[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

@@ -16,4 +16,3 @@ POSTGRES_PORT=
 # MAIL
 EMAIL_HOST_USER=
 EMAIL_HOST_PASSWORD=
-

.gitignore

@@ -5,4 +5,8 @@ static/admin/
 static/django_extensions/
 .env
 debug.log
-scratches/
+scratches/
+
+data/
+
+.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

@@ -1 +1 @@
-3.10
+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

@@ -2,4 +2,4 @@
 # Django starts so that shared_task will use this app.
 from .celery import app as celery_app
 
-__all__ = ('celery_app',)
+__all__ = ("celery_app",)

envipath/api.py

@@ -4,8 +4,6 @@ from ninja import NinjaAPI
 
 api = NinjaAPI()
 
-from ninja import NinjaAPI
-
 api_v1 = NinjaAPI(title="API V1 Docs", urls_namespace="api-v1")
 api_legacy = NinjaAPI(title="Legacy API Docs", urls_namespace="api-legacy")
 

envipath/asgi.py

@@ -11,6 +11,6 @@ import os
 
 from django.core.asgi import get_asgi_application
 
-os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'envipath.settings')
+os.environ.setdefault("DJANGO_SETTINGS_MODULE", "envipath.settings")
 
 application = get_asgi_application()

envipath/celery.py

@@ -4,15 +4,15 @@ 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')
+os.environ.setdefault("DJANGO_SETTINGS_MODULE", "envipath.settings")
 
-app = Celery('envipath')
+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')
+app.config_from_object("django.conf:settings", namespace="CELERY")
 
 
 @setup_logging.connect

envipath/settings.py

@@ -9,6 +9,7 @@ https://docs.djangoproject.com/en/4.2/topics/settings/
 For the full list of settings and their values, see
 https://docs.djangoproject.com/en/4.2/ref/settings/
 """
+
 import os
 from pathlib import Path
 
@@ -20,34 +21,35 @@ 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)
+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 = '7!VTW`aZqg/UBLsM.P=m)2]lWqg>{+:xUgG1"WO@bCyaHR2Up8XW&g<*3.F4l2gi9c.E3}dHyA0D`&z?u#U%^7HYbj],eP"g_MS|3BNMD[mI>s#<i/%2ngZ~Oy+/w&@]'
+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'
+DEBUG = os.environ.get("DEBUG", "False") == "True"
-ALLOWED_HOSTS = os.environ['ALLOWED_HOSTS'].split(',')
+
+ALLOWED_HOSTS = os.environ["ALLOWED_HOSTS"].split(",")
+
 
 # Application definition
 
 INSTALLED_APPS = [
-    'django.contrib.admin',
+    "django.contrib.admin",
-    'django.contrib.auth',
+    "django.contrib.auth",
-    'django.contrib.contenttypes',
+    "django.contrib.contenttypes",
-    'django.contrib.sessions',
+    "django.contrib.sessions",
-    'django.contrib.messages',
+    "django.contrib.messages",
-    'django.contrib.staticfiles',
+    "django.contrib.staticfiles",
     # 3rd party
-    'django_extensions',
+    "django_extensions",
-    'oauth2_provider',
+    "oauth2_provider",
     # Custom
-    'epdb',
+    "epdb",
-    'migration',
+    "migration",
-    'epauth',
 ]
 
 AUTHENTICATION_BACKENDS = [
@@ -55,42 +57,42 @@ AUTHENTICATION_BACKENDS = [
 ]
 
 MIDDLEWARE = [
-    'django.middleware.security.SecurityMiddleware',
+    "django.middleware.security.SecurityMiddleware",
-    'django.contrib.sessions.middleware.SessionMiddleware',
+    "django.contrib.sessions.middleware.SessionMiddleware",
-    'django.middleware.common.CommonMiddleware',
+    "django.middleware.common.CommonMiddleware",
-    'django.middleware.csrf.CsrfViewMiddleware',
+    "django.middleware.csrf.CsrfViewMiddleware",
-    'django.contrib.auth.middleware.AuthenticationMiddleware',
+    "django.contrib.auth.middleware.AuthenticationMiddleware",
-    'django.contrib.messages.middleware.MessageMiddleware',
+    "django.contrib.messages.middleware.MessageMiddleware",
-    'django.middleware.clickjacking.XFrameOptionsMiddleware',
+    "django.middleware.clickjacking.XFrameOptionsMiddleware",
-    'oauth2_provider.middleware.OAuth2TokenMiddleware',
+    "oauth2_provider.middleware.OAuth2TokenMiddleware",
 ]
 
 OAUTH2_PROVIDER = {
     "PKCE_REQUIRED": False,  # Accept PKCE requests but dont require them
 }
 
-if os.environ.get('REGISTRATION_MANDATORY', False) == 'True':
+if os.environ.get("REGISTRATION_MANDATORY", False) == "True":
-    MIDDLEWARE.append('epdb.middleware.login_required_middleware.LoginRequiredMiddleware')
+    MIDDLEWARE.append("epdb.middleware.login_required_middleware.LoginRequiredMiddleware")
 
-ROOT_URLCONF = 'envipath.urls'
+ROOT_URLCONF = "envipath.urls"
 
 TEMPLATES = [
     {
-        'BACKEND': 'django.template.backends.django.DjangoTemplates',
+        "BACKEND": "django.template.backends.django.DjangoTemplates",
-        'DIRS': (os.path.join(BASE_DIR, 'templates'),),
+        "DIRS": (os.path.join(BASE_DIR, "templates"),),
-        'APP_DIRS': True,
+        "APP_DIRS": True,
-        'OPTIONS': {
+        "OPTIONS": {
-            'context_processors': [
+            "context_processors": [
-                'django.template.context_processors.debug',
+                "django.template.context_processors.debug",
-                'django.template.context_processors.request',
+                "django.template.context_processors.request",
-                'django.contrib.auth.context_processors.auth',
+                "django.contrib.auth.context_processors.auth",
-                'django.contrib.messages.context_processors.messages',
+                "django.contrib.messages.context_processors.messages",
             ],
         },
     },
 ]
 
-WSGI_APPLICATION = 'envipath.wsgi.application'
+WSGI_APPLICATION = "envipath.wsgi.application"
 
 # Database
 # https://docs.djangoproject.com/en/4.2/ref/settings/#databases
@@ -98,11 +100,11 @@ WSGI_APPLICATION = 'envipath.wsgi.application'
 DATABASES = {
     "default": {
         "ENGINE": "django.db.backends.postgresql",
-        "USER": os.environ['POSTGRES_USER'],
+        "USER": os.environ["POSTGRES_USER"],
-        "NAME": os.environ['POSTGRES_DB'],
+        "NAME": os.environ["POSTGRES_DB"],
-        "PASSWORD": os.environ['POSTGRES_PASSWORD'],
+        "PASSWORD": os.environ["POSTGRES_PASSWORD"],
-        "HOST": os.environ['POSTGRES_SERVICE_NAME'],
+        "HOST": os.environ["POSTGRES_SERVICE_NAME"],
-        "PORT": os.environ['POSTGRES_PORT']
+        "PORT": os.environ["POSTGRES_PORT"],
     }
 }
 
@@ -110,96 +112,87 @@ DATABASES = {
 # 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.UserAttributeSimilarityValidator',
+    {"NAME": "django.contrib.auth.password_validation.MinimumLengthValidator"},
-    },
+    {"NAME": "django.contrib.auth.password_validation.CommonPasswordValidator"},
-    {
+    {"NAME": "django.contrib.auth.password_validation.NumericPasswordValidator"},
-        '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'
+LANGUAGE_CODE = "en-us"
 
-TIME_ZONE = 'UTC'
+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'
+DEFAULT_AUTO_FIELD = "django.db.models.BigAutoField"
 
+EMAIL_SUBJECT_PREFIX = "[enviPath] "
 if DEBUG:
-    EMAIL_BACKEND = 'django.core.mail.backends.console.EmailBackend'
+    EMAIL_BACKEND = "django.core.mail.backends.console.EmailBackend"
 else:
-    EMAIL_BACKEND = 'django.core.mail.backends.smtp.EmailBackend'
+    EMAIL_BACKEND = "django.core.mail.backends.smtp.EmailBackend"
     EMAIL_USE_TLS = True
-    EMAIL_HOST = 'mail.gandi.net'
+    EMAIL_HOST = "mail.gandi.net"
-    EMAIL_HOST_USER = os.environ['EMAIL_HOST_USER']
+    EMAIL_HOST_USER = os.environ["EMAIL_HOST_USER"]
-    EMAIL_HOST_PASSWORD = os.environ['EMAIL_HOST_PASSWORD']
+    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'
+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/'
+LOGIN_URL = "/login/"
 
-SERVER_URL = os.environ.get('SERVER_URL', 'http://localhost:8000')
+SERVER_URL = os.environ.get("SERVER_URL", "http://localhost:8000")
 
 CSRF_TRUSTED_ORIGINS = [SERVER_URL]
 
-AMBIT_URL = 'http://localhost:9001'
+AMBIT_URL = "http://localhost:9001"
-DEFAULT_VALUES = {
+DEFAULT_VALUES = {"description": "no description"}
-    'description': 'no description'
-}
 
-EP_DATA_DIR = os.environ['EP_DATA_DIR']
+EP_DATA_DIR = os.environ["EP_DATA_DIR"]
-MODEL_DIR = os.path.join(EP_DATA_DIR, 'models')
+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')
+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')
+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')
+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/'
+STATIC_URL = "/static/"
 
 # Where the sources are stored...
-STATICFILES_DIRS = (
+STATICFILES_DIRS = (BASE_DIR / "static",)
-    BASE_DIR / 'static',
-)
 
-FIXTURE_DIRS = (
+FIXTURE_DIRS = (BASE_DIR / "fixtures",)
-        BASE_DIR / 'fixtures',
-)
 
 # Logging
 LOGGING = {
@@ -207,8 +200,8 @@ LOGGING = {
     "disable_existing_loggers": True,
     "formatters": {
         "simple": {
-            'format': '[%(asctime)s] %(levelname)s %(module)s - %(message)s',
+            "format": "[%(asctime)s] %(levelname)s %(module)s - %(message)s",
-            'datefmt': '%Y-%m-%d %H:%M:%S',
+            "datefmt": "%Y-%m-%d %H:%M:%S",
         },
     },
     "handlers": {
@@ -221,7 +214,7 @@ LOGGING = {
             "level": "DEBUG",  # Or higher
             "class": "logging.FileHandler",
             "filename": os.path.join(LOG_DIR, "debug.log"),
-            "formatter": "simple"
+            "formatter": "simple",
         },
     },
     "loggers": {
@@ -229,72 +222,66 @@ LOGGING = {
         "epdb": {
             "handlers": ["file"],  # "console",
             "propagate": True,
-            "level": os.environ.get('LOG_LEVEL', 'INFO')
+            "level": os.environ.get("LOG_LEVEL", "INFO"),
         },
         # For everything under envipath/ loaded via getlogger(__name__)
-        'envipath': {
+        "envipath": {
-            'handlers': ['file', 'console'],
+            "handlers": ["file", "console"],
-            'propagate': True,
+            "propagate": True,
-            'level': os.environ.get('LOG_LEVEL', 'INFO')
+            "level": os.environ.get("LOG_LEVEL", "INFO"),
         },
         # For everything under utilities/ loaded via getlogger(__name__)
-        'utilities': {
+        "utilities": {
-            'handlers': ['file', 'console'],
+            "handlers": ["file", "console"],
-            'propagate': True,
+            "propagate": True,
-            'level': os.environ.get('LOG_LEVEL', 'INFO')
+            "level": os.environ.get("LOG_LEVEL", "INFO"),
         },
     },
 }
 
 # Flags
-ENVIFORMER_PRESENT = os.environ.get('ENVIFORMER_PRESENT', 'False') == 'True'
+ENVIFORMER_PRESENT = os.environ.get("ENVIFORMER_PRESENT", "False") == "True"
-if ENVIFORMER_PRESENT:
+ENVIFORMER_DEVICE = os.environ.get("ENVIFORMER_DEVICE", "cpu")
-    print("Loading enviFormer")
-    device = os.environ.get('ENVIFORMER_DEVICE', 'cpu')
-    from enviformer import load
-    ENVIFORMER_INSTANCE = load(device=device)
-    print("loaded")
-
 
 # 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'
+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_BROKER_URL = "redis://localhost:6379/0"  # Use Redis as message broker
-CELERY_RESULT_BACKEND = 'redis://localhost:6379/1'
+CELERY_RESULT_BACKEND = "redis://localhost:6379/1"
-CELERY_ACCEPT_CONTENT = ['json']
+CELERY_ACCEPT_CONTENT = ["json"]
-CELERY_TASK_SERIALIZER = 'json'
+CELERY_TASK_SERIALIZER = "json"
 
-MODEL_BUILDING_ENABLED = os.environ.get('MODEL_BUILDING_ENABLED', 'False') == 'True'
+MODEL_BUILDING_ENABLED = os.environ.get("MODEL_BUILDING_ENABLED", "False") == "True"
-APPLICABILITY_DOMAIN_ENABLED = os.environ.get('APPLICABILITY_DOMAIN_ENABLED', 'False') == 'True'
+APPLICABILITY_DOMAIN_ENABLED = os.environ.get("APPLICABILITY_DOMAIN_ENABLED", "False") == "True"
 DEFAULT_RF_MODEL_PARAMS = {
-    'base_clf': RandomForestClassifier(
+    "base_clf": RandomForestClassifier(
         n_estimators=100,
-        max_features='log2',
+        max_features="log2",
         random_state=42,
-        criterion='entropy',
+        criterion="entropy",
         ccp_alpha=0.0,
         max_depth=3,
-        min_samples_leaf=1
+        min_samples_leaf=1,
     ),
-    'num_chains': 10,
+    "num_chains": 10,
 }
 
 DEFAULT_MODEL_PARAMS = {
-    'base_clf': DecisionTreeClassifier(
+    "base_clf": DecisionTreeClassifier(
-        criterion='entropy',
+        criterion="entropy",
         max_depth=3,
         min_samples_split=5,
         # min_samples_leaf=5,
-        max_features='sqrt',
+        max_features="sqrt",
         # class_weight='balanced',
-        random_state=42
+        random_state=42,
     ),
-    'num_chains': 10,
+    "num_chains": 10,
 }
 
 DEFAULT_MAX_NUMBER_OF_NODES = 30
@@ -302,9 +289,10 @@ DEFAULT_MAX_DEPTH = 5
 DEFAULT_MODEL_THRESHOLD = 0.25
 
 # Loading Plugins
-PLUGINS_ENABLED = os.environ.get('PLUGINS_ENABLED', 'False') == 'True'
+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)
@@ -313,56 +301,59 @@ else:
     PROPERTY_PLUGINS = {}
     DESCRIPTOR_PLUGINS = {}
 
-SENTRY_ENABLED = os.environ.get('SENTRY_ENABLED', 'False') == 'True'
+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'):
+        if event.get("logger"):
-            for log_path in LOGGING.get('loggers').keys():
+            for log_path in LOGGING.get("loggers").keys():
-                if event['logger'].startswith(log_path):
+                if event["logger"].startswith(log_path):
                     return None
 
         return event
 
     sentry_sdk.init(
-        dsn=os.environ.get('SENTRY_DSN'),
+        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'),
+        environment=os.environ.get("SENTRY_ENVIRONMENT", "development"),
         before_send=before_send,
     )
 
 # compile into digestible flags
 FLAGS = {
-    'MODEL_BUILDING': MODEL_BUILDING_ENABLED,
+    "MODEL_BUILDING": MODEL_BUILDING_ENABLED,
-    'CELERY': FLAG_CELERY_PRESENT,
+    "CELERY": FLAG_CELERY_PRESENT,
-    'PLUGINS': PLUGINS_ENABLED,
+    "PLUGINS": PLUGINS_ENABLED,
-    'SENTRY': SENTRY_ENABLED,
+    "SENTRY": SENTRY_ENABLED,
-    'ENVIFORMER': ENVIFORMER_PRESENT,
+    "ENVIFORMER": ENVIFORMER_PRESENT,
-    'APPLICABILITY_DOMAIN': APPLICABILITY_DOMAIN_ENABLED,
+    "APPLICABILITY_DOMAIN": APPLICABILITY_DOMAIN_ENABLED,
 }
 
 # path of the URL are checked via "startswith"
 # -> /password_reset/done is covered as well
 LOGIN_EXEMPT_URLS = [
-    '/register',
+    "/register",
-    '/api/legacy/',
+    "/api/legacy/",
-    '/o/token/',
+    "/o/token/",
-    '/o/userinfo/',
+    "/o/userinfo/",
-    '/password_reset/',
+    "/password_reset/",
-    '/reset/',
+    "/reset/",
-    '/microsoft/',
+    "/microsoft/",
 ]
 
 # MS AD/Entra
-MS_ENTRA_ENABLED = os.environ.get('MS_ENTRA_ENABLED', 'False') == 'True'
+MS_ENTRA_ENABLED = os.environ.get("MS_ENTRA_ENABLED", "False") == "True"
 if MS_ENTRA_ENABLED:
-    MS_ENTRA_CLIENT_ID = os.environ['MS_CLIENT_ID']
+    # Add app to installed apps
-    MS_ENTRA_CLIENT_SECRET = os.environ['MS_CLIENT_SECRET']
+    INSTALLED_APPS.append("epauth")
-    MS_ENTRA_TENANT_ID = os.environ['MS_TENANT_ID']
+    # 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_REDIRECT_URI = os.environ["MS_REDIRECT_URI"]
-    MS_ENTRA_SCOPES = os.environ.get('MS_SCOPES', '').split(',')
+    MS_ENTRA_SCOPES = os.environ.get("MS_SCOPES", "").split(",")

envipath/urls.py

@@ -14,13 +14,14 @@ 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("epauth.urls")),
     path("", include("epdb.urls")),
     path("", include("migration.urls")),
     path("admin/", admin.site.urls),
@@ -28,3 +29,6 @@ urlpatterns = [
     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

@@ -11,6 +11,6 @@ import os
 
 from django.core.wsgi import get_wsgi_application
 
-os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'envipath.settings')
+os.environ.setdefault("DJANGO_SETTINGS_MODULE", "envipath.settings")
 
 application = get_wsgi_application()

epdb/admin.py

@@ -16,7 +16,9 @@ from .models import (
     Node,
     Edge,
     Scenario,
-    Setting
+    Setting,
+    ExternalDatabase,
+    ExternalIdentifier,
 )
 
 
@@ -37,12 +39,13 @@ class GroupPackagePermissionAdmin(admin.ModelAdmin):
 
 
 class EPAdmin(admin.ModelAdmin):
-    search_fields = ['name', 'description']
+    search_fields = ["name", "description"]
 
 
 class PackageAdmin(EPAdmin):
     pass
 
+
 class MLRelativeReasoningAdmin(EPAdmin):
     pass
 
@@ -87,6 +90,14 @@ 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)
@@ -103,3 +114,5 @@ 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

@@ -21,7 +21,7 @@ class BearerTokenAuth(HttpBearer):
 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')
+    return get_user_model().objects.get(username="anonymous")
 
 
 router = Router(auth=BearerTokenAuth())
@@ -85,7 +85,9 @@ 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!'}
+        return 403, {
+            "message": f"Getting Package with id {package_uuid} failed due to insufficient rights!"
+        }
 
 
 @router.get("/compound", response={200: List[CompoundSchema], 403: Error})
@@ -97,7 +99,9 @@ def get_compounds(request):
     return qs
 
 
-@router.get("/package/{uuid:package_uuid}/compound", response={200: List[CompoundSchema], 403: Error})
+@router.get(
+    "/package/{uuid:package_uuid}/compound", response={200: List[CompoundSchema], 403: Error}
+)
 @paginate
 def get_package_compounds(request, package_uuid):
     try:
@@ -105,4 +109,5 @@ def get_package_compounds(request, 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!'}
+            "message": f"Getting Compounds for Package with id {package_uuid} failed due to insufficient rights!"
+        }

epdb/apps.py

@@ -2,8 +2,8 @@ from django.apps import AppConfig
 
 
 class EPDBConfig(AppConfig):
-    default_auto_field = 'django.db.models.BigAutoField'
+    default_auto_field = "django.db.models.BigAutoField"
-    name = 'epdb'
+    name = "epdb"
 
     def ready(self):
         import epdb.signals  # noqa: F401

epdb/forms.py

@@ -1,5 +0,0 @@
-from django import forms
-
-
-class EmailLoginForm(forms.Form):
-    email = forms.EmailField()

epdb/management/commands/bootstrap.py

@@ -5,32 +5,49 @@ 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
+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():
+        if not User.objects.filter(email="anon@envipath.com").exists():
-            anon = UserManager.create_user("anonymous", "anon@envipath.com", "SuperSafe",
+            anon = UserManager.create_user(
-                                           is_active=True, add_to_group=False, set_setting=False)
+                "anonymous",
+                "anon@envipath.com",
+                "SuperSafe",
+                is_active=True,
+                add_to_group=False,
+                set_setting=False,
+            )
         else:
-            anon = User.objects.get(email='anon@envipath.com')
+            anon = User.objects.get(email="anon@envipath.com")
 
         # Admin User
-        if not User.objects.filter(email='admin@envipath.com').exists():
+        if not User.objects.filter(email="admin@envipath.com").exists():
-            admin = UserManager.create_user("admin", "admin@envipath.com", "SuperSafe",
+            admin = UserManager.create_user(
-                                            is_active=True, add_to_group=False, set_setting=False)
+                "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')
+            admin = User.objects.get(email="admin@envipath.com")
 
         # System Group
-        g = GroupManager.create_group(admin, 'enviPath Users', 'All enviPath Users')
+        g = GroupManager.create_group(admin, "enviPath Users", "All enviPath Users")
         g.public = True
         g.save()
 
@@ -43,14 +60,20 @@ class Command(BaseCommand):
         admin.default_group = g
         admin.save()
 
-        if not User.objects.filter(email='user0@envipath.com').exists():
+        if not User.objects.filter(email="user0@envipath.com").exists():
-            user0 = UserManager.create_user("user0", "user0@envipath.com", "SuperSafe",
+            user0 = UserManager.create_user(
-                                            is_active=True, add_to_group=False, set_setting=False)
+                "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')
+            user0 = User.objects.get(email="user0@envipath.com")
 
         g.user_member.add(user0)
         g.save()
@@ -61,18 +84,20 @@ class Command(BaseCommand):
         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)
+        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',
+            name="Global Default Setting",
-            description='Global Default Setting containing BBD Rules and Max 30 Nodes and Max Depth of 8',
+            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
+            model_threshold=None,
         )
 
         return s
@@ -84,54 +109,51 @@ class Command(BaseCommand):
         """
         databases = [
             {
-                'name': 'PubChem Compound',
+                "name": "PubChem Compound",
-                'full_name': 'PubChem Compound Database',
+                "full_name": "PubChem Compound Database",
-                'description': 'Chemical database of small organic molecules',
+                "description": "Chemical database of small organic molecules",
-                'base_url': 'https://pubchem.ncbi.nlm.nih.gov',
+                "base_url": "https://pubchem.ncbi.nlm.nih.gov",
-                'url_pattern': 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'
+                "url_pattern": "https://pubchem.ncbi.nlm.nih.gov/compound/{id}",
             },
             {
-                'name': 'PubChem Substance',
+                "name": "PubChem Substance",
-                'full_name': 'PubChem Substance Database',
+                "full_name": "PubChem Substance Database",
-                'description': 'Database of chemical substances',
+                "description": "Database of chemical substances",
-                'base_url': 'https://pubchem.ncbi.nlm.nih.gov',
+                "base_url": "https://pubchem.ncbi.nlm.nih.gov",
-                'url_pattern': 'https://pubchem.ncbi.nlm.nih.gov/substance/{id}'
+                "url_pattern": "https://pubchem.ncbi.nlm.nih.gov/substance/{id}",
             },
             {
-                'name': 'ChEBI',
+                "name": "ChEBI",
-                'full_name': 'Chemical Entities of Biological Interest',
+                "full_name": "Chemical Entities of Biological Interest",
-                'description': 'Dictionary of molecular entities',
+                "description": "Dictionary of molecular entities",
-                'base_url': 'https://www.ebi.ac.uk/chebi',
+                "base_url": "https://www.ebi.ac.uk/chebi",
-                'url_pattern': 'https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:{id}'
+                "url_pattern": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:{id}",
             },
             {
-                'name': 'RHEA',
+                "name": "RHEA",
-                'full_name': 'RHEA Reaction Database',
+                "full_name": "RHEA Reaction Database",
-                'description': 'Comprehensive resource of biochemical reactions',
+                "description": "Comprehensive resource of biochemical reactions",
-                'base_url': 'https://www.rhea-db.org',
+                "base_url": "https://www.rhea-db.org",
-                'url_pattern': 'https://www.rhea-db.org/rhea/{id}'
+                "url_pattern": "https://www.rhea-db.org/rhea/{id}",
             },
             {
-                'name': 'KEGG Reaction',
+                "name": "KEGG Reaction",
-                'full_name': 'KEGG Reaction Database',
+                "full_name": "KEGG Reaction Database",
-                'description': 'Database of biochemical reactions',
+                "description": "Database of biochemical reactions",
-                'base_url': 'https://www.genome.jp',
+                "base_url": "https://www.genome.jp",
-                'url_pattern': 'https://www.genome.jp/entry/reaction+{id}'
+                "url_pattern": "https://www.genome.jp/entry/{id}",
             },
             {
-                'name': 'UniProt',
+                "name": "UniProt",
-                'full_name': 'MetaCyc Metabolic Pathway Database',
+                "full_name": "MetaCyc Metabolic Pathway Database",
-                'description': 'UniProt is a freely accessible database of protein sequence and functional information',
+                "description": "UniProt is a freely accessible database of protein sequence and functional information",
-                'base_url': 'https://www.uniprot.org',
+                "base_url": "https://www.uniprot.org",
-                'url_pattern': 'https://www.uniprot.org/uniprotkb?query="{id}"'
+                "url_pattern": 'https://www.uniprot.org/uniprotkb?query="{id}"',
-            }
+            },
         ]
 
         for db_info in databases:
-            ExternalDatabase.objects.get_or_create(
+            ExternalDatabase.objects.get_or_create(name=db_info["name"], defaults=db_info)
-                name=db_info['name'],
-                defaults=db_info
-            )
 
     @transaction.atomic
     def handle(self, *args, **options):
@@ -142,20 +164,24 @@ class Command(BaseCommand):
 
         # Import Packages
         packages = [
-            'EAWAG-BBD.json',
+            "EAWAG-BBD.json",
-            'EAWAG-SOIL.json',
+            "EAWAG-SOIL.json",
-            'EAWAG-SLUDGE.json',
+            "EAWAG-SLUDGE.json",
-            'EAWAG-SEDIMENT.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).read())
+            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
+            mapping[p.replace(".json", "")] = imported_package
 
-        setting = self.create_default_setting(admin, [mapping['EAWAG-BBD']])
+        setting = self.create_default_setting(admin, [mapping["EAWAG-BBD"]])
         setting.public = True
         setting.save()
         setting.make_global_default()
@@ -171,26 +197,28 @@ class Command(BaseCommand):
             usp.save()
 
         # Create Model Package
-        pack = PackageManager.create_package(admin, "Public Prediction Models",
+        pack = PackageManager.create_package(
-                                             "Package to make Prediction Models publicly available")
+            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']],
+            rule_packages=[mapping["EAWAG-BBD"]],
-            data_packages=[mapping['EAWAG-BBD']],
+            data_packages=[mapping["EAWAG-BBD"]],
             eval_packages=[],
             threshold=0.5,
-            name='ECC - BBD - T0.5',
+            name="ECC - BBD - T0.5",
-            description='ML Relative Reasoning',
+            description="ML Relative Reasoning",
         )
 
         ml_model.build_dataset()
         ml_model.build_model()
-        # ml_model.evaluate_model()
 
         # If available, create EnviFormerModel
         if s.ENVIFORMER_PRESENT:
-            enviFormer_model = EnviFormer.create(pack, 'EnviFormer - T0.5', 'EnviFormer Model with Threshold 0.5', 0.5)
+            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

@@ -1,27 +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 *
+from epdb.models import User
 
 
 class Command(BaseCommand):
-
     def add_arguments(self, parser):
         parser.add_argument(
-            '--data',
+            "--data",
             type=str,
-            help='Path of the Package to import.',
+            help="Path of the Package to import.",
             required=True,
         )
         parser.add_argument(
-            '--owner',
+            "--owner",
             type=str,
-            help='Username of the desired Owner.',
+            help="Username of the desired Owner.",
             required=True,
         )
 
     @transaction.atomic
     def handle(self, *args, **options):
-        owner = User.objects.get(username=options['owner'])
+        owner = User.objects.get(username=options["owner"])
-        package_data = json.load(open(options['data']))
+        package_data = json.load(open(options["data"]))
         PackageManager.import_legacy_package(package_data, owner)

epdb/management/commands/localize_urls.py

@@ -1,51 +1,64 @@
 from django.apps import apps
 from django.core.management.base import BaseCommand
 
-from django.db.models import F, Value
+from django.db.models import F, Value, TextField, JSONField
-from django.db.models.functions import Replace
+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',
+            "--old",
             type=str,
-            help='Old Host, most likely https://envipath.org/',
+            help="Old Host, most likely https://envipath.org/",
             required=True,
         )
         parser.add_argument(
-            '--new',
+            "--new",
             type=str,
-            help='New Host, most likely http://localhost:8000/',
+            help="New Host, most likely http://localhost:8000/",
             required=True,
         )
 
     def handle(self, *args, **options):
         MODELS = [
-            'User',
+            "User",
-            'Group',
+            "Group",
-            'Package',
+            "Package",
-            'Compound',
+            "Compound",
-            'CompoundStructure',
+            "CompoundStructure",
-            'Pathway',
+            "Pathway",
-            'Edge',
+            "Edge",
-            'Node',
+            "Node",
-            'Reaction',
+            "Reaction",
-            'SimpleAmbitRule',
+            "SimpleAmbitRule",
-            'SimpleRDKitRule',
+            "SimpleRDKitRule",
-            'ParallelRule',
+            "ParallelRule",
-            'SequentialRule',
+            "SequentialRule",
-            'Scenario',
+            "Scenario",
-            'Setting',
+            "Setting",
-            'MLRelativeReasoning',
+            "MLRelativeReasoning",
-            'RuleBasedRelativeReasoning',
+            "RuleBasedRelativeReasoning",
-            'EnviFormer',
+            "EnviFormer",
-            'ApplicabilityDomain',
+            "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']))
+                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

@@ -3,22 +3,25 @@ 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("login"),
-                               reverse('logout'),
+            reverse("logout"),
-                               reverse('admin:login'),
+            reverse("admin:login"),
-                               reverse('admin:index'),
+            reverse("admin:index"),
-                           ] + getattr(settings, 'LOGIN_EXEMPT_URLS', [])
+        ] + 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.method == "GET":
-                    if request.get_full_path() and request.get_full_path() != '/':
+                    if request.get_full_path() and request.get_full_path() != "/":
-                        return redirect(f"{settings.LOGIN_URL}?next={quote(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/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/tasks.py

@@ -2,55 +2,57 @@ import logging
 from typing import Optional
 
 from celery import shared_task
-from epdb.models import Pathway, Node, Edge, EPModel, Setting
+from epdb.models import Pathway, Node, EPModel, Setting
 from epdb.logic import SPathway
 
 
 logger = logging.getLogger(__name__)
 
 
-@shared_task(queue='background')
+@shared_task(queue="background")
 def mul(a, b):
     return a * b
 
 
-@shared_task(queue='predict')
+@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')
+@shared_task(queue="background")
 def send_registration_mail(user_pk: int):
     pass
 
 
-@shared_task(queue='model')
+@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')
+@shared_task(queue="model")
 def evaluate_model(model_pk: int):
     mod = EPModel.objects.get(id=model_pk)
     mod.evaluate_model()
 
 
-@shared_task(queue='model')
+@shared_task(queue="model")
 def retrain(model_pk: int):
     mod = EPModel.objects.get(id=model_pk)
     mod.retrain()
 
 
-@shared_task(queue='predict')
+@shared_task(queue="predict")
-def predict(pw_pk: int, pred_setting_pk: int, limit: Optional[int] = None, node_pk: Optional[int] = None) -> Pathway:
+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.kv.update(**{"status": "running"})
     pw.save()
 
     try:
@@ -74,12 +76,10 @@ def predict(pw_pk: int, pred_setting_pk: int, limit: Optional[int] = None, node_
         else:
             raise ValueError("Neither limit nor node_pk given!")
 
-
-
     except Exception as e:
-        pw.kv.update({'status': 'failed'})
+        pw.kv.update({"status": "failed"})
         pw.save()
         raise e
 
-    pw.kv.update(**{'status': 'completed'})
+    pw.kv.update(**{"status": "completed"})
-    pw.save()
+    pw.save()

epdb/templatetags/envipytags.py

@@ -2,6 +2,7 @@ from django import template
 
 register = template.Library()
 
+
 @register.filter
 def classname(obj):
-    return obj.__class__.__name__
+    return obj.__class__.__name__

epdb/tests.py

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

epdb/urls.py

@@ -1,99 +1,195 @@
-from django.urls import path, re_path
 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}'
+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'^$', v.index, name='index'),
+    re_path(r"^$", v.index, name="index"),
-
     # Login
-    re_path(r'^login', v.login, name='login'),
+    re_path(r"^login", v.login, name="login"),
-    re_path(r'^logout', v.logout, name='logout'),
+    re_path(r"^logout", v.logout, name="logout"),
-    re_path(r'^register', v.register, name='register'),
+    re_path(r"^register", v.register, name="register"),
-
+    # Built-In views
-    # Built In views
+    path(
-    path('password_reset/', auth_views.PasswordResetView.as_view(
+        "password_reset/",
-        template_name='static/password_reset_form.html'
+        auth_views.PasswordResetView.as_view(template_name="static/password_reset_form.html"),
-    ), name='password_reset'),
+        name="password_reset",
-
+    ),
-    path('password_reset/done/', auth_views.PasswordResetDoneView.as_view(
+    path(
-        template_name='static/password_reset_done.html'
+        "password_reset/done/",
-    ), name='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'
+    path(
-    ), name='password_reset_confirm'),
+        "reset/<uidb64>/<token>/",
-
+        auth_views.PasswordResetConfirmView.as_view(
-    path('reset/done/', auth_views.PasswordResetCompleteView.as_view(
+            template_name="static/password_reset_confirm.html"
-        template_name='static/password_reset_complete.html'
+        ),
-    ), name='password_reset_complete'),
+        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$', v.packages, name='packages'),
+    re_path(r"^package$", v.packages, name="packages"),
-    re_path(r'^compound$', v.compounds, name='compounds'),
+    re_path(r"^compound$", v.compounds, name="compounds"),
-    re_path(r'^rule$', v.rules, name='rules'),
+    re_path(r"^rule$", v.rules, name="rules"),
-    re_path(r'^reaction$', v.reactions, name='reactions'),
+    re_path(r"^reaction$", v.reactions, name="reactions"),
-    re_path(r'^pathway$', v.pathways, name='pathways'),
+    re_path(r"^pathway$", v.pathways, name="pathways"),
-    re_path(r'^scenario$', v.scenarios, name='scenarios'),
+    re_path(r"^scenario$", v.scenarios, name="scenarios"),
-    re_path(r'^model$', v.models, name='model'),
+    re_path(r"^model$", v.models, name="model"),
-    re_path(r'^user$', v.users, name='users'),
+    re_path(r"^user$", v.users, name="users"),
-    re_path(r'^group$', v.groups, name='groups'),
+    re_path(r"^group$", v.groups, name="groups"),
-    re_path(r'^search$', v.search, name='search'),
+    re_path(r"^search$", v.search, name="search"),
-
-
     # User Detail
-    re_path(rf'^user/(?P<user_uuid>{UUID})', v.user, name='user'),
+    re_path(rf"^user/(?P<user_uuid>{UUID})", v.user, name="user"),
     # Group Detail
-    re_path(rf'^group/(?P<group_uuid>{UUID})$', v.group, name='group_detail'),
+    re_path(rf"^group/(?P<group_uuid>{UUID})$", v.group, name="group detail"),
-
     # "in package" urls
-    re_path(rf'^package/(?P<package_uuid>{UUID})$', v.package, name='package_detail'),
+    re_path(rf"^package/(?P<package_uuid>{UUID})$", v.package, name="package detail"),
     # Compound
-    re_path(rf'^package/(?P<package_uuid>{UUID})/compound$', v.package_compounds, name='package compound list'),
+    re_path(
-    re_path(rf'^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})$', v.package_compound, name='package compound detail'),
+        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$', v.package_compound_structures, name='package compound structure list'),
+    re_path(
-    re_path(rf'^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})/structure/(?P<structure_uuid>{UUID})$', v.package_compound_structure, name='package compound structure detail'),
+        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$', v.package_rules, name='package rule list'),
+    re_path(rf"^package/(?P<package_uuid>{UUID})/rule$", v.package_rules, name="package rule list"),
-    re_path(rf'^package/(?P<package_uuid>{UUID})/rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
+    re_path(
-    re_path(rf'^package/(?P<package_uuid>{UUID})/simple-ambit-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
+        rf"^package/(?P<package_uuid>{UUID})/rule/(?P<rule_uuid>{UUID})$",
-    re_path(rf'^package/(?P<package_uuid>{UUID})/simple-rdkit-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
+        v.package_rule,
-    re_path(rf'^package/(?P<package_uuid>{UUID})/parallel-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
+        name="package rule detail",
-    re_path(rf'^package/(?P<package_uuid>{UUID})/sequential-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
+    ),
+    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(
-    re_path(rf'^package/(?P<package_uuid>{UUID})/reaction/(?P<reaction_uuid>{UUID})$', v.package_reaction, name='package reaction detail'),
+        rf"^package/(?P<package_uuid>{UUID})/reaction$",
+        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(
-    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})$', v.package_pathway, name='package pathway detail'),
+        rf"^package/(?P<package_uuid>{UUID})/pathway$",
+        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(
-    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node/(?P<node_uuid>{UUID})$', v.package_pathway_node, name='package pathway node detail'),
+        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node$",
+        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(
-    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge/(?P<edge_uuid>{UUID})$', v.package_pathway_edge, name='package pathway edge detail'),
+        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge$",
+        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(
-    re_path(rf'^package/(?P<package_uuid>{UUID})/scenario/(?P<scenario_uuid>{UUID})$', v.package_scenario, name='package scenario detail'),
+        rf"^package/(?P<package_uuid>{UUID})/scenario$",
+        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(
-    re_path(rf'^package/(?P<package_uuid>{UUID})/model/(?P<model_uuid>{UUID})$', v.package_model,name='package model detail'),
+        rf"^package/(?P<package_uuid>{UUID})/model$", v.package_models, name="package model list"
-
+    ),
-    re_path(r'^setting$', v.settings, name='settings'),
+    re_path(
-    re_path(rf'^setting/(?P<setting_uuid>{UUID})', v.setting, name='setting'),
+        rf"^package/(?P<package_uuid>{UUID})/model/(?P<model_uuid>{UUID})$",
-
+        v.package_model,
-    re_path(r'^indigo/info$', v.indigo, name='indigo_info'),
+        name="package model detail",
-    re_path(r'^indigo/aromatize$', v.aromatize, name='indigo_aromatize'),
+    ),
-    re_path(r'^indigo/dearomatize$', v.dearomatize, name='indigo_dearomatize'),
+    re_path(r"^setting$", v.settings, name="settings"),
-    re_path(r'^indigo/layout$', v.layout, name='indigo_layout'),
+    re_path(rf"^setting/(?P<setting_uuid>{UUID})", v.setting, name="setting"),
-
+    re_path(r"^indigo/info$", v.indigo, name="indigo_info"),
-    re_path(r'^depict$', v.depict, name='depict'),
+    re_path(r"^indigo/aromatize$", 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"),
 ]

migration/urls.py

@@ -12,4 +12,5 @@ urlpatterns = [
     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

@@ -1,80 +1,123 @@
 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
+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':
+    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(
+        if (
-                "force") is None:
+            os.path.exists(s.BASE_DIR / "fixtures" / "migration_status_per_rule.json")
-            migration_status = json.load(open(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:
-            data = json.load(gzip.open(s.BASE_DIR / 'fixtures' / 'ambit_rules.json.gz', 'rb'))
+            BBD = Package.objects.get(
-
+                url="http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1"
-            results = []
+            )
+            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
 
-            num_keys = len(data.keys())
+            for i, r in enumerate(RULES):
-            for i, bt_rule_name in enumerate(data.keys()):
+                logger.debug(f"\r{i + 1:03d}/{num_rules}")
-                print(f"{i + 1}/{num_keys}")
-                bt_rule = data[bt_rule_name]
-                smirks = bt_rule['smirks']
-
-                all_prods = set()
-
                 res = True
+                for smiles in ALL_SMILES:
+                    try:
+                        ambit_res, _, rdkit_res, _ = run_both_engines(smiles, r.smirks)
 
-                for comp, ambit_prod in zip(bt_rule['compounds'], bt_rule['products']):
+                        res &= set(ambit_res) == set(rdkit_res)
-
+                    except Exception as e:
-                    products = FormatConverter.apply(comp['smiles'], smirks)
+                        logger.error(e)
-
-                    all_rdkit_prods = []
-                    for ps in products:
-                        for p in ps:
-                            all_rdkit_prods.append(p)
-
-                    all_rdkit_prods = list(set(all_rdkit_prods))
-
-                    ambit_smiles, ambit_errors = FormatConverter.sanitize_smiles(ambit_prod)
-                    rdkit_smiles, rdkit_errors = FormatConverter.sanitize_smiles(all_rdkit_prods)
-
-                    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=37)
-
-                    # TODO mode = "full ambit"
-                    # partial_res = len(set(ambit_smiles).intersection(set(rdkit_smiles))) == len(ambit_smiles)
-                    # FAILED (failures=46)
-
-                    # TODO mode = "equality"
-                    partial_res = set(ambit_smiles) == set(rdkit_smiles)
-                    # FAILED (failures=69)
-
-                    res &= partial_res
 
                 results.append(
                     {
-                        'name': bt_rule_name,
+                        "name": r.name,
-                        'id': bt_rule['id'].split('/')[-1],
+                        "detail_url": s.SERVER_URL
-                        'url': bt_rule['id'],
+                        + "/migration/"
-                        'status': res,
+                        + r.url.replace("https://envipath.org/", "").replace(
-                        'detail_url': s.SERVER_URL + '/migration/' + bt_rule['id'].replace('https://envipath.org/', '')
+                            "http://localhost:8000/", ""
+                        ),
+                        "id": str(r.uuid),
+                        "url": r.url,
+                        "status": res,
                     }
                 )
 
@@ -84,95 +127,82 @@ def migration(request):
                     error += 1
 
                 total += 1
-
+            results = sorted(results, key=lambda x: (x["status"], x["name"]))
-            results = sorted(results, key=lambda x: (x['status'], x['name']))
 
             migration_status = {
-                'results': results,
+                "results": results,
-                'success': success,
+                "success": success,
-                'error': error,
+                "error": error,
-                'total': total
+                "total": total,
             }
 
-            json.dump(migration_status, open(s.BASE_DIR / 'fixtures' / 'migration_status_per_rule.json', 'w'))
+            json.dump(
+                migration_status,
+                open(s.BASE_DIR / "fixtures" / "migration_status_per_rule.json", "w"),
+            )
 
-        for r in migration_status['results']:
+        for r in migration_status["results"]:
-            r['detail_url'] = r['detail_url'].replace('http://localhost:8000', s.SERVER_URL)
+            r["detail_url"] = r["detail_url"].replace(
+                "http://localhost:8000", s.SERVER_URL
+            )
 
         context.update(**migration_status)
 
-        return render(request, 'migration.html', context)
+        return render(request, "migration.html", context)
 
 
 def migration_detail(request, package_uuid, rule_uuid):
     current_user = _anonymous_or_real(request)
 
-    if request.method == 'GET':
+    if request.method == "GET":
         context = get_base_context(request)
 
-        p = PackageManager.get_package_by_id(current_user, package_uuid)
+        BBD = Package.objects.get(name="EAWAG-BBD")
-        rule = Rule.objects.get(package=p, uuid=rule_uuid)
+        STRUCTURES = CompoundStructure.objects.filter(compound__package=BBD)
+        rule = Rule.objects.get(package=BBD, uuid=rule_uuid)
+
         bt_rule_name = rule.name
-
+        smirks = rule.smirks
-        data = json.load(gzip.open(s.BASE_DIR / 'fixtures' / 'ambit_rules.json.gz', 'rb'))
-
-        bt_rule = data[bt_rule_name]
-        smirks = bt_rule['smirks']
-
-        results = []
 
         res = True
+        results = []
 
         all_prods = set()
-        for comp, ambit_prod in zip(bt_rule['compounds'], bt_rule['products']):
+        for structure in STRUCTURES:
-            # if comp['smiles'] != 'CC1=C(C(=C(C=N1)CO)C=O)O':
+            ambit_smiles, ambit_errors, rdkit_smiles, rdkit_errors = run_both_engines(
-            #     continue
+                structure.smiles, smirks
-
+            )
-            products = FormatConverter.apply(comp['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))
-
-            ambit_smiles, ambit_errors = FormatConverter.sanitize_smiles(ambit_prod)
-            rdkit_smiles, rdkit_errors = FormatConverter.sanitize_smiles(all_rdkit_prods)
 
             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=37)
+            # FAILED (failures=18)
 
             # TODO mode = "full ambit"
-            # partial_res = len(set(ambit_smiles).intersection(set(rdkit_smiles))) == len(ambit_smiles)
+            # partial_res = len(set(ambit_smiles).intersection(set(rdkit_smiles))) == len(set(ambit_smiles))
-            # FAILED (failures=46)
+            # FAILED (failures=34)
 
             # TODO mode = "equality"
             partial_res = set(ambit_smiles) == set(rdkit_smiles)
-            # FAILED (failures=69)
+            # FAILED (failures=30)
 
-            #
             if len(ambit_smiles) or len(rdkit_smiles):
                 temp = {
-                    'url': comp['id'],
+                    "url": structure.url,
-                    'id': comp['id'].split('/')[-1],
+                    "id": str(structure.uuid),
-                    'name': comp['name'],
+                    "name": structure.name,
-                    'initial_smiles': comp['smiles'],
+                    "initial_smiles": structure.smiles,
-                    'ambit_smiles': sorted(list(ambit_smiles)),
+                    "ambit_smiles": sorted(list(ambit_smiles)),
-                    'rdkit_smiles': sorted(list(rdkit_smiles)),
+                    "rdkit_smiles": sorted(list(rdkit_smiles)),
-                    'status': set(ambit_smiles) == set(rdkit_smiles),
+                    "status": set(ambit_smiles) == set(rdkit_smiles),
                 }
-
+                detail = f"""
-                if set(ambit_smiles) != set(rdkit_smiles):
-                    detail = f"""
                         BT: {bt_rule_name}
-                        SMIRKS: {bt_rule['smirks']}
+                        SMIRKS: {smirks}
-                        Compound: {comp['smiles']}
+                        Compound: {structure.smiles}
-                        Compound URL: {comp['id']}
+                        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)))}
@@ -185,15 +215,63 @@ def migration_detail(request, package_uuid, rule_uuid):
                         rdkit_errors: {rdkit_errors}
                     """
 
-                    temp['detail'] = '\n'.join([x.strip() for x in detail.split('\n')])
+                temp["detail"] = "\n".join([x.strip() for x in detail.split("\n")])
-                    # print(detail.strip())
 
                 results.append(temp)
 
             res &= partial_res
 
-        results = sorted(results, key=lambda x: x['status'])
+        results = sorted(results, key=lambda x: x["status"])
-        context['results'] = results
+        context["results"] = results
-        context['res'] = res
+        context["res"] = res
-        context['bt_rule_name'] = bt_rule_name
+        context["bt_rule_name"] = bt_rule_name
-        return render(request, 'migration_detail.html', context)
+        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

@@ -3,7 +3,7 @@ name = "envipy"
 version = "0.1.0"
 description = "Add your description here"
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.12"
 dependencies = [
     "celery>=5.5.2",
     "django>=5.2.1",
@@ -12,9 +12,9 @@ dependencies = [
     "django-ninja>=1.4.1",
     "django-oauth-toolkit>=3.0.1",
     "django-polymorphic>=4.1.0",
-    "django-stubs>=5.2.4",
     "enviformer",
     "envipy-additional-information",
+    "envipy-ambit>=0.1.0",
     "envipy-plugins",
     "epam-indigo>=1.30.1",
     "gunicorn>=23.0.0",
@@ -30,9 +30,62 @@ dependencies = [
 ]
 
 [tool.uv.sources]
-enviformer = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git", rev = "v0.1.0" }
+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 = "v0.1.4"}
+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/images/uzh-logo.svg

@@ -0,0 +1,488 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- Generator: Adobe Illustrator 16.0.0, SVG Export Plug-In . SVG Version: 6.00 Build 0)  -->
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1 Tiny//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-tiny.dtd">
+<svg version="1.1" baseProfile="tiny" id="Universität_Zürich"
+	 xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+	 viewBox="-0.499 -0.501 142.73 49.19" xml:space="preserve">
+<path d="M6.818,32.721C6.296,32.944,6.2,32.986,6.093,33.04c-0.113,0.058-0.156,0.108-0.133,0.231
+	c0.005,0.029,0.026,0.091,0.047,0.139c0.017,0.038,0.019,0.062-0.006,0.071c-0.023,0.011-0.041-0.01-0.062-0.062
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+	c-0.11-0.183-0.217-0.366-0.322-0.553h38.517C43.243,35.148,43.137,35.333,43.027,35.515z M20.275,7.089v0.187
+	C20.27,7.313,20.26,7.368,20.241,7.42c-0.032,0.085-0.111,0.221-0.217,0.386c-0.04,0.064-0.11,0.174-0.188,0.33
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+	 M18.109,6.749c0.017-0.277,0.092-0.805,0.362-1.164c0.204-0.278,0.407-0.443,0.557-0.54C19.096,5,19.151,4.973,19.19,4.954
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+	C18.106,8.091,18.175,8.193,18.245,8.343z M21.164,11.877v0.807h-3.941v-0.807H21.164z M21.164,13.022v3.141H20.21V14.75
+	c0.001-0.469-0.173-0.866-0.459-1.138c-0.153-0.147-0.338-0.258-0.542-0.328c-0.013-0.004-0.012-0.005-0.012-0.005
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+	L21.164,13.022z M19.87,14.75v1.414h-1.35V14.75c0.005-0.546,0.272-0.925,0.675-1.103C19.596,13.824,19.865,14.203,19.87,14.75z
+	 M21.164,16.503v3.995h-0.876v-1.995c0-0.468-0.176-0.875-0.47-1.155c-0.157-0.15-0.344-0.263-0.55-0.333
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+	c-0.294,0.279-0.471,0.688-0.47,1.154v1.995h-0.88v-3.995L21.164,16.503L21.164,16.503z M19.948,18.506v1.992h-1.507v-1.995
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+	c0.226,0.215,0.364,0.525,0.365,0.91L19.948,18.506z M21.164,20.838v4.755h-3.941v-4.755H21.164z M21.164,25.933v3.103h-3.941
+	v-3.103H21.164z M21.164,29.375v5.247h-3.941v-5.247H21.164z M24.634,16.538v1.416l-0.542-0.542l-0.541,0.541v-1.415H24.634z
+	 M23.566,16.13l0.396-1.694l0.163-2.835l0.098,2.833l0.396,1.696H23.566z M24.092,17.988l2.511,2.51h-5.021L24.092,17.988z
+	 M26.603,20.838v1.921h-5.037v-1.921H26.603z M26.603,23.354v2.238h-1.575v-0.561c0-0.516-0.419-0.938-0.938-0.938
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+	H23.155z M26.603,29.375v5.247h-5.037v-5.247H26.603z M30.067,7.089v0.187c-0.005,0.038-0.017,0.093-0.035,0.145
+	C30,7.505,29.921,7.64,29.815,7.805c-0.04,0.064-0.11,0.174-0.188,0.33c-0.101-0.153-0.186-0.256-0.246-0.318
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+	c-0.105-0.165-0.185-0.3-0.217-0.385c-0.031-0.082-0.041-0.177-0.042-0.185V7.089H30.067z M27.901,6.749
+	c0.017-0.277,0.092-0.805,0.362-1.164c0.204-0.278,0.407-0.443,0.557-0.54C28.888,5,28.942,4.973,28.982,4.954
+	c0.04,0.02,0.095,0.046,0.163,0.091c0.147,0.097,0.352,0.262,0.557,0.54c0.271,0.359,0.345,0.887,0.362,1.164H27.901z M30.146,7.988
+	c0.061,0.085,0.125,0.209,0.193,0.359c0.096,0.233,0.121,0.462,0.124,0.63v2.492h-0.642c0-0.548,0-1.756,0-2.491
+	c0.003-0.171,0.033-0.409,0.125-0.632C30.025,8.17,30.088,8.07,30.146,7.988z M29.473,8.994l-0.001,2.476H28.5
+	c0-0.689-0.001-2.477-0.001-2.478c0.008-0.162,0.021-0.386,0.138-0.617c0.122-0.242,0.354-0.386,0.354-0.386h0.001
+	c0,0,0.219,0.144,0.342,0.386C29.455,8.618,29.466,8.828,29.473,8.994z M28.036,8.343c0.091,0.224,0.106,0.465,0.109,0.636
+	l0.003,2.491h-0.635V8.975c0.004-0.168,0.021-0.396,0.116-0.631c0.07-0.149,0.138-0.273,0.194-0.358
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+	 M29.662,14.75v1.414h-1.351V14.75c0.005-0.546,0.272-0.925,0.675-1.103C29.388,13.824,29.657,14.203,29.662,14.75z M30.956,16.503
+	v3.995H30.08v-1.995c0-0.468-0.176-0.875-0.47-1.155c-0.157-0.15-0.344-0.263-0.55-0.333c-0.01-0.005-0.074-0.024-0.074-0.024
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+	L30.956,16.503L30.956,16.503z M29.74,18.506v1.992h-1.506v-1.995c0-0.384,0.141-0.694,0.364-0.909
+	c0.11-0.105,0.241-0.185,0.388-0.241h0.001c0.147,0.058,0.277,0.136,0.388,0.24c0.225,0.215,0.364,0.525,0.365,0.91V18.506z
+	 M30.956,20.838v4.755h-3.941v-4.755H30.956z M30.956,25.933v3.103h-3.941v-3.103H30.956z M30.956,29.375v5.247h-3.941v-5.247
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+	c-0.131,0.324-0.141,0.624-0.145,0.804v2.465h-0.5v23.151H4.646c-1.702-3.133-2.672-6.721-2.672-10.538
+	c0-6.106,2.475-11.635,6.477-15.639c4.003-4.002,9.531-6.479,15.639-6.479c6.108,0,11.637,2.476,15.64,6.479
+	c4.002,4.003,6.478,9.531,6.478,15.639c0,3.817-0.97,7.405-2.672,10.538L31.562,34.622L31.562,34.622z"/>
+</svg>

static/js/pps.js

@@ -646,8 +646,8 @@ function handleAssessmentResponse(depict_url, data) {
     var reactivityCentersImgSrc = null;
 
     if (data['assessment']['node'] !== undefined) {
-        functionalGroupsImgSrc = "<img width='400' src='" + data['assessment']['node']['image'] + "'>";
+        functionalGroupsImgSrc = "<img width='400' src='" + data['assessment']['node']['image'] + "&highlight=true'>";
-        reactivityCentersImgSrc = "<img width='400' src='" + data['assessment']['node']['image'] + "'>"
+        reactivityCentersImgSrc = "<img width='400' src='" + data['assessment']['node']['image'] + "&highlightReactivity=true'>"
     } else {
         functionalGroupsImgSrc = "<img width='400' src=\"" + depict_url + "?smiles=" + encodeURIComponent(data['assessment']['smiles']) + "\">";
         reactivityCentersImgSrc = "<img width='400' src=\"" + depict_url + "?smiles=" + encodeURIComponent(data['assessment']['smiles']) + "\">"
@@ -751,7 +751,7 @@ function handleAssessmentResponse(depict_url, data) {
         var predProb = "<a class='list-group-item'>Predicted probability: " + transObj['probability'].toFixed(2) + "</a>";
         var timesTriggered = "<a class='list-group-item'>This rule has triggered " + transObj['times_triggered'] + " times in the training set</a>";
         var reliability = "<a class='list-group-item'>Reliability: " + transObj['reliability'].toFixed(2) + " (" + (transObj['reliability'] > data['ad_params']['reliability_threshold'] ? "&gt" : "&lt") + " Reliability Threshold of " + data['ad_params']['reliability_threshold'] + ") </a>";
-        var localCompatibility = "<a class='list-group-item'>Local Compatibility: " + transObj['local_compatibility'].toFixed(2) + " (" + (transObj['local_compatibility'] > data['ad_params']['local_compatibilty_threshold'] ? "&gt" : "&lt") + " Local Compatibility Threshold of " + data['ad_params']['local_compatibilty_threshold'] + ")</a>";
+        var localCompatibility = "<a class='list-group-item'>Local Compatibility: " + transObj['local_compatibility'].toFixed(2) + " (" + (transObj['local_compatibility'] > data['ad_params']['local_compatibility_threshold'] ? "&gt" : "&lt") + " Local Compatibility Threshold of " + data['ad_params']['local_compatibility_threshold'] + ")</a>";
 
         var transImg = "<img width='100%' src='" + transObj['rule']['url'] + "?smiles=" + encodeURIComponent(data['assessment']['smiles']) + "'>";
 
@@ -784,4 +784,4 @@ function handleAssessmentResponse(depict_url, data) {
 
     $("#appDomainAssessmentResultTable").append(res);
 
-}
+}

static/js/pw.js

@@ -444,6 +444,13 @@ function serializeSVG(svgElement) {
         line.setAttribute("fill", style.fill);
     });
 
+    svgElement.querySelectorAll("line.link_no_arrow").forEach(line => {
+        const style = getComputedStyle(line);
+        line.setAttribute("stroke", style.stroke);
+        line.setAttribute("stroke-width", style.strokeWidth);
+        line.setAttribute("fill", style.fill);
+    });
+
     const serializer = new XMLSerializer();
     let svgString = serializer.serializeToString(svgElement);
 
@@ -455,7 +462,26 @@ function serializeSVG(svgElement) {
     return svgString;
 }
 
+function shrinkSVG(svgSelector) {
+
+    const svg = d3.select(svgSelector);
+    const node = svg.node();
+
+    // Compute bounding box of everything inside the SVG
+    const bbox = node.getBBox();
+
+    const padding = 10;
+    svg.attr("viewBox",
+        `${bbox.x - padding} ${bbox.y - padding} ${bbox.width + 2 * padding} ${bbox.height + 2 * padding}`
+    )
+        .attr("width", bbox.width + 2 * padding)
+        .attr("height", bbox.height + 2 * padding);
+
+    return bbox;
+}
+
 function downloadSVG(svgElement, filename = 'chart.svg') {
+    shrinkSVG("#" + svgElement.id);
     const svgString = serializeSVG(svgElement);
     const blob = new Blob([svgString], {type: 'image/svg+xml;charset=utf-8'});
     const url = URL.createObjectURL(blob);

templates/actions/objects/compound.html

@@ -3,6 +3,10 @@
         <a role="button" data-toggle="modal" data-target="#edit_compound_modal">
             <i class="glyphicon glyphicon-edit"></i> Edit Compound</a>
     </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
+    </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#add_structure_modal">
             <i class="glyphicon glyphicon-plus"></i> Add Structure</a>
@@ -11,6 +15,10 @@
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
             <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
     </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#generic_set_external_reference_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set External Reference</a>
+    </li>
 {% endif %}
     <li>
         <a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
@@ -21,4 +29,4 @@
         <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
             <i class="glyphicon glyphicon-trash"></i> Delete Compound</a>
     </li>
-{% endif %}
+{% endif %}

templates/actions/objects/compound_structure.html

@@ -3,12 +3,20 @@
         <a role="button" data-toggle="modal" data-target="#edit_compound_structure_modal">
             <i class="glyphicon glyphicon-edit"></i> Edit Compound Structure</a>
     </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
+    </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
             <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
     </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#generic_set_external_reference_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set External Reference</a>
+    </li>
     <li>
         <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
             <i class="glyphicon glyphicon-trash"></i> Delete Compound Structure</a>
     </li>
-{% endif %}
+{% endif %}

templates/actions/objects/edge.html

@@ -1,4 +1,8 @@
 {% if meta.can_edit %}
+    <li>
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
+    </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
             <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>

templates/actions/objects/node.html

@@ -3,6 +3,10 @@
         <a role="button" data-toggle="modal" data-target="#edit_node_modal">
             <i class="glyphicon glyphicon-edit"></i> Edit Node</a>
     </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
+    </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
             <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>

templates/actions/objects/pathway.html

@@ -31,6 +31,10 @@
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
             <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
     </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
+    </li>
     {#    <li>#}
     {#        <a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">#}
     {#            <i class="glyphicon glyphicon-plus"></i> Calculate Compound Properties</a>#}
@@ -48,4 +52,4 @@
         <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
             <i class="glyphicon glyphicon-trash"></i> Delete Pathway</a>
     </li>
-{% endif %}
+{% endif %}

templates/actions/objects/reaction.html

@@ -3,10 +3,18 @@
         <a role="button" data-toggle="modal" data-target="#edit_reaction_modal">
             <i class="glyphicon glyphicon-edit"></i> Edit Reaction</a>
     </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
+    </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
             <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
     </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#generic_set_external_reference_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set External Reference</a>
+    </li>
 {% endif %}
     <li>
         <a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
@@ -17,4 +25,4 @@
         <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
             <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a>
     </li>
-{% endif %}
+{% endif %}

templates/actions/objects/rule.html

@@ -3,6 +3,10 @@
         <a role="button" data-toggle="modal" data-target="#edit_rule_modal">
             <i class="glyphicon glyphicon-edit"></i> Edit Rule</a>
     </li>
+    <li>
+        <a role="button" data-toggle="modal" data-target="#set_aliases_modal">
+            <i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
+    </li>
     <li>
         <a role="button" data-toggle="modal" data-target="#set_scenario_modal">
             <i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
@@ -17,4 +21,4 @@
         <a class="button" data-toggle="modal" data-target="#generic_delete_modal">
             <i class="glyphicon glyphicon-trash"></i> Delete Rule</a>
     </li>
-{% endif %}
+{% endif %}

templates/compare.html

@@ -0,0 +1,55 @@
+{% extends "framework.html" %}
+
+{% block content %}
+    <div>
+        <form action="" method="post">
+            {% csrf_token %}
+            <input type="text" class="form-control" id="smiles" name="smiles" placeholder="SMILES"
+                   value="{{ smiles }}"/>
+            <input type="text" class="form-control" id="smiles" name="smirks" placeholder="SMIRKS"
+                   value="{{ smirks }}"/>
+            <button type="submit" class="btn btn-primary">Test</button>
+        </form>
+    </div>
+    {% if result %}
+        {{ smiles }}<p></p>
+        <img width='400' src='{% url 'depict' %}?smiles={{ smiles|urlencode }}'><br>
+        <p></p>
+        {% if rule %}
+            {{ smirks }}
+            <p></p>
+            {{ rule.reactants_smarts }}
+            <p></p>
+            {{ rule.products_smarts }}
+            <p></p>
+            <div>
+                {{ rule.as_svg|safe }}
+            </div>
+        {% endif %}
+        <h2>Diff</h2>
+        {% if diff %}
+            {% for d in diff %}
+                {{ d }}
+            {% endfor %}
+        {% else %}
+            {{ "No diff" }}
+        {% endif %}
+        <div>
+            <div class="col-md-6">
+                <h2>Ambit</h2>
+                {% for p in ambit_res %}
+                    {{ p }}<br>
+                    <img width='400' src='{% url 'depict' %}?smiles={{ p|urlencode }}'><br>
+                {% endfor %}
+            </div>
+
+            <div class="col-md-6">
+                <h2>RDKit</h2>
+                {% for p in rdkit_res %}
+                    {{ p }}<br>
+                    <img width='400' src='{% url 'depict' %}?smiles={{ p|urlencode }}'><br>
+                {% endfor %}
+            </div>
+        </div>
+    {% endif %}
+{% endblock content %}

templates/errors/error.html

@@ -6,8 +6,7 @@
         <h4 class="alert-heading">{{ error_message }}</h4>
         <hr>
         <p class="mb-0">
-            {{ error_detail }}<br>
+            {{ error_detail }}
-            The error was logged and will be investigated.
         </p>
     </div>
 

templates/framework.html

@@ -89,7 +89,7 @@
         <div class="collapse navbar-collapse collapse-framework navbar-collapse-framework" id="navbarCollapse">
             <ul class="nav navbar-nav navbar-nav-framework">
                 <li>
-                    <a class="button" data-toggle="modal" data-target="#predict_modal">
+                    <a href="#" data-toggle="modal" data-target="#predict_modal">
                         Predict Pathway
                     </a>
                 </li>
@@ -134,7 +134,7 @@
                     <a data-toggle="dropdown" class="dropdown-toggle" href="#">Info <b class="caret"></b></a>
                     <ul role="menu" class="dropdown-menu">
                         <!--<li><a href="{{ meta.server_url }}/funding" id="fundingLink">Funding</a></li>-->
-                        <li><a href="https://envipath.com/license/" id="licenceLink">Licences</a></li>
+                        <li><a href="https://community.envipath.org/t/envipath-license/109" id="licenceLink">Licences</a></li>
                         <li class="divider"></li>
                         <li><a target="_blank" href="https://wiki.envipath.org/" id="wikiLink">Documentation Wiki</a>
                         </li>
@@ -227,21 +227,23 @@
     <div class="row">
         <div class="col-lg-12">
             <ul class="nav nav-pills nav-justified">
-                <li><a href="http://eawag.ch" target="_blank">
-                    <img id="image-ealogo"
-                         height="60"
-                         src='{% static "/images/ealogo.gif" %}'
-                         alt="Eawag"/>
-                </a>
-                </li>
                 <li>
                     <a href="http://ml.auckland.ac.nz" target="_blank">
-                        <img id="image-uoalogo"
+                        <img id="image-uoalogo" height="60" src='{% static "/images/UoA-Logo-Primary-RGB-Small.png" %}'
-                             height="60"
-                             src='{% static "/images/uoa.png" %}'
                              alt="The Univserity of Auckland"/>
                     </a>
                 </li>
+                <li>
+                    <a href="https://eawag.ch" target="_blank">
+                        <img id="image-ealogo" height="60" src='{% static "/images/ealogo.gif" %}' alt="Eawag"/>
+                    </a>
+                </li>
+                <li>
+                    <a href="https://www.uzh.ch/" target="_blank">
+                        <img id="image-ufzlogo" height="60" src='{% static "/images/uzh-logo.svg" %}'
+                             alt="University of Zurich"/>
+                    </a>
+                </li>
             </ul>
         </div>
     </div>

templates/index/index.html

@@ -103,6 +103,7 @@
             var textSmiles = $('#index-form-text-input').val().trim();
 
             if (textSmiles === '') {
+                $(this).prop("disabled", false);
                 return;
             }
 

templates/migration_detail.html

@@ -1,50 +1,45 @@
 {% extends "framework.html" %}
 
 {% block content %}
-<div class="panel-group" id="migration-detail">
+    <div class="panel-group" id="migration-detail">
-    <div class="panel panel-default">
+        <div class="panel panel-default">
-        <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
+            <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
-            Migration Status for {{ bt_rule_name }}
+                Migration Status for {{ bt_rule_name }}
-        </div>
-        <div class="panel-body">
-            <p>A package contains pathways, rules, etc. and can reflect specific experimental
-                conditions. <a target="_blank" href="https://wiki.envipath.org/index.php/packages" role="button">Learn
-                    more &gt;&gt;</a></p>
-        </div>
-
-        {% for obj in results %}
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-            {% if obj.status %}
-            <span class="glyphicon glyphicon-ok" aria-hidden="true"
-                  style="float:right" data-toggle="tooltip"
-                  data-placement="top" title="" data-original-title="Reviewed">
-            </span>
-            {% else %}
-            <span class="glyphicon glyphicon-remove" aria-hidden="true"
-                  style="float:right" data-toggle="tooltip"
-                  data-placement="top" title="" data-original-title="Reviewed">
-            </span>
-            {% endif %}
-            <h4 class="panel-title">
-                <a id="{{ obj.id }}-link" data-toggle="collapse" data-parent="#migration-detail"
-                   href="#{{ obj.id }}">{{ obj.name }}</a>
-            </h4>
-        </div>
-        <div id="{{ obj.id }}" class="panel-collapse collapse {% if not obj.status %}in{% endif %}">
-            <div class="panel-body list-group-item">
-                {% if obj.status %}
-                <p>Products generated by AMBIT: {{ obj.ambit_smiles }}</p>
-                <p>Products generated by RDKit: {{ obj.rdkit_smiles }}</p>
-                {% else %}
-                    <pre>{{ obj.detail }}</pre>
-                {% endif %}
             </div>
+            <div class="panel-body">
+                <p>A package contains pathways, rules, etc. and can reflect specific experimental
+                    conditions. <a target="_blank" href="https://wiki.envipath.org/index.php/packages" role="button">Learn
+                        more &gt;&gt;</a></p>
+            </div>
+
+            {% for obj in results %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    {% if obj.status %}
+                        <span class="glyphicon glyphicon-ok" aria-hidden="true"
+                              style="float:right" data-toggle="tooltip"
+                              data-placement="top" title="" data-original-title="Reviewed">
+                        </span>
+                    {% else %}
+                        <span class="glyphicon glyphicon-remove" aria-hidden="true"
+                              style="float:right" data-toggle="tooltip"
+                              data-placement="top" title="" data-original-title="Reviewed">
+                        </span>
+                    {% endif %}
+                    <h4 class="panel-title">
+                        <a id="{{ obj.id }}-link" data-toggle="collapse" data-parent="#migration-detail"
+                           href="#{{ obj.id }}">{{ obj.name }}</a>
+                    </h4>
+                </div>
+                <div id="{{ obj.id }}" class="panel-collapse collapse {% if not obj.status %}in{% endif %}">
+                    <div class="panel-body list-group-item">
+                        <pre>{{ obj.detail }}</pre>
+                    </div>
+                </div>
+            {% endfor %}
         </div>
-        {% endfor %}
     </div>
-</div>
 
-<script>
+    <script>
 
-</script>
+    </script>
 {% endblock content %}

templates/modals/collections/import_legacy_package_modal.html

@@ -15,12 +15,12 @@
                       enctype="multipart/form-data">
                     {% csrf_token %}
                     <p>
-                        <label class="btn btn-primary" for="jsonFile">
+                        <label class="btn btn-primary" for="legacyJsonFile">
-                            <input id="jsonFile" name="file" type="file" style="display:none;"
+                            <input id="legacyJsonFile" name="file" type="file" style="display:none;"
-                                   onchange="$('#upload-file-info').html(this.files[0].name)">
+                                   onchange="$('#upload-legacy-file-info').html(this.files[0].name)">
                             Choose JSON File
                         </label>
-                        <span class="label label-info" id="upload-file-info"></span>
+                        <span class="label label-info" id="upload-legacy-file-info"></span>
                         <input type="hidden" value="import-legacy-package-json" name="hidden" readonly="">
                     </p>
                 </form>

templates/modals/collections/new_scenario_modal.html

@@ -29,11 +29,11 @@
                         <tr>
                             <th>
                                 <input type="number" id="dateYear" name="scenario-date-year" class="form-control"
-                                       placeholder="YYYY">
+                                       placeholder="YYYY" max="{% now "Y" %}">
                             </th>
                             <th>
                                 <input type="number" id="dateMonth" name="scenario-date-month" min="1" max="12"
-                                       class="form-control" placeholder="MM" align="">
+                                       class="form-control" placeholder="MM" >
                             </th>
                             <th>
                                 <input type="number" id="dateDay" name="scenario-date-day" min="1" max="31" class="form-control"
@@ -88,8 +88,15 @@
             $('#new_scenario_form').submit();
         });
 
-    });
+        var dateYear = document.getElementById("dateYear");
+        dateYear.addEventListener("change", () => {
+            console.log("Final value after editing:", dateYear.value);
+            if (dateYear.value.length < 4) {
+                dateYear.value = {% now "Y" %};
+            }
+        });
 
+    });
 
 </script>
 

templates/modals/objects/edit_compound_structure_modal.html

@@ -15,12 +15,12 @@
                     {% csrf_token %}
                     <p>
                         <label for="compound-structure-name">Name</label>
-                        <input id="compound-structure-name" class="form-control" name="compound-structure-name" value="{{ structure.name }}">
+                        <input id="compound-structure-name" class="form-control" name="compound-structure-name" value="{{ compound_structure.name }}">
                     </p>
                     <p>
                         <label for="compound-structure-description">Description</label>
                         <input id="compound-structure-description" type="text" class="form-control"
-                               value="{{ structure.description }}" name="compound-structure-description">
+                               value="{{ compound_structure.description }}" name="compound-structure-description">
                     </p>
                 </form>
             </div>

templates/modals/objects/generic_copy_object_modal.html

@@ -23,6 +23,8 @@
                     </select>
                     <input type="hidden" name="hidden" value="copy">
                 </form>
+                <div id="copy-object-error-message" class="alert alert-danger" role="alert" style="display: none">
+                </div>
             </div>
             <div class="modal-footer">
                 <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
@@ -38,6 +40,7 @@
 
         $('#generic-copy-object-modal-form-submit').click(function (e) {
             e.preventDefault();
+            $('#copy-object-error-message').hide()
 
             const packageUrl = $('#target-package').find(":selected").val();
 
@@ -49,12 +52,22 @@
                 object_to_copy: '{{ current_object.url }}',
             }
 
-            $.post(packageUrl, formData, function (response) {
+            $.ajax({
-                if (response.success) {
+                type: 'post',
-                    window.location.href = response.success;
+                data: formData,
+                url: packageUrl,
+                success: function (data, textStatus) {
+                    window.location.href = data.success;
+                },
+                error: function (jqXHR, textStatus, errorThrown) {
+                    if (jqXHR.responseJSON.error.indexOf('to the same package') > -1) {
+                        $('#copy-object-error-message').append('<p>The target Package is the same as the source Package. Please select another target!</p>');
+                    } else {
+                        $('#copy-object-error-message').append('<p>' + jqXHR.responseJSON.error + '</p>');
+                    }
+                    $('#copy-object-error-message').show();
                 }
             });
-
         });
 
     })

templates/modals/objects/generic_set_aliases_modal.html

@@ -0,0 +1,169 @@
+{% load static %}
+
+<style>
+    .alias-container {
+        display: flex;
+        flex-wrap: wrap;
+        align-items: center;
+        border: 1px solid #ccc;
+        border-radius: 4px;
+        padding: 4px 6px;
+        cursor: text;
+        min-height: 38px;
+        background-color: #fff;
+    }
+
+    .alias {
+        display: inline-flex;
+        align-items: center;
+        background-color: #5bc0de;
+        color: white;
+        padding: 4px 8px;
+        margin: 3px 3px;
+        border-radius: 4px;
+        font-size: 13px;
+        line-height: 1.4;
+    }
+
+    .alias .remove {
+        margin-left: 6px;
+        cursor: pointer;
+        font-weight: bold;
+        line-height: 1;
+    }
+
+    .alias-input {
+        flex: 1;
+        min-width: 120px;
+        border: none;
+        outline: none;
+        margin: 3px 3px;
+        font-size: 14px;
+    }
+
+    .form-control.alias-container {
+        height: auto;
+        box-shadow: none;
+    }
+</style>
+
+<div class="modal fade bs-modal-lg" id="set_aliases_modal" tabindex="-1" aria-labelledby="set_aliases_modal"
+     aria-modal="true" role="dialog">
+    <div class="modal-dialog modal-lg">
+        <div class="modal-content">
+            <div class="modal-header">
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">×</span>
+                </button>
+                <h4 class="modal-title">Set Aliases for {{ current_object.name }}</h4>
+            </div>
+            <div class="modal-body">
+                <form id="set_aliases_modal_form" accept-charset="UTF-8" action="{{ current_object.url }}"
+                      data-remote="true" method="post">
+                    {% csrf_token %}
+                    <label for="alias-input">Aliases:</label>
+                    <div class="form-control alias-container" id="alias-box">
+                        {% for alias in current_object.aliases %}
+                        <span class="alias">{{ alias|escape }}<span class="remove">&times;</span></span>
+                        {% endfor %}
+                        <input type="text" id="alias-input" class="alias-input" placeholder="Add Alias...">
+                    </div>
+                </form>
+                <div id="add-alias-error-message" class="alert alert-danger" role="alert" style="display: none">
+                </div>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary pull-left" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="set_aliases_modal_form_submit">Submit</button>
+            </div>
+        </div>
+    </div>
+
+</div>
+<script>
+    $(function () {
+
+        function addAlias(aliasText) {
+            aliasText = aliasText.trim();
+            if (aliasText === '') return;
+
+            // Avoid duplicate aliass
+            var exists = false;
+            $('#alias-box .alias').each(function () {
+                if ($(this).text().replace('×', '').trim().toLowerCase() === aliasText.toLowerCase()) {
+                    exists = true;
+                    return false;
+                }
+            });
+
+            if (!exists) {
+                var aliasHtml = '<span class="alias">' + $('<div>').text(aliasText).html() +
+                    '<span class="remove">&times;</span></span>';
+                $(aliasHtml).insertBefore('#alias-input');
+            }
+
+            $('#alias-input').val('');
+        }
+
+        // Add alias when Enter is pressed
+        $('#alias-input').on('keypress', function (e) {
+            if (e.which === 13) {
+                e.preventDefault();
+                addAlias($(this).val());
+            }
+        });
+
+        // Add alias when input loses focus
+        $('#alias-input').on('blur', function () {
+            var val = $(this).val();
+            if (val.trim() !== '') {
+                addAlias(val);
+            }
+        });
+
+        // Remove alias when clicking ×
+        $('#alias-box').on('click', '.remove', function () {
+            $(this).closest('.alias').remove();
+        });
+
+        // Focus input when clicking the container
+        $('#alias-box').on('click', function () {
+            $('#alias-input').focus();
+        });
+
+
+        $('#set_aliases_modal_form_submit').on('click', function (e) {
+            e.preventDefault();
+
+            let aliases = [];
+            $('#alias-box .alias').each(function () {
+                aliases.push($(this).text().replace('×', '').trim())
+            });
+
+            if (aliases.length === 0) {
+                // Set empty string for deletion of all aliases
+                // If empty list is sent, its gets removed entirely from post data
+                aliases = ['']
+            }
+
+            formData = {
+                'aliases': aliases
+            }
+
+            $.ajax({
+                type: 'post',
+                data: formData,
+                url: '{{ current_object.url }}',
+                traditional: true,
+                success: function (data, textStatus) {
+                    window.location.href = data.success;
+                },
+                error: function (jqXHR, textStatus, errorThrown) {
+                    $('#add-alias-error-message').append('<p>Setting aliases failed!</p>');
+                    $('#add-alias-error-message').show();                }
+            });
+
+        });
+
+    });
+</script>

templates/modals/objects/generic_set_external_reference_modal.html

@@ -0,0 +1,60 @@
+{% load static %}
+<!-- Delete Object -->
+<div id="generic_set_external_reference_modal" class="modal" tabindex="-1">
+    <div class="modal-dialog">
+        <div class="modal-content">
+            <div class="modal-header">
+                <h3 class="modal-title">Add External References</h3>
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                    <span aria-hidden="true">&times;</span>
+                </button>
+            </div>
+            <div class="modal-body">
+                <form id="generic-set-external-reference-modal-form" accept-charset="UTF-8"
+                      action="{{ current_object.url }}"
+                      data-remote="true" method="post">
+                    {% csrf_token %}
+                    <label for="database-select">Select the Database you want to attach an External Reference
+                        for</label>
+                    <select id="database-select" name="selected-database" data-actions-box='true' class="form-control"
+                            data-width='100%'>
+                        <option disabled selected>Select Database</option>
+                        {% for entity, databases in meta.external_databases.items %}
+                            {% if entity == object_type %}
+                                {% for db in databases %}
+                                    <option id="db-select-{{ db.database.pk }}" data-input-placeholder="{{ db.placeholder }}"
+                                            value="{{ db.database.id }}">{{ db.database.name }}</option>`
+                                {% endfor %}
+                            {% endif %}
+                        {% endfor %}
+                    </select>
+                    <p></p>
+                    <div id="input-div" style="display: none">
+                        <label for="identifier" >The reference</label>
+                        <input type="text" id="identifier" name="identifier" class="form-control" placeholder="">
+                    </div>
+                </form>
+            </div>
+            <div class="modal-footer">
+                <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                <button type="button" class="btn btn-primary" id="generic-set-external-reference-modal-form-submit">Submit</button>
+            </div>
+        </div>
+    </div>
+</div>
+<script>
+    $(function () {
+
+        $("#database-select").on("change", function () {
+            let selected = $(this).val();
+            $("#identifier").attr("placeholder", $('#db-select-' + selected).data('input-placeholder'));
+            $("#input-div").show();
+        });
+
+        $('#generic-set-external-reference-modal-form-submit').click(function (e) {
+            e.preventDefault();
+            $('#generic-set-external-reference-modal-form').submit();
+        });
+
+    })
+</script>

templates/modals/objects/generic_set_scenario_modal.html

@@ -18,6 +18,7 @@
                     <select id="scenario-select" name="selected-scenarios" data-actions-box='true' class="form-control"
                             multiple data-width='100%'>
                         <option disabled>Select Scenarios</option>
+                        <option value="" hidden></option>
                     </select>
                 </form>
             </div>
@@ -64,6 +65,9 @@
 
             $('#set_scenario_modal_form_submit').on('click', function (e) {
                 e.preventDefault();
+                if ($('#scenario-select').val().length == 0) {
+                    $('#scenario-select').val("")
+                }
                 $('#set_scenario_modal_form').submit();
             });
         });

templates/objects/composite_rule.html

@@ -2,12 +2,13 @@
 
 {% block content %}
 
-{% block action_modals %}
+    {% block action_modals %}
-{% include "modals/objects/edit_rule_modal.html" %}
+        {% include "modals/objects/edit_rule_modal.html" %}
-{% include "modals/objects/generic_set_scenario_modal.html" %}
+        {% include "modals/objects/generic_set_aliases_modal.html" %}
-{% include "modals/objects/generic_copy_object_modal.html" %}
+        {% include "modals/objects/generic_set_scenario_modal.html" %}
-{% include "modals/objects/generic_delete_modal.html" %}
+        {% include "modals/objects/generic_copy_object_modal.html" %}
-{% endblock action_modals %}
+        {% include "modals/objects/generic_delete_modal.html" %}
+    {% endblock action_modals %}
 
 <div class="panel-group" id="rule-detail">
     <div class="panel panel-default">
@@ -28,10 +29,27 @@
         </div>
         <div class="panel-body">
             <p>
-                {{ rule.description }}
+                {{ rule.description|safe }}
             </p>
         </div>
 
+        {% if rule.aliases %}
+            <!-- Aliases -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="rule-aliases-link" data-toggle="collapse" data-parent="#rule-detail"
+                       href="#rule-aliases">Aliases</a>
+                </h4>
+            </div>
+            <div id="rule-aliases" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    {% for alias in rule.aliases %}
+                        <a class="list-group-item">{{ alias }}</a>
+                    {% endfor %}
+                </div>
+            </div>
+        {% endif %}
+
         <!-- Reaction Patterns -->
         <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
             <h4 class="panel-title">
@@ -69,19 +87,41 @@
             </div>
         {% endif %}
 
-        <!-- EC Numbers -->
+        {% if rule.enzymelinks %}
-        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+            <!-- EC Numbers -->
-            <h4 class="panel-title">
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
-                <a id="rule-ec-numbers-link" data-toggle="collapse" data-parent="#rule-detail"
+                <h4 class="panel-title">
-                   href="#rule-ec-numbers">EC Numbers</a>
+                    <a id="rule-ec-numbers-link" data-toggle="collapse" data-parent="#rule-detail"
-            </h4>
+                       href="#rule-ec-numbers">EC Numbers</a>
-        </div>
+                </h4>
-        <div id="rule-ec-numbers" class="panel-collapse collapse">
-            <div class="panel-body list-group-item">
-
             </div>
-        </div>
+            <div id="rule-ec-numbers" class="panel-collapse collapse in">
-
+                <div class="panel-body list-group-item">
+                    {% for k, v in rule.get_grouped_enzymelinks.items %}
+                        <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                            <h4 class="panel-title">
+                                <a id="{{ k|slugify }}_Link" data-toggle="collapse"
+                                   data-parent="#{{ k|slugify }}_Accordion"
+                                   href="#{{ k|slugify }}">
+                                    {{ k }}
+                                </a>
+                            </h4>
+                        </div>
+                        <div id="{{ k|slugify }}" class="panel-collapse collapse in">
+                            <div class="panel-body list-group-item">
+                                {% for enzyme in v %}
+                                    <a class="list-group-item" href="{{ enzyme.url }}">
+                                        {{ enzyme.ec_number }}
+                                        <div style="position:absolute;bottom:10px;left:100px;">{{ enzyme.name }}</div>
+                                        <div style="float:right;">{{ enzyme.linking_method }}</div>
+                                    </a>
+                                {% endfor %}
+                            </div>
+                        </div>
+                    {% endfor %}
+                </div>
+            </div>
+        {% endif %}
     </div>
 </div>
 {% endblock content %}

templates/objects/compound.html

@@ -4,8 +4,10 @@
 
     {% block action_modals %}
         {% include "modals/objects/edit_compound_modal.html" %}
+        {% include "modals/objects/generic_set_aliases_modal.html" %}
         {% include "modals/objects/add_structure_modal.html" %}
         {% include "modals/objects/generic_set_scenario_modal.html" %}
+        {% include "modals/objects/generic_set_external_reference_modal.html" %}
         {% include "modals/objects/generic_copy_object_modal.html" %}
         {% include "modals/objects/generic_delete_modal.html" %}
     {% endblock action_modals %}
@@ -36,6 +38,23 @@
                 </p>
             </div>
 
+            {% if compound.aliases %}
+                <!-- Aliases -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="compound-aliases-link" data-toggle="collapse" data-parent="#compound-detail"
+                           href="#compound-aliases">Aliases</a>
+                    </h4>
+                </div>
+                <div id="compound-aliases" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for alias in compound.aliases %}
+                            <a class="list-group-item">{{ alias }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
             <!-- Description -->
             <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                 <h4 class="panel-title">

templates/objects/compound_structure.html

@@ -2,11 +2,13 @@
 
 {% block content %}
 
-{% block action_modals %}
+    {% block action_modals %}
-{% include "modals/objects/edit_compound_structure_modal.html" %}
+        {% include "modals/objects/edit_compound_structure_modal.html" %}
-{% include "modals/objects/generic_set_scenario_modal.html" %}
+        {% include "modals/objects/generic_set_aliases_modal.html" %}
-{% include "modals/objects/generic_delete_modal.html" %}
+        {% include "modals/objects/generic_set_scenario_modal.html" %}
-{% endblock action_modals %}
+        {% include "modals/objects/generic_set_external_reference_modal.html" %}
+        {% include "modals/objects/generic_delete_modal.html" %}
+    {% endblock action_modals %}
 
 <div class="panel-group" id="compound-structure-detail">
     <div class="panel panel-default">
@@ -32,34 +34,52 @@
         <!-- Image -->
         <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
             <h4 class="panel-title">
-                <a id="compound-image-link" data-toggle="collapse" data-parent="#compound-detail"
+                <a id="compound-structure-image-link" data-toggle="collapse" data-parent="#compound-structure-detail"
-                   href="#compound-image">Image Representation</a>
+                   href="#compound-structure-image">Image Representation</a>
             </h4>
         </div>
-        <div id="compound-image" class="panel-collapse collapse in">
+        <div id="compound-structure-image" class="panel-collapse collapse in">
             <div class="panel-body list-group-item">
                 <div id="image-div" align="center">
                     {{ compound_structure.as_svg|safe }}
                 </div>
             </div>
         </div>
+
         <!-- SMILES -->
         <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
             <h4 class="panel-title">
-                <a id="compound-smiles-link" data-toggle="collapse" data-parent="#compound-detail"
+                <a id="compound-structure-smiles-link" data-toggle="collapse" data-parent="#compound-structure-detail"
-                   href="#compound-smiles">SMILES Representation</a>
+                   href="#compound-structure-smiles">SMILES Representation</a>
             </h4>
         </div>
-        <div id="compound-smiles" class="panel-collapse collapse in">
+        <div id="compound-structure-smiles" class="panel-collapse collapse in">
             <div class="panel-body list-group-item">
                 {{ compound_structure.smiles }}
             </div>
         </div>
 
+        {% if compound_structure.aliases %}
+            <!-- Aliases -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="compound-structure-aliases-link" data-toggle="collapse" data-parent="#compound-structure-detail"
+                       href="#compound-structure-aliases">Aliases</a>
+                </h4>
+            </div>
+            <div id="compound-structure-aliases" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    {% for alias in compound_structure.aliases %}
+                        <a class="list-group-item">{{ alias }}</a>
+                    {% endfor %}
+                </div>
+            </div>
+        {% endif %}
+
         {% if compound_structure.scenarios.all %}
             <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                 <h4 class="panel-title">
-                    <a id="compound_structure-scenario-link" data-toggle="collapse" data-parent="#compound-structure-detail"
+                    <a id="compound-structure-scenario-link" data-toggle="collapse" data-parent="#compound-structure-detail"
                        href="#compound-structure-scenario">Scenarios</a>
                 </h4>
             </div>

templates/objects/edge.html

@@ -4,6 +4,7 @@
 
     {% block action_modals %}
 {#        {% include "modals/objects/edit_edge_modal.html" %}#}
+        {% include "modals/objects/generic_set_aliases_modal.html" %}
         {% include "modals/objects/generic_set_scenario_modal.html" %}
         {% include "modals/objects/generic_delete_modal.html" %}
     {% endblock action_modals %}
@@ -39,6 +40,23 @@
                 </div>
             </div>
 
+            {% if edge.aliases %}
+                <!-- Aliases -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="edge-aliases-link" data-toggle="collapse" data-parent="#edge-detail"
+                           href="#edge-aliases">Aliases</a>
+                    </h4>
+                </div>
+                <div id="edge-aliases" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for alias in edge.aliases %}
+                            <a class="list-group-item">{{ alias }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
             <!-- Image -->
             <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                 <h4 class="panel-title">

templates/objects/enzymelink.html

@@ -0,0 +1,105 @@
+{% extends "framework.html" %}
+
+{% block content %}
+
+    <div class="panel-group" id="enzyme-detail">
+        <div class="panel panel-default">
+            <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
+                {{ enzymelink.ec_number }}
+            </div>
+
+            <!-- Name -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="enzyme-name-link" data-toggle="collapse" data-parent="#enzyme-detail"
+                       href="#enzyme-name">Enzyme Name</a>
+                </h4>
+            </div>
+            <div id="enzyme-name" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    {{ enzymelink.name }}
+                </div>
+            </div>
+
+            <!-- Linking Method -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="enzyme-linking-link" data-toggle="collapse" data-parent="#enzyme-detail"
+                       href="#enzyme-linking">Linking Method</a>
+                </h4>
+            </div>
+            <div id="enzyme-linking" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    {{ enzymelink.linking_method }}. &nbsp;<a
+                        href="https://wiki.envipath.org/index.php/Rules#EnzymeLinks" target="#">Learn more &gt;&gt;</a>
+                </div>
+            </div>
+
+            {% if enzymelink.kegg_reaction_links %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="enzyme-evidence-link" data-toggle="collapse" data-parent="#enzyme-detail"
+                           href="#enzyme-evidence">Linking Evidence</a>
+                    </h4>
+                </div>
+                <div id="enzyme-evidence" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for kl in enzymelink.kegg_reaction_links %}
+                            <a class="list-group-item"
+                               href="{{ kl.external_url }}">{{ kl.identifier_value }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
+            {% if enzymelink.reaction_evidence.all %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="enzyme-reaction-evidence-link" data-toggle="collapse" data-parent="#enzyme-detail"
+                           href="#enzyme-reaction-evidence">Linking Evidence - enviPath Reactions</a>
+                    </h4>
+                </div>
+                <div id="enzyme-reaction-evidence" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for r in enzymelink.reaction_evidence.all %}
+                            <a class="list-group-item" href="{{ r.url }}">{{ r.name }} <i>({{ r.package.name }})</i></a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
+            {% if enzymelink.edge_evidence.all %}
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="enzyme-edge-evidence-link" data-toggle="collapse" data-parent="#enzyme-detail"
+                           href="#enzyme-edge-evidence">Linking Evidence - enviPath Pathways</a>
+                    </h4>
+                </div>
+                <div id="enzyme-edge-evidence" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for e in enzymelink.edge_evidence.all %}
+                            <a class="list-group-item" href="{{ e.pathway.url }}">{{ e.pathway.name }}
+                                <i>({{ r.package.name }})</i></a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
+            <!-- External DB Reference -->
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="enzyme-external-identifier-link" data-toggle="collapse" data-parent="#enzyme-detail"
+                       href="#enzyme-external-identifier">External DB References</a>
+                </h4>
+            </div>
+            <div id="enzyme-external-identifier" class="panel-collapse collapse in">
+                <div class="panel-body list-group-item">
+                    <a class="list-group-item"
+                       href="http://www.brenda-enzymes.org/enzyme.php?ecno={{ enzymelink.ec_number }}"
+                       target="_blank"> Brenda entry for {{ enzymelink.ec_number }}</a>
+                </div>
+            </div>
+
+        </div>
+    </div>
+{% endblock content %}

templates/objects/model.html

@@ -315,12 +315,18 @@
             $("#predict-button").on("click", function (e) {
                 e.preventDefault();
 
+                clear("predictResultTable");
+
                 data = {
                     "smiles": $("#smiles-to-predict").val(),
                     "classify": "ILikeCats!"
                 }
 
-                clear("predictResultTable");
+                if (data["smiles"].trim() === "") {
+                    $("#predictResultTable").addClass("alert alert-danger");
+                    $("#predictResultTable").append("Please enter a SMILES string to predict!");
+                    return;
+                }
 
                 makeLoadingGif("#predictLoading", "{% static '/images/wait.gif' %}");
                 $.ajax({
@@ -332,17 +338,17 @@
                             $("#predictLoading").empty();
                             handlePredictionResponse(data);
                         } catch (error) {
-                            console.log("Error");
+
                             $("#predictLoading").empty();
                             $("#predictResultTable").addClass("alert alert-danger");
-                            $("#predictResultTable").append("Error while processing request :/");
+                            $("#predictResultTable").append("Error while processing response :/");
                         }
                     },
-                    error: function (jqXHR, textStatus, errorThrown) {
+                    error: function (jqXHR, textStatus, errorThrown, x) {
                         $("#predictLoading").empty();
                         $("#predictResultTable").addClass("alert alert-danger");
-                        $("#predictResultTable").append("Error while processing request :/");
+                        $("#predictResultTable").append(jqXHR.responseJSON.error);
-                    }
+                    },
                 });
             });
         }
@@ -351,12 +357,20 @@
             $("#assess-button").on("click", function (e) {
                 e.preventDefault();
 
+                clear("appDomainAssessmentResultTable");
+
                 data = {
                     "smiles": $("#smiles-to-assess").val(),
                     "app-domain-assessment": "ILikeCats!"
                 }
 
-                clear("appDomainAssessmentResultTable");
+                if (data["smiles"].trim() === "") {
+                    $("#appDomainAssessmentResultTable").addClass("alert alert-danger");
+                    $("#appDomainAssessmentResultTable").append("Please enter a SMILES string to predict!");
+                    return;
+                }
+
+
 
                 makeLoadingGif("#appDomainLoading", "{% static '/images/wait.gif' %}");
                 $.ajax({
@@ -369,16 +383,15 @@
                             handleAssessmentResponse("{% url 'depict' %}", data);
                             console.log(data);
                         } catch (error) {
-                            console.log("Error");
                             $("#appDomainLoading").empty();
                             $("#appDomainAssessmentResultTable").addClass("alert alert-danger");
-                            $("#appDomainAssessmentResultTable").append("Error while processing request :/");
+                            $("#appDomainAssessmentResultTable").append("Error while processing response :/");
                         }
                     },
                     error: function (jqXHR, textStatus, errorThrown) {
                         $("#appDomainLoading").empty();
                         $("#appDomainAssessmentResultTable").addClass("alert alert-danger");
-                        $("#appDomainAssessmentResultTable").append("Error while processing request :/");
+                        $("#appDomainAssessmentResultTable").append(jqXHR.responseJSON.error);
                     }
                 });
             });

templates/objects/node.html

@@ -4,6 +4,7 @@
 
     {% block action_modals %}
         {% include "modals/objects/edit_node_modal.html" %}
+        {% include "modals/objects/generic_set_aliases_modal.html" %}
         {% include "modals/objects/generic_set_scenario_modal.html" %}
         {% include "modals/objects/generic_delete_modal.html" %}
     {% endblock action_modals %}
@@ -42,6 +43,23 @@
                 </div>
             </div>
 
+            {% if node.aliases %}
+                <!-- Aliases -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="node-aliases-link" data-toggle="collapse" data-parent="#node-detail"
+                           href="#node-aliases">Aliases</a>
+                    </h4>
+                </div>
+                <div id="node-aliases" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for alias in node.aliases %}
+                            <a class="list-group-item">{{ alias }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
             <!-- Image -->
             <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                 <h4 class="panel-title">

templates/objects/package.html

@@ -29,7 +29,7 @@
             </div>
         </div>
         <div class="panel-body">
-            <p> {{ package.description }} </p>
+            <p> {{ package.description|safe }} </p>
         </div>
         <ul class="list-group">
             <li class="list-group-item">

templates/objects/pathway.html

@@ -85,6 +85,7 @@
         {% include "modals/objects/download_pathway_image_modal.html" %}
         {% include "modals/objects/generic_copy_object_modal.html" %}
         {% include "modals/objects/edit_pathway_modal.html" %}
+        {% include "modals/objects/generic_set_aliases_modal.html" %}
         {% include "modals/objects/generic_set_scenario_modal.html" %}
         {% include "modals/objects/delete_pathway_node_modal.html" %}
         {% include "modals/objects/delete_pathway_edge_modal.html" %}
@@ -176,9 +177,6 @@
                 </nav>
                 <div id="vizdiv" >
                     <svg id="pwsvg">
-                        {% if debug %}
-                            <rect width="100%" height="100%" fill="aliceblue"/>
-                        {% endif %}
                         <defs>
                             <marker id="arrow" viewBox="0 0 10 10" refX="43" refY="5" markerWidth="6" markerHeight="6"
                                     orient="auto-start-reverse" markerUnits="userSpaceOnUse">
@@ -210,6 +208,23 @@
                 </div>
             </div>
 
+            {% if pathway.aliases %}
+                <!-- Aliases -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="pathway-aliases-link" data-toggle="collapse" data-parent="#pathway-detail"
+                           href="#pathway-aliases">Aliases</a>
+                    </h4>
+                </div>
+                <div id="pathway-aliases" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for alias in pathway.aliases %}
+                            <a class="list-group-item">{{ alias }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
             {% if pathway.scenarios.all %}
                 <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                     <h4 class="panel-title">

templates/objects/reaction.html

@@ -4,8 +4,10 @@
 
     {% block action_modals %}
         {% include "modals/objects/edit_reaction_modal.html" %}
+        {% include "modals/objects/generic_set_aliases_modal.html" %}
         {% include "modals/objects/generic_set_scenario_modal.html" %}
         {% include "modals/objects/generic_copy_object_modal.html" %}
+        {% include "modals/objects/generic_set_external_reference_modal.html" %}
         {% include "modals/objects/generic_delete_modal.html" %}
     {% endblock action_modals %}
 
@@ -40,6 +42,23 @@
                 </div>
             </div>
 
+            {% if reaction.aliases %}
+                <!-- Aliases -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="reaction-aliases-link" data-toggle="collapse" data-parent="#reaction-detail"
+                           href="#reaction-aliases">Aliases</a>
+                    </h4>
+                </div>
+                <div id="reaction-aliases" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for alias in reaction.aliases %}
+                            <a class="list-group-item">{{ alias }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
             <!-- Image -->
             <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                 <h4 class="panel-title">
@@ -105,6 +124,23 @@
                 </div>
             {% endif %}
 
+            {% if reaction.get_related_enzymes %}
+                <!-- EC Numbers -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="rule-ec-numbers-link" data-toggle="collapse" data-parent="#rule-detail"
+                           href="#rule-ec-numbers">EC Numbers</a>
+                    </h4>
+                </div>
+                <div id="rule-ec-numbers" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for e in reaction.get_related_enzymes %}
+                            <a class="list-group-item" href="http://www.brenda-enzymes.org/enzyme.php?ecno={{ e.ec_number }}">{{ e.name }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
             {% if reaction.related_pathways %}
                 <!-- Pathways -->
                 <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">

templates/objects/simple_rule.html

@@ -4,6 +4,7 @@
 
     {% block action_modals %}
         {% include "modals/objects/edit_rule_modal.html" %}
+        {% include "modals/objects/generic_set_aliases_modal.html" %}
         {% include "modals/objects/generic_set_scenario_modal.html" %}
         {% include "modals/objects/generic_copy_object_modal.html" %}
         {% include "modals/objects/generic_delete_modal.html" %}
@@ -32,6 +33,23 @@
                 </p>
             </div>
 
+            {% if rule.aliases %}
+                <!-- Aliases -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="rule-aliases-link" data-toggle="collapse" data-parent="#rule-detail"
+                           href="#rule-aliases">Aliases</a>
+                    </h4>
+                </div>
+                <div id="rule-aliases" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for alias in rule.aliases %}
+                            <a class="list-group-item">{{ alias }}</a>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
+
             <!-- Representation -->
             <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
                 <h4 class="panel-title">
@@ -183,6 +201,43 @@
                     </div>
                 </div>
             {% endif %}
+
+            {% if rule.enzymelinks %}
+                <!-- EC Numbers -->
+                <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                    <h4 class="panel-title">
+                        <a id="rule-ec-numbers-link" data-toggle="collapse" data-parent="#rule-detail"
+                           href="#rule-ec-numbers">EC Numbers</a>
+                    </h4>
+                </div>
+                <div id="rule-ec-numbers" class="panel-collapse collapse in">
+                    <div class="panel-body list-group-item">
+                        {% for k, v in rule.get_grouped_enzymelinks.items %}
+                            <div class="panel panel-default panel-heading list-group-item"
+                                 style="background-color:silver">
+                                <h4 class="panel-title">
+                                    <a id="{{ k|slugify }}_Link" data-toggle="collapse"
+                                       data-parent="#{{ k|slugify }}_Accordion"
+                                       href="#{{ k|slugify }}">
+                                        {{ k }}
+                                    </a>
+                                </h4>
+                            </div>
+                            <div id="{{ k|slugify }}" class="panel-collapse collapse in">
+                                <div class="panel-body list-group-item">
+                                    {% for enzyme in v %}
+                                        <a class="list-group-item" href="{{ enzyme.url }}">
+                                            {{ enzyme.ec_number }}
+                                            <div style="position:absolute;bottom:10px;left:100px;">{{ enzyme.name }}</div>
+                                            <div style="float:right;">{{ enzyme.linking_method }}</div>
+                                        </a>
+                                    {% endfor %}
+                                </div>
+                            </div>
+                        {% endfor %}
+                    </div>
+                </div>
+            {% endif %}
         </div>
     </div>
 {% endblock content %}

tests/test_compound_model.py

@@ -13,91 +13,80 @@ class CompoundTest(TestCase):
     @classmethod
     def setUpClass(cls):
         super(CompoundTest, cls).setUpClass()
-        cls.user = User.objects.get(username='anonymous')
+        cls.user = User.objects.get(username="anonymous")
-        cls.package = PackageManager.create_package(cls.user, 'Anon Test Package', 'No Desc')
+        cls.package = PackageManager.create_package(cls.user, "Anon Test Package", "No Desc")
 
     def test_smoke(self):
         c = Compound.create(
             self.package,
-            smiles='C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F',
+            smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
-            name='Afoxolaner',
+            name="Afoxolaner",
-            description='No Desc'
+            description="No Desc",
         )
 
-        self.assertEqual(c.default_structure.smiles,
+        self.assertEqual(
-                         'C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F')
+            c.default_structure.smiles,
-        self.assertEqual(c.name, 'Afoxolaner')
+            "C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
-        self.assertEqual(c.description, 'No Desc')
+        )
+        self.assertEqual(c.name, "Afoxolaner")
+        self.assertEqual(c.description, "No Desc")
 
     def test_missing_smiles(self):
         with self.assertRaises(ValueError):
-            _ = Compound.create(
+            _ = Compound.create(self.package, smiles=None, name="Afoxolaner", description="No Desc")
-                self.package,
-                smiles=None,
-                name='Afoxolaner',
-                description='No Desc'
-            )
 
         with self.assertRaises(ValueError):
-            _ = Compound.create(
+            _ = Compound.create(self.package, smiles="", name="Afoxolaner", description="No Desc")
-                self.package,
-                smiles='',
-                name='Afoxolaner',
-                description='No Desc'
-            )
 
         with self.assertRaises(ValueError):
-            _ = Compound.create(
+            _ = Compound.create(self.package, smiles="  ", name="Afoxolaner", description="No Desc")
-                self.package,
-                smiles='  ',
-                name='Afoxolaner',
-                description='No Desc'
-            )
 
     def test_smiles_are_trimmed(self):
         c = Compound.create(
             self.package,
-            smiles='   C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F   ',
+            smiles="   C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F   ",
-            name='Afoxolaner',
+            name="Afoxolaner",
-            description='No Desc'
+            description="No Desc",
         )
 
-        self.assertEqual(c.default_structure.smiles,
+        self.assertEqual(
-                         'C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F')
+            c.default_structure.smiles,
+            "C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
+        )
 
     def test_name_and_description_optional(self):
         c = Compound.create(
             self.package,
-            smiles='C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F',
+            smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
         )
 
-        self.assertEqual(c.name, 'Compound 1')
+        self.assertEqual(c.name, "Compound 1")
-        self.assertEqual(c.description, 'no description')
+        self.assertEqual(c.description, "no description")
 
     def test_empty_name_and_description_are_ignored(self):
         c = Compound.create(
             self.package,
-            smiles='C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F',
+            smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
-            name='',
+            name="",
-            description='',
+            description="",
         )
 
-        self.assertEqual(c.name, 'Compound 1')
+        self.assertEqual(c.name, "Compound 1")
-        self.assertEqual(c.description, 'no description')
+        self.assertEqual(c.description, "no description")
 
     def test_deduplication(self):
         c1 = Compound.create(
             self.package,
-            smiles='C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F',
+            smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
-            name='Afoxolaner',
+            name="Afoxolaner",
-            description='No Desc'
+            description="No Desc",
         )
 
         c2 = Compound.create(
             self.package,
-            smiles='C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F',
+            smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
-            name='Afoxolaner',
+            name="Afoxolaner",
-            description='No Desc'
+            description="No Desc",
         )
 
         # Check if create detects that this Compound already exist
@@ -109,36 +98,36 @@ class CompoundTest(TestCase):
         with self.assertRaises(ValueError):
             _ = Compound.create(
                 self.package,
-                smiles='C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F',
+                smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
-                name='Afoxolaner',
+                name="Afoxolaner",
-                description='No Desc'
+                description="No Desc",
             )
 
     def test_create_with_standardized_smiles(self):
         c = Compound.create(
             self.package,
-            smiles='O=C(O)C1=CC=C([N+](=O)[O-])C=C1',
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
-            name='Standardized SMILES',
+            name="Standardized SMILES",
-            description='No Desc'
+            description="No Desc",
         )
         self.assertEqual(len(c.structures.all()), 1)
 
         cs = c.structures.all()[0]
         self.assertEqual(cs.normalized_structure, True)
-        self.assertEqual(cs.smiles, 'O=C(O)C1=CC=C([N+](=O)[O-])C=C1')
+        self.assertEqual(cs.smiles, "O=C(O)C1=CC=C([N+](=O)[O-])C=C1")
 
     def test_create_with_non_standardized_smiles(self):
         c = Compound.create(
             self.package,
-            smiles='[O-][N+](=O)c1ccc(C(=O)[O-])cc1',
+            smiles="[O-][N+](=O)c1ccc(C(=O)[O-])cc1",
-            name='Non Standardized SMILES',
+            name="Non Standardized SMILES",
-            description='No Desc'
+            description="No Desc",
         )
 
         self.assertEqual(len(c.structures.all()), 2)
         for cs in c.structures.all():
             if cs.normalized_structure:
-                self.assertEqual(cs.smiles, 'O=C(O)C1=CC=C([N+](=O)[O-])C=C1')
+                self.assertEqual(cs.smiles, "O=C(O)C1=CC=C([N+](=O)[O-])C=C1")
                 break
         else:
             # Loop finished without break, lets fail...
@@ -147,51 +136,54 @@ class CompoundTest(TestCase):
     def test_add_structure_smoke(self):
         c = Compound.create(
             self.package,
-            smiles='O=C(O)C1=CC=C([N+](=O)[O-])C=C1',
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
-            name='Standardized SMILES',
+            name="Standardized SMILES",
-            description='No Desc'
+            description="No Desc",
         )
 
-        c.add_structure('[O-][N+](=O)c1ccc(C(=O)[O-])cc1', 'Non Standardized SMILES')
+        c.add_structure("[O-][N+](=O)c1ccc(C(=O)[O-])cc1", "Non Standardized SMILES")
 
         self.assertEqual(len(c.structures.all()), 2)
 
     def test_add_structure_with_different_normalized_smiles(self):
         c = Compound.create(
             self.package,
-            smiles='O=C(O)C1=CC=C([N+](=O)[O-])C=C1',
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
-            name='Standardized SMILES',
+            name="Standardized SMILES",
-            description='No Desc'
+            description="No Desc",
         )
 
         with self.assertRaises(ValueError):
             c.add_structure(
-                'C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F',
+                "C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
-                'Different Standardized SMILES')
+                "Different Standardized SMILES",
+            )
 
     def test_delete(self):
         c = Compound.create(
             self.package,
-            smiles='O=C(O)C1=CC=C([N+](=O)[O-])C=C1',
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
-            name='Standardization Test',
+            name="Standardization Test",
-            description='No Desc'
+            description="No Desc",
         )
 
         c.delete()
 
         self.assertEqual(Compound.objects.filter(package=self.package).count(), 0)
-        self.assertEqual(CompoundStructure.objects.filter(compound__package=self.package).count(), 0)
+        self.assertEqual(
+            CompoundStructure.objects.filter(compound__package=self.package).count(), 0
+        )
 
     def test_set_as_default_structure(self):
         c1 = Compound.create(
             self.package,
-            smiles='O=C(O)C1=CC=C([N+](=O)[O-])C=C1',
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
-            name='Standardized SMILES',
+            name="Standardized SMILES",
-            description='No Desc'
+            description="No Desc",
         )
         default_structure = c1.default_structure
 
-        c2 = c1.add_structure('[O-][N+](=O)c1ccc(C(=O)[O-])cc1', 'Non Standardized SMILES')
+        c2 = c1.add_structure("[O-][N+](=O)c1ccc(C(=O)[O-])cc1", "Non Standardized SMILES")
 
         c1.set_default_structure(c2)
         self.assertNotEqual(default_structure, c2)

tests/test_copy_objects.py

@@ -1,6 +1,5 @@
 from django.test import TestCase
 
-from django.test import TestCase
 
 from epdb.logic import PackageManager
 from epdb.models import Compound, User, Reaction
@@ -12,50 +11,47 @@ class CopyTest(TestCase):
     @classmethod
     def setUpClass(cls):
         super(CopyTest, cls).setUpClass()
-        cls.user = User.objects.get(username='anonymous')
+        cls.user = User.objects.get(username="anonymous")
-        cls.package = PackageManager.create_package(cls.user, 'Source Package', 'No Desc')
+        cls.package = PackageManager.create_package(cls.user, "Source Package", "No Desc")
         cls.AFOXOLANER = Compound.create(
             cls.package,
-            smiles='C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F',
+            smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
-            name='Afoxolaner',
+            name="Afoxolaner",
-            description='Test compound for copying'
+            description="Test compound for copying",
         )
 
         cls.FOUR_NITROBENZOIC_ACID = Compound.create(
             cls.package,
-            smiles='[O-][N+](=O)c1ccc(C(=O)[O-])cc1',  # Normalized: O=C(O)C1=CC=C([N+](=O)[O-])C=C1',
+            smiles="[O-][N+](=O)c1ccc(C(=O)[O-])cc1",  # Normalized: O=C(O)C1=CC=C([N+](=O)[O-])C=C1',
-            name='Test Compound',
+            name="Test Compound",
-            description='Compound with multiple structures'
+            description="Compound with multiple structures",
         )
 
         cls.ETHANOL = Compound.create(
-            cls.package,
+            cls.package, smiles="CCO", name="Ethanol", description="Simple alcohol"
-            smiles='CCO',
-            name='Ethanol',
-            description='Simple alcohol'
         )
-        cls.target_package = PackageManager.create_package(cls.user, 'Target Package', 'No Desc')
+        cls.target_package = PackageManager.create_package(cls.user, "Target Package", "No Desc")
 
         cls.reaction_educt = Compound.create(
             cls.package,
-            smiles='C(CCl)Cl',
+            smiles="C(CCl)Cl",
-            name='1,2-Dichloroethane',
+            name="1,2-Dichloroethane",
-            description='Eawag BBD compound c0001'
+            description="Eawag BBD compound c0001",
         ).default_structure
 
         cls.reaction_product = Compound.create(
             cls.package,
-            smiles='C(CO)Cl',
+            smiles="C(CO)Cl",
-            name='2-Chloroethanol',
+            name="2-Chloroethanol",
-            description='Eawag BBD compound c0005'
+            description="Eawag BBD compound c0005",
         ).default_structure
 
         cls.REACTION = Reaction.create(
             package=cls.package,
-            name='Eawag BBD reaction r0001',
+            name="Eawag BBD reaction r0001",
             educts=[cls.reaction_educt],
             products=[cls.reaction_product],
-            multi_step=False
+            multi_step=False,
         )
 
     def test_compound_copy_basic(self):
@@ -68,7 +64,9 @@ class CopyTest(TestCase):
         self.assertEqual(self.AFOXOLANER.description, copied_compound.description)
         self.assertEqual(copied_compound.package, self.target_package)
         self.assertEqual(self.AFOXOLANER.package, self.package)
-        self.assertEqual(self.AFOXOLANER.default_structure.smiles, copied_compound.default_structure.smiles)
+        self.assertEqual(
+            self.AFOXOLANER.default_structure.smiles, copied_compound.default_structure.smiles
+        )
 
     def test_compound_copy_with_multiple_structures(self):
         """Test copying a compound with multiple structures"""
@@ -86,7 +84,7 @@ class CopyTest(TestCase):
         self.assertIsNotNone(copied_compound.default_structure)
         self.assertEqual(
             copied_compound.default_structure.smiles,
-            self.FOUR_NITROBENZOIC_ACID.default_structure.smiles
+            self.FOUR_NITROBENZOIC_ACID.default_structure.smiles,
         )
 
     def test_compound_copy_preserves_aliases(self):
@@ -95,15 +93,15 @@ class CopyTest(TestCase):
         original_compound = self.ETHANOL
 
         # Add aliases if the method exists
-        if hasattr(original_compound, 'add_alias'):
+        if hasattr(original_compound, "add_alias"):
-            original_compound.add_alias('Ethyl alcohol')
+            original_compound.add_alias("Ethyl alcohol")
-            original_compound.add_alias('Grain alcohol')
+            original_compound.add_alias("Grain alcohol")
 
         mapping = dict()
         copied_compound = original_compound.copy(self.target_package, mapping)
 
         # Verify aliases were copied if they exist
-        if hasattr(original_compound, 'aliases') and hasattr(copied_compound, 'aliases'):
+        if hasattr(original_compound, "aliases") and hasattr(copied_compound, "aliases"):
             original_aliases = original_compound.aliases
             copied_aliases = copied_compound.aliases
             self.assertEqual(original_aliases, copied_aliases)
@@ -113,10 +111,10 @@ class CopyTest(TestCase):
         original_compound = self.ETHANOL
 
         # Add external identifiers if the methods exist
-        if hasattr(original_compound, 'add_cas_number'):
+        if hasattr(original_compound, "add_cas_number"):
-            original_compound.add_cas_number('64-17-5')
+            original_compound.add_cas_number("64-17-5")
-        if hasattr(original_compound, 'add_pubchem_compound_id'):
+        if hasattr(original_compound, "add_pubchem_compound_id"):
-            original_compound.add_pubchem_compound_id('702')
+            original_compound.add_pubchem_compound_id("702")
 
         mapping = dict()
         copied_compound = original_compound.copy(self.target_package, mapping)
@@ -146,7 +144,9 @@ class CopyTest(TestCase):
         self.assertEqual(original_structure.smiles, copied_structure.smiles)
         self.assertEqual(original_structure.canonical_smiles, copied_structure.canonical_smiles)
         self.assertEqual(original_structure.inchikey, copied_structure.inchikey)
-        self.assertEqual(original_structure.normalized_structure, copied_structure.normalized_structure)
+        self.assertEqual(
+            original_structure.normalized_structure, copied_structure.normalized_structure
+        )
 
         # Verify they are different objects
         self.assertNotEqual(original_structure.uuid, copied_structure.uuid)
@@ -177,7 +177,9 @@ class CopyTest(TestCase):
             self.assertEqual(orig_educt.compound.package, self.package)
             self.assertEqual(orig_educt.smiles, copy_educt.smiles)
 
-        for orig_product, copy_product in zip(self.REACTION.products.all(), copied_reaction.products.all()):
+        for orig_product, copy_product in zip(
+            self.REACTION.products.all(), copied_reaction.products.all()
+        ):
             self.assertNotEqual(orig_product.uuid, copy_product.uuid)
             self.assertEqual(orig_product.name, copy_product.name)
             self.assertEqual(orig_product.description, copy_product.description)

tests/test_dataset.py

@@ -11,21 +11,21 @@ class DatasetTest(TestCase):
     def setUp(self):
         self.cs1 = Compound.create(
             self.package,
-            name='2,6-Dibromohydroquinone',
+            name="2,6-Dibromohydroquinone",
-            description='http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/d6435251-1a54-4327-b4b1-fd6e9a8f4dc9/structure/d8a0225c-dbb5-4e6c-a642-730081c09c5b',
+            description="http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/d6435251-1a54-4327-b4b1-fd6e9a8f4dc9/structure/d8a0225c-dbb5-4e6c-a642-730081c09c5b",
-            smiles='C1=C(C(=C(C=C1O)Br)O)Br',
+            smiles="C1=C(C(=C(C=C1O)Br)O)Br",
         ).default_structure
 
         self.cs2 = Compound.create(
             self.package,
-            smiles='O=C(O)CC(=O)/C=C(/Br)C(=O)O',
+            smiles="O=C(O)CC(=O)/C=C(/Br)C(=O)O",
         ).default_structure
 
         self.rule1 = Rule.create(
-            rule_type='SimpleAmbitRule',
+            rule_type="SimpleAmbitRule",
             package=self.package,
-            smirks='[#8:8]([H])-[c:4]1[c:3]([H])[c:2](-[#1,#17,#35:9])[c:1](-[#8:7]([H]))[c:6](-[#1,#17,#35])[c:5]([H])1>>[#8-]-[#6:6](=O)-[#6:5]-[#6:4](=[O:8])\[#6:3]=[#6:2](\[#1,#17,#35:9])-[#6:1](-[#8-])=[O:7]',
+            smirks="[#8:8]([H])-[c:4]1[c:3]([H])[c:2](-[#1,#17,#35:9])[c:1](-[#8:7]([H]))[c:6](-[#1,#17,#35])[c:5]([H])1>>[#8-]-[#6:6](=O)-[#6:5]-[#6:4](=[O:8])\\[#6:3]=[#6:2](\\[#1,#17,#35:9])-[#6:1](-[#8-])=[O:7]",
-            description='http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/f6a56c0f-a4a0-4ee3-b006-d765b4767cf6'
+            description="http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/f6a56c0f-a4a0-4ee3-b006-d765b4767cf6",
         )
 
         self.reaction1 = Reaction.create(
@@ -33,14 +33,14 @@ class DatasetTest(TestCase):
             educts=[self.cs1],
             products=[self.cs2],
             rules=[self.rule1],
-            multi_step=False
+            multi_step=False,
         )
 
     @classmethod
     def setUpClass(cls):
         super(DatasetTest, cls).setUpClass()
-        cls.user = User.objects.get(username='anonymous')
+        cls.user = User.objects.get(username="anonymous")
-        cls.package = PackageManager.create_package(cls.user, 'Anon Test Package', 'No Desc')
+        cls.package = PackageManager.create_package(cls.user, "Anon Test Package", "No Desc")
 
     def test_smoke(self):
         reactions = [r for r in Reaction.objects.filter(package=self.package)]

tests/test_enviformer.py

@@ -0,0 +1,35 @@
+from tempfile import TemporaryDirectory
+from django.test import TestCase, tag
+from epdb.logic import PackageManager
+from epdb.models import User, EnviFormer, Package
+
+
+@tag("slow")
+class EnviFormerTest(TestCase):
+    fixtures = ["test_fixtures.jsonl.gz"]
+
+    @classmethod
+    def setUpClass(cls):
+        super(EnviFormerTest, cls).setUpClass()
+        cls.user = User.objects.get(username="anonymous")
+        cls.package = PackageManager.create_package(cls.user, "Anon Test Package", "No Desc")
+        cls.BBD_SUBSET = Package.objects.get(name="Fixtures")
+
+    def test_model_flow(self):
+        """Test the full flow of EnviFormer, dataset build -> model finetune -> model evaluate -> model inference"""
+        with TemporaryDirectory() as tmpdir:
+            with self.settings(MODEL_DIR=tmpdir):
+                threshold = float(0.5)
+                data_package_objs = [self.BBD_SUBSET]
+                eval_packages_objs = [self.BBD_SUBSET]
+                mod = EnviFormer.create(
+                    self.package, data_package_objs, eval_packages_objs, threshold=threshold
+                )
+
+                mod.build_dataset()
+                mod.build_model()
+                mod.multigen_eval = True
+                mod.save()
+                mod.evaluate_model()
+
+                mod.predict("CCN(CC)C(=O)C1=CC(=CC=C1)C")

tests/test_formatconverter.py

@@ -4,8 +4,7 @@ from utilities.chem import FormatConverter
 
 
 class FormatConverterTestCase(TestCase):
-
     def test_standardization(self):
-        smiles = 'C[n+]1c([N-](C))cccc1'
+        smiles = "C[n+]1c([N-](C))cccc1"
         standardized_smiles = FormatConverter.standardize(smiles)
-        self.assertEqual(standardized_smiles, 'CN=C1C=CC=CN1C')
+        self.assertEqual(standardized_smiles, "CN=C1C=CC=CN1C")

tests/test_model.py

@@ -4,7 +4,7 @@ import numpy as np
 from django.test import TestCase
 
 from epdb.logic import PackageManager
-from epdb.models import User, MLRelativeReasoning, RuleBasedRelativeReasoning, Package
+from epdb.models import User, MLRelativeReasoning, Package
 
 
 class ModelTest(TestCase):
@@ -13,9 +13,9 @@ class ModelTest(TestCase):
     @classmethod
     def setUpClass(cls):
         super(ModelTest, cls).setUpClass()
-        cls.user = User.objects.get(username='anonymous')
+        cls.user = User.objects.get(username="anonymous")
-        cls.package = PackageManager.create_package(cls.user, 'Anon Test Package', 'No Desc')
+        cls.package = PackageManager.create_package(cls.user, "Anon Test Package", "No Desc")
-        cls.BBD_SUBSET = Package.objects.get(name='Fixtures')
+        cls.BBD_SUBSET = Package.objects.get(name="Fixtures")
 
     def test_smoke(self):
         with TemporaryDirectory() as tmpdir:
@@ -24,7 +24,7 @@ class ModelTest(TestCase):
 
                 rule_package_objs = [self.BBD_SUBSET]
                 data_package_objs = [self.BBD_SUBSET]
-                eval_packages_objs = []
+                eval_packages_objs = [self.BBD_SUBSET]
 
                 mod = MLRelativeReasoning.create(
                     self.package,
@@ -32,8 +32,8 @@ class ModelTest(TestCase):
                     data_package_objs,
                     eval_packages_objs,
                     threshold=threshold,
-                    name='ECC - BBD - 0.5',
+                    name="ECC - BBD - 0.5",
-                    description='Created MLRelativeReasoning in Testcase',
+                    description="Created MLRelativeReasoning in Testcase",
                 )
 
                 # mod = RuleBasedRelativeReasoning.create(
@@ -52,9 +52,9 @@ class ModelTest(TestCase):
                 mod.build_model()
                 mod.multigen_eval = True
                 mod.save()
-                # mod.evaluate_model()
+                mod.evaluate_model()
 
-                results = mod.predict('CCN(CC)C(=O)C1=CC(=CC=C1)C')
+                results = mod.predict("CCN(CC)C(=O)C1=CC(=CC=C1)C")
 
                 products = dict()
                 for r in results:
@@ -62,8 +62,11 @@ class ModelTest(TestCase):
                         products[tuple(sorted(ps.product_set))] = (r.rule.name, r.probability)
 
                 expected = {
-                    ('CC=O', 'CCNC(=O)C1=CC(C)=CC=C1'): ('bt0243-4301', np.float64(0.33333333333333337)),
+                    ("CC=O", "CCNC(=O)C1=CC(C)=CC=C1"): (
-                    ('CC1=CC=CC(C(=O)O)=C1', 'CCNCC'): ('bt0430-4011', np.float64(0.25)),
+                        "bt0243-4301",
+                        np.float64(0.33333333333333337),
+                    ),
+                    ("CC1=CC=CC(C(=O)O)=C1", "CCNCC"): ("bt0430-4011", np.float64(0.25)),
                 }
 
                 self.assertEqual(products, expected)

tests/test_multigen_eval.py

@@ -1,4 +1,3 @@
-import json
 from django.test import TestCase
 from networkx.utils.misc import graphs_equal
 from epdb.logic import PackageManager, SPathway
@@ -12,9 +11,11 @@ class MultiGenTest(TestCase):
     @classmethod
     def setUpClass(cls):
         super(MultiGenTest, cls).setUpClass()
-        cls.user: 'User' = User.objects.get(username='anonymous')
+        cls.user: "User" = User.objects.get(username="anonymous")
-        cls.package: 'Package' = PackageManager.create_package(cls.user, 'Anon Test Package', 'No Desc')
+        cls.package: "Package" = PackageManager.create_package(
-        cls.BBD_SUBSET: 'Package' = Package.objects.get(name='Fixtures')
+            cls.user, "Anon Test Package", "No Desc"
+        )
+        cls.BBD_SUBSET: "Package" = Package.objects.get(name="Fixtures")
 
     def test_equal_pathways(self):
         """Test that two identical pathways return a precision and recall of 1.0"""
@@ -23,14 +24,23 @@ class MultiGenTest(TestCase):
             if len(pathway.edge_set.all()) == 0:  # Do not test pathways with no edges
                 continue
             score, precision, recall = multigen_eval(pathway, pathway)
-            self.assertEqual(precision, 1.0, f"Precision should be one for identical pathways. "
+            self.assertEqual(
-                                             f"Failed on pathway: {pathway.name}")
+                precision,
-            self.assertEqual(recall, 1.0, f"Recall should be one for identical pathways. "
+                1.0,
-                                          f"Failed on pathway: {pathway.name}")
+                f"Precision should be one for identical pathways. "
+                f"Failed on pathway: {pathway.name}",
+            )
+            self.assertEqual(
+                recall,
+                1.0,
+                f"Recall should be one for identical pathways. Failed on pathway: {pathway.name}",
+            )
 
     def test_intermediates(self):
         """Test that an intermediate can be correctly identified and the metrics are correctly adjusted"""
-        score, precision, recall, intermediates = multigen_eval(*self.intermediate_case(), return_intermediates=True)
+        score, precision, recall, intermediates = multigen_eval(
+            *self.intermediate_case(), return_intermediates=True
+        )
         self.assertEqual(len(intermediates), 1, "There should be 1 found intermediate")
         self.assertEqual(precision, 1, "Precision should be 1")
         self.assertEqual(recall, 1, "Recall should be 1")
@@ -49,7 +59,9 @@ class MultiGenTest(TestCase):
 
     def test_all(self):
         """Test an intermediate, false-positive and false-negative together"""
-        score, precision, recall, intermediates = multigen_eval(*self.all_case(), return_intermediates=True)
+        score, precision, recall, intermediates = multigen_eval(
+            *self.all_case(), return_intermediates=True
+        )
         self.assertEqual(len(intermediates), 1, "There should be 1 found intermediate")
         self.assertAlmostEqual(precision, 0.6, 3, "Precision should be 0.6")
         self.assertAlmostEqual(recall, 0.75, 3, "Recall should be 0.75")
@@ -57,19 +69,23 @@ class MultiGenTest(TestCase):
     def test_shallow_pathway(self):
         pathways = self.BBD_SUBSET.pathways.all()
         for pathway in pathways:
-            pathway_name = pathway.name
             if len(pathway.edge_set.all()) == 0:  # Do not test pathways with no edges
                 continue
+
             shallow_pathway = graph_from_pathway(SPathway.from_pathway(pathway))
             pathway = graph_from_pathway(pathway)
+
             if not graphs_equal(shallow_pathway, pathway):
-                print('\n\nS', shallow_pathway.adj)
+                print("\n\nS", shallow_pathway.adj)
-                print('\n\nPW', pathway.adj)
+                print("\n\nPW", pathway.adj)
                 # print(shallow_pathway.nodes, pathway.nodes)
                 # print(shallow_pathway.graph, pathway.graph)
 
-            self.assertTrue(graphs_equal(shallow_pathway, pathway), f"Networkx graph from shallow pathway not "
+            self.assertTrue(
-                                                                    f"equal to pathway for pathway {pathway.name}")
+                graphs_equal(shallow_pathway, pathway),
+                f"Networkx graph from shallow pathway not "
+                f"equal to pathway for pathway {pathway.name}",
+            )
 
     def test_graph_edit_eval(self):
         """Performs all the previous tests but with graph_edit_eval
@@ -79,10 +95,16 @@ class MultiGenTest(TestCase):
             if len(pathway.edge_set.all()) == 0:  # Do not test pathways with no edges
                 continue
             score = pathway_edit_eval(pathway, pathway)
-            self.assertEqual(score, 0.0, "Pathway edit distance should be zero for identical pathways. "
+            self.assertEqual(
-                                         f"Failed on pathway: {pathway.name}")
+                score,
+                0.0,
+                "Pathway edit distance should be zero for identical pathways. "
+                f"Failed on pathway: {pathway.name}",
+            )
         inter_score = pathway_edit_eval(*self.intermediate_case())
-        self.assertAlmostEqual(inter_score, 1.75, 3, "Pathway edit distance failed on intermediate case")
+        self.assertAlmostEqual(
+            inter_score, 1.75, 3, "Pathway edit distance failed on intermediate case"
+        )
         fp_score = pathway_edit_eval(*self.fp_case())
         self.assertAlmostEqual(fp_score, 1.25, 3, "Pathway edit distance failed on fp case")
         fn_score = pathway_edit_eval(*self.fn_case())
@@ -93,22 +115,30 @@ class MultiGenTest(TestCase):
     def intermediate_case(self):
         """Create an example with an intermediate in the predicted pathway"""
         true_pathway = Pathway.create(self.package, "CCO")
-        true_pathway.add_edge([true_pathway.root_nodes.all()[0]], [true_pathway.add_node("CC(=O)O", depth=1)])
+        true_pathway.add_edge(
+            [true_pathway.root_nodes.all()[0]], [true_pathway.add_node("CC(=O)O", depth=1)]
+        )
         pred_pathway = Pathway.create(self.package, "CCO")
-        pred_pathway.add_edge([pred_pathway.root_nodes.all()[0]],
+        pred_pathway.add_edge(
-                              [acetaldehyde := pred_pathway.add_node("CC=O", depth=1)])
+            [pred_pathway.root_nodes.all()[0]],
+            [acetaldehyde := pred_pathway.add_node("CC=O", depth=1)],
+        )
         pred_pathway.add_edge([acetaldehyde], [pred_pathway.add_node("CC(=O)O", depth=2)])
         return true_pathway, pred_pathway
 
     def fp_case(self):
         """Create an example with an extra compound in the predicted pathway"""
         true_pathway = Pathway.create(self.package, "CCO")
-        true_pathway.add_edge([true_pathway.root_nodes.all()[0]],
+        true_pathway.add_edge(
-                              [acetaldehyde := true_pathway.add_node("CC=O", depth=1)])
+            [true_pathway.root_nodes.all()[0]],
+            [acetaldehyde := true_pathway.add_node("CC=O", depth=1)],
+        )
         true_pathway.add_edge([acetaldehyde], [true_pathway.add_node("CC(=O)O", depth=2)])
         pred_pathway = Pathway.create(self.package, "CCO")
-        pred_pathway.add_edge([pred_pathway.root_nodes.all()[0]],
+        pred_pathway.add_edge(
-                              [acetaldehyde := pred_pathway.add_node("CC=O", depth=1)])
+            [pred_pathway.root_nodes.all()[0]],
+            [acetaldehyde := pred_pathway.add_node("CC=O", depth=1)],
+        )
         pred_pathway.add_edge([acetaldehyde], [pred_pathway.add_node("CC(=O)O", depth=2)])
         pred_pathway.add_edge([acetaldehyde], [pred_pathway.add_node("C", depth=2)])
         return true_pathway, pred_pathway
@@ -116,22 +146,30 @@ class MultiGenTest(TestCase):
     def fn_case(self):
         """Create an example with a missing compound in the predicted pathway"""
         true_pathway = Pathway.create(self.package, "CCO")
-        true_pathway.add_edge([true_pathway.root_nodes.all()[0]],
+        true_pathway.add_edge(
-                              [acetaldehyde := true_pathway.add_node("CC=O", depth=1)])
+            [true_pathway.root_nodes.all()[0]],
+            [acetaldehyde := true_pathway.add_node("CC=O", depth=1)],
+        )
         true_pathway.add_edge([acetaldehyde], [true_pathway.add_node("CC(=O)O", depth=2)])
         pred_pathway = Pathway.create(self.package, "CCO")
-        pred_pathway.add_edge([pred_pathway.root_nodes.all()[0]], [pred_pathway.add_node("CC=O", depth=1)])
+        pred_pathway.add_edge(
+            [pred_pathway.root_nodes.all()[0]], [pred_pathway.add_node("CC=O", depth=1)]
+        )
         return true_pathway, pred_pathway
 
     def all_case(self):
         """Create an example with an intermediate, extra compound and missing compound"""
         true_pathway = Pathway.create(self.package, "CCO")
-        true_pathway.add_edge([true_pathway.root_nodes.all()[0]],
+        true_pathway.add_edge(
-                              [acetaldehyde := true_pathway.add_node("CC=O", depth=1)])
+            [true_pathway.root_nodes.all()[0]],
+            [acetaldehyde := true_pathway.add_node("CC=O", depth=1)],
+        )
         true_pathway.add_edge([acetaldehyde], [true_pathway.add_node("C", depth=2)])
         true_pathway.add_edge([acetaldehyde], [true_pathway.add_node("CC(=O)O", depth=2)])
         pred_pathway = Pathway.create(self.package, "CCO")
-        pred_pathway.add_edge([pred_pathway.root_nodes.all()[0]], [methane := pred_pathway.add_node("C", depth=1)])
+        pred_pathway.add_edge(
+            [pred_pathway.root_nodes.all()[0]], [methane := pred_pathway.add_node("C", depth=1)]
+        )
         pred_pathway.add_edge([methane], [true_pathway.add_node("CC=O", depth=2)])
         pred_pathway.add_edge([methane], [true_pathway.add_node("c1ccccc1", depth=2)])
         return true_pathway, pred_pathway

tests/test_reaction_model.py

@@ -10,127 +10,127 @@ class ReactionTest(TestCase):
     @classmethod
     def setUpClass(cls):
         super(ReactionTest, cls).setUpClass()
-        cls.user = User.objects.get(username='anonymous')
+        cls.user = User.objects.get(username="anonymous")
-        cls.package = PackageManager.create_package(cls.user, 'Anon Test Package', 'No Desc')
+        cls.package = PackageManager.create_package(cls.user, "Anon Test Package", "No Desc")
 
     def test_smoke(self):
         educt = Compound.create(
             self.package,
-            smiles='C(CCl)Cl',
+            smiles="C(CCl)Cl",
-            name='1,2-Dichloroethane',
+            name="1,2-Dichloroethane",
-            description='Eawag BBD compound c0001'
+            description="Eawag BBD compound c0001",
         ).default_structure
 
         product = Compound.create(
             self.package,
-            smiles='C(CO)Cl',
+            smiles="C(CO)Cl",
-            name='2-Chloroethanol',
+            name="2-Chloroethanol",
-            description='Eawag BBD compound c0005'
+            description="Eawag BBD compound c0005",
         ).default_structure
 
         r = Reaction.create(
             package=self.package,
-            name='Eawag BBD reaction r0001',
+            name="Eawag BBD reaction r0001",
             educts=[educt],
             products=[product],
-            multi_step=False
+            multi_step=False,
         )
 
-        self.assertEqual(r.smirks(), 'C(CCl)Cl>>C(CO)Cl')
+        self.assertEqual(r.smirks(), "C(CCl)Cl>>C(CO)Cl")
-        self.assertEqual(r.name, 'Eawag BBD reaction r0001')
+        self.assertEqual(r.name, "Eawag BBD reaction r0001")
-        self.assertEqual(r.description, 'no description')
+        self.assertEqual(r.description, "no description")
 
     def test_string_educts_and_products(self):
         r = Reaction.create(
             package=self.package,
-            name='Eawag BBD reaction r0001',
+            name="Eawag BBD reaction r0001",
-            educts=['C(CCl)Cl'],
+            educts=["C(CCl)Cl"],
-            products=['C(CO)Cl'],
+            products=["C(CO)Cl"],
-            multi_step=False
+            multi_step=False,
         )
 
-        self.assertEqual(r.smirks(), 'C(CCl)Cl>>C(CO)Cl')
+        self.assertEqual(r.smirks(), "C(CCl)Cl>>C(CO)Cl")
 
     def test_missing_smiles(self):
         educt = Compound.create(
             self.package,
-            smiles='C(CCl)Cl',
+            smiles="C(CCl)Cl",
-            name='1,2-Dichloroethane',
+            name="1,2-Dichloroethane",
-            description='Eawag BBD compound c0001'
+            description="Eawag BBD compound c0001",
         ).default_structure
 
         product = Compound.create(
             self.package,
-            smiles='C(CO)Cl',
+            smiles="C(CO)Cl",
-            name='2-Chloroethanol',
+            name="2-Chloroethanol",
-            description='Eawag BBD compound c0005'
+            description="Eawag BBD compound c0005",
         ).default_structure
 
         with self.assertRaises(ValueError):
             _ = Reaction.create(
                 package=self.package,
-                name='Eawag BBD reaction r0001',
+                name="Eawag BBD reaction r0001",
                 educts=[educt],
                 products=[],
-                multi_step=False
+                multi_step=False,
             )
 
         with self.assertRaises(ValueError):
             _ = Reaction.create(
                 package=self.package,
-                name='Eawag BBD reaction r0001',
+                name="Eawag BBD reaction r0001",
                 educts=[],
                 products=[product],
-                multi_step=False
+                multi_step=False,
             )
 
         with self.assertRaises(ValueError):
             _ = Reaction.create(
                 package=self.package,
-                name='Eawag BBD reaction r0001',
+                name="Eawag BBD reaction r0001",
                 educts=[],
                 products=[],
-                multi_step=False
+                multi_step=False,
             )
 
     def test_empty_name_and_description_are_ignored(self):
         r = Reaction.create(
             package=self.package,
-            name='',
+            name="",
-            description='',
+            description="",
-            educts=['C(CCl)Cl'],
+            educts=["C(CCl)Cl"],
-            products=['C(CO)Cl'],
+            products=["C(CO)Cl"],
             multi_step=False,
         )
 
-        self.assertEqual(r.name, 'no name')
+        self.assertEqual(r.name, "no name")
-        self.assertEqual(r.description, 'no description')
+        self.assertEqual(r.description, "no description")
 
     def test_deduplication(self):
         rule = Rule.create(
             package=self.package,
-            rule_type='SimpleAmbitRule',
+            rule_type="SimpleAmbitRule",
-            name='bt0022-2833',
+            name="bt0022-2833",
-            description='Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative',
+            description="Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative",
-            smirks='[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]',
+            smirks="[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
         )
 
         r1 = Reaction.create(
             package=self.package,
-            name='Eawag BBD reaction r0001',
+            name="Eawag BBD reaction r0001",
-            educts=['C(CCl)Cl'],
+            educts=["C(CCl)Cl"],
-            products=['C(CO)Cl'],
+            products=["C(CO)Cl"],
             rules=[rule],
-            multi_step=False
+            multi_step=False,
         )
 
         r2 = Reaction.create(
             package=self.package,
-            name='Eawag BBD reaction r0001',
+            name="Eawag BBD reaction r0001",
-            educts=['C(CCl)Cl'],
+            educts=["C(CCl)Cl"],
-            products=['C(CO)Cl'],
+            products=["C(CO)Cl"],
             rules=[rule],
-            multi_step=False
+            multi_step=False,
         )
 
         # Check if create detects that this Compound already exist
@@ -141,18 +141,18 @@ class ReactionTest(TestCase):
     def test_deduplication_without_rules(self):
         r1 = Reaction.create(
             package=self.package,
-            name='Eawag BBD reaction r0001',
+            name="Eawag BBD reaction r0001",
-            educts=['C(CCl)Cl'],
+            educts=["C(CCl)Cl"],
-            products=['C(CO)Cl'],
+            products=["C(CO)Cl"],
-            multi_step=False
+            multi_step=False,
         )
 
         r2 = Reaction.create(
             package=self.package,
-            name='Eawag BBD reaction r0001',
+            name="Eawag BBD reaction r0001",
-            educts=['C(CCl)Cl'],
+            educts=["C(CCl)Cl"],
-            products=['C(CO)Cl'],
+            products=["C(CO)Cl"],
-            multi_step=False
+            multi_step=False,
         )
 
         # Check if create detects that this Compound already exist
@@ -164,19 +164,19 @@ class ReactionTest(TestCase):
         with self.assertRaises(ValueError):
             _ = Reaction.create(
                 package=self.package,
-                name='Eawag BBD reaction r0001',
+                name="Eawag BBD reaction r0001",
-                educts=['ASDF'],
+                educts=["ASDF"],
-                products=['C(CO)Cl'],
+                products=["C(CO)Cl"],
-                multi_step=False
+                multi_step=False,
             )
 
     def test_delete(self):
         r = Reaction.create(
             package=self.package,
-            name='Eawag BBD reaction r0001',
+            name="Eawag BBD reaction r0001",
-            educts=['C(CCl)Cl'],
+            educts=["C(CCl)Cl"],
-            products=['C(CO)Cl'],
+            products=["C(CO)Cl"],
-            multi_step=False
+            multi_step=False,
         )
 
         r.delete()

tests/test_rule_model.py

@@ -10,73 +10,79 @@ class RuleTest(TestCase):
     @classmethod
     def setUpClass(cls):
         super(RuleTest, cls).setUpClass()
-        cls.user = User.objects.get(username='anonymous')
+        cls.user = User.objects.get(username="anonymous")
-        cls.package = PackageManager.create_package(cls.user, 'Anon Test Package', 'No Desc')
+        cls.package = PackageManager.create_package(cls.user, "Anon Test Package", "No Desc")
 
     def test_smoke(self):
         r = Rule.create(
-            rule_type='SimpleAmbitRule',
+            rule_type="SimpleAmbitRule",
             package=self.package,
-            name='bt0022-2833',
+            name="bt0022-2833",
-            description='Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative',
+            description="Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative",
-            smirks='[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]',
+            smirks="[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
         )
 
-        self.assertEqual(r.smirks,
+        self.assertEqual(
-                         '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]')
+            r.smirks,
-        self.assertEqual(r.name, 'bt0022-2833')
+            "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
-        self.assertEqual(r.description,
+        )
-                         'Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative')
+        self.assertEqual(r.name, "bt0022-2833")
+        self.assertEqual(
+            r.description,
+            "Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative",
+        )
 
     def test_smirks_are_trimmed(self):
         r = Rule.create(
-            rule_type='SimpleAmbitRule',
+            rule_type="SimpleAmbitRule",
             package=self.package,
-            name='bt0022-2833',
+            name="bt0022-2833",
-            description='Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative',
+            description="Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative",
-            smirks='   [H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]   ',
+            smirks="   [H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]   ",
         )
 
-        self.assertEqual(r.smirks,
+        self.assertEqual(
-                         '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]')
+            r.smirks,
+            "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+        )
 
     def test_name_and_description_optional(self):
         r = Rule.create(
-            rule_type='SimpleAmbitRule',
+            rule_type="SimpleAmbitRule",
             package=self.package,
-            smirks='[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]',
+            smirks="[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
         )
 
-        self.assertRegex(r.name, 'Rule \\d+')
+        self.assertRegex(r.name, "Rule \\d+")
-        self.assertEqual(r.description, 'no description')
+        self.assertEqual(r.description, "no description")
 
     def test_empty_name_and_description_are_ignored(self):
         r = Rule.create(
-            rule_type='SimpleAmbitRule',
+            rule_type="SimpleAmbitRule",
             package=self.package,
-            smirks='[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]',
+            smirks="[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
-            name='',
+            name="",
-            description='',
+            description="",
         )
 
-        self.assertRegex(r.name, 'Rule \\d+')
+        self.assertRegex(r.name, "Rule \\d+")
-        self.assertEqual(r.description, 'no description')
+        self.assertEqual(r.description, "no description")
 
     def test_deduplication(self):
         r1 = Rule.create(
-            rule_type='SimpleAmbitRule',
+            rule_type="SimpleAmbitRule",
             package=self.package,
-            smirks='[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]',
+            smirks="[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
-            name='',
+            name="",
-            description='',
+            description="",
         )
 
         r2 = Rule.create(
-            rule_type='SimpleAmbitRule',
+            rule_type="SimpleAmbitRule",
             package=self.package,
-            smirks='[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]',
+            smirks="[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
-            name='',
+            name="",
-            description='',
+            description="",
         )
 
         self.assertEqual(r1.pk, r2.pk)
@@ -84,21 +90,21 @@ class RuleTest(TestCase):
 
     def test_valid_smirks(self):
         with self.assertRaises(ValueError):
-            r = Rule.create(
+            Rule.create(
-                rule_type='SimpleAmbitRule',
+                rule_type="SimpleAmbitRule",
                 package=self.package,
-                smirks='This is not a valid SMIRKS',
+                smirks="This is not a valid SMIRKS",
-                name='',
+                name="",
-                description='',
+                description="",
             )
 
     def test_delete(self):
         r = Rule.create(
-            rule_type='SimpleAmbitRule',
+            rule_type="SimpleAmbitRule",
             package=self.package,
-            smirks='[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]',
+            smirks="[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
-            name='',
+            name="",
-            description='',
+            description="",
         )
 
         r.delete()

tests/test_simpleambitrule.py

@@ -12,34 +12,32 @@ class SimpleAmbitRuleTest(TestCase):
     @classmethod
     def setUpClass(cls):
         super(SimpleAmbitRuleTest, cls).setUpClass()
-        cls.user = User.objects.get(username='anonymous')
+        cls.user = User.objects.get(username="anonymous")
-        cls.package = PackageManager.create_package(cls.user, 'Simple Ambit Rule Test Package',
+        cls.package = PackageManager.create_package(
-                                                    'Test Package for SimpleAmbitRule')
+            cls.user, "Simple Ambit Rule Test Package", "Test Package for SimpleAmbitRule"
+        )
 
     def test_create_basic_rule(self):
         """Test creating a basic SimpleAmbitRule with minimal parameters."""
-        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'
+        smirks = "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]"
 
-        rule = SimpleAmbitRule.create(
+        rule = SimpleAmbitRule.create(package=self.package, smirks=smirks)
-            package=self.package,
-            smirks=smirks
-        )
 
         self.assertIsInstance(rule, SimpleAmbitRule)
         self.assertEqual(rule.smirks, smirks)
         self.assertEqual(rule.package, self.package)
-        self.assertRegex(rule.name, r'Rule \d+')
+        self.assertRegex(rule.name, r"Rule \d+")
-        self.assertEqual(rule.description, 'no description')
+        self.assertEqual(rule.description, "no description")
         self.assertIsNone(rule.reactant_filter_smarts)
         self.assertIsNone(rule.product_filter_smarts)
 
     def test_create_with_all_parameters(self):
         """Test creating SimpleAmbitRule with all parameters."""
-        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'
+        smirks = "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]"
-        name = 'Test Rule'
+        name = "Test Rule"
-        description = 'A test biotransformation rule'
+        description = "A test biotransformation rule"
-        reactant_filter = '[CH2X4]'
+        reactant_filter = "[CH2X4]"
-        product_filter = '[OH]'
+        product_filter = "[OH]"
 
         rule = SimpleAmbitRule.create(
             package=self.package,
@@ -47,7 +45,7 @@ class SimpleAmbitRuleTest(TestCase):
             description=description,
             smirks=smirks,
             reactant_filter_smarts=reactant_filter,
-            product_filter_smarts=product_filter
+            product_filter_smarts=product_filter,
         )
 
         self.assertEqual(rule.name, name)
@@ -60,127 +58,114 @@ class SimpleAmbitRuleTest(TestCase):
         """Test that SMIRKS is required for rule creation."""
         with self.assertRaises(ValueError) as cm:
             SimpleAmbitRule.create(package=self.package, smirks=None)
-        self.assertIn('SMIRKS is required', str(cm.exception))
+        self.assertIn("SMIRKS is required", str(cm.exception))
 
         with self.assertRaises(ValueError) as cm:
-            SimpleAmbitRule.create(package=self.package, smirks='')
+            SimpleAmbitRule.create(package=self.package, smirks="")
-        self.assertIn('SMIRKS is required', str(cm.exception))
+        self.assertIn("SMIRKS is required", str(cm.exception))
 
         with self.assertRaises(ValueError) as cm:
-            SimpleAmbitRule.create(package=self.package, smirks='   ')
+            SimpleAmbitRule.create(package=self.package, smirks="   ")
-        self.assertIn('SMIRKS is required', str(cm.exception))
+        self.assertIn("SMIRKS is required", str(cm.exception))
 
-    @patch('epdb.models.FormatConverter.is_valid_smirks')
+    @patch("epdb.models.FormatConverter.is_valid_smirks")
     def test_invalid_smirks_validation(self, mock_is_valid):
         """Test validation of SMIRKS format."""
         mock_is_valid.return_value = False
 
-        invalid_smirks = 'invalid_smirks_string'
+        invalid_smirks = "invalid_smirks_string"
         with self.assertRaises(ValueError) as cm:
-            SimpleAmbitRule.create(
+            SimpleAmbitRule.create(package=self.package, smirks=invalid_smirks)
-                package=self.package,
-                smirks=invalid_smirks
-            )
 
         self.assertIn(f'SMIRKS "{invalid_smirks}" is invalid', str(cm.exception))
         mock_is_valid.assert_called_once_with(invalid_smirks)
 
     def test_smirks_trimming(self):
         """Test that SMIRKS strings are trimmed during creation."""
-        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'
+        smirks = "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]"
-        smirks_with_whitespace = f'   {smirks}   '
+        smirks_with_whitespace = f"   {smirks}   "
 
-        rule = SimpleAmbitRule.create(
+        rule = SimpleAmbitRule.create(package=self.package, smirks=smirks_with_whitespace)
-            package=self.package,
-            smirks=smirks_with_whitespace
-        )
 
         self.assertEqual(rule.smirks, smirks)
 
     def test_empty_name_and_description_handling(self):
         """Test that empty name and description are handled appropriately."""
-        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'
+        smirks = "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]"
 
         rule = SimpleAmbitRule.create(
-            package=self.package,
+            package=self.package, smirks=smirks, name="", description="   "
-            smirks=smirks,
-            name='',
-            description='   '
         )
 
-        self.assertRegex(rule.name, r'Rule \d+')
+        self.assertRegex(rule.name, r"Rule \d+")
-        self.assertEqual(rule.description, 'no description')
+        self.assertEqual(rule.description, "no description")
 
     def test_deduplication_basic(self):
         """Test that identical rules are deduplicated."""
-        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'
+        smirks = "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]"
 
-        rule1 = SimpleAmbitRule.create(
+        rule1 = SimpleAmbitRule.create(package=self.package, smirks=smirks, name="Rule 1")
-            package=self.package,
-            smirks=smirks,
-            name='Rule 1'
-        )
 
         rule2 = SimpleAmbitRule.create(
             package=self.package,
             smirks=smirks,
-            name='Rule 2'  # Different name, but same SMIRKS
+            name="Rule 2",  # Different name, but same SMIRKS
         )
 
         self.assertEqual(rule1.pk, rule2.pk)
-        self.assertEqual(SimpleAmbitRule.objects.filter(package=self.package, smirks=smirks).count(), 1)
+        self.assertEqual(
+            SimpleAmbitRule.objects.filter(package=self.package, smirks=smirks).count(), 1
+        )
 
     def test_deduplication_with_filters(self):
         """Test deduplication with filter SMARTS."""
-        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'
+        smirks = "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]"
-        reactant_filter = '[CH2X4]'
+        reactant_filter = "[CH2X4]"
-        product_filter = '[OH]'
+        product_filter = "[OH]"
 
         rule1 = SimpleAmbitRule.create(
             package=self.package,
             smirks=smirks,
             reactant_filter_smarts=reactant_filter,
-            product_filter_smarts=product_filter
+            product_filter_smarts=product_filter,
         )
 
         rule2 = SimpleAmbitRule.create(
             package=self.package,
             smirks=smirks,
             reactant_filter_smarts=reactant_filter,
-            product_filter_smarts=product_filter
+            product_filter_smarts=product_filter,
         )
 
         self.assertEqual(rule1.pk, rule2.pk)
 
     def test_no_deduplication_different_filters(self):
         """Test that rules with different filters are not deduplicated."""
-        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'
+        smirks = "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]"
 
         rule1 = SimpleAmbitRule.create(
-            package=self.package,
+            package=self.package, smirks=smirks, reactant_filter_smarts="[CH2X4]"
-            smirks=smirks,
-            reactant_filter_smarts='[CH2X4]'
         )
 
         rule2 = SimpleAmbitRule.create(
-            package=self.package,
+            package=self.package, smirks=smirks, reactant_filter_smarts="[CH3X4]"
-            smirks=smirks,
-            reactant_filter_smarts='[CH3X4]'
         )
 
         self.assertNotEqual(rule1.pk, rule2.pk)
-        self.assertEqual(SimpleAmbitRule.objects.filter(package=self.package, smirks=smirks).count(), 2)
+        self.assertEqual(
+            SimpleAmbitRule.objects.filter(package=self.package, smirks=smirks).count(), 2
+        )
 
     def test_filter_smarts_trimming(self):
         """Test that filter SMARTS are trimmed and handled correctly."""
-        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'
+        smirks = "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]"
 
         # Test with whitespace-only filters (should be treated as None)
         rule = SimpleAmbitRule.create(
             package=self.package,
             smirks=smirks,
-            reactant_filter_smarts='   ',
+            reactant_filter_smarts="   ",
-            product_filter_smarts='   '
+            product_filter_smarts="   ",
         )
 
         self.assertIsNone(rule.reactant_filter_smarts)
@@ -188,94 +173,85 @@ class SimpleAmbitRuleTest(TestCase):
 
     def test_url_property(self):
         """Test the URL property generation."""
-        rule = SimpleAmbitRule.create(
+        rule = SimpleAmbitRule.create(package=self.package, smirks="[H:1][C:2]>>[H:1][O:2]")
-            package=self.package,
-            smirks='[H:1][C:2]>>[H:1][O:2]'
-        )
 
-        expected_url = f'{self.package.url}/simple-ambit-rule/{rule.uuid}'
+        expected_url = f"{self.package.url}/simple-ambit-rule/{rule.uuid}"
         self.assertEqual(rule.url, expected_url)
 
-    @patch('epdb.models.FormatConverter.apply')
+    @patch("epdb.models.FormatConverter.apply")
     def test_apply_method(self, mock_apply):
         """Test the apply method delegates to FormatConverter."""
-        mock_apply.return_value = ['product1', 'product2']
+        mock_apply.return_value = ["product1", "product2"]
 
-        rule = SimpleAmbitRule.create(
+        rule = SimpleAmbitRule.create(package=self.package, smirks="[H:1][C:2]>>[H:1][O:2]")
-            package=self.package,
-            smirks='[H:1][C:2]>>[H:1][O:2]'
-        )
 
-        test_smiles = 'CCO'
+        test_smiles = "CCO"
         result = rule.apply(test_smiles)
 
         mock_apply.assert_called_once_with(test_smiles, rule.smirks)
-        self.assertEqual(result, ['product1', 'product2'])
+        self.assertEqual(result, ["product1", "product2"])
 
     def test_reactants_smarts_property(self):
         """Test reactants_smarts property extracts correct part of SMIRKS."""
-        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'
+        smirks = "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]"
-        expected_reactants = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]'
+        expected_reactants = "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]"
 
-        rule = SimpleAmbitRule.create(
+        rule = SimpleAmbitRule.create(package=self.package, smirks=smirks)
-            package=self.package,
-            smirks=smirks
-        )
 
         self.assertEqual(rule.reactants_smarts, expected_reactants)
 
     def test_products_smarts_property(self):
         """Test products_smarts property extracts correct part of SMIRKS."""
-        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'
+        smirks = "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]"
-        expected_products = '[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'
+        expected_products = "[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]"
 
-        rule = SimpleAmbitRule.create(
+        rule = SimpleAmbitRule.create(package=self.package, smirks=smirks)
-            package=self.package,
-            smirks=smirks
-        )
 
         self.assertEqual(rule.products_smarts, expected_products)
 
-    @patch('epdb.models.Package.objects')
+    @patch("epdb.models.Package.objects")
     def test_related_reactions_property(self, mock_package_objects):
         """Test related_reactions property returns correct queryset."""
         mock_qs = MagicMock()
         mock_package_objects.filter.return_value = mock_qs
 
-        rule = SimpleAmbitRule.create(
+        rule = SimpleAmbitRule.create(package=self.package, smirks="[H:1][C:2]>>[H:1][O:2]")
-            package=self.package,
-            smirks='[H:1][C:2]>>[H:1][O:2]'
-        )
 
         # Instead of directly assigning, patch the property or use with patch.object
-        with patch.object(type(rule), 'reaction_rule', new_callable=PropertyMock) as mock_reaction_rule:
+        with patch.object(
-            mock_reaction_rule.return_value.filter.return_value.order_by.return_value = ['reaction1', 'reaction2']
+            type(rule), "reaction_rule", new_callable=PropertyMock
+        ) as mock_reaction_rule:
+            mock_reaction_rule.return_value.filter.return_value.order_by.return_value = [
+                "reaction1",
+                "reaction2",
+            ]
 
             result = rule.related_reactions
 
             mock_package_objects.filter.assert_called_once_with(reviewed=True)
             mock_reaction_rule.return_value.filter.assert_called_once_with(package__in=mock_qs)
-            mock_reaction_rule.return_value.filter.return_value.order_by.assert_called_once_with('name')
+            mock_reaction_rule.return_value.filter.return_value.order_by.assert_called_once_with(
-            self.assertEqual(result, ['reaction1', 'reaction2'])
+                "name"
+            )
+            self.assertEqual(result, ["reaction1", "reaction2"])
 
-    @patch('epdb.models.Pathway.objects')
+    @patch("epdb.models.Pathway.objects")
-    @patch('epdb.models.Edge.objects')
+    @patch("epdb.models.Edge.objects")
     def test_related_pathways_property(self, mock_edge_objects, mock_pathway_objects):
         """Test related_pathways property returns correct queryset."""
 
-        mock_related_reactions = ['reaction1', 'reaction2']
+        mock_related_reactions = ["reaction1", "reaction2"]
 
-        with patch.object(SimpleAmbitRule, "related_reactions", new_callable=PropertyMock) as mock_prop:
+        with patch.object(
+            SimpleAmbitRule, "related_reactions", new_callable=PropertyMock
+        ) as mock_prop:
             mock_prop.return_value = mock_related_reactions
 
-            rule = SimpleAmbitRule.create(
+            rule = SimpleAmbitRule.create(package=self.package, smirks="[H:1][C:2]>>[H:1][O:2]")
-                package=self.package,
-                smirks='[H:1][C:2]>>[H:1][O:2]'
-            )
 
             # Mock Edge objects query
             mock_edge_values = MagicMock()
-            mock_edge_values.values.return_value = ['pathway_id1', 'pathway_id2']
+            mock_edge_values.values.return_value = ["pathway_id1", "pathway_id2"]
             mock_edge_objects.filter.return_value = mock_edge_values
 
             # Mock Pathway objects query
@@ -285,52 +261,49 @@ class SimpleAmbitRuleTest(TestCase):
             result = rule.related_pathways
 
             mock_edge_objects.filter.assert_called_once_with(edge_label__in=mock_related_reactions)
-            mock_edge_values.values.assert_called_once_with('pathway_id')
+            mock_edge_values.values.assert_called_once_with("pathway_id")
             mock_pathway_objects.filter.assert_called_once()
             self.assertEqual(result, mock_pathway_qs)
 
-    @patch('epdb.models.IndigoUtils.smirks_to_svg')
+    @patch("epdb.models.IndigoUtils.smirks_to_svg")
     def test_as_svg_property(self, mock_smirks_to_svg):
         """Test as_svg property calls IndigoUtils correctly."""
-        mock_smirks_to_svg.return_value = '<svg>test_svg</svg>'
+        mock_smirks_to_svg.return_value = "<svg>test_svg</svg>"
 
-        rule = SimpleAmbitRule.create(
+        rule = SimpleAmbitRule.create(package=self.package, smirks="[H:1][C:2]>>[H:1][O:2]")
-            package=self.package,
-            smirks='[H:1][C:2]>>[H:1][O:2]'
-        )
 
         result = rule.as_svg
         mock_smirks_to_svg.assert_called_once_with(rule.smirks, True, width=800, height=400)
-        self.assertEqual(result, '<svg>test_svg</svg>')
+        self.assertEqual(result, "<svg>test_svg</svg>")
 
     def test_atomic_transaction(self):
         """Test that rule creation is atomic."""
-        smirks = '[H:1][C:2]>>[H:1][O:2]'
+        smirks = "[H:1][C:2]>>[H:1][O:2]"
 
         # This should work normally
         rule = SimpleAmbitRule.create(package=self.package, smirks=smirks)
         self.assertIsInstance(rule, SimpleAmbitRule)
 
         # Test transaction rollback on error
-        with patch('epdb.models.SimpleAmbitRule.save', side_effect=Exception('Database error')):
+        with patch("epdb.models.SimpleAmbitRule.save", side_effect=Exception("Database error")):
             with self.assertRaises(Exception):
-                SimpleAmbitRule.create(package=self.package, smirks='[H:3][C:4]>>[H:3][O:4]')
+                SimpleAmbitRule.create(package=self.package, smirks="[H:3][C:4]>>[H:3][O:4]")
 
         # Verify no partial data was saved
         self.assertEqual(SimpleAmbitRule.objects.filter(package=self.package).count(), 1)
 
     def test_multiple_duplicate_warning(self):
         """Test logging when multiple duplicates are found."""
-        smirks = '[H:1][C:2]>>[H:1][O:2]'
+        smirks = "[H:1][C:2]>>[H:1][O:2]"
 
         # Create first rule
         rule1 = SimpleAmbitRule.create(package=self.package, smirks=smirks)
 
         # Manually create a duplicate to simulate the error condition
-        rule2 = SimpleAmbitRule(package=self.package, smirks=smirks, name='Manual Rule')
+        rule2 = SimpleAmbitRule(package=self.package, smirks=smirks, name="Manual Rule")
         rule2.save()
 
-        with patch('epdb.models.logger') as mock_logger:
+        with patch("epdb.models.logger") as mock_logger:
             # This should find the existing rule and log an error about multiple matches
             result = SimpleAmbitRule.create(package=self.package, smirks=smirks)
 
@@ -339,24 +312,28 @@ class SimpleAmbitRuleTest(TestCase):
 
             # Should log an error about multiple matches
             mock_logger.error.assert_called()
-            self.assertIn('More than one rule matched', mock_logger.error.call_args[0][0])
+            self.assertIn("More than one rule matched", mock_logger.error.call_args[0][0])
 
     def test_model_fields(self):
         """Test model field properties."""
         rule = SimpleAmbitRule.create(
             package=self.package,
-            smirks='[H:1][C:2]>>[H:1][O:2]',
+            smirks="[H:1][C:2]>>[H:1][O:2]",
-            reactant_filter_smarts='[CH3]',
+            reactant_filter_smarts="[CH3]",
-            product_filter_smarts='[OH]'
+            product_filter_smarts="[OH]",
         )
 
         # Test field properties
-        self.assertFalse(rule._meta.get_field('smirks').blank)
+        self.assertFalse(rule._meta.get_field("smirks").blank)
-        self.assertFalse(rule._meta.get_field('smirks').null)
+        self.assertFalse(rule._meta.get_field("smirks").null)
-        self.assertTrue(rule._meta.get_field('reactant_filter_smarts').null)
+        self.assertTrue(rule._meta.get_field("reactant_filter_smarts").null)
-        self.assertTrue(rule._meta.get_field('product_filter_smarts').null)
+        self.assertTrue(rule._meta.get_field("product_filter_smarts").null)
 
         # Test verbose names
-        self.assertEqual(rule._meta.get_field('smirks').verbose_name, 'SMIRKS')
+        self.assertEqual(rule._meta.get_field("smirks").verbose_name, "SMIRKS")
-        self.assertEqual(rule._meta.get_field('reactant_filter_smarts').verbose_name, 'Reactant Filter SMARTS')
+        self.assertEqual(
-        self.assertEqual(rule._meta.get_field('product_filter_smarts').verbose_name, 'Product Filter SMARTS')
+            rule._meta.get_field("reactant_filter_smarts").verbose_name, "Reactant Filter SMARTS"
+        )
+        self.assertEqual(
+            rule._meta.get_field("product_filter_smarts").verbose_name, "Product Filter SMARTS"
+        )

tests/test_sobjects.py

@@ -1,32 +1,29 @@
 from django.test import TestCase
 
-from epdb.logic import SNode, SEdge, SPathway
+from epdb.logic import SNode, SEdge
 
 
 class SObjectTest(TestCase):
-
     def setUp(self):
         pass
 
     def test_snode_eq(self):
-        snode1 = SNode('CN1C2C(N(C(N(C)C=2N=C1)=O)C)=O', 0)
+        snode1 = SNode("CN1C2C(N(C(N(C)C=2N=C1)=O)C)=O", 0)
-        snode2 = SNode('CN1C2C(N(C(N(C)C=2N=C1)=O)C)=O', 0)
+        snode2 = SNode("CN1C2C(N(C(N(C)C=2N=C1)=O)C)=O", 0)
         assert snode1 == snode2
 
     def test_snode_hash(self):
         pass
 
     def test_sedge_eq(self):
-        sedge1 = SEdge([SNode('CN1C2C(N(C(N(C)C=2N=C1)=O)C)=O', 0)],
+        sedge1 = SEdge(
-                       [SNode('CN1C(=O)NC2=C(C1=O)N(C)C=N2', 1), SNode('C=O', 1)],
+            [SNode("CN1C2C(N(C(N(C)C=2N=C1)=O)C)=O", 0)],
-                       rule=None)
+            [SNode("CN1C(=O)NC2=C(C1=O)N(C)C=N2", 1), SNode("C=O", 1)],
-        sedge2 = SEdge([SNode('CN1C2C(N(C(N(C)C=2N=C1)=O)C)=O', 0)],
+            rule=None,
-                       [SNode('CN1C(=O)NC2=C(C1=O)N(C)C=N2', 1), SNode('C=O', 1)],
+        )
-                       rule=None)
+        sedge2 = SEdge(
+            [SNode("CN1C2C(N(C(N(C)C=2N=C1)=O)C)=O", 0)],
+            [SNode("CN1C(=O)NC2=C(C1=O)N(C)C=N2", 1), SNode("C=O", 1)],
+            rule=None,
+        )
         assert sedge1 == sedge2
-
-    def test_sedge_hash(self):
-        pass
-
-    def test_spathway(self):
-        pw = SPathway()

tests/views/test_compound_views.py

@@ -0,0 +1,396 @@
+from django.test import TestCase
+from django.urls import reverse
+from envipy_additional_information import Temperature, Interval
+
+from epdb.logic import UserManager, PackageManager
+from epdb.models import Compound, Scenario, ExternalDatabase
+
+
+class CompoundViewTest(TestCase):
+    fixtures = ["test_fixtures.jsonl.gz"]
+
+    @classmethod
+    def setUpClass(cls):
+        super(CompoundViewTest, cls).setUpClass()
+        cls.user1 = UserManager.create_user(
+            "user1",
+            "user1@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=True,
+            is_active=True,
+        )
+        cls.user1_default_package = cls.user1.default_package
+        cls.package = PackageManager.create_package(cls.user1, "Test", "Test Pack")
+
+    def setUp(self):
+        self.client.force_login(self.user1)
+
+    def test_create_compound(self):
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "1,2-Dichloroethane",
+                "compound-description": "Eawag BBD compound c0001",
+                "compound-smiles": "C(CCl)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        compound_url = response.url
+
+        c = Compound.objects.get(url=compound_url)
+
+        self.assertEqual(c.package, self.user1_default_package)
+        self.assertEqual(c.name, "1,2-Dichloroethane")
+        self.assertEqual(c.description, "Eawag BBD compound c0001")
+        self.assertEqual(c.default_structure.smiles, "C(CCl)Cl")
+        self.assertEqual(c.default_structure.canonical_smiles, "ClCCCl")
+        self.assertEqual(c.structures.all().count(), 2)
+        self.assertEqual(self.user1_default_package.compounds.count(), 1)
+
+        # Adding the same rule again should return the existing one, hence not increasing the number of rules
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "1,2-Dichloroethane",
+                "compound-description": "Eawag BBD compound c0001",
+                "compound-smiles": "C(CCl)Cl",
+            },
+        )
+
+        self.assertEqual(response.url, compound_url)
+        self.assertEqual(response.status_code, 302)
+        self.assertEqual(self.user1_default_package.compounds.count(), 1)
+
+        # Adding the same rule in a different package should create a new rule
+        response = self.client.post(
+            reverse("package compound list", kwargs={"package_uuid": self.package.uuid}),
+            {
+                "compound-name": "1,2-Dichloroethane",
+                "compound-description": "Eawag BBD compound c0001",
+                "compound-smiles": "C(CCl)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        self.assertNotEqual(compound_url, response.url)
+
+        # adding another reaction should increase count
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "2-Chloroethanol",
+                "compound-description": "Eawag BBD compound c0005",
+                "compound-smiles": "C(CO)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        self.assertEqual(self.user1_default_package.compounds.count(), 2)
+
+    # Edit
+    def test_edit_rule(self):
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "1,2-Dichloroethane",
+                "compound-description": "Eawag BBD compound c0001",
+                "compound-smiles": "C(CCl)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        compound_url = response.url
+
+        c = Compound.objects.get(url=compound_url)
+
+        response = self.client.post(
+            reverse(
+                "package compound detail",
+                kwargs={
+                    "package_uuid": str(self.user1_default_package.uuid),
+                    "compound_uuid": str(c.uuid),
+                },
+            ),
+            {
+                "compound-name": "Test Compound Adjusted",
+                "compound-description": "New Description",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        c = Compound.objects.get(url=compound_url)
+        self.assertEqual(c.name, "Test Compound Adjusted")
+        self.assertEqual(c.description, "New Description")
+
+        # Rest stays untouched
+        self.assertEqual(c.default_structure.smiles, "C(CCl)Cl")
+        self.assertEqual(self.user1_default_package.compounds.count(), 1)
+
+    # Scenario
+    def test_set_scenario(self):
+        s1 = Scenario.create(
+            self.user1_default_package,
+            "Test Scen",
+            "Test Desc",
+            "2025-10",
+            "soil",
+            [Temperature(interval=Interval(start=20, end=30))],
+        )
+
+        s2 = Scenario.create(
+            self.user1_default_package,
+            "Test Scen2",
+            "Test Desc2",
+            "2025-10",
+            "soil",
+            [Temperature(interval=Interval(start=10, end=20))],
+        )
+
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "1,2-Dichloroethane",
+                "compound-description": "Eawag BBD compound c0001",
+                "compound-smiles": "C(CCl)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        compound_url = response.url
+
+        c = Compound.objects.get(url=compound_url)
+
+        response = self.client.post(
+            reverse(
+                "package compound detail",
+                kwargs={"package_uuid": str(c.package.uuid), "compound_uuid": str(c.uuid)},
+            ),
+            {"selected-scenarios": [s1.url, s2.url]},
+        )
+
+        self.assertEqual(len(c.scenarios.all()), 2)
+
+        response = self.client.post(
+            reverse(
+                "package compound detail",
+                kwargs={"package_uuid": str(c.package.uuid), "compound_uuid": str(c.uuid)},
+            ),
+            {"selected-scenarios": [s1.url]},
+        )
+
+        self.assertEqual(len(c.scenarios.all()), 1)
+        self.assertEqual(c.scenarios.first().url, s1.url)
+
+        response = self.client.post(
+            reverse(
+                "package compound detail",
+                kwargs={"package_uuid": str(c.package.uuid), "compound_uuid": str(c.uuid)},
+            ),
+            {
+                # We have to set an empty string to avoid that the parameter is removed
+                "selected-scenarios": ""
+            },
+        )
+
+        self.assertEqual(len(c.scenarios.all()), 0)
+
+    #
+    def test_copy(self):
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "1,2-Dichloroethane",
+                "compound-description": "Eawag BBD compound c0001",
+                "compound-smiles": "C(CCl)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        compound_url = response.url
+        c = Compound.objects.get(url=compound_url)
+
+        response = self.client.post(
+            reverse(
+                "package detail",
+                kwargs={
+                    "package_uuid": str(self.package.uuid),
+                },
+            ),
+            {"hidden": "copy", "object_to_copy": c.url},
+        )
+
+        self.assertEqual(response.status_code, 200)
+
+        copied_object_url = response.json()["success"]
+        copied_compound = Compound.objects.get(url=copied_object_url)
+
+        self.assertEqual(copied_compound.name, c.name)
+        self.assertEqual(copied_compound.description, c.description)
+        self.assertEqual(copied_compound.default_structure.smiles, c.default_structure.smiles)
+
+        # Copy to the same package should fail
+        response = self.client.post(
+            reverse(
+                "package detail",
+                kwargs={
+                    "package_uuid": str(c.package.uuid),
+                },
+            ),
+            {"hidden": "copy", "object_to_copy": c.url},
+        )
+
+        self.assertEqual(response.status_code, 400)
+        self.assertEqual(
+            response.json()["error"], f"Can't copy object {compound_url} to the same package!"
+        )
+
+    def test_references(self):
+        ext_db, _ = ExternalDatabase.objects.get_or_create(
+            name="PubChem Compound",
+            defaults={
+                "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}",
+            },
+        )
+
+        ext_db2, _ = ExternalDatabase.objects.get_or_create(
+            name="PubChem Substance",
+            defaults={
+                "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}",
+            },
+        )
+
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "1,2-Dichloroethane",
+                "compound-description": "Eawag BBD compound c0001",
+                "compound-smiles": "C(CCl)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        compound_url = response.url
+        c = Compound.objects.get(url=compound_url)
+
+        response = self.client.post(
+            reverse(
+                "package compound detail",
+                kwargs={
+                    "package_uuid": str(c.package.uuid),
+                    "compound_uuid": str(c.uuid),
+                },
+            ),
+            {"selected-database": ext_db.pk, "identifier": "25154249"},
+        )
+
+        self.assertEqual(c.external_identifiers.count(), 1)
+        self.assertEqual(c.external_identifiers.first().database, ext_db)
+        self.assertEqual(c.external_identifiers.first().identifier_value, "25154249")
+        self.assertEqual(
+            c.external_identifiers.first().url, "https://pubchem.ncbi.nlm.nih.gov/compound/25154249"
+        )
+
+        response = self.client.post(
+            reverse(
+                "package compound detail",
+                kwargs={
+                    "package_uuid": str(c.package.uuid),
+                    "compound_uuid": str(c.uuid),
+                },
+            ),
+            {"selected-database": ext_db2.pk, "identifier": "25154249"},
+        )
+
+        self.assertEqual(c.external_identifiers.count(), 2)
+        self.assertEqual(c.external_identifiers.last().database, ext_db2)
+        self.assertEqual(c.external_identifiers.last().identifier_value, "25154249")
+        self.assertEqual(
+            c.external_identifiers.last().url, "https://pubchem.ncbi.nlm.nih.gov/substance/25154249"
+        )
+
+    def test_delete(self):
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "1,2-Dichloroethane",
+                "compound-description": "Eawag BBD compound c0001",
+                "compound-smiles": "C(CCl)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        compound_url = response.url
+
+        c = Compound.objects.get(url=compound_url)
+
+        response = self.client.post(
+            reverse(
+                "package compound detail",
+                kwargs={"package_uuid": str(c.package.uuid), "compound_uuid": str(c.uuid)},
+            ),
+            {"hidden": "delete"},
+        )
+
+        self.assertEqual(self.user1_default_package.compounds.count(), 0)
+
+    def test_set_aliases(self):
+        alias_1 = "Alias 1"
+        alias_2 = "Alias 2"
+
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "1,2-Dichloroethane",
+                "compound-description": "Eawag BBD compound c0001",
+                "compound-smiles": "C(CCl)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        compound_url = response.url
+
+        c = Compound.objects.get(url=compound_url)
+
+        response = self.client.post(
+            reverse(
+                "package compound detail",
+                kwargs={"package_uuid": str(c.package.uuid), "compound_uuid": str(c.uuid)},
+            ),
+            {"aliases": [alias_1, alias_2]},
+        )
+
+        c = Compound.objects.get(url=compound_url)
+        self.assertEqual(len(c.aliases), 2)
+
+        response = self.client.post(
+            reverse(
+                "package compound detail",
+                kwargs={"package_uuid": str(c.package.uuid), "compound_uuid": str(c.uuid)},
+            ),
+            {"aliases": [alias_1]},
+        )
+
+        c = Compound.objects.get(url=compound_url)
+        self.assertEqual(len(c.aliases), 1)
+
+        response = self.client.post(
+            reverse(
+                "package compound detail",
+                kwargs={"package_uuid": str(c.package.uuid), "compound_uuid": str(c.uuid)},
+            ),
+            {
+                # We have to set an empty string to avoid that the parameter is removed
+                "aliases": ""
+            },
+        )
+
+        c = Compound.objects.get(url=compound_url)
+        self.assertEqual(len(c.aliases), 0)

tests/views/test_model_views.py

@@ -0,0 +1,125 @@
+from django.test import TestCase, override_settings
+from django.urls import reverse
+from django.conf import settings as s
+
+from epdb.logic import UserManager
+from epdb.models import Package, User
+
+
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models")
+class PathwayViewTest(TestCase):
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
+
+    @classmethod
+    def setUpClass(cls):
+        super(PathwayViewTest, cls).setUpClass()
+        cls.user1 = UserManager.create_user(
+            "user1",
+            "user1@envipath.com",
+            "SuperSafe",
+            set_setting=True,
+            add_to_group=True,
+            is_active=True,
+        )
+        cls.user1_default_package = cls.user1.default_package
+        cls.model_package = Package.objects.get(name="Fixtures")
+
+    def setUp(self):
+        self.client.force_login(self.user1)
+
+    def test_predict(self):
+        self.client.force_login(User.objects.get(username="admin"))
+        response = self.client.get(
+            reverse(
+                "package model detail",
+                kwargs={
+                    "package_uuid": str(self.model_package.uuid),
+                    "model_uuid": str(self.model_package.models.first().uuid),
+                },
+            ),
+            {
+                "classify": "ILikeCats!",
+                "smiles": "CCN(CC)C(=O)C1=CC(=CC=C1)CO",
+            },
+        )
+
+        expected = [
+            {
+                "products": [["O=C(O)C1=CC(CO)=CC=C1", "CCNCC"]],
+                "probability": 0.25,
+                "btrule": {
+                    "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/0e6e9290-b658-4450-b291-3ec19fa19206",
+                    "name": "bt0430-4011",
+                },
+            },
+            {
+                "products": [["CCNC(=O)C1=CC(CO)=CC=C1", "CC=O"]],
+                "probability": 0.0,
+                "btrule": {
+                    "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/27a3a353-0b66-4228-bd16-e407949e90df",
+                    "name": "bt0243-4301",
+                },
+            },
+            {
+                "products": [["CCN(CC)C(=O)C1=CC(C=O)=CC=C1"]],
+                "probability": 0.75,
+                "btrule": {
+                    "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/2f2e0c39-e109-4836-959f-2bda2524f022",
+                    "name": "bt0001-3568",
+                },
+            },
+        ]
+
+        actual = response.json()
+        self.assertEqual(actual, expected)
+
+        response = self.client.get(
+            reverse(
+                "package model detail",
+                kwargs={
+                    "package_uuid": str(self.model_package.uuid),
+                    "model_uuid": str(self.model_package.models.first().uuid),
+                },
+            ),
+            {
+                "classify": "ILikeCats!",
+                "smiles": "",
+            },
+        )
+
+        self.assertEqual(response.status_code, 400)
+        self.assertEqual(response.json()["error"], "Received empty SMILES")
+
+        response = self.client.get(
+            reverse(
+                "package model detail",
+                kwargs={
+                    "package_uuid": str(self.model_package.uuid),
+                    "model_uuid": str(self.model_package.models.first().uuid),
+                },
+            ),
+            {
+                "classify": "ILikeCats!",
+                "smiles": "  ",  # Input should be stripped
+            },
+        )
+
+        self.assertEqual(response.status_code, 400)
+        self.assertEqual(response.json()["error"], "Received empty SMILES")
+
+        response = self.client.get(
+            reverse(
+                "package model detail",
+                kwargs={
+                    "package_uuid": str(self.model_package.uuid),
+                    "model_uuid": str(self.model_package.models.first().uuid),
+                },
+            ),
+            {
+                "classify": "ILikeCats!",
+                "smiles": "RandomInput",
+            },
+        )
+
+        self.assertEqual(response.status_code, 400)
+        self.assertEqual(response.json()["error"], '"RandomInput" is not a valid SMILES')

tests/views/test_package_views.py

@@ -13,19 +13,34 @@ class PackageViewTest(TestCase):
     @classmethod
     def setUpClass(cls):
         super(PackageViewTest, cls).setUpClass()
-        cls.user1 = UserManager.create_user("user1", "user1@envipath.com", "SuperSafe",
+        cls.user1 = UserManager.create_user(
-                                            set_setting=False, add_to_group=True, is_active=True)
+            "user1",
-        cls.user2 = UserManager.create_user("user2", "user2@envipath.com", "SuperSafe",
+            "user1@envipath.com",
-                                            set_setting=False, add_to_group=True, is_active=True)
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=True,
+            is_active=True,
+        )
+        cls.user2 = UserManager.create_user(
+            "user2",
+            "user2@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=True,
+            is_active=True,
+        )
 
     def setUp(self):
         self.client.force_login(self.user1)
 
     def test_create_package(self):
-        response = self.client.post(reverse("packages"), {
+        response = self.client.post(
-            "package-name": "Test Package",
+            reverse("packages"),
-            "package-description": "Just a Description",
+            {
-        })
+                "package-name": "Test Package",
+                "package-description": "Just a Description",
+            },
+        )
         self.assertEqual(response.status_code, 302)
         package_url = response.url
 
@@ -41,13 +56,12 @@ class PackageViewTest(TestCase):
         file = SimpleUploadedFile(
             "Fixture_Package.json",
             open(s.FIXTURE_DIRS[0] / "Fixture_Package.json", "rb").read(),
-            content_type="application/json"
+            content_type="application/json",
         )
 
-        response = self.client.post(reverse("packages"), {
+        response = self.client.post(
-            "file": file,
+            reverse("packages"), {"file": file, "hidden": "import-package-json"}
-            "hidden": "import-package-json"
+        )
-        })
 
         self.assertEqual(response.status_code, 302)
         package_url = response.url
@@ -67,13 +81,12 @@ class PackageViewTest(TestCase):
         file = SimpleUploadedFile(
             "EAWAG-BBD.json",
             open(s.FIXTURE_DIRS[0] / "packages" / "2025-07-18" / "EAWAG-BBD.json", "rb").read(),
-            content_type="application/json"
+            content_type="application/json",
         )
 
-        response = self.client.post(reverse("packages"), {
+        response = self.client.post(
-            "file": file,
+            reverse("packages"), {"file": file, "hidden": "import-legacy-package-json"}
-            "hidden": "import-legacy-package-json"
+        )
-        })
 
         self.assertEqual(response.status_code, 302)
         package_url = response.url
@@ -90,17 +103,23 @@ class PackageViewTest(TestCase):
         self.assertEqual(upp.permission, Permission.ALL[0])
 
     def test_edit_package(self):
-        response = self.client.post(reverse("packages"), {
+        response = self.client.post(
-            "package-name": "Test Package",
+            reverse("packages"),
-            "package-description": "Just a Description",
+            {
-        })
+                "package-name": "Test Package",
+                "package-description": "Just a Description",
+            },
+        )
         self.assertEqual(response.status_code, 302)
         package_url = response.url
 
-        self.client.post(package_url, {
+        self.client.post(
-            "package-name": "New Name",
+            package_url,
-            "package-description": "New Description",
+            {
-        })
+                "package-name": "New Name",
+                "package-description": "New Description",
+            },
+        )
 
         p = Package.objects.get(url=package_url)
 
@@ -108,10 +127,13 @@ class PackageViewTest(TestCase):
         self.assertEqual(p.description, "New Description")
 
     def test_edit_package_permissions(self):
-        response = self.client.post(reverse("packages"), {
+        response = self.client.post(
-            "package-name": "Test Package",
+            reverse("packages"),
-            "package-description": "Just a Description",
+            {
-        })
+                "package-name": "Test Package",
+                "package-description": "Just a Description",
+            },
+        )
         self.assertEqual(response.status_code, 302)
         package_url = response.url
         p = Package.objects.get(url=package_url)
@@ -119,57 +141,63 @@ class PackageViewTest(TestCase):
         with self.assertRaises(UserPackagePermission.DoesNotExist):
             UserPackagePermission.objects.get(package=p, user=self.user2)
 
-        self.client.post(package_url, {
+        self.client.post(
-            "grantee": self.user2.url,
+            package_url,
-            "read": "on",
+            {
-            "write": "on",
+                "grantee": self.user2.url,
-        })
+                "read": "on",
+                "write": "on",
+            },
+        )
 
         upp = UserPackagePermission.objects.get(package=p, user=self.user2)
 
         self.assertEqual(upp.permission, Permission.WRITE[0])
 
     def test_publish_package(self):
-        response = self.client.post(reverse("packages"), {
+        response = self.client.post(
-            "package-name": "Test Package",
+            reverse("packages"),
-            "package-description": "Just a Description",
+            {
-        })
+                "package-name": "Test Package",
+                "package-description": "Just a Description",
+            },
+        )
         self.assertEqual(response.status_code, 302)
         package_url = response.url
         p = Package.objects.get(url=package_url)
 
-        self.client.post(package_url, {
+        self.client.post(package_url, {"hidden": "publish-package"})
-            "hidden": "publish-package"
-        })
 
         self.assertEqual(Group.objects.filter(public=True).count(), 1)
         g = Group.objects.get(public=True)
         gpp = GroupPackagePermission.objects.get(package=p, group=g)
         self.assertEqual(gpp.permission, Permission.READ[0])
 
-
     def test_set_package_license(self):
-        response = self.client.post(reverse("packages"), {
+        response = self.client.post(
-            "package-name": "Test Package",
+            reverse("packages"),
-            "package-description": "Just a Description",
+            {
-        })
+                "package-name": "Test Package",
+                "package-description": "Just a Description",
+            },
+        )
 
         package_url = response.url
         p = Package.objects.get(url=package_url)
 
-        self.client.post(package_url, {
+        self.client.post(package_url, {"license": "no-license"})
-            "license": "no-license"
-        })
 
         self.assertIsNone(p.license)
         # TODO test others
 
-
     def test_delete_package(self):
-        response = self.client.post(reverse("packages"), {
+        response = self.client.post(
-            "package-name": "Test Package",
+            reverse("packages"),
-            "package-description": "Just a Description",
+            {
-        })
+                "package-name": "Test Package",
+                "package-description": "Just a Description",
+            },
+        )
 
         package_url = response.url
         p = Package.objects.get(url=package_url)
@@ -178,3 +206,15 @@ class PackageViewTest(TestCase):
 
         response = self.client.get(package_url)
         self.assertEqual(response.status_code, 404)
+
+    def test_delete_default_package(self):
+        self.client.force_login(self.user1)
+        # Try to delete the default package
+        response = self.client.post(self.user1.default_package.url, {"hidden": "delete"})
+
+        self.assertEqual(response.status_code, 400)
+        self.assertTrue(
+            "You cannot delete the default package. "
+            "If you want to delete this package you have to "
+            "set another default package first" in response.content.decode()
+        )

tests/views/test_pathway_views.py

@@ -0,0 +1,168 @@
+from django.test import TestCase, override_settings
+from django.urls import reverse
+from django.conf import settings as s
+
+from epdb.logic import UserManager, PackageManager
+from epdb.models import Pathway, Edge
+
+
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models")
+class PathwayViewTest(TestCase):
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
+
+    @classmethod
+    def setUpClass(cls):
+        super(PathwayViewTest, cls).setUpClass()
+        cls.user1 = UserManager.create_user(
+            "user1",
+            "user1@envipath.com",
+            "SuperSafe",
+            set_setting=True,
+            add_to_group=True,
+            is_active=True,
+        )
+        cls.user1_default_package = cls.user1.default_package
+        cls.package = PackageManager.create_package(cls.user1, "Test", "Test Pack")
+
+    def setUp(self):
+        self.client.force_login(self.user1)
+
+    def test_predict_pathway(self):
+        response = self.client.post(
+            reverse("pathways"),
+            {
+                "name": "Test Pathway",
+                "description": "Just a Description",
+                "predict": "predict",
+                "smiles": "CCN(CC)C(=O)C1=CC(=CC=C1)CO",
+            },
+        )
+        self.assertEqual(response.status_code, 302)
+        pathway_url = response.url
+
+        pw = Pathway.objects.get(url=pathway_url)
+        self.assertEqual(self.user1_default_package, pw.package)
+
+        self.assertEqual(pw.name, "Test Pathway")
+        self.assertEqual(pw.description, "Just a Description")
+        self.assertEqual(len(pw.root_nodes), 1)
+        self.assertEqual(
+            pw.root_nodes.first().default_node_label.smiles, "CCN(CC)C(=O)C1=CC(CO)=CC=C1"
+        )
+
+        first_level_nodes = {
+            # Edge 1
+            "CCN(CC)C(=O)C1=CC(C=O)=CC=C1",
+            # Edge 2
+            "CCNC(=O)C1=CC(CO)=CC=C1",
+            "CC=O",
+            # Edge 3
+            "CCNCC",
+            "O=C(O)C1=CC(CO)=CC=C1",
+        }
+
+        predicted_nodes = set()
+        edges = Edge.objects.filter(start_nodes__in=[pw.root_nodes.first()])
+
+        for edge in edges:
+            for n in edge.end_nodes.all():
+                predicted_nodes.add(n.default_node_label.smiles)
+
+        self.assertEqual(first_level_nodes, predicted_nodes)
+
+    def test_predict_package_pathway(self):
+        response = self.client.post(
+            reverse("package pathway list", kwargs={"package_uuid": str(self.package.uuid)}),
+            {
+                "name": "Test Pathway",
+                "description": "Just a Description",
+                "predict": "predict",
+                "smiles": "CCN(CC)C(=O)C1=CC(=CC=C1)CO",
+            },
+        )
+        self.assertEqual(response.status_code, 302)
+        pathway_url = response.url
+
+        pw = Pathway.objects.get(url=pathway_url)
+        self.assertEqual(self.package, pw.package)
+
+        self.assertEqual(pw.name, "Test Pathway")
+        self.assertEqual(pw.description, "Just a Description")
+        self.assertEqual(len(pw.root_nodes), 1)
+        self.assertEqual(
+            pw.root_nodes.first().default_node_label.smiles, "CCN(CC)C(=O)C1=CC(CO)=CC=C1"
+        )
+
+        first_level_nodes = {
+            # Edge 1
+            "CCN(CC)C(=O)C1=CC(C=O)=CC=C1",
+            # Edge 2
+            "CCNC(=O)C1=CC(CO)=CC=C1",
+            "CC=O",
+            # Edge 3
+            "CCNCC",
+            "O=C(O)C1=CC(CO)=CC=C1",
+        }
+
+        predicted_nodes = set()
+        edges = Edge.objects.filter(start_nodes__in=[pw.root_nodes.first()])
+
+        for edge in edges:
+            for n in edge.end_nodes.all():
+                predicted_nodes.add(n.default_node_label.smiles)
+
+        self.assertEqual(first_level_nodes, predicted_nodes)
+
+    def test_set_aliases(self):
+        alias_1 = "Alias 1"
+        alias_2 = "Alias 2"
+
+        response = self.client.post(
+            reverse("package pathway list", kwargs={"package_uuid": str(self.package.uuid)}),
+            {
+                "name": "Test Pathway",
+                "description": "Just a Description",
+                "predict": "predict",
+                "smiles": "CCN(CC)C(=O)C1=CC(=CC=C1)CO",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        pathway_url = response.url
+        pw = Pathway.objects.get(url=pathway_url)
+
+        response = self.client.post(
+            reverse(
+                "package pathway detail",
+                kwargs={"package_uuid": str(pw.package.uuid), "pathway_uuid": str(pw.uuid)},
+            ),
+            {"aliases": [alias_1, alias_2]},
+        )
+
+        pw = Pathway.objects.get(url=pathway_url)
+        self.assertEqual(len(pw.aliases), 2)
+
+        response = self.client.post(
+            reverse(
+                "package pathway detail",
+                kwargs={"package_uuid": str(pw.package.uuid), "pathway_uuid": str(pw.uuid)},
+            ),
+            {"aliases": [alias_1]},
+        )
+
+        pw = Pathway.objects.get(url=pathway_url)
+        self.assertEqual(len(pw.aliases), 1)
+
+        response = self.client.post(
+            reverse(
+                "package pathway detail",
+                kwargs={"package_uuid": str(pw.package.uuid), "pathway_uuid": str(pw.uuid)},
+            ),
+            {
+                # We have to set an empty string to avoid that the parameter is removed
+                "aliases": ""
+            },
+        )
+
+        pw = Pathway.objects.get(url=pathway_url)
+        self.assertEqual(len(pw.aliases), 0)

tests/views/test_reaction_views.py

@@ -0,0 +1,390 @@
+from django.test import TestCase
+from django.urls import reverse
+from envipy_additional_information import Temperature, Interval
+
+from epdb.logic import UserManager, PackageManager
+from epdb.models import Reaction, Scenario, ExternalDatabase
+
+
+class ReactionViewTest(TestCase):
+    fixtures = ["test_fixtures.jsonl.gz"]
+
+    @classmethod
+    def setUpClass(cls):
+        super(ReactionViewTest, cls).setUpClass()
+        cls.user1 = UserManager.create_user(
+            "user1",
+            "user1@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=True,
+            is_active=True,
+        )
+        cls.user1_default_package = cls.user1.default_package
+        cls.package = PackageManager.create_package(cls.user1, "Test", "Test Pack")
+
+    def setUp(self):
+        self.client.force_login(self.user1)
+
+    def test_create_reaction(self):
+        response = self.client.post(
+            reverse("reactions"),
+            {
+                "reaction-name": "Eawag BBD reaction r0001",
+                "reaction-description": "Description for Eawag BBD reaction r0001",
+                "reaction-smirks": "C(CCl)Cl>>C(CO)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        reaction_url = response.url
+
+        r = Reaction.objects.get(url=reaction_url)
+
+        self.assertEqual(r.package, self.user1_default_package)
+        self.assertEqual(r.name, "Eawag BBD reaction r0001")
+        self.assertEqual(r.description, "Description for Eawag BBD reaction r0001")
+        self.assertEqual(r.smirks(), "C(CCl)Cl>>C(CO)Cl")
+        self.assertEqual(self.user1_default_package.reactions.count(), 1)
+
+        # Adding the same rule again should return the existing one, hence not increasing the number of rules
+        response = self.client.post(
+            reverse("reactions"),
+            {
+                "reaction-name": "Eawag BBD reaction r0001",
+                "reaction-description": "Description for Eawag BBD reaction r0001",
+                "reaction-smirks": "C(CCl)Cl>>C(CO)Cl",
+            },
+        )
+
+        self.assertEqual(response.url, reaction_url)
+        self.assertEqual(response.status_code, 302)
+        self.assertEqual(self.user1_default_package.reactions.count(), 1)
+
+        # Adding the same rule in a different package should create a new rule
+        response = self.client.post(
+            reverse("package reaction list", kwargs={"package_uuid": self.package.uuid}),
+            {
+                "reaction-name": "Eawag BBD reaction r0001",
+                "reaction-description": "Description for Eawag BBD reaction r0001",
+                "reaction-smirks": "C(CCl)Cl>>C(CO)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        self.assertNotEqual(reaction_url, response.url)
+
+        # adding another reaction should increase count
+        response = self.client.post(
+            reverse("reactions"),
+            {
+                "reaction-name": "Eawag BBD reaction r0002",
+                "reaction-description": "Description for Eawag BBD reaction r0002",
+                "reaction-smirks": "C(CO)Cl>>C(C=O)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        self.assertEqual(self.user1_default_package.reactions.count(), 2)
+
+    # Edit
+    def test_edit_rule(self):
+        response = self.client.post(
+            reverse("reactions"),
+            {
+                "reaction-name": "Eawag BBD reaction r0001",
+                "reaction-description": "Description for Eawag BBD reaction r0001",
+                "reaction-smirks": "C(CCl)Cl>>C(CO)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        reaction_url = response.url
+
+        r = Reaction.objects.get(url=reaction_url)
+
+        response = self.client.post(
+            reverse(
+                "package reaction detail",
+                kwargs={
+                    "package_uuid": str(self.user1_default_package.uuid),
+                    "reaction_uuid": str(r.uuid),
+                },
+            ),
+            {
+                "reaction-name": "Test Reaction Adjusted",
+                "reaction-description": "New Description",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        r = Reaction.objects.get(url=reaction_url)
+        self.assertEqual(r.name, "Test Reaction Adjusted")
+        self.assertEqual(r.description, "New Description")
+
+        # Rest stays untouched
+        self.assertEqual(r.smirks(), "C(CCl)Cl>>C(CO)Cl")
+        self.assertEqual(self.user1_default_package.reactions.count(), 1)
+
+    # Scenario
+    def test_set_scenario(self):
+        s1 = Scenario.create(
+            self.user1_default_package,
+            "Test Scen",
+            "Test Desc",
+            "2025-10",
+            "soil",
+            [Temperature(interval=Interval(start=20, end=30))],
+        )
+
+        s2 = Scenario.create(
+            self.user1_default_package,
+            "Test Scen2",
+            "Test Desc2",
+            "2025-10",
+            "soil",
+            [Temperature(interval=Interval(start=10, end=20))],
+        )
+
+        response = self.client.post(
+            reverse("reactions"),
+            {
+                "reaction-name": "Eawag BBD reaction r0001",
+                "reaction-description": "Description for Eawag BBD reaction r0001",
+                "reaction-smirks": "C(CCl)Cl>>C(CO)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        reaction_url = response.url
+        r = Reaction.objects.get(url=reaction_url)
+
+        response = self.client.post(
+            reverse(
+                "package reaction detail",
+                kwargs={"package_uuid": str(r.package.uuid), "reaction_uuid": str(r.uuid)},
+            ),
+            {"selected-scenarios": [s1.url, s2.url]},
+        )
+
+        self.assertEqual(len(r.scenarios.all()), 2)
+
+        response = self.client.post(
+            reverse(
+                "package reaction detail",
+                kwargs={"package_uuid": str(r.package.uuid), "reaction_uuid": str(r.uuid)},
+            ),
+            {"selected-scenarios": [s1.url]},
+        )
+
+        self.assertEqual(len(r.scenarios.all()), 1)
+        self.assertEqual(r.scenarios.first().url, s1.url)
+
+        response = self.client.post(
+            reverse(
+                "package reaction detail",
+                kwargs={"package_uuid": str(r.package.uuid), "reaction_uuid": str(r.uuid)},
+            ),
+            {
+                # We have to set an empty string to avoid that the parameter is removed
+                "selected-scenarios": ""
+            },
+        )
+
+        self.assertEqual(len(r.scenarios.all()), 0)
+
+    def test_copy(self):
+        response = self.client.post(
+            reverse("reactions"),
+            {
+                "reaction-name": "Eawag BBD reaction r0001",
+                "reaction-description": "Description for Eawag BBD reaction r0001",
+                "reaction-smirks": "C(CCl)Cl>>C(CO)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        reaction_url = response.url
+        r = Reaction.objects.get(url=reaction_url)
+
+        response = self.client.post(
+            reverse(
+                "package detail",
+                kwargs={
+                    "package_uuid": str(self.package.uuid),
+                },
+            ),
+            {"hidden": "copy", "object_to_copy": r.url},
+        )
+
+        self.assertEqual(response.status_code, 200)
+
+        copied_object_url = response.json()["success"]
+        copied_reaction = Reaction.objects.get(url=copied_object_url)
+
+        self.assertEqual(copied_reaction.name, r.name)
+        self.assertEqual(copied_reaction.description, r.description)
+        self.assertEqual(copied_reaction.smirks(), r.smirks())
+
+        # Copy to the same package should fail
+        response = self.client.post(
+            reverse(
+                "package detail",
+                kwargs={
+                    "package_uuid": str(r.package.uuid),
+                },
+            ),
+            {"hidden": "copy", "object_to_copy": r.url},
+        )
+
+        self.assertEqual(response.status_code, 400)
+        self.assertEqual(
+            response.json()["error"], f"Can't copy object {reaction_url} to the same package!"
+        )
+
+    def test_references(self):
+        ext_db, _ = ExternalDatabase.objects.get_or_create(
+            name="KEGG Reaction",
+            defaults={
+                "full_name": "KEGG Reaction Database",
+                "description": "Database of biochemical reactions",
+                "base_url": "https://www.genome.jp",
+                "url_pattern": "https://www.genome.jp/entry/{id}",
+            },
+        )
+
+        ext_db2, _ = ExternalDatabase.objects.get_or_create(
+            name="RHEA",
+            defaults={
+                "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}",
+            },
+        )
+
+        response = self.client.post(
+            reverse("reactions"),
+            {
+                "reaction-name": "Eawag BBD reaction r0001",
+                "reaction-description": "Description for Eawag BBD reaction r0001",
+                "reaction-smirks": "C(CCl)Cl>>C(CO)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        reaction_url = response.url
+        r = Reaction.objects.get(url=reaction_url)
+
+        response = self.client.post(
+            reverse(
+                "package reaction detail",
+                kwargs={
+                    "package_uuid": str(r.package.uuid),
+                    "reaction_uuid": str(r.uuid),
+                },
+            ),
+            {"selected-database": ext_db.pk, "identifier": "C12345"},
+        )
+
+        self.assertEqual(r.external_identifiers.count(), 1)
+        self.assertEqual(r.external_identifiers.first().database, ext_db)
+        self.assertEqual(r.external_identifiers.first().identifier_value, "C12345")
+        # TODO Fixture contains old url template there the real test fails, use old value instead
+        # self.assertEqual(r.external_identifiers.first().url, 'https://www.genome.jp/entry/C12345')
+        self.assertEqual(
+            r.external_identifiers.first().url, "https://www.genome.jp/entry/reaction+C12345"
+        )
+
+        response = self.client.post(
+            reverse(
+                "package reaction detail",
+                kwargs={
+                    "package_uuid": str(r.package.uuid),
+                    "reaction_uuid": str(r.uuid),
+                },
+            ),
+            {"selected-database": ext_db2.pk, "identifier": "60116"},
+        )
+
+        self.assertEqual(r.external_identifiers.count(), 2)
+        self.assertEqual(r.external_identifiers.last().database, ext_db2)
+        self.assertEqual(r.external_identifiers.last().identifier_value, "60116")
+        self.assertEqual(r.external_identifiers.last().url, "https://www.rhea-db.org/rhea/60116")
+
+    def test_delete(self):
+        response = self.client.post(
+            reverse("reactions"),
+            {
+                "reaction-name": "Eawag BBD reaction r0001",
+                "reaction-description": "Description for Eawag BBD reaction r0001",
+                "reaction-smirks": "C(CCl)Cl>>C(CO)Cl",
+            },
+        )
+        self.assertEqual(response.status_code, 302)
+
+        reaction_url = response.url
+        r = Reaction.objects.get(url=reaction_url)
+
+        response = self.client.post(
+            reverse(
+                "package reaction detail",
+                kwargs={"package_uuid": str(r.package.uuid), "reaction_uuid": str(r.uuid)},
+            ),
+            {"hidden": "delete"},
+        )
+
+        self.assertEqual(self.user1_default_package.reactions.count(), 0)
+
+    def test_set_aliases(self):
+        alias_1 = "Alias 1"
+        alias_2 = "Alias 2"
+
+        response = self.client.post(
+            reverse("reactions"),
+            {
+                "reaction-name": "Eawag BBD reaction r0001",
+                "reaction-description": "Description for Eawag BBD reaction r0001",
+                "reaction-smirks": "C(CCl)Cl>>C(CO)Cl",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        reaction_url = response.url
+        r = Reaction.objects.get(url=reaction_url)
+
+        response = self.client.post(
+            reverse(
+                "package reaction detail",
+                kwargs={"package_uuid": str(r.package.uuid), "reaction_uuid": str(r.uuid)},
+            ),
+            {"aliases": [alias_1, alias_2]},
+        )
+
+        r = Reaction.objects.get(url=reaction_url)
+        self.assertEqual(len(r.aliases), 2)
+
+        response = self.client.post(
+            reverse(
+                "package reaction detail",
+                kwargs={"package_uuid": str(r.package.uuid), "reaction_uuid": str(r.uuid)},
+            ),
+            {"aliases": [alias_1]},
+        )
+
+        r = Reaction.objects.get(url=reaction_url)
+        self.assertEqual(len(r.aliases), 1)
+
+        response = self.client.post(
+            reverse(
+                "package reaction detail",
+                kwargs={"package_uuid": str(r.package.uuid), "reaction_uuid": str(r.uuid)},
+            ),
+            {
+                # We have to set an empty string to avoid that the parameter is removed
+                "aliases": ""
+            },
+        )
+
+        r = Reaction.objects.get(url=reaction_url)
+        self.assertEqual(len(r.aliases), 0)

tests/views/test_rule_views.py

@@ -0,0 +1,314 @@
+from django.test import TestCase
+from django.urls import reverse
+from envipy_additional_information import Temperature, Interval
+
+from epdb.logic import UserManager, PackageManager
+from epdb.models import Rule, Scenario
+
+
+class RuleViewTest(TestCase):
+    fixtures = ["test_fixtures.jsonl.gz"]
+
+    @classmethod
+    def setUpClass(cls):
+        super(RuleViewTest, cls).setUpClass()
+        cls.user1 = UserManager.create_user(
+            "user1",
+            "user1@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=True,
+            is_active=True,
+        )
+        cls.user1_default_package = cls.user1.default_package
+        cls.package = PackageManager.create_package(cls.user1, "Test", "Test Pack")
+
+    def setUp(self):
+        self.client.force_login(self.user1)
+
+    def test_create_rule(self):
+        response = self.client.post(
+            reverse("rules"),
+            {
+                "rule-name": "Test Rule",
+                "rule-description": "Just a Description",
+                "rule-smirks": "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+                "rule-type": "SimpleAmbitRule",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        rule_url = response.url
+
+        r = Rule.objects.get(url=rule_url)
+
+        self.assertEqual(r.package, self.user1_default_package)
+        self.assertEqual(r.name, "Test Rule")
+        self.assertEqual(r.description, "Just a Description")
+        self.assertEqual(
+            r.smirks,
+            "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+        )
+        self.assertEqual(self.user1_default_package.rules.count(), 1)
+
+        # Adding the same rule again should return the existing one, hence not increasing the number of rules
+        response = self.client.post(
+            reverse("rules"),
+            {
+                "rule-name": "Test Rule",
+                "rule-description": "Just a Description",
+                "rule-smirks": "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+                "rule-type": "SimpleAmbitRule",
+            },
+        )
+
+        self.assertEqual(response.url, rule_url)
+        self.assertEqual(response.status_code, 302)
+        self.assertEqual(self.user1_default_package.rules.count(), 1)
+
+        # Adding the same rule in a different package should create a new rule
+        response = self.client.post(
+            reverse("package rule list", kwargs={"package_uuid": self.package.uuid}),
+            {
+                "rule-name": "Test Rule",
+                "rule-description": "Just a Description",
+                "rule-smirks": "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+                "rule-type": "SimpleAmbitRule",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        self.assertNotEqual(rule_url, response.url)
+
+    # Edit
+    def test_edit_rule(self):
+        response = self.client.post(
+            reverse("rules"),
+            {
+                "rule-name": "Test Rule",
+                "rule-description": "Just a Description",
+                "rule-smirks": "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+                "rule-type": "SimpleAmbitRule",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        rule_url = response.url
+
+        r = Rule.objects.get(url=rule_url)
+
+        response = self.client.post(
+            reverse(
+                "package rule detail",
+                kwargs={
+                    "package_uuid": str(self.user1_default_package.uuid),
+                    "rule_uuid": str(r.uuid),
+                },
+            ),
+            {
+                "rule-name": "Test Rule Adjusted",
+                "rule-description": "New Description",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        r = Rule.objects.get(url=rule_url)
+        self.assertEqual(r.name, "Test Rule Adjusted")
+        self.assertEqual(r.description, "New Description")
+
+    # Scenario
+    def test_set_scenario(self):
+        s1 = Scenario.create(
+            self.user1_default_package,
+            "Test Scen",
+            "Test Desc",
+            "2025-10",
+            "soil",
+            [Temperature(interval=Interval(start=20, end=30))],
+        )
+
+        s2 = Scenario.create(
+            self.user1_default_package,
+            "Test Scen2",
+            "Test Desc2",
+            "2025-10",
+            "soil",
+            [Temperature(interval=Interval(start=10, end=20))],
+        )
+
+        response = self.client.post(
+            reverse("rules"),
+            {
+                "rule-name": "Test Rule",
+                "rule-description": "Just a Description",
+                "rule-smirks": "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+                "rule-type": "SimpleAmbitRule",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        rule_url = response.url
+        r = Rule.objects.get(url=rule_url)
+
+        response = self.client.post(
+            reverse(
+                "package rule detail",
+                kwargs={"package_uuid": str(r.package.uuid), "rule_uuid": str(r.uuid)},
+            ),
+            {"selected-scenarios": [s1.url, s2.url]},
+        )
+
+        self.assertEqual(len(r.scenarios.all()), 2)
+
+        response = self.client.post(
+            reverse(
+                "package rule detail",
+                kwargs={"package_uuid": str(r.package.uuid), "rule_uuid": str(r.uuid)},
+            ),
+            {"selected-scenarios": [s1.url]},
+        )
+
+        self.assertEqual(len(r.scenarios.all()), 1)
+        self.assertEqual(r.scenarios.first().url, s1.url)
+
+        response = self.client.post(
+            reverse(
+                "package rule detail",
+                kwargs={"package_uuid": str(r.package.uuid), "rule_uuid": str(r.uuid)},
+            ),
+            {
+                # We have to set an empty string to avoid that the parameter is removed
+                "selected-scenarios": ""
+            },
+        )
+
+        self.assertEqual(len(r.scenarios.all()), 0)
+
+    def test_copy(self):
+        response = self.client.post(
+            reverse("rules"),
+            {
+                "rule-name": "Test Rule",
+                "rule-description": "Just a Description",
+                "rule-smirks": "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+                "rule-type": "SimpleAmbitRule",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        rule_url = response.url
+        r = Rule.objects.get(url=rule_url)
+
+        response = self.client.post(
+            reverse(
+                "package detail",
+                kwargs={
+                    "package_uuid": str(self.package.uuid),
+                },
+            ),
+            {"hidden": "copy", "object_to_copy": r.url},
+        )
+
+        self.assertEqual(response.status_code, 200)
+
+        copied_object_url = response.json()["success"]
+        copied_rule = Rule.objects.get(url=copied_object_url)
+
+        self.assertEqual(copied_rule.name, r.name)
+        self.assertEqual(copied_rule.description, r.description)
+        self.assertEqual(copied_rule.smirks, r.smirks)
+
+        # Copy to the same package should fail
+        response = self.client.post(
+            reverse(
+                "package detail",
+                kwargs={
+                    "package_uuid": str(r.package.uuid),
+                },
+            ),
+            {"hidden": "copy", "object_to_copy": r.url},
+        )
+
+        self.assertEqual(response.status_code, 400)
+        self.assertEqual(
+            response.json()["error"], f"Can't copy object {rule_url} to the same package!"
+        )
+
+    def test_delete(self):
+        response = self.client.post(
+            reverse("rules"),
+            {
+                "rule-name": "Test Rule",
+                "rule-description": "Just a Description",
+                "rule-smirks": "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+                "rule-type": "SimpleAmbitRule",
+            },
+        )
+        self.assertEqual(response.status_code, 302)
+
+        rule_url = response.url
+        r = Rule.objects.get(url=rule_url)
+
+        response = self.client.post(
+            reverse(
+                "package rule detail",
+                kwargs={"package_uuid": str(r.package.uuid), "rule_uuid": str(r.uuid)},
+            ),
+            {"hidden": "delete"},
+        )
+
+        self.assertEqual(self.user1_default_package.rules.count(), 0)
+
+    def test_set_aliases(self):
+        alias_1 = "Alias 1"
+        alias_2 = "Alias 2"
+
+        response = self.client.post(
+            reverse("rules"),
+            {
+                "rule-name": "Test Rule",
+                "rule-description": "Just a Description",
+                "rule-smirks": "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+                "rule-type": "SimpleAmbitRule",
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        rule_url = response.url
+        r = Rule.objects.get(url=rule_url)
+
+        response = self.client.post(
+            reverse(
+                "package rule detail",
+                kwargs={"package_uuid": str(r.package.uuid), "rule_uuid": str(r.uuid)},
+            ),
+            {"aliases": [alias_1, alias_2]},
+        )
+
+        r = Rule.objects.get(url=rule_url)
+        self.assertEqual(len(r.aliases), 2)
+
+        response = self.client.post(
+            reverse(
+                "package rule detail",
+                kwargs={"package_uuid": str(r.package.uuid), "rule_uuid": str(r.uuid)},
+            ),
+            {"aliases": [alias_1]},
+        )
+
+        r = Rule.objects.get(url=rule_url)
+        self.assertEqual(len(r.aliases), 1)
+
+        response = self.client.post(
+            reverse(
+                "package rule detail",
+                kwargs={"package_uuid": str(r.package.uuid), "rule_uuid": str(r.uuid)},
+            ),
+            {
+                # We have to set an empty string to avoid that the parameter is removed
+                "aliases": ""
+            },
+        )
+
+        r = Rule.objects.get(url=rule_url)
+        self.assertEqual(len(r.aliases), 0)

tests/views/test_user_views.py

@@ -11,70 +11,81 @@ class UserViewTest(TestCase):
     @classmethod
     def setUpClass(cls):
         super(UserViewTest, cls).setUpClass()
-        cls.user = User.objects.get(username='anonymous')
+        cls.user = User.objects.get(username="anonymous")
-        cls.package = PackageManager.create_package(cls.user, 'Anon Test Package', 'No Desc')
+        cls.package = PackageManager.create_package(cls.user, "Anon Test Package", "No Desc")
-        cls.BBD_SUBSET = Package.objects.get(name='Fixtures')
+        cls.BBD_SUBSET = Package.objects.get(name="Fixtures")
 
     def test_login_with_valid_credentials(self):
-        response = self.client.post(reverse("login"), {
+        response = self.client.post(
-            "username": "user0",
+            reverse("login"),
-            "password": 'SuperSafe',
+            {
-        })
+                "username": "user0",
+                "password": "SuperSafe",
+            },
+        )
         self.assertRedirects(response, reverse("index"))
         self.assertTrue(response.wsgi_request.user.is_authenticated)
 
     def test_login_with_invalid_credentials(self):
-        response = self.client.post(reverse("login"), {
+        response = self.client.post(
-            "username": "user0",
+            reverse("login"),
-            "password": "wrongpassword",
+            {
-        })
+                "username": "user0",
+                "password": "wrongpassword",
+            },
+        )
         self.assertEqual(response.status_code, 200)
         self.assertFalse(response.wsgi_request.user.is_authenticated)
 
     def test_register(self):
-        response = self.client.post(reverse("register"), {
+        response = self.client.post(
-            "username": "user1",
+            reverse("register"),
-            "email": "user1@envipath.com",
+            {
-            "password": "SuperSafe",
+                "username": "user1",
-            "rpassword": "SuperSafe",
+                "email": "user1@envipath.com",
-        })
+                "password": "SuperSafe",
+                "rpassword": "SuperSafe",
+            },
+        )
         self.assertEqual(response.status_code, 200)
         # TODO currently fails as the fixture does not provide a global setting...
         self.assertContains(response, "Registration failed!")
 
     def test_register_password_mismatch(self):
-        response = self.client.post(reverse("register"), {
+        response = self.client.post(
-            "username": "user1",
+            reverse("register"),
-            "email": "user1@envipath.com",
+            {
-            "password": "SuperSafe",
+                "username": "user1",
-            "rpassword": "SuperSaf3",
+                "email": "user1@envipath.com",
-        })
+                "password": "SuperSafe",
+                "rpassword": "SuperSaf3",
+            },
+        )
         self.assertEqual(response.status_code, 200)
         self.assertContains(response, "Registration failed, provided passwords differ")
 
     def test_logout(self):
-        response = self.client.post(reverse("login"), {
+        response = self.client.post(
-            "username": "user0",
+            reverse("login"), {"username": "user0", "password": "SuperSafe", "login": "true"}
-            "password": 'SuperSafe',
+        )
-            "login": "true"
-        })
         self.assertTrue(response.wsgi_request.user.is_authenticated)
 
-        response = self.client.post(reverse('logout'), {
+        response = self.client.post(
-            "logout": "true",
+            reverse("logout"),
-        })
+            {
+                "logout": "true",
+            },
+        )
         self.assertFalse(response.wsgi_request.user.is_authenticated)
 
     def test_next_param_properly_handled(self):
-        response = self.client.get(reverse('packages'))
+        response = self.client.get(reverse("packages"))
 
         self.assertRedirects(response, f"{reverse('login')}/?next=/package")
 
-        response = self.client.post(reverse('login'), {
+        response = self.client.post(
-            "username": "user0",
+            reverse("login"),
-            "password": 'SuperSafe',
+            {"username": "user0", "password": "SuperSafe", "login": "true", "next": "/package"},
-            "login": "true",
+        )
-            "next": "/package"
-        })
 
-        self.assertRedirects(response, reverse('packages'))
+        self.assertRedirects(response, reverse("packages"))

utilities/biodeg.py

@@ -1,13 +0,0 @@
-import abc
-from enviPy.epdb import Pathway
-
-class PredictionSchema(abc.ABC):
-    pass
-
-class DFS(PredictionSchema):
-
-    def __init__(self, pw: Pathway, settings=None):
-        self.setting = settings or pw.prediction_settings
-
-    def predict(self):
-        pass

utilities/chem.py

@@ -2,12 +2,11 @@ import logging
 import re
 from abc import ABC
 from collections import defaultdict
-from typing import List, Optional, Dict
+from typing import List, Optional, Dict, TYPE_CHECKING
 
 from indigo import Indigo, IndigoException, IndigoObject
 from indigo.renderer import IndigoRenderer
-from rdkit import Chem
+from rdkit import Chem, rdBase
-from rdkit import RDLogger
 from rdkit.Chem import MACCSkeys, Descriptors
 from rdkit.Chem import rdChemReactions
 from rdkit.Chem.Draw import rdMolDraw2D
@@ -15,9 +14,11 @@ from rdkit.Chem.MolStandardize import rdMolStandardize
 from rdkit.Chem.rdmolops import GetMolFrags
 from rdkit.Contrib.IFG import ifg
 
-logger = logging.getLogger(__name__)
+if TYPE_CHECKING:
-RDLogger.DisableLog('rdApp.*')
+    from epdb.models import Rule
 
+logger = logging.getLogger(__name__)
+rdBase.DisableLog("rdApp.*")
 
 # from rdkit import rdBase
 # rdBase.LogToPythonLogger()
@@ -28,7 +29,6 @@ RDLogger.DisableLog('rdApp.*')
 
 
 class ProductSet(object):
-
     def __init__(self, product_set: List[str]):
         self.product_set = product_set
 
@@ -42,15 +42,18 @@ class ProductSet(object):
         return iter(self.product_set)
 
     def __eq__(self, other):
-        return isinstance(other, ProductSet) and sorted(self.product_set) == sorted(other.product_set)
+        return isinstance(other, ProductSet) and sorted(self.product_set) == sorted(
+            other.product_set
+        )
 
     def __hash__(self):
-        return hash('-'.join(sorted(self.product_set)))
+        return hash("-".join(sorted(self.product_set)))
 
 
 class PredictionResult(object):
-
+    def __init__(
-    def __init__(self, product_sets: List['ProductSet'], probability: float, rule: Optional['Rule'] = None):
+        self, product_sets: List["ProductSet"], probability: float, rule: Optional["Rule"] = None
+    ):
         self.product_sets = product_sets
         self.probability = probability
         self.rule = rule
@@ -66,7 +69,6 @@ class PredictionResult(object):
 
 
 class FormatConverter(object):
-
     @staticmethod
     def mass(smiles):
         return Descriptors.MolWt(FormatConverter.from_smiles(smiles))
@@ -127,7 +129,7 @@ class FormatConverter(object):
         if kekulize:
             try:
                 mol = Chem.Kekulize(mol)
-            except:
+            except Exception:
                 mol = Chem.Mol(mol.ToBinary())
 
         if not mol.GetNumConformers():
@@ -139,8 +141,8 @@ class FormatConverter(object):
         opts.clearBackground = False
         drawer.DrawMolecule(mol)
         drawer.FinishDrawing()
-        svg = drawer.GetDrawingText().replace('svg:', '')
+        svg = drawer.GetDrawingText().replace("svg:", "")
-        svg = re.sub("<\?xml.*\?>", '', svg)
+        svg = re.sub("<\?xml.*\?>", "", svg)
 
         return svg
 
@@ -151,7 +153,7 @@ class FormatConverter(object):
         if kekulize:
             try:
                 Chem.Kekulize(mol)
-            except:
+            except Exception:
                 mc = Chem.Mol(mol.ToBinary())
 
         if not mc.GetNumConformers():
@@ -178,7 +180,7 @@ class FormatConverter(object):
                     smiles = tmp_smiles
 
             if change is False:
-                print(f"nothing changed")
+                print("nothing changed")
 
         return smiles
 
@@ -198,7 +200,9 @@ class FormatConverter(object):
         parent_clean_mol = rdMolStandardize.FragmentParent(clean_mol)
 
         # try to neutralize molecule
-        uncharger = rdMolStandardize.Uncharger()  # annoying, but necessary as no convenience method exists
+        uncharger = (
+            rdMolStandardize.Uncharger()
+        )  # annoying, but necessary as no convenience method exists
         uncharged_parent_clean_mol = uncharger.uncharge(parent_clean_mol)
 
         # note that no attempt is made at reionization at this step
@@ -239,17 +243,24 @@ class FormatConverter(object):
         try:
             rdChemReactions.ReactionFromSmarts(smirks)
             return True
-        except:
+        except Exception:
             return False
 
     @staticmethod
-    def apply(smiles: str, smirks: str, preprocess_smiles: bool = True, bracketize: bool = True,
+    def apply(
-              standardize: bool = True, kekulize: bool = True) -> List['ProductSet']:
+        smiles: str,
-        logger.debug(f'Applying {smirks} on {smiles}')
+        smirks: str,
+        preprocess_smiles: bool = True,
+        bracketize: bool = True,
+        standardize: bool = True,
+        kekulize: bool = True,
+        remove_stereo: bool = True,
+    ) -> List["ProductSet"]:
+        logger.debug(f"Applying {smirks} on {smiles}")
 
         # If explicitly wanted or rule generates multiple products add brackets around products to capture all
         if bracketize:  # or "." in smirks:
-            smirks = smirks.split('>>')[0] + ">>(" + smirks.split('>>')[1] + ")"
+            smirks = smirks.split(">>")[0] + ">>(" + smirks.split(">>")[1] + ")"
 
         # List of ProductSet objects
         pss = set()
@@ -274,7 +285,9 @@ class FormatConverter(object):
                             Chem.SanitizeMol(product)
                             product = GetMolFrags(product, asMols=True)
                             for p in product:
-                                p = FormatConverter.standardize(Chem.MolToSmiles(p))
+                                p = FormatConverter.standardize(
+                                    Chem.MolToSmiles(p), remove_stereo=remove_stereo
+                                )
                                 prods.append(p)
 
                             # if kekulize:
@@ -300,9 +313,8 @@ class FormatConverter(object):
                             #     #     bond.SetIsAromatic(False)
                             #     Chem.Kekulize(product)
 
-
                         except ValueError as e:
-                            logger.error(f'Sanitizing and converting failed:\n{e}')
+                            logger.error(f"Sanitizing and converting failed:\n{e}")
                             continue
 
                     if len(prods):
@@ -310,34 +322,14 @@ class FormatConverter(object):
                         pss.add(ps)
 
         except Exception as e:
-            logger.error(f'Applying {smirks} on {smiles} failed:\n{e}')
+            logger.error(f"Applying {smirks} on {smiles} failed:\n{e}")
 
         return pss
 
-    # @staticmethod
-    # def apply(reaction, smiles):
-    #     rxn = AllChem.ReactionFromSmarts(reaction)
-    #     return [Chem.MolToSmiles(x, 1) for x in rxn.RunReactants((Chem.MolFromSmiles(smiles),))[0]]
-
     @staticmethod
     def MACCS(smiles):
         return MACCSkeys.GenMACCSKeys(FormatConverter.from_smiles(smiles))
 
-    @staticmethod
-    def neutralize_atoms(mol):
-        pattern = Chem.MolFromSmarts("[+1!h0!$([*]~[-1,-2,-3,-4]),-1!$([*]~[+1,+2,+3,+4])]")
-        at_matches = mol.GetSubstructMatches(pattern)
-        at_matches_list = [y[0] for y in at_matches]
-        if len(at_matches_list) > 0:
-            for at_idx in at_matches_list:
-                atom = mol.GetAtomWithIdx(at_idx)
-                chg = atom.GetFormalCharge()
-                hcount = atom.GetTotalNumHs()
-                atom.SetFormalCharge(0)
-                atom.SetNumExplicitHs(hcount - chg)
-                atom.UpdatePropertyCache()
-        return mol
-
     @staticmethod
     def sanitize_smiles(smiles_list: List):
         parsed_smiles = []
@@ -353,28 +345,26 @@ class FormatConverter(object):
                 #     smi = smi.replace("@", "")
 
                 mol = Chem.MolFromSmiles(smi)
-                mol = FormatConverter.neutralize_atoms(mol)
+                mol = FormatConverter.neutralize_molecule(mol)
+                Chem.RemoveStereochemistry(mol)
                 mol = Chem.RemoveAllHs(mol)
                 Chem.Kekulize(mol)
                 smi_p = Chem.MolToSmiles(mol, kekuleSmiles=True)
                 smi_p = Chem.CanonSmiles(smi_p)
 
-                if '~' in smi_p:
+                if "~" in smi_p:
-                    smi_p1 = smi_p.replace('~', '')
+                    smi_p1 = smi_p.replace("~", "")
                     parsed_smiles.append(smi_p1)
                 else:
                     parsed_smiles.append(smi_p)
-            except Exception as e:
+            except Exception:
                 errors += 1
                 pass
 
         return parsed_smiles, errors
 
 
-
-
 class Standardizer(ABC):
-
     def __init__(self, name):
         self.name = name
 
@@ -383,7 +373,6 @@ class Standardizer(ABC):
 
 
 class RuleStandardizer(Standardizer):
-
     def __init__(self, name, smirks):
         super().__init__(name)
         self.smirks = smirks
@@ -392,8 +381,8 @@ class RuleStandardizer(Standardizer):
         standardized_smiles = list(set(FormatConverter.apply(smiles, self.smirks)))
 
         if len(standardized_smiles) > 1:
-            logger.warning(f'{self.smirks} generated more than 1 compound {standardized_smiles}')
+            logger.warning(f"{self.smirks} generated more than 1 compound {standardized_smiles}")
-            print(f'{self.smirks} generated more than 1 compound {standardized_smiles}')
+            print(f"{self.smirks} generated more than 1 compound {standardized_smiles}")
             standardized_smiles = standardized_smiles[:1]
 
         if standardized_smiles:
@@ -403,7 +392,6 @@ class RuleStandardizer(Standardizer):
 
 
 class RegExStandardizer(Standardizer):
-
     def __init__(self, name, replacements: dict):
         super().__init__(name)
         self.replacements = replacements
@@ -423,28 +411,39 @@ class RegExStandardizer(Standardizer):
         return super().standardize(smi)
 
 
-FLATTEN = [
+FLATTEN = [RegExStandardizer("Remove Stereo", {"@": ""})]
-    RegExStandardizer("Remove Stereo", {"@": ""})
-]
 
-UN_CIS_TRANS = [
+UN_CIS_TRANS = [RegExStandardizer("Un-Cis-Trans", {"/": "", "\\": ""})]
-    RegExStandardizer("Un-Cis-Trans", {"/": "", "\\": ""})
-]
 
 BASIC = [
     RuleStandardizer("ammoniumstandardization", "[H][N+:1]([H])([H])[#6:2]>>[H][#7:1]([H])-[#6:2]"),
     RuleStandardizer("cyanate", "[H][#8:1][C:2]#[N:3]>>[#8-:1][C:2]#[N:3]"),
     RuleStandardizer("deprotonatecarboxyls", "[H][#8:1]-[#6:2]=[O:3]>>[#8-:1]-[#6:2]=[O:3]"),
     RuleStandardizer("forNOOH", "[H][#8:1]-[#7+:2](-[*:3])=[O:4]>>[#8-:1]-[#7+:2](-[*:3])=[O:4]"),
-    RuleStandardizer("Hydroxylprotonation", "[#6;A:1][#6:2](-[#8-:3])=[#6;A:4]>>[#6:1]-[#6:2](-[#8:3][H])=[#6;A:4]"),
+    RuleStandardizer(
-    RuleStandardizer("phosphatedeprotonation", "[H][#8:1]-[$([#15]);!$(P([O-])):2]>>[#8-:1]-[#15:2]"),
+        "Hydroxylprotonation",
-    RuleStandardizer("PicricAcid",
+        "[#6;A:1][#6:2](-[#8-:3])=[#6;A:4]>>[#6:1]-[#6:2](-[#8:3][H])=[#6;A:4]",
-                     "[H][#8:1]-[c:2]1[c:3][c:4][c:5]([c:6][c:7]1-[#7+:8](-[#8-:9])=[O:10])-[#7+:11](-[#8-:12])=[O:13]>>[#8-:1]-[c:2]1[c:3][c:4][c:5]([c:6][c:7]1-[#7+:8](-[#8-:9])=[O:10])-[#7+:11](-[#8-:12])=[O:13]"),
+    ),
-    RuleStandardizer("Sulfate1", "[H][#8:1][S:2]([#8:3][H])(=[O:4])=[O:5]>>[#8-:1][S:2]([#8-:3])(=[O:4])=[O:5]"),
+    RuleStandardizer(
-    RuleStandardizer("Sulfate2",
+        "phosphatedeprotonation", "[H][#8:1]-[$([#15]);!$(P([O-])):2]>>[#8-:1]-[#15:2]"
-                     "[#6:1]-[#8:2][S:3]([#8:4][H])(=[O:5])=[O:6]>>[#6:1]-[#8:2][S:3]([#8-:4])(=[O:5])=[O:6]"),
+    ),
-    RuleStandardizer("Sulfate3", "[H][#8:3][S:2]([#6:1])(=[O:4])=[O:5]>>[#6:1][S:2]([#8-:3])(=[O:4])=[O:5]"),
+    RuleStandardizer(
-    RuleStandardizer("Transform_c1353forSOOH", "[H][#8:1][S:2]([*:3])=[O:4]>>[#8-:1][S:2]([*:3])=[O:4]"),
+        "PicricAcid",
+        "[H][#8:1]-[c:2]1[c:3][c:4][c:5]([c:6][c:7]1-[#7+:8](-[#8-:9])=[O:10])-[#7+:11](-[#8-:12])=[O:13]>>[#8-:1]-[c:2]1[c:3][c:4][c:5]([c:6][c:7]1-[#7+:8](-[#8-:9])=[O:10])-[#7+:11](-[#8-:12])=[O:13]",
+    ),
+    RuleStandardizer(
+        "Sulfate1", "[H][#8:1][S:2]([#8:3][H])(=[O:4])=[O:5]>>[#8-:1][S:2]([#8-:3])(=[O:4])=[O:5]"
+    ),
+    RuleStandardizer(
+        "Sulfate2",
+        "[#6:1]-[#8:2][S:3]([#8:4][H])(=[O:5])=[O:6]>>[#6:1]-[#8:2][S:3]([#8-:4])(=[O:5])=[O:6]",
+    ),
+    RuleStandardizer(
+        "Sulfate3", "[H][#8:3][S:2]([#6:1])(=[O:4])=[O:5]>>[#6:1][S:2]([#8-:3])(=[O:4])=[O:5]"
+    ),
+    RuleStandardizer(
+        "Transform_c1353forSOOH", "[H][#8:1][S:2]([*:3])=[O:4]>>[#8-:1][S:2]([*:3])=[O:4]"
+    ),
 ]
 
 ENHANCED = BASIC + [
@@ -452,28 +451,30 @@ ENHANCED = BASIC + [
 ]
 
 EXOTIC = ENHANCED + [
-    RuleStandardizer("ThioPhosphate1", "[H][S:1]-[#15:2]=[$([#16]),$([#8]):3]>>[S-:1]-[#15:2]=[$([#16]),$([#8]):3]")
+    RuleStandardizer(
+        "ThioPhosphate1",
+        "[H][S:1]-[#15:2]=[$([#16]),$([#8]):3]>>[S-:1]-[#15:2]=[$([#16]),$([#8]):3]",
+    )
 ]
 
 COA_CUTTER = [
-    RuleStandardizer("CutCoEnzymeAOff",
+    RuleStandardizer(
-                     "CC(C)(COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)n1cnc2c(N)ncnc12)C(O)C(=O)NCCC(=O)NCCS[$(*):1]>>[O-][$(*):1]")
+        "CutCoEnzymeAOff",
+        "CC(C)(COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)n1cnc2c(N)ncnc12)C(O)C(=O)NCCC(=O)NCCS[$(*):1]>>[O-][$(*):1]",
+    )
 ]
 
-ENOL_KETO = [
+ENOL_KETO = [RuleStandardizer("enol2Ketone", "[H][#8:2]-[#6:3]=[#6:1]>>[#6:1]-[#6:3]=[O:2]")]
-    RuleStandardizer("enol2Ketone", "[H][#8:2]-[#6:3]=[#6:1]>>[#6:1]-[#6:3]=[O:2]")
-]
 
 MATCH_STANDARDIZER = EXOTIC + FLATTEN + UN_CIS_TRANS + COA_CUTTER + ENOL_KETO
 
 
 class IndigoUtils(object):
-
     @staticmethod
     def layout(mol_data):
         i = Indigo()
         try:
-            if mol_data.startswith('$RXN') or '>>' in mol_data:
+            if mol_data.startswith("$RXN") or ">>" in mol_data:
                 rxn = i.loadQueryReaction(mol_data)
                 rxn.layout()
                 return rxn.rxnfile()
@@ -481,14 +482,14 @@ class IndigoUtils(object):
                 mol = i.loadQueryMolecule(mol_data)
                 mol.layout()
                 return mol.molfile()
-        except IndigoException as e:
+        except IndigoException:
             try:
                 logger.info("layout() failed, trying loadReactionSMARTS as fallback!")
                 rxn = IndigoUtils.load_reaction_SMARTS(mol_data)
                 rxn.layout()
                 return rxn.molfile()
             except IndigoException as e2:
-                logger.error(f'layout() failed due to {e2}!')
+                logger.error(f"layout() failed due to {e2}!")
 
     @staticmethod
     def load_reaction_SMARTS(mol):
@@ -498,7 +499,7 @@ class IndigoUtils(object):
     def aromatize(mol_data, is_query):
         i = Indigo()
         try:
-            if mol_data.startswith('$RXN'):
+            if mol_data.startswith("$RXN"):
                 if is_query:
                     rxn = i.loadQueryReaction(mol_data)
                 else:
@@ -514,20 +515,20 @@ class IndigoUtils(object):
 
                 mol.aromatize()
                 return mol.molfile()
-        except IndigoException as e:
+        except IndigoException:
             try:
                 logger.info("Aromatizing failed, trying loadReactionSMARTS as fallback!")
                 rxn = IndigoUtils.load_reaction_SMARTS(mol_data)
                 rxn.aromatize()
                 return rxn.molfile()
             except IndigoException as e2:
-                logger.error(f'Aromatizing failed due to {e2}!')
+                logger.error(f"Aromatizing failed due to {e2}!")
 
     @staticmethod
     def dearomatize(mol_data, is_query):
         i = Indigo()
         try:
-            if mol_data.startswith('$RXN'):
+            if mol_data.startswith("$RXN"):
                 if is_query:
                     rxn = i.loadQueryReaction(mol_data)
                 else:
@@ -543,14 +544,14 @@ class IndigoUtils(object):
 
                 mol.dearomatize()
                 return mol.molfile()
-        except IndigoException as e:
+        except IndigoException:
             try:
                 logger.info("De-Aromatizing failed, trying loadReactionSMARTS as fallback!")
                 rxn = IndigoUtils.load_reaction_SMARTS(mol_data)
                 rxn.dearomatize()
                 return rxn.molfile()
             except IndigoException as e2:
-                logger.error(f'De-Aromatizing failed due to {e2}!')
+                logger.error(f"De-Aromatizing failed due to {e2}!")
 
     @staticmethod
     def sanitize_functional_group(functional_group: str):
@@ -562,7 +563,7 @@ class IndigoUtils(object):
 
             # special environment handling (amines, hydroxy, esters, ethers)
             # the higher substituted should not contain H env.
-            if functional_group == '[C]=O':
+            if functional_group == "[C]=O":
                 functional_group = "[H][C](=O)[CX4,c]"
 
             # aldamines
@@ -596,15 +597,20 @@ class IndigoUtils(object):
                 functional_group = "[nH1,nX2](a)a"  # pyrrole (with H) or pyridine (no other connections); currently overlaps with neighboring aromatic atoms
 
             # substituted aromatic nitrogen
-            functional_group = functional_group.replace("N*(R)R",
+            functional_group = functional_group.replace(
-                                                        "n(a)a")  # substituent will be before N*; currently overlaps with neighboring aromatic atoms
+                "N*(R)R", "n(a)a"
+            )  # substituent will be before N*; currently overlaps with neighboring aromatic atoms
             # pyridinium
             if functional_group == "RN*(R)(R)(R)R":
-                functional_group = "[CX4,c]n(a)a"  # currently overlaps with neighboring aromatic atoms
+                functional_group = (
+                    "[CX4,c]n(a)a"  # currently overlaps with neighboring aromatic atoms
+                )
 
             # N-oxide
             if functional_group == "[H]ON*(R)(R)(R)R":
-                functional_group = "[O-][n+](a)a"  # currently overlaps with neighboring aromatic atoms
+                functional_group = (
+                    "[O-][n+](a)a"  # currently overlaps with neighboring aromatic atoms
+                )
 
             # other aromatic hetero atoms
             functional_group = functional_group.replace("C*", "c")
@@ -617,7 +623,9 @@ class IndigoUtils(object):
             # other replacement, to accomodate for the standardization rules in enviPath
             # This is not the perfect way to do it; there should be a way to replace substructure SMARTS in SMARTS?
             # nitro groups are broken, due to charge handling. this SMARTS matches both forms (formal charges and hypervalent); Ertl-CDK still treats both forms separately...
-            functional_group = functional_group.replace("[H]O[N](=O)R", "[CX4,c][NX3](~[OX1])~[OX1]")
+            functional_group = functional_group.replace(
+                "[H]O[N](=O)R", "[CX4,c][NX3](~[OX1])~[OX1]"
+            )
             functional_group = functional_group.replace("O=N(=O)R", "[CX4,c][NX3](~[OX1])~[OX1]")
             # carboxylic acid: this SMARTS matches both neutral and anionic form; includes COOH in larger functional_groups
             functional_group = functional_group.replace("[H]OC(=O)", "[OD1]C(=O)")
@@ -635,7 +643,9 @@ class IndigoUtils(object):
         return functional_group
 
     @staticmethod
-    def _colorize(indigo: Indigo, molecule: IndigoObject, functional_groups: Dict[str, int], is_reaction: bool):
+    def _colorize(
+        indigo: Indigo, molecule: IndigoObject, functional_groups: Dict[str, int], is_reaction: bool
+    ):
         indigo.setOption("render-atom-color-property", "color")
         indigo.setOption("aromaticity-model", "generic")
 
@@ -665,7 +675,6 @@ class IndigoUtils(object):
 
                 for match in matcher.iterateMatches(query):
                     if match is not None:
-
                         for atom in query.iterateAtoms():
                             mappedAtom = match.mapAtom(atom)
                             if mappedAtom is None or mappedAtom.index() in environment:
@@ -674,7 +683,7 @@ class IndigoUtils(object):
                             counts[mappedAtom.index()] = max(v, counts[mappedAtom.index()])
 
             except IndigoException as e:
-                logger.debug(f'Colorizing failed due to {e}')
+                logger.debug(f"Colorizing failed due to {e}")
 
         for k, v in counts.items():
             if is_reaction:
@@ -688,8 +697,9 @@ class IndigoUtils(object):
             molecule.addDataSGroup([k], [], "color", color)
 
     @staticmethod
-    def mol_to_svg(mol_data: str, width: int = 0, height: int = 0, functional_groups: Dict[str, int] = None):
+    def mol_to_svg(
-
+        mol_data: str, width: int = 0, height: int = 0, functional_groups: Dict[str, int] = None
+    ):
         if functional_groups is None:
             functional_groups = {}
 
@@ -701,7 +711,7 @@ class IndigoUtils(object):
         i.setOption("render-image-size", width, height)
         i.setOption("render-bond-line-width", 2.0)
 
-        if '~' in mol_data:
+        if "~" in mol_data:
             mol = i.loadSmarts(mol_data)
         else:
             mol = i.loadMolecule(mol_data)
@@ -709,11 +719,18 @@ class IndigoUtils(object):
         if len(functional_groups.keys()) > 0:
             IndigoUtils._colorize(i, mol, functional_groups, False)
 
-        return renderer.renderToBuffer(mol).decode('UTF-8')
+        return renderer.renderToBuffer(mol).decode("UTF-8")
 
     @staticmethod
-    def smirks_to_svg(smirks: str, is_query_smirks, width: int = 0, height: int = 0,
+    def smirks_to_svg(
-                      educt_functional_groups: Dict[str, int] = None, product_functional_groups: Dict[str, int] = None):
+        smirks: str,
+        is_query_smirks,
+        width: int = 0,
+        height: int = 0,
+        educt_functional_groups: Dict[str, int] = None,
+        product_functional_groups: Dict[str, int] = None,
+        debug: bool = False,
+    ):
         if educt_functional_groups is None:
             educt_functional_groups = {}
 
@@ -723,6 +740,11 @@ class IndigoUtils(object):
         i = Indigo()
         renderer = IndigoRenderer(i)
 
+        if debug:
+            i.setOption("render-atom-ids-visible", True)
+            i.setOption("render-bond-ids-visible", False)
+            i.setOption("render-atom-bond-ids-from-one", True)
+
         i.setOption("render-output-format", "svg")
         i.setOption("render-coloring", True)
         i.setOption("render-image-size", width, height)
@@ -740,18 +762,18 @@ class IndigoUtils(object):
                 for prod in obj.iterateProducts():
                     IndigoUtils._colorize(i, prod, product_functional_groups, True)
 
-        return renderer.renderToBuffer(obj).decode('UTF-8')
+        return renderer.renderToBuffer(obj).decode("UTF-8")
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     data = {
         "struct": "\n  Ketcher  2172510 12D 1   1.00000     0.00000     0\n\n  6  6  0     0  0            999 V2000\n    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.5000   -0.8660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.0000   -1.7321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000   -1.7321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.5000   -0.8660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  2  0  0  0  0\n  2  3  1  0  0  0  0\n  3  4  2  0  0  0  0\n  4  5  1  0  0  0  0\n  5  6  2  0  0  0  0\n  6  1  1  0  0  0  0\nM  END\n",
         "options": {
             "smart-layout": True,
             "ignore-stereochemistry-errors": True,
             "mass-skip-error-on-pseudoatoms": False,
-            "gross-formula-add-rsites": True
+            "gross-formula-add-rsites": True,
-        }
+        },
     }
 
-    print(IndigoUtils.aromatize(data['struct'], False))
+    print(IndigoUtils.aromatize(data["struct"], False))