Merge branch 'develop' into fix/frontpage_predict

Modal now opens on badge click.
Modal now closes on random click around

Reviewed-on: enviPath/enviPy#192
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>

.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 +16,5 @@ POSTGRES_PORT=
 # MAIL
 EMAIL_HOST_USER=
 EMAIL_HOST_PASSWORD=
-
+# MATOMO
+MATOMO_SITE_ID

.gitea/workflows/ci.yaml

@@ -0,0 +1,116 @@
+name: CI
+
+on:
+  pull_request:
+    branches:
+      - develop
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    services:
+      postgres:
+        image: postgres:16
+        env:
+          POSTGRES_USER: ${{ vars.POSTGRES_USER }}
+          POSTGRES_PASSWORD: ${{ secrets.POSTGRES_PASSWORD }}
+          POSTGRES_DB: ${{ vars.POSTGRES_DB }}
+        ports:
+          - ${{ vars.POSTGRES_PORT}}:5432
+        options: >-
+          --health-cmd="pg_isready -U postgres"
+          --health-interval=10s
+          --health-timeout=5s
+          --health-retries=5
+
+      #redis:
+      #  image: redis:7
+      #  ports:
+      #    - 6379:6379
+      #  options: >-
+      #    --health-cmd "redis-cli ping"
+      #    --health-interval=10s
+      #    --health-timeout=5s
+      #    --health-retries=5
+
+    env:
+      RUNNER_TOOL_CACHE: /toolcache
+      EP_DATA_DIR: /opt/enviPy/
+      ALLOWED_HOSTS: 127.0.0.1,localhost
+      DEBUG: True
+      LOG_LEVEL: DEBUG
+      MODEL_BUILDING_ENABLED: True
+      APPLICABILITY_DOMAIN_ENABLED: True
+      ENVIFORMER_PRESENT: True
+      ENVIFORMER_DEVICE: cpu
+      FLAG_CELERY_PRESENT: False
+      PLUGINS_ENABLED: True
+      SERVER_URL: http://localhost:8000
+      ADMIN_APPROVAL_REQUIRED: True
+      REGISTRATION_MANDATORY: True
+      LOG_DIR: ''
+      # DB
+      POSTGRES_SERVICE_NAME: postgres
+      POSTGRES_DB: ${{ vars.POSTGRES_DB }}
+      POSTGRES_USER: ${{ vars.POSTGRES_USER }}
+      POSTGRES_PASSWORD: ${{ secrets.POSTGRES_PASSWORD }}
+      POSTGRES_PORT: 5432
+      # SENTRY
+      SENTRY_ENABLED: False
+      # MS ENTRA
+      MS_ENTRA_ENABLED: False
+
+    steps:
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install system tools via apt
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y postgresql-client redis-tools openjdk-11-jre-headless
+
+      - name: Setup ssh
+        run: |
+          echo "${{ secrets.ENVIPY_CI_PRIVATE_KEY }}" > ~/.ssh/id_ed25519
+          chmod 600 ~/.ssh/id_ed25519
+          ssh-keyscan git.envipath.com >> ~/.ssh/known_hosts
+          eval $(ssh-agent -s)
+          ssh-add ~/.ssh/id_ed25519
+
+      - name: Install pnpm
+        uses: pnpm/action-setup@v4
+        with:
+          version: 10
+
+      - name: Use Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: 20
+          cache: "pnpm"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
+      - name: Setup venv
+        run: |
+          uv sync --locked --all-extras --dev
+
+      - name: Wait for services
+        run: |
+          until pg_isready -h postgres -U postgres; do sleep 2; done
+          # until redis-cli -h redis ping; do sleep 2; done
+
+      - name: Run Django Migrations
+        run: |
+          source .venv/bin/activate
+          python manage.py migrate --noinput
+
+      - name: Run Django tests
+        run: |
+          source .venv/bin/activate
+          python manage.py test tests --exclude-tag slow

.gitignore

@@ -6,3 +6,12 @@ static/django_extensions/
 .env
 debug.log
 scratches/
+
+data/
+
+.DS_Store
+
+node_modules/
+static/css/output.css
+
+*.code-workspace

.pre-commit-config.yaml

@@ -0,0 +1,40 @@
+# 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
+        exclude: ^static/images/
+
+  - 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: prettier-jinja-templates
+        name: Format Jinja templates with Prettier
+        entry: pnpm exec prettier --plugin=prettier-plugin-jinja-template --parser=jinja-template --write
+        language: system
+        types: [file]
+        files: ^templates/.*\.html$
+
+  # - repo: local
+  #   hooks:
+  #     - id: django-check
+  #       name: Run Django Check
+  #       entry: uv run python manage.py check
+  #       language: system
+  #       pass_filenames: false
+  #       types: [python]

.prettierrc.json

@@ -0,0 +1,11 @@
+{
+  "plugins": ["prettier-plugin-jinja-template", "prettier-plugin-tailwindcss"],
+  "overrides": [
+    {
+      "files": "templates/**/*.html",
+      "options": {
+        "parser": "jinja-template"
+      }
+    }
+  ]
+}

.python-version

@@ -1 +1 @@
-3.10
+3.12

README.md

@@ -1,2 +1,103 @@
 # 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) - Python package manager
+- **Docker and Docker Compose** - Required for running PostgreSQL database
+- Git
+- Make
+
+> **Note:** This application requires PostgreSQL (uses `ArrayField`). Docker is the easiest 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 installation: if you have rdkit installed on your system globally with a different version of python, the installation will try to link against that and subsequent calls fail. Only option remove global rdkit and rerun sync.
+
+---
+
+The frontend requires `pnpm` to correctly display in development.
+[Install it here](https://pnpm.io/installation).
+
+### 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
+```
+
+This will start the css-watcher as well as the django-development server,
+The application will be available at `http://localhost:8000`.
+
+**Note:** The development server automatically starts a CSS watcher (`pnpm run dev`) alongside the Django server to rebuild CSS files when changes are detected. This ensures your styles are always up-to-date during development.
+
+#### 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 build         # Build frontend assets and collect static files
+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 +57,45 @@ 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",
+                "epdb.context_processors.package_context",
             ],
         },
     },
 ]
 
-WSGI_APPLICATION = 'envipath.wsgi.application'
+ALLOWED_HTML_TAGS = {"b", "i", "u", "br", "em", "mark", "p", "s", "strong"}
+
+WSGI_APPLICATION = "envipath.wsgi.application"
 
 # Database
 # https://docs.djangoproject.com/en/4.2/ref/settings/#databases
@@ -98,11 +103,11 @@ 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 +115,87 @@ 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 +203,8 @@ 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 +217,7 @@ LOGGING = {
             "level": "DEBUG",  # Or higher
             "class": "logging.FileHandler",
             "filename": os.path.join(LOG_DIR, "debug.log"),
-            "formatter": "simple"
+            "formatter": "simple",
         },
     },
     "loggers": {
@@ -229,72 +225,67 @@ 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 +293,10 @@ 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 +305,70 @@ 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/",
+    "/terms",
+    "/privacy",
+    "/cookie-policy",
+    "/about",
+    "/contact",
+    "/jobs",
+    "/cite",
+    "/legal",
 ]
 
 # 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(",")
+
+# Site ID 10 -> beta.envipath.org
+MATOMO_SITE_ID = os.environ.get("MATOMO_SITE_ID", "10")

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

@@ -7,6 +7,7 @@ from .models import (
     GroupPackagePermission,
     Package,
     MLRelativeReasoning,
+    EnviFormer,
     Compound,
     CompoundStructure,
     SimpleAmbitRule,
@@ -16,12 +17,16 @@ from .models import (
     Node,
     Edge,
     Scenario,
-    Setting
+    Setting,
+    ExternalDatabase,
+    ExternalIdentifier,
+    JobLog,
+    License,
 )
 
 
 class UserAdmin(admin.ModelAdmin):
-    pass
+    list_display = ["username", "email", "is_active"]
 
 
 class UserPackagePermissionAdmin(admin.ModelAdmin):
@@ -36,17 +41,32 @@ class GroupPackagePermissionAdmin(admin.ModelAdmin):
     pass
 
 
+class JobLogAdmin(admin.ModelAdmin):
+    pass
+
+
 class EPAdmin(admin.ModelAdmin):
-    search_fields = ['name', 'description']
+    search_fields = ["name", "description"]
+    list_display = ["name", "url", "created"]
+    ordering = ["-created"]
 
 
 class PackageAdmin(EPAdmin):
     pass
 
+
 class MLRelativeReasoningAdmin(EPAdmin):
     pass
 
 
+class EnviFormerAdmin(EPAdmin):
+    pass
+
+
+class LicenseAdmin(admin.ModelAdmin):
+    list_display = ["cc_string", "link", "image_link"]
+
+
 class CompoundAdmin(EPAdmin):
     pass
 
@@ -87,12 +107,23 @@ class SettingAdmin(EPAdmin):
     pass
 
 
+class ExternalDatabaseAdmin(admin.ModelAdmin):
+    pass
+
+
+class ExternalIdentifierAdmin(admin.ModelAdmin):
+    pass
+
+
 admin.site.register(User, UserAdmin)
 admin.site.register(UserPackagePermission, UserPackagePermissionAdmin)
 admin.site.register(Group, GroupAdmin)
 admin.site.register(GroupPackagePermission, GroupPackagePermissionAdmin)
+admin.site.register(JobLog, JobLogAdmin)
 admin.site.register(Package, PackageAdmin)
 admin.site.register(MLRelativeReasoning, MLRelativeReasoningAdmin)
+admin.site.register(EnviFormer, EnviFormerAdmin)
+admin.site.register(License, LicenseAdmin)
 admin.site.register(Compound, CompoundAdmin)
 admin.site.register(CompoundStructure, CompoundStructureAdmin)
 admin.site.register(SimpleAmbitRule, SimpleAmbitRuleAdmin)
@@ -103,3 +134,5 @@ 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/context_processors.py

@@ -0,0 +1,32 @@
+"""
+Context processors for enviPy application.
+
+Context processors automatically make variables available to all templates.
+"""
+
+from .logic import PackageManager
+from .models import Package
+
+
+def package_context(request):
+    """
+    Provides package data for the search modal which is included globally
+    in framework_modern.html.
+
+    Returns:
+        dict: Context dictionary with reviewed and unreviewed packages
+    """
+    current_user = request.user
+
+    reviewed_package_qs = PackageManager.get_reviewed_packages()
+
+    unreviewed_package_qs = Package.objects.none()
+
+    # Only get user-specific packages if user is authenticated
+    if current_user.is_authenticated:
+        unreviewed_package_qs = PackageManager.get_all_readable_packages(current_user)
+
+    return {
+        "reviewed_packages": reviewed_package_qs,
+        "unreviewed_packages": unreviewed_package_qs,
+    }

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 +5,55 @@ 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,
+    License,
+)
 
 
 class Command(BaseCommand):
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "-ol", "--only-licenses", action="store_true", help="Only create licenses."
+        )
 
     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 +66,20 @@ 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()
@@ -60,19 +89,32 @@ class Command(BaseCommand):
 
         return anon, admin, g, user0
 
+    def create_licenses(self):
+        """Create the six default licenses supported by enviPath"""
+        cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
+        for cc_string in cc_strings:
+            if not License.objects.filter(cc_string=cc_string).exists():
+                new_license = License()
+                new_license.cc_string = cc_string
+                new_license.link = f"https://creativecommons.org/licenses/{cc_string}/4.0/"
+                new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
+                new_license.save()
+
     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
@@ -84,57 +126,58 @@ 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):
+        # Create licenses
+        self.create_licenses()
+        if options.get("only_licenses", False):
+            return
         # Create users
         anon, admin, g, user0 = self.create_users()
 
@@ -142,20 +185,24 @@ 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 +218,28 @@ 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 +1,119 @@
+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] FOR MLRR ONLY: -r [rule_packages]
+                                        OPTIONAL: -e [eval_packages] -t threshold`
+    For example, to train both EnviFormer and MLRelativeReasoning on BBD and SOIL and evaluate them on SLUDGE with a
+    threshold of 0.6, the below command would be used:
+    `python manage.py create_ml_models enviformer mlrr -d bbd soil -e sludge -t 0.6
+    """
+
+    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=[],
+        )
+        parser.add_argument(
+            "-t",
+            "--threshold",
+            type=float,
+            help="Model prediction threshold",
+            default=0.5,
+        )
+
+    @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']}\n"
+              f"Data packages: {options['data_packages']}\n"
+              f"Rule Packages (only for MLRR): {options['rule_packages']}\n"
+              f"Eval Packages: {options['eval_packages']}\n"
+              f"Threshold: {options['threshold']:.2f}")
+        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=options['threshold'],
+                    name=f"EnviFormer - {', '.join(options['data_packages'])} - T{options['threshold']:.2f}",
+                    description=f"EnviFormer transformer trained on {options['data_packages']} "
+                                f"evaluated on {options['eval_packages']}.",
+                )
+            elif model_name == "mlrr":
+                model = MLRelativeReasoning.create(
+                    package=pack,
+                    rule_packages=rule_packages,
+                    data_packages=data_packages,
+                    eval_packages=eval_packages,
+                    threshold=options['threshold'],
+                    name=f"ECC - {', '.join(options['data_packages'])} - T{options['threshold']:.2f}",
+                    description=f"ML Relative Reasoning trained on {options['data_packages']} with rules from "
+                                f"{options['rule_packages']} and evaluated on {options['eval_packages']}.",
+                )
+            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(False, eval_packages=eval_packages)
+            print(f"Saving {model_name}")
+            model.save()

epdb/management/commands/dump_enviformer.py

@@ -0,0 +1,59 @@
+import json
+import os
+import tarfile
+from tempfile import TemporaryDirectory
+
+from django.conf import settings as s
+from django.core.management.base import BaseCommand
+from django.db import transaction
+
+from epdb.models import EnviFormer
+
+
+class Command(BaseCommand):
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "model",
+            type=str,
+            help="Model UUID of the Model to Dump",
+        )
+        parser.add_argument("--output", type=str)
+
+    def package_dict_and_folder(self, dict_data, folder_path, output_path):
+        with TemporaryDirectory() as tmpdir:
+            dict_filename = os.path.join(tmpdir, "data.json")
+
+            with open(dict_filename, "w", encoding="utf-8") as f:
+                json.dump(dict_data, f, indent=2)
+
+            with tarfile.open(output_path, "w:gz") as tar:
+                tar.add(dict_filename, arcname="data.json")
+                tar.add(folder_path, arcname=os.path.basename(folder_path))
+
+            os.remove(dict_filename)
+
+    @transaction.atomic
+    def handle(self, *args, **options):
+        output = options["output"]
+
+        if os.path.exists(output):
+            raise ValueError(f"Output file {output} already exists")
+
+        model = EnviFormer.objects.get(uuid=options["model"])
+
+        data = {
+            "uuid": str(model.uuid),
+            "name": model.name,
+            "description": model.description,
+            "kv": model.kv,
+            "data_packages_uuids": [str(p.uuid) for p in model.data_packages.all()],
+            "eval_packages_uuids": [str(p.uuid) for p in model.data_packages.all()],
+            "threshold": model.threshold,
+            "eval_results": model.eval_results,
+            "multigen_eval": model.multigen_eval,
+            "model_status": model.model_status,
+        }
+
+        model_folder = os.path.join(s.MODEL_DIR, "enviformer", str(model.uuid))
+
+        self.package_dict_and_folder(data, model_folder, output)

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/load_enviformer.py

@@ -0,0 +1,81 @@
+import json
+import os
+import shutil
+import tarfile
+from tempfile import TemporaryDirectory
+
+from django.conf import settings as s
+from django.core.management.base import BaseCommand
+from django.db import transaction
+
+from epdb.models import EnviFormer, Package
+
+
+class Command(BaseCommand):
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "input",
+            type=str,
+            help=".tar.gz file containing the Model dump.",
+        )
+        parser.add_argument(
+            "package",
+            type=str,
+            help="Package UUID where the Model should be loaded to.",
+        )
+
+    def read_dict_and_folder_from_archive(self, archive_path, extract_to="extracted_folder"):
+        with tarfile.open(archive_path, "r:gz") as tar:
+            tar.extractall(extract_to)
+
+            dict_path = os.path.join(extract_to, "data.json")
+
+            if not os.path.exists(dict_path):
+                raise FileNotFoundError("data.json not found in the archive.")
+
+            with open(dict_path, "r", encoding="utf-8") as f:
+                data_dict = json.load(f)
+
+            extracted_items = os.listdir(extract_to)
+            folders = [item for item in extracted_items if item != "data.json"]
+            folder_path = os.path.join(extract_to, folders[0]) if folders else None
+
+        return data_dict, folder_path
+
+    @transaction.atomic
+    def handle(self, *args, **options):
+        if not os.path.exists(options["input"]):
+            raise ValueError(f"Input file {options['input']} does not exist.")
+
+        target_package = Package.objects.get(uuid=options["package"])
+
+        with TemporaryDirectory() as tmpdir:
+            data, folder = self.read_dict_and_folder_from_archive(options["input"], tmpdir)
+
+            model = EnviFormer()
+            model.package = target_package
+            # model.uuid = data["uuid"]
+            model.name = data["name"]
+            model.description = data["description"]
+            model.kv = data["kv"]
+            model.threshold = float(data["threshold"])
+            model.eval_results = data["eval_results"]
+            model.multigen_eval = data["multigen_eval"]
+            model.model_status = data["model_status"]
+            model.save()
+
+            for p_uuid in data["data_packages_uuids"]:
+                p = Package.objects.get(uuid=p_uuid)
+                model.data_packages.add(p)
+
+            for p_uuid in data["eval_packages_uuids"]:
+                p = Package.objects.get(uuid=p_uuid)
+                model.eval_packages.add(p)
+
+            target_folder = os.path.join(s.MODEL_DIR, "enviformer", str(model.uuid))
+
+            shutil.copytree(folder, target_folder)
+            os.rename(
+                os.path.join(s.MODEL_DIR, "enviformer", str(model.uuid), f"{data['uuid']}.ckpt"),
+                os.path.join(s.MODEL_DIR, "enviformer", str(model.uuid), f"{model.uuid}.ckpt"),
+            )

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/management/commands/update_job_logs.py

@@ -0,0 +1,38 @@
+from datetime import date, timedelta
+
+from django.core.management.base import BaseCommand
+from django.db import transaction
+
+from epdb.models import JobLog
+
+
+class Command(BaseCommand):
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "--cleanup",
+            type=int,
+            default=None,
+            help="Remove all logs older than this number of days. Default is None, which does not remove any logs.",
+        )
+
+    @transaction.atomic
+    def handle(self, *args, **options):
+        if options["cleanup"] is not None:
+            cleanup_dt = date.today() - timedelta(days=options["cleanup"])
+            print(JobLog.objects.filter(created__lt=cleanup_dt).delete())
+
+        logs = JobLog.objects.filter(status="INITIAL")
+        print(f"Found {logs.count()} logs to update")
+        updated = 0
+        for log in logs:
+            res = log.check_for_update()
+            if res:
+                updated += 1
+
+        print(f"Updated {updated} logs")
+
+        from django.db.models import Count
+
+        qs = JobLog.objects.values("status").annotate(total=Count("status"))
+        for r in qs:
+            print(r["status"], r["total"])

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/migrations/0009_joblog.py

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

epdb/migrations/0010_license_cc_string.py

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

epdb/migrations/0011_auto_20251111_1413.py

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

epdb/tasks.py

@@ -1,58 +1,154 @@
+import csv
+import io
 import logging
-from typing import Optional
+from typing import Any, Callable, List, Optional
+from uuid import uuid4
 
 from celery import shared_task
-from epdb.models import Pathway, Node, Edge, EPModel, Setting
+from celery.utils.functional import LRUCache
-from epdb.logic import SPathway
+from django.utils import timezone
 
+from epdb.logic import SPathway
+from epdb.models import Edge, EPModel, JobLog, Node, Package, Pathway, Rule, Setting, User
 
 logger = logging.getLogger(__name__)
+ML_CACHE = LRUCache(3)  # Cache the three most recent ML models to reduce load times.
 
 
-@shared_task(queue='background')
+def get_ml_model(model_pk: int):
+    if model_pk not in ML_CACHE:
+        ML_CACHE[model_pk] = EPModel.objects.get(id=model_pk)
+    return ML_CACHE[model_pk]
+
+
+def dispatch_eager(user: "User", job: Callable, *args, **kwargs):
+    try:
+        x = job(*args, **kwargs)
+        log = JobLog()
+        log.user = user
+        log.task_id = uuid4()
+        log.job_name = job.__name__
+        log.status = "SUCCESS"
+        log.done_at = timezone.now()
+        log.task_result = str(x) if x else None
+        log.save()
+
+        return x
+    except Exception as e:
+        logger.exception(e)
+        raise e
+
+
+def dispatch(user: "User", job: Callable, *args, **kwargs):
+    try:
+        x = job.delay(*args, **kwargs)
+        log = JobLog()
+        log.user = user
+        log.task_id = x.task_id
+        log.job_name = job.__name__
+        log.status = "INITIAL"
+        log.save()
+
+        return x.result
+    except Exception as e:
+        logger.exception(e)
+        raise e
+
+
+@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)
+    mod = get_ml_model(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(bind=True, queue="model")
-def build_model(model_pk: int):
+def build_model(self, model_pk: int):
     mod = EPModel.objects.get(id=model_pk)
+
+    if JobLog.objects.filter(task_id=self.request.id).exists():
+        JobLog.objects.filter(task_id=self.request.id).update(status="RUNNING", task_result=mod.url)
+
+    try:
         mod.build_dataset()
         mod.build_model()
+    except Exception as e:
+        if JobLog.objects.filter(task_id=self.request.id).exists():
+            JobLog.objects.filter(task_id=self.request.id).update(
+                status="FAILED", task_result=mod.url
+            )
+
+        raise e
+
+    if JobLog.objects.filter(task_id=self.request.id).exists():
+        JobLog.objects.filter(task_id=self.request.id).update(status="SUCCESS", task_result=mod.url)
+
+    return mod.url
 
 
-@shared_task(queue='model')
+@shared_task(bind=True, queue="model")
-def evaluate_model(model_pk: int):
+def evaluate_model(self, model_pk: int, multigen: bool, package_pks: Optional[list] = None):
+    packages = None
+
+    if package_pks:
+        packages = Package.objects.filter(pk__in=package_pks)
+
     mod = EPModel.objects.get(id=model_pk)
-    mod.evaluate_model()
+    if JobLog.objects.filter(task_id=self.request.id).exists():
+        JobLog.objects.filter(task_id=self.request.id).update(status="RUNNING", task_result=mod.url)
+
+    try:
+        mod.evaluate_model(multigen, eval_packages=packages)
+    except Exception as e:
+        if JobLog.objects.filter(task_id=self.request.id).exists():
+            JobLog.objects.filter(task_id=self.request.id).update(
+                status="FAILED", task_result=mod.url
+            )
+
+        raise e
+
+    if JobLog.objects.filter(task_id=self.request.id).exists():
+        JobLog.objects.filter(task_id=self.request.id).update(status="SUCCESS", task_result=mod.url)
+
+    return mod.url
 
 
-@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(bind=True, queue="predict")
-def predict(pw_pk: int, pred_setting_pk: int, limit: Optional[int] = None, node_pk: Optional[int] = None) -> Pathway:
+def predict(
+    self,
+    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)
+    # If the setting has a model add/restore it from the cache
+    if setting.model is not None:
+        setting.model = get_ml_model(setting.model.pk)
 
-    pw.kv.update(**{'status': 'running'})
+    pw.kv.update(**{"status": "running"})
     pw.save()
 
+    if JobLog.objects.filter(task_id=self.request.id).exists():
+        JobLog.objects.filter(task_id=self.request.id).update(status="RUNNING", task_result=pw.url)
+
     try:
         # regular prediction
         if limit is not None:
@@ -74,12 +170,114 @@ 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()
+
+        if JobLog.objects.filter(task_id=self.request.id).exists():
+            JobLog.objects.filter(task_id=self.request.id).update(
+                status="FAILED", task_result=pw.url
+            )
+
         raise e
 
-    pw.kv.update(**{'status': 'completed'})
+    pw.kv.update(**{"status": "completed"})
     pw.save()
+
+    if JobLog.objects.filter(task_id=self.request.id).exists():
+        JobLog.objects.filter(task_id=self.request.id).update(status="SUCCESS", task_result=pw.url)
+
+    return pw.url
+
+
+@shared_task(bind=True, queue="background")
+def identify_missing_rules(
+    self,
+    pw_pks: List[int],
+    rule_package_pk: int,
+):
+    from utilities.misc import PathwayUtils
+
+    rules = Package.objects.get(pk=rule_package_pk).get_applicable_rules()
+
+    rows: List[Any] = []
+    header = [
+        "Package Name",
+        "Pathway Name",
+        "Educt Name",
+        "Educt SMILES",
+        "Reaction Name",
+        "Reaction SMIRKS",
+        "Triggered Rules",
+        "Reactant SMARTS",
+        "Product SMARTS",
+        "Product Names",
+        "Product SMILES",
+    ]
+
+    rows.append(header)
+
+    for pw in Pathway.objects.filter(pk__in=pw_pks):
+        pu = PathwayUtils(pw)
+
+        missing_rules = pu.find_missing_rules(rules)
+
+        package_name = pw.package.name
+        pathway_name = pw.name
+
+        for edge_url, rule_chain in missing_rules.items():
+            row: List[Any] = [package_name, pathway_name]
+            edge = Edge.objects.get(url=edge_url)
+            educts = edge.start_nodes.all()
+
+            for educt in educts:
+                row.append(educt.default_node_label.name)
+                row.append(educt.default_node_label.smiles)
+
+            row.append(edge.edge_label.name)
+            row.append(edge.edge_label.smirks())
+
+            rule_names = []
+            reactant_smarts = []
+            product_smarts = []
+
+            for r in rule_chain:
+                r = Rule.objects.get(url=r[0])
+                rule_names.append(r.name)
+
+                rs = r.reactants_smarts
+                if isinstance(rs, set):
+                    rs = list(rs)
+
+                ps = r.products_smarts
+                if isinstance(ps, set):
+                    ps = list(ps)
+
+                reactant_smarts.append(rs)
+                product_smarts.append(ps)
+
+            row.append(rule_names)
+            row.append(reactant_smarts)
+            row.append(product_smarts)
+
+            products = edge.end_nodes.all()
+            product_names = []
+            product_smiles = []
+
+            for product in products:
+                product_names.append(product.default_node_label.name)
+                product_smiles.append(product.default_node_label.smiles)
+
+            row.append(product_names)
+            row.append(product_smiles)
+
+            rows.append(row)
+
+    buffer = io.StringIO()
+
+    writer = csv.writer(buffer)
+    writer.writerows(rows)
+
+    buffer.seek(0)
+
+    return buffer.getvalue()

epdb/templatetags/envipytags.py

@@ -1,7 +1,21 @@
 from django import template
+from pydantic import AnyHttpUrl, ValidationError
+from pydantic.type_adapter import TypeAdapter
 
 register = template.Library()
 
+url_adapter = TypeAdapter(AnyHttpUrl)
+
+
 @register.filter
 def classname(obj):
     return obj.__class__.__name__
+
+
+@register.filter
+def is_url(value):
+    try:
+        url_adapter.validate_python(value)
+        return True
+    except ValidationError:
+        return False

epdb/tests.py

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

epdb/urls.py

@@ -1,99 +1,206 @@
-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"),
-
+    re_path(r"^predict$", v.predict_pathway, name="predict_pathway"),
-
     # User Detail
-    re_path(rf'^user/(?P<user_uuid>{UUID})', v.user, name='user'),
+    re_path(rf"^user/(?P<user_uuid>{UUID})", v.user, name="user"),
     # Group Detail
-    re_path(rf'^group/(?P<group_uuid>{UUID})$', 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"),
+    re_path(r"^jobs", v.jobs, name="jobs"),
     # OAuth Stuff
     path("o/userinfo/", v.userinfo, name="oauth_userinfo"),
+    # Static Pages
+    re_path(r"^terms$", v.static_terms_of_use, name="terms_of_use"),
+    re_path(r"^privacy$", v.static_privacy_policy, name="privacy_policy"),
+    re_path(r"^cookie-policy$", v.static_cookie_policy, name="cookie_policy"),
+    re_path(r"^about$", v.static_about_us, name="about_us"),
+    re_path(r"^contact$", v.static_contact_support, name="contact_support"),
+    re_path(r"^careers$", v.static_careers, name="careers"),
+    re_path(r"^cite$", v.static_cite, name="cite"),
+    re_path(r"^legal$", v.static_legal, name="legal"),
 ]

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

@@ -1,45 +1,52 @@
 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
 
 
-def migration(request):
+from rdkit import Chem
-    if request.method == 'GET':
+from rdkit.Chem.MolStandardize import rdMolStandardize
-        context = get_base_context(request)
 
-        if os.path.exists(s.BASE_DIR / 'fixtures' / 'migration_status_per_rule.json') and request.GET.get(
+logger = logging.getLogger(__name__)
-                "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'))
 
-            results = []
 
-            success = 0
+def normalize_smiles(smiles):
-            error = 0
+    m1 = Chem.MolFromSmiles(smiles)
-            total = 0
+    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)
 
-            num_keys = len(data.keys())
-            for i, bt_rule_name in enumerate(data.keys()):
-                print(f"{i + 1}/{num_keys}")
-                bt_rule = data[bt_rule_name]
-                smirks = bt_rule['smirks']
 
-                all_prods = set()
+def run_both_engines(SMILES, SMIRKS):
+    from envipy_ambit import apply
 
-                res = True
+    ambit_res = apply(SMIRKS, SMILES)
+    # ambit_res, ambit_errors = FormatConverter.sanitize_smiles([str(s) for s in ambit_res])
 
-                for comp, ambit_prod in zip(bt_rule['compounds'], bt_rule['products']):
+    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(comp['smiles'], smirks)
+    products = FormatConverter.apply(SMILES, SMIRKS)
 
     all_rdkit_prods = []
     for ps in products:
@@ -47,34 +54,70 @@ def migration(request):
             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
 
-                    ambit_smiles, ambit_errors = FormatConverter.sanitize_smiles(ambit_prod)
-                    rdkit_smiles, rdkit_errors = FormatConverter.sanitize_smiles(all_rdkit_prods)
 
-                    for x in ambit_smiles:
+def migration(request):
-                        all_prods.add(x)
+    if request.method == "GET":
+        context = get_base_context(request)
 
-                    # TODO mode "intersection"
+        if (
-                    # partial_res = (len(set(ambit_smiles).intersection(set(rdkit_smiles))) > 0) or (len(ambit_smiles) == 0)
+            os.path.exists(s.BASE_DIR / "fixtures" / "migration_status_per_rule.json")
-                    # FAILED (failures=37)
+            and request.GET.get("force") is None
+        ):
+            migration_status = json.load(
+                open(s.BASE_DIR / "fixtures" / "migration_status_per_rule.json")
+            )
+        else:
+            BBD = Package.objects.get(
+                url="http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1"
+            )
+            ALL_SMILES = [
+                cs.smiles
+                for cs in CompoundStructure.objects.filter(compound__package=BBD)
+            ]
+            RULES = SimpleAmbitRule.objects.filter(package=BBD)
 
-                    # TODO mode = "full ambit"
+            results = list()
-                    # partial_res = len(set(ambit_smiles).intersection(set(rdkit_smiles))) == len(ambit_smiles)
+            num_rules = len(RULES)
-                    # FAILED (failures=46)
+            success = 0
+            error = 0
+            total = 0
 
-                    # TODO mode = "equality"
+            for i, r in enumerate(RULES):
-                    partial_res = set(ambit_smiles) == set(rdkit_smiles)
+                logger.debug(f"\r{i + 1:03d}/{num_rules}")
-                    # FAILED (failures=69)
+                res = True
+                for smiles in ALL_SMILES:
+                    try:
+                        ambit_res, _, rdkit_res, _ = run_both_engines(smiles, r.smirks)
 
-                    res &= partial_res
+                        res &= set(ambit_res) == set(rdkit_res)
+                    except Exception as e:
+                        logger.error(e)
 
                 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),
                 }
-
-                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"])

package.json

@@ -0,0 +1,25 @@
+{
+  "name": "envipy",
+  "version": "1.0.0",
+  "private": true,
+  "description": "enviPath UI - Tailwind CSS + DaisyUI",
+  "scripts": {
+    "dev": "tailwindcss -i static/css/input.css -o static/css/output.css --watch=always",
+    "build": "tailwindcss -i static/css/input.css -o static/css/output.css --minify"
+  },
+  "devDependencies": {
+    "@tailwindcss/cli": "^4.1.16",
+    "@tailwindcss/postcss": "^4.1.16",
+    "daisyui": "^5.4.3",
+    "postcss": "^8.5.6",
+    "prettier": "^3.6.2",
+    "prettier-plugin-jinja-template": "^2.1.0",
+    "prettier-plugin-tailwindcss": "^0.7.1",
+    "tailwindcss": "^4.1.16"
+  },
+  "keywords": [
+    "django",
+    "tailwindcss",
+    "daisyui"
+  ]
+}

pnpm-lock.yaml

@@ -0,0 +1,740 @@
+lockfileVersion: '9.0'
+
+settings:
+  autoInstallPeers: true
+  excludeLinksFromLockfile: false
+
+importers:
+
+  .:
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+        version: 4.1.16
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+        version: 4.1.16
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+        version: 5.4.3
+      postcss:
+        specifier: ^8.5.6
+        version: 8.5.6
+      prettier:
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+        version: 3.6.2
+      prettier-plugin-jinja-template:
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+        version: 2.1.0(prettier@3.6.2)
+      prettier-plugin-tailwindcss:
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+        version: 0.7.1(prettier@3.6.2)
+      tailwindcss:
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+        version: 4.1.16
+
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+    hasBin: true
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+      - '@emnapi/runtime'
+      - '@tybys/wasm-util'
+      - '@emnapi/wasi-threads'
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+
+  lightningcss-win32-x64-msvc@1.30.2:
+    resolution: {integrity: sha512-5g1yc73p+iAkid5phb4oVFMB45417DkRevRbt/El/gKXJk4jid+vPFF/AXbxn05Aky8PapwzZrdJShv5C0avjw==}
+    engines: {node: '>= 12.0.0'}
+    cpu: [x64]
+    os: [win32]
+
+  lightningcss@1.30.2:
+    resolution: {integrity: sha512-utfs7Pr5uJyyvDETitgsaqSyjCb2qNRAtuqUeWIAKztsOYdcACf2KtARYXg2pSvhkt+9NfoaNY7fxjl6nuMjIQ==}
+    engines: {node: '>= 12.0.0'}
+
+  magic-string@0.30.21:
+    resolution: {integrity: sha512-vd2F4YUyEXKGcLHoq+TEyCjxueSeHnFxyyjNp80yg0XV4vUhnDer/lvvlqM/arB5bXQN5K2/3oinyCRyx8T2CQ==}
+
+  micromatch@4.0.8:
+    resolution: {integrity: sha512-PXwfBhYu0hBCPw8Dn0E+WDYb7af3dSLVWKi3HGv84IdF4TyFoC0ysxFd0Goxw7nSv4T/PzEJQxsYsEiFCKo2BA==}
+    engines: {node: '>=8.6'}
+
+  mri@1.2.0:
+    resolution: {integrity: sha512-tzzskb3bG8LvYGFF/mDTpq3jpI6Q9wc3LEmBaghu+DdCssd1FakN7Bc0hVNmEyGq1bq3RgfkCb3cmQLpNPOroA==}
+    engines: {node: '>=4'}
+
+  nanoid@3.3.11:
+    resolution: {integrity: sha512-N8SpfPUnUp1bK+PMYW8qSWdl9U+wwNWI4QKxOYDy9JAro3WMX7p2OeVRF9v+347pnakNevPmiHhNmZ2HbFA76w==}
+    engines: {node: ^10 || ^12 || ^13.7 || ^14 || >=15.0.1}
+    hasBin: true
+
+  node-addon-api@7.1.1:
+    resolution: {integrity: sha512-5m3bsyrjFWE1xf7nz7YXdN4udnVtXK6/Yfgn5qnahL6bCkf2yKt4k3nuTKAtT4r3IG8JNR2ncsIMdZuAzJjHQQ==}
+
+  picocolors@1.1.1:
+    resolution: {integrity: sha512-xceH2snhtb5M9liqDsmEw56le376mTZkEX/jEb/RxNFyegNul7eNslCXP9FDj/Lcu0X8KEyMceP2ntpaHrDEVA==}
+
+  picomatch@2.3.1:
+    resolution: {integrity: sha512-JU3teHTNjmE2VCGFzuY8EXzCDVwEqB2a8fsIvwaStHhAWJEeVd1o1QD80CU6+ZdEXXSLbSsuLwJjkCBWqRQUVA==}
+    engines: {node: '>=8.6'}
+
+  postcss@8.5.6:
+    resolution: {integrity: sha512-3Ybi1tAuwAP9s0r1UQ2J4n5Y0G05bJkpUIO0/bI9MhwmD70S5aTWbXGBwxHrelT+XM1k6dM0pk+SwNkpTRN7Pg==}
+    engines: {node: ^10 || ^12 || >=14}
+
+  prettier-plugin-jinja-template@2.1.0:
+    resolution: {integrity: sha512-mzoCp2Oy9BDSug80fw3B3J4n4KQj1hRvoQOL1akqcDKBb5nvYxrik9zUEDs4AEJ6nK7QDTGoH0y9rx7AlnQ78Q==}
+    peerDependencies:
+      prettier: ^3.0.0
+
+  prettier-plugin-tailwindcss@0.7.1:
+    resolution: {integrity: sha512-Bzv1LZcuiR1Sk02iJTS1QzlFNp/o5l2p3xkopwOrbPmtMeh3fK9rVW5M3neBQzHq+kGKj/4LGQMTNcTH4NGPtQ==}
+    engines: {node: '>=20.19'}
+    peerDependencies:
+      '@ianvs/prettier-plugin-sort-imports': '*'
+      '@prettier/plugin-hermes': '*'
+      '@prettier/plugin-oxc': '*'
+      '@prettier/plugin-pug': '*'
+      '@shopify/prettier-plugin-liquid': '*'
+      '@trivago/prettier-plugin-sort-imports': '*'
+      '@zackad/prettier-plugin-twig': '*'
+      prettier: ^3.0
+      prettier-plugin-astro: '*'
+      prettier-plugin-css-order: '*'
+      prettier-plugin-jsdoc: '*'
+      prettier-plugin-marko: '*'
+      prettier-plugin-multiline-arrays: '*'
+      prettier-plugin-organize-attributes: '*'
+      prettier-plugin-organize-imports: '*'
+      prettier-plugin-sort-imports: '*'
+      prettier-plugin-svelte: '*'
+    peerDependenciesMeta:
+      '@ianvs/prettier-plugin-sort-imports':
+        optional: true
+      '@prettier/plugin-hermes':
+        optional: true
+      '@prettier/plugin-oxc':
+        optional: true
+      '@prettier/plugin-pug':
+        optional: true
+      '@shopify/prettier-plugin-liquid':
+        optional: true
+      '@trivago/prettier-plugin-sort-imports':
+        optional: true
+      '@zackad/prettier-plugin-twig':
+        optional: true
+      prettier-plugin-astro:
+        optional: true
+      prettier-plugin-css-order:
+        optional: true
+      prettier-plugin-jsdoc:
+        optional: true
+      prettier-plugin-marko:
+        optional: true
+      prettier-plugin-multiline-arrays:
+        optional: true
+      prettier-plugin-organize-attributes:
+        optional: true
+      prettier-plugin-organize-imports:
+        optional: true
+      prettier-plugin-sort-imports:
+        optional: true
+      prettier-plugin-svelte:
+        optional: true
+
+  prettier@3.6.2:
+    resolution: {integrity: sha512-I7AIg5boAr5R0FFtJ6rCfD+LFsWHp81dolrFD8S79U9tb8Az2nGrJncnMSnys+bpQJfRUzqs9hnA81OAA3hCuQ==}
+    engines: {node: '>=14'}
+    hasBin: true
+
+  source-map-js@1.2.1:
+    resolution: {integrity: sha512-UXWMKhLOwVKb728IUtQPXxfYU+usdybtUrK/8uGE8CQMvrhOpwvzDBwj0QhSL7MQc7vIsISBG8VQ8+IDQxpfQA==}
+    engines: {node: '>=0.10.0'}
+
+  tailwindcss@4.1.16:
+    resolution: {integrity: sha512-pONL5awpaQX4LN5eiv7moSiSPd/DLDzKVRJz8Q9PgzmAdd1R4307GQS2ZpfiN7ZmekdQrfhZZiSE5jkLR4WNaA==}
+
+  tapable@2.3.0:
+    resolution: {integrity: sha512-g9ljZiwki/LfxmQADO3dEY1CbpmXT5Hm2fJ+QaGKwSXUylMybePR7/67YW7jOrrvjEgL1Fmz5kzyAjWVWLlucg==}
+    engines: {node: '>=6'}
+
+  to-regex-range@5.0.1:
+    resolution: {integrity: sha512-65P7iz6X5yEr1cwcgvQxbbIw7Uk3gOy5dIdtZ4rDveLqhrdJP+Li/Hx6tyK0NEb+2GCyneCMJiGqrADCSNk8sQ==}
+    engines: {node: '>=8.0'}
+
+snapshots:
+
+  '@alloc/quick-lru@5.2.0': {}
+
+  '@jridgewell/gen-mapping@0.3.13':
+    dependencies:
+      '@jridgewell/sourcemap-codec': 1.5.5
+      '@jridgewell/trace-mapping': 0.3.31
+
+  '@jridgewell/remapping@2.3.5':
+    dependencies:
+      '@jridgewell/gen-mapping': 0.3.13
+      '@jridgewell/trace-mapping': 0.3.31
+
+  '@jridgewell/resolve-uri@3.1.2': {}
+
+  '@jridgewell/sourcemap-codec@1.5.5': {}
+
+  '@jridgewell/trace-mapping@0.3.31':
+    dependencies:
+      '@jridgewell/resolve-uri': 3.1.2
+      '@jridgewell/sourcemap-codec': 1.5.5
+
+  '@parcel/watcher-android-arm64@2.5.1':
+    optional: true
+
+  '@parcel/watcher-darwin-arm64@2.5.1':
+    optional: true
+
+  '@parcel/watcher-darwin-x64@2.5.1':
+    optional: true
+
+  '@parcel/watcher-freebsd-x64@2.5.1':
+    optional: true
+
+  '@parcel/watcher-linux-arm-glibc@2.5.1':
+    optional: true
+
+  '@parcel/watcher-linux-arm-musl@2.5.1':
+    optional: true
+
+  '@parcel/watcher-linux-arm64-glibc@2.5.1':
+    optional: true
+
+  '@parcel/watcher-linux-arm64-musl@2.5.1':
+    optional: true
+
+  '@parcel/watcher-linux-x64-glibc@2.5.1':
+    optional: true
+
+  '@parcel/watcher-linux-x64-musl@2.5.1':
+    optional: true
+
+  '@parcel/watcher-win32-arm64@2.5.1':
+    optional: true
+
+  '@parcel/watcher-win32-ia32@2.5.1':
+    optional: true
+
+  '@parcel/watcher-win32-x64@2.5.1':
+    optional: true
+
+  '@parcel/watcher@2.5.1':
+    dependencies:
+      detect-libc: 1.0.3
+      is-glob: 4.0.3
+      micromatch: 4.0.8
+      node-addon-api: 7.1.1
+    optionalDependencies:
+      '@parcel/watcher-android-arm64': 2.5.1
+      '@parcel/watcher-darwin-arm64': 2.5.1
+      '@parcel/watcher-darwin-x64': 2.5.1
+      '@parcel/watcher-freebsd-x64': 2.5.1
+      '@parcel/watcher-linux-arm-glibc': 2.5.1
+      '@parcel/watcher-linux-arm-musl': 2.5.1
+      '@parcel/watcher-linux-arm64-glibc': 2.5.1
+      '@parcel/watcher-linux-arm64-musl': 2.5.1
+      '@parcel/watcher-linux-x64-glibc': 2.5.1
+      '@parcel/watcher-linux-x64-musl': 2.5.1
+      '@parcel/watcher-win32-arm64': 2.5.1
+      '@parcel/watcher-win32-ia32': 2.5.1
+      '@parcel/watcher-win32-x64': 2.5.1
+
+  '@tailwindcss/cli@4.1.16':
+    dependencies:
+      '@parcel/watcher': 2.5.1
+      '@tailwindcss/node': 4.1.16
+      '@tailwindcss/oxide': 4.1.16
+      enhanced-resolve: 5.18.3
+      mri: 1.2.0
+      picocolors: 1.1.1
+      tailwindcss: 4.1.16
+
+  '@tailwindcss/node@4.1.16':
+    dependencies:
+      '@jridgewell/remapping': 2.3.5
+      enhanced-resolve: 5.18.3
+      jiti: 2.6.1
+      lightningcss: 1.30.2
+      magic-string: 0.30.21
+      source-map-js: 1.2.1
+      tailwindcss: 4.1.16
+
+  '@tailwindcss/oxide-android-arm64@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-darwin-arm64@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-darwin-x64@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-freebsd-x64@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-linux-arm-gnueabihf@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-linux-arm64-gnu@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-linux-arm64-musl@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-linux-x64-gnu@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-linux-x64-musl@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-wasm32-wasi@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-win32-arm64-msvc@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-win32-x64-msvc@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide@4.1.16':
+    optionalDependencies:
+      '@tailwindcss/oxide-android-arm64': 4.1.16
+      '@tailwindcss/oxide-darwin-arm64': 4.1.16
+      '@tailwindcss/oxide-darwin-x64': 4.1.16
+      '@tailwindcss/oxide-freebsd-x64': 4.1.16
+      '@tailwindcss/oxide-linux-arm-gnueabihf': 4.1.16
+      '@tailwindcss/oxide-linux-arm64-gnu': 4.1.16
+      '@tailwindcss/oxide-linux-arm64-musl': 4.1.16
+      '@tailwindcss/oxide-linux-x64-gnu': 4.1.16
+      '@tailwindcss/oxide-linux-x64-musl': 4.1.16
+      '@tailwindcss/oxide-wasm32-wasi': 4.1.16
+      '@tailwindcss/oxide-win32-arm64-msvc': 4.1.16
+      '@tailwindcss/oxide-win32-x64-msvc': 4.1.16
+
+  '@tailwindcss/postcss@4.1.16':
+    dependencies:
+      '@alloc/quick-lru': 5.2.0
+      '@tailwindcss/node': 4.1.16
+      '@tailwindcss/oxide': 4.1.16
+      postcss: 8.5.6
+      tailwindcss: 4.1.16
+
+  braces@3.0.3:
+    dependencies:
+      fill-range: 7.1.1
+
+  daisyui@5.4.3: {}
+
+  detect-libc@1.0.3: {}
+
+  detect-libc@2.1.2: {}
+
+  enhanced-resolve@5.18.3:
+    dependencies:
+      graceful-fs: 4.2.11
+      tapable: 2.3.0
+
+  fill-range@7.1.1:
+    dependencies:
+      to-regex-range: 5.0.1
+
+  graceful-fs@4.2.11: {}
+
+  is-extglob@2.1.1: {}
+
+  is-glob@4.0.3:
+    dependencies:
+      is-extglob: 2.1.1
+
+  is-number@7.0.0: {}
+
+  jiti@2.6.1: {}
+
+  lightningcss-android-arm64@1.30.2:
+    optional: true
+
+  lightningcss-darwin-arm64@1.30.2:
+    optional: true
+
+  lightningcss-darwin-x64@1.30.2:
+    optional: true
+
+  lightningcss-freebsd-x64@1.30.2:
+    optional: true
+
+  lightningcss-linux-arm-gnueabihf@1.30.2:
+    optional: true
+
+  lightningcss-linux-arm64-gnu@1.30.2:
+    optional: true
+
+  lightningcss-linux-arm64-musl@1.30.2:
+    optional: true
+
+  lightningcss-linux-x64-gnu@1.30.2:
+    optional: true
+
+  lightningcss-linux-x64-musl@1.30.2:
+    optional: true
+
+  lightningcss-win32-arm64-msvc@1.30.2:
+    optional: true
+
+  lightningcss-win32-x64-msvc@1.30.2:
+    optional: true
+
+  lightningcss@1.30.2:
+    dependencies:
+      detect-libc: 2.1.2
+    optionalDependencies:
+      lightningcss-android-arm64: 1.30.2
+      lightningcss-darwin-arm64: 1.30.2
+      lightningcss-darwin-x64: 1.30.2
+      lightningcss-freebsd-x64: 1.30.2
+      lightningcss-linux-arm-gnueabihf: 1.30.2
+      lightningcss-linux-arm64-gnu: 1.30.2
+      lightningcss-linux-arm64-musl: 1.30.2
+      lightningcss-linux-x64-gnu: 1.30.2
+      lightningcss-linux-x64-musl: 1.30.2
+      lightningcss-win32-arm64-msvc: 1.30.2
+      lightningcss-win32-x64-msvc: 1.30.2
+
+  magic-string@0.30.21:
+    dependencies:
+      '@jridgewell/sourcemap-codec': 1.5.5
+
+  micromatch@4.0.8:
+    dependencies:
+      braces: 3.0.3
+      picomatch: 2.3.1
+
+  mri@1.2.0: {}
+
+  nanoid@3.3.11: {}
+
+  node-addon-api@7.1.1: {}
+
+  picocolors@1.1.1: {}
+
+  picomatch@2.3.1: {}
+
+  postcss@8.5.6:
+    dependencies:
+      nanoid: 3.3.11
+      picocolors: 1.1.1
+      source-map-js: 1.2.1
+
+  prettier-plugin-jinja-template@2.1.0(prettier@3.6.2):
+    dependencies:
+      prettier: 3.6.2
+
+  prettier-plugin-tailwindcss@0.7.1(prettier@3.6.2):
+    dependencies:
+      prettier: 3.6.2
+
+  prettier@3.6.2: {}
+
+  source-map-js@1.2.1: {}
+
+  tailwindcss@4.1.16: {}
+
+  tapable@2.3.0: {}
+
+  to-regex-range@5.0.1:
+    dependencies:
+      is-number: 7.0.0

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",
@@ -27,12 +27,103 @@ dependencies = [
     "scikit-learn>=1.6.1",
     "sentry-sdk[django]>=2.32.0",
     "setuptools>=80.8.0",
+    "nh3==0.3.2",
+    "polars==1.35.1",
 ]
 
 [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 = "v0.1.4" }
 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]+?))$"
+
+[tool.ruff.format]
+docstring-code-format = true
+
+# 4. Ignore `E402` (import violations) in all `__init__.py` files, and in selected subdirectories.
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["E402"]
+"**/{tests,docs,tools}/*" = ["E402"]
+
+[tool.poe.tasks]
+# Main tasks
+setup = { sequence = ["db-up", "migrate", "bootstrap"], help = "Complete setup: start database, run migrations, and bootstrap data" }
+dev = { shell = """
+# Start pnpm CSS watcher in background
+pnpm run dev &
+PNPM_PID=$!
+echo "Started CSS watcher (PID: $PNPM_PID)"
+
+# Cleanup function
+cleanup() {
+    echo "\nShutting down..."
+    if kill -0 $PNPM_PID 2>/dev/null; then
+        kill $PNPM_PID
+        echo "✓ CSS watcher stopped"
+    fi
+    if [ ! -z "${DJ_PID:-}" ] && kill -0 $DJ_PID 2>/dev/null; then
+        kill $DJ_PID
+        echo "✓ Django server stopped"
+    fi
+}
+
+# Set trap for cleanup
+trap cleanup EXIT INT TERM
+
+# Start Django dev server in background
+uv run python manage.py runserver &
+DJ_PID=$!
+
+# Wait for Django to finish
+wait $DJ_PID
+""", help = "Start the development server with CSS watcher", deps = ["db-up", "js-deps"] }
+build = { sequence = ["build-frontend", "collectstatic"], help = "Build frontend assets and collect static files" }
+
+# 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" }
+
+# Frontend tasks
+js-deps = { cmd = "pnpm install", help = "Install frontend dependencies" }
+
+# 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 = "uv run python manage.py migrate", help = "Run database migrations" }
+bootstrap = { shell = """
+echo "Bootstrapping initial data..."
+echo "This will take a bit ⏱️. Get yourself some coffee..."
+uv run 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 = "uv run python manage.py shell", help = "Open Django shell" }
+
+# Build tasks
+build-frontend = { cmd = "pnpm run build", help = "Build frontend assets using pnpm", deps = ["js-deps"] }
+collectstatic = { cmd = "uv run python manage.py collectstatic --noinput", help = "Collect static files for production", deps = ["build-frontend"] }

static/css/daisyui-theme.css

@@ -0,0 +1,84 @@
+/**
+ * DaisyUI Themes - Generated by Style Dictionary
+ * Theme mappings defined in tokens/daisyui-themes.json
+ */
+
+/* Light theme (default) */
+@plugin "daisyui/theme" {
+  name: "envipath";
+  default: true;
+  color-scheme: light;
+
+  --color-base-100: var(--color-neutral-50);
+  --color-base-200: var(--color-neutral-100);
+  --color-base-300: var(--color-neutral-200);
+  --color-base-content: var(--color-neutral-900);
+  --color-primary: var(--color-primary-500);
+  --color-primary-content: var(--color-primary-50);
+  --color-secondary: var(--color-secondary-500);
+  --color-secondary-content: var(--color-secondary-50);
+  --color-accent: var(--color-accent-500);
+  --color-accent-content: var(--color-accent-50);
+  --color-neutral: var(--color-neutral-950);
+  --color-neutral-content: var(--color-neutral-100);
+  --color-info: var(--color-info-500);
+  --color-info-content: var(--color-info-950);
+  --color-success: var(--color-success-500);
+  --color-success-content: var(--color-success-950);
+  --color-warning: var(--color-warning-500);
+  --color-warning-content: var(--color-warning-950);
+  --color-error: var(--color-error-500);
+  --color-error-content: var(--color-error-950);
+
+  /* border radius */
+  --radius-selector: 1rem;
+  --radius-field: 0.25rem;
+  --radius-box: 0.5rem;
+
+  /* base sizes */
+  --size-selector: 0.25rem;
+  --size-field: 0.25rem;
+
+  /* border size */
+  --border: 1px;
+
+  /* effects */
+  --depth: 1;
+  --noise: 0;
+}
+
+/* Dark theme (prefers-color-scheme: dark) */
+@plugin "daisyui/theme" {
+  name: "envipath-dark";
+  prefersdark: true;
+  color-scheme: dark;
+
+  --color-primary: var(--color-primary-400);
+  --color-primary-content: var(--color-neutral-950);
+  --color-secondary: var(--color-secondary-400);
+  --color-secondary-content: var(--color-neutral-950);
+  --color-accent: var(--color-primary-500);
+  --color-accent-content: var(--color-neutral-950);
+  --color-neutral: var(--color-neutral-300);
+  --color-neutral-content: var(--color-neutral-900);
+  --color-base-100: var(--color-neutral-900);
+  --color-base-200: var(--color-neutral-800);
+  --color-base-300: var(--color-neutral-700);
+  --color-base-content: var(--color-neutral-50);
+  --color-info: var(--color-primary-400);
+  --color-info-content: var(--color-neutral-950);
+  --color-success: var(--color-success-400);
+  --color-success-content: var(--color-neutral-950);
+  --color-warning: var(--color-warning-400);
+  --color-warning-content: var(--color-neutral-950);
+  --color-error: var(--color-error-400);
+  --color-error-content: var(--color-neutral-950);
+  --radius-selector: 1rem;
+  --radius-field: 0.25rem;
+  --radius-box: 0.5rem;
+  --size-selector: 0.25rem;
+  --size-field: 0.25rem;
+  --border: 1px;
+  --depth: 1;
+  --noise: 0;
+}

static/css/input.css

@@ -0,0 +1,36 @@
+@import "tailwindcss";
+
+/* fira-code-latin-wght-normal */
+@font-face {
+  font-family: 'Fira Code Variable';
+  font-style: normal;
+  font-display: swap;
+  font-weight: 300 700;
+  src: url(https://cdn.jsdelivr.net/fontsource/fonts/fira-code:vf@latest/latin-wght-normal.woff2) format('woff2-variations');
+  unicode-range: U+0000-00FF,U+0131,U+0152-0153,U+02BB-02BC,U+02C6,U+02DA,U+02DC,U+0304,U+0308,U+0329,U+2000-206F,U+20AC,U+2122,U+2191,U+2193,U+2212,U+2215,U+FEFF,U+FFFD;
+}
+
+/* inter-latin-wght-normal */
+@font-face {
+  font-family: 'Inter Variable';
+  font-style: normal;
+  font-display: swap;
+  font-weight: 100 900;
+  src: url(https://cdn.jsdelivr.net/fontsource/fonts/inter:vf@latest/latin-wght-normal.woff2) format('woff2-variations');
+  unicode-range: U+0000-00FF,U+0131,U+0152-0153,U+02BB-02BC,U+02C6,U+02DA,U+02DC,U+0304,U+0308,U+0329,U+2000-206F,U+20AC,U+2122,U+2191,U+2193,U+2212,U+2215,U+FEFF,U+FFFD;
+}
+
+
+/* Tell Tailwind where to find Django templates and Python files */
+@source "../../templates";
+
+/* Custom theme configuration - must come before plugins */
+@import "./theme.css";
+
+/* Import DaisyUI plugin */
+@plugin "daisyui" {
+  logs: true;
+  exclude: rootscrollgutter;
+}
+
+@import "./daisyui-theme.css";

static/css/theme.css

@@ -0,0 +1,111 @@
+/**
+ * Tailwind v4 Theme - Generated by Style Dictionary
+ * This creates Tailwind utility classes from design tokens
+ */
+
+@theme {
+  /* Colors */
+  --color-primary-50: oklch(0.98 0.02 201);
+  --color-primary-100: oklch(0.96 0.04 203);
+  --color-primary-200: oklch(0.92 0.08 205);
+  --color-primary-300: oklch(0.87 0.12 207);
+  --color-primary-400: oklch(0.80 0.13 212);
+  --color-primary-500: oklch(0.71 0.13 215);
+  --color-primary-600: oklch(0.61 0.11 222);
+  --color-primary-700: oklch(0.52 0.09 223);
+  --color-primary-800: oklch(0.45 0.08 224);
+  --color-primary-900: oklch(0.40 0.07 227);
+  --color-primary-950: oklch(0.30 0.05 230);
+  --color-secondary-50: oklch(0.98 0.02 166);
+  --color-secondary-100: oklch(0.95 0.05 163);
+  --color-secondary-200: oklch(0.90 0.09 164);
+  --color-secondary-300: oklch(0.85 0.13 165);
+  --color-secondary-400: oklch(0.77 0.15 163);
+  --color-secondary-500: oklch(0.70 0.15 162);
+  --color-secondary-600: oklch(0.60 0.13 163);
+  --color-secondary-700: oklch(0.51 0.10 166);
+  --color-secondary-800: oklch(0.43 0.09 167);
+  --color-secondary-900: oklch(0.38 0.07 169);
+  --color-secondary-950: oklch(0.26 0.05 173);
+  --color-success-50: oklch(0.98 0.02 156);
+  --color-success-100: oklch(0.96 0.04 157);
+  --color-success-200: oklch(0.93 0.08 156);
+  --color-success-300: oklch(0.87 0.14 154);
+  --color-success-400: oklch(0.80 0.18 152);
+  --color-success-500: oklch(0.72 0.19 150);
+  --color-success-600: oklch(0.63 0.17 149);
+  --color-success-700: oklch(0.53 0.14 150);
+  --color-success-800: oklch(0.45 0.11 151);
+  --color-success-900: oklch(0.39 0.09 153);
+  --color-success-950: oklch(0.27 0.06 153);
+  --color-warning-50: oklch(0.99 0.03 102);
+  --color-warning-100: oklch(0.97 0.07 103);
+  --color-warning-200: oklch(0.95 0.12 102);
+  --color-warning-300: oklch(0.91 0.17 98);
+  --color-warning-400: oklch(0.86 0.17 92);
+  --color-warning-500: oklch(0.80 0.16 86);
+  --color-warning-600: oklch(0.68 0.14 76);
+  --color-warning-700: oklch(0.55 0.12 66);
+  --color-warning-800: oklch(0.48 0.10 62);
+  --color-warning-900: oklch(0.42 0.09 58);
+  --color-warning-950: oklch(0.29 0.06 54);
+  --color-error-50: oklch(0.97 0.01 17);
+  --color-error-100: oklch(0.94 0.03 18);
+  --color-error-200: oklch(0.88 0.06 18);
+  --color-error-300: oklch(0.81 0.10 20);
+  --color-error-400: oklch(0.71 0.17 22);
+  --color-error-500: oklch(0.64 0.21 25);
+  --color-error-600: oklch(0.58 0.22 27);
+  --color-error-700: oklch(0.51 0.19 28);
+  --color-error-800: oklch(0.44 0.16 27);
+  --color-error-900: oklch(0.40 0.13 26);
+  --color-error-950: oklch(0.26 0.09 26);
+  --color-neutral-50: oklch(0.98 0.00 248);
+  --color-neutral-100: oklch(0.97 0.01 248);
+  --color-neutral-200: oklch(0.93 0.01 256);
+  --color-neutral-300: oklch(0.87 0.02 253);
+  --color-neutral-400: oklch(0.71 0.04 257);
+  --color-neutral-500: oklch(0.55 0.04 257);
+  --color-neutral-600: oklch(0.45 0.04 257);
+  --color-neutral-700: oklch(0.37 0.04 257);
+  --color-neutral-800: oklch(0.28 0.04 260);
+  --color-neutral-900: oklch(0.28 0.04 260);
+  --color-neutral-950: oklch(0.28 0.04 260);
+
+  /* Spacing */
+  --spacing-0: 0;
+  --spacing-1: 0.25rem;
+  --spacing-2: 0.5rem;
+  --spacing-3: 0.75rem;
+  --spacing-4: 1rem;
+  --spacing-5: 1.25rem;
+  --spacing-6: 1.5rem;
+  --spacing-7: 1.75rem;
+  --spacing-8: 2rem;
+  --spacing-10: 2.5rem;
+  --spacing-12: 3rem;
+  --spacing-16: 4rem;
+  --spacing-20: 5rem;
+  --spacing-24: 6rem;
+  --spacing-32: 8rem;
+  --spacing-40: 10rem;
+  --spacing-48: 12rem;
+  --spacing-56: 14rem;
+  --spacing-64: 16rem;
+
+  /* Typography */
+  --font-family-sans: 'Inter Variable', system-ui, -apple-system, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+  --font-family-mono: 'Fira Code Variable', 'Cascadia Code', 'Source Code Pro', Menlo, Consolas, monospace;
+  --font-family-base: 'Inter Variable', system-ui, -apple-system, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+  --font-size-xs: 0.75rem;
+  --font-size-sm: 0.875rem;
+  --font-size-base: 1rem;
+  --font-size-lg: 1.125rem;
+  --font-size-xl: 1.25rem;
+  --font-size-2xl: 1.5rem;
+  --font-size-3xl: 1.875rem;
+  --font-size-4xl: 2.25rem;
+  --font-size-5xl: 3rem;
+  --font-size-6xl: 3.75rem;
+  --font-size-7xl: 4.5rem;
+}

static/images/logo-long.svg

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+</svg>

static/js/discourse-api.js

@@ -0,0 +1,170 @@
+/**
+ * Discourse API Integration for enviPath Community
+ * Handles fetching topics from the Discourse forum API
+ */
+
+class DiscourseAPI {
+    constructor() {
+        this.baseUrl = 'https://community.envipath.org';
+        this.categoryId = 10; // Announcements category
+        this.limit = 3; // Number of topics to fetch
+    }
+
+    /**
+     * Fetch topics from Discourse API
+     * @param {number} limit - Number of topics to fetch
+     * @returns {Promise<Array>} Array of topic objects
+     */
+    async fetchTopics(limit = this.limit) {
+        try {
+            const url = `${this.baseUrl}/c/announcements/${this.categoryId}.json`;
+            const response = await fetch(url);
+
+            if (!response.ok) {
+                throw new Error(`HTTP error! status: ${response.status}`);
+            }
+
+            const data = await response.json();
+            return this.processTopics(data.topic_list.topics, limit);
+        } catch (error) {
+            console.error('Error fetching Discourse topics:', error);
+            return this.getFallbackTopics();
+        }
+    }
+
+    /**
+     * Process raw Discourse topics into standardized format
+     * @param {Array} topics - Raw topics from Discourse API
+     * @param {number} limit - Number of topics to return
+     * @returns {Array} Processed topics
+     */
+    processTopics(topics, limit) {
+        return topics
+            .slice(0, limit)
+            .map(topic => ({
+                id: topic.id,
+                title: topic.title,
+                excerpt: this.extractExcerpt(topic.excerpt),
+                url: `${this.baseUrl}/t/${topic.slug}/${topic.id}`,
+                replies: topic.reply_count,
+                views: topic.views,
+                created_at: topic.created_at,
+                category: 'Announcements',
+                category_id: this.categoryId,
+                author: topic.last_poster_username,
+                author_avatar: this.getAvatarUrl(topic.last_poster_username)
+            }))
+            .sort((a, b) => new Date(b.created_at) - new Date(a.created_at)); // Latest first
+    }
+
+    /**
+     * Extract excerpt from topic content
+     * @param {string} excerpt - Raw excerpt from Discourse
+     * @returns {string} Cleaned excerpt
+     */
+    extractExcerpt(excerpt) {
+        if (!excerpt) return 'Click to read more';
+
+        // Remove HTML tags and clean up; collapse whitespace; do not add manual ellipsis
+        return excerpt
+            .replace(/<[^>]*>/g, '') // Remove HTML tags
+            .replace(/&nbsp;/g, ' ') // Replace &nbsp; with spaces
+            .replace(/&amp;/g, '&') // Replace &amp; with &
+            .replace(/&lt;/g, '<') // Replace &lt; with <
+            .replace(/&gt;/g, '>') // Replace &gt; with >
+            .replace(/\s+/g, ' ') // Collapse all whitespace/newlines
+            .trim()
+    }
+
+    /**
+     * Get avatar URL for user
+     * @param {string} username - Username
+     * @returns {string} Avatar URL
+     */
+    getAvatarUrl(username) {
+        if (!username) return `${this.baseUrl}/letter_avatar_proxy/v4/letter/u/1.png`;
+        return `${this.baseUrl}/user_avatar/${this.baseUrl.replace('https://', '')}/${username}/40/1_1.png`;
+    }
+
+    /**
+     * Get fallback topics when API fails
+     * @returns {Array} Fallback topics
+     */
+    getFallbackTopics() {
+        return [
+            {
+                id: 110,
+                title: "enviPath Beta Update: Major Improvements to Prediction, Analysis & Collaboration!",
+                excerpt: "We're excited to announce major updates to the enviPath beta platform! This release includes significant improvements to our prediction algorithms, enhanced analysis tools, and new collaboration features that will make environmental biotransformation research more accessible and efficient.",
+                url: "https://community.envipath.org/t/envipath-beta-update-major-improvements-to-prediction-analysis-collaboration/110",
+                replies: 0,
+                views: 16,
+                created_at: "2025-09-23T00:00:00Z",
+                category: "Announcements",
+                category_id: 10,
+                author: "wicker",
+                author_avatar: "https://community.envipath.org/user_avatar/community.envipath.org/wicker/40/1_1.png"
+            }
+        ];
+    }
+
+    /**
+     * Format date for display
+     * @param {string} dateString - ISO date string
+     * @returns {string} Formatted date
+     */
+    formatDate(dateString) {
+        const date = new Date(dateString);
+        return date.toLocaleDateString();
+    }
+
+
+    /**
+     * Load topics and call render function
+     * @param {string} containerId - ID of container element
+     * @param {Function} renderCallback - Function to render topics
+     */
+    async loadTopics(containerId = 'community-news-container', renderCallback = null) {
+        const container = document.getElementById(containerId);
+        if (!container) {
+            console.error(`Container with ID '${containerId}' not found`);
+            return;
+        }
+
+        // Hide loading spinner
+        const loading = document.getElementById('loading');
+        if (loading) {
+            loading.style.display = 'none';
+        }
+
+        try {
+            const topics = await this.fetchTopics();
+
+            if (renderCallback && typeof renderCallback === 'function') {
+                renderCallback(topics);
+            } else {
+                // Default rendering - just log topics
+                console.log('Topics loaded:', topics);
+            }
+        } catch (error) {
+            console.error('Error loading topics:', error);
+            container.innerHTML = '<p class="text-neutral">No updates found. Head over to the <a href="https://community.envipath.org" target="_blank" class="link link-primary">community</a> to see the latest discussions.</p>';
+        }
+    }
+}
+
+// Export for use in other scripts
+window.DiscourseAPI = DiscourseAPI;
+
+// Auto-initialize if container exists
+document.addEventListener('DOMContentLoaded', function() {
+    if (document.getElementById('community-news-container')) {
+        const discourseAPI = new DiscourseAPI();
+        discourseAPI.loadTopics('community-news-container', function(topics) {
+            // This will be handled by the template's render function
+            if (window.renderDiscourseTopics) {
+                window.renderDiscourseTopics(topics);
+            }
+        });
+    }
+});

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']) + "'>";
 

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/collections/pathway.html

@@ -1,6 +1,6 @@
 {% if meta.can_edit %}
     <li>
-        <a role="button" data-toggle="modal" data-target="#predict_modal">
+        <a href="{{ meta.server_url }}/predict">
             <span class="glyphicon glyphicon-plus"></span> New Pathway</a>
     </li>
 {% endif %}

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">

templates/actions/objects/compound_structure.html

@@ -3,10 +3,18 @@
         <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>

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

@@ -22,6 +22,10 @@
             <i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as Image</a>
     </li>
 {% if meta.can_edit %}
+    <li>
+        <a class="button" data-toggle="modal" data-target="#identify_missing_rules_modal">
+            <i class="glyphicon glyphicon-question-sign"></i> Identify Missing Rules</a>
+    </li>
     <li role="separator" class="divider"></li>
     <li>
         <a class="button" data-toggle="modal" data-target="#edit_pathway_modal">
@@ -31,6 +35,10 @@
         <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>#}

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">

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>

templates/collections/joblog.html

@@ -0,0 +1,70 @@
+{% extends "framework.html" %}
+{% load static %}
+{% block content %}
+
+    <div class="panel-group" id="reviewListAccordion">
+        <div class="panel panel-default">
+            <div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
+                Jobs
+            </div>
+            <div class="panel-body">
+                <p>
+                    Job Logs Desc
+                </p>
+
+            </div>
+
+            <div class="panel panel-default panel-heading list-group-item" style="background-color:silver">
+                <h4 class="panel-title">
+                    <a id="job-accordion-link" data-toggle="collapse" data-parent="#job-accordion" href="#jobs">
+                        Jobs
+                    </a>
+                </h4>
+            </div>
+            <div id="jobs"
+                 class="panel-collapse collapse in">
+                <div class="panel-body list-group-item" id="job-content">
+                    <table class="table table-bordered table-hover">
+                        <tr style="background-color: rgba(0, 0, 0, 0.08);">
+                            <th scope="col">ID</th>
+                            <th scope="col">Name</th>
+                            <th scope="col">Status</th>
+                            <th scope="col">Queued</th>
+                            <th scope="col">Done</th>
+                            <th scope="col">Result</th>
+                        </tr>
+                        <tbody>
+                        {% for job in jobs %}
+                            <tr>
+                                <td>{{ job.task_id }}</td>
+                                <td>{{ job.job_name }}</td>
+                                <td>{{ job.status }}</td>
+                                <td>{{ job.created }}</td>
+                                <td>{{ job.done_at }}</td>
+                                {% if job.task_result and job.task_result|is_url == True %}
+                                    <td><a href="{{ job.task_result }}">Result</a></td>
+                                {% elif job.task_result %}
+                                    <td>{{ job.task_result|slice:"40" }}...</td>
+                                {% else %}
+                                    <td>Empty</td>
+                                {% endif %}
+                            </tr>
+                        {% endfor %}
+                        </tbody>
+                    </table>
+                </div>
+            </div>
+
+            <!-- Unreviewable objects such as User / Group / Setting -->
+            <ul class='list-group'>
+                {% for obj in objects %}
+                    {% if object_type == 'user' %}
+                        <a class="list-group-item" href="{{ obj.url }}">{{ obj.username }}</a>
+                    {% else %}
+                        <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
+                    {% endif %}
+                {% endfor %}
+            </ul>
+        </div>
+    </div>
+{% endblock content %}

templates/collections/objects_list.html

@@ -192,7 +192,7 @@
             <div class="panel-body list-group-item" id="ReviewedContent">
                 {% if object_type == 'package' %}
                 {% for obj in reviewed_objects %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}
                     <span class="glyphicon glyphicon-star" aria-hidden="true"
                           style="float:right" data-toggle="tooltip"
                           data-placement="top" title="" data-original-title="Reviewed">
@@ -201,7 +201,7 @@
                 {% endfor %}
                 {% else %}
                 {% for obj in reviewed_objects|slice:":50" %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}{# <i>({{ obj.package.name }})</i> #}
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}{# <i>({{ obj.package.name }})</i> #}
                     <span class="glyphicon glyphicon-star" aria-hidden="true"
                           style="float:right" data-toggle="tooltip"
                           data-placement="top" title="" data-original-title="Reviewed">
@@ -221,11 +221,11 @@
             <div class="panel-body list-group-item" id="UnreviewedContent">
                 {% if object_type == 'package' %}
                 {% for obj in unreviewed_objects %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
                 {% endfor %}
                 {% else %}
                 {% for obj in unreviewed_objects|slice:":50" %}
-                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
+                <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
                 {% endfor %}
                 {% endif %}
             </div>
@@ -236,9 +236,9 @@
         <ul class='list-group'>
             {% for obj in objects %}
             {% if object_type == 'user' %}
-            <a class="list-group-item" href="{{ obj.url }}">{{ obj.username }}</a>
+            <a class="list-group-item" href="{{ obj.url }}">{{ obj.username|safe }}</a>
             {% else %}
-            <a class="list-group-item" href="{{ obj.url }}">{{ obj.name }}</a>
+            <a class="list-group-item" href="{{ obj.url }}">{{ obj.name|safe }}</a>
             {% endif %}
             {% endfor %}
         </ul>

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

@@ -1,46 +1,68 @@
-<!DOCTYPE html>
+<!doctype html>
-<html>
+<html data-theme="envipath">
-{% load static %}
+  {% load static %}
-<head>
+  <head>
     <title>{{ title }}</title>
+    <meta name="csrf-token" content="{{ csrf_token }}" />
+    {# Favicon #}
+    <link
+      rel="shortcut icon"
+      type="image/png"
+      href="{% static 'images/favicon.ico' %}"
+    />
+
+    {# Tailwind CSS disabled for legacy Bootstrap framework #}
+    {# Pages using this framework will be migrated to framework_modern.html incrementally #}
+    {# <link href="{% static 'css/output.css' %}" rel="stylesheet" type="text/css"/> #}
+
+    {# Legacy Bootstrap 3.3.7 - scoped to .legacy-bootstrap #}
+    <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.1/jquery.min.js"></script>
+    <link
+      rel="stylesheet"
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+    />
+    <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"></script>
+    <script src="https://ajax.aspnetcdn.com/ajax/jquery.templates/beta1/jquery.tmpl.js"></script>
+    <link
+      href="https://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css"
+      rel="stylesheet"
+    />
+    <link
+      rel="stylesheet"
+      href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.7.3/css/bootstrap-select.min.css"
+    />
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.7.3/js/bootstrap-select.min.js"></script>
+    <script src="https://community.envipath.org/javascripts/embed-topics.js"></script>
+    <!-- CDN END -->
+
+    {# Bootstrap compatibility styles #}
     <style>
-        html, body {
+      /* Ensure proper viewport behavior */
+      html,
+      body {
         height: 100%; /* ensure body fills viewport */
         overflow-x: hidden; /* prevent horizontal scroll */
       }
     </style>
-    {# TODO use bundles from bootstrap 3.3.7 #}
+
-    <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.1/jquery.min.js"></script>
-    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css">
-    <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"></script>
-    <script src="https://ajax.aspnetcdn.com/ajax/jquery.templates/beta1/jquery.tmpl.js"></script>
-    <link href="https://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css" rel="stylesheet">
-    <link rel="stylesheet"
-          href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.7.3/css/bootstrap-select.min.css">
-    <script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.7.3/js/bootstrap-select.min.js"></script>
-    <script src="https://community.envipath.org/javascripts/embed-topics.js"></script>
-    <!-- CDN END -->
-    <meta name="csrf-token" content="{{ csrf_token }}">
     <script>
-        const csrftoken = document.querySelector('[name=csrf-token]').content;
+      const csrftoken = document.querySelector("[name=csrf-token]").content;
 
       // Setup CSRF header for all jQuery AJAX requests
       $.ajaxSetup({
-            beforeSend: function(xhr, settings) {
+        beforeSend: function (xhr, settings) {
           if (!/^(GET|HEAD|OPTIONS|TRACE)$/i.test(settings.type)) {
             xhr.setRequestHeader("X-CSRFToken", csrftoken);
           }
-            }
+        },
       });
     </script>
-    {# Favicon #}
+
-    <link rel="shortcut icon" type="image/png" href="{% static 'images/favicon.ico' %}"/>
     <!--    {# C3 CSS #}-->
     <!--    <link id="css-c3" href="{% static 'css/c3.css' %}" rel="stylesheet" type="text/css"/>-->
     <!--    {# EP CSS #}-->
     <!--    <link id="css-pps_white_general" href="{% static 'css/epp.css' %}" rel="stylesheet" type="text/css"/>-->
 
-
     {# General EP JS #}
     <script src="{% static 'js/pps.js' %}"></script>
     {# Modal Steps for Stepwise Modal Wizards #}
@@ -49,26 +71,33 @@
     {% if not debug %}
       <!-- Matomo -->
       <script>
-            var _paq = window._paq = window._paq || [];
+        var _paq = (window._paq = window._paq || []);
         /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
-            _paq.push(['trackPageView']);
+        _paq.push(["trackPageView"]);
-            _paq.push(['enableLinkTracking']);
+        _paq.push(["enableLinkTracking"]);
         (function () {
           var u = "//matomo.envipath.com/";
-                _paq.push(['setTrackerUrl', u + 'matomo.php']);
+          _paq.push(["setTrackerUrl", u + "matomo.php"]);
-                _paq.push(['setSiteId', '10']);
+          _paq.push(["setSiteId", "{{ meta.site_id }}"]);
-                var d = document, g = d.createElement('script'), s = d.getElementsByTagName('script')[0];
+          var d = document,
+            g = d.createElement("script"),
+            s = d.getElementsByTagName("script")[0];
           g.async = true;
-                g.src = u + 'matomo.js';
+          g.src = u + "matomo.js";
           s.parentNode.insertBefore(g, s);
         })();
       </script>
       <!-- End Matomo Code -->
     {% endif %}
-
+  </head>
-</head>
+  <body>
-<body>
+    <!-- Legacy Bootstrap navbar - isolated from Tailwind -->
-<nav class="navbar navbar-default navbar-inverse" style="border-radius:0px;" role="navigation">
+    <div class="legacy-bootstrap">
+      <nav
+        class="navbar navbar-default navbar-inverse"
+        style="border-radius:0px;"
+        role="navigation"
+      >
         <div class="container-fluid">
           <!-- Brand and toggle get grouped for better mobile display -->
           <div class="navbar-header navbar-header-framework">
@@ -79,96 +108,186 @@
             <!--                <span class="icon-bar"></span>-->
             <!--                <span class="icon-bar"></span>-->
             <!--            </button>-->
-            <a id="pictureLink" href="{{ meta.server_url }}" class="navbar-brand">
+            <a
-                <img id="image-logo-short-white.svg" src='{% static "/images/logo-short-white.svg" %}' width="100"
+              id="pictureLink"
-                     alt="enviPath">
+              href="{{ meta.server_url }}"
+              class="navbar-brand"
+            >
+              <img
+                id="image-logo-short-white.svg"
+                src="{% static "/images/logo-short-white.svg" %}"
+                width="100"
+                alt="enviPath"
+              />
             </a>
           </div>
 
           <!-- Collect the nav links, forms, and other content for toggling -->
-        <div class="collapse navbar-collapse collapse-framework navbar-collapse-framework" id="navbarCollapse">
+          <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="{{ meta.server_url }}/predict"> Predict Pathway </a>
-                        Predict Pathway
+              </li>
-                    </a>
+              {#                <li class="dropdown">#}
+              {#                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">Predict Pathway<b class="caret"></b></a>#}
+              {#                    <ul role="menu" class="dropdown-menu">#}
+              {#                        <li>#}
+              {#                            <a class="button" data-toggle="modal" data-target="#predict_modal">#}
+              {#                                <i class="	glyphicon glyphicon-tag"></i> Predict Pathway#}
+              {#                            </a>#}
+              {#                        </li>#}
+              {#                        <li>#}
+              {#                            <a class="button" data-toggle="modal" data-target="#batch_predict_modal">#}
+              {#                                <i class="	glyphicon glyphicon-tags"></i> Batch Prediction#}
+              {#                            </a>#}
+              {#                        </li>#}
+              {#                    </ul>#}
+              {#                </li>#}
+              <li>
+                <a href="{{ meta.server_url }}/package" id="packageLink"
+                  >Package</a
+                >
+              </li>
+              <li>
+                <a href="{{ meta.server_url }}/search" id="searchLink"
+                  >Search</a
+                >
+              </li>
+              <li>
+                <a href="{{ meta.server_url }}/model" id="modelLink"
+                  >Modelling</a
+                >
               </li>
-{#                <li class="dropdown">#}
-{#                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">Predict Pathway<b class="caret"></b></a>#}
-{#                    <ul role="menu" class="dropdown-menu">#}
-{#                        <li>#}
-{#                            <a class="button" data-toggle="modal" data-target="#predict_modal">#}
-{#                                <i class="	glyphicon glyphicon-tag"></i> Predict Pathway#}
-{#                            </a>#}
-{#                        </li>#}
-{#                        <li>#}
-{#                            <a class="button" data-toggle="modal" data-target="#batch_predict_modal">#}
-{#                                <i class="	glyphicon glyphicon-tags"></i> Batch Prediction#}
-{#                            </a>#}
-{#                        </li>#}
-{#                    </ul>#}
-{#                </li>#}
-                <li><a href="{{ meta.server_url }}/package" id="packageLink">Package</a></li>
-                <li><a href="{{ meta.server_url }}/search" id="searchLink">Search</a></li>
-                <li><a href="{{ meta.server_url }}/model" id="modelLink">Modelling</a></li>
               <li class="dropdown">
-                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">Browse Data<b class="caret"></b></a>
+                <a data-toggle="dropdown" class="dropdown-toggle" href="#"
+                  >Browse Data<b class="caret"></b
+                ></a>
                 <ul role="menu" class="dropdown-menu">
-                        <li><a href="{{ meta.server_url }}/pathway" id="pathwayLink">Pathway</a></li>
+                  <li>
-                        <li><a href="{{ meta.server_url }}/rule" id="ruleLink">Rule</a></li>
+                    <a href="{{ meta.server_url }}/pathway" id="pathwayLink"
-                        <li><a href="{{ meta.server_url }}/compound" id="compoundLink">Compound</a></li>
+                      >Pathway</a
-                        <li><a href="{{ meta.server_url }}/reaction" id="reactionLink">Reaction</a></li>
+                    >
-                        <li><a href="{{ meta.server_url }}/model" id="relative-reasoningLink">Model</a></li>
+                  </li>
-                        <li><a href="{{ meta.server_url }}/scenario" id="scenarioLink">Scenario</a></li>
+                  <li>
+                    <a href="{{ meta.server_url }}/rule" id="ruleLink">Rule</a>
+                  </li>
+                  <li>
+                    <a href="{{ meta.server_url }}/compound" id="compoundLink"
+                      >Compound</a
+                    >
+                  </li>
+                  <li>
+                    <a href="{{ meta.server_url }}/reaction" id="reactionLink"
+                      >Reaction</a
+                    >
+                  </li>
+                  <li>
+                    <a
+                      href="{{ meta.server_url }}/model"
+                      id="relative-reasoningLink"
+                      >Model</a
+                    >
+                  </li>
+                  <li>
+                    <a href="{{ meta.server_url }}/scenario" id="scenarioLink"
+                      >Scenario</a
+                    >
+                  </li>
                   {#                        <li><a href="{{ meta.server_url }}/setting" id="settingLink">Setting</a></li>#}
                   {#                        <li><a href="{{ meta.server_url }}/user" id="userLink">User</a></li>#}
                   {#                        <li><a href="{{ meta.server_url }}/group" id="groupLink">Group</a></li>#}
                 </ul>
               </li>
-
             </ul>
 
-            <ul class="nav navbar-nav navbar-right navbar-nav-framework navbar-right-framework">
+            <ul
-                <li><a href="https://community.envipath.org/" id="communityLink">Community</a></li>
+              class="nav navbar-nav navbar-right navbar-nav-framework navbar-right-framework"
+            >
+              <li>
+                <a href="https://community.envipath.org/" id="communityLink"
+                  >Community</a
+                >
+              </li>
               <li class="dropdown">
-                    <a data-toggle="dropdown" class="dropdown-toggle" href="#">Info <b class="caret"></b></a>
+                <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>
-                        <li class="divider"></li>
+                    <a
-                        <li><a target="_blank" href="https://wiki.envipath.org/" id="wikiLink">Documentation Wiki</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>
+                  <li>
+                    <a
+                      href="#"
+                      id="citeButton"
+                      data-toggle="modal"
+                      data-target="#citemodal"
+                      >How to cite enviPath</a
+                    >
                   </li>
-                        <li><a href="#" id="citeButton" data-toggle="modal" data-target="#citemodal">How to cite
-                            enviPath</a></li>
                   <li class="divider"></li>
                   <li><a>Version: {{ meta.version }}</a></li>
                 </ul>
               </li>
               {% if meta.user.username == 'anonymous' %}
                 <li>
-                        <a href="#signup" id="loginButton" data-toggle="modal" data-target="#signupmodal"
+                  <a
-                           style="margin-right:10px">Login</a>
+                    href="{% url 'login' %}"
+                    id="loginButton"
+                    style="margin-right:10px"
+                    >Login</a
+                  >
                 </li>
               {% else %}
                 <li class="dropdown">
-                        <a data-toggle="dropdown" id="loggedInButton" class="dropdown-toggle" id="logedInButton"
+                  <a
-                           href="#">
+                    data-toggle="dropdown"
+                    id="loggedInButton"
+                    class="dropdown-toggle"
+                    id="logedInButton"
+                    href="#"
+                  >
                     <div id="username">
                       {{ user.username }}<b class="caret"></b>
                     </div>
                   </a>
                   <ul role="menu" class="dropdown-menu">
                     <li>
-                                <a href="{{ meta.user.url }}" id="accountbutton">My Account</a>
+                      <a href="{{ meta.user.url }}" id="accountbutton"
+                        >My Account</a
+                      >
                     </li>
                     <li class="divider"></li>
-                            <form class="navbar-form navbar-left navbar-left-framework" role="logout"
+                    <form
-                                  action="{% url 'logout' %}" method="post">
+                      class="navbar-form navbar-left navbar-left-framework"
+                      role="logout"
+                      action="{% url 'logout' %}"
+                      method="post"
+                    >
                       {% csrf_token %}
                       <div class="form-group">
-                                    <input type="hidden" name="logout" value="true">
+                        <input type="hidden" name="logout" value="true" />
                       </div>
-                                <button type="submit" class="btn btn-default">Logout</button>
+                      <button type="submit" class="btn btn-default">
+                        Logout
+                      </button>
                     </form>
                   </ul>
                 </li>
@@ -176,8 +295,11 @@
             </ul>
           </div>
         </div>
-</nav>
+      </nav>
-<div id="docContent" class="content container">
+    </div>
+    <!-- End legacy Bootstrap navbar -->
+
+    <div id="docContent" class="content container">
       {% if breadcrumbs %}
         <div id="bread">
           <ol class="breadcrumb">
@@ -196,79 +318,105 @@
         </div>
       {% endif %}
       {% if message %}
-        <div id="message">
+        <div id="message">{{ message }}</div>
-            {{ message }}
-        </div>
       {% endif %}
       {% block content %}
       {% endblock content %}
       {% if meta.url_contains_package and meta.current_package.license %}
         <p></p>
         <div class="panel-group" id="license_accordion">
-            <div class="panel panel-default list-group-item" style="background-color:#f5f5f5">
+          <div
+            class="panel panel-default list-group-item"
+            style="background-color:#f5f5f5"
+          >
             <div class="panel-title">
-                    <a data-toggle="collapse" data-parent="#licence_accordion" href="#license">License</a>
+              <a
+                data-toggle="collapse"
+                data-parent="#licence_accordion"
+                href="#license"
+                >License</a
+              >
             </div>
           </div>
           <div id="license" class="panel-collapse collapse in">
             <div class="panel-body list-group-item">
               <a target="_blank" href="{{ meta.current_package.license.link }}">
-                        <img src="{{ meta.current_package.license.image_link }}">
+                <img src="{{ meta.current_package.license.image_link }}" />
               </a>
             </div>
           </div>
         </div>
       {% endif %}
-</div>
+    </div>
 
-<!-- FOOTER -->
+    <!-- FOOTER - Legacy Bootstrap -->
-<div class="container text-center">
+    <div class="legacy-bootstrap">
-    <hr/>
+      <div class="container text-center">
+        <hr />
         <div class="row">
           <div class="col-lg-12">
             <ul class="nav nav-pills nav-justified">
-                <li><a href="http://eawag.ch" target="_blank">
+              <li>
-                    <img id="image-ealogo"
+                <a href="http://ml.auckland.ac.nz" target="_blank">
+                  <img
+                    id="image-uoalogo"
                     height="60"
-                         src='{% static "/images/ealogo.gif" %}'
+                    src="{% static "/images/UoA-Logo-Primary-RGB-Small.png" %}"
-                         alt="Eawag"/>
+                    alt="The Univserity of Auckland"
+                  />
                 </a>
               </li>
               <li>
-                    <a href="http://ml.auckland.ac.nz" target="_blank">
+                <a href="https://eawag.ch" target="_blank">
-                        <img id="image-uoalogo"
+                  <img
+                    id="image-ealogo"
                     height="60"
-                             src='{% static "/images/uoa.png" %}'
+                    src="{% static "/images/ealogo.gif" %}"
-                             alt="The Univserity of Auckland"/>
+                    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>
-</div>
+      </div>
-<div class="row">
+      <div class="row">
         <div class="col-lg-12">
           <ul class="nav nav-pills nav-justified">
             <!--            <li><a href="https://envipath.com/imprint/" target="_blank">Impressum/Imprint</a></li>-->
-            <li><a href="mailto:admin@envipath.org" target="_blank">Contact</a></li>
+            <li>
+              <a href="mailto:admin@envipath.org" target="_blank">Contact</a>
+            </li>
             <!--            <li><a href="http://envipath.com" target="_blank"> enviPath UG (haftungsbeschr&auml;nkt) &amp; Co. KG &copy;-->
             <!--                {{ YEAR }}</a></li>-->
           </ul>
         </div>
-</div>
+      </div>
-<script>
+    </div>
+    <!-- End legacy Bootstrap footer -->
+
+    <script>
       $(function () {
         // Hide actionsbutton if theres no action defined
-        if ($('#actionsButton ul').children().length > 0) {
+        if ($("#actionsButton ul").children().length > 0) {
-            $('#actionsButton').show();
+          $("#actionsButton").show();
         }
       });
-</script>
+    </script>
-{% block modals %}
+    {% block modals %}
       {% include "modals/cite_modal.html" %}
-    {% include "modals/signup_modal.html" %}
       {% include "modals/predict_modal.html" %}
       {% include "modals/batch_predict_modal.html" %}
-{% endblock %}
+    {% endblock %}
-</body>
+  </body>
 </html>

templates/framework_modern.html

@@ -0,0 +1,223 @@
+<!doctype html>
+<html data-theme="envipath" lang="en">
+  {% load static %}
+  <head>
+    <title>{{ title }}</title>
+    <meta charset="UTF-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <meta name="csrf-token" content="{{ csrf_token }}" />
+
+    {# Favicon #}
+    <link
+      rel="shortcut icon"
+      type="image/png"
+      href="{% static 'images/favicon.ico' %}"
+    />
+
+    {# Tailwind CSS + DaisyUI Output #}
+    <link
+      href="{% static 'css/output.css' %}"
+      rel="stylesheet"
+      type="text/css"
+    />
+
+    {# jQuery - Keep for compatibility with existing JS #}
+    <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.1/jquery.min.js"></script>
+
+    {# Font Awesome #}
+    <link
+      href="https://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css"
+      rel="stylesheet"
+    />
+
+    {# Discourse embed for community #}
+    <script src="https://community.envipath.org/javascripts/embed-topics.js"></script>
+
+    <script>
+      const csrftoken = document.querySelector("[name=csrf-token]").content;
+
+      // Setup CSRF header for all jQuery AJAX requests
+      $.ajaxSetup({
+        beforeSend: function (xhr, settings) {
+          if (!/^(GET|HEAD|OPTIONS|TRACE)$/i.test(settings.type)) {
+            xhr.setRequestHeader("X-CSRFToken", csrftoken);
+          }
+        },
+      });
+    </script>
+
+    {# General EP JS #}
+    <script src="{% static 'js/pps.js' %}"></script>
+    {# Modal Steps for Stepwise Modal Wizards #}
+    <script src="{% static 'js/jquery-bootstrap-modal-steps.js' %}"></script>
+
+    {% if not debug %}
+      <!-- Matomo -->
+      <script>
+        var _paq = (window._paq = window._paq || []);
+        _paq.push(["trackPageView"]);
+        _paq.push(["enableLinkTracking"]);
+        (function () {
+          var u = "//matomo.envipath.com/";
+          _paq.push(["setTrackerUrl", u + "matomo.php"]);
+          _paq.push(["setSiteId", "{{ meta.site_id }}"]);
+          var d = document,
+            g = d.createElement("script"),
+            s = d.getElementsByTagName("script")[0];
+          g.async = true;
+          g.src = u + "matomo.js";
+          s.parentNode.insertBefore(g, s);
+        })();
+      </script>
+      <!-- End Matomo Code -->
+    {% endif %}
+  </head>
+  <body class="bg-base-300 min-h-screen">
+    {% include "includes/navbar.html" %}
+
+    {# Main Content Area #}
+    <main class="w-full">
+      {% block main_content %}
+        {# Breadcrumbs - outside main content, optional #}
+        {% if breadcrumbs %}
+          <div id="bread" class="max-w-7xl mx-auto px-4 py-4">
+            <div class="breadcrumbs text-sm">
+              <ul>
+                {% for elem in breadcrumbs %}
+                  {% for name, url in elem.items %}
+                    {% if forloop.parentloop.last %}
+                      <li>{{ name }}</li>
+                    {% else %}
+                      <li><a href="{{ url }}">{{ name }}</a></li>
+                    {% endif %}
+                  {% endfor %}
+                {% endfor %}
+              </ul>
+            </div>
+          </div>
+        {% endif %}
+
+        {# Main content container - paper effect on medium+ screens #}
+        <div
+          id="docContent"
+          class="bg-base-100 mx-auto md:my-8 md:max-w-6xl md:rounded-lg md:shadow-xl"
+        >
+          {# Messages - inside paper #}
+          {% if message %}
+            <div id="message" class="alert alert-info m-4">{{ message }}</div>
+          {% endif %}
+
+          {# Page content - no enforced styles #}
+          {% block content %}
+          {% endblock content %}
+
+          {# License - inside paper if present #}
+          {% if meta.url_contains_package and meta.current_package.license %}
+            <div class="collapse collapse-arrow bg-base-200 m-8">
+              <input type="checkbox" checked />
+              <div class="collapse-title text-xl font-medium">License</div>
+              <div class="collapse-content">
+                <a
+                  target="_blank"
+                  href="{{ meta.current_package.license.link }}"
+                >
+                  <img
+                    src="{{ meta.current_package.license.image_link }}"
+                    alt="License"
+                  />
+                </a>
+              </div>
+            </div>
+          {% endif %}
+        </div>
+      {% endblock main_content %}
+    </main>
+
+    {% include "includes/footer.html" %}
+
+    {# Floating Help Tab #}
+    {% if not public_mode %}
+      <div class="fixed right-0 top-1/2 -translate-y-1/2 z-50">
+        <a
+          href="https://community.envipath.org/"
+          target="_blank"
+          class="btn btn-secondary hover:btn-secondary-focus text-secondary-content flex items-center justify-center text-sm shadow-lg transition-all duration-300 hover:-translate-x-1 hover:scale-105"
+          title="Get Help from the Community"
+        >
+          <svg
+            xmlns="http://www.w3.org/2000/svg"
+            width="24"
+            height="24"
+            viewBox="0 0 24 24"
+            fill="none"
+            stroke="currentColor"
+            stroke-width="2"
+            stroke-linecap="round"
+            stroke-linejoin="round"
+            class="lucide lucide-message-circle-question-mark-icon lucide-message-circle-question-mark"
+          >
+            <path
+              d="M2.992 16.342a2 2 0 0 1 .094 1.167l-1.065 3.29a1 1 0 0 0 1.236 1.168l3.413-.998a2 2 0 0 1 1.099.092 10 10 0 1 0-4.777-4.719"
+            />
+            <path d="M9.09 9a3 3 0 0 1 5.83 1c0 2-3 3-3 3" />
+            <path d="M12 17h.01" />
+          </svg>
+        </a>
+      </div>
+    {% endif %}
+
+    {% block modals %}
+      {% include "modals/search_modal.html" %}
+    {% endblock %}
+
+    <script>
+      $(function () {
+        // Hide actionsbutton if there's no action defined
+        if ($("#actionsButton ul").children().length > 0) {
+          $("#actionsButton").show();
+        }
+      });
+
+      // Open search modal function
+      function openSearchModal() {
+        const searchModal = document.getElementById("search_modal");
+        if (searchModal) {
+          searchModal.showModal();
+        }
+      }
+
+      // Click handler for search badge
+      const searchTrigger = document.getElementById("search-trigger");
+      if (searchTrigger) {
+        searchTrigger.addEventListener("click", function (event) {
+          event.preventDefault();
+          openSearchModal();
+        });
+      }
+
+      // Global keyboard shortcut for search (Cmd+K on Mac, Ctrl+K on Windows/Linux)
+      document.addEventListener("keydown", function (event) {
+        // Check if user is typing in an input field
+        const activeElement = document.activeElement;
+        const isInputField =
+          activeElement &&
+          (activeElement.tagName === "INPUT" ||
+            activeElement.tagName === "TEXTAREA" ||
+            activeElement.contentEditable === "true");
+
+        if (isInputField) {
+          return; // Don't trigger shortcut when typing in input fields
+        }
+
+        // Check for Cmd+K (Mac) or Ctrl+K (Windows/Linux)
+        const isMac = /Mac/.test(navigator.platform);
+        const isCorrectModifier = isMac ? event.metaKey : event.ctrlKey;
+
+        if (isCorrectModifier && event.key === "k") {
+          event.preventDefault();
+          openSearchModal();
+        }
+      });
+    </script>
+  </body>
+</html>

templates/includes/footer.html

@@ -0,0 +1,69 @@
+{% load static %}
+<div class="lg:max-w-5xl mt-10 mx-auto bg-base-300 text-base-content">
+
+    <footer class="footer sm:footer-horizontal p-10">
+        {% if not public_mode %}
+        <nav>
+            <h6 class="footer-title">Services</h6>
+            <a class="link link-hover" href="/">Predict</a>
+            <a class="link link-hover" href="/search">Search</a>
+            <a class="link link-hover" href="/package">Browse</a>
+            {% if user.is_authenticated %}
+            <a class="link link-hover" href="/model">Your Collections</a>
+            {% endif %}
+            <a href="https://wiki.envipath.org/" target="_blank" class="link link-hover">Documentation</a>
+    </nav>
+        {% endif %}
+    <nav>
+      <h6 class="footer-title">Company</h6>
+      <a class="link link-hover" href="/about">About us</a>
+      <a class="link link-hover" href="/contact">Contact us</a>
+      <a class="link link-hover" href="/careers">Careers</a>
+      <a class="link link-hover" href="/legal">Legal</a>
+    </nav>
+    <nav>
+      <h6 class="footer-title">Legal</h6>
+      <a class="link link-hover" href="/terms">Terms of use</a>
+      <a class="link link-hover" href="/privacy">Privacy policy</a>
+      <a class="link link-hover" href="/cookie-policy">Cookie policy</a>
+      <a class="link link-hover" href="/cite">Cite enviPath</a>
+    </nav>
+  </footer>
+  <footer class="footer border-neutral-300 border-t-2 px-10 py-4">
+    <div class="flex flex-row justify-between w-full items-start">
+      <aside class="grid-flow-col items-center">
+          <svg class="fill-neutral-content flex-shrink-0 h-14 m-2" viewbox="0 0 65 65" >
+              <use
+                href="{% static "/images/logo-square.svg" %}#ep-logo-square"
+              >
+              </use>
+            </svg>
+
+          enviPath Ltd.
+          <br />
+          Biodegredation prediction since 2015.
+        </p>
+      </aside>
+      <aside class="text-sm text-base-200 mt-2"><span class="text-xs tracking-tight">Version</span> <span class="text-base font-bold">{{ meta.version }}</span></aside>
+    </div>
+    <nav class="md:place-self-center md:justify-self-end">
+      <div class="grid grid-flow-col gap-4">
+        <a href="https://www.youtube.com/@envipath7231" target="_blank">
+            <svg role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg" class="w-6 h-6 fill-current">
+                <title>YouTube</title>
+                <path d="M23.498 6.186a3.016 3.016 0 0 0-2.122-2.136C19.505 3.545 12 3.545 12 3.545s-7.505 0-9.377.505A3.017 3.017 0 0 0 .502 6.186C0 8.07 0 12 0 12s0 3.93.502 5.814a3.016 3.016 0 0 0 2.122 2.136c1.871.505 9.376.505 9.376.505s7.505 0 9.377-.505a3.015 3.015 0 0 0 2.122-2.136C24 15.93 24 12 24 12s0-3.93-.502-5.814zM9.545 15.568V8.432L15.818 12l-6.273 3.568z"/>
+            </svg>
+        </a>
+        <a href="https://community.envipath.org/" target="_blank">
+            <svg role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg" class="w-6 h-6 fill-current">
+                <title>Discourse</title>
+                <path d="M12.103 0C18.666 0 24 5.485 24 11.997c0 6.51-5.33 11.99-11.9 11.99L0 24V11.79C0 5.28 5.532 0 12.103 0zm.116 4.563c-2.593-.003-4.996 1.352-6.337 3.57-1.33 2.208-1.387 4.957-.148 7.22L4.4 19.61l4.794-1.074c2.745 1.225 5.965.676 8.136-1.39 2.17-2.054 2.86-5.228 1.737-7.997-1.135-2.778-3.84-4.59-6.84-4.585h-.008z"/>
+            </svg>
+        </a>
+        <a href="https://www.linkedin.com/company/envipath/" target="_blank">
+            <img src="{% static "/images/linkedin.png" %}" alt="LinkedIn" class="w-6 h-6">
+        </a>
+      </div>
+    </nav>
+  </footer>
+</div>

templates/includes/navbar.html

@@ -0,0 +1,147 @@
+{% load static %}
+{# Modern DaisyUI Navbar #}
+<div class="navbar bg-neutral-50 text-neutral-950 shadow-lg x-50">
+  <div class="navbar-start">
+    <a href="{{ meta.server_url }}" class="btn btn-ghost normal-case text-xl">
+      <svg class="h-8 fill-base-content" viewBox="0 0 104 26" role="img">
+        <use href="{% static "/images/logo-name.svg" %}#ep-logo-name" />
+      </svg>
+    </a>
+  </div>
+
+  {% if not public_mode %}
+    <div class="navbar-center hidden lg:flex">
+      <a
+        href="{{ meta.server_url }}/predict"
+        role="button"
+        class="btn btn-ghost"
+        id="predictLink"
+        >Predict</a
+      >
+      <!-- <li><a href="{{ meta.server_url }}/package" id="packageLink">Package</a></li> -->
+      <!--<li><a href="{{ meta.server_url }}/browse" id="browseLink">Browse</a></li>-->
+      <div class="dropdown dropdown-center">
+        <div tabindex="0" role="button" class="btn btn-ghost">Browse</div>
+        <ul
+          tabindex="-1"
+          class="dropdown-content menu bg-base-100 rounded-box z-1 w-52 p-2 shadow-sm"
+        >
+          <li>
+            <a href="{{ meta.server_url }}/pathway" id="pathwayLink">Pathway</a>
+          </li>
+          <li><a href="{{ meta.server_url }}/rule" id="ruleLink">Rule</a></li>
+          <li>
+            <a href="{{ meta.server_url }}/compound" id="compoundLink"
+              >Compound</a
+            >
+          </li>
+          <li>
+            <a href="{{ meta.server_url }}/reaction" id="reactionLink"
+              >Reaction</a
+            >
+          </li>
+          <li>
+            <a href="{{ meta.server_url }}/model" id="relative-reasoningLink"
+              >Model</a
+            >
+          </li>
+          <li>
+            <a href="{{ meta.server_url }}/scenario" id="scenarioLink"
+              >Scenario</a
+            >
+          </li>
+        </ul>
+      </div>
+    </div>
+  {% endif %}
+
+  <div class="navbar-end">
+    {% if not public_mode %}
+      <a id="search-trigger" role="button" class="cursor-pointer">
+        <div
+          class="flex items-center badge badge-dash space-x-1 bg-base-200 text-base-content/50 p-2 m-1"
+        >
+          <svg
+            xmlns="http://www.w3.org/2000/svg"
+            width="16"
+            height="16"
+            viewBox="0 0 24 24"
+            fill="none"
+            stroke="currentColor"
+            stroke-width="2"
+            stroke-linecap="round"
+            stroke-linejoin="round"
+            class="lucide lucide-search-icon lucide-search"
+          >
+            <path d="m21 21-4.34-4.34" />
+            <circle cx="11" cy="11" r="8" />
+          </svg>
+          <span id="search-shortcut">⌘K</span>
+        </div>
+      </a>
+    {% endif %}
+    {% if meta.user.username == 'anonymous' or public_mode %}
+      <a href="{% url 'login' %}" id="loginButton" class="p-2">Login</a>
+    {% else %}
+      <div class="dropdown dropdown-end">
+        <div
+          tabindex="0"
+          role="button"
+          class="btn btn-ghost m-1 btn-circle"
+          id="loggedInButton"
+        >
+          <svg
+            xmlns="http://www.w3.org/2000/svg"
+            width="24"
+            height="24"
+            viewBox="0 0 24 24"
+            fill="none"
+            stroke="currentColor"
+            stroke-width="2"
+            stroke-linecap="round"
+            stroke-linejoin="round"
+            class="lucide lucide-circle-user-icon lucide-circle-user"
+          >
+            <circle cx="12" cy="12" r="10" />
+            <circle cx="12" cy="10" r="3" />
+            <path d="M7 20.662V19a2 2 0 0 1 2-2h6a2 2 0 0 1 2 2v1.662" />
+          </svg>
+        </div>
+        <ul
+          tabindex="-1"
+          class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2 shadow-sm"
+        >
+          <li><a href="{{ meta.user.url }}" id="accountbutton">Settings</a></li>
+          <li>
+            <form
+              id="logoutForm"
+              action="{% url 'logout' %}"
+              method="post"
+              style="display: none;"
+            >
+              {% csrf_token %}
+              <input type="hidden" name="logout" value="true" />
+            </form>
+            <a
+              href="#"
+              id="logoutButton"
+              onclick="event.preventDefault(); document.getElementById('logoutForm').submit();"
+              >Logout</a
+            >
+          </li>
+        </ul>
+      </div>
+    {% endif %}
+  </div>
+</div>
+
+<script>
+  // OS-aware search shortcut display
+  (function () {
+    const isMac = /Mac/.test(navigator.platform);
+    const shortcutElement = document.getElementById("search-shortcut");
+    if (shortcutElement) {
+      shortcutElement.textContent = isMac ? "⌘K" : "Ctrl+K";
+    }
+  })();
+</script>

templates/index/index.html

@@ -1,185 +1,453 @@
-{% extends "framework.html" %}
+{% extends "framework_modern.html" %}
 {% load static %}
-{% block content %}
+{% block main_content %}
-    <!-- TODO rename ids as well as remove pathways if modal is closed!-->
+  <!-- Hero Section with Logo and Search -->
-    <div class="modal fade" tabindex="-1" id="foundMatching" role="dialog" aria-labelledby="foundModal"
+  <section class="hero relative mx-auto h-fit w-full max-w-5xl shadow-none">
-         aria-hidden="true">
+    <div
-        <div class="modal-dialog">
+      class="hero from-primary-800 to-primary-600 min-h-[calc(100vh*0.4)] bg-gradient-to-br"
-            <div class="modal-content">
+      style="background-image: url('{% static "/images/hero.png" %}'); background-size: cover; background-position: center;"
-                <div class="modal-header">
+    >
-                    <button type="button" class="close" data-dismiss="modal">
+      <div class="hero-overlay"></div>
-                        <span aria-hidden="true">&times;</span>
+      <!-- Predict Pathway text over the image -->
-                        <span class="sr-only">Close</span>
+      <div class="absolute bottom-40 left-1/8 z-10 -translate-x-8">
-                    </button>
+        <h2 class="text-base-100 text-left text-3xl text-shadow-lg">
-                    <h4 class="modal-title" id="newPackMod">Found Pathway in Database</h4>
+          Predict Your Pathway
-                </div>
+        </h2>
-                <div class="modal-body">
-                    <p>We found at least one pathway in the database with the given root
-                        compound. Do you want to open any of the existing pathways or
-                        predict a new one? To open an existing pathway, simply click
-                        on the pathway, to predict a new one, click Predict. The predicted
-                        pathway might differ from the ones in the database due to the
-                        settings used in the prediction.</p>
-                    <div id="foundPathways"></div>
-                </div>
-                <div class="modal-footer">
-                    <a id="modal-predict" class="btn btn-primary" href="#">Predict</a>
-                    <button type="button" id="cancel-predict" class="btn btn-default" data-dismiss="modal">Cancel
-                    </button>
       </div>
     </div>
+  </section>
+
+  <div class="bg-base-200 mx-auto max-w-5xl shadow-md">
+    <!-- Predict Pathway Section -->
+    <div
+      class="relative z-20 mx-auto -mt-32 mb-10 w-full flex-col lg:flex-row-reverse"
+    >
+      <div
+        class="card bg-base-100 mx-auto w-3/4 shrink-0 shadow-xl transition-all duration-300 ease-in-out"
+      >
+        <div class="card-body">
+          <div class="my-4 ml-8 flex h-fit flex-row items-center justify-start">
+            <div class="flex items-center gap-1">
+              <label class="swap btn btn-ghost btn-sm p-1" title="Input Mode">
+                <input type="checkbox" />
+                <span class="swap-on flex items-center gap-1">
+                  <div
+                    class="bg-neutral/50 text-neutral-content flex items-center justify-center rounded-full p-1"
+                  >
+                    <svg
+                      aria-label="smiles mode"
+                      xmlns="http://www.w3.org/2000/svg"
+                      viewBox="0 0 20 20"
+                      class="size-5"
+                    >
+                      <g
+                        stroke-linejoin="round"
+                        stroke-linecap="round"
+                        stroke-width="2"
+                        fill="currentColor"
+                        stroke="none"
+                      >
+                        <path
+                          fill-rule="evenodd"
+                          d="M8 2.75A.75.75 0 0 1 8.75 2h7.5a.75.75 0 0 1 0 1.5h-3.215l-4.483 13h2.698a.75.75 0 0 1 0 1.5h-7.5a.75.75 0 0 1 0-1.5h3.215l4.483-13H8.75A.75.75 0 0 1 8 2.75Z"
+                          clip-rule="evenodd"
+                        />
+                      </g>
+                    </svg>
                   </div>
+                  <span class="ext-xs">SMILES</span>
+                </span>
+                <span class="swap-off flex items-center gap-1">
+                  <div
+                    class="bg-neutral/50 text-neutral-content flex items-center justify-center rounded-full p-1"
+                  >
+                    <svg
+                      aria-label="draw mode"
+                      xmlns="http://www.w3.org/2000/svg"
+                      viewBox="0 0 20 20"
+                      fill="currentColor"
+                      stroke="none"
+                      class="size-5"
+                    >
+                      <path
+                        d="m2.695 14.762-1.262 3.155a.5.5 0 0 0 .65.65l3.155-1.262a4 4 0 0 0 1.343-.886L17.5 5.501a2.121 2.121 0 0 0-3-3L3.58 13.419a4 4 0 0 0-.885 1.343Z"
+                      />
+                    </svg>
+                  </div>
+                  <span class="text-base/50 text-xs">Draw</span>
+                </span>
+              </label>
             </div>
-    <div class="row">
-        <div class="col-xs-8">
-            <div class="jumbotron">
-                <h1>
-                    <img id="image-logo-long" class="img-responsive" alt="enviPath" width="1000ex"
-                         src='{% static "/images/logo-long.svg" %}'/>
-                </h1>
-                <p>enviPath is a database and prediction system for the microbial
-                    biotransformation of organic environmental contaminants. The
-                    database provides the possibility to store and view experimentally
-                    observed biotransformation pathways. The pathway prediction system
-                    provides different relative reasoning models to predict likely biotransformation
-                    pathways and products. You can try it out below.
-                </p>
-                <p>
-                    <a class="btn" style="background-color:#222222;color:#9d9d9d" role="button" target="_blank"
-                       href="https://wiki.envipath.org/index.php/Main_Page">Learn more &gt;&gt;</a>
-                </p>
           </div>
 
-        </div>
+          <fieldset
-        <div id="loading"></div>
+            class="fieldset overflow-hidden transition-all duration-300 ease-in-out"
-        <div class="col-xs-4">
+          >
-            <d-topics-list discourse-url="https://community.envipath.org" per-page="10" category="10"
+            <form
-                           template="complete"></d-topics-list>
+              id="index-form"
-        </div>
+              action="{{ meta.current_package.url }}/pathway"
-    </div>
+              method="POST"
-    <div class="row">
+            >
-        <form id="index-form" action="{{ meta.current_package.url }}/pathway" method="POST">
               {% csrf_token %}
-            <div class="input-group" id="index-form-bar">
+              <div
-                <div class="input-group-btn">
+                id="text-input-container"
-                    <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown"
+                class="scale-100 transform opacity-100 transition-all duration-300 ease-in-out"
-                            aria-expanded="false">
+              >
-                        <span class="caret"></span>
+                <div class="join mx-auto w-full">
-                    </button>
+                  <input
-                    <ul class="dropdown-menu" role="menu">
+                    type="text"
-                        <li>
+                    id="index-form-text-input"
-                            <iframe id="index-form-ketcher" src="{% static '/js/ketcher2/ketcher.html' %}" width="100%"
+                    placeholder="canonical SMILES string"
-                                    height="510"></iframe>
+                    class="input input-md join-item grow"
-                        </li>
+                  />
-                    </ul>
+                  <button class="btn btn-neutral join-item">Predict!</button>
-                </div>
+                </div>
-                <input type="text" class="form-control" id='index-form-text-input'
+                <div class="label relative mt-1 w-full">
-                       placeholder="Enter a SMILES to predict a Pathway or type something to search">
+                  <div class="flex gap-2">
-                <div class="input-group-btn">
+                    <a
-                    <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown"
+                      href="#"
-                            aria-haspopup="true"
+                      class="example-link hover:text-primary cursor-pointer"
-                            aria-expanded="false" id="action-button">Predict <span class="caret"></span></button>
+                      data-smiles="CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
-                    <ul class="dropdown-menu">
+                      title="load example"
-                        <li><a id="dropdown-predict">Predict</a></li>
+                      >Caffeine</a
-                        <li><a id="dropdown-search">Search</a></li>
+                    >
-                    </ul>
+                    <a
-                    <button class="btn" style="background-color:#222222;color:#9d9d9d" type="button" id="run-button">Go!
+                      href="#"
+                      class="example-link hover:text-primary cursor-pointer"
+                      data-smiles="CC(C)CC1=CC=C(C=C1)C(C)C(=O)O"
+                      title="load example"
+                      >Ibuprofen</a
+                    >
+                  </div>
+                  <a class="absolute top-0 left-[calc(100%-5.4rem)]" href="#"
+                    >Advanced</a
+                  >
+                </div>
+              </div>
+              <div
+                id="ketcher-container"
+                class="hidden w-full scale-95 transform opacity-0 transition-all duration-300 ease-in-out"
+              >
+                <iframe
+                  id="index-ketcher"
+                  src="{% static '/js/ketcher2/ketcher.html' %}"
+                  width="100%"
+                  height="400"
+                  class="rounded-lg"
+                ></iframe>
+                <button
+                  class="btn btn-lg bg-primary-950 text-primary-50 join-item mt-2 w-full"
+                >
+                  Predict!
                 </button>
+                <div class="mt-1 flex w-full justify-end">
+                  <a class="label justify-end" href="/predict">Advanced</a>
                 </div>
               </div>
-            <input type="hidden" id="index-form-smiles" name="smiles" value="smiles">
+              <input
-            <input type="hidden" id="index-form-predict" name="predict" value="predict">
+                type="hidden"
+                id="index-form-smiles"
+                name="smiles"
+                value="smiles"
+              />
+              <input
+                type="hidden"
+                id="index-form-predict"
+                name="predict"
+                value="predict"
+              />
+              <input type="hidden" id="current-action" value="predict" />
             </form>
+          </fieldset>
         </div>
-    <p></p>
+      </div>
+    </div>
+
+    <!-- Community News Section -->
+    <section class="bg-base-200 z-10 mx-8 py-16">
+      <div class="mx-auto max-w-7xl px-4">
+        <h2 class="h2 mb-8 text-left font-bold">Community Updates</h2>
+
+        <div id="community-news-container" class="flex justify-center gap-4">
+          <!-- News cards will be populated here -->
+          <div id="loading" class="flex w-full justify-center">
+            <span class="loading loading-spinner loading-lg"></span>
+          </div>
+        </div>
+
+        <div class="mt-6 text-right">
+          <a
+            href="https://community.envipath.org/c/announcements/10"
+            target="_blank"
+            class="btn btn-ghost btn-sm"
+          >
+            Read More Announcements
+          </a>
+        </div>
+
+        <!-- Discourse API integration -->
+        <script src="{% static 'js/discourse-api.js' %}"></script>
+      </div>
+    </section>
+
+    <!-- Mission Statement Section -->
+    <section class="from-base-200 to-base-100 bg-gradient-to-b py-16">
+      <div class="mx-auto px-8 md:px-12">
+        <div class="flex flex-row gap-4">
+          <div class="w-1/3">
+            <img
+              src="{% static "/images/ep-rule-artwork.png" %}"
+              alt="rule-based iterative tree greneration"
+              class="h-full w-full object-contain"
+            />
+          </div>
+          <div class="mr-8 w-2/3 space-y-4 text-left">
+            <h2 class="h2 mb-8 font-bold">About enviPath</h2>
+            <p class="">
+              enviPath is a database and prediction system for the microbial
+              biotransformation of organic environmental contaminants. The
+              database provides the possibility to store and view experimentally
+              observed biotransformation pathways.
+            </p>
+            <p class="">
+              The pathway prediction system provides different relative
+              reasoning models to predict likely biotransformation pathways and
+              products. Explore our tools and contribute to advancing
+              environmental biotransformation research.
+            </p>
+            <div class="float-right flex flex-row gap-4">
+              <a href="/about" class="btn btn-ghost-neutral">Read More</a>
+              <a href="/about" class="btn btn-neutral">Publications</a>
+            </div>
+          </div>
+        </div>
+      </div>
+    </section>
+
+    <!-- Partners Section -->
+    <section class="bg-base-100 py-14 sm:py-12">
+      <div class="mx-auto px-6 lg:px-8">
+        <div class="divider">
+          <h2 class="text-center text-lg/8 font-semibold">Backed by Science</h2>
+        </div>
+        <div
+          class="mx-auto mt-10 grid max-w-lg grid-cols-4 items-center gap-x-8 gap-y-10 sm:max-w-xl sm:grid-cols-6 sm:gap-x-10 lg:mx-0 lg:max-w-none lg:grid-cols-3"
+        >
+          <img
+            src="{% static "/images/uoa-logo-small.png" %}"
+            alt="The University of Auckland"
+            class="max-h-20 w-full object-contain lg:col-span-1"
+          />
+          <img
+            src="{% static "/images/logo-eawag.svg" %}"
+            alt="Eawag"
+            class="max-h-12 w-full object-contain lg:col-span-1"
+          />
+          <img
+            src="{% static "/images/uzh-logo.svg" %}"
+            alt="University of Zurich"
+            class="2 max-h-16 w-full object-contain lg:col-span-1"
+          />
+        </div>
+      </div>
+    </section>
+  </div>
+
   <script language="javascript">
     var currentPackage = "{{ meta.current_package.url }}";
 
-        function goButtonClicked() {
+    // Discourse API integration is now handled by discourse-api.js
-            $(this).prop("disabled", true);
 
-            var action = $('#action-button').text().trim();
+    // Function to render Discourse topics into cards
+    function renderDiscourseTopics(topics) {
+      const container = document.getElementById("community-news-container");
+      if (!container) return;
 
-            var textSmiles = $('#index-form-text-input').val().trim();
+      // Clear container
+      container.innerHTML = "";
 
-            if (textSmiles === '') {
+      // Create cards for each topic
-                return;
+      topics.forEach((topic) => {
+        const card = createDiscourseCard(topic);
+        container.insertAdjacentHTML("beforeend", card);
+      });
     }
 
-            var ketcherSmiles = getKetcher('index-form-ketcher').getSmiles().trim();
+    // Function to create HTML card for a topic
+    function createDiscourseCard(topic) {
+      const date = new Date(topic.created_at).toLocaleDateString();
 
-            if (action !== 'Search' && ketcherSmiles !== '' && textSmiles !== ketcherSmiles) {
+      return `
-                console.log("Ketcher and TextInput differ!");
+                <div class="card bg-white shadow-xs hover:shadow-lg transition-shadow duration-300 h-64 w-75 flex-shrink-0">
+                    <div class="card-body flex flex-col h-full">
+                        <h3 class="card-title leading-tight font-normal tracking-tight h-12 mb-2 line-clamp-2 text-ellipsis wrap-break-word overflow-hidden">
+                            <a href="${topic.url}" target="_blank" class="hover:text-primary">
+                                ${topic.title}
+                            </a>
+                        </h3>
+                        <div class="text-sm line-clamp-4 break-words" >
+                            ${topic.excerpt}
+                        </div>
+
+                        <div class="flex flex-row items-center justify-between">
+                            <div class="flex items-center gap-2">
+                                <div class="avatar tooltip tooltip-right" data-tip="${topic.author}">
+                                    <div class="w-8 rounded-full">
+                                        <img src="${topic.author_avatar}" alt="${topic.author}" />
+                                    </div>
+                                </div>
+                                <span class="text-xs text-gray-500">${date}</span>
+                            </div>
+                            <a href="${topic.url}" target="_blank" class="btn btn-ghost text-neutral-500 rounded-full p-2">
+                                <svg xmlns="http://www.w3.org/2000/svg" class="h-5 w-5" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round">
+                                    <path d="M12 7v14"/>
+                                    <path d="M3 18a1 1 0 0 1-1-1V4a1 1 0 0 1 1-1h5a4 4 0 0 1 4 4 4 4 0 0 1 4-4h5a1 1 0 0 1 1 1v13a1 1 0 0 1-1 1h-6a3 3 0 0 0-3 3 3 3 0 0 0-3-3z"/>
+                                </svg>
+                            </a>
+                        </div>
+                    </div>
+                </div>
+            `;
     }
 
-            if (action === 'Search') {
+    // Make render function globally available
-                var par = {};
+    window.renderDiscourseTopics = renderDiscourseTopics;
-                par['search'] = textSmiles;
+
-                par['mode'] = 'text';
+    // Toggle functionality with smooth animations
-                var queryString = $.param(par, true);
+    function toggleInputMode() {
-                window.location.href = "/search?" + queryString;
+      const toggle = $('input[type="checkbox"]');
+      const textContainer = $("#text-input-container");
+      const ketcherContainer = $("#ketcher-container");
+      const formCard = $(".card");
+      const fieldset = $(".fieldset");
+
+      if (toggle.is(":checked")) {
+        // Draw mode - show Ketcher, hide text input
+        textContainer.addClass("opacity-0 transform scale-95");
+        textContainer.removeClass("opacity-100 transform scale-100");
+
+        // Adjust fieldset padding for Ketcher mode - reduce padding and make more compact
+        fieldset.removeClass("p-8");
+        fieldset.addClass("p-4");
+
+        // Wait for fade out to complete, then hide and show new content
+        setTimeout(() => {
+          textContainer.addClass("hidden");
+          ketcherContainer.removeClass("hidden opacity-0 transform scale-95");
+          ketcherContainer.addClass("opacity-100 transform scale-100");
+
+          // Force re-evaluation of iframe size
+          const iframe = document.getElementById("index-ketcher");
+          if (iframe) {
+            iframe.style.height = "400px";
+          }
+        }, 300);
       } else {
-                $('#index-form-smiles').val(textSmiles);
+        // SMILES mode - show text input, hide Ketcher
-                $('#index-form').submit();
+        ketcherContainer.addClass("opacity-0 transform scale-95");
+        ketcherContainer.removeClass("opacity-100 transform scale-100");
+
+        // Restore fieldset padding for text input mode
+        fieldset.removeClass("p-4");
+        fieldset.addClass("p-8");
+
+        // Wait for fade out to complete, then hide and show new content
+        setTimeout(() => {
+          ketcherContainer.addClass("hidden");
+          textContainer.removeClass("hidden opacity-0 transform scale-95");
+          textContainer.addClass("opacity-100 transform scale-100");
+        }, 300);
+
+        // Transfer SMILES from Ketcher to text input if available
+        if (window.indexKetcher && window.indexKetcher.getSmiles) {
+          const smiles = window.indexKetcher.getSmiles();
+          if (smiles && smiles.trim() !== "") {
+            $("#index-form-text-input").val(smiles);
+          }
+        }
       }
     }
 
-        function actionDropdownClicked() {
+    // Ketcher integration
-            var suffix = ' <span class="caret"></span>';
+    function indexKetcherToTextInput() {
-            var dropdownVal = $(this).text();
+      $("#index-form-smiles").val(this.ketcher.getSmiles());
-
-            if (dropdownVal === 'Search') {
-                $("#index-form").attr("action", '/search');
-                $("#index-form").attr("method", 'GET');
-            } else {
-                $("#index-form").attr("action", currentPackage + "/pathway");
-            }
-
-            $('#action-button').html(dropdownVal + suffix);
-        }
-
-        function ketcherToTextInput() {
-            $('#index-form-text-input').val(this.ketcher.getSmiles());
     }
 
     $(function () {
+      // Initialize fieldset with proper padding
+      $(".fieldset").addClass("p-8");
 
-            $('#index-form').on("keydown", function (e) {
+      // Toggle event listener
-                if (e.key === "Enter") {
+      $('input[type="checkbox"]').on("change", toggleInputMode);
-                    e.preventDefault();
-                    goButtonClicked();
-                }
-            });
 
-            // Code that should be executed once DOM is ready goes here
+      // Ketcher iframe load handler
-            $('#dropdown-predict').on('click', actionDropdownClicked);
+      $("#index-ketcher").on("load", function () {
-            $('#dropdown-search').on('click', actionDropdownClicked);
-
-            $('#run-button').on('click', goButtonClicked);
-
-            // Update Ketcher Width
-            var fullWidth = $('#index-form-bar').width();
-            $('#index-form-ketcher').width(fullWidth);
-
-            // add a listener that gets triggered whenever the structure in ketcher has changed
-            $('#index-form-ketcher').on('load', function () {
         const checkKetcherReady = () => {
-                    win = this.contentWindow
+          const win = this.contentWindow;
-                    if (win.ketcher && 'editor' in win.ketcher) {
+          if (win.ketcher && "editor" in win.ketcher) {
+            window.indexKetcher = win.ketcher;
             win.ketcher.editor.event.change.handlers.push({
               once: false,
               priority: 0,
-                            f: ketcherToTextInput,
+              f: indexKetcherToTextInput,
-                            ketcher: win.ketcher
+              ketcher: win.ketcher,
             });
           } else {
             setTimeout(checkKetcherReady, 100);
           }
         };
-
         checkKetcherReady();
       });
 
+      // Handle example link clicks
+      $(".example-link").on("click", function (e) {
+        e.preventDefault();
+        const smiles = $(this).data("smiles");
+        const title = $(this).attr("title");
+
+        // Check if we're in Ketcher mode or text input mode
+        if ($('input[type="checkbox"]').is(":checked")) {
+          // In Ketcher mode - set the SMILES in Ketcher
+          if (window.indexKetcher && window.indexKetcher.setMolecule) {
+            window.indexKetcher.setMolecule(smiles);
+          }
+        } else {
+          // In text input mode - set the SMILES in the text input
+          $("#index-form-text-input").val(smiles);
+        }
+
+        // Show a brief feedback
+        const originalText = $(this).text();
+        $(this).text(`loaded!`);
+        setTimeout(() => {
+          $(this).text(originalText);
+        }, 1000);
+      });
+
+      // Handle form submission on Enter
+      $("#index-form").on("submit", function (e) {
+        e.preventDefault();
+
+        var textSmiles = "";
+
+        // Check if we're in Ketcher mode and extract SMILES
+        if ($('input[type="checkbox"]').is(":checked") && window.indexKetcher) {
+          textSmiles = window.indexKetcher.getSmiles().trim();
+        } else {
+          textSmiles = $("#index-form-text-input").val().trim();
+        }
+
+        if (textSmiles === "") {
+          return;
+        }
+
+        $("#index-form-smiles").val(textSmiles);
+        $("#index-form").attr("action", currentPackage + "/pathway");
+        $("#index-form").attr("method", "POST");
+        this.submit();
+      });
+
+      // Discourse topics are now loaded automatically by discourse-api.js
     });
   </script>
-{% endblock content %}
+{% endblock main_content %}

templates/migration.html

@@ -26,12 +26,12 @@
             {% endif %}
             <h4 class="panel-title">
                 <a id="{{ obj.id }}-link" data-toggle="collapse" data-parent="#migration-detail"
-                   href="#{{ obj.id }}">{{ obj.name }}</a>
+                   href="#{{ obj.id }}">{{ obj.name|safe }}</a>
             </h4>
         </div>
         <div id="{{ obj.id }}" class="panel-collapse collapse {% if not obj.status %}in{% endif %}">
             <div class="panel-body list-group-item">
-                <a class="list-group-item" href="{{ obj.detail_url }}">{{ obj.name }} Migration Detail Page</a>
+                <a class="list-group-item" href="{{ obj.detail_url }}">{{ obj.name|safe }} Migration Detail Page</a>
             </div>
         </div>
         {% endfor %}

templates/migration_detail.html

@@ -1,7 +1,7 @@
 {% 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-heading" id="headingPanel" style="font-size:2rem;height: 46px">
                 Migration Status for {{ bt_rule_name }}
@@ -27,24 +27,19 @@
                     {% endif %}
                     <h4 class="panel-title">
                         <a id="{{ obj.id }}-link" data-toggle="collapse" data-parent="#migration-detail"
-                   href="#{{ obj.id }}">{{ obj.name }}</a>
+                           href="#{{ obj.id }}">{{ obj.name|safe }}</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>
             {% endfor %}
         </div>
-</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_model_modal.html

@@ -1,3 +1,4 @@
+
 <div class="modal fade" tabindex="-1" id="new_model_modal" role="dialog" aria-labelledby="new_model_modal"
      aria-hidden="true">
     <div class="modal-dialog modal-lg">
@@ -18,13 +19,19 @@
                         prediction. You just need to set a name and the packages
                         you want the object to be based on. There are multiple types of models available.
                         For additional information have a look at our
-                        <a target="_blank" href="https://wiki.envipath.org/index.php/relative-reasoning" role="button">wiki &gt;&gt;</a>
+                        <a target="_blank" href="https://wiki.envipath.org/index.php/relative-reasoning" role="button">wiki
+                            &gt;&gt;</a>
                     </div>
+                    <!-- Name -->
                     <label for="model-name">Name</label>
                     <input id="model-name" name="model-name" class="form-control" placeholder="Name"/>
+
+                    <!-- Description -->
                     <label for="model-description">Description</label>
                     <input id="model-description" name="model-description" class="form-control"
                            placeholder="Description"/>
+
+                    <!-- Model Type -->
                     <label for="model-type">Model Type</label>
                     <select id="model-type" name="model-type" class="form-control" data-width='100%'>
                         <option disabled selected>Select Model Type</option>
@@ -32,70 +39,72 @@
                             <option value="{{ v }}">{{ k }}</option>
                         {% endfor %}
                     </select>
-                    <!-- ML and Rule Based Based Form-->
+
-                    <div id="package-based-relative-reasoning-specific-form">
                     <!-- Rule Packages -->
-                        <label for="package-based-relative-reasoning-rule-packages">Rule Packages</label>
+                    <div id="rule-packages" class="ep-model-param mlrr rbrr">
-                        <select id="package-based-relative-reasoning-rule-packages" name="package-based-relative-reasoning-rule-packages"
+                        <label for="model-rule-packages">Rule Packages</label>
-                                data-actions-box='true' class="form-control" multiple data-width='100%'>
+                        <select id="model-rule-packages" name="model-rule-packages" data-actions-box='true'
+                                class="form-control" multiple data-width='100%'>
                             <option disabled>Reviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                                 {% if obj.reviewed %}
-                            <option value="{{ obj.url }}">{{ obj.name }}</option>
+                                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                                 {% endif %}
                             {% endfor %}
 
                             <option disabled>Unreviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                                 {% if not obj.reviewed %}
-                            <option value="{{ obj.url }}">{{ obj.name }}</option>
+                                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                                 {% endif %}
                             {% endfor %}
                         </select>
+                    </div>
+
                     <!-- Data Packages -->
-                        <label for="package-based-relative-reasoning-data-packages" >Data Packages</label>
+                    <div id="data-packages" class="ep-model-param mlrr rbrr enviformer">
-                        <select id="package-based-relative-reasoning-data-packages" name="package-based-relative-reasoning-data-packages"
+                        <label for="model-data-packages">Data Packages</label>
-                                data-actions-box='true' class="form-control" multiple data-width='100%'>
+                        <select id="model-data-packages" name="model-data-packages" data-actions-box='true'
+                                class="form-control" multiple data-width='100%'>
                             <option disabled>Reviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                                 {% if obj.reviewed %}
-                            <option value="{{ obj.url }}">{{ obj.name }}</option>
+                                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                                 {% endif %}
                             {% endfor %}
 
                             <option disabled>Unreviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                                 {% if not obj.reviewed %}
-                            <option value="{{ obj.url }}">{{ obj.name }}</option>
+                                    <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                                 {% endif %}
                             {% endfor %}
                         </select>
+                    </div>
 
-                        <div id="ml-relative-reasoning-specific-form">
                     <!-- Fingerprinter -->
-                            <label for="ml-relative-reasoning-fingerprinter">Fingerprinter</label>
+                    <div id="fingerprinter" class="ep-model-param mlrr">
-                            <select id="ml-relative-reasoning-fingerprinter" name="ml-relative-reasoning-fingerprinter"
+                        <label for="model-fingerprinter">Fingerprinter</label>
-                                    class="form-control">
+                        <select id="model-fingerprinter" name="model-fingerprinter" data-actions-box='true'
+                                class="form-control" multiple data-width='100%'>
                             <option value="MACCS" selected>MACCS Fingerprinter</option>
-                            </select>
                             {% if meta.enabled_features.PLUGINS and additional_descriptors %}
-                                <!-- Property Plugins go here -->
-                                <label for="ml-relative-reasoning-additional-fingerprinter">Additional Fingerprinter /
-                                    Descriptors</label>
-                                <select id="ml-relative-reasoning-additional-fingerprinter"
-                                        name="ml-relative-reasoning-additional-fingerprinter" class="form-control">
                                 <option disabled selected>Select Additional Fingerprinter / Descriptor</option>
                                 {% for k, v in additional_descriptors.items %}
                                     <option value="{{ v }}">{{ k }}</option>
                                 {% endfor %}
-                                </select>
                             {% endif %}
-
+                        </select>
-                            <label for="ml-relative-reasoning-threshold">Threshold</label>
-                            <input type="number" min="0" max="1" step="0.05" value="0.5"
-                                   id="ml-relative-reasoning-threshold"
-                                   name="ml-relative-reasoning-threshold" class="form-control">
                     </div>
+
+                    <!-- Threshold -->
+                    <div id="threshold" class="ep-model-param mlrr enviformer">
+                        <label for="model-threshold">Threshold</label>
+                        <input type="number" min="0" max="1" step="0.05" value="0.5" id="model-threshold"
+                               name="model-threshold" class="form-control">
+                    </div>
+
+                    <div id="appdomain" class="ep-model-param mlrr">
                         {% if meta.enabled_features.APPLICABILITY_DOMAIN %}
                             <!-- Build AD? -->
                             <div class="checkbox">
@@ -107,11 +116,13 @@
                             <div id="ad-params" style="display:none">
                                 <!-- Num Neighbors -->
                                 <label for="num-neighbors">Number of Neighbors</label>
-                            <input id="num-neighbors" name="num-neighbors" type="number" class="form-control" value="5"
+                                <input id="num-neighbors" name="num-neighbors" type="number" class="form-control"
+                                       value="5"
                                        step="1" min="0" max="10">
                                 <!-- Local Compatibility -->
                                 <label for="local-compatibility-threshold">Local Compatibility Threshold</label>
-                            <input id="local-compatibility-threshold" name="local-compatibility-threshold" type="number"
+                                <input id="local-compatibility-threshold" name="local-compatibility-threshold"
+                                       type="number"
                                        class="form-control" value="0.5" step="0.01" min="0" max="1">
                                 <!-- Reliability -->
                                 <label for="reliability-threshold">Reliability Threshold</label>
@@ -120,12 +131,6 @@
                             </div>
                         {% endif %}
                     </div>
-                    <!-- EnviFormer-->
-                    <div id="enviformer-specific-form">
-                        <label for="enviformer-threshold">Threshold</label>
-                        <input type="number" min="0" max="1" step="0.05" value="0.5" id="enviformer-threshold"
-                               name="enviformer-threshold" class="form-control">
-                    </div>
                 </form>
             </div>
             <div class="modal-footer">
@@ -137,20 +142,23 @@
 </div>
 
 <script>
-$(function() {
+    $(function () {
+        // Built in Model Types
+        var nativeModelTypes = [
+            "mlrr",
+            "rbrr",
+            "enviformer",
+        ]
+
         // Initially hide all "specific" forms
-    $("div[id$='-specific-form']").each( function() {
+        $(".ep-model-param").each(function () {
             $(this).hide();
         });
 
         $('#model-type').selectpicker();
-    $("#ml-relative-reasoning-fingerprinter").selectpicker();
+        $("#model-fingerprinter").selectpicker();
-    $("#package-based-relative-reasoning-rule-packages").selectpicker();
+        $("#model-rule-packages").selectpicker();
-    $("#package-based-relative-reasoning-data-packages").selectpicker();
+        $("#model-data-packages").selectpicker();
-    $("#package-based-relative-reasoning-evaluation-packages").selectpicker();
-    if ($('#ml-relative-reasoning-additional-fingerprinter').length > 0) {
-        $("#ml-relative-reasoning-additional-fingerprinter").selectpicker();
-    }
 
         $("#build-app-domain").change(function () {
             if ($(this).is(":checked")) {
@@ -161,29 +169,20 @@ $(function() {
         });
 
         // On change hide all and show only selected
-    $("#model-type").change(function() {
+        $("#model-type").change(function () {
-        $("div[id$='-specific-form']").each( function() {
+            $('.ep-model-param').hide();
-            $(this).hide();
+            var modelType = $('#model-type').val();
-        });
+            if (nativeModelTypes.indexOf(modelType) !== -1) {
-        val = $('option:selected', this).val();
+                $('.' + modelType).show();
-
-        if (val === 'ml-relative-reasoning' || val === 'rule-based-relative-reasoning') {
-            $("#package-based-relative-reasoning-specific-form").show();
-            if (val === 'ml-relative-reasoning') {
-                 $("#ml-relative-reasoning-specific-form").show();
-            }
             } else {
-            $("#" + val + "-specific-form").show();
+                // do nothing
             }
         });
 
-    $('#new_model_modal_form_submit').on('click', function(e){
+        $('#new_model_modal_form_submit').on('click', function (e) {
             e.preventDefault();
             $('#new_model_form').submit();
         });
 
-});
+    });
-
-
-
 </script>

templates/modals/collections/new_pathway_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <div class="modal fade" tabindex="-1" id="new_pathway_modal" role="dialog" aria-labelledby="new_pathway_modal"
      aria-hidden="true" style="overflow-y: auto;">
@@ -111,7 +112,7 @@
 
                     <select id="settingSelect" name="settingSelect" class="form-control">
                         {% for setting in available_settings %}
-                        <option value="{{ setting.id }}">{{ setting.name }}</option>
+                        <option value="{{ setting.id }}">{{ setting.name|safe }}</option>
                         {% endfor %}
                     </select>
                     <p></p>

templates/modals/collections/new_prediction_setting_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 
 <div id="new_prediction_setting_modal" class="modal" tabindex="-1">
@@ -40,14 +41,14 @@
                             <option disabled>Reviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                             {% if obj.reviewed %}
-                            <option value="{{ obj.url }}">{{ obj.name }}</option>
+                            <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                             {% endif %}
                             {% endfor %}
 
                             <option disabled>Unreviewed Packages</option>
                             {% for obj in meta.readable_packages %}
                             {% if not obj.reviewed %}
-                            <option value="{{ obj.url }}">{{ obj.name }}</option>
+                            <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
                             {% endif %}
                             {% endfor %}
                         </select>
@@ -57,7 +58,7 @@
                         <select id="model-based-prediction-setting-model" name="model-based-prediction-setting-model" class="form-control" data-width='100%'>
                         <option disabled selected>Select the model</option>
                         {% for m in models %}
-                        <option value="{{ m.url }}">{{ m.name }}</option>
+                        <option value="{{ m.url }}">{{ m.name|safe }}</option>
                         {% endfor %}
                         </select>
                         <label for="model-based-prediction-setting-threshold">Threshold</label>

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/add_pathway_edge_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <div class="modal fade bs-modal-lg" id="add_pathway_edge_modal" tabindex="-1" aria-labelledby="add_pathway_edge_modal"
      aria-modal="true"
@@ -36,7 +37,7 @@
                             <select id="add_pathway_edge_substrates" name="edge-substrates"
                                     data-actions-box='true' class="form-control" multiple data-width='100%'>
                                 {% for n in pathway.nodes %}
-                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name }}</option>
+                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
                                 {% endfor %}
                             </select>
                         </div>
@@ -47,7 +48,7 @@
                             <select id="add_pathway_edge_products" name="edge-products"
                                     data-actions-box='true' class="form-control" multiple data-width='100%'>
                                 {% for n in pathway.nodes %}
-                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name }}</option>
+                                    <option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
                                 {% endfor %}
                             </select>
                         </div>

templates/modals/objects/delete_pathway_edge_modal.html

@@ -1,3 +1,4 @@
+
 {% load static %}
 <!-- Delete Edge -->
 <div id="delete_pathway_edge_modal" class="modal" tabindex="-1">
@@ -19,7 +20,7 @@
                             data-actions-box='true' class="form-control" data-width='100%'>
                         <option value="" disabled selected>Select Reaction to delete</option>
                         {% for e in pathway.edges %}
-                            <option value="{{ e.url }}">{{ e.edge_label.name }}</option>
+                            <option value="{{ e.url }}">{{ e.edge_label.name|safe }}</option>
                         {% endfor %}
                     </select>
                     <input type="hidden" id="hidden" name="hidden" value="delete"/>