Initial

Adding users to a group or setting permissions on a package now filter for active users. Also any inactive members of group/package get marked as such.

<img width="490" alt="{3B906C71-F3AE-41E4-A61C-B8377D79F685}.png" src="attachments/09cf149a-9d7a-4560-8ce7-9f3487527ee2">

Reviewed-on: enviPath/enviPy#329
Co-authored-by: Liam Brydon <lbry121@aucklanduni.ac.nz>
Co-committed-by: Liam Brydon <lbry121@aucklanduni.ac.nz>

.env.local.example

@@ -0,0 +1,35 @@
+# 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'
+EMAIL_HOST_USER='admin@envipath.com'
+EMAIL_HOST_PASSWORD='dummy-password'
+
+DEFAULT_FROM_EMAIL="test@test.com"
+SERVER_EMAIL='test@test.com'
+
+# Testing settings VScode
+DJANGO_SETTINGS_MODULE='envipath.settings'
+MANAGE_PY_PATH='./manage.py'
+
+APPLICABILITY_DOMAIN_ENABLED=True
+ENVIFORMER_PRESENT=True
+MODEL_BUILDING_ENABLED=True

.env.prod.example

@@ -16,4 +16,5 @@ POSTGRES_PORT=
 # MAIL
 EMAIL_HOST_USER=
 EMAIL_HOST_PASSWORD=
-
+# MATOMO
+MATOMO_SITE_ID

.gitea/actions/setup-envipy/action.yaml

@@ -0,0 +1,67 @@
+name: 'Setup enviPy Environment'
+description: 'Shared setup for enviPy CI - installs dependencies and prepares environment'
+
+inputs:
+  skip-frontend:
+    description: 'Skip frontend build steps (pnpm, tailwind)'
+    required: false
+    default: 'false'
+  skip-playwright:
+    description: 'Skip Playwright installation'
+    required: false
+    default: 'false'
+  ssh-private-key:
+    description: 'SSH private key for git access'
+    required: true
+  run-migrations:
+    description: 'Run Django migrations after setup'
+    required: false
+    default: 'true'
+
+runs:
+  using: "composite"
+  steps:
+    - name: Setup ssh
+      shell: bash
+      run: |
+        mkdir -p ~/.ssh
+        echo "${{ inputs.ssh-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: Setup Python venv
+      shell: bash
+      run: |
+        uv sync --locked --all-extras --dev
+
+    - name: Install Playwright
+      if: inputs.skip-playwright == 'false'
+      shell: bash
+      run: |
+        source .venv/bin/activate
+        playwright install --with-deps
+
+    - name: Build Frontend
+      if: inputs.skip-frontend == 'false'
+      shell: bash
+      run: |
+        uv run python scripts/pnpm_wrapper.py install
+        uv run python scripts/pnpm_wrapper.py run build
+
+    - name: Wait for Postgres
+      shell: bash
+      run: |
+        until pg_isready -h postgres -U ${{ env.POSTGRES_USER }}; do
+          echo "Waiting for postgres..."
+          sleep 2
+        done
+        echo "Postgres is ready!"
+
+    - name: Run Django Migrations
+      if: inputs.run-migrations == 'true'
+      shell: bash
+      run: |
+        source .venv/bin/activate
+        python manage.py migrate --noinput

.gitea/docker/Dockerfile.ci

@@ -0,0 +1,53 @@
+# Custom CI Docker image for Gitea runners
+# Pre-installs Node.js 24, pnpm 10, uv, and system dependencies
+# to eliminate setup time in CI workflows
+
+FROM ubuntu:24.04
+
+# Prevent interactive prompts during package installation
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install system dependencies
+RUN apt-get update && \
+    apt-get install -y \
+      postgresql-client \
+      redis-tools \
+      openjdk-11-jre-headless \
+      curl \
+      ca-certificates \
+      gnupg \
+      lsb-release \
+      git \
+      ssh \
+      libxrender1 \
+      libxext6 \
+      libfontconfig1 \
+      libfreetype6 \
+      libcairo2 \
+      libglib2.0-0t64 \
+      && rm -rf /var/lib/apt/lists/*
+
+# Install Node.js 24 via NodeSource
+RUN curl -fsSL https://deb.nodesource.com/setup_24.x | bash - && \
+    apt-get install -y nodejs && \
+    rm -rf /var/lib/apt/lists/*
+
+# Enable corepack and install pnpm 10
+RUN corepack enable && \
+    corepack prepare pnpm@10 --activate
+
+# Install uv https://docs.astral.sh/uv/guides/integration/docker/#available-images
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
+ENV PATH="/root/.cargo/bin:${PATH}"
+
+# Verify installations
+RUN node --version && \
+    npm --version && \
+    pnpm --version && \
+    uv --version && \
+    pg_isready --version && \
+    redis-cli --version && \
+    java -version
+
+# Set working directory
+WORKDIR /workspace

.gitea/workflows/api-ci.yaml

@@ -0,0 +1,86 @@
+name: API CI
+
+on:
+  pull_request:
+    branches:
+      - develop
+    paths:
+      - 'epapi/**'
+      - 'epdb/models.py'  # API depends on models
+      - 'epdb/logic.py'   # API depends on business logic
+      - 'tests/fixtures/**'  # API tests use fixtures
+  workflow_dispatch:
+
+jobs:
+  api-tests:
+    if: ${{ !contains(gitea.event.pull_request.title, 'WIP') }}
+    runs-on: ubuntu-latest
+    container:
+      image: git.envipath.com/envipath/envipy-ci: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
+
+    env:
+      RUNNER_TOOL_CACHE: /toolcache
+      EP_DATA_DIR: /opt/enviPy/
+      ALLOWED_HOSTS: 127.0.0.1,localhost
+      DEBUG: True
+      LOG_LEVEL: INFO
+      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
+
+      # Use shared setup action - skips frontend builds for API-only tests
+      - name: Setup enviPy Environment
+        uses: ./.gitea/actions/setup-envipy
+        with:
+          skip-frontend: 'true'
+          skip-playwright: 'false'
+          ssh-private-key: ${{ secrets.ENVIPY_CI_PRIVATE_KEY }}
+          run-migrations: 'true'
+
+      - name: Run API tests
+        run: |
+          .venv/bin/python manage.py test epapi -v 2
+
+      - name: Test API endpoints availability
+        run: |
+          .venv/bin/python manage.py runserver 0.0.0.0:8000 &
+          SERVER_PID=$!
+          sleep 5
+          curl -f http://localhost:8000/api/v1/docs || echo "API docs not available"
+          kill $SERVER_PID

.gitea/workflows/build-ci-image.yaml

@@ -0,0 +1,48 @@
+name: Build CI Docker Image
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - develop
+      - main
+    paths:
+      - '.gitea/docker/Dockerfile.ci'
+      - '.gitea/workflows/build-ci-image.yaml'
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to container registry
+        uses: docker/login-action@v3
+        with:
+          registry: git.envipath.com
+          username: ${{ secrets.CI_REGISTRY_USER }}
+          password: ${{ secrets.CI_REGISTRY_PASSWORD }}
+
+      - name: Extract metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: git.envipath.com/envipath/envipy-ci
+          tags: |
+            type=raw,value=latest
+            type=sha,prefix={{branch}}-
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: .gitea/docker/Dockerfile.ci
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=registry,ref=git.envipath.com/envipath/envipy-ci:latest
+          cache-to: type=inline

.gitea/workflows/ci.yaml

@@ -0,0 +1,87 @@
+name: CI
+
+on:
+  pull_request:
+    branches:
+      - develop
+  workflow_dispatch:
+
+jobs:
+  test:
+    if: ${{ !contains(gitea.event.pull_request.title, 'WIP') }}
+    runs-on: ubuntu-latest
+    container:
+      image: git.envipath.com/envipath/envipy-ci: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: INFO
+      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
+
+      # Use shared setup action - includes all dependencies and migrations
+      - name: Setup enviPy Environment
+        uses: ./.gitea/actions/setup-envipy
+        with:
+          skip-frontend: 'false'
+          skip-playwright: 'false'
+          ssh-private-key: ${{ secrets.ENVIPY_CI_PRIVATE_KEY }}
+          run-migrations: 'true'
+
+      - name: Run frontend tests
+        run: |
+          .venv/bin/python manage.py test --tag frontend
+
+      - name: Run Django tests
+        run: |
+          .venv/bin/python manage.py test tests --exclude-tag slow --exclude-tag frontend

.gitignore

@@ -1,8 +1,375 @@
-*.pyc
+
+
+
+### Python ###
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#   Usually these files are written by a python script from a template
+#   before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
 db.sqlite3
-.idea/
+db.sqlite3-journal
 static/admin/
 static/django_extensions/
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+# pdm.lock
+# pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+# pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# Redis
+*.rdb
+*.aof
+*.pid
+
+# RabbitMQ
+mnesia/
+rabbitmq/
+rabbitmq-data/
+
+# ActiveMQ
+activemq-data/
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
 .env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#   JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#   be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#   and can be added to the global gitignore or merged into this file.  For a more nuclear
+#   option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+# Abstra
+#   Abstra is an AI-powered process automation framework.
+#   Ignore directories containing user credentials, local state, and settings.
+#   Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#   and can be added to the global gitignore or merged into this file. However, if you prefer,
+#   you could uncomment the following to ignore the entire vscode folder
+.vscode/
+*.code-workspace
+
+# Ruff stuff:
+.ruff_cache/
+
+# UV cache
+.uv-cache/
+
+# PyPI configuration file
+.pypirc
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml
+
+### Agents ###
+.claude/
+.codex/
+.cursor/
+.github/prompts/
+.junie/
+.windsurf/
+
+AGENTS.md
+CLAUDE.md
+GEMINI.md
+.aider.*
+
+### Node.js ###
+
+# Logs
+logs
+*.log
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+lerna-debug.log*
+
+# Diagnostic reports (https://nodejs.org/api/report.html)
+report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
+
+# Runtime data
+pids
+*.pid
+*.seed
+*.pid.lock
+
+# Directory for instrumented libs generated by jscoverage/JSCover
+lib-cov
+
+# Coverage directory used by tools like istanbul
+coverage
+*.lcov
+
+# nyc test coverage
+.nyc_output
+
+# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
+.grunt
+
+# Bower dependency directory (https://bower.io/)
+bower_components
+
+# node-waf configuration
+.lock-wscript
+
+# Compiled binary addons (https://nodejs.org/api/addons.html)
+build/Release
+
+# Dependency directories
+node_modules/
+jspm_packages/
+
+# Snowpack dependency directory (https://snowpack.dev/)
+web_modules/
+
+# TypeScript cache
+*.tsbuildinfo
+
+# Optional npm cache directory
+.npm
+
+# Optional eslint cache
+.eslintcache
+
+# Optional stylelint cache
+.stylelintcache
+
+# Optional REPL history
+.node_repl_history
+
+# Output of 'npm pack'
+*.tgz
+
+# Yarn Integrity file
+.yarn-integrity
+
+# dotenv environment variable files
+.env
+.env.*
+!.env.example
+
+# parcel-bundler cache (https://parceljs.org/)
+.cache
+.parcel-cache
+
+# Next.js build output
+.next
+out
+
+# Nuxt.js build / generate output
+.nuxt
+dist
+.output
+
+# Gatsby files
+.cache/
+# Comment in the public line in if your project uses Gatsby and not Next.js
+# https://nextjs.org/blog/next-9-1#public-directory-support
+# public
+
+# vuepress build output
+.vuepress/dist
+
+# vuepress v2.x temp and cache directory
+.temp
+.cache
+
+# Sveltekit cache directory
+.svelte-kit/
+
+# vitepress build output
+**/.vitepress/dist
+
+# vitepress cache directory
+**/.vitepress/cache
+
+# Docusaurus cache and generated files
+.docusaurus
+
+# Serverless directories
+.serverless/
+
+# FuseBox cache
+.fusebox/
+
+# DynamoDB Local files
+.dynamodb/
+
+# Firebase cache directory
+.firebase/
+
+# TernJS port file
+.tern-port
+
+# Stores VSCode versions used for testing VSCode extensions
+.vscode-test
+
+# yarn v3
+.pnp.*
+.yarn/*
+!.yarn/patches
+!.yarn/plugins
+!.yarn/releases
+!.yarn/sdks
+!.yarn/versions
+
+# Vite files
+vite.config.js.timestamp-*
+vite.config.ts.timestamp-*
+.vite/
+
+### Custom ###
+
 debug.log
-scratches/
+scratches/
+test-results/
+data/
+*.arff
+
+# Auto generated
+static/css/output.css
+
+# macOS system files
+.DS_Store
+.Trashes
+._*

.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 +1,125 @@
 # 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 and Redis (for async Celery tasks)
+- 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)
+uv run poe celery        # Start Celery worker for async task processing
+uv run poe celery-dev    # Start database and Celery worker
+```
+
+### 4. Async Celery Setup (Optional)
+
+By default, Celery tasks run synchronously (`CELERY_TASK_ALWAYS_EAGER = True`), which means prediction tasks block the HTTP request until completion. To enable asynchronous task processing with live status updates on pathway pages:
+
+1. **Set the Celery flag in your `.env` file:**
+
+   ```bash
+   FLAG_CELERY_PRESENT=True
+   ```
+
+2. **Start Redis and Celery worker:**
+
+   ```bash
+   uv run poe celery-dev
+   ```
+
+3. **Start the development server** (in another terminal):
+   ```bash
+   uv run poe dev
+   ```
+
+### 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
+        ```

bayer/admin.py

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

bayer/apps.py

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

bayer/migrations/0001_initial.py

@@ -0,0 +1,35 @@
+# Generated by Django 5.2.7 on 2026-02-12 12:36
+
+import django.utils.timezone
+import model_utils.fields
+import uuid
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Package',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('name', models.TextField(default='no name', verbose_name='Name')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
+                ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('reviewed', models.BooleanField(default=False, verbose_name='Reviewstatus')),
+                ('classification_level', models.IntegerField(choices=[(0, 'Internal'), (10, 'Restricted'), (20, 'Secret')], default=10)),
+            ],
+            options={
+                'db_table': 'epdb_package',
+            },
+        ),
+    ]

bayer/migrations/0002_initial.py

@@ -0,0 +1,22 @@
+# Generated by Django 5.2.7 on 2026-02-12 12:36
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+        ('bayer', '0001_initial'),
+        ('epdb', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='package',
+            name='license',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.license', verbose_name='License'),
+        ),
+    ]

bayer/models.py

@@ -0,0 +1,95 @@
+from typing import List
+
+from django.conf import settings as s
+from django.db import models
+from django.db.models import QuerySet
+
+from epdb.models import (
+    EnviPathModel,
+    ParallelRule,
+    SequentialRule,
+    SimpleAmbitRule,
+    SimpleRDKitRule,
+)
+
+
+class Package(EnviPathModel):
+    reviewed = models.BooleanField(verbose_name="Reviewstatus", default=False)
+    license = models.ForeignKey(
+        "epdb.License", on_delete=models.SET_NULL, blank=True, null=True, verbose_name="License"
+    )
+
+    class Classification(models.IntegerChoices):
+        INTERNAL = 0, "Internal"
+        RESTRICTED = 10 , "Restricted"
+        SECRET = 20, "Secret"
+
+    classification_level = models.IntegerField(
+        choices=Classification,
+        default=Classification.RESTRICTED,
+    )
+
+    def delete(self, *args, **kwargs):
+        # explicitly handle related Rules
+        for r in self.rules.all():
+            r.delete()
+        super().delete(*args, **kwargs)
+
+    def __str__(self):
+        return f"{self.name} (pk={self.pk})"
+
+    @property
+    def compounds(self) -> QuerySet:
+        return self.compound_set.all()
+
+    @property
+    def rules(self) -> QuerySet:
+        return self.rule_set.all()
+
+    @property
+    def reactions(self) -> QuerySet:
+        return self.reaction_set.all()
+
+    @property
+    def pathways(self) -> QuerySet:
+        return self.pathway_set.all()
+
+    @property
+    def scenarios(self) -> QuerySet:
+        return self.scenario_set.all()
+
+    @property
+    def models(self) -> QuerySet:
+        return self.epmodel_set.all()
+
+    def _url(self):
+        return "{}/package/{}".format(s.SERVER_URL, self.uuid)
+
+    def get_applicable_rules(self) -> List["Rule"]:
+        """
+        Returns a ordered set of rules where the following applies:
+        1. All Composite will be added to result
+        2. All SimpleRules will be added if theres no CompositeRule present using the SimpleRule
+        Ordering is based on "url" field.
+        """
+        rules = []
+        rule_qs = self.rules
+
+        reflected_simple_rules = set()
+
+        for r in rule_qs:
+            if isinstance(r, ParallelRule) or isinstance(r, SequentialRule):
+                rules.append(r)
+                for sr in r.simple_rules.all():
+                    reflected_simple_rules.add(sr)
+
+        for r in rule_qs:
+            if isinstance(r, SimpleAmbitRule) or isinstance(r, SimpleRDKitRule):
+                if r not in reflected_simple_rules:
+                    rules.append(r)
+
+        rules = sorted(rules, key=lambda x: x.url)
+        return rules
+
+    class Meta:
+        db_table = "epdb_package"

bayer/templates/objects/package.html

@@ -0,0 +1,97 @@
+{% extends "framework_modern.html" %}
+
+{% block content %}
+
+  {% block action_modals %}
+    {% include "modals/objects/edit_package_modal.html" %}
+    {% include "modals/objects/edit_package_permissions_modal.html" %}
+    {% include "modals/objects/publish_package_modal.html" %}
+    {% include "modals/objects/set_license_modal.html" %}
+    {% include "modals/objects/export_package_modal.html" %}
+    {% include "modals/objects/generic_delete_modal.html" %}
+  {% endblock action_modals %}
+
+  <div class="space-y-2 p-4">
+    <!-- Header Section -->
+    <div class="card bg-base-100">
+      <div class="card-body">
+        <div class="flex items-center justify-between">
+          <h2 class="card-title text-2xl">{{ package.name }} - <i>{{ package.get_classification_level_display }}</i></h2>
+          <div id="actionsButton" class="dropdown dropdown-e nd hidden">
+            <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
+              <svg
+                xmlns="http://www.w3.org/2000/svg"
+                width="16"
+                height="16"
+                viewBox="0 0 24 24"
+                fill="none"
+                stroke="currentColor"
+                stroke-width="2"
+                stroke-linecap="round"
+                stroke-linejoin="round"
+                class="lucide lucide-wrench"
+              >
+                <path
+                  d="M14.7 6.3a1 1 0 0 0 0 1.4l1.6 1.6a1 1 0 0 0 1.4 0l3.77-3.77a6 6 0 0 1-7.94 7.94l-6.91 6.91a2.12 2.12 0 0 1-3-3l6.91-6.91a6 6 0 0 1 7.94-7.94l-3.76 3.76z"
+                />
+              </svg>
+              Actions
+            </div>
+            <ul
+              tabindex="-1"
+              class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
+            >
+              {% block actions %}
+                {% include "actions/objects/package.html" %}
+              {% endblock %}
+            </ul>
+          </div>
+        </div>
+        <p class="mt-2">{{ package.description|safe }}</p>
+        <ul class="menu bg-base-200 rounded-box mt-4 w-full">
+          <li>
+            <a href="{{ package.url }}/pathway" class="hover:bg-base-300"
+              >Pathways ({{ package.pathways.count }})</a
+            >
+          </li>
+          <li>
+            <a href="{{ package.url }}/rule" class="hover:bg-base-300"
+              >Rules ({{ package.rules.count }})</a
+            >
+          </li>
+          <li>
+            <a href="{{ package.url }}/compound" class="hover:bg-base-300"
+              >Compounds ({{ package.compounds.count }})</a
+            >
+          </li>
+          <li>
+            <a href="{{ package.url }}/reaction" class="hover:bg-base-300"
+              >Reactions ({{ package.reactions.count }})</a
+            >
+          </li>
+          <li>
+            <a href="{{ package.url }}/model" class="hover:bg-base-300"
+              >Models ({{ package.models.count }})</a
+            >
+          </li>
+          <li>
+            <a href="{{ package.url }}/scenario" class="hover:bg-base-300"
+              >Scenarios ({{ package.scenarios.count }})</a
+            >
+          </li>
+        </ul>
+      </div>
+    </div>
+  </div>
+
+  <script>
+    // Show actions button if there are actions
+    document.addEventListener("DOMContentLoaded", function () {
+      const actionsButton = document.getElementById("actionsButton");
+      const actionsList = actionsButton?.querySelector("ul");
+      if (actionsList && actionsList.children.length > 0) {
+        actionsButton?.classList.remove("hidden");
+      }
+    });
+  </script>
+{% endblock content %}

bayer/views.py

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

docker-compose.dev.yml

@@ -0,0 +1,26 @@
+services:
+  db:
+    image: postgres:18
+    container_name: envipath-postgres
+    environment:
+      POSTGRES_USER: postgres
+      POSTGRES_PASSWORD: postgres
+      POSTGRES_DB: envipath
+    ports:
+      - "5432:5432"
+    volumes:
+      - postgres_data:/var/lib/postgresql
+    healthcheck:
+      test: ["CMD-SHELL", "pg_isready -U postgres"]
+      interval: 5s
+      timeout: 5s
+      retries: 5
+
+  redis:
+    image: redis:7-alpine
+    container_name: envipath-redis
+    ports:
+      - "6379:6379"
+
+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

@@ -1,14 +1,12 @@
-from epdb.api import router as epdb_app_router
+from epapi.v1.router import router as v1_router  # Refactored API from epdb.api_v2
 from epdb.legacy_api import router as epdb_legacy_app_router
 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")
 
 # Add routers
-api_v1.add_router("/", epdb_app_router)
+api_v1.add_router("/", v1_router)
 api_legacy.add_router("/", epdb_legacy_app_router)

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
 
@@ -20,77 +21,104 @@ 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)
+ENV_PATH = os.environ.get("ENV_PATH", BASE_DIR / ".env")
+print(f"Loading env from {ENV_PATH}")
+load_dotenv(ENV_PATH, 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'
-ALLOWED_HOSTS = os.environ['ALLOWED_HOSTS'].split(',')
+DEBUG = os.environ.get("DEBUG", "False") == "True"
+
+ALLOWED_HOSTS = os.environ["ALLOWED_HOSTS"].split(",")
+
 
 # Application definition
 
 INSTALLED_APPS = [
-    'django.contrib.admin',
-    'django.contrib.auth',
-    'django.contrib.contenttypes',
-    'django.contrib.sessions',
-    'django.contrib.messages',
-    'django.contrib.staticfiles',
+    "django.contrib.admin",
+    "django.contrib.auth",
+    "django.contrib.contenttypes",
+    "django.contrib.sessions",
+    "django.contrib.messages",
+    "django.contrib.staticfiles",
     # 3rd party
-    'django_extensions',
-    'oauth2_provider',
+    "django_extensions",
+    "oauth2_provider",
     # Custom
-    'epdb',
-    'migration',
-    'epauth',
+    "epapi",  # API endpoints (v1, etc.)
+    "epdb",
+    "migration",
+    "bayer",
 ]
 
+TENANT = os.environ.get("TENANT", "public")
+
+if TENANT != "public":
+    INSTALLED_APPS.append(TENANT)
+
+EPDB_PACKAGE_MODEL = os.environ.get("EPDB_PACKAGE_MODEL", "epdb.Package")
+
+
+def GET_PACKAGE_MODEL():
+    from django.apps import apps
+
+    return apps.get_model(EPDB_PACKAGE_MODEL)
+
+
 AUTHENTICATION_BACKENDS = [
     "django.contrib.auth.backends.ModelBackend",
 ]
 
 MIDDLEWARE = [
-    'django.middleware.security.SecurityMiddleware',
-    'django.contrib.sessions.middleware.SessionMiddleware',
-    'django.middleware.common.CommonMiddleware',
-    'django.middleware.csrf.CsrfViewMiddleware',
-    'django.contrib.auth.middleware.AuthenticationMiddleware',
-    'django.contrib.messages.middleware.MessageMiddleware',
-    'django.middleware.clickjacking.XFrameOptionsMiddleware',
-    'oauth2_provider.middleware.OAuth2TokenMiddleware',
+    "django.middleware.security.SecurityMiddleware",
+    "django.contrib.sessions.middleware.SessionMiddleware",
+    "django.middleware.common.CommonMiddleware",
+    "django.middleware.csrf.CsrfViewMiddleware",
+    "django.contrib.auth.middleware.AuthenticationMiddleware",
+    "django.contrib.messages.middleware.MessageMiddleware",
+    "django.middleware.clickjacking.XFrameOptionsMiddleware",
+    "oauth2_provider.middleware.OAuth2TokenMiddleware",
 ]
 
 OAUTH2_PROVIDER = {
     "PKCE_REQUIRED": False,  # Accept PKCE requests but dont require them
 }
 
-if os.environ.get('REGISTRATION_MANDATORY', False) == 'True':
-    MIDDLEWARE.append('epdb.middleware.login_required_middleware.LoginRequiredMiddleware')
+if os.environ.get("REGISTRATION_MANDATORY", False) == "True":
+    MIDDLEWARE.append("epdb.middleware.login_required_middleware.LoginRequiredMiddleware")
 
-ROOT_URLCONF = 'envipath.urls'
+ROOT_URLCONF = "envipath.urls"
+
+TEMPLATE_DIRS = [
+    os.path.join(BASE_DIR, "bayer", "templates"),
+    os.path.join(BASE_DIR, "templates"),
+]
 
 TEMPLATES = [
     {
-        'BACKEND': 'django.template.backends.django.DjangoTemplates',
-        'DIRS': (os.path.join(BASE_DIR, 'templates'),),
-        'APP_DIRS': True,
-        'OPTIONS': {
-            'context_processors': [
-                'django.template.context_processors.debug',
-                'django.template.context_processors.request',
-                'django.contrib.auth.context_processors.auth',
-                'django.contrib.messages.context_processors.messages',
+        "BACKEND": "django.template.backends.django.DjangoTemplates",
+        "DIRS": TEMPLATE_DIRS,
+        "APP_DIRS": True,
+        "OPTIONS": {
+            "context_processors": [
+                "django.template.context_processors.debug",
+                "django.template.context_processors.request",
+                "django.contrib.auth.context_processors.auth",
+                "django.contrib.messages.context_processors.messages",
+                "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 +126,11 @@ WSGI_APPLICATION = 'envipath.wsgi.application'
 DATABASES = {
     "default": {
         "ENGINE": "django.db.backends.postgresql",
-        "USER": os.environ['POSTGRES_USER'],
-        "NAME": os.environ['POSTGRES_DB'],
-        "PASSWORD": os.environ['POSTGRES_PASSWORD'],
-        "HOST": os.environ['POSTGRES_SERVICE_NAME'],
-        "PORT": os.environ['POSTGRES_PORT']
+        "USER": os.environ["POSTGRES_USER"],
+        "NAME": os.environ["POSTGRES_DB"],
+        "PASSWORD": os.environ["POSTGRES_PASSWORD"],
+        "HOST": os.environ["POSTGRES_SERVICE_NAME"],
+        "PORT": os.environ["POSTGRES_PORT"],
     }
 }
 
@@ -110,96 +138,93 @@ 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.MinimumLengthValidator',
-    },
-    {
-        'NAME': 'django.contrib.auth.password_validation.CommonPasswordValidator',
-    },
-    {
-        'NAME': 'django.contrib.auth.password_validation.NumericPasswordValidator',
-    },
+    {"NAME": "django.contrib.auth.password_validation.UserAttributeSimilarityValidator"},
+    {"NAME": "django.contrib.auth.password_validation.MinimumLengthValidator"},
+    {"NAME": "django.contrib.auth.password_validation.CommonPasswordValidator"},
+    {"NAME": "django.contrib.auth.password_validation.NumericPasswordValidator"},
 ]
 
 # Internationalization
 # https://docs.djangoproject.com/en/4.2/topics/i18n/
 
-LANGUAGE_CODE = 'en-us'
+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_USER = os.environ['EMAIL_HOST_USER']
-    EMAIL_HOST_PASSWORD = os.environ['EMAIL_HOST_PASSWORD']
+    EMAIL_HOST = "mail.gandi.net"
+    EMAIL_HOST_USER = os.environ["EMAIL_HOST_USER"]
+    EMAIL_HOST_PASSWORD = os.environ["EMAIL_HOST_PASSWORD"]
     EMAIL_PORT = 587
+    DEFAULT_FROM_EMAIL = os.environ["DEFAULT_FROM_EMAIL"]
+    SERVER_EMAIL = os.environ["SERVER_EMAIL"]
 
 AUTH_USER_MODEL = "epdb.User"
-ADMIN_APPROVAL_REQUIRED = os.environ.get('ADMIN_APPROVAL_REQUIRED', 'False') == 'True'
+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'
-DEFAULT_VALUES = {
-    'description': 'no description'
-}
+AMBIT_URL = "http://localhost:9001"
+DEFAULT_VALUES = {"description": "no description"}
 
-EP_DATA_DIR = os.environ['EP_DATA_DIR']
-MODEL_DIR = os.path.join(EP_DATA_DIR, 'models')
+EP_DATA_DIR = os.environ["EP_DATA_DIR"]
+if not os.path.exists(EP_DATA_DIR):
+    os.mkdir(EP_DATA_DIR)
+
+MODEL_DIR = os.path.join(EP_DATA_DIR, "models")
 if not os.path.exists(MODEL_DIR):
     os.mkdir(MODEL_DIR)
 
-STATIC_DIR = os.path.join(EP_DATA_DIR, 'static')
+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")
+
+API_PAGINATION_DEFAULT_PAGE_SIZE = int(os.environ.get("API_PAGINATION_DEFAULT_PAGE_SIZE", 50))
+PAGINATION_MAX_PER_PAGE_SIZE = int(
+    os.environ.get("API_PAGINATION_MAX_PAGE_SIZE", 100)
+)  # Ninja override
+
 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 = (
-    BASE_DIR / 'static',
-)
+STATICFILES_DIRS = (BASE_DIR / "static",)
 
-FIXTURE_DIRS = (
-        BASE_DIR / 'fixtures',
-)
+FIXTURE_DIRS = (BASE_DIR / "fixtures",)
 
 # Logging
 LOGGING = {
@@ -207,8 +232,8 @@ LOGGING = {
     "disable_existing_loggers": True,
     "formatters": {
         "simple": {
-            'format': '[%(asctime)s] %(levelname)s %(module)s - %(message)s',
-            'datefmt': '%Y-%m-%d %H:%M:%S',
+            "format": "[%(asctime)s] %(levelname)s %(module)s - %(message)s",
+            "datefmt": "%Y-%m-%d %H:%M:%S",
         },
     },
     "handlers": {
@@ -221,7 +246,7 @@ LOGGING = {
             "level": "DEBUG",  # Or higher
             "class": "logging.FileHandler",
             "filename": os.path.join(LOG_DIR, "debug.log"),
-            "formatter": "simple"
+            "formatter": "simple",
         },
     },
     "loggers": {
@@ -229,72 +254,67 @@ 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': {
-            'handlers': ['file', 'console'],
-            'propagate': True,
-            'level': os.environ.get('LOG_LEVEL', 'INFO')
+        "envipath": {
+            "handlers": ["file", "console"],
+            "propagate": True,
+            "level": os.environ.get("LOG_LEVEL", "INFO"),
         },
         # For everything under utilities/ loaded via getlogger(__name__)
-        'utilities': {
-            'handlers': ['file', 'console'],
-            'propagate': True,
-            'level': os.environ.get('LOG_LEVEL', 'INFO')
+        "utilities": {
+            "handlers": ["file", "console"],
+            "propagate": True,
+            "level": os.environ.get("LOG_LEVEL", "INFO"),
         },
     },
 }
 
 # Flags
-ENVIFORMER_PRESENT = os.environ.get('ENVIFORMER_PRESENT', 'False') == 'True'
-if ENVIFORMER_PRESENT:
-    print("Loading enviFormer")
-    device = os.environ.get('ENVIFORMER_DEVICE', 'cpu')
-    from enviformer import load
-    ENVIFORMER_INSTANCE = load(device=device)
-    print("loaded")
+ENVIFORMER_PRESENT = os.environ.get("ENVIFORMER_PRESENT", "False") == "True"
+ENVIFORMER_DEVICE = os.environ.get("ENVIFORMER_DEVICE", "cpu")
 
 
 # If celery is not present set always eager to true which will cause delayed tasks to block until finished
-FLAG_CELERY_PRESENT = os.environ.get('FLAG_CELERY_PRESENT', 'False') == 'True'
+FLAG_CELERY_PRESENT = os.environ.get("FLAG_CELERY_PRESENT", "False") == "True"
 if not FLAG_CELERY_PRESENT:
     CELERY_TASK_ALWAYS_EAGER = True
 
 # Celery Configuration Options
 CELERY_TIMEZONE = "Europe/Berlin"
 # Celery Configuration
-CELERY_BROKER_URL = 'redis://localhost:6379/0'  # Use Redis as message broker
-CELERY_RESULT_BACKEND = 'redis://localhost:6379/1'
-CELERY_ACCEPT_CONTENT = ['json']
-CELERY_TASK_SERIALIZER = 'json'
+CELERY_BROKER_URL = "redis://localhost:6379/0"  # Use Redis as message broker
+CELERY_RESULT_BACKEND = "redis://localhost:6379/1"
+CELERY_ACCEPT_CONTENT = ["json"]
+CELERY_TASK_SERIALIZER = "json"
 
-MODEL_BUILDING_ENABLED = os.environ.get('MODEL_BUILDING_ENABLED', 'False') == 'True'
-APPLICABILITY_DOMAIN_ENABLED = os.environ.get('APPLICABILITY_DOMAIN_ENABLED', 'False') == 'True'
+MODEL_BUILDING_ENABLED = os.environ.get("MODEL_BUILDING_ENABLED", "False") == "True"
+APPLICABILITY_DOMAIN_ENABLED = os.environ.get("APPLICABILITY_DOMAIN_ENABLED", "False") == "True"
 DEFAULT_RF_MODEL_PARAMS = {
-    'base_clf': RandomForestClassifier(
+    "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(
-        criterion='entropy',
+    "base_clf": DecisionTreeClassifier(
+        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 +322,10 @@ 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 +334,71 @@ 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'):
-            for log_path in LOGGING.get('loggers').keys():
-                if event['logger'].startswith(log_path):
+        if event.get("logger"):
+            for log_path in LOGGING.get("loggers").keys():
+                if event["logger"].startswith(log_path):
                     return None
 
         return event
 
     sentry_sdk.init(
-        dsn=os.environ.get('SENTRY_DSN'),
+        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,
-    'CELERY': FLAG_CELERY_PRESENT,
-    'PLUGINS': PLUGINS_ENABLED,
-    'SENTRY': SENTRY_ENABLED,
-    'ENVIFORMER': ENVIFORMER_PRESENT,
-    'APPLICABILITY_DOMAIN': APPLICABILITY_DOMAIN_ENABLED,
+    "MODEL_BUILDING": MODEL_BUILDING_ENABLED,
+    "CELERY": FLAG_CELERY_PRESENT,
+    "PLUGINS": PLUGINS_ENABLED,
+    "SENTRY": SENTRY_ENABLED,
+    "ENVIFORMER": ENVIFORMER_PRESENT,
+    "APPLICABILITY_DOMAIN": APPLICABILITY_DOMAIN_ENABLED,
 }
 
 # path of the URL are checked via "startswith"
 # -> /password_reset/done is covered as well
 LOGIN_EXEMPT_URLS = [
-    '/register',
-    '/api/legacy/',
-    '/o/token/',
-    '/o/userinfo/',
-    '/password_reset/',
-    '/reset/',
-    '/microsoft/',
+    "/register",
+    "/api/v1/",  # Let API handle its own authentication
+    "/api/legacy/",
+    "/o/token/",
+    "/o/userinfo/",
+    "/password_reset/",
+    "/reset/",
+    "/microsoft/",
+    "/terms",
+    "/privacy",
+    "/cookie-policy",
+    "/about",
+    "/contact",
+    "/careers",
+    "/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']
-    MS_ENTRA_CLIENT_SECRET = os.environ['MS_CLIENT_SECRET']
-    MS_ENTRA_TENANT_ID = os.environ['MS_TENANT_ID']
+    # Add app to installed apps
+    INSTALLED_APPS.append("epauth")
+    # Set vars required by app
+    MS_ENTRA_CLIENT_ID = os.environ["MS_CLIENT_ID"]
+    MS_ENTRA_CLIENT_SECRET = os.environ["MS_CLIENT_SECRET"]
+    MS_ENTRA_TENANT_ID = os.environ["MS_TENANT_ID"]
     MS_ENTRA_AUTHORITY = f"https://login.microsoftonline.com/{MS_ENTRA_TENANT_ID}"
-    MS_ENTRA_REDIRECT_URI = os.environ['MS_REDIRECT_URI']
-    MS_ENTRA_SCOPES = os.environ.get('MS_SCOPES', '').split(',')
+    MS_ENTRA_REDIRECT_URI = os.environ["MS_REDIRECT_URI"]
+    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

@@ -14,17 +14,29 @@ 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),
     path("api/v1/", api_v1.urls),
     path("api/legacy/", api_legacy.urls),
     path("o/", include("oauth2_provider.urls", namespace="oauth2_provider")),
 ]
+
+if "migration" in s.INSTALLED_APPS:
+    urlpatterns.append(path("", include("migration.urls")))
+
+if s.MS_ENTRA_ENABLED:
+    urlpatterns.append(path("", include("epauth.urls")))
+
+# Custom error handlers
+handler400 = "epdb.views.handler400"
+handler403 = "epdb.views.handler403"
+handler404 = "epdb.views.handler404"
+handler500 = "epdb.views.handler500"

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()

epapi/apps.py

@@ -0,0 +1,6 @@
+from django.apps import AppConfig
+
+
+class EpapiConfig(AppConfig):
+    default_auto_field = "django.db.models.BigAutoField"
+    name = "epapi"

epapi/tests/__init__.py

@@ -0,0 +1 @@
+# Tests for epapi app

epapi/tests/utils/__init__.py

@@ -0,0 +1 @@
+"""Tests for epapi utility modules."""

epapi/tests/utils/test_validation_errors.py

@@ -0,0 +1,218 @@
+"""
+Tests for validation error utilities.
+
+Tests the format_validation_error() and handle_validation_error() functions
+that transform Pydantic validation errors into user-friendly messages.
+"""
+
+from django.test import TestCase, tag
+import json
+from pydantic import BaseModel, ValidationError, field_validator
+from typing import Literal
+
+from ninja.errors import HttpError
+from epapi.utils.validation_errors import format_validation_error, handle_validation_error
+
+
+@tag("api", "utils")
+class ValidationErrorUtilityTests(TestCase):
+    """Test validation error utility functions."""
+
+    def test_format_missing_field_error(self):
+        """Test formatting of missing required field error."""
+
+        # Create a model with required field
+        class TestModel(BaseModel):
+            required_field: str
+
+        # Trigger validation error
+        try:
+            TestModel()
+        except ValidationError as e:
+            errors = e.errors()
+            self.assertEqual(len(errors), 1)
+            formatted = format_validation_error(errors[0])
+            self.assertEqual(formatted, "This field is required")
+
+    def test_format_enum_error(self):
+        """Test formatting of enum validation error."""
+
+        class TestModel(BaseModel):
+            status: Literal["active", "inactive"]
+
+        try:
+            TestModel(status="invalid")
+        except ValidationError as e:
+            errors = e.errors()
+            self.assertEqual(len(errors), 1)
+            formatted = format_validation_error(errors[0])
+            # Literal errors get formatted as "Please enter ..." with the valid options
+            self.assertIn("Please enter", formatted)
+            self.assertIn("active", formatted)
+            self.assertIn("inactive", formatted)
+
+    def test_format_type_errors(self):
+        """Test formatting of type validation errors (string, int, float)."""
+        test_cases = [
+            # (field_type, invalid_value, expected_message)
+            # Note: We don't check exact error_type as Pydantic may use different types
+            # (e.g., int_type vs int_parsing) but we verify the formatted message is correct
+            (str, 123, "Please enter a valid string"),
+            (int, "not_a_number", "Please enter a valid int"),
+            (float, "not_a_float", "Please enter a valid float"),
+        ]
+
+        for field_type, invalid_value, expected_message in test_cases:
+            with self.subTest(field_type=field_type.__name__):
+
+                class TestModel(BaseModel):
+                    field: field_type
+
+                try:
+                    TestModel(field=invalid_value)
+                except ValidationError as e:
+                    errors = e.errors()
+                    self.assertEqual(len(errors), 1)
+                    formatted = format_validation_error(errors[0])
+                    self.assertEqual(formatted, expected_message)
+
+    def test_format_value_error(self):
+        """Test formatting of value error from custom validator."""
+
+        class TestModel(BaseModel):
+            age: int
+
+            @field_validator("age")
+            @classmethod
+            def validate_age(cls, v):
+                if v < 0:
+                    raise ValueError("Age must be positive")
+                return v
+
+        try:
+            TestModel(age=-5)
+        except ValidationError as e:
+            errors = e.errors()
+            self.assertEqual(len(errors), 1)
+            formatted = format_validation_error(errors[0])
+            self.assertEqual(formatted, "Age must be positive")
+
+    def test_format_unknown_error_type_fallback(self):
+        """Test that unknown error types fall back to default formatting."""
+        # Mock an error with an unknown type
+        mock_error = {
+            "type": "unknown_custom_type",
+            "msg": "Input should be a valid email address",
+            "ctx": {},
+        }
+
+        formatted = format_validation_error(mock_error)
+        # Should use the else branch which does replacements on the message
+        self.assertEqual(formatted, "Please enter a valid email address")
+
+    def test_handle_validation_error_structure(self):
+        """Test that handle_validation_error raises HttpError with correct structure."""
+
+        class TestModel(BaseModel):
+            name: str
+            count: int
+
+        try:
+            TestModel(name=123, count="invalid")
+        except ValidationError as e:
+            # handle_validation_error should raise HttpError
+            with self.assertRaises(HttpError) as context:
+                handle_validation_error(e)
+
+            http_error = context.exception
+            self.assertEqual(http_error.status_code, 400)
+
+            # Parse the JSON from the error message
+            error_data = json.loads(http_error.message)
+
+            # Check structure
+            self.assertEqual(error_data["type"], "validation_error")
+            self.assertIn("field_errors", error_data)
+            self.assertIn("message", error_data)
+            self.assertEqual(error_data["message"], "Please correct the errors below")
+
+            # Check that both fields have errors
+            self.assertIn("name", error_data["field_errors"])
+            self.assertIn("count", error_data["field_errors"])
+
+    def test_handle_validation_error_no_pydantic_internals(self):
+        """Test that handle_validation_error doesn't expose Pydantic internals."""
+
+        class TestModel(BaseModel):
+            email: str
+
+        try:
+            TestModel(email=123)
+        except ValidationError as e:
+            with self.assertRaises(HttpError) as context:
+                handle_validation_error(e)
+
+            http_error = context.exception
+            error_data = json.loads(http_error.message)
+            error_str = json.dumps(error_data)
+
+            # Ensure no Pydantic internals are exposed
+            self.assertNotIn("pydantic", error_str.lower())
+            self.assertNotIn("https://errors.pydantic.dev", error_str)
+            self.assertNotIn("loc", error_str)
+
+    def test_handle_validation_error_user_friendly_messages(self):
+        """Test that all error messages are user-friendly."""
+
+        class TestModel(BaseModel):
+            name: str
+            age: int
+            status: Literal["active", "inactive"]
+
+        try:
+            TestModel(name=123, status="invalid")  # Multiple errors
+        except ValidationError as e:
+            with self.assertRaises(HttpError) as context:
+                handle_validation_error(e)
+
+            http_error = context.exception
+            error_data = json.loads(http_error.message)
+
+            # All messages should be user-friendly (contain "Please" or "This field")
+            for field, messages in error_data["field_errors"].items():
+                for message in messages:
+                    # User-friendly messages start with "Please" or "This field"
+                    self.assertTrue(
+                        message.startswith("Please") or message.startswith("This field"),
+                        f"Message '{message}' is not user-friendly",
+                    )
+
+    def test_handle_validation_error_multiple_errors_same_field(self):
+        """Test handling multiple validation errors for the same field."""
+
+        class TestModel(BaseModel):
+            value: int
+
+            @field_validator("value")
+            @classmethod
+            def validate_range(cls, v):
+                if v < 0:
+                    raise ValueError("Must be non-negative")
+                if v > 100:
+                    raise ValueError("Must be at most 100")
+                return v
+
+        # Test with string (type error) - this will fail before the validator runs
+        try:
+            TestModel(value="invalid")
+        except ValidationError as e:
+            with self.assertRaises(HttpError) as context:
+                handle_validation_error(e)
+
+            http_error = context.exception
+            error_data = json.loads(http_error.message)
+
+            # Should have error for 'value' field
+            self.assertIn("value", error_data["field_errors"])
+            self.assertIsInstance(error_data["field_errors"]["value"], list)
+            self.assertGreater(len(error_data["field_errors"]["value"]), 0)

epapi/tests/v1/__init__.py

@@ -0,0 +1 @@
+# Tests for epapi v1 API

epapi/tests/v1/test_additional_information.py

@@ -0,0 +1,448 @@
+"""
+Tests for Additional Information API endpoints.
+
+Tests CRUD operations on scenario additional information including the new PATCH endpoint.
+"""
+
+from django.test import TestCase, tag
+import json
+from uuid import uuid4
+
+from epdb.logic import PackageManager, UserManager
+from epdb.models import Scenario
+
+
+@tag("api", "additional_information")
+class AdditionalInformationAPITests(TestCase):
+    """Test additional information API endpoints."""
+
+    @classmethod
+    def setUpTestData(cls):
+        """Set up test data: user, package, and scenario."""
+        cls.user = UserManager.create_user(
+            "ai-test-user",
+            "ai-test@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=False,
+            is_active=True,
+        )
+        cls.other_user = UserManager.create_user(
+            "ai-other-user",
+            "ai-other@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=False,
+            is_active=True,
+        )
+        cls.package = PackageManager.create_package(
+            cls.user, "AI Test Package", "Test package for additional information"
+        )
+        # Package owned by other_user (no access for cls.user)
+        cls.other_package = PackageManager.create_package(
+            cls.other_user, "Other Package", "Package without access"
+        )
+        # Create a scenario for testing
+        cls.scenario = Scenario.objects.create(
+            package=cls.package,
+            name="Test Scenario",
+            description="Test scenario for additional information tests",
+            scenario_type="biodegradation",
+            scenario_date="2024-01-01",
+            additional_information={},  # Initialize with empty dict
+        )
+        cls.other_scenario = Scenario.objects.create(
+            package=cls.other_package,
+            name="Other Scenario",
+            description="Scenario in package without access",
+            scenario_type="biodegradation",
+            scenario_date="2024-01-01",
+            additional_information={},
+        )
+
+    def test_list_all_schemas(self):
+        """Test GET /api/v1/information/schema/ returns all schemas."""
+        self.client.force_login(self.user)
+
+        response = self.client.get("/api/v1/information/schema/")
+
+        self.assertEqual(response.status_code, 200)
+        data = response.json()
+        self.assertIsInstance(data, dict)
+        # Should have multiple schemas
+        self.assertGreater(len(data), 0)
+        # Each schema should have RJSF format
+        for name, schema in data.items():
+            self.assertIn("schema", schema)
+            self.assertIn("uiSchema", schema)
+            self.assertIn("formData", schema)
+            self.assertIn("groups", schema)
+
+    def test_get_specific_schema(self):
+        """Test GET /api/v1/information/schema/{model_name}/ returns specific schema."""
+        self.client.force_login(self.user)
+
+        # Assuming 'temperature' is a valid model
+        response = self.client.get("/api/v1/information/schema/temperature/")
+
+        self.assertEqual(response.status_code, 200)
+        data = response.json()
+        self.assertIn("schema", data)
+        self.assertIn("uiSchema", data)
+
+    def test_get_nonexistent_schema_returns_404(self):
+        """Test GET for non-existent schema returns 404."""
+        self.client.force_login(self.user)
+
+        response = self.client.get("/api/v1/information/schema/nonexistent/")
+
+        self.assertEqual(response.status_code, 404)
+
+    def test_list_scenario_information_empty(self):
+        """Test GET /api/v1/scenario/{uuid}/information/ returns empty list initially."""
+        self.client.force_login(self.user)
+
+        response = self.client.get(f"/api/v1/scenario/{self.scenario.uuid}/information/")
+
+        self.assertEqual(response.status_code, 200)
+        data = response.json()
+        self.assertIsInstance(data, list)
+        self.assertEqual(len(data), 0)
+
+    def test_create_additional_information(self):
+        """Test POST creates additional information."""
+        self.client.force_login(self.user)
+
+        # Create temperature information (assuming temperature model exists)
+        payload = {"interval": {"start": 20, "end": 25}}
+        response = self.client.post(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/temperature/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 200)
+        data = response.json()
+        self.assertEqual(data["status"], "created")
+        self.assertIn("uuid", data)
+        self.assertIsNotNone(data["uuid"])
+
+    def test_create_with_invalid_data_returns_400(self):
+        """Test POST with invalid data returns 400 with validation errors."""
+        self.client.force_login(self.user)
+
+        # Invalid data (missing required fields or wrong types)
+        payload = {"invalid_field": "value"}
+        response = self.client.post(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/temperature/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 400)
+        data = response.json()
+        # Should have validation error details in 'detail' field
+        self.assertIn("detail", data)
+
+    def test_validation_errors_are_user_friendly(self):
+        """Test that validation errors are user-friendly and field-specific."""
+        self.client.force_login(self.user)
+
+        # Invalid data - wrong type (string instead of number in interval)
+        payload = {"interval": {"start": "not_a_number", "end": 25}}
+        response = self.client.post(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/temperature/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 400)
+        data = response.json()
+
+        # Parse the error response - Django Ninja wraps errors in 'detail'
+        error_str = data.get("detail") or data.get("error")
+        self.assertIsNotNone(error_str, "Response should contain error details")
+
+        # Parse the JSON error string
+        error_data = json.loads(error_str)
+
+        # Check structure
+        self.assertEqual(error_data.get("type"), "validation_error")
+        self.assertIn("field_errors", error_data)
+        self.assertIn("message", error_data)
+
+        # Ensure error messages are user-friendly (no Pydantic URLs or technical jargon)
+        error_str = json.dumps(error_data)
+        self.assertNotIn("pydantic", error_str.lower())
+        self.assertNotIn("https://errors.pydantic.dev", error_str)
+        self.assertNotIn("loc", error_str)  # No technical field like 'loc'
+
+        # Check that error message is helpful
+        self.assertIn("Please", error_data["message"])  # User-friendly language
+
+    def test_patch_additional_information(self):
+        """Test PATCH updates existing additional information."""
+        self.client.force_login(self.user)
+
+        # First create an item
+        create_payload = {"interval": {"start": 20, "end": 25}}
+        create_response = self.client.post(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/temperature/",
+            data=json.dumps(create_payload),
+            content_type="application/json",
+        )
+        item_uuid = create_response.json()["uuid"]
+
+        # Then update it with PATCH
+        update_payload = {"interval": {"start": 30, "end": 35}}
+        patch_response = self.client.patch(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/item/{item_uuid}/",
+            data=json.dumps(update_payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(patch_response.status_code, 200)
+        data = patch_response.json()
+        self.assertEqual(data["status"], "updated")
+        self.assertEqual(data["uuid"], item_uuid)  # UUID preserved
+
+        # Verify the data was updated
+        list_response = self.client.get(f"/api/v1/scenario/{self.scenario.uuid}/information/")
+        items = list_response.json()
+        self.assertEqual(len(items), 1)
+        updated_item = items[0]
+        self.assertEqual(updated_item["uuid"], item_uuid)
+        self.assertEqual(updated_item["data"]["interval"]["start"], 30)
+        self.assertEqual(updated_item["data"]["interval"]["end"], 35)
+
+    def test_patch_nonexistent_item_returns_404(self):
+        """Test PATCH on non-existent item returns 404."""
+        self.client.force_login(self.user)
+
+        fake_uuid = str(uuid4())
+        payload = {"interval": {"start": 30, "end": 35}}
+        response = self.client.patch(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/item/{fake_uuid}/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 404)
+
+    def test_patch_with_invalid_data_returns_400(self):
+        """Test PATCH with invalid data returns 400."""
+        self.client.force_login(self.user)
+
+        # First create an item
+        create_payload = {"interval": {"start": 20, "end": 25}}
+        create_response = self.client.post(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/temperature/",
+            data=json.dumps(create_payload),
+            content_type="application/json",
+        )
+        item_uuid = create_response.json()["uuid"]
+
+        # Try to update with invalid data
+        invalid_payload = {"invalid_field": "value"}
+        patch_response = self.client.patch(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/item/{item_uuid}/",
+            data=json.dumps(invalid_payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(patch_response.status_code, 400)
+
+    def test_patch_validation_errors_are_user_friendly(self):
+        """Test that PATCH validation errors are user-friendly and field-specific."""
+        self.client.force_login(self.user)
+
+        # First create an item
+        create_payload = {"interval": {"start": 20, "end": 25}}
+        create_response = self.client.post(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/temperature/",
+            data=json.dumps(create_payload),
+            content_type="application/json",
+        )
+        item_uuid = create_response.json()["uuid"]
+
+        # Update with invalid data - wrong type (string instead of number in interval)
+        invalid_payload = {"interval": {"start": "not_a_number", "end": 25}}
+        patch_response = self.client.patch(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/item/{item_uuid}/",
+            data=json.dumps(invalid_payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(patch_response.status_code, 400)
+        data = patch_response.json()
+
+        # Parse the error response - Django Ninja wraps errors in 'detail'
+        error_str = data.get("detail") or data.get("error")
+        self.assertIsNotNone(error_str, "Response should contain error details")
+
+        # Parse the JSON error string
+        error_data = json.loads(error_str)
+
+        # Check structure
+        self.assertEqual(error_data.get("type"), "validation_error")
+        self.assertIn("field_errors", error_data)
+        self.assertIn("message", error_data)
+
+        # Ensure error messages are user-friendly (no Pydantic URLs or technical jargon)
+        error_str = json.dumps(error_data)
+        self.assertNotIn("pydantic", error_str.lower())
+        self.assertNotIn("https://errors.pydantic.dev", error_str)
+        self.assertNotIn("loc", error_str)  # No technical field like 'loc'
+
+        # Check that error message is helpful
+        self.assertIn("Please", error_data["message"])  # User-friendly language
+
+    def test_delete_additional_information(self):
+        """Test DELETE removes additional information."""
+        self.client.force_login(self.user)
+
+        # Create an item
+        create_payload = {"interval": {"start": 20, "end": 25}}
+        create_response = self.client.post(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/temperature/",
+            data=json.dumps(create_payload),
+            content_type="application/json",
+        )
+        item_uuid = create_response.json()["uuid"]
+
+        # Delete it
+        delete_response = self.client.delete(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/item/{item_uuid}/"
+        )
+
+        self.assertEqual(delete_response.status_code, 200)
+        data = delete_response.json()
+        self.assertEqual(data["status"], "deleted")
+
+        # Verify deletion
+        list_response = self.client.get(f"/api/v1/scenario/{self.scenario.uuid}/information/")
+        items = list_response.json()
+        self.assertEqual(len(items), 0)
+
+    def test_delete_nonexistent_item_returns_404(self):
+        """Test DELETE on non-existent item returns 404."""
+        self.client.force_login(self.user)
+
+        fake_uuid = str(uuid4())
+        response = self.client.delete(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/item/{fake_uuid}/"
+        )
+
+        self.assertEqual(response.status_code, 404)
+
+    def test_multiple_items_crud(self):
+        """Test creating, updating, and deleting multiple items."""
+        self.client.force_login(self.user)
+
+        # Create first item
+        item1_payload = {"interval": {"start": 20, "end": 25}}
+        response1 = self.client.post(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/temperature/",
+            data=json.dumps(item1_payload),
+            content_type="application/json",
+        )
+        item1_uuid = response1.json()["uuid"]
+
+        # Create second item (different type if available, or same type)
+        item2_payload = {"interval": {"start": 30, "end": 35}}
+        response2 = self.client.post(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/temperature/",
+            data=json.dumps(item2_payload),
+            content_type="application/json",
+        )
+        item2_uuid = response2.json()["uuid"]
+
+        # Verify both exist
+        list_response = self.client.get(f"/api/v1/scenario/{self.scenario.uuid}/information/")
+        items = list_response.json()
+        self.assertEqual(len(items), 2)
+
+        # Update first item
+        update_payload = {"interval": {"start": 15, "end": 20}}
+        self.client.patch(
+            f"/api/v1/scenario/{self.scenario.uuid}/information/item/{item1_uuid}/",
+            data=json.dumps(update_payload),
+            content_type="application/json",
+        )
+
+        # Delete second item
+        self.client.delete(f"/api/v1/scenario/{self.scenario.uuid}/information/item/{item2_uuid}/")
+
+        # Verify final state: one item with updated data
+        list_response = self.client.get(f"/api/v1/scenario/{self.scenario.uuid}/information/")
+        items = list_response.json()
+        self.assertEqual(len(items), 1)
+        self.assertEqual(items[0]["uuid"], item1_uuid)
+        self.assertEqual(items[0]["data"]["interval"]["start"], 15)
+
+    def test_list_info_denied_without_permission(self):
+        """User cannot list info for scenario in package they don't have access to"""
+        self.client.force_login(self.user)
+        response = self.client.get(f"/api/v1/scenario/{self.other_scenario.uuid}/information/")
+        self.assertEqual(response.status_code, 403)
+
+    def test_add_info_denied_without_permission(self):
+        """User cannot add info to scenario in package they don't have access to"""
+        self.client.force_login(self.user)
+        payload = {"interval": {"start": 25, "end": 30}}
+        response = self.client.post(
+            f"/api/v1/scenario/{self.other_scenario.uuid}/information/temperature/",
+            json.dumps(payload),
+            content_type="application/json",
+        )
+        self.assertEqual(response.status_code, 403)
+
+    def test_update_info_denied_without_permission(self):
+        """User cannot update info in scenario they don't have access to"""
+        self.client.force_login(self.other_user)
+        # First create an item as other_user
+        create_payload = {"interval": {"start": 20, "end": 25}}
+        create_response = self.client.post(
+            f"/api/v1/scenario/{self.other_scenario.uuid}/information/temperature/",
+            data=json.dumps(create_payload),
+            content_type="application/json",
+        )
+        item_uuid = create_response.json()["uuid"]
+
+        # Try to update as user (who doesn't have access)
+        self.client.force_login(self.user)
+        update_payload = {"interval": {"start": 30, "end": 35}}
+        response = self.client.patch(
+            f"/api/v1/scenario/{self.other_scenario.uuid}/information/item/{item_uuid}/",
+            data=json.dumps(update_payload),
+            content_type="application/json",
+        )
+        self.assertEqual(response.status_code, 403)
+
+    def test_delete_info_denied_without_permission(self):
+        """User cannot delete info from scenario they don't have access to"""
+        self.client.force_login(self.other_user)
+        # First create an item as other_user
+        create_payload = {"interval": {"start": 20, "end": 25}}
+        create_response = self.client.post(
+            f"/api/v1/scenario/{self.other_scenario.uuid}/information/temperature/",
+            data=json.dumps(create_payload),
+            content_type="application/json",
+        )
+        item_uuid = create_response.json()["uuid"]
+
+        # Try to delete as user (who doesn't have access)
+        self.client.force_login(self.user)
+        response = self.client.delete(
+            f"/api/v1/scenario/{self.other_scenario.uuid}/information/item/{item_uuid}/"
+        )
+        self.assertEqual(response.status_code, 403)
+
+    def test_nonexistent_scenario_returns_404(self):
+        """Test operations on non-existent scenario return 404."""
+        self.client.force_login(self.user)
+
+        fake_uuid = uuid4()
+        response = self.client.get(f"/api/v1/scenario/{fake_uuid}/information/")
+
+        self.assertEqual(response.status_code, 404)

epapi/tests/v1/test_api_permissions.py

@@ -0,0 +1,477 @@
+from django.test import TestCase, tag
+
+from epdb.logic import GroupManager, PackageManager, UserManager
+from epdb.models import (
+    Compound,
+    GroupPackagePermission,
+    Permission,
+    UserPackagePermission,
+)
+
+
+@tag("api", "end2end")
+class APIPermissionTestBase(TestCase):
+    """
+    Base class for API permission tests.
+
+    Sets up common test data:
+    - user1: Owner of packages
+    - user2: User with various permissions
+    - user3: User with no permissions
+    - reviewed_package: Public package (reviewed=True)
+    - unreviewed_package_owned: Unreviewed package owned by user1
+    - unreviewed_package_read: Unreviewed package with READ permission for user2
+    - unreviewed_package_write: Unreviewed package with WRITE permission for user2
+    - unreviewed_package_all: Unreviewed package with ALL permission for user2
+    - unreviewed_package_no_access: Unreviewed package with no permissions for user2/user3
+    - group_package: Unreviewed package accessible via group permission
+    - test_group: Group containing user2
+    """
+
+    @classmethod
+    def setUpTestData(cls):
+        # Create users
+        cls.user1 = UserManager.create_user(
+            "permission-user1",
+            "permission-user1@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=False,
+            is_active=True,
+        )
+        cls.user2 = UserManager.create_user(
+            "permission-user2",
+            "permission-user2@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=False,
+            is_active=True,
+        )
+        cls.user3 = UserManager.create_user(
+            "permission-user3",
+            "permission-user3@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=False,
+            is_active=True,
+        )
+
+        # Delete default packages to ensure clean test data
+        for user in [cls.user1, cls.user2, cls.user3]:
+            default_pkg = user.default_package
+            user.default_package = None
+            user.save()
+            if default_pkg:
+                default_pkg.delete()
+
+        # Create reviewed package (public)
+        cls.reviewed_package = PackageManager.create_package(
+            cls.user1, "Reviewed Package", "Public package"
+        )
+        cls.reviewed_package.reviewed = True
+        cls.reviewed_package.save()
+
+        # Create unreviewed packages with various permissions
+        cls.unreviewed_package_owned = PackageManager.create_package(
+            cls.user1, "User1 Owned Package", "Owned by user1"
+        )
+
+        cls.unreviewed_package_read = PackageManager.create_package(
+            cls.user1, "User2 Read Package", "User2 has READ permission"
+        )
+        UserPackagePermission.objects.create(
+            user=cls.user2, package=cls.unreviewed_package_read, permission=Permission.READ[0]
+        )
+
+        cls.unreviewed_package_write = PackageManager.create_package(
+            cls.user1, "User2 Write Package", "User2 has WRITE permission"
+        )
+        UserPackagePermission.objects.create(
+            user=cls.user2, package=cls.unreviewed_package_write, permission=Permission.WRITE[0]
+        )
+
+        cls.unreviewed_package_all = PackageManager.create_package(
+            cls.user1, "User2 All Package", "User2 has ALL permission"
+        )
+        UserPackagePermission.objects.create(
+            user=cls.user2, package=cls.unreviewed_package_all, permission=Permission.ALL[0]
+        )
+
+        cls.unreviewed_package_no_access = PackageManager.create_package(
+            cls.user1, "No Access Package", "No permissions for user2/user3"
+        )
+
+        # Create group and group package
+        cls.test_group = GroupManager.create_group(
+            cls.user1, "Test Group", "Group for permission testing"
+        )
+        cls.test_group.user_member.add(cls.user2)
+        cls.test_group.save()
+
+        cls.group_package = PackageManager.create_package(
+            cls.user1, "Group Package", "Accessible via group permission"
+        )
+        GroupPackagePermission.objects.create(
+            group=cls.test_group, package=cls.group_package, permission=Permission.READ[0]
+        )
+
+        # Create test compounds in each package
+        cls.reviewed_compound = Compound.create(
+            cls.reviewed_package, "C", "Reviewed Compound", "Test compound"
+        )
+        cls.owned_compound = Compound.create(
+            cls.unreviewed_package_owned, "CC", "Owned Compound", "Test compound"
+        )
+        cls.read_compound = Compound.create(
+            cls.unreviewed_package_read, "CCC", "Read Compound", "Test compound"
+        )
+        cls.write_compound = Compound.create(
+            cls.unreviewed_package_write, "CCCC", "Write Compound", "Test compound"
+        )
+        cls.all_compound = Compound.create(
+            cls.unreviewed_package_all, "CCCCC", "All Compound", "Test compound"
+        )
+        cls.no_access_compound = Compound.create(
+            cls.unreviewed_package_no_access, "CCCCCC", "No Access Compound", "Test compound"
+        )
+        cls.group_compound = Compound.create(
+            cls.group_package, "CCCCCCC", "Group Compound", "Test compound"
+        )
+
+
+@tag("api", "end2end")
+class PackageListPermissionTest(APIPermissionTestBase):
+    """
+    Test permissions for /api/v1/packages/ endpoint.
+
+    Special case: This endpoint allows anonymous access (auth=None)
+    """
+
+    ENDPOINT = "/api/v1/packages/"
+
+    def test_anonymous_user_sees_only_reviewed_packages(self):
+        """Anonymous users should only see reviewed packages."""
+        self.client.logout()
+        response = self.client.get(self.ENDPOINT)
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        # Should only see reviewed package
+        self.assertEqual(payload["total_items"], 1)
+        self.assertEqual(payload["items"][0]["uuid"], str(self.reviewed_package.uuid))
+        self.assertEqual(payload["items"][0]["review_status"], "reviewed")
+
+    def test_authenticated_user_sees_all_readable_packages(self):
+        """Authenticated users see reviewed + packages they have access to."""
+        self.client.force_login(self.user2)
+        response = self.client.get(self.ENDPOINT)
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        # user2 should see:
+        # - reviewed_package (public)
+        # - unreviewed_package_read (READ permission)
+        # - unreviewed_package_write (WRITE permission)
+        # - unreviewed_package_all (ALL permission)
+        # - group_package (via group membership)
+        # Total: 5 packages
+        self.assertEqual(payload["total_items"], 5)
+
+        visible_uuids = {item["uuid"] for item in payload["items"]}
+        expected_uuids = {
+            str(self.reviewed_package.uuid),
+            str(self.unreviewed_package_read.uuid),
+            str(self.unreviewed_package_write.uuid),
+            str(self.unreviewed_package_all.uuid),
+            str(self.group_package.uuid),
+        }
+        self.assertEqual(visible_uuids, expected_uuids)
+
+    def test_owner_sees_all_owned_packages(self):
+        """Package owner sees all packages they created."""
+        self.client.force_login(self.user1)
+        response = self.client.get(self.ENDPOINT)
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        # user1 owns all packages
+        # Total: 7 packages (all packages created in setUpTestData)
+        self.assertEqual(payload["total_items"], 7)
+
+    def test_filter_by_review_status_true(self):
+        """Filter to show only reviewed packages."""
+        self.client.force_login(self.user2)
+        response = self.client.get(self.ENDPOINT, {"review_status": True})
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        # Only reviewed_package
+        self.assertEqual(payload["total_items"], 1)
+        self.assertTrue(all(item["review_status"] == "reviewed" for item in payload["items"]))
+
+    def test_filter_by_review_status_false(self):
+        """Filter to show only unreviewed packages."""
+        self.client.force_login(self.user2)
+        response = self.client.get(self.ENDPOINT, {"review_status": False})
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        # user2's accessible unreviewed packages: 4
+        self.assertEqual(payload["total_items"], 4)
+        self.assertTrue(all(item["review_status"] == "unreviewed" for item in payload["items"]))
+
+    def test_anonymous_filter_unreviewed_returns_empty(self):
+        """Anonymous users get no results when filtering for unreviewed."""
+        self.client.logout()
+        response = self.client.get(self.ENDPOINT, {"review_status": False})
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        self.assertEqual(payload["total_items"], 0)
+
+
+@tag("api", "end2end")
+class GlobalCompoundListPermissionTest(APIPermissionTestBase):
+    """
+    Test permissions for /api/v1/compounds/ endpoint.
+
+    This endpoint requires authentication.
+    """
+
+    ENDPOINT = "/api/v1/compounds/"
+
+    def test_anonymous_user_cannot_access(self):
+        """Anonymous users should get 401 Unauthorized."""
+        self.client.logout()
+        response = self.client.get(self.ENDPOINT)
+
+        self.assertEqual(response.status_code, 401)
+
+    def test_authenticated_user_sees_compounds_from_readable_packages(self):
+        """Authenticated users see compounds from packages they can read."""
+        self.client.force_login(self.user2)
+        response = self.client.get(self.ENDPOINT)
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        self.assertEqual(payload["total_items"], 5)
+
+        visible_uuids = {item["uuid"] for item in payload["items"]}
+        expected_uuids = {
+            str(self.reviewed_compound.uuid),
+            str(self.read_compound.uuid),
+            str(self.write_compound.uuid),
+            str(self.all_compound.uuid),
+            str(self.group_compound.uuid),
+        }
+        self.assertEqual(visible_uuids, expected_uuids)
+
+    def test_user_without_permission_cannot_see_compound(self):
+        """User without permission to package cannot see its compounds."""
+        self.client.force_login(self.user3)
+        response = self.client.get(self.ENDPOINT)
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        # user3 should only see compounds from reviewed_package
+        self.assertEqual(payload["total_items"], 1)
+        self.assertEqual(payload["items"][0]["uuid"], str(self.reviewed_compound.uuid))
+
+    def test_owner_sees_all_compounds(self):
+        """Package owner sees all compounds they created."""
+        self.client.force_login(self.user1)
+        response = self.client.get(self.ENDPOINT)
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        # user1 owns all packages, so sees all compounds
+        self.assertEqual(payload["total_items"], 7)
+
+
+@tag("api", "end2end")
+class PackageScopedCompoundListPermissionTest(APIPermissionTestBase):
+    """
+    Test permissions for /api/v1/package/{uuid}/compound/ endpoint.
+
+    This endpoint requires authentication AND package access.
+    """
+
+    def test_anonymous_user_cannot_access_reviewed_package(self):
+        """Anonymous users should get 401 even for reviewed packages."""
+        self.client.logout()
+        endpoint = f"/api/v1/package/{self.reviewed_package.uuid}/compound/"
+        response = self.client.get(endpoint)
+
+        self.assertEqual(response.status_code, 401)
+
+    def test_authenticated_user_can_access_reviewed_package(self):
+        """Authenticated users can access reviewed packages."""
+        self.client.force_login(self.user3)
+        endpoint = f"/api/v1/package/{self.reviewed_package.uuid}/compound/"
+        response = self.client.get(endpoint)
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        self.assertEqual(payload["total_items"], 1)
+        self.assertEqual(payload["items"][0]["uuid"], str(self.reviewed_compound.uuid))
+
+    def test_user_can_access_package_with_read_permission(self):
+        """User with READ permission can access package-scoped endpoint."""
+        self.client.force_login(self.user2)
+        endpoint = f"/api/v1/package/{self.unreviewed_package_read.uuid}/compound/"
+        response = self.client.get(endpoint)
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        self.assertEqual(payload["total_items"], 1)
+        self.assertEqual(payload["items"][0]["uuid"], str(self.read_compound.uuid))
+
+    def test_user_can_access_package_with_write_permission(self):
+        """User with WRITE permission can access package-scoped endpoint."""
+        self.client.force_login(self.user2)
+        endpoint = f"/api/v1/package/{self.unreviewed_package_write.uuid}/compound/"
+        response = self.client.get(endpoint)
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        self.assertEqual(payload["total_items"], 1)
+        self.assertEqual(payload["items"][0]["uuid"], str(self.write_compound.uuid))
+
+    def test_user_can_access_package_with_all_permission(self):
+        """User with ALL permission can access package-scoped endpoint."""
+        self.client.force_login(self.user2)
+        endpoint = f"/api/v1/package/{self.unreviewed_package_all.uuid}/compound/"
+        response = self.client.get(endpoint)
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        self.assertEqual(payload["total_items"], 1)
+        self.assertEqual(payload["items"][0]["uuid"], str(self.all_compound.uuid))
+
+    def test_user_cannot_access_package_without_permission(self):
+        """User without permission gets 403 Forbidden."""
+        self.client.force_login(self.user2)
+        endpoint = f"/api/v1/package/{self.unreviewed_package_no_access.uuid}/compound/"
+        response = self.client.get(endpoint)
+
+        self.assertEqual(response.status_code, 403)
+
+    def test_nonexistent_package_returns_404(self):
+        """Request for non-existent package returns 404."""
+        self.client.force_login(self.user2)
+        fake_uuid = "00000000-0000-0000-0000-000000000000"
+        endpoint = f"/api/v1/package/{fake_uuid}/compound/"
+        response = self.client.get(endpoint)
+
+        self.assertEqual(response.status_code, 404)
+
+    def test_owner_can_access_owned_package(self):
+        """Package owner can access their package."""
+        self.client.force_login(self.user1)
+        endpoint = f"/api/v1/package/{self.unreviewed_package_owned.uuid}/compound/"
+        response = self.client.get(endpoint)
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        self.assertEqual(payload["total_items"], 1)
+        self.assertEqual(payload["items"][0]["uuid"], str(self.owned_compound.uuid))
+
+    def test_group_member_can_access_group_package(self):
+        """Group member can access package via group permission."""
+        self.client.force_login(self.user2)
+        endpoint = f"/api/v1/package/{self.group_package.uuid}/compound/"
+        response = self.client.get(endpoint)
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        self.assertEqual(payload["total_items"], 1)
+        self.assertEqual(payload["items"][0]["uuid"], str(self.group_compound.uuid))
+
+    def test_non_group_member_cannot_access_group_package(self):
+        """Non-group member cannot access package with only group permission."""
+        self.client.force_login(self.user3)
+        endpoint = f"/api/v1/package/{self.group_package.uuid}/compound/"
+        response = self.client.get(endpoint)
+
+        self.assertEqual(response.status_code, 403)
+
+
+@tag("api", "end2end")
+class MultiResourcePermissionTest(APIPermissionTestBase):
+    """
+    Test that permission system works consistently across all resource types.
+
+    Tests a sample of other endpoints to ensure permission logic is consistent.
+    """
+
+    def test_rules_endpoint_respects_permissions(self):
+        """Rules endpoint uses same permission logic."""
+        from epdb.models import SimpleAmbitRule
+
+        # Create rule in no-access package
+        rule = SimpleAmbitRule.create(
+            self.unreviewed_package_no_access, "Test Rule", "Test", "[C:1]>>[C:1]O"
+        )
+
+        self.client.force_login(self.user2)
+        response = self.client.get("/api/v1/rules/")
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        # user2 should not see the rule from no_access_package
+        rule_uuids = [item["uuid"] for item in payload["items"]]
+        self.assertNotIn(str(rule.uuid), rule_uuids)
+
+    def test_reactions_endpoint_respects_permissions(self):
+        """Reactions endpoint uses same permission logic."""
+        from epdb.models import Reaction
+
+        # Create reaction in no-access package
+        reaction = Reaction.create(
+            self.unreviewed_package_no_access, "Test Reaction", "Test", ["C"], ["CO"]
+        )
+
+        self.client.force_login(self.user2)
+        response = self.client.get("/api/v1/reactions/")
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        # user2 should not see the reaction from no_access_package
+        reaction_uuids = [item["uuid"] for item in payload["items"]]
+        self.assertNotIn(str(reaction.uuid), reaction_uuids)
+
+    def test_pathways_endpoint_respects_permissions(self):
+        """Pathways endpoint uses same permission logic."""
+        from epdb.models import Pathway
+
+        # Create pathway in no-access package
+        pathway = Pathway.objects.create(
+            package=self.unreviewed_package_no_access, name="Test Pathway", description="Test"
+        )
+
+        self.client.force_login(self.user2)
+        response = self.client.get("/api/v1/pathways/")
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        # user2 should not see the pathway from no_access_package
+        pathway_uuids = [item["uuid"] for item in payload["items"]]
+        self.assertNotIn(str(pathway.uuid), pathway_uuids)

epapi/tests/v1/test_contract_get_entities.py

@@ -0,0 +1,477 @@
+from django.test import TestCase, tag
+
+from epdb.logic import PackageManager, UserManager
+from epdb.models import Compound, Reaction, Pathway, EPModel, SimpleAmbitRule, Scenario
+
+
+class BaseTestAPIGetPaginated:
+    """
+    Mixin class for API pagination tests.
+
+    Subclasses must inherit from both this class and TestCase, e.g.:
+        class MyTest(BaseTestAPIGetPaginated, TestCase):
+            ...
+
+    Subclasses must define:
+    - resource_name: Singular name (e.g., "compound")
+    - resource_name_plural: Plural name (e.g., "compounds")
+    - global_endpoint: Global listing endpoint (e.g., "/api/v1/compounds/")
+    - package_endpoint_template: Template for package-scoped endpoint or None
+    - total_reviewed: Number of reviewed items to create
+    - total_unreviewed: Number of unreviewed items to create
+    - create_reviewed_resource(cls, package, idx): Factory method
+    - create_unreviewed_resource(cls, package, idx): Factory method
+    """
+
+    # Configuration to be overridden by subclasses
+    resource_name = None
+    resource_name_plural = None
+    global_endpoint = None
+    package_endpoint_template = None
+    total_reviewed = 50
+    total_unreviewed = 20
+    default_page_size = 50
+    max_page_size = 100
+
+    @classmethod
+    def setUpTestData(cls):
+        # Create test user
+        cls.user = UserManager.create_user(
+            f"{cls.resource_name}-user",
+            f"{cls.resource_name}-user@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=False,
+            is_active=True,
+        )
+
+        # Delete the auto-created default package to ensure clean test data
+        default_pkg = cls.user.default_package
+        cls.user.default_package = None
+        cls.user.save()
+        default_pkg.delete()
+
+        # Create reviewed package
+        cls.reviewed_package = PackageManager.create_package(
+            cls.user, "Reviewed Package", f"Reviewed package for {cls.resource_name} tests"
+        )
+        cls.reviewed_package.reviewed = True
+        cls.reviewed_package.save()
+
+        # Create unreviewed package
+        cls.unreviewed_package = PackageManager.create_package(
+            cls.user, "Draft Package", f"Unreviewed package for {cls.resource_name} tests"
+        )
+
+        # Create reviewed resources
+        for idx in range(cls.total_reviewed):
+            cls.create_reviewed_resource(cls.reviewed_package, idx)
+
+        # Create unreviewed resources
+        for idx in range(cls.total_unreviewed):
+            cls.create_unreviewed_resource(cls.unreviewed_package, idx)
+
+        # Set up package-scoped endpoints if applicable
+        if cls.package_endpoint_template:
+            cls.reviewed_package_endpoint = cls.package_endpoint_template.format(
+                uuid=cls.reviewed_package.uuid
+            )
+            cls.unreviewed_package_endpoint = cls.package_endpoint_template.format(
+                uuid=cls.unreviewed_package.uuid
+            )
+
+    @classmethod
+    def create_reviewed_resource(cls, package, idx):
+        """
+        Create a single reviewed resource.
+        Must be implemented by subclass.
+
+        Args:
+            package: The package to create the resource in
+            idx: Index of the resource (0-based)
+        """
+        raise NotImplementedError(f"{cls.__name__} must implement create_reviewed_resource()")
+
+    @classmethod
+    def create_unreviewed_resource(cls, package, idx):
+        """
+        Create a single unreviewed resource.
+        Must be implemented by subclass.
+
+        Args:
+            package: The package to create the resource in
+            idx: Index of the resource (0-based)
+        """
+        raise NotImplementedError(f"{cls.__name__} must implement create_unreviewed_resource()")
+
+    def setUp(self):
+        self.client.force_login(self.user)
+
+    def test_requires_session_authentication(self):
+        """Test that the global endpoint requires authentication."""
+        self.client.logout()
+        response = self.client.get(self.global_endpoint)
+        self.assertEqual(response.status_code, 401)
+
+    def test_global_listing_uses_default_page_size(self):
+        """Test that the global endpoint uses default pagination settings."""
+        response = self.client.get(self.global_endpoint, {"review_status": True})
+        self.assertEqual(response.status_code, 200)
+
+        payload = response.json()
+        self.assertEqual(payload["page"], 1)
+        self.assertEqual(payload["page_size"], self.default_page_size)
+        self.assertEqual(payload["total_items"], self.total_reviewed)
+
+        # Verify only reviewed items are returned
+        self.assertTrue(all(item["review_status"] == "reviewed" for item in payload["items"]))
+
+    def test_can_request_later_page(self):
+        """Test that pagination works for later pages."""
+        if self.total_reviewed <= self.default_page_size:
+            self.skipTest(
+                f"Not enough items to test pagination "
+                f"({self.total_reviewed} <= {self.default_page_size})"
+            )
+
+        response = self.client.get(self.global_endpoint, {"page": 2, "review_status": True})
+        self.assertEqual(response.status_code, 200)
+
+        payload = response.json()
+        self.assertEqual(payload["page"], 2)
+
+        # Calculate expected items on page 2
+        expected_items = min(self.default_page_size, self.total_reviewed - self.default_page_size)
+        self.assertEqual(len(payload["items"]), expected_items)
+
+        # Verify only reviewed items are returned
+        self.assertTrue(all(item["review_status"] == "reviewed" for item in payload["items"]))
+
+    def test_page_size_is_capped(self):
+        """Test that page size is capped at the maximum."""
+        if self.total_reviewed <= self.max_page_size:
+            self.skipTest(
+                f"Not enough items to test page size cap "
+                f"({self.total_reviewed} <= {self.max_page_size})"
+            )
+
+        response = self.client.get(self.global_endpoint, {"page_size": 150})
+        self.assertEqual(response.status_code, 200)
+
+        payload = response.json()
+        self.assertEqual(payload["page_size"], self.max_page_size)
+        self.assertEqual(len(payload["items"]), self.max_page_size)
+
+    def test_package_endpoint_for_reviewed_package(self):
+        """Test the package-scoped endpoint for reviewed packages."""
+        if not self.package_endpoint_template:
+            self.skipTest("No package endpoint for this resource")
+
+        response = self.client.get(self.reviewed_package_endpoint)
+        self.assertEqual(response.status_code, 200)
+
+        payload = response.json()
+        self.assertEqual(payload["total_items"], self.total_reviewed)
+
+        # Verify only reviewed items are returned
+        self.assertTrue(all(item["review_status"] == "reviewed" for item in payload["items"]))
+
+    def test_package_endpoint_for_unreviewed_package(self):
+        """Test the package-scoped endpoint for unreviewed packages."""
+        if not self.package_endpoint_template:
+            self.skipTest("No package endpoint for this resource")
+
+        response = self.client.get(self.unreviewed_package_endpoint)
+        self.assertEqual(response.status_code, 200)
+
+        payload = response.json()
+        self.assertEqual(payload["total_items"], self.total_unreviewed)
+
+        # Verify only unreviewed items are returned
+        self.assertTrue(all(item["review_status"] == "unreviewed" for item in payload["items"]))
+
+
+@tag("api", "end2end")
+class PackagePaginationAPITest(TestCase):
+    ENDPOINT = "/api/v1/packages/"
+
+    @classmethod
+    def setUpTestData(cls):
+        cls.user = UserManager.create_user(
+            "package-user",
+            "package-user@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=False,
+            is_active=True,
+        )
+
+        # Delete the auto-created default package to ensure clean test data
+        default_pkg = cls.user.default_package
+        cls.user.default_package = None
+        cls.user.save()
+        default_pkg.delete()
+
+        # Create reviewed packages
+        cls.total_reviewed = 25
+        for idx in range(cls.total_reviewed):
+            package = PackageManager.create_package(
+                cls.user, f"Reviewed Package {idx:03d}", "Reviewed package for tests"
+            )
+            package.reviewed = True
+            package.save()
+
+        # Create unreviewed packages
+        cls.total_unreviewed = 15
+        for idx in range(cls.total_unreviewed):
+            PackageManager.create_package(
+                cls.user, f"Draft Package {idx:03d}", "Unreviewed package for tests"
+            )
+
+    def setUp(self):
+        self.client.force_login(self.user)
+
+    def test_anonymous_can_access_reviewed_packages(self):
+        self.client.logout()
+        response = self.client.get(self.ENDPOINT)
+        self.assertEqual(response.status_code, 200)
+
+        payload = response.json()
+        # Anonymous users can only see reviewed packages
+        self.assertEqual(payload["total_items"], self.total_reviewed)
+        self.assertTrue(all(item["review_status"] == "reviewed" for item in payload["items"]))
+
+    def test_listing_uses_default_page_size(self):
+        response = self.client.get(self.ENDPOINT)
+        self.assertEqual(response.status_code, 200)
+
+        payload = response.json()
+        self.assertEqual(payload["page"], 1)
+        self.assertEqual(payload["page_size"], 50)
+        self.assertEqual(payload["total_items"], self.total_reviewed + self.total_unreviewed)
+
+    def test_reviewed_filter_true(self):
+        response = self.client.get(self.ENDPOINT, {"review_status": True})
+        self.assertEqual(response.status_code, 200)
+
+        payload = response.json()
+        self.assertEqual(payload["total_items"], self.total_reviewed)
+        self.assertTrue(all(item["review_status"] == "reviewed" for item in payload["items"]))
+
+    def test_reviewed_filter_false(self):
+        response = self.client.get(self.ENDPOINT, {"review_status": False})
+        self.assertEqual(response.status_code, 200)
+
+        payload = response.json()
+        self.assertEqual(payload["total_items"], self.total_unreviewed)
+        self.assertTrue(all(item["review_status"] == "unreviewed" for item in payload["items"]))
+
+    def test_reviewed_filter_false_anonymous(self):
+        self.client.logout()
+        response = self.client.get(self.ENDPOINT, {"review_status": False})
+        self.assertEqual(response.status_code, 200)
+
+        payload = response.json()
+        # Anonymous users cannot access unreviewed packages
+        self.assertEqual(payload["total_items"], 0)
+
+
+@tag("api", "end2end")
+class CompoundPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
+    """Compound pagination tests using base class."""
+
+    resource_name = "compound"
+    resource_name_plural = "compounds"
+    global_endpoint = "/api/v1/compounds/"
+    package_endpoint_template = "/api/v1/package/{uuid}/compound/"
+    total_reviewed = 125
+    total_unreviewed = 35
+
+    @classmethod
+    def create_reviewed_resource(cls, package, idx):
+        simple_smiles = ["C", "CC", "CCC", "CCCC", "CCCCC"]
+        smiles = simple_smiles[idx % len(simple_smiles)] + ("O" * (idx // len(simple_smiles)))
+        return Compound.create(
+            package,
+            smiles,
+            f"Reviewed Compound {idx:03d}",
+            "Compound for pagination tests",
+        )
+
+    @classmethod
+    def create_unreviewed_resource(cls, package, idx):
+        simple_smiles = ["C", "CC", "CCC", "CCCC", "CCCCC"]
+        smiles = simple_smiles[idx % len(simple_smiles)] + ("N" * (idx // len(simple_smiles)))
+        return Compound.create(
+            package,
+            smiles,
+            f"Draft Compound {idx:03d}",
+            "Compound for pagination tests",
+        )
+
+
+@tag("api", "end2end")
+class RulePaginationAPITest(BaseTestAPIGetPaginated, TestCase):
+    """Rule pagination tests using base class."""
+
+    resource_name = "rule"
+    resource_name_plural = "rules"
+    global_endpoint = "/api/v1/rules/"
+    package_endpoint_template = "/api/v1/package/{uuid}/rule/"
+    total_reviewed = 125
+    total_unreviewed = 35
+
+    @classmethod
+    def create_reviewed_resource(cls, package, idx):
+        # Create unique SMIRKS by combining chain length and functional group variations
+        # This ensures each idx gets a truly unique SMIRKS pattern
+        carbon_chain = "C" * (idx + 1)  # C, CC, CCC, ... (grows with idx)
+        smirks = f"[{carbon_chain}:1]>>[{carbon_chain}:1]O"
+        return SimpleAmbitRule.create(
+            package,
+            f"Reviewed Rule {idx:03d}",
+            f"Rule {idx} for pagination tests",
+            smirks,
+        )
+
+    @classmethod
+    def create_unreviewed_resource(cls, package, idx):
+        # Create unique SMIRKS by varying the carbon chain length
+        carbon_chain = "C" * (idx + 1)  # C, CC, CCC, ... (grows with idx)
+        smirks = f"[{carbon_chain}:1]>>[{carbon_chain}:1]N"
+        return SimpleAmbitRule.create(
+            package,
+            f"Draft Rule {idx:03d}",
+            f"Rule {idx} for pagination tests",
+            smirks,
+        )
+
+
+@tag("api", "end2end")
+class ReactionPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
+    """Reaction pagination tests using base class."""
+
+    resource_name = "reaction"
+    resource_name_plural = "reactions"
+    global_endpoint = "/api/v1/reactions/"
+    package_endpoint_template = "/api/v1/package/{uuid}/reaction/"
+    total_reviewed = 125
+    total_unreviewed = 35
+
+    @classmethod
+    def create_reviewed_resource(cls, package, idx):
+        # Generate unique SMILES with growing chain lengths to avoid duplicates
+        # Each idx gets a unique chain length
+        educt_smiles = "C" * (idx + 1)  # C, CC, CCC, ... (grows with idx)
+        product_smiles = educt_smiles + "O"
+        return Reaction.create(
+            package=package,
+            name=f"Reviewed Reaction {idx:03d}",
+            description="Reaction for pagination tests",
+            educts=[educt_smiles],
+            products=[product_smiles],
+        )
+
+    @classmethod
+    def create_unreviewed_resource(cls, package, idx):
+        # Generate unique SMILES with growing chain lengths to avoid duplicates
+        # Each idx gets a unique chain length
+        educt_smiles = "C" * (idx + 1)  # C, CC, CCC, ... (grows with idx)
+        product_smiles = educt_smiles + "N"
+        return Reaction.create(
+            package=package,
+            name=f"Draft Reaction {idx:03d}",
+            description="Reaction for pagination tests",
+            educts=[educt_smiles],
+            products=[product_smiles],
+        )
+
+
+@tag("api", "end2end")
+class PathwayPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
+    """Pathway pagination tests using base class."""
+
+    resource_name = "pathway"
+    resource_name_plural = "pathways"
+    global_endpoint = "/api/v1/pathways/"
+    package_endpoint_template = "/api/v1/package/{uuid}/pathway/"
+    total_reviewed = 125
+    total_unreviewed = 35
+
+    @classmethod
+    def create_reviewed_resource(cls, package, idx):
+        return Pathway.objects.create(
+            package=package,
+            name=f"Reviewed Pathway {idx:03d}",
+            description="Pathway for pagination tests",
+        )
+
+    @classmethod
+    def create_unreviewed_resource(cls, package, idx):
+        return Pathway.objects.create(
+            package=package,
+            name=f"Draft Pathway {idx:03d}",
+            description="Pathway for pagination tests",
+        )
+
+
+@tag("api", "end2end")
+class ModelPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
+    """Model pagination tests using base class."""
+
+    resource_name = "model"
+    resource_name_plural = "models"
+    global_endpoint = "/api/v1/models/"
+    package_endpoint_template = "/api/v1/package/{uuid}/model/"
+    total_reviewed = 125
+    total_unreviewed = 35
+
+    @classmethod
+    def create_reviewed_resource(cls, package, idx):
+        return EPModel.objects.create(
+            package=package,
+            name=f"Reviewed Model {idx:03d}",
+            description="Model for pagination tests",
+        )
+
+    @classmethod
+    def create_unreviewed_resource(cls, package, idx):
+        return EPModel.objects.create(
+            package=package,
+            name=f"Draft Model {idx:03d}",
+            description="Model for pagination tests",
+        )
+
+
+@tag("api", "end2end")
+class ScenarioPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
+    """Scenario pagination tests using base class."""
+
+    resource_name = "scenario"
+    resource_name_plural = "scenarios"
+    global_endpoint = "/api/v1/scenarios/"
+    package_endpoint_template = "/api/v1/package/{uuid}/scenario/"
+    total_reviewed = 125
+    total_unreviewed = 35
+
+    @classmethod
+    def create_reviewed_resource(cls, package, idx):
+        return Scenario.create(
+            package,
+            f"Reviewed Scenario {idx:03d}",
+            "Scenario for pagination tests",
+            "2025-01-01",
+            "lab",
+            [],
+        )
+
+    @classmethod
+    def create_unreviewed_resource(cls, package, idx):
+        return Scenario.create(
+            package,
+            f"Draft Scenario {idx:03d}",
+            "Scenario for pagination tests",
+            "2025-01-01",
+            "field",
+            [],
+        )

epapi/tests/v1/test_scenario_creation.py

@@ -0,0 +1,301 @@
+"""
+Tests for Scenario Creation Endpoint Error Handling.
+
+Tests comprehensive error handling for POST /api/v1/package/{uuid}/scenario/
+including package not found, permission denied, validation errors, and database errors.
+"""
+
+from django.test import TestCase, tag
+import json
+from uuid import uuid4
+
+from epdb.logic import PackageManager, UserManager
+from epdb.models import Scenario
+
+
+@tag("api", "scenario_creation")
+class ScenarioCreationAPITests(TestCase):
+    """Test scenario creation endpoint error handling."""
+
+    @classmethod
+    def setUpTestData(cls):
+        """Set up test data: users and packages."""
+        cls.user = UserManager.create_user(
+            "scenario-test-user",
+            "scenario-test@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=False,
+            is_active=True,
+        )
+        cls.other_user = UserManager.create_user(
+            "other-user",
+            "other@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=False,
+            is_active=True,
+        )
+        cls.package = PackageManager.create_package(
+            cls.user, "Test Package", "Test package for scenario creation"
+        )
+
+    def test_create_scenario_package_not_found(self):
+        """Test that non-existent package UUID returns 404."""
+        self.client.force_login(self.user)
+
+        fake_uuid = uuid4()
+        payload = {
+            "name": "Test Scenario",
+            "description": "Test description",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{fake_uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 404)
+        self.assertIn("Package not found", response.json()["detail"])
+
+    def test_create_scenario_insufficient_permissions(self):
+        """Test that unauthorized access returns 403."""
+        self.client.force_login(self.other_user)
+
+        payload = {
+            "name": "Test Scenario",
+            "description": "Test description",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 403)
+        self.assertIn("permission", response.json()["detail"].lower())
+
+    def test_create_scenario_invalid_ai_type(self):
+        """Test that unknown additional information type returns 400."""
+        self.client.force_login(self.user)
+
+        payload = {
+            "name": "Test Scenario",
+            "description": "Test description",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [
+                {"type": "invalid_type_that_does_not_exist", "data": {"some_field": "some_value"}}
+            ],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 400)
+        response_data = response.json()
+        self.assertIn("Validation errors", response_data["detail"])
+
+    def test_create_scenario_validation_error(self):
+        """Test that invalid additional information data returns 400."""
+        self.client.force_login(self.user)
+
+        # Use malformed data structure for an actual AI type
+        payload = {
+            "name": "Test Scenario",
+            "description": "Test description",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [
+                {
+                    "type": "invalid_type_name",
+                    "data": None,  # This should cause a validation error
+                }
+            ],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        # Should return 422 for validation errors
+        self.assertEqual(response.status_code, 422)
+
+    def test_create_scenario_success(self):
+        """Test that valid scenario creation returns 200."""
+        self.client.force_login(self.user)
+
+        payload = {
+            "name": "Test Scenario",
+            "description": "Test description",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 200)
+        data = response.json()
+        self.assertEqual(data["name"], "Test Scenario")
+        self.assertEqual(data["description"], "Test description")
+
+        # Verify scenario was actually created
+        scenario = Scenario.objects.get(name="Test Scenario")
+        self.assertEqual(scenario.package, self.package)
+        self.assertEqual(scenario.scenario_type, "biodegradation")
+
+    def test_create_scenario_auto_name(self):
+        """Test that empty name triggers auto-generation."""
+        self.client.force_login(self.user)
+
+        payload = {
+            "name": "",  # Empty name should be auto-generated
+            "description": "Test description",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 200)
+        data = response.json()
+        # Auto-generated name should follow pattern "Scenario N"
+        self.assertTrue(data["name"].startswith("Scenario "))
+
+    def test_create_scenario_xss_protection(self):
+        """Test that XSS attempts are sanitized."""
+        self.client.force_login(self.user)
+
+        payload = {
+            "name": "<script>alert('xss')</script>Clean Name",
+            "description": "<img src=x onerror=alert('xss')>Description",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 200)
+        data = response.json()
+        # XSS should be cleaned out
+        self.assertNotIn("<script>", data["name"])
+        self.assertNotIn("onerror", data["description"])
+
+    def test_create_scenario_missing_required_field(self):
+        """Test that missing required fields returns validation error."""
+        self.client.force_login(self.user)
+
+        # Missing 'name' field entirely
+        payload = {
+            "description": "Test description",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        # Should return 422 for schema validation errors
+        self.assertEqual(response.status_code, 422)
+
+    def test_create_scenario_type_error_in_ai(self):
+        """Test that TypeError in AI instantiation returns 400."""
+        self.client.force_login(self.user)
+
+        payload = {
+            "name": "Test Scenario",
+            "description": "Test description",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [
+                {
+                    "type": "invalid_type_name",
+                    "data": "string instead of dict",  # Wrong type
+                }
+            ],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        # Should return 422 for validation errors
+        self.assertEqual(response.status_code, 422)
+
+    def test_create_scenario_default_values(self):
+        """Test that default values are applied correctly."""
+        self.client.force_login(self.user)
+
+        # Minimal payload with only name
+        payload = {"name": "Minimal Scenario"}
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 200)
+        data = response.json()
+        self.assertEqual(data["name"], "Minimal Scenario")
+        # Check defaults are applied
+        scenario = Scenario.objects.get(name="Minimal Scenario")
+        # Default description from model is "no description"
+        self.assertIn(scenario.description.lower(), ["", "no description"])
+
+    def test_create_scenario_unicode_characters(self):
+        """Test that unicode characters are handled properly."""
+        self.client.force_login(self.user)
+
+        payload = {
+            "name": "Test Scenario 测试 🧪",
+            "description": "Description with émojis and spëcial çhars",
+            "scenario_date": "2024-01-01",
+            "scenario_type": "biodegradation",
+            "additional_information": [],
+        }
+
+        response = self.client.post(
+            f"/api/v1/package/{self.package.uuid}/scenario/",
+            data=json.dumps(payload),
+            content_type="application/json",
+        )
+
+        self.assertEqual(response.status_code, 200)
+        data = response.json()
+        self.assertIn("测试", data["name"])
+        self.assertIn("émojis", data["description"])

epapi/tests/v1/test_schema_generation.py

@@ -0,0 +1,114 @@
+"""
+Property-based tests for schema generation.
+
+Tests that verify schema generation works correctly for all models,
+regardless of their structure.
+"""
+
+import pytest
+from typing import Type
+from pydantic import BaseModel
+
+from envipy_additional_information import registry, EnviPyModel
+from epapi.utils.schema_transformers import build_rjsf_output
+
+
+class TestSchemaGeneration:
+    """Test that all models can generate valid RJSF schemas."""
+
+    @pytest.mark.parametrize("model_name,model_cls", list(registry.list_models().items()))
+    def test_all_models_generate_rjsf(self, model_name: str, model_cls: Type[BaseModel]):
+        """Every model in the registry should generate valid RJSF format."""
+        # Skip non-EnviPyModel classes (parsers, etc.)
+        if not issubclass(model_cls, EnviPyModel):
+            pytest.skip(f"{model_name} is not an EnviPyModel")
+
+        # Should not raise exception
+        result = build_rjsf_output(model_cls)
+
+        # Verify structure
+        assert isinstance(result, dict), f"{model_name}: Result should be a dict"
+        assert "schema" in result, f"{model_name}: Missing 'schema' key"
+        assert "uiSchema" in result, f"{model_name}: Missing 'uiSchema' key"
+        assert "formData" in result, f"{model_name}: Missing 'formData' key"
+        assert "groups" in result, f"{model_name}: Missing 'groups' key"
+
+        # Verify types
+        assert isinstance(result["schema"], dict), f"{model_name}: schema should be dict"
+        assert isinstance(result["uiSchema"], dict), f"{model_name}: uiSchema should be dict"
+        assert isinstance(result["formData"], dict), f"{model_name}: formData should be dict"
+        assert isinstance(result["groups"], list), f"{model_name}: groups should be list"
+
+        # Verify schema has properties
+        assert "properties" in result["schema"], f"{model_name}: schema should have 'properties'"
+        assert isinstance(result["schema"]["properties"], dict), (
+            f"{model_name}: properties should be dict"
+        )
+
+    @pytest.mark.parametrize("model_name,model_cls", list(registry.list_models().items()))
+    def test_ui_schema_matches_schema_fields(self, model_name: str, model_cls: Type[BaseModel]):
+        """uiSchema keys should match schema properties (or be nested for intervals)."""
+        if not issubclass(model_cls, EnviPyModel):
+            pytest.skip(f"{model_name} is not an EnviPyModel")
+
+        result = build_rjsf_output(model_cls)
+        schema_props = set(result["schema"]["properties"].keys())
+        ui_schema_keys = set(result["uiSchema"].keys())
+
+        # uiSchema should have entries for all top-level properties
+        # (intervals may have nested start/end, but the main field should be present)
+        assert ui_schema_keys.issubset(schema_props), (
+            f"{model_name}: uiSchema has keys not in schema: {ui_schema_keys - schema_props}"
+        )
+
+    @pytest.mark.parametrize("model_name,model_cls", list(registry.list_models().items()))
+    def test_groups_is_list_of_strings(self, model_name: str, model_cls: Type[BaseModel]):
+        """Groups should be a list of strings."""
+        if not issubclass(model_cls, EnviPyModel):
+            pytest.skip(f"{model_name} is not an EnviPyModel")
+
+        result = build_rjsf_output(model_cls)
+        groups = result["groups"]
+
+        assert isinstance(groups, list), f"{model_name}: groups should be list"
+        assert all(isinstance(g, str) for g in groups), (
+            f"{model_name}: all groups should be strings, got {groups}"
+        )
+        assert len(groups) > 0, f"{model_name}: should have at least one group"
+
+    @pytest.mark.parametrize("model_name,model_cls", list(registry.list_models().items()))
+    def test_form_data_matches_schema(self, model_name: str, model_cls: Type[BaseModel]):
+        """formData keys should match schema properties."""
+        if not issubclass(model_cls, EnviPyModel):
+            pytest.skip(f"{model_name} is not an EnviPyModel")
+
+        result = build_rjsf_output(model_cls)
+        schema_props = set(result["schema"]["properties"].keys())
+        form_data_keys = set(result["formData"].keys())
+
+        # formData should only contain keys that are in schema
+        assert form_data_keys.issubset(schema_props), (
+            f"{model_name}: formData has keys not in schema: {form_data_keys - schema_props}"
+        )
+
+
+class TestWidgetTypes:
+    """Test that widget types are valid."""
+
+    @pytest.mark.parametrize("model_name,model_cls", list(registry.list_models().items()))
+    def test_widget_types_are_valid(self, model_name: str, model_cls: Type[BaseModel]):
+        """All widget types in uiSchema should be valid WidgetType values."""
+        from envipy_additional_information.ui_config import WidgetType
+
+        if not issubclass(model_cls, EnviPyModel):
+            pytest.skip(f"{model_name} is not an EnviPyModel")
+
+        result = build_rjsf_output(model_cls)
+        valid_widgets = {wt.value for wt in WidgetType}
+
+        for field_name, ui_config in result["uiSchema"].items():
+            widget = ui_config.get("ui:widget")
+            if widget:
+                assert widget in valid_widgets, (
+                    f"{model_name}.{field_name}: Invalid widget '{widget}'. Valid: {valid_widgets}"
+                )

epapi/tests/v1/test_token_auth.py

@@ -0,0 +1,94 @@
+from datetime import timedelta
+
+from django.test import TestCase, tag
+from django.utils import timezone
+
+from epdb.logic import PackageManager, UserManager
+from epdb.models import APIToken
+
+
+@tag("api", "auth")
+class BearerTokenAuthTests(TestCase):
+    @classmethod
+    def setUpTestData(cls):
+        cls.user = UserManager.create_user(
+            "token-user",
+            "token-user@envipath.com",
+            "SuperSafe",
+            set_setting=False,
+            add_to_group=False,
+            is_active=True,
+        )
+
+        default_pkg = cls.user.default_package
+        cls.user.default_package = None
+        cls.user.save()
+        if default_pkg:
+            default_pkg.delete()
+
+        cls.unreviewed_package = PackageManager.create_package(
+            cls.user, "Token Auth Package", "Package for token auth tests"
+        )
+
+    def _auth_header(self, raw_token):
+        return {"HTTP_AUTHORIZATION": f"Bearer {raw_token}"}
+
+    def test_valid_token_allows_access(self):
+        _, raw_token = APIToken.create_token(self.user, name="Valid Token", expires_days=1)
+
+        response = self.client.get("/api/v1/compounds/", **self._auth_header(raw_token))
+
+        self.assertEqual(response.status_code, 200)
+
+    def test_expired_token_rejected(self):
+        token, raw_token = APIToken.create_token(self.user, name="Expired Token", expires_days=1)
+        token.expires_at = timezone.now() - timedelta(days=1)
+        token.save(update_fields=["expires_at"])
+
+        response = self.client.get("/api/v1/compounds/", **self._auth_header(raw_token))
+
+        self.assertEqual(response.status_code, 401)
+
+    def test_inactive_token_rejected(self):
+        token, raw_token = APIToken.create_token(self.user, name="Inactive Token", expires_days=1)
+        token.is_active = False
+        token.save(update_fields=["is_active"])
+
+        response = self.client.get("/api/v1/compounds/", **self._auth_header(raw_token))
+
+        self.assertEqual(response.status_code, 401)
+
+    def test_invalid_token_rejected(self):
+        response = self.client.get("/api/v1/compounds/", HTTP_AUTHORIZATION="Bearer invalid-token")
+
+        self.assertEqual(response.status_code, 401)
+
+    def test_no_token_rejected(self):
+        self.client.logout()
+        response = self.client.get("/api/v1/compounds/")
+
+        self.assertEqual(response.status_code, 401)
+
+    def test_bearer_populates_request_user_for_packages(self):
+        response = self.client.get("/api/v1/packages/")
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+        uuids = {item["uuid"] for item in payload["items"]}
+        self.assertNotIn(str(self.unreviewed_package.uuid), uuids)
+
+        _, raw_token = APIToken.create_token(self.user, name="Package Token", expires_days=1)
+        response = self.client.get("/api/v1/packages/", **self._auth_header(raw_token))
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+        uuids = {item["uuid"] for item in payload["items"]}
+        self.assertIn(str(self.unreviewed_package.uuid), uuids)
+
+    def test_session_auth_still_works_without_bearer(self):
+        self.client.force_login(self.user)
+        response = self.client.get("/api/v1/packages/")
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+        uuids = {item["uuid"] for item in payload["items"]}
+        self.assertIn(str(self.unreviewed_package.uuid), uuids)

epapi/utils/schema_transformers.py

@@ -0,0 +1,181 @@
+"""
+Schema transformation utilities for converting Pydantic models to RJSF format.
+
+This module provides functions to extract UI configuration from Pydantic models
+and transform them into React JSON Schema Form (RJSF) compatible format.
+"""
+
+from typing import Type, Optional, Any
+
+import jsonref
+from pydantic import BaseModel
+
+from envipy_additional_information.ui_config import UIConfig
+from envipy_additional_information import registry
+
+
+def extract_groups(model_cls: Type[BaseModel]) -> list[str]:
+    """
+    Extract groups from registry-stored group information.
+
+    Args:
+        model_cls: The model class
+
+    Returns:
+        List of group names the model belongs to
+    """
+    return registry.get_groups(model_cls)
+
+
+def extract_ui_metadata(model_cls: Type[BaseModel]) -> dict[str, Any]:
+    """
+    Extract model-level UI metadata from UI class.
+
+    Returns metadata attributes that are NOT UIConfig instances.
+    Common metadata includes: unit, description, title.
+    """
+    metadata: dict[str, Any] = {}
+
+    if not hasattr(model_cls, "UI"):
+        return metadata
+
+    ui_class = getattr(model_cls, "UI")
+
+    # Iterate over all attributes in the UI class
+    for attr_name in dir(ui_class):
+        # Skip private attributes
+        if attr_name.startswith("_"):
+            continue
+
+        # Get the attribute value
+        try:
+            attr_value = getattr(ui_class, attr_name)
+        except AttributeError:
+            continue
+
+        # Skip callables but keep types/classes
+        if callable(attr_value) and not isinstance(attr_value, type):
+            continue
+
+        # Skip UIConfig instances (these are field-level configs, not metadata)
+        # This includes both UIConfig and IntervalConfig
+        if isinstance(attr_value, UIConfig):
+            continue
+
+        metadata[attr_name] = attr_value
+
+    return metadata
+
+
+def extract_ui_config_from_model(model_cls: Type[BaseModel]) -> dict[str, Any]:
+    """
+    Extract UI configuration from model's UI class.
+
+    Returns a dictionary mapping field names to their UI schema configurations.
+    Trusts the config classes to handle their own transformation logic.
+    """
+    ui_configs: dict[str, Any] = {}
+
+    if not hasattr(model_cls, "UI"):
+        return ui_configs
+
+    ui_class = getattr(model_cls, "UI")
+    schema = model_cls.model_json_schema()
+    field_names = schema.get("properties", {}).keys()
+
+    # Extract config for each field
+    for field_name in field_names:
+        # Skip if UI config doesn't exist for this field (field may be hidden from UI)
+        if not hasattr(ui_class, field_name):
+            continue
+
+        ui_config = getattr(ui_class, field_name)
+
+        if isinstance(ui_config, UIConfig):
+            ui_configs[field_name] = ui_config.to_ui_schema_field()
+
+    return ui_configs
+
+
+def build_ui_schema(model_cls: Type[BaseModel]) -> dict:
+    """Generate RJSF uiSchema from model's UI class."""
+    ui_schema = {}
+
+    # Extract field-level UI configs
+    field_configs = extract_ui_config_from_model(model_cls)
+
+    for field_name, config in field_configs.items():
+        ui_schema[field_name] = config
+
+    return ui_schema
+
+
+def build_schema(model_cls: Type[BaseModel]) -> dict[str, Any]:
+    """
+    Build JSON schema from Pydantic model, applying UI metadata.
+
+    Dereferences all $ref pointers to produce fully inlined schema.
+    This ensures the frontend receives schemas with enum values and nested
+    properties fully resolved, without needing client-side ref resolution.
+
+    Extracts model-level metadata from UI class (title, unit, etc.) and applies
+    it to the generated schema. This ensures UI metadata is the single source of truth.
+    """
+    schema = model_cls.model_json_schema()
+
+    # Dereference $ref pointers (inlines $defs) using jsonref
+    # This ensures the frontend receives schemas with enum values and nested
+    # properties fully resolved, currently necessary for client-side rendering.
+    # FIXME: This is a hack to get the schema to work with alpine schema-form.js replace once we migrate to client-side framework.
+    schema = jsonref.replace_refs(schema, proxies=False)
+
+    # Remove $defs section as all refs are now inlined
+    if "$defs" in schema:
+        del schema["$defs"]
+
+    # Extract and apply UI metadata (title, unit, description, etc.)
+    ui_metadata = extract_ui_metadata(model_cls)
+
+    # Apply all metadata consistently as custom properties with x- prefix
+    # This ensures consistency and avoids conflicts with standard JSON Schema properties
+    for key, value in ui_metadata.items():
+        if value is not None:
+            schema[f"x-{key}"] = value
+
+    # Set standard title property from UI metadata for JSON Schema compliance
+    if "title" in ui_metadata:
+        schema["title"] = ui_metadata["title"]
+    elif "label" in ui_metadata:
+        schema["title"] = ui_metadata["label"]
+
+    return schema
+
+
+def build_rjsf_output(model_cls: Type[BaseModel], initial_data: Optional[dict] = None) -> dict:
+    """
+    Main function that returns complete RJSF format.
+
+    Trusts the config classes to handle their own transformation logic.
+    No special-case handling - if a config knows how to transform itself, it will.
+
+    Returns:
+        dict with keys: schema, uiSchema, formData, groups
+    """
+    # Build schema with UI metadata applied
+    schema = build_schema(model_cls)
+
+    # Build UI schema - config classes handle their own transformation
+    ui_schema = build_ui_schema(model_cls)
+
+    # Extract groups from marker interfaces
+    groups = extract_groups(model_cls)
+
+    # Use provided initial_data or empty dict
+    form_data = initial_data if initial_data is not None else {}
+
+    return {
+        "schema": schema,
+        "uiSchema": ui_schema,
+        "formData": form_data,
+        "groups": groups,
+    }

epapi/utils/validation_errors.py

@@ -0,0 +1,82 @@
+"""Shared utilities for handling Pydantic validation errors."""
+
+import json
+from pydantic import ValidationError
+from pydantic_core import ErrorDetails
+from ninja.errors import HttpError
+
+
+def format_validation_error(error: ErrorDetails) -> str:
+    """Format a Pydantic validation error into a user-friendly message.
+
+    Args:
+        error: A Pydantic error details dictionary containing 'msg', 'type', 'ctx', etc.
+
+    Returns:
+        A user-friendly error message string.
+    """
+    msg = error.get("msg") or "Invalid value"
+    error_type = error.get("type") or ""
+
+    # Handle common validation types with friendly messages
+    if error_type == "enum":
+        ctx = error.get("ctx", {})
+        expected = ctx.get("expected", "") if ctx else ""
+        return f"Please select a valid option{': ' + expected if expected else ''}"
+    elif error_type == "literal_error":
+        # Literal errors (like Literal["active", "inactive"])
+        return msg.replace("Input should be ", "Please enter ")
+    elif error_type == "missing":
+        return "This field is required"
+    elif error_type == "string_type":
+        return "Please enter a valid string"
+    elif error_type == "int_type":
+        return "Please enter a valid int"
+    elif error_type == "int_parsing":
+        return "Please enter a valid int"
+    elif error_type == "float_type":
+        return "Please enter a valid float"
+    elif error_type == "float_parsing":
+        return "Please enter a valid float"
+    elif error_type == "value_error":
+        # Strip "Value error, " prefix from custom validator messages
+        return msg.replace("Value error, ", "")
+    else:
+        # Default: use the message from Pydantic but clean it up
+        return msg.replace("Input should be ", "Please enter ").replace("Value error, ", "")
+
+
+def handle_validation_error(e: ValidationError) -> None:
+    """Convert a Pydantic ValidationError into a structured HttpError.
+
+    This function transforms Pydantic validation errors into a JSON structure
+    that the frontend expects for displaying field-level errors.
+
+    Args:
+        e: The Pydantic ValidationError to handle.
+
+    Raises:
+        HttpError: Always raises a 400 error with structured JSON containing
+                   type, field_errors, and message fields.
+    """
+    # Transform Pydantic validation errors into user-friendly format
+    field_errors: dict[str, list[str]] = {}
+    for error in e.errors():
+        # Get the field name from location tuple
+        loc = error.get("loc", ())
+        field = str(loc[-1]) if loc else "root"
+
+        # Format the error message
+        friendly_msg = format_validation_error(error)
+
+        if field not in field_errors:
+            field_errors[field] = []
+        field_errors[field].append(friendly_msg)
+
+    # Return structured error for frontend parsing
+    error_response = {
+        "type": "validation_error",
+        "field_errors": field_errors,
+        "message": "Please correct the errors below",
+    }
+    raise HttpError(400, json.dumps(error_response))

epapi/v1/auth.py

@@ -0,0 +1,34 @@
+import hashlib
+
+from ninja.security import HttpBearer
+from ninja.errors import HttpError
+
+from epdb.models import APIToken
+
+
+class BearerTokenAuth(HttpBearer):
+    def authenticate(self, request, token):
+        if token is None:
+            return None
+
+        hashed_token = hashlib.sha256(token.encode()).hexdigest()
+        user = APIToken.authenticate(hashed_token, hashed=True)
+        if not user:
+            raise HttpError(401, "Invalid or expired token")
+
+        request.user = user
+        return user
+
+
+class OptionalBearerTokenAuth:
+    """Bearer auth that allows unauthenticated access.
+
+    Validates the Bearer token if present (401 on invalid token),
+    otherwise lets the request through for anonymous/session access.
+    """
+
+    def __init__(self):
+        self._bearer = BearerTokenAuth()
+
+    def __call__(self, request):
+        return self._bearer(request) or request.user

epapi/v1/dal.py

@@ -0,0 +1,119 @@
+from django.db.models import Model
+from epdb.logic import PackageManager
+from epdb.models import CompoundStructure, User, Package, Compound, Scenario
+from uuid import UUID
+
+from .errors import EPAPINotFoundError, EPAPIPermissionDeniedError
+
+
+def get_compound_for_read(user, compound_uuid: UUID):
+    """
+    Get compound by UUID with permission check.
+    """
+    try:
+        compound = Compound.objects.get(uuid=compound_uuid)
+        package = compound.package
+    except Compound.DoesNotExist:
+        raise EPAPINotFoundError(f"Compound with UUID {compound_uuid} not found")
+
+    # FIXME: optimize package manager to exclusively work with UUIDs
+    if not user or user.is_anonymous or not PackageManager.readable(user, package):
+        raise EPAPIPermissionDeniedError("Insufficient permissions to access this compound.")
+
+    return compound
+
+
+def get_package_for_read(user, package_uuid: UUID):
+    """
+    Get package by UUID with permission check.
+    """
+
+    # FIXME: update package manager with custom exceptions to avoid manual checks here
+    try:
+        package = Package.objects.get(uuid=package_uuid)
+    except Package.DoesNotExist:
+        raise EPAPINotFoundError(f"Package with UUID {package_uuid} not found")
+
+    # FIXME: optimize package manager to exclusively work with UUIDs
+    if not user or user.is_anonymous or not PackageManager.readable(user, package):
+        raise EPAPIPermissionDeniedError("Insufficient permissions to access this package.")
+
+    return package
+
+
+def get_scenario_for_read(user, scenario_uuid: UUID):
+    """Get scenario by UUID with read permission check."""
+    try:
+        scenario = Scenario.objects.select_related("package").get(uuid=scenario_uuid)
+    except Scenario.DoesNotExist:
+        raise EPAPINotFoundError(f"Scenario with UUID {scenario_uuid} not found")
+
+    if not user or user.is_anonymous or not PackageManager.readable(user, scenario.package):
+        raise EPAPIPermissionDeniedError("Insufficient permissions to access this scenario.")
+
+    return scenario
+
+
+def get_scenario_for_write(user, scenario_uuid: UUID):
+    """Get scenario by UUID with write permission check."""
+    try:
+        scenario = Scenario.objects.select_related("package").get(uuid=scenario_uuid)
+    except Scenario.DoesNotExist:
+        raise EPAPINotFoundError(f"Scenario with UUID {scenario_uuid} not found")
+
+    if not user or user.is_anonymous or not PackageManager.writable(user, scenario.package):
+        raise EPAPIPermissionDeniedError("Insufficient permissions to modify this scenario.")
+
+    return scenario
+
+
+def get_user_packages_for_read(user: User | None):
+    """Get all packages readable by the user."""
+    if not user or user.is_anonymous:
+        return PackageManager.get_reviewed_packages()
+    return PackageManager.get_all_readable_packages(user, include_reviewed=True)
+
+
+def get_user_entities_for_read(model_class: Model, user: User | None):
+    """Build queryset for reviewed package entities."""
+
+    if not user or user.is_anonymous:
+        return model_class.objects.filter(package__reviewed=True).select_related("package")
+
+    qs = model_class.objects.filter(
+        package__in=PackageManager.get_all_readable_packages(user, include_reviewed=True)
+    ).select_related("package")
+    return qs
+
+
+def get_package_entities_for_read(model_class: Model, package_uuid: UUID, user: User | None = None):
+    """Build queryset for specific package entities."""
+    package = get_package_for_read(user, package_uuid)
+    qs = model_class.objects.filter(package=package).select_related("package")
+    return qs
+
+
+def get_user_structure_for_read(user: User | None):
+    """Build queryset for structures accessible to the user (via compound->package)."""
+
+    if not user or user.is_anonymous:
+        return CompoundStructure.objects.filter(compound__package__reviewed=True).select_related(
+            "compound__package"
+        )
+
+    qs = CompoundStructure.objects.filter(
+        compound__package__in=PackageManager.get_all_readable_packages(user, include_reviewed=True)
+    ).select_related("compound__package")
+    return qs
+
+
+def get_package_compound_structure_for_read(
+    package_uuid: UUID, compound_uuid: UUID, user: User | None = None
+):
+    """Build queryset for specific package compound structures."""
+
+    get_package_for_read(user, package_uuid)
+    compound = get_compound_for_read(user, compound_uuid)
+
+    qs = CompoundStructure.objects.filter(compound=compound).select_related("compound__package")
+    return qs

epapi/v1/endpoints/additional_information.py

@@ -0,0 +1,174 @@
+from ninja import Router, Body
+from ninja.errors import HttpError
+from uuid import UUID
+from pydantic import ValidationError
+from typing import Dict, Any
+import logging
+
+from envipy_additional_information import registry
+from envipy_additional_information.groups import GroupEnum
+from epapi.utils.schema_transformers import build_rjsf_output
+from epapi.utils.validation_errors import handle_validation_error
+from ..dal import get_scenario_for_read, get_scenario_for_write
+
+logger = logging.getLogger(__name__)
+
+router = Router(tags=["Additional Information"])
+
+
+@router.get("/information/schema/")
+def list_all_schemas(request):
+    """Return all schemas in RJSF format with lowercase class names as keys."""
+    result = {}
+    for name, cls in registry.list_models().items():
+        try:
+            result[name] = build_rjsf_output(cls)
+        except Exception as e:
+            logger.warning(f"Failed to generate schema for {name}: {e}")
+            continue
+    return result
+
+
+@router.get("/information/schema/{model_name}/")
+def get_model_schema(request, model_name: str):
+    """Return RJSF schema for specific model."""
+    cls = registry.get_model(model_name.lower())
+    if not cls:
+        raise HttpError(404, f"Unknown model: {model_name}")
+    return build_rjsf_output(cls)
+
+
+@router.get("/scenario/{uuid:scenario_uuid}/information/")
+def list_scenario_info(request, scenario_uuid: UUID):
+    """List all additional information for a scenario"""
+    scenario = get_scenario_for_read(request.user, scenario_uuid)
+
+    result = []
+    for ai in scenario.get_additional_information():
+        result.append(
+            {
+                "type": ai.__class__.__name__,
+                "uuid": getattr(ai, "uuid", None),
+                "data": ai.model_dump(mode="json"),
+            }
+        )
+    return result
+
+
+@router.post("/scenario/{uuid:scenario_uuid}/information/{model_name}/")
+def add_scenario_info(
+    request, scenario_uuid: UUID, model_name: str, payload: Dict[str, Any] = Body(...)
+):
+    """Add new additional information to scenario"""
+    cls = registry.get_model(model_name.lower())
+    if not cls:
+        raise HttpError(404, f"Unknown model: {model_name}")
+
+    try:
+        instance = cls(**payload)  # Pydantic validates
+    except ValidationError as e:
+        handle_validation_error(e)
+
+    scenario = get_scenario_for_write(request.user, scenario_uuid)
+
+    # Model method now returns the UUID
+    created_uuid = scenario.add_additional_information(instance)
+
+    return {"status": "created", "uuid": created_uuid}
+
+
+@router.patch("/scenario/{uuid:scenario_uuid}/information/item/{uuid:ai_uuid}/")
+def update_scenario_info(
+    request, scenario_uuid: UUID, ai_uuid: UUID, payload: Dict[str, Any] = Body(...)
+):
+    """Update existing additional information for a scenario"""
+    scenario = get_scenario_for_write(request.user, scenario_uuid)
+    ai_uuid_str = str(ai_uuid)
+
+    # Find item to determine type for validation
+    found_type = None
+    for type_name, items in scenario.additional_information.items():
+        if any(item.get("uuid") == ai_uuid_str for item in items):
+            found_type = type_name
+            break
+
+    if found_type is None:
+        raise HttpError(404, f"Additional information not found: {ai_uuid}")
+
+    # Get the model class for validation
+    cls = registry.get_model(found_type.lower())
+    if not cls:
+        raise HttpError(500, f"Unknown model type in data: {found_type}")
+
+    # Validate the payload against the model
+    try:
+        instance = cls(**payload)
+    except ValidationError as e:
+        handle_validation_error(e)
+
+    # Use model method for update
+    try:
+        scenario.update_additional_information(ai_uuid_str, instance)
+    except ValueError as e:
+        raise HttpError(404, str(e))
+
+    return {"status": "updated", "uuid": ai_uuid_str}
+
+
+@router.delete("/scenario/{uuid:scenario_uuid}/information/item/{uuid:ai_uuid}/")
+def delete_scenario_info(request, scenario_uuid: UUID, ai_uuid: UUID):
+    """Delete additional information from scenario"""
+    scenario = get_scenario_for_write(request.user, scenario_uuid)
+
+    try:
+        scenario.remove_additional_information(str(ai_uuid))
+    except ValueError as e:
+        raise HttpError(404, str(e))
+
+    return {"status": "deleted"}
+
+
+@router.get("/information/groups/")
+def list_groups(request):
+    """Return list of available group names."""
+    return {"groups": GroupEnum.values()}
+
+
+@router.get("/information/groups/{group_name}/")
+def get_group_models(request, group_name: str):
+    """
+    Return models for a specific group organized by subcategory.
+
+    Args:
+        group_name: One of "sludge", "soil", or "sediment" (string)
+
+    Returns:
+        Dictionary with subcategories (exp, spike, comp, misc, or group name)
+        as keys and lists of model info as values
+    """
+    # Convert string to enum (raises ValueError if invalid)
+    try:
+        group_enum = GroupEnum(group_name)
+    except ValueError:
+        valid = ", ".join(GroupEnum.values())
+        raise HttpError(400, f"Invalid group '{group_name}'. Valid: {valid}")
+
+    try:
+        group_data = registry.collect_group(group_enum)
+    except (ValueError, TypeError) as e:
+        raise HttpError(400, str(e))
+
+    result = {}
+    for subcategory, models in group_data.items():
+        result[subcategory] = [
+            {
+                "name": cls.__name__.lower(),
+                "class": cls.__name__,
+                "title": getattr(cls.UI, "title", cls.__name__)
+                if hasattr(cls, "UI")
+                else cls.__name__,
+            }
+            for cls in models
+        ]
+
+    return result

epapi/v1/endpoints/compounds.py

@@ -0,0 +1,41 @@
+from django.conf import settings as s
+from ninja import Router
+from ninja_extra.pagination import paginate
+from uuid import UUID
+
+from epdb.models import Compound
+from ..pagination import EnhancedPageNumberPagination
+from ..schemas import CompoundOutSchema, ReviewStatusFilter
+from ..dal import get_user_entities_for_read, get_package_entities_for_read
+
+router = Router()
+
+
+@router.get("/compounds/", response=EnhancedPageNumberPagination.Output[CompoundOutSchema])
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+    filter_schema=ReviewStatusFilter,
+)
+def list_all_compounds(request):
+    """
+    List all compounds from reviewed packages.
+    """
+    return get_user_entities_for_read(Compound, request.user).order_by("name").all()
+
+
+@router.get(
+    "/package/{uuid:package_uuid}/compound/",
+    response=EnhancedPageNumberPagination.Output[CompoundOutSchema],
+)
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+    filter_schema=ReviewStatusFilter,
+)
+def list_package_compounds(request, package_uuid: UUID):
+    """
+    List all compounds for a specific package.
+    """
+    user = request.user
+    return get_package_entities_for_read(Compound, package_uuid, user).order_by("name").all()

epapi/v1/endpoints/models.py

@@ -0,0 +1,41 @@
+from django.conf import settings as s
+from ninja import Router
+from ninja_extra.pagination import paginate
+from uuid import UUID
+
+from epdb.models import EPModel
+from ..pagination import EnhancedPageNumberPagination
+from ..schemas import ModelOutSchema, ReviewStatusFilter
+from ..dal import get_user_entities_for_read, get_package_entities_for_read
+
+router = Router()
+
+
+@router.get("/models/", response=EnhancedPageNumberPagination.Output[ModelOutSchema])
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+    filter_schema=ReviewStatusFilter,
+)
+def list_all_models(request):
+    """
+    List all models from reviewed packages.
+    """
+    return get_user_entities_for_read(EPModel, request.user).order_by("name").all()
+
+
+@router.get(
+    "/package/{uuid:package_uuid}/model/",
+    response=EnhancedPageNumberPagination.Output[ModelOutSchema],
+)
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+    filter_schema=ReviewStatusFilter,
+)
+def list_package_models(request, package_uuid: UUID):
+    """
+    List all models for a specific package.
+    """
+    user = request.user
+    return get_package_entities_for_read(EPModel, package_uuid, user).order_by("name").all()

epapi/v1/endpoints/packages.py

@@ -0,0 +1,32 @@
+from django.conf import settings as s
+from ninja import Router
+from ninja_extra.pagination import paginate
+import logging
+
+from ..auth import OptionalBearerTokenAuth
+from ..dal import get_user_packages_for_read
+from ..pagination import EnhancedPageNumberPagination
+from ..schemas import PackageOutSchema, SelfReviewStatusFilter
+
+router = Router()
+logger = logging.getLogger(__name__)
+
+
+@router.get(
+    "/packages/",
+    response=EnhancedPageNumberPagination.Output[PackageOutSchema],
+    auth=OptionalBearerTokenAuth(),
+)
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+    filter_schema=SelfReviewStatusFilter,
+)
+def list_all_packages(request):
+    """
+    List packages accessible to the user.
+
+    """
+    user = request.user
+    qs = get_user_packages_for_read(user)
+    return qs.order_by("name").all()

epapi/v1/endpoints/pathways.py

@@ -0,0 +1,42 @@
+from django.conf import settings as s
+from ninja import Router
+from ninja_extra.pagination import paginate
+from uuid import UUID
+
+from epdb.models import Pathway
+from ..pagination import EnhancedPageNumberPagination
+from ..schemas import PathwayOutSchema, ReviewStatusFilter
+from ..dal import get_user_entities_for_read, get_package_entities_for_read
+
+router = Router()
+
+
+@router.get("/pathways/", response=EnhancedPageNumberPagination.Output[PathwayOutSchema])
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+    filter_schema=ReviewStatusFilter,
+)
+def list_all_pathways(request):
+    """
+    List all pathways from reviewed packages.
+    """
+    user = request.user
+    return get_user_entities_for_read(Pathway, user).order_by("name").all()
+
+
+@router.get(
+    "/package/{uuid:package_uuid}/pathway/",
+    response=EnhancedPageNumberPagination.Output[PathwayOutSchema],
+)
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+    filter_schema=ReviewStatusFilter,
+)
+def list_package_pathways(request, package_uuid: UUID):
+    """
+    List all pathways for a specific package.
+    """
+    user = request.user
+    return get_package_entities_for_read(Pathway, package_uuid, user).order_by("name").all()

epapi/v1/endpoints/reactions.py

@@ -0,0 +1,42 @@
+from django.conf import settings as s
+from ninja import Router
+from ninja_extra.pagination import paginate
+from uuid import UUID
+
+from epdb.models import Reaction
+from ..pagination import EnhancedPageNumberPagination
+from ..schemas import ReactionOutSchema, ReviewStatusFilter
+from ..dal import get_user_entities_for_read, get_package_entities_for_read
+
+router = Router()
+
+
+@router.get("/reactions/", response=EnhancedPageNumberPagination.Output[ReactionOutSchema])
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+    filter_schema=ReviewStatusFilter,
+)
+def list_all_reactions(request):
+    """
+    List all reactions from reviewed packages.
+    """
+    user = request.user
+    return get_user_entities_for_read(Reaction, user).order_by("name").all()
+
+
+@router.get(
+    "/package/{uuid:package_uuid}/reaction/",
+    response=EnhancedPageNumberPagination.Output[ReactionOutSchema],
+)
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+    filter_schema=ReviewStatusFilter,
+)
+def list_package_reactions(request, package_uuid: UUID):
+    """
+    List all reactions for a specific package.
+    """
+    user = request.user
+    return get_package_entities_for_read(Reaction, package_uuid, user).order_by("name").all()

epapi/v1/endpoints/rules.py

@@ -0,0 +1,42 @@
+from django.conf import settings as s
+from ninja import Router
+from ninja_extra.pagination import paginate
+from uuid import UUID
+
+from epdb.models import Rule
+from ..pagination import EnhancedPageNumberPagination
+from ..schemas import ReviewStatusFilter, RuleOutSchema
+from ..dal import get_user_entities_for_read, get_package_entities_for_read
+
+router = Router()
+
+
+@router.get("/rules/", response=EnhancedPageNumberPagination.Output[RuleOutSchema])
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+    filter_schema=ReviewStatusFilter,
+)
+def list_all_rules(request):
+    """
+    List all rules from reviewed packages.
+    """
+    user = request.user
+    return get_user_entities_for_read(Rule, user).order_by("name").all()
+
+
+@router.get(
+    "/package/{uuid:package_uuid}/rule/",
+    response=EnhancedPageNumberPagination.Output[RuleOutSchema],
+)
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+    filter_schema=ReviewStatusFilter,
+)
+def list_package_rules(request, package_uuid: UUID):
+    """
+    List all rules for a specific package.
+    """
+    user = request.user
+    return get_package_entities_for_read(Rule, package_uuid, user).order_by("name").all()

epapi/v1/endpoints/scenarios.py

@@ -0,0 +1,130 @@
+from django.conf import settings as s
+from django.db import IntegrityError, OperationalError, DatabaseError
+from ninja import Router, Body
+from ninja.errors import HttpError
+from ninja_extra.pagination import paginate
+from uuid import UUID
+from pydantic import ValidationError
+import logging
+import json
+
+from epdb.models import Scenario
+from epdb.logic import PackageManager
+from epdb.views import _anonymous_or_real
+from ..pagination import EnhancedPageNumberPagination
+from ..schemas import (
+    ScenarioOutSchema,
+    ScenarioCreateSchema,
+    ScenarioReviewStatusAndRelatedFilter,
+)
+from ..dal import get_user_entities_for_read, get_package_entities_for_read
+from envipy_additional_information import registry
+
+logger = logging.getLogger(__name__)
+
+router = Router()
+
+
+@router.get("/scenarios/", response=EnhancedPageNumberPagination.Output[ScenarioOutSchema])
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+    filter_schema=ScenarioReviewStatusAndRelatedFilter,
+)
+def list_all_scenarios(request):
+    user = request.user
+    items = get_user_entities_for_read(Scenario, user)
+    return items.order_by("name").all()
+
+
+@router.get(
+    "/package/{uuid:package_uuid}/scenario/",
+    response=EnhancedPageNumberPagination.Output[ScenarioOutSchema],
+)
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+    filter_schema=ScenarioReviewStatusAndRelatedFilter,
+)
+def list_package_scenarios(request, package_uuid: UUID):
+    user = request.user
+    items = get_package_entities_for_read(Scenario, package_uuid, user)
+    return items.order_by("name").all()
+
+
+@router.post("/package/{uuid:package_uuid}/scenario/", response=ScenarioOutSchema)
+def create_scenario(request, package_uuid: UUID, payload: ScenarioCreateSchema = Body(...)):
+    """Create a new scenario with optional additional information."""
+    user = _anonymous_or_real(request)
+
+    try:
+        current_package = PackageManager.get_package_by_id(user, package_uuid)
+    except ValueError as e:
+        error_msg = str(e)
+        if "does not exist" in error_msg:
+            raise HttpError(404, f"Package not found: {package_uuid}")
+        elif "Insufficient permissions" in error_msg:
+            raise HttpError(403, "You do not have permission to access this package")
+        else:
+            logger.error(f"Unexpected ValueError from get_package_by_id: {error_msg}")
+            raise HttpError(400, "Invalid package request")
+
+    # Build additional information models from payload
+    additional_information_models = []
+    validation_errors = []
+
+    for ai_item in payload.additional_information:
+        # Get model class from registry
+        model_cls = registry.get_model(ai_item.type.lower())
+        if not model_cls:
+            validation_errors.append(f"Unknown additional information type: {ai_item.type}")
+            continue
+
+        try:
+            # Validate and create model instance
+            instance = model_cls(**ai_item.data)
+            additional_information_models.append(instance)
+        except ValidationError as e:
+            # Collect validation errors to return to user
+            error_messages = [err.get("msg", "Validation error") for err in e.errors()]
+            validation_errors.append(f"{ai_item.type}: {', '.join(error_messages)}")
+        except (TypeError, AttributeError, KeyError) as e:
+            logger.warning(f"Failed to instantiate {ai_item.type} model: {str(e)}")
+            validation_errors.append(f"{ai_item.type}: Invalid data structure - {str(e)}")
+        except Exception as e:
+            logger.error(f"Unexpected error instantiating {ai_item.type}: {str(e)}")
+            validation_errors.append(f"{ai_item.type}: Failed to process - please check your data")
+
+    # If there are validation errors, return them
+    if validation_errors:
+        raise HttpError(
+            400,
+            json.dumps(
+                {
+                    "error": "Validation errors in additional information",
+                    "details": validation_errors,
+                }
+            ),
+        )
+
+    # Create scenario using the existing Scenario.create method
+    try:
+        new_scenario = Scenario.create(
+            package=current_package,
+            name=payload.name,
+            description=payload.description,
+            scenario_date=payload.scenario_date,
+            scenario_type=payload.scenario_type,
+            additional_information=additional_information_models,
+        )
+    except IntegrityError as e:
+        logger.error(f"Database integrity error creating scenario: {str(e)}")
+        raise HttpError(400, "Scenario creation failed - data constraint violation")
+    except OperationalError as e:
+        logger.error(f"Database operational error creating scenario: {str(e)}")
+        raise HttpError(503, "Database temporarily unavailable - please try again")
+    except (DatabaseError, AttributeError) as e:
+        logger.error(f"Error creating scenario: {str(e)}")
+        raise HttpError(500, "Failed to create scenario due to database error")
+
+    return new_scenario

epapi/v1/endpoints/settings.py

@@ -0,0 +1,23 @@
+from django.conf import settings as s
+from ninja import Router
+from ninja_extra.pagination import paginate
+
+from epdb.logic import SettingManager
+
+from ..pagination import EnhancedPageNumberPagination
+from ..schemas import SettingOutSchema
+
+router = Router()
+
+
+@router.get("/settings/", response=EnhancedPageNumberPagination.Output[SettingOutSchema])
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+)
+def list_all_pathways(request):
+    """
+    List all pathways from reviewed packages.
+    """
+    user = request.user
+    return SettingManager.get_all_settings(user)

epapi/v1/endpoints/structure.py

@@ -0,0 +1,50 @@
+from django.conf import settings as s
+from ninja import Router
+from ninja_extra.pagination import paginate
+from uuid import UUID
+
+from ..pagination import EnhancedPageNumberPagination
+from ..schemas import CompoundStructureOutSchema, StructureReviewStatusFilter
+from ..dal import (
+    get_user_structure_for_read,
+    get_package_compound_structure_for_read,
+)
+
+router = Router()
+
+
+@router.get(
+    "/structures/", response=EnhancedPageNumberPagination.Output[CompoundStructureOutSchema]
+)
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+    filter_schema=StructureReviewStatusFilter,
+)
+def list_all_structures(request):
+    """
+    List all structures from all packages.
+    """
+    user = request.user
+    return get_user_structure_for_read(user).order_by("name").all()
+
+
+@router.get(
+    "/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure/",
+    response=EnhancedPageNumberPagination.Output[CompoundStructureOutSchema],
+)
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+    filter_schema=StructureReviewStatusFilter,
+)
+def list_package_structures(request, package_uuid: UUID, compound_uuid: UUID):
+    """
+    List all structures for a specific package and compound.
+    """
+    user = request.user
+    return (
+        get_package_compound_structure_for_read(package_uuid, compound_uuid, user)
+        .order_by("name")
+        .all()
+    )

epapi/v1/errors.py

@@ -0,0 +1,28 @@
+from ninja.errors import HttpError
+
+
+class EPAPIError(HttpError):
+    status_code: int = 500
+
+    def __init__(self, message: str) -> None:
+        super().__init__(status_code=self.status_code, message=message)
+
+    @classmethod
+    def from_exception(cls, exc: Exception):
+        return cls(message=str(exc))
+
+
+class EPAPIUnauthorizedError(EPAPIError):
+    status_code = 401
+
+
+class EPAPIPermissionDeniedError(EPAPIError):
+    status_code = 403
+
+
+class EPAPINotFoundError(EPAPIError):
+    status_code = 404
+
+
+class EPAPIValidationError(EPAPIError):
+    status_code = 422

epapi/v1/pagination.py

@@ -0,0 +1,60 @@
+import math
+from typing import Any, Generic, List, TypeVar
+
+from django.db.models import QuerySet
+from ninja import Schema
+from ninja.pagination import PageNumberPagination
+
+T = TypeVar("T")
+
+
+class EnhancedPageNumberPagination(PageNumberPagination):
+    class Output(Schema, Generic[T]):
+        items: List[T]
+        page: int
+        page_size: int
+        total_items: int
+        total_pages: int
+
+    def paginate_queryset(
+        self,
+        queryset: QuerySet,
+        pagination: PageNumberPagination.Input,
+        **params: Any,
+    ) -> Any:
+        page_size = self._get_page_size(pagination.page_size)
+        offset = (pagination.page - 1) * page_size
+        total_items = self._items_count(queryset)
+        total_pages = math.ceil(total_items / page_size) if page_size > 0 else 0
+
+        return {
+            "items": queryset[offset : offset + page_size],
+            "page": pagination.page,
+            "page_size": page_size,
+            "total_items": total_items,
+            "total_pages": total_pages,
+        }
+
+    async def apaginate_queryset(
+        self,
+        queryset: QuerySet,
+        pagination: PageNumberPagination.Input,
+        **params: Any,
+    ) -> Any:
+        page_size = self._get_page_size(pagination.page_size)
+        offset = (pagination.page - 1) * page_size
+        total_items = await self._aitems_count(queryset)
+        total_pages = math.ceil(total_items / page_size) if page_size > 0 else 0
+
+        if isinstance(queryset, QuerySet):
+            items = [obj async for obj in queryset[offset : offset + page_size]]
+        else:
+            items = queryset[offset : offset + page_size]
+
+        return {
+            "items": items,
+            "page": pagination.page,
+            "page_size": page_size,
+            "total_items": total_items,
+            "total_pages": total_pages,
+        }

epapi/v1/router.py

@@ -0,0 +1,36 @@
+from ninja import Router
+from ninja.security import SessionAuth
+
+from .auth import BearerTokenAuth
+from .endpoints import (
+    packages,
+    scenarios,
+    compounds,
+    rules,
+    reactions,
+    pathways,
+    models,
+    structure,
+    additional_information,
+    settings,
+)
+
+# Main router with authentication
+router = Router(
+    auth=[
+        SessionAuth(),
+        BearerTokenAuth(),
+    ]
+)
+
+# Include all endpoint routers
+router.add_router("", packages.router)
+router.add_router("", scenarios.router)
+router.add_router("", compounds.router)
+router.add_router("", rules.router)
+router.add_router("", reactions.router)
+router.add_router("", pathways.router)
+router.add_router("", models.router)
+router.add_router("", structure.router)
+router.add_router("", additional_information.router)
+router.add_router("", settings.router)

epapi/v1/schemas.py

@@ -0,0 +1,134 @@
+from ninja import FilterSchema, FilterLookup, Schema
+from typing import Annotated, Optional, List, Dict, Any
+from uuid import UUID
+
+
+# Filter schema for query parameters
+class ReviewStatusFilter(FilterSchema):
+    """Filter schema for review_status query parameter."""
+
+    review_status: Annotated[Optional[bool], FilterLookup("package__reviewed")] = None
+
+
+class SelfReviewStatusFilter(FilterSchema):
+    """Filter schema for review_status query parameter on self-reviewed entities."""
+
+    review_status: Annotated[Optional[bool], FilterLookup("reviewed")] = None
+
+
+class StructureReviewStatusFilter(FilterSchema):
+    """Filter schema for review_status on structures (via compound->package)."""
+
+    review_status: Annotated[Optional[bool], FilterLookup("compound__package__reviewed")] = None
+
+
+class ScenarioReviewStatusAndRelatedFilter(ReviewStatusFilter):
+    """Filter schema for review_status and parent query parameter."""
+
+    exclude_related: Annotated[Optional[bool], FilterLookup("parent__isnull")] = None
+
+
+# Base schema for all package-scoped entities
+class PackageEntityOutSchema(Schema):
+    """Base schema for entities belonging to a package."""
+
+    uuid: UUID
+    url: str = ""
+    name: str
+    description: str
+    review_status: str = ""
+    package: str = ""
+
+    @staticmethod
+    def resolve_url(obj):
+        return obj.url
+
+    @staticmethod
+    def resolve_package(obj):
+        return obj.package.url
+
+    @staticmethod
+    def resolve_review_status(obj):
+        return "reviewed" if obj.package.reviewed else "unreviewed"
+
+
+# All package-scoped entities inherit from base
+class ScenarioOutSchema(PackageEntityOutSchema):
+    pass
+
+
+class AdditionalInformationItemSchema(Schema):
+    """Schema for additional information item in scenario creation."""
+
+    type: str
+    data: Dict[str, Any]
+
+
+class ScenarioCreateSchema(Schema):
+    """Schema for creating a new scenario."""
+
+    name: str
+    description: str = ""
+    scenario_date: str = "No date"
+    scenario_type: str = "Not specified"
+    additional_information: List[AdditionalInformationItemSchema] = []
+
+
+class CompoundOutSchema(PackageEntityOutSchema):
+    pass
+
+
+class RuleOutSchema(PackageEntityOutSchema):
+    pass
+
+
+class ReactionOutSchema(PackageEntityOutSchema):
+    pass
+
+
+class PathwayOutSchema(PackageEntityOutSchema):
+    pass
+
+
+class ModelOutSchema(PackageEntityOutSchema):
+    pass
+
+
+class CompoundStructureOutSchema(PackageEntityOutSchema):
+    compound: str = ""
+
+    @staticmethod
+    def resolve_compound(obj):
+        return obj.compound.url
+
+    @staticmethod
+    def resolve_package(obj):
+        return obj.compound.package.url
+
+    @staticmethod
+    def resolve_review_status(obj):
+        return "reviewed" if obj.compound.package.reviewed else "unreviewed"
+
+
+# Package is special (no package FK)
+class PackageOutSchema(Schema):
+    uuid: UUID
+    url: str = ""
+    name: str
+    description: str
+    review_status: str = ""
+
+    @staticmethod
+    def resolve_url(obj):
+        return obj.url
+
+    @staticmethod
+    def resolve_review_status(obj):
+        return "reviewed" if obj.reviewed else "unreviewed"
+
+
+class SettingOutSchema(Schema):
+    uuid: UUID
+    url: str = ""
+    name: str
+    description: str

epdb/admin.py

@@ -1,27 +1,34 @@
+from django.conf import settings as s
 from django.contrib import admin
 
 from .models import (
-    User,
-    UserPackagePermission,
-    Group,
-    GroupPackagePermission,
-    Package,
-    MLRelativeReasoning,
     Compound,
     CompoundStructure,
-    SimpleAmbitRule,
-    ParallelRule,
-    Reaction,
-    Pathway,
-    Node,
     Edge,
+    EnviFormer,
+    ExternalDatabase,
+    ExternalIdentifier,
+    Group,
+    GroupPackagePermission,
+    JobLog,
+    License,
+    MLRelativeReasoning,
+    Node,
+    ParallelRule,
+    Pathway,
+    Reaction,
     Scenario,
-    Setting
+    Setting,
+    SimpleAmbitRule,
+    User,
+    UserPackagePermission,
 )
 
+Package = s.GET_PACKAGE_MODEL()
+
 
 class UserAdmin(admin.ModelAdmin):
-    pass
+    list_display = ["username", "email", "is_active", "is_staff", "is_superuser"]
 
 
 class UserPackagePermissionAdmin(admin.ModelAdmin):
@@ -36,17 +43,32 @@ class GroupPackagePermissionAdmin(admin.ModelAdmin):
     pass
 
 
+class JobLogAdmin(admin.ModelAdmin):
+    pass
+
+
 class EPAdmin(admin.ModelAdmin):
-    search_fields = ['name', 'description']
+    search_fields = ["name", "description", "url", "uuid"]
+    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 +109,23 @@ 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 +136,5 @@ 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

@@ -2,26 +2,18 @@ from typing import List
 
 from django.contrib.auth import get_user_model
 from ninja import Router, Schema, Field
-from ninja.errors import HttpError
 from ninja.pagination import paginate
-from ninja.security import HttpBearer
+
+from epapi.v1.auth import BearerTokenAuth
 
 from .logic import PackageManager
-from .models import User, Compound, APIToken
-
-
-class BearerTokenAuth(HttpBearer):
-    def authenticate(self, request, token):
-        for token_obj in APIToken.objects.select_related("user").all():
-            if token_obj.check_token(token) and token_obj.is_valid():
-                return token_obj.user
-        raise HttpError(401, "Invalid or expired token")
+from .models import User, Compound
 
 
 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 +77,9 @@ 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 +91,9 @@ 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 +101,5 @@ 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

@@ -1,9 +1,17 @@
+import logging
+
 from django.apps import AppConfig
+from django.conf import settings
+
+logger = logging.getLogger(__name__)
 
 
 class EPDBConfig(AppConfig):
-    default_auto_field = 'django.db.models.BigAutoField'
-    name = 'epdb'
+    default_auto_field = "django.db.models.BigAutoField"
+    name = "epdb"
 
     def ready(self):
         import epdb.signals  # noqa: F401
+
+        model_name = getattr(settings, "EPDB_PACKAGE_MODEL", "epdb.Package")
+        logger.info(f"Using Package model: {model_name}")

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 django.conf import settings as s
+
+
+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 = s.GET_PACKAGE_MODEL().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 +5,54 @@ 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,
+    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():
-            anon = UserManager.create_user("anonymous", "anon@envipath.com", "SuperSafe",
-                                           is_active=True, add_to_group=False, set_setting=False)
+        if not User.objects.filter(email="anon@envipath.com").exists():
+            anon = UserManager.create_user(
+                "anonymous",
+                "anon@envipath.com",
+                "SuperSafe",
+                is_active=True,
+                add_to_group=False,
+                set_setting=False,
+            )
         else:
-            anon = User.objects.get(email='anon@envipath.com')
+            anon = User.objects.get(email="anon@envipath.com")
 
         # Admin User
-        if not User.objects.filter(email='admin@envipath.com').exists():
-            admin = UserManager.create_user("admin", "admin@envipath.com", "SuperSafe",
-                                            is_active=True, add_to_group=False, set_setting=False)
+        if not User.objects.filter(email="admin@envipath.com").exists():
+            admin = UserManager.create_user(
+                "admin",
+                "admin@envipath.com",
+                "SuperSafe",
+                is_active=True,
+                add_to_group=False,
+                set_setting=False,
+            )
             admin.is_staff = True
             admin.is_superuser = True
             admin.save()
         else:
-            admin = User.objects.get(email='admin@envipath.com')
+            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 +65,20 @@ class Command(BaseCommand):
         admin.default_group = g
         admin.save()
 
-        if not User.objects.filter(email='user0@envipath.com').exists():
-            user0 = UserManager.create_user("user0", "user0@envipath.com", "SuperSafe",
-                                            is_active=True, add_to_group=False, set_setting=False)
+        if not User.objects.filter(email="user0@envipath.com").exists():
+            user0 = UserManager.create_user(
+                "user0",
+                "user0@envipath.com",
+                "SuperSafe",
+                is_active=True,
+                add_to_group=False,
+                set_setting=False,
+            )
             user0.is_staff = True
             user0.is_superuser = True
             user0.save()
         else:
-            user0 = User.objects.get(email='user0@envipath.com')
+            user0 = User.objects.get(email="user0@envipath.com")
 
         g.user_member.add(user0)
         g.save()
@@ -60,19 +88,32 @@ 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',
-            description='Global Default Setting containing BBD Rules and Max 30 Nodes and Max Depth of 8',
+            name="Global Default Setting",
+            description="Global Default Setting containing BBD Rules and Max 30 Nodes and Max Depth of 8",
             max_nodes=30,
             max_depth=5,
             rule_packages=packages,
             model=None,
-            model_threshold=None
+            model_threshold=None,
         )
 
         return s
@@ -84,57 +125,58 @@ class Command(BaseCommand):
         """
         databases = [
             {
-                'name': 'PubChem Compound',
-                'full_name': 'PubChem Compound Database',
-                'description': 'Chemical database of small organic molecules',
-                'base_url': 'https://pubchem.ncbi.nlm.nih.gov',
-                'url_pattern': 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'
+                "name": "PubChem Compound",
+                "full_name": "PubChem Compound Database",
+                "description": "Chemical database of small organic molecules",
+                "base_url": "https://pubchem.ncbi.nlm.nih.gov",
+                "url_pattern": "https://pubchem.ncbi.nlm.nih.gov/compound/{id}",
             },
             {
-                'name': 'PubChem Substance',
-                'full_name': 'PubChem Substance Database',
-                'description': 'Database of chemical substances',
-                'base_url': 'https://pubchem.ncbi.nlm.nih.gov',
-                'url_pattern': 'https://pubchem.ncbi.nlm.nih.gov/substance/{id}'
+                "name": "PubChem Substance",
+                "full_name": "PubChem Substance Database",
+                "description": "Database of chemical substances",
+                "base_url": "https://pubchem.ncbi.nlm.nih.gov",
+                "url_pattern": "https://pubchem.ncbi.nlm.nih.gov/substance/{id}",
             },
             {
-                'name': 'ChEBI',
-                'full_name': 'Chemical Entities of Biological Interest',
-                'description': 'Dictionary of molecular entities',
-                'base_url': 'https://www.ebi.ac.uk/chebi',
-                'url_pattern': 'https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:{id}'
+                "name": "ChEBI",
+                "full_name": "Chemical Entities of Biological Interest",
+                "description": "Dictionary of molecular entities",
+                "base_url": "https://www.ebi.ac.uk/chebi",
+                "url_pattern": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:{id}",
             },
             {
-                'name': 'RHEA',
-                'full_name': 'RHEA Reaction Database',
-                'description': 'Comprehensive resource of biochemical reactions',
-                'base_url': 'https://www.rhea-db.org',
-                'url_pattern': 'https://www.rhea-db.org/rhea/{id}'
+                "name": "RHEA",
+                "full_name": "RHEA Reaction Database",
+                "description": "Comprehensive resource of biochemical reactions",
+                "base_url": "https://www.rhea-db.org",
+                "url_pattern": "https://www.rhea-db.org/rhea/{id}",
             },
             {
-                'name': 'KEGG Reaction',
-                'full_name': 'KEGG Reaction Database',
-                'description': 'Database of biochemical reactions',
-                'base_url': 'https://www.genome.jp',
-                'url_pattern': 'https://www.genome.jp/entry/reaction+{id}'
+                "name": "KEGG Reaction",
+                "full_name": "KEGG Reaction Database",
+                "description": "Database of biochemical reactions",
+                "base_url": "https://www.genome.jp",
+                "url_pattern": "https://www.genome.jp/entry/{id}",
             },
             {
-                'name': 'UniProt',
-                'full_name': 'MetaCyc Metabolic Pathway Database',
-                'description': 'UniProt is a freely accessible database of protein sequence and functional information',
-                'base_url': 'https://www.uniprot.org',
-                'url_pattern': 'https://www.uniprot.org/uniprotkb?query="{id}"'
-            }
+                "name": "UniProt",
+                "full_name": "MetaCyc Metabolic Pathway Database",
+                "description": "UniProt is a freely accessible database of protein sequence and functional information",
+                "base_url": "https://www.uniprot.org",
+                "url_pattern": 'https://www.uniprot.org/uniprotkb?query="{id}"',
+            },
         ]
 
         for db_info in databases:
-            ExternalDatabase.objects.get_or_create(
-                name=db_info['name'],
-                defaults=db_info
-            )
+            ExternalDatabase.objects.get_or_create(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 +184,24 @@ class Command(BaseCommand):
 
         # Import Packages
         packages = [
-            'EAWAG-BBD.json',
-            'EAWAG-SOIL.json',
-            'EAWAG-SLUDGE.json',
-            'EAWAG-SEDIMENT.json',
+            "EAWAG-BBD.json",
+            "EAWAG-SOIL.json",
+            "EAWAG-SLUDGE.json",
+            "EAWAG-SEDIMENT.json",
         ]
 
         mapping = {}
         for p in packages:
             print(f"Importing {p}...")
-            package_data = json.loads(open(s.BASE_DIR / 'fixtures' / 'packages' / '2025-07-18' / p).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 +217,23 @@ class Command(BaseCommand):
             usp.save()
 
         # Create Model Package
-        pack = PackageManager.create_package(admin, "Public Prediction Models",
-                                             "Package to make Prediction Models publicly available")
+        pack = PackageManager.create_package(
+            admin,
+            "Public Prediction Models",
+            "Package to make Prediction Models publicly available",
+        )
         pack.reviewed = True
         pack.save()
 
         # Create RR
         ml_model = MLRelativeReasoning.create(
             package=pack,
-            rule_packages=[mapping['EAWAG-BBD']],
-            data_packages=[mapping['EAWAG-BBD']],
-            eval_packages=[],
+            rule_packages=[mapping["EAWAG-BBD"]],
+            data_packages=[mapping["EAWAG-BBD"]],
             threshold=0.5,
-            name='ECC - BBD - T0.5',
-            description='ML Relative Reasoning',
+            name="ECC - BBD - T0.5",
+            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)

epdb/management/commands/create_api_token.py

@@ -0,0 +1,92 @@
+from django.conf import settings as s
+from django.contrib.auth import get_user_model
+from django.core.management.base import BaseCommand, CommandError
+
+from epdb.models import APIToken
+
+
+class Command(BaseCommand):
+    help = "Create an API token for a user"
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "--username",
+            required=True,
+            help="Username of the user who will own the token",
+        )
+        parser.add_argument(
+            "--name",
+            required=True,
+            help="Descriptive name for the token",
+        )
+        parser.add_argument(
+            "--expires-days",
+            type=int,
+            default=90,
+            help="Days until expiration (0 for no expiration)",
+        )
+        parser.add_argument(
+            "--inactive",
+            action="store_true",
+            help="Create the token as inactive",
+        )
+        parser.add_argument(
+            "--curl",
+            action="store_true",
+            help="Print a curl example using the token",
+        )
+        parser.add_argument(
+            "--base-url",
+            default=None,
+            help="Base URL for curl example (default SERVER_URL or http://localhost:8000)",
+        )
+        parser.add_argument(
+            "--endpoint",
+            default="/api/v1/compounds/",
+            help="Endpoint path for curl example",
+        )
+
+    def handle(self, *args, **options):
+        username = options["username"]
+        name = options["name"]
+        expires_days = options["expires_days"]
+
+        if expires_days < 0:
+            raise CommandError("--expires-days must be >= 0")
+
+        if expires_days == 0:
+            expires_days = None
+
+        user_model = get_user_model()
+        try:
+            user = user_model.objects.get(username=username)
+        except user_model.DoesNotExist as exc:
+            raise CommandError(f"User not found for username '{username}'") from exc
+
+        token, raw_token = APIToken.create_token(user, name=name, expires_days=expires_days)
+
+        if options["inactive"]:
+            token.is_active = False
+            token.save(update_fields=["is_active"])
+
+        self.stdout.write(f"User: {user.username} ({user.email})")
+        self.stdout.write(f"Token name: {token.name}")
+        self.stdout.write(f"Token id: {token.id}")
+        if token.expires_at:
+            self.stdout.write(f"Expires at: {token.expires_at.isoformat()}")
+        else:
+            self.stdout.write("Expires at: never")
+        self.stdout.write(f"Active: {token.is_active}")
+        self.stdout.write("Raw token:")
+        self.stdout.write(raw_token)
+
+        if options["curl"]:
+            base_url = (
+                options["base_url"] or getattr(s, "SERVER_URL", None) or "http://localhost:8000"
+            )
+            endpoint = options["endpoint"]
+            endpoint = endpoint if endpoint.startswith("/") else f"/{endpoint}"
+            url = f"{base_url.rstrip('/')}{endpoint}"
+            curl_cmd = f'curl -H "Authorization: Bearer {raw_token}" "{url}"'
+            self.stdout.write("Curl:")
+            self.stdout.write(curl_cmd)

epdb/management/commands/create_ml_models.py

@@ -0,0 +1,121 @@
+from django.conf import settings as s
+from django.core.management.base import BaseCommand
+from django.db import transaction
+
+from epdb.models import EnviFormer, MLRelativeReasoning
+
+Package = s.GET_PACKAGE_MODEL()
+
+
+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,
+                    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,
+                    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.eval_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'])
-        package_data = json.load(open(options['data']))
+        owner = User.objects.get(username=options["owner"])
+        package_data = json.load(open(options["data"]))
         PackageManager.import_legacy_package(package_data, owner)

epdb/management/commands/load_enviformer.py

@@ -0,0 +1,83 @@
+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 = s.GET_PACKAGE_MODEL()
+
+
+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 +1,65 @@
 from django.apps import apps
+from django.conf import settings as s
 from django.core.management.base import BaseCommand
+from django.db.models import F, JSONField, TextField, Value
+from django.db.models.functions import Cast, Replace
 
-from django.db.models import F, Value
-from django.db.models.functions import Replace
+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):
+        Package = s.GET_PACKAGE_MODEL()
+        Package.objects.update(url=Replace(F("url"), Value(options["old"]), Value(options["new"])))
+
         MODELS = [
-            'User',
-            'Group',
-            'Package',
-            'Compound',
-            'CompoundStructure',
-            'Pathway',
-            'Edge',
-            'Node',
-            'Reaction',
-            'SimpleAmbitRule',
-            'SimpleRDKitRule',
-            'ParallelRule',
-            'SequentialRule',
-            'Scenario',
-            'Setting',
-            'MLRelativeReasoning',
-            'RuleBasedRelativeReasoning',
-            'EnviFormer',
-            'ApplicabilityDomain',
+            "User",
+            "Group",
+            "Compound",
+            "CompoundStructure",
+            "Pathway",
+            "Edge",
+            "Node",
+            "Reaction",
+            "SimpleAmbitRule",
+            "SimpleRDKitRule",
+            "ParallelRule",
+            "SequentialRule",
+            "Scenario",
+            "Setting",
+            "MLRelativeReasoning",
+            "RuleBasedRelativeReasoning",
+            "EnviFormer",
+            "ApplicabilityDomain",
+            "EnzymeLink",
         ]
         for model in MODELS:
             obj_cls = apps.get_model("epdb", model)
-            print(f"Localizing urls for {model}")
             obj_cls.objects.update(
-                url=Replace(F('url'), Value(options['old']), Value(options['new']))
+                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('logout'),
-                               reverse('admin:login'),
-                               reverse('admin:index'),
-                           ] + getattr(settings, 'LOGIN_EXEMPT_URLS', [])
+            reverse("login"),
+            reverse("logout"),
+            reverse("admin:login"),
+            reverse("admin:index"),
+        ] + getattr(settings, "LOGIN_EXEMPT_URLS", [])
 
     def __call__(self, request):
         if not request.user.is_authenticated:
             path = request.path_info
             if not any(path.startswith(url) for url in self.exempt_urls):
-                if request.method == 'GET':
-                    if request.get_full_path() and request.get_full_path() != '/':
-                        return redirect(f"{settings.LOGIN_URL}?next={quote(request.get_full_path())}")
+                if request.method == "GET":
+                    if request.get_full_path() and request.get_full_path() != "/":
+                        return redirect(
+                            f"{settings.LOGIN_URL}?next={quote(request.get_full_path())}"
+                        )
                 return redirect(settings.LOGIN_URL)
         return self.get_response(request)

epdb/migrations/0001_initial.py

@@ -1,6 +1,5 @@
-# Generated by Django 5.2.1 on 2025-07-22 20:58
+# Generated by Django 5.2.7 on 2026-02-12 12:36
 
-import datetime
 import django.contrib.auth.models
 import django.contrib.auth.validators
 import django.contrib.postgres.fields
@@ -19,11 +18,12 @@ class Migration(migrations.Migration):
     dependencies = [
         ('auth', '0012_alter_user_first_name_max_length'),
         ('contenttypes', '0002_remove_content_type_name'),
+        migrations.swappable_dependency(settings.EPDB_PACKAGE_MODEL),
     ]
 
     operations = [
         migrations.CreateModel(
-            name='Compound',
+            name='ApplicabilityDomain',
             fields=[
                 ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
                 ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
@@ -31,9 +31,33 @@ class Migration(migrations.Migration):
                 ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
                 ('name', models.TextField(default='no name', verbose_name='Name')),
                 ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
+                ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('num_neighbours', models.IntegerField(default=5)),
+                ('reliability_threshold', models.FloatField(default=0.5)),
+                ('local_compatibilty_threshold', models.FloatField(default=0.5)),
+                ('functional_groups', models.JSONField(blank=True, default=dict, null=True)),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.CreateModel(
+            name='Edge',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('name', models.TextField(default='no name', verbose_name='Name')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
                 ('kv', models.JSONField(blank=True, default=dict, null=True)),
                 ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
             ],
+            options={
+                'abstract': False,
+            },
         ),
         migrations.CreateModel(
             name='EPModel',
@@ -44,7 +68,9 @@ class Migration(migrations.Migration):
                 ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
                 ('name', models.TextField(default='no name', verbose_name='Name')),
                 ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
                 ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
                 ('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
             ],
             options={
@@ -52,6 +78,27 @@ class Migration(migrations.Migration):
                 'base_manager_name': 'objects',
             },
         ),
+        migrations.CreateModel(
+            name='ExternalDatabase',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
+                ('name', models.CharField(max_length=100, unique=True, verbose_name='Database Name')),
+                ('full_name', models.CharField(blank=True, max_length=255, verbose_name='Full Database Name')),
+                ('description', models.TextField(blank=True, verbose_name='Description')),
+                ('base_url', models.URLField(blank=True, null=True, verbose_name='Base URL')),
+                ('url_pattern', models.CharField(blank=True, help_text="URL pattern with {id} placeholder, e.g., 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'", max_length=500, verbose_name='URL Pattern')),
+                ('is_active', models.BooleanField(default=True, verbose_name='Is Active')),
+            ],
+            options={
+                'verbose_name': 'External Database',
+                'verbose_name_plural': 'External Databases',
+                'db_table': 'epdb_external_database',
+                'ordering': ['name'],
+            },
+        ),
         migrations.CreateModel(
             name='Permission',
             fields=[
@@ -65,6 +112,7 @@ class Migration(migrations.Migration):
             name='License',
             fields=[
                 ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('cc_string', models.TextField(verbose_name='CC string')),
                 ('link', models.URLField(verbose_name='link')),
                 ('image_link', models.URLField(verbose_name='Image link')),
             ],
@@ -78,8 +126,11 @@ class Migration(migrations.Migration):
                 ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
                 ('name', models.TextField(default='no name', verbose_name='Name')),
                 ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
                 ('kv', models.JSONField(blank=True, default=dict, null=True)),
                 ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
+                ('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
             ],
             options={
                 'abstract': False,
@@ -101,6 +152,9 @@ class Migration(migrations.Migration):
                 ('date_joined', models.DateTimeField(default=django.utils.timezone.now, verbose_name='date joined')),
                 ('email', models.EmailField(max_length=254, unique=True)),
                 ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
+                ('is_reviewer', models.BooleanField(default=False)),
+                ('default_package', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Default Package')),
                 ('groups', models.ManyToManyField(blank=True, help_text='The groups this user belongs to. A user will get all permissions granted to each of their groups.', related_name='user_set', related_query_name='user', to='auth.group', verbose_name='groups')),
                 ('user_permissions', models.ManyToManyField(blank=True, help_text='Specific permissions for this user.', related_name='user_set', related_query_name='user', to='auth.permission', verbose_name='user permissions')),
             ],
@@ -117,11 +171,34 @@ class Migration(migrations.Migration):
             name='APIToken',
             fields=[
                 ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('hashed_key', models.CharField(max_length=128, unique=True)),
-                ('created', models.DateTimeField(auto_now_add=True)),
-                ('expires_at', models.DateTimeField(blank=True, default=datetime.datetime(2025, 10, 20, 20, 58, 48, 351675, tzinfo=datetime.timezone.utc), null=True)),
-                ('name', models.CharField(blank=True, help_text='Optional name for the token', max_length=100)),
-                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('hashed_key', models.CharField(help_text='SHA-256 hash of the token key', max_length=128, unique=True)),
+                ('expires_at', models.DateTimeField(blank=True, help_text='Token expiration time (null for no expiration)', null=True)),
+                ('name', models.CharField(help_text='Descriptive name for this token', max_length=100)),
+                ('is_active', models.BooleanField(default=True, help_text='Whether this token is active')),
+                ('user', models.ForeignKey(help_text='User who owns this token', on_delete=django.db.models.deletion.CASCADE, related_name='api_tokens', to=settings.AUTH_USER_MODEL)),
+            ],
+            options={
+                'verbose_name': 'API Token',
+                'verbose_name_plural': 'API Tokens',
+                'db_table': 'epdb_api_token',
+                'ordering': ['-created'],
+            },
+        ),
+        migrations.CreateModel(
+            name='Compound',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('name', models.TextField(default='no name', verbose_name='Name')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
+                ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
             ],
         ),
         migrations.CreateModel(
@@ -133,6 +210,7 @@ class Migration(migrations.Migration):
                 ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
                 ('name', models.TextField(default='no name', verbose_name='Name')),
                 ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
                 ('kv', models.JSONField(blank=True, default=dict, null=True)),
                 ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
                 ('smiles', models.TextField(verbose_name='SMILES')),
@@ -150,36 +228,6 @@ class Migration(migrations.Migration):
             name='default_structure',
             field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='compound_default_structure', to='epdb.compoundstructure', verbose_name='Default Structure'),
         ),
-        migrations.CreateModel(
-            name='Edge',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('polymorphic_ctype', models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-        ),
-        migrations.CreateModel(
-            name='EnviFormer',
-            fields=[
-                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
-                ('threshold', models.FloatField(default=0.5)),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.epmodel',),
-        ),
         migrations.CreateModel(
             name='PluginModel',
             fields=[
@@ -191,17 +239,6 @@ class Migration(migrations.Migration):
             },
             bases=('epdb.epmodel',),
         ),
-        migrations.CreateModel(
-            name='RuleBaseRelativeReasoning',
-            fields=[
-                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
-            ],
-            options={
-                'abstract': False,
-                'base_manager_name': 'objects',
-            },
-            bases=('epdb.epmodel',),
-        ),
         migrations.CreateModel(
             name='Group',
             fields=[
@@ -209,10 +246,11 @@ class Migration(migrations.Migration):
                 ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
                 ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
                 ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
                 ('name', models.TextField(verbose_name='Group name')),
                 ('public', models.BooleanField(default=False, verbose_name='Public Group')),
                 ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('group_member', models.ManyToManyField(related_name='groups_in_group', to='epdb.group', verbose_name='Group member')),
+                ('group_member', models.ManyToManyField(blank=True, related_name='groups_in_group', to='epdb.group', verbose_name='Group member')),
                 ('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Group Owner')),
                 ('user_member', models.ManyToManyField(related_name='users_in_group', to=settings.AUTH_USER_MODEL, verbose_name='User members')),
             ],
@@ -225,6 +263,41 @@ class Migration(migrations.Migration):
             name='default_group',
             field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='default_group', to='epdb.group', verbose_name='Default Group'),
         ),
+        migrations.CreateModel(
+            name='JobLog',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('task_id', models.UUIDField(unique=True)),
+                ('job_name', models.TextField()),
+                ('status', models.CharField(choices=[('INITIAL', 'Initial'), ('SUCCESS', 'Success'), ('FAILURE', 'Failure'), ('REVOKED', 'Revoked'), ('IGNORED', 'Ignored')], default='INITIAL', max_length=20)),
+                ('done_at', models.DateTimeField(blank=True, default=None, null=True)),
+                ('task_result', models.TextField(blank=True, default=None, null=True)),
+                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+        migrations.CreateModel(
+            name='Package',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('name', models.TextField(default='no name', verbose_name='Name')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
+                ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('reviewed', models.BooleanField(default=False, verbose_name='Reviewstatus')),
+                ('license', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.license', verbose_name='License')),
+            ],
+            options={
+                'swappable': 'EPDB_PACKAGE_MODEL',
+            },
+        ),
         migrations.CreateModel(
             name='Node',
             fields=[
@@ -234,9 +307,11 @@ class Migration(migrations.Migration):
                 ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
                 ('name', models.TextField(default='no name', verbose_name='Name')),
                 ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
                 ('kv', models.JSONField(blank=True, default=dict, null=True)),
                 ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
                 ('depth', models.IntegerField(verbose_name='Node depth')),
+                ('stereo_removed', models.BooleanField(default=False)),
                 ('default_node_label', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='default_node_structure', to='epdb.compoundstructure', verbose_name='Default Node Label')),
                 ('node_labels', models.ManyToManyField(related_name='node_structures', to='epdb.compoundstructure', verbose_name='All Node Labels')),
                 ('out_edges', models.ManyToManyField(to='epdb.edge', verbose_name='Outgoing Edges')),
@@ -255,38 +330,6 @@ class Migration(migrations.Migration):
             name='start_nodes',
             field=models.ManyToManyField(related_name='edge_educts', to='epdb.node', verbose_name='Start Nodes'),
         ),
-        migrations.CreateModel(
-            name='Package',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('reviewed', models.BooleanField(default=False, verbose_name='Reviewstatus')),
-                ('license', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.license', verbose_name='License')),
-            ],
-            options={
-                'abstract': False,
-            },
-        ),
-        migrations.AddField(
-            model_name='epmodel',
-            name='package',
-            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package'),
-        ),
-        migrations.AddField(
-            model_name='compound',
-            name='package',
-            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package'),
-        ),
-        migrations.AddField(
-            model_name='user',
-            name='default_package',
-            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.package', verbose_name='Default Package'),
-        ),
         migrations.CreateModel(
             name='SequentialRule',
             fields=[
@@ -309,16 +352,6 @@ class Migration(migrations.Migration):
             },
             bases=('epdb.rule',),
         ),
-        migrations.AddField(
-            model_name='rule',
-            name='package',
-            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package'),
-        ),
-        migrations.AddField(
-            model_name='rule',
-            name='polymorphic_ctype',
-            field=models.ForeignKey(editable=False, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='polymorphic_%(app_label)s.%(class)s_set+', to='contenttypes.contenttype'),
-        ),
         migrations.CreateModel(
             name='Pathway',
             fields=[
@@ -328,9 +361,11 @@ class Migration(migrations.Migration):
                 ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
                 ('name', models.TextField(default='no name', verbose_name='Name')),
                 ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
                 ('kv', models.JSONField(blank=True, default=dict, null=True)),
                 ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
+                ('predicted', models.BooleanField(default=False)),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
             ],
             options={
                 'abstract': False,
@@ -355,12 +390,13 @@ class Migration(migrations.Migration):
                 ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
                 ('name', models.TextField(default='no name', verbose_name='Name')),
                 ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
                 ('kv', models.JSONField(blank=True, default=dict, null=True)),
                 ('aliases', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), default=list, size=None, verbose_name='Aliases')),
                 ('multi_step', models.BooleanField(verbose_name='Multistep Reaction')),
                 ('medline_references', django.contrib.postgres.fields.ArrayField(base_field=models.TextField(), null=True, size=None, verbose_name='Medline References')),
                 ('educts', models.ManyToManyField(related_name='reaction_educts', to='epdb.compoundstructure', verbose_name='Educts')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
                 ('products', models.ManyToManyField(related_name='reaction_products', to='epdb.compoundstructure', verbose_name='Products')),
                 ('rules', models.ManyToManyField(related_name='reaction_rule', to='epdb.rule', verbose_name='Rule')),
             ],
@@ -368,6 +404,28 @@ class Migration(migrations.Migration):
                 'abstract': False,
             },
         ),
+        migrations.CreateModel(
+            name='EnzymeLink',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
+                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('name', models.TextField(default='no name', verbose_name='Name')),
+                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
+                ('kv', models.JSONField(blank=True, default=dict, null=True)),
+                ('ec_number', models.TextField(verbose_name='EC Number')),
+                ('classification_level', models.IntegerField(verbose_name='Classification Level')),
+                ('linking_method', models.TextField(verbose_name='Linking Method')),
+                ('edge_evidence', models.ManyToManyField(to='epdb.edge')),
+                ('rule', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.rule')),
+                ('reaction_evidence', models.ManyToManyField(to='epdb.reaction')),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
         migrations.AddField(
             model_name='edge',
             name='edge_label',
@@ -382,11 +440,12 @@ class Migration(migrations.Migration):
                 ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
                 ('name', models.TextField(default='no name', verbose_name='Name')),
                 ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
                 ('kv', models.JSONField(blank=True, default=dict, null=True)),
                 ('scenario_date', models.CharField(default='No date', max_length=256)),
                 ('scenario_type', models.CharField(default='Not specified', max_length=256)),
                 ('additional_information', models.JSONField(verbose_name='Additional Information')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Package')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Package')),
                 ('parent', models.ForeignKey(default=None, null=True, on_delete=django.db.models.deletion.CASCADE, to='epdb.scenario')),
             ],
             options={
@@ -437,14 +496,16 @@ class Migration(migrations.Migration):
                 ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
                 ('name', models.TextField(default='no name', verbose_name='Name')),
                 ('description', models.TextField(default='no description', verbose_name='Descriptions')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
                 ('kv', models.JSONField(blank=True, default=dict, null=True)),
                 ('public', models.BooleanField(default=False)),
                 ('global_default', models.BooleanField(default=False)),
                 ('max_depth', models.IntegerField(default=5, verbose_name='Setting Max Depth')),
                 ('max_nodes', models.IntegerField(default=30, verbose_name='Setting Max Number of Nodes')),
                 ('model_threshold', models.FloatField(blank=True, default=0.25, null=True, verbose_name='Setting Model Threshold')),
+                ('expansion_scheme', models.CharField(choices=[('BFS', 'Breadth First Search'), ('DFS', 'Depth First Search'), ('GREEDY', 'Greedy')], default='BFS', max_length=20)),
                 ('model', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.epmodel', verbose_name='Setting EPModel')),
-                ('rule_packages', models.ManyToManyField(blank=True, related_name='setting_rule_packages', to='epdb.package', verbose_name='Setting Rule Packages')),
+                ('rule_packages', models.ManyToManyField(blank=True, related_name='setting_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Setting Rule Packages')),
             ],
             options={
                 'abstract': False,
@@ -461,39 +522,86 @@ class Migration(migrations.Migration):
             field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.setting', verbose_name='The users default settings'),
         ),
         migrations.CreateModel(
-            name='MLRelativeReasoning',
+            name='EnviFormer',
             fields=[
                 ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
                 ('threshold', models.FloatField(default=0.5)),
-                ('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
                 ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
-                ('data_packages', models.ManyToManyField(related_name='data_packages', to='epdb.package', verbose_name='Data Packages')),
-                ('eval_packages', models.ManyToManyField(related_name='eval_packages', to='epdb.package', verbose_name='Evaluation Packages')),
-                ('rule_packages', models.ManyToManyField(related_name='rule_packages', to='epdb.package', verbose_name='Rule Packages')),
+                ('multigen_eval', models.BooleanField(default=False)),
+                ('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
+                ('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
+                ('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
+                ('eval_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
+                ('rule_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
             ],
             options={
                 'abstract': False,
-                'base_manager_name': 'objects',
             },
             bases=('epdb.epmodel',),
         ),
         migrations.CreateModel(
-            name='ApplicabilityDomain',
+            name='MLRelativeReasoning',
+            fields=[
+                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
+                ('threshold', models.FloatField(default=0.5)),
+                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
+                ('multigen_eval', models.BooleanField(default=False)),
+                ('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
+                ('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
+                ('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
+                ('eval_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
+                ('rule_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
+            ],
+            options={
+                'abstract': False,
+            },
+            bases=('epdb.epmodel',),
+        ),
+        migrations.AddField(
+            model_name='applicabilitydomain',
+            name='model',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.mlrelativereasoning'),
+        ),
+        migrations.CreateModel(
+            name='RuleBasedRelativeReasoning',
+            fields=[
+                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
+                ('threshold', models.FloatField(default=0.5)),
+                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
+                ('multigen_eval', models.BooleanField(default=False)),
+                ('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
+                ('min_count', models.IntegerField(default=10)),
+                ('max_count', models.IntegerField(default=0)),
+                ('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
+                ('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Data Packages')),
+                ('eval_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Evaluation Packages')),
+                ('rule_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to=settings.EPDB_PACKAGE_MODEL, verbose_name='Rule Packages')),
+            ],
+            options={
+                'abstract': False,
+            },
+            bases=('epdb.epmodel',),
+        ),
+        migrations.CreateModel(
+            name='ExternalIdentifier',
             fields=[
                 ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
                 ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
                 ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
-                ('name', models.TextField(default='no name', verbose_name='Name')),
-                ('description', models.TextField(default='no description', verbose_name='Descriptions')),
-                ('kv', models.JSONField(blank=True, default=dict, null=True)),
-                ('num_neighbours', models.FloatField(default=5)),
-                ('reliability_threshold', models.FloatField(default=0.5)),
-                ('local_compatibilty_threshold', models.FloatField(default=0.5)),
-                ('model', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.mlrelativereasoning')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
+                ('object_id', models.IntegerField()),
+                ('identifier_value', models.CharField(max_length=255, verbose_name='Identifier Value')),
+                ('url', models.URLField(blank=True, null=True, verbose_name='Direct URL')),
+                ('is_primary', models.BooleanField(default=False, help_text='Mark this as the primary identifier for this database', verbose_name='Is Primary')),
+                ('content_type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
+                ('database', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.externaldatabase', verbose_name='External Database')),
             ],
             options={
-                'abstract': False,
+                'verbose_name': 'External Identifier',
+                'verbose_name_plural': 'External Identifiers',
+                'db_table': 'epdb_external_identifier',
+                'indexes': [models.Index(fields=['content_type', 'object_id'], name='epdb_extern_content_b76813_idx'), models.Index(fields=['database', 'identifier_value'], name='epdb_extern_databas_486422_idx')],
+                'unique_together': {('content_type', 'object_id', 'database', 'identifier_value')},
             },
         ),
         migrations.CreateModel(
@@ -558,7 +666,7 @@ class Migration(migrations.Migration):
                 ('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
                 ('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
                 ('group', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.group', verbose_name='Permission to')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Permission on')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Permission on')),
             ],
             options={
                 'unique_together': {('package', 'group')},
@@ -570,7 +678,7 @@ class Migration(migrations.Migration):
             fields=[
                 ('permission_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, to='epdb.permission')),
                 ('uuid', models.UUIDField(default=uuid.uuid4, primary_key=True, serialize=False, verbose_name='UUID of this object')),
-                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.package', verbose_name='Permission on')),
+                ('package', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.EPDB_PACKAGE_MODEL, verbose_name='Permission on')),
                 ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Permission to')),
             ],
             options={

epdb/migrations/0002_auto_20260212_1240.py

@@ -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("bayer", "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", "0001_initial"),
+    ]
+
+    operations = [migrations.RunPython(set_cc)]

epdb/migrations/0002_externaldatabase_alter_apitoken_options_and_more.py

@@ -1,128 +0,0 @@
-# Generated by Django 5.2.1 on 2025-08-25 18:07
-
-import django.db.models.deletion
-import django.utils.timezone
-import model_utils.fields
-import uuid
-from django.conf import settings
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('contenttypes', '0002_remove_content_type_name'),
-        ('epdb', '0001_initial'),
-    ]
-
-    operations = [
-        migrations.CreateModel(
-            name='ExternalDatabase',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
-                ('name', models.CharField(max_length=100, unique=True, verbose_name='Database Name')),
-                ('full_name', models.CharField(blank=True, max_length=255, verbose_name='Full Database Name')),
-                ('description', models.TextField(blank=True, verbose_name='Description')),
-                ('base_url', models.URLField(blank=True, null=True, verbose_name='Base URL')),
-                ('url_pattern', models.CharField(blank=True, help_text="URL pattern with {id} placeholder, e.g., 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'", max_length=500, verbose_name='URL Pattern')),
-                ('is_active', models.BooleanField(default=True, verbose_name='Is Active')),
-            ],
-            options={
-                'verbose_name': 'External Database',
-                'verbose_name_plural': 'External Databases',
-                'db_table': 'epdb_external_database',
-                'ordering': ['name'],
-            },
-        ),
-        migrations.AlterModelOptions(
-            name='apitoken',
-            options={'ordering': ['-created'], 'verbose_name': 'API Token', 'verbose_name_plural': 'API Tokens'},
-        ),
-        migrations.AlterModelOptions(
-            name='edge',
-            options={},
-        ),
-        migrations.RemoveField(
-            model_name='edge',
-            name='polymorphic_ctype',
-        ),
-        migrations.AddField(
-            model_name='apitoken',
-            name='is_active',
-            field=models.BooleanField(default=True, help_text='Whether this token is active'),
-        ),
-        migrations.AddField(
-            model_name='apitoken',
-            name='modified',
-            field=model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified'),
-        ),
-        migrations.AddField(
-            model_name='applicabilitydomain',
-            name='functional_groups',
-            field=models.JSONField(blank=True, default=dict, null=True),
-        ),
-        migrations.AddField(
-            model_name='mlrelativereasoning',
-            name='app_domain',
-            field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain'),
-        ),
-        migrations.AlterField(
-            model_name='apitoken',
-            name='created',
-            field=model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created'),
-        ),
-        migrations.AlterField(
-            model_name='apitoken',
-            name='expires_at',
-            field=models.DateTimeField(blank=True, help_text='Token expiration time (null for no expiration)', null=True),
-        ),
-        migrations.AlterField(
-            model_name='apitoken',
-            name='hashed_key',
-            field=models.CharField(help_text='SHA-256 hash of the token key', max_length=128, unique=True),
-        ),
-        migrations.AlterField(
-            model_name='apitoken',
-            name='name',
-            field=models.CharField(help_text='Descriptive name for this token', max_length=100),
-        ),
-        migrations.AlterField(
-            model_name='apitoken',
-            name='user',
-            field=models.ForeignKey(help_text='User who owns this token', on_delete=django.db.models.deletion.CASCADE, related_name='api_tokens', to=settings.AUTH_USER_MODEL),
-        ),
-        migrations.AlterField(
-            model_name='applicabilitydomain',
-            name='num_neighbours',
-            field=models.IntegerField(default=5),
-        ),
-        migrations.AlterModelTable(
-            name='apitoken',
-            table='epdb_api_token',
-        ),
-        migrations.CreateModel(
-            name='ExternalIdentifier',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('created', model_utils.fields.AutoCreatedField(default=django.utils.timezone.now, editable=False, verbose_name='created')),
-                ('modified', model_utils.fields.AutoLastModifiedField(default=django.utils.timezone.now, editable=False, verbose_name='modified')),
-                ('uuid', models.UUIDField(default=uuid.uuid4, editable=False, unique=True)),
-                ('object_id', models.IntegerField()),
-                ('identifier_value', models.CharField(max_length=255, verbose_name='Identifier Value')),
-                ('url', models.URLField(blank=True, null=True, verbose_name='Direct URL')),
-                ('is_primary', models.BooleanField(default=False, help_text='Mark this as the primary identifier for this database', verbose_name='Is Primary')),
-                ('content_type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
-                ('database', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='epdb.externaldatabase', verbose_name='External Database')),
-            ],
-            options={
-                'verbose_name': 'External Identifier',
-                'verbose_name_plural': 'External Identifiers',
-                'db_table': 'epdb_external_identifier',
-                'indexes': [models.Index(fields=['content_type', 'object_id'], name='epdb_extern_content_b76813_idx'), models.Index(fields=['database', 'identifier_value'], name='epdb_extern_databas_486422_idx')],
-                'unique_together': {('content_type', 'object_id', 'database', 'identifier_value')},
-            },
-        ),
-    ]

epdb/migrations/0003_applicabilitydomain_url_compound_url_and_more.py

@@ -1,228 +0,0 @@
-# Generated by Django 5.2.1 on 2025-08-26 17:05
-
-from django.db import migrations, models
-
-
-def populate_url(apps, schema_editor):
-    MODELS = [
-        'User',
-        'Group',
-        'Package',
-        'Compound',
-        'CompoundStructure',
-        'Pathway',
-        'Edge',
-        'Node',
-        'Reaction',
-        'SimpleAmbitRule',
-        'SimpleRDKitRule',
-        'ParallelRule',
-        'SequentialRule',
-        'Scenario',
-        'Setting',
-        'MLRelativeReasoning',
-        'EnviFormer',
-        'ApplicabilityDomain',
-    ]
-    for model in MODELS:
-        obj_cls = apps.get_model("epdb", model)
-        for obj in obj_cls.objects.all():
-            obj.url = assemble_url(obj)
-            if obj.url is None:
-                raise ValueError(f"Could not assemble url for {obj}")
-            obj.save()
-
-
-def assemble_url(obj):
-    from django.conf import settings as s
-    match obj.__class__.__name__:
-        case 'User':
-            return '{}/user/{}'.format(s.SERVER_URL, obj.uuid)
-        case 'Group':
-            return '{}/group/{}'.format(s.SERVER_URL, obj.uuid)
-        case 'Package':
-            return '{}/package/{}'.format(s.SERVER_URL, obj.uuid)
-        case 'Compound':
-            return '{}/compound/{}'.format(obj.package.url, obj.uuid)
-        case 'CompoundStructure':
-            return '{}/structure/{}'.format(obj.compound.url, obj.uuid)
-        case 'SimpleAmbitRule':
-            return '{}/simple-ambit-rule/{}'.format(obj.package.url, obj.uuid)
-        case 'SimpleRDKitRule':
-            return '{}/simple-rdkit-rule/{}'.format(obj.package.url, obj.uuid)
-        case 'ParallelRule':
-            return '{}/parallel-rule/{}'.format(obj.package.url, obj.uuid)
-        case 'SequentialRule':
-            return '{}/sequential-rule/{}'.format(obj.compound.url, obj.uuid)
-        case 'Reaction':
-            return '{}/reaction/{}'.format(obj.package.url, obj.uuid)
-        case 'Pathway':
-            return '{}/pathway/{}'.format(obj.package.url, obj.uuid)
-        case 'Node':
-            return '{}/node/{}'.format(obj.pathway.url, obj.uuid)
-        case 'Edge':
-            return '{}/edge/{}'.format(obj.pathway.url, obj.uuid)
-        case 'MLRelativeReasoning':
-            return '{}/model/{}'.format(obj.package.url, obj.uuid)
-        case 'EnviFormer':
-            return '{}/model/{}'.format(obj.package.url, obj.uuid)
-        case 'ApplicabilityDomain':
-            return '{}/model/{}/applicability-domain/{}'.format(obj.model.package.url, obj.model.uuid, obj.uuid)
-        case 'Scenario':
-            return '{}/scenario/{}'.format(obj.package.url, obj.uuid)
-        case 'Setting':
-            return '{}/setting/{}'.format(s.SERVER_URL, obj.uuid)
-        case _:
-            raise ValueError(f"Unknown model {obj.__class__.__name__}")
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ('epdb', '0002_externaldatabase_alter_apitoken_options_and_more'),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name='applicabilitydomain',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='compound',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='compoundstructure',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='edge',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='epmodel',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='group',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='node',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='package',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='pathway',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='reaction',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='rule',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='scenario',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='setting',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-        migrations.AddField(
-            model_name='user',
-            name='url',
-            field=models.TextField(null=True, unique=False, verbose_name='URL'),
-        ),
-
-        migrations.RunPython(populate_url, reverse_code=migrations.RunPython.noop),
-
-        migrations.AlterField(
-            model_name='applicabilitydomain',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='compound',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='compoundstructure',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='edge',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='epmodel',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='group',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='node',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='package',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='pathway',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='reaction',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='rule',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='scenario',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='setting',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-        migrations.AlterField(
-            model_name='user',
-            name='url',
-            field=models.TextField(null=True, unique=True, verbose_name='URL'),
-        ),
-    ]

epdb/migrations/0004_alter_mlrelativereasoning_options_and_more.py

@@ -1,55 +0,0 @@
-# Generated by Django 5.2.1 on 2025-09-09 09:21
-
-import django.db.models.deletion
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('epdb', '0001_squashed_0003_applicabilitydomain_url_compound_url_and_more'),
-    ]
-
-    operations = [
-        migrations.AlterModelOptions(
-            name='mlrelativereasoning',
-            options={},
-        ),
-        migrations.AlterField(
-            model_name='mlrelativereasoning',
-            name='data_packages',
-            field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to='epdb.package', verbose_name='Data Packages'),
-        ),
-        migrations.AlterField(
-            model_name='mlrelativereasoning',
-            name='eval_packages',
-            field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to='epdb.package', verbose_name='Evaluation Packages'),
-        ),
-        migrations.AlterField(
-            model_name='mlrelativereasoning',
-            name='rule_packages',
-            field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to='epdb.package', verbose_name='Rule Packages'),
-        ),
-        migrations.CreateModel(
-            name='RuleBasedRelativeReasoning',
-            fields=[
-                ('epmodel_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.epmodel')),
-                ('threshold', models.FloatField(default=0.5)),
-                ('eval_results', models.JSONField(blank=True, default=dict, null=True)),
-                ('model_status', models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL')),
-                ('min_count', models.IntegerField(default=10)),
-                ('max_count', models.IntegerField(default=0)),
-                ('app_domain', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain')),
-                ('data_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to='epdb.package', verbose_name='Data Packages')),
-                ('eval_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to='epdb.package', verbose_name='Evaluation Packages')),
-                ('rule_packages', models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to='epdb.package', verbose_name='Rule Packages')),
-            ],
-            options={
-                'abstract': False,
-            },
-            bases=('epdb.epmodel',),
-        ),
-        migrations.DeleteModel(
-            name='RuleBaseRelativeReasoning',
-        ),
-    ]

epdb/migrations/0005_alter_group_group_member.py

@@ -1,18 +0,0 @@
-# Generated by Django 5.2.1 on 2025-09-11 06:21
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('epdb', '0004_alter_mlrelativereasoning_options_and_more'),
-    ]
-
-    operations = [
-        migrations.AlterField(
-            model_name='group',
-            name='group_member',
-            field=models.ManyToManyField(blank=True, related_name='groups_in_group', to='epdb.group', verbose_name='Group member'),
-        ),
-    ]

epdb/migrations/0006_mlrelativereasoning_multigen_eval_and_more.py

@@ -1,23 +0,0 @@
-# Generated by Django 5.2.1 on 2025-09-18 06:42
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('epdb', '0005_alter_group_group_member'),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name='mlrelativereasoning',
-            name='multigen_eval',
-            field=models.BooleanField(default=False),
-        ),
-        migrations.AddField(
-            model_name='rulebasedrelativereasoning',
-            name='multigen_eval',
-            field=models.BooleanField(default=False),
-        ),
-    ]

epdb/tasks.py

@@ -1,58 +1,194 @@
+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 epdb.logic import SPathway
+from celery.utils.functional import LRUCache
+from django.conf import settings as s
+from django.core.mail import EmailMultiAlternatives
+from django.utils import timezone
 
+from epdb.logic import SPathway
+from epdb.models import Edge, EPModel, JobLog, Node, Pathway, Rule, Setting, User
+from utilities.chem import FormatConverter
 
 logger = logging.getLogger(__name__)
+ML_CACHE = LRUCache(3)  # Cache the three most recent ML models to reduce load times.
+
+Package = s.GET_PACKAGE_MODEL()
 
 
-@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 log, 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 log
+    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
+    u = User.objects.get(id=user_pk)
+
+    tpl = """Welcome {username}!,
+
+Thank you for your interest in enviPath.
+
+The public system is intended for non-commercial use only.
+We will review your account details and usually activate your account within 24 hours.
+Once activated, you will be notified by email.
+
+If we have any questions, we will contact you at this email address.
+
+Best regards,
+
+enviPath team"""
+
+    msg = EmailMultiAlternatives(
+        "Your enviPath account",
+        tpl.format(username=u.username),
+        "admin@envipath.org",
+        [u.email],
+        bcc=["admin@envipath.org"],
+    )
+
+    msg.send(fail_silently=False)
 
 
-@shared_task(queue='model')
-def build_model(model_pk: int):
+@shared_task(bind=True, queue="model")
+def build_model(self, model_pk: int):
     mod = EPModel.objects.get(id=model_pk)
-    mod.build_dataset()
-    mod.build_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.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')
-def evaluate_model(model_pk: int):
+@shared_task(bind=True, queue="model")
+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')
-def predict(pw_pk: int, pred_setting_pk: int, limit: Optional[int] = None, node_pk: Optional[int] = None) -> Pathway:
+@shared_task(bind=True, queue="predict")
+def predict(
+    self,
+    pw_pk: int,
+    pred_setting_pk: int,
+    limit: Optional[int] = None,
+    node_pk: Optional[int] = None,
+    setting_overrides: Optional[dict] = None,
+) -> Pathway:
     pw = Pathway.objects.get(id=pw_pk)
     setting = Setting.objects.get(id=pred_setting_pk)
 
-    pw.kv.update(**{'status': 'running'})
+    if setting_overrides:
+        for k, v in setting_overrides.items():
+            setattr(setting, k, v)
+
+    # 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)
+
+    kv = {"status": "running"}
+
+    if setting_overrides:
+        kv["setting_overrides"] = setting_overrides
+
+    pw.kv.update(**kv)
     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:
@@ -72,14 +208,259 @@ def predict(pw_pk: int, pred_setting_pk: int, limit: Optional[int] = None, node_
             spw = SPathway.from_pathway(pw)
             spw.predict_step(from_node=n)
         else:
-            raise ValueError("Neither limit nor node_pk given!")
-
-
+            spw = SPathway(prediction_setting=setting, persist=pw)
+            spw.predict()
 
     except Exception as e:
-        pw.kv.update({'status': 'failed'})
+        pw.kv.update({"status": "failed"})
+        pw.kv.update(**{"error": str(e)})
         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.save()
+    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()
+
+
+@shared_task(bind=True, queue="background")
+def engineer_pathways(self, pw_pks: List[int], setting_pk: int, target_package_pk: int):
+    from utilities.misc import PathwayUtils
+
+    setting = Setting.objects.get(pk=setting_pk)
+    # Temporarily set model_threshold to 0.0 to keep all tps
+    setting.model_threshold = 0.0
+
+    target = Package.objects.get(pk=target_package_pk)
+
+    intermediate_pathways = []
+    predicted_pathways = []
+
+    for pw in Pathway.objects.filter(pk__in=pw_pks):
+        pu = PathwayUtils(pw)
+
+        eng_pw, node_to_snode_mapping, intermediates = pu.engineer(setting)
+
+        # If we've found intermediates, do the following
+        # - Get a copy of the original pathway and add intermediates
+        # - Store the predicted pathway for further investigation
+        if len(intermediates):
+            copy_mapping = {}
+            copied_pw = pw.copy(target, copy_mapping)
+            copied_pw.name = f"{copied_pw.name} (Engineered)"
+            copied_pw.description = f"The original Pathway can be found here: {pw.url}"
+            copied_pw.save()
+
+            for inter in intermediates:
+                start = copy_mapping[inter[0]]
+                end = copy_mapping[inter[1]]
+                start_snode = inter[2]
+                end_snode = inter[3]
+                for idx, intermediate_edge in enumerate(inter[4]):
+                    smiles_to_node = {}
+
+                    snodes_to_create = list(
+                        set(intermediate_edge.educts + intermediate_edge.products)
+                    )
+
+                    for snode in snodes_to_create:
+                        if snode == start_snode or snode == end_snode:
+                            smiles_to_node[snode.smiles] = start if snode == start_snode else end
+                            continue
+
+                        if snode.smiles not in smiles_to_node:
+                            n = Node.create(copied_pw, smiles=snode.smiles, depth=snode.depth)
+                            # Used in viz to highlight intermediates
+                            n.kv.update({"is_engineered_intermediate": True})
+                            n.save()
+                            smiles_to_node[snode.smiles] = n
+
+                    Edge.create(
+                        copied_pw,
+                        [smiles_to_node[educt.smiles] for educt in intermediate_edge.educts],
+                        [smiles_to_node[product.smiles] for product in intermediate_edge.products],
+                        rule=intermediate_edge.rule,
+                    )
+
+            # Persist the predicted pathway
+            pred_pw = pu.spathway_to_pathway(target, eng_pw, name=f"{pw.name} (Predicted)")
+
+            intermediate_pathways.append(copied_pw.url)
+            predicted_pathways.append(pred_pw.url)
+
+    return intermediate_pathways, predicted_pathways
+
+
+@shared_task(bind=True, queue="background")
+def batch_predict(
+    self,
+    substrates: List[str] | List[List[str]],
+    prediction_setting_pk: int,
+    target_package_pk: int,
+    num_tps: int = 50,
+):
+    target_package = Package.objects.get(pk=target_package_pk)
+    prediction_setting = Setting.objects.get(pk=prediction_setting_pk)
+
+    if len(substrates) == 0:
+        raise ValueError("No substrates given!")
+
+    is_pair = isinstance(substrates[0], list)
+
+    substrate_and_names = []
+    if not is_pair:
+        for sub in substrates:
+            substrate_and_names.append([sub, None])
+    else:
+        substrate_and_names = substrates
+
+    # Check prerequisite that we can standardize all substrates
+    standardized_substrates_and_smiles = []
+    for substrate in substrate_and_names:
+        try:
+            stand_smiles = FormatConverter.standardize(substrate[0])
+            standardized_substrates_and_smiles.append([stand_smiles, substrate[1]])
+        except ValueError:
+            raise ValueError(
+                f'Pathway prediction failed as standardization of SMILES "{substrate}" failed!'
+            )
+
+    pathways = []
+
+    for pair in standardized_substrates_and_smiles:
+        pw = Pathway.create(
+            target_package,
+            pair[0],
+            name=pair[1],
+            predicted=True,
+        )
+
+        # set mode and setting
+        pw.setting = prediction_setting
+        pw.kv.update({"mode": "predict"})
+        pw.save()
+
+        predict(
+            pw.pk,
+            prediction_setting.pk,
+            limit=None,
+            setting_overrides={
+                "max_nodes": num_tps,
+                "max_depth": num_tps,
+                "model_threshold": 0.001,
+            },
+        )
+
+        pathways.append(pw)
+
+    buffer = io.StringIO()
+
+    for idx, pw in enumerate(pathways):
+        # Carry out header only for the first pathway
+        buffer.write(pw.to_csv(include_header=idx == 0, include_pathway_url=True))
+
+    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__
+    return obj.__class__.__name__
+
+
+@register.filter
+def is_url(value):
+    try:
+        url_adapter.validate_python(value)
+        return True
+    except ValidationError:
+        return False

epdb/urls.py

@@ -1,99 +1,212 @@
-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'^logout', v.logout, name='logout'),
-    re_path(r'^register', v.register, name='register'),
-
-    # Built In views
-    path('password_reset/', auth_views.PasswordResetView.as_view(
-        template_name='static/password_reset_form.html'
-    ), name='password_reset'),
-
-    path('password_reset/done/', auth_views.PasswordResetDoneView.as_view(
-        template_name='static/password_reset_done.html'
-    ), name='password_reset_done'),
-
-    path('reset/<uidb64>/<token>/', auth_views.PasswordResetConfirmView.as_view(
-        template_name='static/password_reset_confirm.html'
-    ), name='password_reset_confirm'),
-
-    path('reset/done/', auth_views.PasswordResetCompleteView.as_view(
-        template_name='static/password_reset_complete.html'
-    ), name='password_reset_complete'),
-
-
+    re_path(r"^login", v.login, name="login"),
+    re_path(r"^logout", v.logout, name="logout"),
+    re_path(r"^register", v.register, name="register"),
+    # Built-In views
+    path(
+        "password_reset/",
+        auth_views.PasswordResetView.as_view(template_name="static/password_reset_form.html"),
+        name="password_reset",
+    ),
+    path(
+        "password_reset/done/",
+        auth_views.PasswordResetDoneView.as_view(template_name="static/password_reset_done.html"),
+        name="password_reset_done",
+    ),
+    path(
+        "reset/<uidb64>/<token>/",
+        auth_views.PasswordResetConfirmView.as_view(
+            template_name="static/password_reset_confirm.html"
+        ),
+        name="password_reset_confirm",
+    ),
+    path(
+        "reset/done/",
+        auth_views.PasswordResetCompleteView.as_view(
+            template_name="static/password_reset_complete.html"
+        ),
+        name="password_reset_complete",
+    ),
     # Top level urls
-    re_path(r'^package$', v.packages, name='packages'),
-    re_path(r'^compound$', v.compounds, name='compounds'),
-    re_path(r'^rule$', v.rules, name='rules'),
-    re_path(r'^reaction$', v.reactions, name='reactions'),
-    re_path(r'^pathway$', v.pathways, name='pathways'),
-    re_path(r'^scenario$', v.scenarios, name='scenarios'),
-    re_path(r'^model$', v.models, name='model'),
-    re_path(r'^user$', v.users, name='users'),
-    re_path(r'^group$', v.groups, name='groups'),
-    re_path(r'^search$', v.search, name='search'),
-
-
+    re_path(r"^package$", v.packages, name="packages"),
+    re_path(r"^compound$", v.compounds, name="compounds"),
+    re_path(r"^rule$", v.rules, name="rules"),
+    re_path(r"^reaction$", v.reactions, name="reactions"),
+    re_path(r"^pathway$", v.pathways, name="pathways"),
+    re_path(r"^scenario$", v.scenarios, name="scenarios"),
+    re_path(r"^model$", v.models, name="model"),
+    re_path(r"^user$", v.users, name="users"),
+    re_path(r"^group$", v.groups, name="groups"),
+    re_path(r"^search$", v.search, name="search"),
+    re_path(r"^predict$", v.predict_pathway, name="predict_pathway"),
+    re_path(r"^batch-predict$", v.batch_predict_pathway, name="batch_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$', v.package_compounds, name='package compound list'),
-    re_path(rf'^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})$', v.package_compound, name='package compound detail'),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/compound$",
+        v.package_compounds,
+        name="package compound list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})$",
+        v.package_compound,
+        name="package compound detail",
+    ),
     # Compound Structure
-    re_path(rf'^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})/structure$', v.package_compound_structures, name='package compound structure list'),
-    re_path(rf'^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})/structure/(?P<structure_uuid>{UUID})$', v.package_compound_structure, name='package compound structure detail'),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})/structure$",
+        v.package_compound_structures,
+        name="package compound structure list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})/structure/(?P<structure_uuid>{UUID})$",
+        v.package_compound_structure,
+        name="package compound structure detail",
+    ),
     # Rule
-    re_path(rf'^package/(?P<package_uuid>{UUID})/rule$', v.package_rules, name='package rule list'),
-    re_path(rf'^package/(?P<package_uuid>{UUID})/rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
-    re_path(rf'^package/(?P<package_uuid>{UUID})/simple-ambit-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
-    re_path(rf'^package/(?P<package_uuid>{UUID})/simple-rdkit-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
-    re_path(rf'^package/(?P<package_uuid>{UUID})/parallel-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
-    re_path(rf'^package/(?P<package_uuid>{UUID})/sequential-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
+    re_path(rf"^package/(?P<package_uuid>{UUID})/rule$", v.package_rules, name="package rule list"),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/rule/(?P<rule_uuid>{UUID})$",
+        v.package_rule,
+        name="package rule detail",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/simple-ambit-rule/(?P<rule_uuid>{UUID})$",
+        v.package_rule,
+        name="package rule detail",
+    ),
+    # re_path(
+    #     rf"^package/(?P<package_uuid>{UUID})/simple-rdkit-rule/(?P<rule_uuid>{UUID})$",
+    #     v.package_rule,
+    #     name="package rule detail",
+    # ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/parallel-rule/(?P<rule_uuid>{UUID})$",
+        v.package_rule,
+        name="package rule detail",
+    ),
+    # re_path(
+    #     rf"^package/(?P<package_uuid>{UUID})/sequential-rule/(?P<rule_uuid>{UUID})$",
+    #     v.package_rule,
+    #     name="package rule detail",
+    # ),
+    # EnzymeLinks
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/rule/(?P<rule_uuid>{UUID})/enzymelink/(?P<enzymelink_uuid>{UUID})$",
+        v.package_rule_enzymelink,
+        name="package rule enzymelink detail",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/simple-ambit-rule/(?P<rule_uuid>{UUID})/enzymelink/(?P<enzymelink_uuid>{UUID})$",
+        v.package_rule_enzymelink,
+        name="package rule enzymelink detail",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/parallel-rule/(?P<rule_uuid>{UUID})/enzymelink/(?P<enzymelink_uuid>{UUID})$",
+        v.package_rule_enzymelink,
+        name="package rule enzymelink detail",
+    ),
     # Reaction
-    re_path(rf'^package/(?P<package_uuid>{UUID})/reaction$', v.package_reactions, name='package reaction list'),
-    re_path(rf'^package/(?P<package_uuid>{UUID})/reaction/(?P<reaction_uuid>{UUID})$', v.package_reaction, name='package reaction detail'),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/reaction$",
+        v.package_reactions,
+        name="package reaction list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/reaction/(?P<reaction_uuid>{UUID})$",
+        v.package_reaction,
+        name="package reaction detail",
+    ),
     # # Pathway
-    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway$', v.package_pathways, name='package pathway list'),
-    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})$', v.package_pathway, name='package pathway detail'),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/pathway$",
+        v.package_pathways,
+        name="package pathway list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})$",
+        v.package_pathway,
+        name="package pathway detail",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/predict$",
+        v.package_predict_pathway,
+        name="package predict pathway",
+    ),
     # Pathway Nodes
-    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node$', v.package_pathway_nodes, name='package pathway node list'),
-    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node/(?P<node_uuid>{UUID})$', v.package_pathway_node, name='package pathway node detail'),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node$",
+        v.package_pathway_nodes,
+        name="package pathway node list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node/(?P<node_uuid>{UUID})$",
+        v.package_pathway_node,
+        name="package pathway node detail",
+    ),
     # Pathway Edges
-    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge$', v.package_pathway_edges, name='package pathway edge list'),
-    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge/(?P<edge_uuid>{UUID})$', v.package_pathway_edge, name='package pathway edge detail'),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge$",
+        v.package_pathway_edges,
+        name="package pathway edge list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge/(?P<edge_uuid>{UUID})$",
+        v.package_pathway_edge,
+        name="package pathway edge detail",
+    ),
     # Scenario
-    re_path(rf'^package/(?P<package_uuid>{UUID})/scenario$', v.package_scenarios, name='package scenario list'),
-    re_path(rf'^package/(?P<package_uuid>{UUID})/scenario/(?P<scenario_uuid>{UUID})$', v.package_scenario, name='package scenario detail'),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/scenario$",
+        v.package_scenarios,
+        name="package scenario list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/scenario/(?P<scenario_uuid>{UUID})$",
+        v.package_scenario,
+        name="package scenario detail",
+    ),
     # Model
-    re_path(rf'^package/(?P<package_uuid>{UUID})/model$', v.package_models, name='package model list'),
-    re_path(rf'^package/(?P<package_uuid>{UUID})/model/(?P<model_uuid>{UUID})$', v.package_model,name='package model detail'),
-
-    re_path(r'^setting$', v.settings, name='settings'),
-    re_path(rf'^setting/(?P<setting_uuid>{UUID})', v.setting, name='setting'),
-
-    re_path(r'^indigo/info$', v.indigo, name='indigo_info'),
-    re_path(r'^indigo/aromatize$', v.aromatize, name='indigo_aromatize'),
-    re_path(r'^indigo/dearomatize$', v.dearomatize, name='indigo_dearomatize'),
-    re_path(r'^indigo/layout$', v.layout, name='indigo_layout'),
-
-    re_path(r'^depict$', v.depict, name='depict'),
-
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/model$", v.package_models, name="package model list"
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/model/(?P<model_uuid>{UUID})$",
+        v.package_model,
+        name="package model detail",
+    ),
+    re_path(r"^setting$", v.settings, name="settings"),
+    re_path(rf"^setting/(?P<setting_uuid>{UUID})", v.setting, name="setting"),
+    re_path(r"^indigo/info$", v.indigo, name="indigo_info"),
+    re_path(r"^indigo/aromatize$", v.aromatize, name="indigo_aromatize"),
+    re_path(r"^indigo/dearomatize$", v.dearomatize, name="indigo_dearomatize"),
+    re_path(r"^indigo/layout$", v.layout, name="indigo_layout"),
+    re_path(r"^depict$", v.depict, name="depict"),
+    path("jobs", v.jobs, name="jobs"),
+    path("jobs/<uuid:job_uuid>", v.job, name="job detail"),
     # 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"),
 ]