```

docker-compose.dev.yml

@@ -0,0 +1,20 @@
+services:
+  db:
+    image: postgres:15
+    container_name: envipath-postgres
+    environment:
+      POSTGRES_USER: postgres
+      POSTGRES_PASSWORD: postgres
+      POSTGRES_DB: envipath
+    ports:
+      - "5432:5432"
+    volumes:
+      - postgres_data:/var/lib/postgresql/data
+    healthcheck:
+      test: ["CMD-SHELL", "pg_isready -U postgres"]
+      interval: 5s
+      timeout: 5s
+      retries: 5
+
+volumes:
+  postgres_data:

envipath/__init__.py

@@ -0,0 +1,5 @@
+# This will make sure the app is always imported when
+# Django starts so that shared_task will use this app.
+from .celery import app as celery_app
+
+__all__ = ("celery_app",)

envipath/api.py

@@ -0,0 +1,12 @@
+from epdb.api import router as epdb_app_router
+from epdb.legacy_api import router as epdb_legacy_app_router
+from ninja import NinjaAPI
+
+api = NinjaAPI()
+
+api_v1 = NinjaAPI(title="API V1 Docs", urls_namespace="api-v1")
+api_legacy = NinjaAPI(title="Legacy API Docs", urls_namespace="api-legacy")
+
+# Add routers
+api_v1.add_router("/", epdb_app_router)
+api_legacy.add_router("/", epdb_legacy_app_router)

envipath/asgi.py

@@ -0,0 +1,16 @@
+"""
+ASGI config for envipath project.
+
+It exposes the ASGI callable as a module-level variable named ``application``.
+
+For more information on this file, see
+https://docs.djangoproject.com/en/4.2/howto/deployment/asgi/
+"""
+
+import os
+
+from django.core.asgi import get_asgi_application
+
+os.environ.setdefault("DJANGO_SETTINGS_MODULE", "envipath.settings")
+
+application = get_asgi_application()

envipath/celery.py

@@ -0,0 +1,27 @@
+import os
+
+from celery import Celery
+from celery.signals import setup_logging
+
+# Set the default Django settings module for the 'celery' program.
+os.environ.setdefault("DJANGO_SETTINGS_MODULE", "envipath.settings")
+
+app = Celery("envipath")
+
+# Using a string here means the worker doesn't have to serialize
+# the configuration object to child processes.
+# - namespace='CELERY' means all celery-related configuration keys
+#   should have a `CELERY_` prefix.
+app.config_from_object("django.conf:settings", namespace="CELERY")
+
+
+@setup_logging.connect
+def config_loggers(*args, **kwargs):
+    from logging.config import dictConfig
+    from django.conf import settings
+
+    dictConfig(settings.LOGGING)
+
+
+# Load task modules from all registered Django apps.
+app.autodiscover_tasks()

envipath/settings.py

@@ -0,0 +1,359 @@
+"""
+Django settings for envipath project.
+
+Generated by 'django-admin startproject' using Django 4.2.17.
+
+For more information on this file, see
+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 os
+from pathlib import Path
+
+from dotenv import load_dotenv
+from envipy_plugins import Classifier, Property, Descriptor
+from sklearn.ensemble import RandomForestClassifier
+from sklearn.tree import DecisionTreeClassifier
+
+# Build paths inside the project like this: BASE_DIR / 'subdir'.
+BASE_DIR = Path(__file__).resolve().parent.parent
+
+load_dotenv(BASE_DIR / ".env", override=False)
+
+# Quick-start development settings - unsuitable for production
+# See https://docs.djangoproject.com/en/4.2/howto/deployment/checklist/
+
+# SECURITY WARNING: keep the secret key used in production secret!
+SECRET_KEY = os.environ.get("SECRET_KEY", "secret-key")
+
+# SECURITY WARNING: don't run with debug turned on in production!
+DEBUG = os.environ.get("DEBUG", "False") == "True"
+
+ALLOWED_HOSTS = os.environ["ALLOWED_HOSTS"].split(",")
+
+
+# Application definition
+
+INSTALLED_APPS = [
+    "django.contrib.admin",
+    "django.contrib.auth",
+    "django.contrib.contenttypes",
+    "django.contrib.sessions",
+    "django.contrib.messages",
+    "django.contrib.staticfiles",
+    # 3rd party
+    "django_extensions",
+    "oauth2_provider",
+    # Custom
+    "epdb",
+    "migration",
+]
+
+AUTHENTICATION_BACKENDS = [
+    "django.contrib.auth.backends.ModelBackend",
+]
+
+MIDDLEWARE = [
+    "django.middleware.security.SecurityMiddleware",
+    "django.contrib.sessions.middleware.SessionMiddleware",
+    "django.middleware.common.CommonMiddleware",
+    "django.middleware.csrf.CsrfViewMiddleware",
+    "django.contrib.auth.middleware.AuthenticationMiddleware",
+    "django.contrib.messages.middleware.MessageMiddleware",
+    "django.middleware.clickjacking.XFrameOptionsMiddleware",
+    "oauth2_provider.middleware.OAuth2TokenMiddleware",
+]
+
+OAUTH2_PROVIDER = {
+    "PKCE_REQUIRED": False,  # Accept PKCE requests but dont require them
+}
+
+if os.environ.get("REGISTRATION_MANDATORY", False) == "True":
+    MIDDLEWARE.append("epdb.middleware.login_required_middleware.LoginRequiredMiddleware")
+
+ROOT_URLCONF = "envipath.urls"
+
+TEMPLATES = [
+    {
+        "BACKEND": "django.template.backends.django.DjangoTemplates",
+        "DIRS": (os.path.join(BASE_DIR, "templates"),),
+        "APP_DIRS": True,
+        "OPTIONS": {
+            "context_processors": [
+                "django.template.context_processors.debug",
+                "django.template.context_processors.request",
+                "django.contrib.auth.context_processors.auth",
+                "django.contrib.messages.context_processors.messages",
+            ],
+        },
+    },
+]
+
+WSGI_APPLICATION = "envipath.wsgi.application"
+
+# Database
+# https://docs.djangoproject.com/en/4.2/ref/settings/#databases
+
+DATABASES = {
+    "default": {
+        "ENGINE": "django.db.backends.postgresql",
+        "USER": os.environ["POSTGRES_USER"],
+        "NAME": os.environ["POSTGRES_DB"],
+        "PASSWORD": os.environ["POSTGRES_PASSWORD"],
+        "HOST": os.environ["POSTGRES_SERVICE_NAME"],
+        "PORT": os.environ["POSTGRES_PORT"],
+    }
+}
+
+# Password validation
+# https://docs.djangoproject.com/en/4.2/ref/settings/#auth-password-validators
+
+AUTH_PASSWORD_VALIDATORS = [
+    {"NAME": "django.contrib.auth.password_validation.UserAttributeSimilarityValidator"},
+    {"NAME": "django.contrib.auth.password_validation.MinimumLengthValidator"},
+    {"NAME": "django.contrib.auth.password_validation.CommonPasswordValidator"},
+    {"NAME": "django.contrib.auth.password_validation.NumericPasswordValidator"},
+]
+
+# Internationalization
+# https://docs.djangoproject.com/en/4.2/topics/i18n/
+
+LANGUAGE_CODE = "en-us"
+
+TIME_ZONE = "UTC"
+
+USE_I18N = True
+
+USE_TZ = True
+
+
+# Default primary key field type
+# https://docs.djangoproject.com/en/4.2/ref/settings/#default-auto-field
+
+DEFAULT_AUTO_FIELD = "django.db.models.BigAutoField"
+
+EMAIL_SUBJECT_PREFIX = "[enviPath] "
+if DEBUG:
+    EMAIL_BACKEND = "django.core.mail.backends.console.EmailBackend"
+else:
+    EMAIL_BACKEND = "django.core.mail.backends.smtp.EmailBackend"
+    EMAIL_USE_TLS = True
+    EMAIL_HOST = "mail.gandi.net"
+    EMAIL_HOST_USER = os.environ["EMAIL_HOST_USER"]
+    EMAIL_HOST_PASSWORD = os.environ["EMAIL_HOST_PASSWORD"]
+    EMAIL_PORT = 587
+    DEFAULT_FROM_EMAIL = os.environ["DEFAULT_FROM_EMAIL"]
+    SERVER_EMAIL = os.environ["SERVER_EMAIL"]
+
+AUTH_USER_MODEL = "epdb.User"
+ADMIN_APPROVAL_REQUIRED = os.environ.get("ADMIN_APPROVAL_REQUIRED", "False") == "True"
+
+# # SESAME
+# SESAME_MAX_AGE = 300
+# # TODO set to "home"
+# LOGIN_REDIRECT_URL = "/"
+LOGIN_URL = "/login/"
+
+SERVER_URL = os.environ.get("SERVER_URL", "http://localhost:8000")
+
+CSRF_TRUSTED_ORIGINS = [SERVER_URL]
+
+AMBIT_URL = "http://localhost:9001"
+DEFAULT_VALUES = {"description": "no description"}
+
+EP_DATA_DIR = os.environ["EP_DATA_DIR"]
+if not os.path.exists(EP_DATA_DIR):
+    os.mkdir(EP_DATA_DIR)
+
+MODEL_DIR = os.path.join(EP_DATA_DIR, "models")
+if not os.path.exists(MODEL_DIR):
+    os.mkdir(MODEL_DIR)
+
+STATIC_DIR = os.path.join(EP_DATA_DIR, "static")
+if not os.path.exists(STATIC_DIR):
+    os.mkdir(STATIC_DIR)
+
+LOG_DIR = os.path.join(EP_DATA_DIR, "log")
+if not os.path.exists(LOG_DIR):
+    os.mkdir(LOG_DIR)
+
+PLUGIN_DIR = os.path.join(EP_DATA_DIR, "plugins")
+if not os.path.exists(PLUGIN_DIR):
+    os.mkdir(PLUGIN_DIR)
+
+# Set this as our static root dir
+STATIC_ROOT = STATIC_DIR
+
+STATIC_URL = "/static/"
+
+# Where the sources are stored...
+STATICFILES_DIRS = (BASE_DIR / "static",)
+
+FIXTURE_DIRS = (BASE_DIR / "fixtures",)
+
+# Logging
+LOGGING = {
+    "version": 1,
+    "disable_existing_loggers": True,
+    "formatters": {
+        "simple": {
+            "format": "[%(asctime)s] %(levelname)s %(module)s - %(message)s",
+            "datefmt": "%Y-%m-%d %H:%M:%S",
+        },
+    },
+    "handlers": {
+        "console": {
+            "level": "INFO",
+            "class": "logging.StreamHandler",
+            "formatter": "simple",
+        },
+        "file": {
+            "level": "DEBUG",  # Or higher
+            "class": "logging.FileHandler",
+            "filename": os.path.join(LOG_DIR, "debug.log"),
+            "formatter": "simple",
+        },
+    },
+    "loggers": {
+        # For everything under epdb/ loaded via getlogger(__name__)
+        "epdb": {
+            "handlers": ["file"],  # "console",
+            "propagate": True,
+            "level": os.environ.get("LOG_LEVEL", "INFO"),
+        },
+        # For everything under envipath/ loaded via getlogger(__name__)
+        "envipath": {
+            "handlers": ["file", "console"],
+            "propagate": True,
+            "level": os.environ.get("LOG_LEVEL", "INFO"),
+        },
+        # For everything under utilities/ loaded via getlogger(__name__)
+        "utilities": {
+            "handlers": ["file", "console"],
+            "propagate": True,
+            "level": os.environ.get("LOG_LEVEL", "INFO"),
+        },
+    },
+}
+
+# Flags
+ENVIFORMER_PRESENT = os.environ.get("ENVIFORMER_PRESENT", "False") == "True"
+ENVIFORMER_DEVICE = os.environ.get("ENVIFORMER_DEVICE", "cpu")
+
+# If celery is not present set always eager to true which will cause delayed tasks to block until finished
+FLAG_CELERY_PRESENT = os.environ.get("FLAG_CELERY_PRESENT", "False") == "True"
+if not FLAG_CELERY_PRESENT:
+    CELERY_TASK_ALWAYS_EAGER = True
+
+# Celery Configuration Options
+CELERY_TIMEZONE = "Europe/Berlin"
+# Celery Configuration
+CELERY_BROKER_URL = "redis://localhost:6379/0"  # Use Redis as message broker
+CELERY_RESULT_BACKEND = "redis://localhost:6379/1"
+CELERY_ACCEPT_CONTENT = ["json"]
+CELERY_TASK_SERIALIZER = "json"
+
+MODEL_BUILDING_ENABLED = os.environ.get("MODEL_BUILDING_ENABLED", "False") == "True"
+APPLICABILITY_DOMAIN_ENABLED = os.environ.get("APPLICABILITY_DOMAIN_ENABLED", "False") == "True"
+DEFAULT_RF_MODEL_PARAMS = {
+    "base_clf": RandomForestClassifier(
+        n_estimators=100,
+        max_features="log2",
+        random_state=42,
+        criterion="entropy",
+        ccp_alpha=0.0,
+        max_depth=3,
+        min_samples_leaf=1,
+    ),
+    "num_chains": 10,
+}
+
+DEFAULT_MODEL_PARAMS = {
+    "base_clf": DecisionTreeClassifier(
+        criterion="entropy",
+        max_depth=3,
+        min_samples_split=5,
+        # min_samples_leaf=5,
+        max_features="sqrt",
+        # class_weight='balanced',
+        random_state=42,
+    ),
+    "num_chains": 10,
+}
+
+DEFAULT_MAX_NUMBER_OF_NODES = 30
+DEFAULT_MAX_DEPTH = 5
+DEFAULT_MODEL_THRESHOLD = 0.25
+
+# Loading Plugins
+PLUGINS_ENABLED = os.environ.get("PLUGINS_ENABLED", "False") == "True"
+if PLUGINS_ENABLED:
+    from utilities.plugin import discover_plugins
+
+    CLASSIFIER_PLUGINS = discover_plugins(_cls=Classifier)
+    PROPERTY_PLUGINS = discover_plugins(_cls=Property)
+    DESCRIPTOR_PLUGINS = discover_plugins(_cls=Descriptor)
+else:
+    CLASSIFIER_PLUGINS = {}
+    PROPERTY_PLUGINS = {}
+    DESCRIPTOR_PLUGINS = {}
+
+SENTRY_ENABLED = os.environ.get("SENTRY_ENABLED", "False") == "True"
+if SENTRY_ENABLED:
+    import sentry_sdk
+
+    def before_send(event, hint):
+        # Check if was a handled exception by one of our loggers
+        if event.get("logger"):
+            for log_path in LOGGING.get("loggers").keys():
+                if event["logger"].startswith(log_path):
+                    return None
+
+        return event
+
+    sentry_sdk.init(
+        dsn=os.environ.get("SENTRY_DSN"),
+        # Add data like request headers and IP for users,
+        # see https://docs.sentry.io/platforms/python/data-management/data-collected/ for more info
+        send_default_pii=True,
+        environment=os.environ.get("SENTRY_ENVIRONMENT", "development"),
+        before_send=before_send,
+    )
+
+# compile into digestible flags
+FLAGS = {
+    "MODEL_BUILDING": MODEL_BUILDING_ENABLED,
+    "CELERY": FLAG_CELERY_PRESENT,
+    "PLUGINS": PLUGINS_ENABLED,
+    "SENTRY": SENTRY_ENABLED,
+    "ENVIFORMER": ENVIFORMER_PRESENT,
+    "APPLICABILITY_DOMAIN": APPLICABILITY_DOMAIN_ENABLED,
+}
+
+# path of the URL are checked via "startswith"
+# -> /password_reset/done is covered as well
+LOGIN_EXEMPT_URLS = [
+    "/register",
+    "/api/legacy/",
+    "/o/token/",
+    "/o/userinfo/",
+    "/password_reset/",
+    "/reset/",
+    "/microsoft/",
+]
+
+# MS AD/Entra
+MS_ENTRA_ENABLED = os.environ.get("MS_ENTRA_ENABLED", "False") == "True"
+if MS_ENTRA_ENABLED:
+    # Add app to installed apps
+    INSTALLED_APPS.append("epauth")
+    # Set vars required by app
+    MS_ENTRA_CLIENT_ID = os.environ["MS_CLIENT_ID"]
+    MS_ENTRA_CLIENT_SECRET = os.environ["MS_CLIENT_SECRET"]
+    MS_ENTRA_TENANT_ID = os.environ["MS_TENANT_ID"]
+    MS_ENTRA_AUTHORITY = f"https://login.microsoftonline.com/{MS_ENTRA_TENANT_ID}"
+    MS_ENTRA_REDIRECT_URI = os.environ["MS_REDIRECT_URI"]
+    MS_ENTRA_SCOPES = os.environ.get("MS_SCOPES", "").split(",")

envipath/urls.py

@@ -0,0 +1,34 @@
+"""
+URL configuration for envipath project.
+
+The `urlpatterns` list routes URLs to views. For more information please see:
+    https://docs.djangoproject.com/en/4.2/topics/http/urls/
+Examples:
+Function views
+    1. Add an import:  from my_app import views
+    2. Add a URL to urlpatterns:  path('', views.home, name='home')
+Class-based views
+    1. Add an import:  from other_app.views import Home
+    2. Add a URL to urlpatterns:  path('', Home.as_view(), name='home')
+Including another URLconf
+    1. Import the include() function: from django.urls import include, path
+    2. Add a URL to urlpatterns:  path('blog/', include('blog.urls'))
+"""
+
+from django.conf import settings as s
+from django.contrib import admin
+from django.urls import include, path
+
+from .api import api_v1, api_legacy
+
+urlpatterns = [
+    path("", include("epdb.urls")),
+    path("", include("migration.urls")),
+    path("admin/", admin.site.urls),
+    path("api/v1/", api_v1.urls),
+    path("api/legacy/", api_legacy.urls),
+    path("o/", include("oauth2_provider.urls", namespace="oauth2_provider")),
+]
+
+if s.MS_ENTRA_ENABLED:
+    urlpatterns.append(path("", include("epauth.urls")))

envipath/wsgi.py

@@ -0,0 +1,16 @@
+"""
+WSGI config for envipath project.
+
+It exposes the WSGI callable as a module-level variable named ``application``.
+
+For more information on this file, see
+https://docs.djangoproject.com/en/4.2/howto/deployment/wsgi/
+"""
+
+import os
+
+from django.core.wsgi import get_wsgi_application
+
+os.environ.setdefault("DJANGO_SETTINGS_MODULE", "envipath.settings")
+
+application = get_wsgi_application()

epauth/admin.py

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

epauth/apps.py

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

epauth/models.py

@@ -0,0 +1,3 @@
+from django.db import models
+
+# Create your models here.

epauth/tests.py

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

epauth/urls.py

@@ -0,0 +1,8 @@
+from django.urls import path
+
+from . import views
+
+urlpatterns = [
+    path("microsoft/login/", views.microsoft_login, name="microsoft_login"),
+    path("microsoft/callback/", views.microsoft_callback, name="microsoft_callback"),
+]

epauth/views.py

@@ -0,0 +1,66 @@
+import msal
+from django.conf import settings as s
+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 microsoft_login(request):
+    msal_app = msal.ConfidentialClientApplication(
+        client_id=s.MS_ENTRA_CLIENT_ID,
+        client_credential=s.MS_ENTRA_CLIENT_SECRET,
+        authority=s.MS_ENTRA_AUTHORITY
+    )
+
+    flow = msal_app.initiate_auth_code_flow(
+        scopes=s.MS_ENTRA_SCOPES,
+        redirect_uri=s.MS_ENTRA_REDIRECT_URI
+    )
+
+    request.session["msal_auth_flow"] = flow
+    return redirect(flow["auth_uri"])
+
+
+def microsoft_callback(request):
+    msal_app = msal.ConfidentialClientApplication(
+        client_id=s.MS_ENTRA_CLIENT_ID,
+        client_credential=s.MS_ENTRA_CLIENT_SECRET,
+        authority=s.MS_ENTRA_AUTHORITY
+    )
+
+    flow = request.session.pop("msal_auth_flow", None)
+    if not flow:
+        return redirect("/")
+
+    # Acquire token using the flow and callback request
+    result = msal_app.acquire_token_by_auth_code_flow(flow, request.GET)
+
+    if "access_token" in result:
+        # Optional: Fetch user info from Microsoft Graph
+        import requests
+        resp = requests.get(
+            "https://graph.microsoft.com/v1.0/me",
+            headers={"Authorization": f"Bearer {result['access_token']}"}
+        )
+        user_info = resp.json()
+
+        user_name = user_info["displayName"]
+        user_email = user_info["mail"]
+        user_oid = user_info["id"]
+
+        # Get implementing class
+        User = get_user_model()
+
+        if User.objects.filter(uuid=user_oid).exists():
+            login(request, User.objects.get(uuid=user_oid))
+        else:
+            u = UserManager.create_user(user_name, user_email, None, uuid=user_oid, is_active=True)
+            login(request, u)
+
+        # TODO Group Sync
+
+        return redirect("/")
+
+    return redirect("/")  # Handle errors

epdb/admin.py

@@ -0,0 +1,118 @@
+from django.contrib import admin
+
+from .models import (
+    User,
+    UserPackagePermission,
+    Group,
+    GroupPackagePermission,
+    Package,
+    MLRelativeReasoning,
+    Compound,
+    CompoundStructure,
+    SimpleAmbitRule,
+    ParallelRule,
+    Reaction,
+    Pathway,
+    Node,
+    Edge,
+    Scenario,
+    Setting,
+    ExternalDatabase,
+    ExternalIdentifier,
+)
+
+
+class UserAdmin(admin.ModelAdmin):
+    pass
+
+
+class UserPackagePermissionAdmin(admin.ModelAdmin):
+    pass
+
+
+class GroupAdmin(admin.ModelAdmin):
+    pass
+
+
+class GroupPackagePermissionAdmin(admin.ModelAdmin):
+    pass
+
+
+class EPAdmin(admin.ModelAdmin):
+    search_fields = ["name", "description"]
+
+
+class PackageAdmin(EPAdmin):
+    pass
+
+
+class MLRelativeReasoningAdmin(EPAdmin):
+    pass
+
+
+class CompoundAdmin(EPAdmin):
+    pass
+
+
+class CompoundStructureAdmin(EPAdmin):
+    pass
+
+
+class SimpleAmbitRuleAdmin(EPAdmin):
+    pass
+
+
+class ParallelRuleAdmin(EPAdmin):
+    pass
+
+
+class ReactionAdmin(EPAdmin):
+    pass
+
+
+class PathwayAdmin(EPAdmin):
+    pass
+
+
+class NodeAdmin(EPAdmin):
+    pass
+
+
+class EdgeAdmin(EPAdmin):
+    pass
+
+
+class ScenarioAdmin(EPAdmin):
+    pass
+
+
+class SettingAdmin(EPAdmin):
+    pass
+
+
+class ExternalDatabaseAdmin(admin.ModelAdmin):
+    pass
+
+
+class ExternalIdentifierAdmin(admin.ModelAdmin):
+    pass
+
+
+admin.site.register(User, UserAdmin)
+admin.site.register(UserPackagePermission, UserPackagePermissionAdmin)
+admin.site.register(Group, GroupAdmin)
+admin.site.register(GroupPackagePermission, GroupPackagePermissionAdmin)
+admin.site.register(Package, PackageAdmin)
+admin.site.register(MLRelativeReasoning, MLRelativeReasoningAdmin)
+admin.site.register(Compound, CompoundAdmin)
+admin.site.register(CompoundStructure, CompoundStructureAdmin)
+admin.site.register(SimpleAmbitRule, SimpleAmbitRuleAdmin)
+admin.site.register(ParallelRule, ParallelRuleAdmin)
+admin.site.register(Reaction, ReactionAdmin)
+admin.site.register(Pathway, PathwayAdmin)
+admin.site.register(Node, NodeAdmin)
+admin.site.register(Edge, EdgeAdmin)
+admin.site.register(Setting, SettingAdmin)
+admin.site.register(Scenario, ScenarioAdmin)
+admin.site.register(ExternalDatabase, ExternalDatabaseAdmin)
+admin.site.register(ExternalIdentifier, ExternalIdentifierAdmin)

epdb/api.py

@@ -0,0 +1,113 @@
+from typing import List
+
+from django.contrib.auth import get_user_model
+from ninja import Router, Schema, Field
+from ninja.errors import HttpError
+from ninja.pagination import paginate
+from ninja.security import HttpBearer
+
+from .logic import PackageManager
+from .models import User, Compound, APIToken
+
+
+class BearerTokenAuth(HttpBearer):
+    def authenticate(self, request, token):
+        for token_obj in APIToken.objects.select_related("user").all():
+            if token_obj.check_token(token) and token_obj.is_valid():
+                return token_obj.user
+        raise HttpError(401, "Invalid or expired token")
+
+
+def _anonymous_or_real(request):
+    if request.user.is_authenticated and not request.user.is_anonymous:
+        return request.user
+    return get_user_model().objects.get(username="anonymous")
+
+
+router = Router(auth=BearerTokenAuth())
+
+
+class UserSchema(Schema):
+    email: str
+    username: str
+    id: str = Field(None, alias="url")
+
+
+class PackageIn(Schema):
+    name: str
+    description: str
+
+
+class PackageOut(Schema):
+    id: str = Field(None, alias="url")
+    name: str
+    reviewed: bool
+    compound_links: str = None
+
+    @staticmethod
+    def resolve_compound_links(obj):
+        return f"{obj.url}/compound"
+
+
+class Error(Schema):
+    message: str
+
+
+class CompoundSchema(Schema):
+    name: str = Field(None, alias="name")
+    id: str = Field(None, alias="url")
+    smiles: str = Field(None, alias="default_structure.smiles")
+    reviewed: bool = Field(None, alias="package.reviewed")
+
+
+@router.get("/user", response={200: List[UserSchema], 403: Error})
+def get_users(request):
+    return User.objects.all()
+
+
+@router.get("/package", response={200: List[PackageOut], 403: Error})
+def get_packages(request):
+    return PackageManager.get_all_readable_packages(request.user, include_reviewed=True)
+
+
+@router.post("/package", response=PackageOut)
+def create_package(request, package: PackageIn):
+    user = request.auth
+    name = package.name.strip()
+    description = package.description.strip()
+
+    p = PackageManager.create_package(user, name, description=description)
+    return p
+
+
+@router.get("/package/{uuid:package_uuid}", response={200: PackageOut, 403: Error})
+def get_package(request, package_uuid):
+    try:
+        return PackageManager.get_package_by_id(request.auth, package_id=package_uuid)
+    except ValueError:
+        return 403, {
+            "message": f"Getting Package with id {package_uuid} failed due to insufficient rights!"
+        }
+
+
+@router.get("/compound", response={200: List[CompoundSchema], 403: Error})
+@paginate
+def get_compounds(request):
+    qs = Compound.objects.none()
+    for p in PackageManager.get_reviewed_packages():
+        qs |= Compound.objects.filter(package=p)
+    return qs
+
+
+@router.get(
+    "/package/{uuid:package_uuid}/compound", response={200: List[CompoundSchema], 403: Error}
+)
+@paginate
+def get_package_compounds(request, package_uuid):
+    try:
+        p = PackageManager.get_package_by_id(request.auth, package_uuid)
+        return Compound.objects.filter(package=p)
+    except ValueError:
+        return 403, {
+            "message": f"Getting Compounds for Package with id {package_uuid} failed due to insufficient rights!"
+        }

epdb/apps.py

@@ -0,0 +1,9 @@
+from django.apps import AppConfig
+
+
+class EPDBConfig(AppConfig):
+    default_auto_field = "django.db.models.BigAutoField"
+    name = "epdb"
+
+    def ready(self):
+        import epdb.signals  # noqa: F401

epdb/management/commands/bootstrap.py

@@ -0,0 +1,224 @@
+import json
+
+from django.conf import settings as s
+from django.core.management.base import BaseCommand
+from django.db import transaction
+
+from epdb.logic import UserManager, GroupManager, PackageManager, SettingManager
+from epdb.models import (
+    UserSettingPermission,
+    MLRelativeReasoning,
+    EnviFormer,
+    Permission,
+    User,
+    ExternalDatabase,
+)
+
+
+class Command(BaseCommand):
+    def create_users(self):
+        # Anonymous User
+        if not User.objects.filter(email="anon@envipath.com").exists():
+            anon = UserManager.create_user(
+                "anonymous",
+                "anon@envipath.com",
+                "SuperSafe",
+                is_active=True,
+                add_to_group=False,
+                set_setting=False,
+            )
+        else:
+            anon = User.objects.get(email="anon@envipath.com")
+
+        # Admin User
+        if not User.objects.filter(email="admin@envipath.com").exists():
+            admin = UserManager.create_user(
+                "admin",
+                "admin@envipath.com",
+                "SuperSafe",
+                is_active=True,
+                add_to_group=False,
+                set_setting=False,
+            )
+            admin.is_staff = True
+            admin.is_superuser = True
+            admin.save()
+        else:
+            admin = User.objects.get(email="admin@envipath.com")
+
+        # System Group
+        g = GroupManager.create_group(admin, "enviPath Users", "All enviPath Users")
+        g.public = True
+        g.save()
+
+        g.user_member.add(anon)
+        g.save()
+
+        anon.default_group = g
+        anon.save()
+
+        admin.default_group = g
+        admin.save()
+
+        if not User.objects.filter(email="user0@envipath.com").exists():
+            user0 = UserManager.create_user(
+                "user0",
+                "user0@envipath.com",
+                "SuperSafe",
+                is_active=True,
+                add_to_group=False,
+                set_setting=False,
+            )
+            user0.is_staff = True
+            user0.is_superuser = True
+            user0.save()
+        else:
+            user0 = User.objects.get(email="user0@envipath.com")
+
+        g.user_member.add(user0)
+        g.save()
+
+        user0.default_group = g
+        user0.save()
+
+        return anon, admin, g, user0
+
+    def import_package(self, data, owner):
+        return PackageManager.import_legacy_package(
+            data, owner, keep_ids=True, add_import_timestamp=False, trust_reviewed=True
+        )
+
+    def create_default_setting(self, owner, packages):
+        s = SettingManager.create_setting(
+            owner,
+            name="Global Default Setting",
+            description="Global Default Setting containing BBD Rules and Max 30 Nodes and Max Depth of 8",
+            max_nodes=30,
+            max_depth=5,
+            rule_packages=packages,
+            model=None,
+            model_threshold=None,
+        )
+
+        return s
+
+    def populate_common_external_databases(self):
+        """
+        Helper function to populate common external databases.
+        This can be called from a Django management command.
+        """
+        databases = [
+            {
+                "name": "PubChem Compound",
+                "full_name": "PubChem Compound Database",
+                "description": "Chemical database of small organic molecules",
+                "base_url": "https://pubchem.ncbi.nlm.nih.gov",
+                "url_pattern": "https://pubchem.ncbi.nlm.nih.gov/compound/{id}",
+            },
+            {
+                "name": "PubChem Substance",
+                "full_name": "PubChem Substance Database",
+                "description": "Database of chemical substances",
+                "base_url": "https://pubchem.ncbi.nlm.nih.gov",
+                "url_pattern": "https://pubchem.ncbi.nlm.nih.gov/substance/{id}",
+            },
+            {
+                "name": "ChEBI",
+                "full_name": "Chemical Entities of Biological Interest",
+                "description": "Dictionary of molecular entities",
+                "base_url": "https://www.ebi.ac.uk/chebi",
+                "url_pattern": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:{id}",
+            },
+            {
+                "name": "RHEA",
+                "full_name": "RHEA Reaction Database",
+                "description": "Comprehensive resource of biochemical reactions",
+                "base_url": "https://www.rhea-db.org",
+                "url_pattern": "https://www.rhea-db.org/rhea/{id}",
+            },
+            {
+                "name": "KEGG Reaction",
+                "full_name": "KEGG Reaction Database",
+                "description": "Database of biochemical reactions",
+                "base_url": "https://www.genome.jp",
+                "url_pattern": "https://www.genome.jp/entry/{id}",
+            },
+            {
+                "name": "UniProt",
+                "full_name": "MetaCyc Metabolic Pathway Database",
+                "description": "UniProt is a freely accessible database of protein sequence and functional information",
+                "base_url": "https://www.uniprot.org",
+                "url_pattern": 'https://www.uniprot.org/uniprotkb?query="{id}"',
+            },
+        ]
+
+        for db_info in databases:
+            ExternalDatabase.objects.get_or_create(name=db_info["name"], defaults=db_info)
+
+    @transaction.atomic
+    def handle(self, *args, **options):
+        # Create users
+        anon, admin, g, user0 = self.create_users()
+
+        self.populate_common_external_databases()
+
+        # Import Packages
+        packages = [
+            "EAWAG-BBD.json",
+            "EAWAG-SOIL.json",
+            "EAWAG-SLUDGE.json",
+            "EAWAG-SEDIMENT.json",
+        ]
+
+        mapping = {}
+        for p in packages:
+            print(f"Importing {p}...")
+            package_data = json.loads(
+                open(
+                    s.BASE_DIR / "fixtures" / "packages" / "2025-07-18" / p, encoding="utf-8"
+                ).read()
+            )
+            imported_package = self.import_package(package_data, admin)
+            mapping[p.replace(".json", "")] = imported_package
+
+        setting = self.create_default_setting(admin, [mapping["EAWAG-BBD"]])
+        setting.public = True
+        setting.save()
+        setting.make_global_default()
+
+        for u in [anon, user0]:
+            u.default_setting = setting
+            u.save()
+
+            usp = UserSettingPermission()
+            usp.user = u
+            usp.setting = setting
+            usp.permission = Permission.READ[0]
+            usp.save()
+
+        # Create Model Package
+        pack = PackageManager.create_package(
+            admin,
+            "Public Prediction Models",
+            "Package to make Prediction Models publicly available",
+        )
+        pack.reviewed = True
+        pack.save()
+
+        # Create RR
+        ml_model = MLRelativeReasoning.create(
+            package=pack,
+            rule_packages=[mapping["EAWAG-BBD"]],
+            data_packages=[mapping["EAWAG-BBD"]],
+            eval_packages=[],
+            threshold=0.5,
+            name="ECC - BBD - T0.5",
+            description="ML Relative Reasoning",
+        )
+
+        ml_model.build_dataset()
+        ml_model.build_model()
+
+        # If available, create EnviFormerModel
+        if s.ENVIFORMER_PRESENT:
+            EnviFormer.create(pack, "EnviFormer - T0.5", "EnviFormer Model with Threshold 0.5", 0.5)

epdb/management/commands/create_ml_models.py

@@ -0,0 +1,105 @@
+from django.conf import settings as s
+from django.core.management.base import BaseCommand
+from django.db import transaction
+
+from epdb.models import MLRelativeReasoning, EnviFormer, Package
+
+
+class Command(BaseCommand):
+    """This command can be run with
+    `python manage.py create_ml_models [model_names] -d [data_packages] OPTIONAL: -e [eval_packages]`
+    For example, to train both EnviFormer and MLRelativeReasoning on BBD and SOIL and evaluate them on SLUDGE
+    the below command would be used:
+    `python manage.py create_ml_models enviformer mlrr -d bbd soil -e sludge
+    """
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "model_names",
+            nargs="+",
+            type=str,
+            help="The names of models to train. Options are: enviformer, mlrr",
+        )
+        parser.add_argument(
+            "-d", "--data-packages", nargs="+", type=str, help="Packages for training"
+        )
+        parser.add_argument(
+            "-e", "--eval-packages", nargs="*", type=str, help="Packages for evaluation", default=[]
+        )
+        parser.add_argument(
+            "-r",
+            "--rule-packages",
+            nargs="*",
+            type=str,
+            help="Rule Packages mandatory for MLRR",
+            default=[],
+        )
+
+    @transaction.atomic
+    def handle(self, *args, **options):
+        # Find Public Prediction Models package to add new models to
+        try:
+            pack = Package.objects.filter(name="Public Prediction Models")[0]
+            bbd = Package.objects.filter(name="EAWAG-BBD")[0]
+            soil = Package.objects.filter(name="EAWAG-SOIL")[0]
+            sludge = Package.objects.filter(name="EAWAG-SLUDGE")[0]
+            sediment = Package.objects.filter(name="EAWAG-SEDIMENT")[0]
+        except IndexError:
+            raise IndexError(
+                "Can't find correct packages. They should be created with the bootstrap command"
+            )
+
+        def decode_packages(package_list):
+            """Decode package strings into their respective packages"""
+            packages = []
+            for p in package_list:
+                p = p.lower()
+                if p == "bbd":
+                    packages.append(bbd)
+                elif p == "soil":
+                    packages.append(soil)
+                elif p == "sludge":
+                    packages.append(sludge)
+                elif p == "sediment":
+                    packages.append(sediment)
+                else:
+                    raise ValueError(f"Unknown package {p}")
+            return packages
+
+        # Iteratively create models in options["model_names"]
+        print(f"Creating models: {options['model_names']}")
+        data_packages = decode_packages(options["data_packages"])
+        eval_packages = decode_packages(options["eval_packages"])
+        rule_packages = decode_packages(options["rule_packages"])
+        for model_name in options["model_names"]:
+            model_name = model_name.lower()
+            if model_name == "enviformer" and s.ENVIFORMER_PRESENT:
+                model = EnviFormer.create(
+                    pack,
+                    data_packages=data_packages,
+                    eval_packages=eval_packages,
+                    threshold=0.5,
+                    name="EnviFormer - T0.5",
+                    description="EnviFormer transformer",
+                )
+            elif model_name == "mlrr":
+                model = MLRelativeReasoning.create(
+                    package=pack,
+                    rule_packages=rule_packages,
+                    data_packages=data_packages,
+                    eval_packages=eval_packages,
+                    threshold=0.5,
+                    name="ECC - BBD - T0.5",
+                    description="ML Relative Reasoning",
+                )
+            else:
+                raise ValueError(f"Cannot create model of type {model_name}, unknown model type")
+            # Build the dataset for the model, train it, evaluate it and save it
+            print(f"Building dataset for {model_name}")
+            model.build_dataset()
+            print(f"Training {model_name}")
+            model.build_model()
+            print(f"Evaluating {model_name}")
+            model.evaluate_model()
+            print(f"Saving {model_name}")
+            model.save()

epdb/management/commands/import_external_identifiers.py

@@ -0,0 +1,58 @@
+from csv import DictReader
+
+from django.core.management.base import BaseCommand
+from django.db import transaction
+
+from epdb.models import Compound, CompoundStructure, Reaction, ExternalDatabase, ExternalIdentifier
+
+
+class Command(BaseCommand):
+    STR_TO_MODEL = {
+        "Compound": Compound,
+        "CompoundStructure": CompoundStructure,
+        "Reaction": Reaction,
+    }
+
+    STR_TO_DATABASE = {
+        "ChEBI": ExternalDatabase.objects.get(name="ChEBI"),
+        "RHEA": ExternalDatabase.objects.get(name="RHEA"),
+        "KEGG Reaction": ExternalDatabase.objects.get(name="KEGG Reaction"),
+        "PubChem Compound": ExternalDatabase.objects.get(name="PubChem Compound"),
+        "PubChem Substance": ExternalDatabase.objects.get(name="PubChem Substance"),
+    }
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "--data",
+            type=str,
+            help="Path of the ID Mapping file.",
+            required=True,
+        )
+
+        parser.add_argument(
+            "--replace-host",
+            type=str,
+            help="Replace https://envipath.org/ with this host, e.g. http://localhost:8000/",
+        )
+
+    @transaction.atomic
+    def handle(self, *args, **options):
+        with open(options["data"]) as fh:
+            reader = DictReader(fh)
+            for row in reader:
+                clz = self.STR_TO_MODEL[row["model"]]
+
+                url = row["url"]
+                if options["replace_host"]:
+                    url = url.replace("https://envipath.org/", options["replace_host"])
+
+                instance = clz.objects.get(url=url)
+                db = self.STR_TO_DATABASE[row["identifier_type"]]
+
+                ExternalIdentifier.objects.create(
+                    content_object=instance,
+                    database=db,
+                    identifier_value=row["identifier_value"],
+                    url=db.url_pattern.format(id=row["identifier_value"]),
+                    is_primary=False,
+                )

epdb/management/commands/import_legacy_package.py

@@ -0,0 +1,29 @@
+import json
+
+from django.core.management.base import BaseCommand
+from django.db import transaction
+
+from epdb.logic import PackageManager
+from epdb.models import User
+
+
+class Command(BaseCommand):
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "--data",
+            type=str,
+            help="Path of the Package to import.",
+            required=True,
+        )
+        parser.add_argument(
+            "--owner",
+            type=str,
+            help="Username of the desired Owner.",
+            required=True,
+        )
+
+    @transaction.atomic
+    def handle(self, *args, **options):
+        owner = User.objects.get(username=options["owner"])
+        package_data = json.load(open(options["data"]))
+        PackageManager.import_legacy_package(package_data, owner)

epdb/management/commands/localize_urls.py

@@ -0,0 +1,64 @@
+from django.apps import apps
+from django.core.management.base import BaseCommand
+
+from django.db.models import F, Value, TextField, JSONField
+from django.db.models.functions import Replace, Cast
+
+from epdb.models import EnviPathModel
+
+
+class Command(BaseCommand):
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "--old",
+            type=str,
+            help="Old Host, most likely https://envipath.org/",
+            required=True,
+        )
+        parser.add_argument(
+            "--new",
+            type=str,
+            help="New Host, most likely http://localhost:8000/",
+            required=True,
+        )
+
+    def handle(self, *args, **options):
+        MODELS = [
+            "User",
+            "Group",
+            "Package",
+            "Compound",
+            "CompoundStructure",
+            "Pathway",
+            "Edge",
+            "Node",
+            "Reaction",
+            "SimpleAmbitRule",
+            "SimpleRDKitRule",
+            "ParallelRule",
+            "SequentialRule",
+            "Scenario",
+            "Setting",
+            "MLRelativeReasoning",
+            "RuleBasedRelativeReasoning",
+            "EnviFormer",
+            "ApplicabilityDomain",
+            "EnzymeLink",
+        ]
+        for model in MODELS:
+            obj_cls = apps.get_model("epdb", model)
+            print(f"Localizing urls for {model}")
+            obj_cls.objects.update(
+                url=Replace(F("url"), Value(options["old"]), Value(options["new"]))
+            )
+            if issubclass(obj_cls, EnviPathModel):
+                obj_cls.objects.update(
+                    kv=Cast(
+                        Replace(
+                            Cast(F("kv"), output_field=TextField()),
+                            Value(options["old"]),
+                            Value(options["new"]),
+                        ),
+                        output_field=JSONField(),
+                    )
+                )

epdb/middleware/login_required_middleware.py

@@ -0,0 +1,27 @@
+from django.conf import settings
+from django.shortcuts import redirect
+from django.urls import reverse
+from urllib.parse import quote
+
+
+class LoginRequiredMiddleware:
+    def __init__(self, get_response):
+        self.get_response = get_response
+        self.exempt_urls = [
+            reverse("login"),
+            reverse("logout"),
+            reverse("admin:login"),
+            reverse("admin:index"),
+        ] + getattr(settings, "LOGIN_EXEMPT_URLS", [])
+
+    def __call__(self, request):
+        if not request.user.is_authenticated:
+            path = request.path_info
+            if not any(path.startswith(url) for url in self.exempt_urls):
+                if request.method == "GET":
+                    if request.get_full_path() and request.get_full_path() != "/":
+                        return redirect(
+                            f"{settings.LOGIN_URL}?next={quote(request.get_full_path())}"
+                        )
+                return redirect(settings.LOGIN_URL)
+        return self.get_response(request)

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/signals.py

@@ -0,0 +1,37 @@
+import logging
+import os
+
+from django.conf import settings as s
+from django.db import transaction
+from django.db.models.signals import pre_delete, post_delete
+from django.dispatch import receiver
+
+from epdb.models import Node, Edge, EPModel
+
+logger = logging.getLogger(__name__)
+
+
+@receiver(pre_delete, sender=Node)
+@transaction.atomic
+def delete_orphan_edges(sender, instance, **kwargs):
+    # check if the node that is about to be deleted is the only start node
+    for edge in Edge.objects.filter(start_nodes=instance):
+        if edge.start_nodes.count() == 1:
+            edge.delete()
+
+    # same for end_nodes
+    for edge in Edge.objects.filter(end_nodes=instance):
+        # check if the node that is about to be deleted is the only start node
+        if edge.end_nodes.count() == 1:
+            edge.delete()
+
+
+@receiver(post_delete, sender=EPModel)
+def delete_epmodel_files(sender, instance, **kwargs):
+    # Delete the files on disk for the deleted model
+    mod_uuid = str(instance.uuid)
+
+    for f in os.listdir(s.MODEL_DIR):
+        if f.startswith(mod_uuid):
+            logger.info(f"Deleting {os.path.join(s.MODEL_DIR, f)}")
+            os.remove(os.path.join(s.MODEL_DIR, f))

epdb/tasks.py

@@ -0,0 +1,85 @@
+import logging
+from typing import Optional
+
+from celery import shared_task
+from epdb.models import Pathway, Node, EPModel, Setting
+from epdb.logic import SPathway
+
+
+logger = logging.getLogger(__name__)
+
+
+@shared_task(queue="background")
+def mul(a, b):
+    return a * b
+
+
+@shared_task(queue="predict")
+def predict_simple(model_pk: int, smiles: str):
+    mod = EPModel.objects.get(id=model_pk)
+    res = mod.predict(smiles)
+    return res
+
+
+@shared_task(queue="background")
+def send_registration_mail(user_pk: int):
+    pass
+
+
+@shared_task(queue="model")
+def build_model(model_pk: int):
+    mod = EPModel.objects.get(id=model_pk)
+    mod.build_dataset()
+    mod.build_model()
+
+
+@shared_task(queue="model")
+def evaluate_model(model_pk: int):
+    mod = EPModel.objects.get(id=model_pk)
+    mod.evaluate_model()
+
+
+@shared_task(queue="model")
+def retrain(model_pk: int):
+    mod = EPModel.objects.get(id=model_pk)
+    mod.retrain()
+
+
+@shared_task(queue="predict")
+def predict(
+    pw_pk: int, pred_setting_pk: int, limit: Optional[int] = None, node_pk: Optional[int] = None
+) -> Pathway:
+    pw = Pathway.objects.get(id=pw_pk)
+    setting = Setting.objects.get(id=pred_setting_pk)
+
+    pw.kv.update(**{"status": "running"})
+    pw.save()
+
+    try:
+        # regular prediction
+        if limit is not None:
+            spw = SPathway(prediction_setting=setting, persist=pw)
+            level = 0
+            while not spw.done:
+                spw.predict_step(from_depth=level)
+                level += 1
+
+                # break in case we are in incremental mode
+                if limit != -1:
+                    if level >= limit:
+                        break
+
+        elif node_pk is not None:
+            n = Node.objects.get(id=node_pk, pathway=pw)
+            spw = SPathway.from_pathway(pw)
+            spw.predict_step(from_node=n)
+        else:
+            raise ValueError("Neither limit nor node_pk given!")
+
+    except Exception as e:
+        pw.kv.update({"status": "failed"})
+        pw.save()
+        raise e
+
+    pw.kv.update(**{"status": "completed"})
+    pw.save()

epdb/templatetags/envipytags.py

@@ -0,0 +1,8 @@
+from django import template
+
+register = template.Library()
+
+
+@register.filter
+def classname(obj):
+    return obj.__class__.__name__

epdb/urls.py

@@ -0,0 +1,195 @@
+from django.contrib.auth import views as auth_views
+from django.urls import path, re_path
+
+from . import views as v
+
+UUID = "[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}"
+
+urlpatterns = [
+    # Home
+    re_path(r"^$", v.index, name="index"),
+    # Login
+    re_path(r"^login", v.login, name="login"),
+    re_path(r"^logout", v.logout, name="logout"),
+    re_path(r"^register", v.register, name="register"),
+    # Built-In views
+    path(
+        "password_reset/",
+        auth_views.PasswordResetView.as_view(template_name="static/password_reset_form.html"),
+        name="password_reset",
+    ),
+    path(
+        "password_reset/done/",
+        auth_views.PasswordResetDoneView.as_view(template_name="static/password_reset_done.html"),
+        name="password_reset_done",
+    ),
+    path(
+        "reset/<uidb64>/<token>/",
+        auth_views.PasswordResetConfirmView.as_view(
+            template_name="static/password_reset_confirm.html"
+        ),
+        name="password_reset_confirm",
+    ),
+    path(
+        "reset/done/",
+        auth_views.PasswordResetCompleteView.as_view(
+            template_name="static/password_reset_complete.html"
+        ),
+        name="password_reset_complete",
+    ),
+    # Top level urls
+    re_path(r"^package$", v.packages, name="packages"),
+    re_path(r"^compound$", v.compounds, name="compounds"),
+    re_path(r"^rule$", v.rules, name="rules"),
+    re_path(r"^reaction$", v.reactions, name="reactions"),
+    re_path(r"^pathway$", v.pathways, name="pathways"),
+    re_path(r"^scenario$", v.scenarios, name="scenarios"),
+    re_path(r"^model$", v.models, name="model"),
+    re_path(r"^user$", v.users, name="users"),
+    re_path(r"^group$", v.groups, name="groups"),
+    re_path(r"^search$", v.search, name="search"),
+    # User Detail
+    re_path(rf"^user/(?P<user_uuid>{UUID})", v.user, name="user"),
+    # Group Detail
+    re_path(rf"^group/(?P<group_uuid>{UUID})$", v.group, name="group detail"),
+    # "in package" urls
+    re_path(rf"^package/(?P<package_uuid>{UUID})$", v.package, name="package detail"),
+    # Compound
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/compound$",
+        v.package_compounds,
+        name="package compound list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})$",
+        v.package_compound,
+        name="package compound detail",
+    ),
+    # Compound Structure
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})/structure$",
+        v.package_compound_structures,
+        name="package compound structure list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})/structure/(?P<structure_uuid>{UUID})$",
+        v.package_compound_structure,
+        name="package compound structure detail",
+    ),
+    # Rule
+    re_path(rf"^package/(?P<package_uuid>{UUID})/rule$", v.package_rules, name="package rule list"),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/rule/(?P<rule_uuid>{UUID})$",
+        v.package_rule,
+        name="package rule detail",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/simple-ambit-rule/(?P<rule_uuid>{UUID})$",
+        v.package_rule,
+        name="package rule detail",
+    ),
+    # re_path(
+    #     rf"^package/(?P<package_uuid>{UUID})/simple-rdkit-rule/(?P<rule_uuid>{UUID})$",
+    #     v.package_rule,
+    #     name="package rule detail",
+    # ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/parallel-rule/(?P<rule_uuid>{UUID})$",
+        v.package_rule,
+        name="package rule detail",
+    ),
+    # re_path(
+    #     rf"^package/(?P<package_uuid>{UUID})/sequential-rule/(?P<rule_uuid>{UUID})$",
+    #     v.package_rule,
+    #     name="package rule detail",
+    # ),
+    # EnzymeLinks
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/rule/(?P<rule_uuid>{UUID})/enzymelink/(?P<enzymelink_uuid>{UUID})$",
+        v.package_rule_enzymelink,
+        name="package rule enzymelink detail",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/simple-ambit-rule/(?P<rule_uuid>{UUID})/enzymelink/(?P<enzymelink_uuid>{UUID})$",
+        v.package_rule_enzymelink,
+        name="package rule enzymelink detail",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/parallel-rule/(?P<rule_uuid>{UUID})/enzymelink/(?P<enzymelink_uuid>{UUID})$",
+        v.package_rule_enzymelink,
+        name="package rule enzymelink detail",
+    ),
+    # Reaction
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/reaction$",
+        v.package_reactions,
+        name="package reaction list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/reaction/(?P<reaction_uuid>{UUID})$",
+        v.package_reaction,
+        name="package reaction detail",
+    ),
+    # # Pathway
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/pathway$",
+        v.package_pathways,
+        name="package pathway list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})$",
+        v.package_pathway,
+        name="package pathway detail",
+    ),
+    # Pathway Nodes
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node$",
+        v.package_pathway_nodes,
+        name="package pathway node list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node/(?P<node_uuid>{UUID})$",
+        v.package_pathway_node,
+        name="package pathway node detail",
+    ),
+    # Pathway Edges
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge$",
+        v.package_pathway_edges,
+        name="package pathway edge list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge/(?P<edge_uuid>{UUID})$",
+        v.package_pathway_edge,
+        name="package pathway edge detail",
+    ),
+    # Scenario
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/scenario$",
+        v.package_scenarios,
+        name="package scenario list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/scenario/(?P<scenario_uuid>{UUID})$",
+        v.package_scenario,
+        name="package scenario detail",
+    ),
+    # Model
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/model$", v.package_models, name="package model list"
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/model/(?P<model_uuid>{UUID})$",
+        v.package_model,
+        name="package model detail",
+    ),
+    re_path(r"^setting$", v.settings, name="settings"),
+    re_path(rf"^setting/(?P<setting_uuid>{UUID})", v.setting, name="setting"),
+    re_path(r"^indigo/info$", v.indigo, name="indigo_info"),
+    re_path(r"^indigo/aromatize$", v.aromatize, name="indigo_aromatize"),
+    re_path(r"^indigo/dearomatize$", v.dearomatize, name="indigo_dearomatize"),
+    re_path(r"^indigo/layout$", v.layout, name="indigo_layout"),
+    re_path(r"^depict$", v.depict, name="depict"),
+    # OAuth Stuff
+    path("o/userinfo/", v.userinfo, name="oauth_userinfo"),
+]

manage.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python
+"""Django's command-line utility for administrative tasks."""
+import os
+import sys
+
+
+def main():
+    """Run administrative tasks."""
+    os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'envipath.settings')
+    try:
+        from django.core.management import execute_from_command_line
+    except ImportError as exc:
+        raise ImportError(
+            "Couldn't import Django. Are you sure it's installed and "
+            "available on your PYTHONPATH environment variable? Did you "
+            "forget to activate a virtual environment?"
+        ) from exc
+    execute_from_command_line(sys.argv)
+
+
+if __name__ == '__main__':
+    main()

migration/admin.py

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

migration/apps.py

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

migration/models.py

@@ -0,0 +1,3 @@
+from django.db import models
+
+# Create your models here.

migration/tests.py

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

migration/urls.py

@@ -0,0 +1,16 @@
+from django.urls import re_path
+
+from . import views as v
+
+UUID = '[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}'
+
+urlpatterns = [
+    re_path(rf'^migration$', v.migration, name='migration'),
+    re_path(rf'^migration/package/(?P<package_uuid>{UUID})/rule/(?P<rule_uuid>{UUID})$', v.migration_detail, name='migration detail'),
+    re_path(rf'^migration/package/(?P<package_uuid>{UUID})/simple-rule/(?P<rule_uuid>{UUID})$',v.migration_detail, name='migration detail'),
+    re_path(rf'^migration/package/(?P<package_uuid>{UUID})/simple-ambit-rule/(?P<rule_uuid>{UUID})$', v.migration_detail, name='migration detail'),
+    re_path(rf'^migration/package/(?P<package_uuid>{UUID})/simple-rdkit-rule/(?P<rule_uuid>{UUID})$', v.migration_detail, name='migration detail'),
+    re_path(rf'^migration/package/(?P<package_uuid>{UUID})/parallel-rule/(?P<rule_uuid>{UUID})$', v.migration_detail, name='migration detail'),
+    re_path(rf'^migration/package/(?P<package_uuid>{UUID})/sequential-rule/(?P<rule_uuid>{UUID})$', v.migration_detail, name='migration detail'),
+    re_path(rf'^migration/compare$', v.compare, name='compare'),
+]

migration/views.py

@@ -0,0 +1,277 @@
+import gzip
+import json
+import logging
+import os.path
+from datetime import datetime
+
+from django.conf import settings as s
+from django.http import HttpResponseNotAllowed
+from django.shortcuts import render
+
+from epdb.logic import PackageManager
+from epdb.models import Rule, SimpleAmbitRule, Package, CompoundStructure
+from epdb.views import get_base_context, _anonymous_or_real
+from utilities.chem import FormatConverter
+
+
+from rdkit import Chem
+from rdkit.Chem.MolStandardize import rdMolStandardize
+
+logger = logging.getLogger(__name__)
+
+
+def normalize_smiles(smiles):
+    m1 = Chem.MolFromSmiles(smiles)
+    if m1 is None:
+        print("Couldnt read smi: ", smiles)
+        return smiles
+    Chem.RemoveStereochemistry(m1)
+    # Normalizer takes care of charge/tautomer/resonance standardization
+    normalizer = rdMolStandardize.Normalizer()
+    return Chem.MolToSmiles(normalizer.normalize(m1), canonical=True)
+
+
+def run_both_engines(SMILES, SMIRKS):
+    from envipy_ambit import apply
+
+    ambit_res = apply(SMIRKS, SMILES)
+    # ambit_res, ambit_errors = FormatConverter.sanitize_smiles([str(s) for s in ambit_res])
+
+    ambit_res = list(
+        set(
+            [
+                normalize_smiles(str(x))
+                for x in FormatConverter.sanitize_smiles([str(s) for s in ambit_res])[0]
+            ]
+        )
+    )
+
+    products = FormatConverter.apply(SMILES, SMIRKS)
+
+    all_rdkit_prods = []
+    for ps in products:
+        for p in ps:
+            all_rdkit_prods.append(p)
+
+    all_rdkit_prods = list(set(all_rdkit_prods))
+    # all_rdkit_res, rdkit_errors = FormatConverter.sanitize_smiles(all_rdkit_prods)
+    all_rdkit_res = list(
+        set(
+            [
+                normalize_smiles(str(x))
+                for x in FormatConverter.sanitize_smiles(
+                    [str(s) for s in all_rdkit_prods]
+                )[0]
+            ]
+        )
+    )
+    # return ambit_res, ambit_errors, all_rdkit_res, rdkit_errors
+    return ambit_res, 0, all_rdkit_res, 0
+
+
+def migration(request):
+    if request.method == "GET":
+        context = get_base_context(request)
+
+        if (
+            os.path.exists(s.BASE_DIR / "fixtures" / "migration_status_per_rule.json")
+            and request.GET.get("force") is None
+        ):
+            migration_status = json.load(
+                open(s.BASE_DIR / "fixtures" / "migration_status_per_rule.json")
+            )
+        else:
+            BBD = Package.objects.get(
+                url="http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1"
+            )
+            ALL_SMILES = [
+                cs.smiles
+                for cs in CompoundStructure.objects.filter(compound__package=BBD)
+            ]
+            RULES = SimpleAmbitRule.objects.filter(package=BBD)
+
+            results = list()
+            num_rules = len(RULES)
+            success = 0
+            error = 0
+            total = 0
+
+            for i, r in enumerate(RULES):
+                logger.debug(f"\r{i + 1:03d}/{num_rules}")
+                res = True
+                for smiles in ALL_SMILES:
+                    try:
+                        ambit_res, _, rdkit_res, _ = run_both_engines(smiles, r.smirks)
+
+                        res &= set(ambit_res) == set(rdkit_res)
+                    except Exception as e:
+                        logger.error(e)
+
+                results.append(
+                    {
+                        "name": r.name,
+                        "detail_url": s.SERVER_URL
+                        + "/migration/"
+                        + r.url.replace("https://envipath.org/", "").replace(
+                            "http://localhost:8000/", ""
+                        ),
+                        "id": str(r.uuid),
+                        "url": r.url,
+                        "status": res,
+                    }
+                )
+
+                if res:
+                    success += 1
+                else:
+                    error += 1
+
+                total += 1
+            results = sorted(results, key=lambda x: (x["status"], x["name"]))
+
+            migration_status = {
+                "results": results,
+                "success": success,
+                "error": error,
+                "total": total,
+            }
+
+            json.dump(
+                migration_status,
+                open(s.BASE_DIR / "fixtures" / "migration_status_per_rule.json", "w"),
+            )
+
+        for r in migration_status["results"]:
+            r["detail_url"] = r["detail_url"].replace(
+                "http://localhost:8000", s.SERVER_URL
+            )
+
+        context.update(**migration_status)
+
+        return render(request, "migration.html", context)
+
+
+def migration_detail(request, package_uuid, rule_uuid):
+    current_user = _anonymous_or_real(request)
+
+    if request.method == "GET":
+        context = get_base_context(request)
+
+        BBD = Package.objects.get(name="EAWAG-BBD")
+        STRUCTURES = CompoundStructure.objects.filter(compound__package=BBD)
+        rule = Rule.objects.get(package=BBD, uuid=rule_uuid)
+
+        bt_rule_name = rule.name
+        smirks = rule.smirks
+
+        res = True
+        results = []
+
+        all_prods = set()
+        for structure in STRUCTURES:
+            ambit_smiles, ambit_errors, rdkit_smiles, rdkit_errors = run_both_engines(
+                structure.smiles, smirks
+            )
+
+            for x in ambit_smiles:
+                all_prods.add(x)
+
+            # TODO mode "intersection"
+            # partial_res = (len(set(ambit_smiles).intersection(set(rdkit_smiles))) > 0) or (len(ambit_smiles) == 0)
+            # FAILED (failures=18)
+
+            # TODO mode = "full ambit"
+            # partial_res = len(set(ambit_smiles).intersection(set(rdkit_smiles))) == len(set(ambit_smiles))
+            # FAILED (failures=34)
+
+            # TODO mode = "equality"
+            partial_res = set(ambit_smiles) == set(rdkit_smiles)
+            # FAILED (failures=30)
+
+            if len(ambit_smiles) or len(rdkit_smiles):
+                temp = {
+                    "url": structure.url,
+                    "id": str(structure.uuid),
+                    "name": structure.name,
+                    "initial_smiles": structure.smiles,
+                    "ambit_smiles": sorted(list(ambit_smiles)),
+                    "rdkit_smiles": sorted(list(rdkit_smiles)),
+                    "status": set(ambit_smiles) == set(rdkit_smiles),
+                }
+                detail = f"""
+                        BT: {bt_rule_name}
+                        SMIRKS: {smirks}
+                        Compound: {structure.smiles}
+                        Compound URL: {structure.url}
+                        Num ambit: {len(set(ambit_smiles))}
+                        Num rdkit: {len(set(rdkit_smiles))}
+                        Num Intersection A: {len(set(ambit_smiles).intersection(set(rdkit_smiles)))}
+                        Num Intersection B: {len(set(rdkit_smiles).intersection(set(ambit_smiles)))}
+                        Difference A: {set(ambit_smiles).difference(set(rdkit_smiles))}
+                        Difference B: {set(rdkit_smiles).difference(set(ambit_smiles))}
+                        ambit products: {ambit_smiles}
+                        rdkit products: {rdkit_smiles}
+                        ambit_errors: {ambit_errors}
+                        rdkit_errors: {rdkit_errors}
+                    """
+
+                temp["detail"] = "\n".join([x.strip() for x in detail.split("\n")])
+
+                results.append(temp)
+
+            res &= partial_res
+
+        results = sorted(results, key=lambda x: x["status"])
+        context["results"] = results
+        context["res"] = res
+        context["bt_rule_name"] = bt_rule_name
+        return render(request, "migration_detail.html", context)
+
+
+def compare(request):
+    context = get_base_context(request)
+
+    if request.method == "GET":
+        context["smirks"] = (
+            "[#1,#6:6][#7;X3;!$(NC1CC1)!$([N][C]=O)!$([!#8]CNC=O):1]([#1,#6:7])[#6;A;X4:2][H:3]>>[#1,#6:6][#7;X3:1]([#1,#6:7])[H:3].[#6;A:2]=O"
+        )
+        context["smiles"] = (
+            "C(CC(=O)N[C@@H](CS[Se-])C(=O)NCC(=O)[O-])[C@@H](C(=O)[O-])N"
+        )
+        return render(request, "compare.html", context)
+
+    elif request.method == "POST":
+        smiles = request.POST.get("smiles")
+        smirks = request.POST.get("smirks")
+
+        from envipy_ambit import apply
+
+        ambit_res = apply(smirks, smiles)
+        ambit_res, _ = FormatConverter.sanitize_smiles([str(x) for x in ambit_res])
+
+        products = FormatConverter.apply(smiles, smirks)
+
+        all_rdkit_prods = []
+        for ps in products:
+            for p in ps:
+                all_rdkit_prods.append(p)
+
+        all_rdkit_prods = list(set(all_rdkit_prods))
+
+        rdkit_res, _ = FormatConverter.sanitize_smiles(all_rdkit_prods)
+        context["result"] = True
+        context["ambit_res"] = sorted(set(ambit_res))
+        context["rdkit_res"] = sorted(set(rdkit_res))
+        context["diff"] = sorted(set(ambit_res).difference(set(rdkit_res)))
+        context["smirks"] = smirks
+        context["smiles"] = smiles
+
+        r = SimpleAmbitRule.objects.filter(smirks=smirks)
+
+        if r.exists():
+            context["rule"] = r.first()
+
+        return render(request, "compare.html", context)
+
+    else:
+        return HttpResponseNotAllowed(["GET", "POST"])

pyproject.toml

@@ -0,0 +1,91 @@
+[project]
+name = "envipy"
+version = "0.1.0"
+description = "Add your description here"
+readme = "README.md"
+requires-python = ">=3.12"
+dependencies = [
+    "celery>=5.5.2",
+    "django>=5.2.1",
+    "django-extensions>=4.1",
+    "django-model-utils>=5.0.0",
+    "django-ninja>=1.4.1",
+    "django-oauth-toolkit>=3.0.1",
+    "django-polymorphic>=4.1.0",
+    "enviformer",
+    "envipy-additional-information",
+    "envipy-ambit>=0.1.0",
+    "envipy-plugins",
+    "epam-indigo>=1.30.1",
+    "gunicorn>=23.0.0",
+    "networkx>=3.4.2",
+    "psycopg2-binary>=2.9.10",
+    "python-dotenv>=1.1.0",
+    "rdkit>=2025.3.2",
+    "redis>=6.1.0",
+    "requests>=2.32.3",
+    "scikit-learn>=1.6.1",
+    "sentry-sdk[django]>=2.32.0",
+    "setuptools>=80.8.0",
+]
+
+[tool.uv.sources]
+enviformer = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git", rev = "v0.1.2" }
+envipy-plugins = { git = "ssh://git@git.envipath.com/enviPath/enviPy-plugins.git", rev = "v0.1.0" }
+envipy-additional-information = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git", rev = "v0.1.7"}
+envipy-ambit = { git = "ssh://git@git.envipath.com/enviPath/enviPy-ambit.git" }
+
+[project.optional-dependencies]
+ms-login = ["msal>=1.33.0"]
+dev = [
+    "celery-stubs==0.1.3",
+    "django-stubs>=5.2.4",
+    "poethepoet>=0.37.0",
+    "pre-commit>=4.3.0",
+    "ruff>=0.13.3",
+]
+
+[tool.ruff]
+line-length = 100
+
+[tool.ruff.lint]
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[tool.ruff.format]
+docstring-code-format = true
+
+# 4. Ignore `E402` (import violations) in all `__init__.py` files, and in selected subdirectories.
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["E402"]
+"**/{tests,docs,tools}/*" = ["E402"]
+
+[tool.poe.tasks]
+# Main tasks
+setup = { sequence = ["db-up", "migrate", "bootstrap"], help = "Complete setup: start database, run migrations, and bootstrap data" }
+dev = { cmd = "python manage.py runserver", help = "Start the development server", deps = ["db-up"] }
+
+# Database tasks
+db-up = { cmd = "docker compose -f docker-compose.dev.yml up -d", help = "Start PostgreSQL database using Docker Compose" }
+db-down = { cmd = "docker compose -f docker-compose.dev.yml down", help = "Stop PostgreSQL database" }
+
+# Full cleanup tasks
+clean = { sequence = ["clean-db"], help = "Remove model files and database volumes (WARNING: destroys all data!)" }
+clean-db = { cmd = "docker compose -f docker-compose.dev.yml down -v", help = "Removes the database container and volume." }
+
+# Django tasks
+migrate = { cmd = "python manage.py migrate", help = "Run database migrations" }
+bootstrap = { shell = """
+echo "Bootstrapping initial data..."
+echo "This will take a bit ⏱️. Get yourself some coffee..."
+python manage.py bootstrap
+echo "✓ Bootstrap complete"
+echo ""
+echo "Default admin credentials:"
+echo "  Username: admin"
+echo "  Email: admin@envipath.com"
+echo "  Password: SuperSafe"
+""", help = "Bootstrap initial data (anonymous user, packages, models)"  }
+shell = { cmd = "python manage.py shell", help = "Open Django shell" }

static/css/c3.css

@@ -0,0 +1,168 @@
+/*-- Chart --*/
+.c3 svg {
+  font: 10px sans-serif;
+  -webkit-tap-highlight-color: transparent; }
+
+.c3 path, .c3 line {
+  fill: none;
+  stroke: #000;
+  }
+
+.c3 text {
+  -webkit-user-select: none;
+  -moz-user-select: none;
+  user-select: none; }
+
+.c3-legend-item-tile,
+.c3-xgrid-focus,
+.c3-ygrid,
+.c3-event-rect,
+.c3-bars path {
+  shape-rendering: crispEdges; }
+
+.c3-chart-arc path {
+  stroke: #fff; }
+
+.c3-chart-arc text {
+  fill: #fff;
+  font-size: 13px; }
+
+/*-- Axis --*/
+/*-- Grid --*/
+.c3-grid line {
+  stroke: #aaa; }
+
+.c3-grid text {
+  fill: #aaa; }
+
+.c3-xgrid, .c3-ygrid {
+  stroke-dasharray: 3 3; }
+
+/*-- Text on Chart --*/
+.c3-text.c3-empty {
+  fill: #808080;
+  font-size: 2em; }
+
+/*-- Line --*/
+.c3-line {
+  stroke-width: 1px; }
+
+/*-- Point --*/
+.c3-circle._expanded_ {
+  stroke-width: 1px;
+  stroke: white; }
+
+.c3-selected-circle {
+  fill: white;
+  stroke-width: 2px; }
+
+/*-- Bar --*/
+.c3-bar {
+  stroke-width: 0; }
+
+.c3-bar._expanded_ {
+  fill-opacity: 0.75; }
+
+/*-- Focus --*/
+.c3-target.c3-focused {
+  opacity: 1; }
+
+.c3-target.c3-focused path.c3-line, .c3-target.c3-focused path.c3-step {
+  stroke-width: 2px; }
+
+.c3-target.c3-defocused {
+  opacity: 0.3 !important; }
+
+/*-- Region --*/
+.c3-region {
+  fill: steelblue;
+  fill-opacity: .1; }
+
+/*-- Brush --*/
+.c3-brush .extent {
+  fill-opacity: .1; }
+
+/*-- Select - Drag --*/
+/*-- Legend --*/
+.c3-legend-item {
+  font-size: 12px; }
+
+.c3-legend-item-hidden {
+  opacity: 0.15; }
+
+.c3-legend-background {
+  opacity: 0.75;
+  fill: white;
+  stroke: lightgray;
+  stroke-width: 1; }
+
+/*-- Title --*/
+.c3-title {
+  font: 14px sans-serif; }
+
+/*-- Tooltip --*/
+.c3-tooltip-container {
+  z-index: 10; }
+
+.c3-tooltip {
+  border-collapse: collapse;
+  border-spacing: 0;
+  background-color: #fff;
+  empty-cells: show;
+  -webkit-box-shadow: 7px 7px 12px -9px #777777;
+  -moz-box-shadow: 7px 7px 12px -9px #777777;
+  box-shadow: 7px 7px 12px -9px #777777;
+  opacity: 0.9; }
+
+.c3-tooltip tr {
+  border: 1px solid #CCC; }
+
+.c3-tooltip th {
+  background-color: #aaa;
+  font-size: 14px;
+  padding: 2px 5px;
+  text-align: left;
+  color: #FFF; }
+
+.c3-tooltip td {
+  font-size: 13px;
+  padding: 3px 6px;
+  background-color: #fff;
+  border-left: 1px dotted #999; }
+
+.c3-tooltip td > span {
+  display: inline-block;
+  width: 10px;
+  height: 10px;
+  margin-right: 6px; }
+
+.c3-tooltip td.value {
+  text-align: right; }
+
+/*-- Area --*/
+.c3-area {
+  stroke-width: 0;
+  opacity: 0.2; }
+
+/*-- Arc --*/
+.c3-chart-arcs-title {
+  dominant-baseline: middle;
+  font-size: 1.3em; }
+
+.c3-chart-arcs .c3-chart-arcs-background {
+  fill: #e0e0e0;
+  stroke: none; }
+
+.c3-chart-arcs .c3-chart-arcs-gauge-unit {
+  fill: #000;
+  font-size: 16px; }
+
+.c3-chart-arcs .c3-chart-arcs-gauge-max {
+  fill: #777; }
+
+.c3-chart-arcs .c3-chart-arcs-gauge-min {
+  fill: #777; }
+
+.c3-chart-arc .c3-gauge-value {
+  fill: #000;
+  /*  font-size: 28px !important;*/ }

static/css/epp.css

@@ -0,0 +1,126 @@
+
+.mini-submenu{
+  display:none;
+  background-color: rgba(0, 0, 0, 0);
+  border: 1px solid rgba(0, 0, 0, 0.9);
+  border-radius: 4px;
+  padding: 9px;
+  /*position: relative;*/
+  width: 42px;
+
+}
+
+.mini-submenu:hover{
+  cursor: pointer;
+}
+
+.mini-submenu .icon-bar {
+  border-radius: 1px;
+  display: block;
+  height: 2px;
+  width: 22px;
+  margin-top: 3px;
+}
+
+.mini-submenu .icon-bar {
+  background-color: #000;
+}
+
+#slide-submenu{
+  background: rgba(0, 0, 0, 0.45);
+  display: inline-block;
+  padding: 0 8px;
+  border-radius: 4px;
+  cursor: pointer;
+}
+
+#eductsdiv {
+	float:left;
+}
+#agentsdiv {
+	float:left;
+}
+#productsdiv {
+	float:left;
+}
+#actions {
+	float:left;
+}
+
+.modal.fade .modal-dialog {
+  overflow-y: auto;
+  max-height: 800px;
+}
+
+.modal-dialog-multiple {
+  position: relative;
+  overflow: visible;
+  width: 600px;
+  margin: 30px auto;
+  max-height: 800px;
+ }
+
+.modal-element{
+  padding-top: 10px;
+  margin-top: 5px;
+  margin-bottom: 5px;
+
+  border-top: 1px solid #e5e5e5;
+}
+
+.modal-dialog-pps{
+  position: relative;
+  display: table;
+  margin-left: 35%;
+  margin-right: 35%;
+  overflow-y: auto;
+  overflow-x: auto;
+  width: 30%;
+}
+
+.modal-dialog-pps-big{
+  position: relative;
+  display: table;
+  margin-left: 25%;
+  margin-right: 25%;
+  overflow-y: auto;
+  overflow-x: auto;
+  width: 50%;
+}
+
+    @media (max-width: 1220px) {
+    .navbar-header-framework {
+        float: none;
+    }
+    .navbar-left-framework,.navbar-right-framework {
+        float: none !important;
+    }
+    .navbar-toggle-framework {
+        display: block;
+    }
+    .navbar-collapse-framework {
+        border-top: 1px solid transparent;
+        box-shadow: inset 0 1px 0 rgba(255,255,255,0.1);
+    }
+    .navbar-fixed-top-framework {
+        top: 0;
+        border-width: 0 0 1px;
+    }
+    .navbar-collapse-framework.collapse {
+        display: none!important;
+    }
+    .navbar-nav-framework {
+        float: none!important;
+        margin-top: 7.5px;
+    }
+    .navbar-nav-framework>li {
+        float: none;
+    }
+    .navbar-nav-framework>li>a {
+        padding-top: 10px;
+        padding-bottom: 10px;
+    }
+    .collapse-framework.in{
+        display:block !important;
+    }
+    }

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+
+<svg
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+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns="http://www.w3.org/2000/svg"
+   version="1.1"
+   width="314.98749"
+   height="28.8125"
+   id="svg3004"
+   xml:space="preserve"><metadata
+     id="metadata3010"><rdf:RDF><cc:Work
+         rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" /><dc:title></dc:title></cc:Work></rdf:RDF></metadata><defs
+     id="defs3008" /><g
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+</svg>

static/js/epp/epp.js

@@ -0,0 +1,217 @@
+class Setting {
+  constructor(nameInputId, selectedPackagesId, relativeReasoningSelectId, cutoffInputId, evaluationTypeSelectId,
+              availableTSSelectId, formsId, tableId, summaryTableId) {
+    this.nameInputId = nameInputId;
+    this.selectedPackagesId = selectedPackagesId;
+    this.relativeReasoningSelectId = relativeReasoningSelectId;
+    this.cutoffInputId = cutoffInputId;
+    this.evaluationTypeSelectId = evaluationTypeSelectId;
+    this.availableTSSelectId = availableTSSelectId;
+    this.formsId = formsId;
+    this.tableId = tableId;
+    this.summaryTableId = summaryTableId;
+
+    // General settings
+    this.name = null;
+    this.selectedPackages = [];
+
+    // Relative Reasoning related
+    this.selectedRelativeReasoning = null;
+    this.cutoff = null;
+    this.evaluationType = null;
+
+    // parameters such as { "lowPH": 7, "highPH": 8 }
+    this.tsParams = {};
+  }
+
+  extractName() {
+    var tempName = $('#' + this.nameInputId).val()
+    if (tempName == '') {
+        console.log("Name was empty...");
+        return;
+    }
+    this.name = tempName;
+  }
+
+  extractSelectedPackages() {
+    var selPacks = $("#" + this.selectedPackagesId + " :selected");
+    var ref = this;
+    ref.selectedPackages = [];
+    selPacks.each(function () {
+      var obj = {}
+      obj['id'] = this.value;
+      obj['name'] = this.text;
+      ref.selectedPackages.push(obj);
+    });
+  }
+
+  extractRelativeReasoning() {
+    var tempRR = $('#' + this.relativeReasoningSelectId + " :selected").val()
+    if (tempRR == '') {
+        console.log("RR was empty...");
+        return;
+    }
+    var obj = {}
+    obj['id'] = $('#' + this.relativeReasoningSelectId + " :selected").val()
+    obj['name'] = $('#' + this.relativeReasoningSelectId + " :selected").text()
+    this.selectedRelativeReasoning = obj;
+  }
+
+  extractCutoff() {
+    var tempCutoff = $('#' + this.cutoffInputId).val()
+    if (tempCutoff == '') {
+        console.log("Cutoff was empty...");
+        return;
+    }
+    this.cutoff = tempCutoff;
+  }
+
+  extractEvaluationType() {
+    var tempEvaluationType = $('#' + this.evaluationTypeSelectId).val()
+    if (tempEvaluationType == '') {
+        console.log("EvaluationType was empty...");
+        return;
+    }
+    this.evaluationType = tempEvaluationType;
+  }
+
+  addTruncator() {
+    // triggered by "Add"
+    // will extract values and afterwards updates table + summary
+    var type = $("#" + this.availableTSSelectId + " :selected").val();
+    var text = $("#" + this.availableTSSelectId + " :selected").text();
+    var form = $("#" + type + "_form > :input")
+
+    // flag to check whether at least one input had a valid value
+    var addedValue = false;
+
+    // reference being used in each
+    var ref = this;
+
+    form.each(function() {
+        if(this.value == "" || this.value === "undefined"){
+            console.log(this);
+            console.log("Skipping " + this.name);
+        } else {
+            var obj = {}
+            obj[this.name] = this.value;
+            obj['text'] = text;
+            ref.tsParams[type] = obj
+        }
+    });
+
+    this.updateTable();
+    this.updateSummaryTable();
+  }
+
+  removeTruncator(rowId) {
+    var summary = rowId.startsWith("sum") ? true : false;
+    // plain key
+    var key = rowId.replace(summary ? "sum" : "trunc", "").replace("row", "");
+
+    console.log("Removing " + key);
+
+    // remove the rows
+    $("#trunc"+ key + "row").remove();
+    if($("#sum"+ key + "row").length > 0) {
+        $("#sum"+ key + "row").remove();
+    }
+
+    delete this.tsParams[key];
+  }
+
+  updateTable() {
+    // remove all children
+    $('#'+this.tableId + "Body").empty()
+
+    var innerHTML = "<tr>" +
+                      "<td>Name</td>" +
+                      "<td>Value</td>" +
+                      "<td width='10%'>Action</td>" +
+                    "</tr>";
+
+    for (var x in this.tsParams) {
+      var val = "";
+      for (var y in this.tsParams[x]){
+        if (y == 'text') {
+            continue;
+        }
+        val += this.tsParams[x][y]
+
+      }
+      innerHTML += "<tr id='trunc" + x + "row'>" +
+                     "<td>" + this.tsParams[x]['text'] + "</td>" +
+                     "<td>" + val + "</td>" +
+                     "<td width='10%'>"+
+                       "<button type='button' id='" + x + "button' class='form-control' onclick='s.removeTruncator(\"trunc" + x + "row\")'>Remove</button>" +
+                     "</td>" +
+                   "</tr>";
+    }
+
+    $('#'+this.tableId + "Body").append(innerHTML);
+  }
+
+  packageRows() {
+    var res = '';
+    for(var p in this.selectedPackages) {
+        var obj = this.selectedPackages[p];
+        res += "<tr>" +
+                 "<td>Package</td>" +
+                 "<td>" + obj['name'] + "</td>" +
+                 "<td width='10%'>" +
+                   // "<button type='button' id='relativereasoningbutton' class='form-control' onclick='s.removeTruncator(\"Relative Reasoning\")'>Remove</button>" +
+                 "</td>" +
+               "</tr>";
+    }
+    return res;
+  }
+
+  modelRow() {
+    if(this.selectedRelativeReasoning == null) {
+      return '';
+    }
+    return "<tr>" +
+             "<td>Relative Reasoning</td>" +
+             "<td>" + this.selectedRelativeReasoning['name'] + " " + (this.evaluationType == "singleGen" ? "SG" : "MG") + " with t=" + this.cutoff + " </td>" +
+             "<td width='10%'>" +
+               // "<button type='button' id='relativereasoningbutton' class='form-control' onclick='s.removeTruncator(\"Relative Reasoning\")'>Remove</button>" +
+             "</td>" +
+           "</tr>";
+  }
+
+  updateSummaryTable() {
+    // remove all children
+    $('#'+this.summaryTableId + "Body").empty()
+
+    var innerHTML = "<tr>" +
+                      "<td>Name</td>" +
+                      "<td>Value</td>" +
+                      "<td width='10%'>Action</td>" +
+                    "</tr>";
+
+    innerHTML += this.packageRows();
+    innerHTML += this.modelRow();
+
+    // var innerHTML = ''
+    for (var x in this.tsParams) {
+      var val = "";
+      for (var y in this.tsParams[x]){
+        if (y == 'text') {
+            continue;
+        }
+        val += this.tsParams[x][y]
+
+      }
+      innerHTML += "<tr id='sum" + x + "row'>" +
+                     "<td>" + this.tsParams[x]['text'] + "</td>" +
+                     "<td>" + val + "</td>" +
+                     "<td width='10%'>"+
+                       "<button type='button' id='" + x + "button' class='form-control' onclick='s.removeTruncator(\"sum" + x + "row\")'>Remove</button>" +
+                     "</td>" +
+                   "</tr>";
+    }
+
+    $('#'+this.summaryTableId + "Body").append(innerHTML);
+  }
+
+}

static/js/epp/jquery-bootstrap-modal-steps.js

@@ -0,0 +1 @@
+!function(t){"use strict";t.fn.modalSteps=function(a){var e=this,n=t.extend({btnCancelHtml:"Cancel",btnPreviousHtml:"Previous",btnNextHtml:"Next",btnLastStepHtml:"Complete",disableNextButton:!1,completeCallback:function(){},callbacks:{},getTitleAndStep:function(){}},a),d=function(t){return void 0!==t&&"function"==typeof t&&(t(),!0)};return e.on("show.bs.modal",function(){var a,l,s,i=e.find(".modal-footer"),o=i.find(".js-btn-step[data-orientation=cancel]"),p=i.find(".js-btn-step[data-orientation=previous]"),r=i.find(".js-btn-step[data-orientation=next]"),c=n.callbacks["*"],b=n.callbacks[1];n.disableNextButton&&r.attr("disabled","disabled"),p.attr("disabled","disabled"),function(){var t=n.callbacks["*"];if(void 0!==t&&"function"!=typeof t)throw"everyStepCallback is not a function! I need a function";if("function"!=typeof n.completeCallback)throw"completeCallback is not a function! I need a function";for(var a in n.callbacks)if(n.callbacks.hasOwnProperty(a)){var e=n.callbacks[a];if("*"!==a&&void 0!==e&&"function"!=typeof e)throw"Step "+a+" callback must be a function"}}(),d(c),d(b),o.html(n.btnCancelHtml),p.html(n.btnPreviousHtml),r.html(n.btnNextHtml),a=t("<input>").attr({type:"hidden",id:"actual-step",value:"1"}),e.find("#actual-step").remove(),e.append(a),e.find("[data-step=1]").removeClass("d-none"),r.attr("data-step",2),l=e.find("[data-step=1]").data("title"),s=t("<span>").addClass("label label-success").html(1),e.find(".js-title-step").append(s).append(" "+l),n.getTitleAndStep(a.attr("data-title"),1)}).on("hidden.bs.modal",function(){var t=e.find("#actual-step"),a=e.find(".js-btn-step[data-orientation=next]");e.find("[data-step]").not(e.find(".js-btn-step")).addClass("d-none"),t.not(e.find(".js-btn-step")).remove(),a.attr("data-step",1).html(n.btnNextHtml),e.find(".js-title-step").html("")}),e.find(".js-btn-step").on("click",function(){var a,l,s,i,o=t(this),p=e.find("#actual-step"),r=e.find(".js-btn-step[data-orientation=previous]"),c=e.find(".js-btn-step[data-orientation=next]"),b=e.find(".js-title-step"),f=o.data("orientation"),u=parseInt(p.val()),m=n.callbacks["*"];if(a=e.find("div[data-step]").length,"complete"===o.attr("data-step"))return n.completeCallback(),void e.modal("hide");if("next"===f)l=u+1,r.attr("data-step",u),p.val(l);else{if("previous"!==f)return void e.modal("hide");l=u-1,c.attr("data-step",u),r.attr("data-step",l-1),p.val(u-1)}parseInt(p.val())===a?c.attr("data-step","complete").html(n.btnLastStepHtml):c.attr("data-step",l).html(n.btnNextHtml),n.disableNextButton&&c.attr("disabled","disabled"),e.find("[data-step="+u+"]").not(e.find(".js-btn-step")).addClass("d-none"),e.find("[data-step="+l+"]").not(e.find(".js-btn-step")).removeClass("d-none"),parseInt(r.attr("data-step"))>0?r.removeAttr("disabled"):r.attr("disabled","disabled"),"previous"===f&&c.removeAttr("disabled"),(s=e.find("[data-step="+l+"]")).attr("data-unlock-continue")&&c.removeAttr("disabled"),i=s.attr("data-title");var v=t("<span>").addClass("label label-success").html(l);b.html(v).append(" "+i),n.getTitleAndStep(s.attr("data-title"),l);var h=n.callbacks[p.val()];d(m),d(h)}),this}}(jQuery);

static/js/epp/pathway.js

@@ -0,0 +1,191 @@
+// drawarea
+var svg;
+
+// colors
+var border = "thin solid lightgrey";
+
+
+// nodes
+
+
+// links
+
+// tree
+var compoundSize = 75; // = diameter of nodes of small compounds
+var maxCompoundSize = function(){ return 1.5 * compoundSize }; // limit increased size of larger compounds
+var maxCompoundPopupSize = function(){ return 5 * compoundSize };
+var compoundImageMargin = 0.15;  // compounds images are rectangles, reduce size to fit into nodes
+
+var treeLayoutLinkDistance = function(){ return 2.5 * compoundSize };
+var treeLayoutCharge = -1000; // compounds push each other apart
+var treeLayoutPseudoCharge = treeLayoutCharge * 0.1; // relaxes forces on pseudo nodes
+var treeLayoutLevelGravity = 0.5; // pulls compounds back to their depth level
+var treeLayoutXCenterGravity = 0.03; // pulls compounds to x center
+var treeLayoutLevels = function(){ return treeLayoutLinkDistance() }; // distance between depth levels
+var treeLayoutXInitMargin = function(){ return treeLayoutLinkDistance() }; // initial x-distance between nodes of same depth
+
+
+// Convenience method to check wether a given node is a leaf
+function isLeaf(node) {
+    return node.children.length == 0;
+}
+
+function getMaxNodeDepth(graph) {
+    maxDepth = 0
+    graph.nodes.forEach(function(node, i) {
+        if (node.depth > maxDepth)
+            maxDepth = node.depth;
+    });
+    return maxDepth;
+}
+
+// adds a parents[] and a children[] array for each node set treeSize
+function setChildrenAndParents(graph) {
+    // Init arrays on each node
+    graph.nodes.forEach(function(node, i) {
+        node.parents = []
+        node.children = []
+    });
+
+    // loop through links, determine source and target and populate
+    // their parent/children arrays
+    graph.links.forEach(function(link, j) {
+        source = graph.nodes[link.source];
+        target = graph.nodes[link.target];
+        source.children.push(target);
+        target.parents.push(source);
+    });
+
+    // Recursively traverses the tree to count the nodes that can be reached
+    function count(node) {
+        node.touch = true;
+        c = 1;
+        node.children.forEach(function(child, i) {
+            if (!child.touch) {
+                c += count(child);
+            }
+        });
+        node.count = false;
+        return c;
+    }
+
+    // Check how many nodes can be reached from each given node
+    // by traversing the children property
+    graph.nodes.forEach(function(node, i) {
+        // reset touch on all nodes
+        graph.nodes.forEach(function(n, i) {
+            n.touch = false;
+        });
+        // get count
+        node.downstreamNodeCount = count(node);
+    });
+
+    // determine siblings for each links
+    graph.links.forEach(function(link, j) {
+        p = graph.nodes[link.source].children.length;
+        c = graph.nodes[link.target].parents.length;
+        link.siblings = Math.max(p, c);
+    });
+}
+
+// sets all links to pseudo that are connected to a pseudo node
+function setPseudoLinks(graph) {
+    graph.links.forEach(function(link, j) {
+        if (graph.nodes[link.source].pseudo || graph.nodes[link.target].pseudo) {
+            link.pseudo = true;
+        } else {
+            link.pseudo = false;
+        }
+    });
+}
+
+function redraw() {
+    svg.attr("transform", "translate(" + d3.event.translate + ")" + " scale(" + d3.event.scale + ")");
+}
+
+function reset() {
+    // remove all;
+    svg.selectAll("g.node").remove();
+    svg.selectAll("rect").remove();
+    svg.selectAll("image").remove();
+    svg.selectAll("line").remove();
+    svg.selectAll("marker").remove();
+    svg.selectAll("text").remove();
+    svg.selectAll("g").remove();
+    svg.selectAll("defs").remove();
+    //start(__graph);
+}
+
+function _drawPathway(elem, graph, options) {
+    width = document.getElementById(elem).offsetWidth;
+    height = width * 0.75;
+
+    svg = d3.select("#" + elem)
+            .append("svg")
+            .attr("width", "100%")
+            .attr("height", height)
+            .style("border", border)
+            .attr("inline", "block")
+            .attr("margin", "auto")
+            .attr("pointer-events", "all")
+            .append('svg:g')
+            .call(d3.behavior.zoom().on("zoom", redraw))
+            .attr("preserveAspectRatio", "xMidYMid meet")
+            .append('svg:g');
+
+    // Background rectangle to enable zoom function
+    // even cursor is not on a node or path
+    svg.append('svg:rect')
+        .attr('width', 9 * width)
+        .attr('height', 9 * height)
+        .attr('fill', 'white')
+        .attr("x", -4 * width)
+        .attr("y", -4 * height)
+        .attr("opacity", 0.0);
+
+    setChildrenAndParents(graph)
+    setPseudoLinks(graph)
+    var maxDepths = getMaxNodeDepth(graph);
+
+//    if(options.treeLayout) {
+//
+//    } else {
+//
+//    }
+    force = d3.layout.force()
+                .charge(function(d) {
+                    if (d.pseudo) {
+                        return treeLayoutPseudoCharge;
+                    } else {
+                        return treeLayoutCharge;
+                    }
+                })
+                .gravity(0)
+                .linkDistance(function(d) {
+                    dist = Math.abs(d.target.treeLevel - d.source.treeLevel) * treeLayoutLinkDistance();
+                    if (dist == 0) {
+                        // nodes with depth in brackets: A (0) -> B (1) + C (2)
+                        // then there is a pseudo node that is on the same level as B
+                        dist = 0.5 * treeLayoutLinkDistance();
+                    }
+                    return dist;
+                })
+                .linkStrength(function(d) {
+                    return strength = 1 / d.siblings;
+                })
+                .size([width, height]);
+
+    force.nodes(graph.nodes).links(graph.links).start();
+
+}
+
+function drawPathway(elem, options) {
+
+    d3.json("", function(error, graph) {
+        if (graph) {
+            _drawPathway(elem, graph, options);
+        } else {
+            throw new Error("Graph not defined: " + error);
+        }
+    });
+}

static/js/jquery-bootstrap-modal-steps.js

@@ -0,0 +1,228 @@
+/* global jQuery */
+
+(function($){
+    'use strict';
+
+    $.fn.modalSteps = function(options){
+        var $modal = this;
+
+        var settings = $.extend({
+            btnCancelHtml: 'Cancel',
+            btnPreviousHtml: 'Previous',
+            btnNextHtml: 'Next',
+            btnLastStepHtml: 'Complete',
+            disableNextButton: false,
+            completeCallback: function(){},
+            callbacks: {}
+        }, options);
+
+
+        var validCallbacks = function(){
+            var everyStepCallback = settings.callbacks['*'];
+
+            if (everyStepCallback !== undefined && typeof(everyStepCallback) !== 'function'){
+                throw 'everyStepCallback is not a function! I need a function';
+            }
+
+            if (typeof(settings.completeCallback) !== 'function') {
+                throw 'completeCallback is not a function! I need a function';
+            }
+
+            for(var step in settings.callbacks){
+                if (settings.callbacks.hasOwnProperty(step)){
+                    var callback = settings.callbacks[step];
+
+                    if (step !== '*' && callback !== undefined && typeof(callback) !== 'function'){
+                        throw 'Step ' + step + ' callback must be a function';
+                    }
+                }
+            }
+        };
+
+        var executeCallback = function(callback){
+            if (callback !== undefined && typeof(callback) === 'function'){
+                callback();
+                return true;
+            }
+            return false;
+        };
+
+        $modal
+            .on('show.bs.modal', function(){
+                var $modalFooter = $modal.find('.modal-footer'),
+                    $btnCancel = $modalFooter.find('.js-btn-step[data-orientation=cancel]'),
+                    $btnPrevious = $modalFooter.find('.js-btn-step[data-orientation=previous]'),
+                    $btnNext = $modalFooter.find('.js-btn-step[data-orientation=next]'),
+                    everyStepCallback = settings.callbacks['*'],
+                    stepCallback = settings.callbacks['1'],
+                    actualStep,
+                    $actualStep,
+                    titleStep,
+                    $titleStepSpan,
+                    nextStep;
+
+                if (settings.disableNextButton){
+                    $btnNext.attr('disabled', 'disabled');
+                }
+                $btnPrevious.attr('disabled', 'disabled');
+
+                validCallbacks();
+                executeCallback(everyStepCallback);
+                executeCallback(stepCallback);
+
+                // Setting buttons
+                $btnCancel.html(settings.btnCancelHtml);
+                $btnPrevious.html(settings.btnPreviousHtml);
+                $btnNext.html(settings.btnNextHtml);
+
+                $actualStep = $('<input>').attr({
+                    'type': 'hidden',
+                    'id': 'actual-step',
+                    'value': '1',
+                });
+
+                $modal.find('#actual-step').remove();
+                $modal.append($actualStep);
+
+                actualStep = 1;
+                nextStep = actualStep + 1;
+
+                $modal.find('[data-step=' + actualStep + ']').removeClass('hide');
+                $btnNext.attr('data-step', nextStep);
+
+                titleStep = $modal.find('[data-step=' + actualStep + ']').data('title');
+                $titleStepSpan = $('<span>')
+                                    .addClass('label label-success')
+                                    .html(actualStep);
+
+                $modal
+                    .find('.js-title-step')
+                    .append($titleStepSpan)
+                    .append(' ' + titleStep);
+            })
+            .on('hidden.bs.modal', function(){
+                var $actualStep = $modal.find('#actual-step'),
+                    $btnNext = $modal.find('.js-btn-step[data-orientation=next]');
+
+                $modal
+                    .find('[data-step]')
+                    .not($modal.find('.js-btn-step'))
+                    .addClass('hide');
+
+                $actualStep
+                    .not($modal.find('.js-btn-step'))
+                    .remove();
+
+                $btnNext
+                    .attr('data-step', 1)
+                    .html(settings.btnNextHtml);
+
+                $modal.find('.js-title-step').html('');
+            });
+
+        $modal.find('.js-btn-step').on('click', function(){
+            var $btn = $(this),
+                $actualStep = $modal.find('#actual-step'),
+                $btnPrevious = $modal.find('.js-btn-step[data-orientation=previous]'),
+                $btnNext = $modal.find('.js-btn-step[data-orientation=next]'),
+                $title = $modal.find('.js-title-step'),
+                orientation = $btn.data('orientation'),
+                actualStep = parseInt($actualStep.val()),
+                everyStepCallback = settings.callbacks['*'],
+                steps,
+                nextStep,
+                $nextStep,
+                newTitle;
+
+            steps = $modal.find('div[data-step]').length;
+
+            // Callback on Complete
+            if ($btn.attr('data-step') === 'complete'){
+                settings.completeCallback();
+                $modal.modal('hide');
+
+                return;
+            }
+
+            // Check the orientation to make logical operations with actualStep/nextStep
+            if (orientation === 'next'){
+                nextStep = actualStep + 1;
+
+                $btnPrevious.attr('data-step', actualStep);
+                $actualStep.val(nextStep);
+
+            } else if (orientation === 'previous'){
+                nextStep = actualStep - 1;
+
+                $btnNext.attr('data-step', actualStep);
+                $btnPrevious.attr('data-step', nextStep - 1);
+
+                $actualStep.val(actualStep - 1);
+
+            } else {
+                $modal.modal('hide');
+                return;
+            }
+
+            if (parseInt($actualStep.val()) === steps){
+                $btnNext
+                    .attr('data-step', 'complete')
+                    .html(settings.btnLastStepHtml);
+            } else {
+                $btnNext
+                    .attr('data-step', nextStep)
+                    .html(settings.btnNextHtml);
+            }
+
+            if (settings.disableNextButton){
+                $btnNext.attr('disabled', 'disabled');
+            }
+
+            // Hide and Show steps
+            $modal
+                .find('[data-step=' + actualStep + ']')
+                .not($modal.find('.js-btn-step'))
+                .addClass('hide');
+
+            $modal
+                .find('[data-step=' + nextStep + ']')
+                .not($modal.find('.js-btn-step'))
+                .removeClass('hide');
+
+            // Just a check for the class of previous button
+            if (parseInt($btnPrevious.attr('data-step')) > 0 ){
+                $btnPrevious.removeAttr('disabled');
+            } else {
+                $btnPrevious.attr('disabled', 'disabled');
+            }
+
+            if (orientation === 'previous'){
+                $btnNext.removeAttr('disabled');
+            }
+
+            // Get the next step
+            $nextStep = $modal.find('[data-step=' + nextStep + ']');
+
+            // Verify if we need to unlock continue btn of the next step
+            if ($nextStep.attr('data-unlock-continue')){
+                $btnNext.removeAttr('disabled');
+            }
+
+            // Set the title of step
+            newTitle = $nextStep.attr('data-title');
+            var $titleStepSpan = $('<span>')
+                                .addClass('label label-success')
+                                .html(nextStep);
+
+            $title
+                .html($titleStepSpan)
+                .append(' ' + newTitle);
+
+            var stepCallback = settings.callbacks[$actualStep.val()];
+            executeCallback(everyStepCallback);
+            executeCallback(stepCallback);
+        });
+
+        return this;
+    };
+}(jQuery));

static/js/ketcher2/DEVNOTES.md

@@ -0,0 +1,57 @@
+## 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

@@ -0,0 +1,184 @@
+                               Apache License
+                         Version 2.0, January 2004
+                      http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+    "License" shall mean the terms and conditions for use, reproduction,
+    and distribution as defined by Sections 1 through 9 of this document.
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+    the copyright owner that is granting the License.
+    "Legal Entity" shall mean the union of the acting entity and all
+    other entities that control, are controlled by, or are under common
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+    direction or management of such entity, whether by contract or
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+    outstanding shares, or (iii) beneficial ownership of such entity.
+    "You" (or "Your") shall mean an individual or Legal Entity
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+    "Work" shall mean the work of authorship, whether in Source or
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+ END OF TERMS AND CONDITIONS
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+ APPENDIX: How to apply the Apache License to your work.
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+ Copyright 2017 EPAM Systems
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static/js/ketcher2/LICENSE-history

@@ -0,0 +1,5 @@
+ 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

@@ -0,0 +1,19 @@
+ 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/