[Feature] Prediction settings list on User page (#276)

I have added a list of other prediction settings to the User page and a way to change a setting to the default.
<img width="500" alt="{4EFA1273-E53A-4333-948B-8AE3597821A8}.png" src="attachments/048fdc83-1c3e-41d2-a59b-44b0337a05bf">

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#276
Reviewed-by: jebus <lorsbach@envipath.com>
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 +1,72 @@
+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
+        cat << 'EOF' > pnpm-workspace.yaml
+        onlyBuiltDependencies:
+          - '@parcel/watcher'
+          - '@tailwindcss/oxide'
+        EOF
+        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/
+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 +1,103 @@
 # enviPy
 
+## Local Development Setup
+
+These instructions will guide you through setting up the project for local development.
+
+### Prerequisites
+
+- Python 3.11 or later
+- [uv](https://github.com/astral-sh/uv) - Python package manager
+- **Docker and Docker Compose** - Required for running PostgreSQL database
+- Git
+- Make
+
+> **Note:** This application requires PostgreSQL (uses `ArrayField`). Docker is the easiest way to run PostgreSQL locally.
+
+
+### 1. Install Dependencies
+
+This project uses `uv` to manage dependencies and `poe-the-poet` for task running. First, [install `uv` if you don't have it yet](https://docs.astral.sh/uv/guides/install-python/).
+
+Then, sync the project dependencies. This will create a virtual environment in `.venv` and install all necessary packages, including `poe-the-poet`.
+
+```bash
+uv sync --dev
+```
+
+Note on RDkit installation: if you have rdkit installed on your system globally with a different version of python, the installation will try to link against that and subsequent calls fail. Only option remove global rdkit and rerun sync.
+
+---
+
+The frontend requires `pnpm` to correctly display in development.
+[Install it here](https://pnpm.io/installation).
+
+### 2. Set Up Environment File
+
+Copy the example environment file for local setup:
+
+```bash
+cp .env.local.example .env
+```
+
+This file contains the necessary environment variables for local development.
+
+### 3. Quick Setup with Poe
+
+The easiest way to set up the development environment is by using the `poe` task runner, which is executed via `uv run`.
+
+```bash
+uv run poe setup
+```
+
+This single command will:
+
+1. Start the PostgreSQL database using Docker Compose.
+2. Run database migrations.
+3. Bootstrap initial data (anonymous user, default packages, models).
+
+After setup, start the development server:
+
+```bash
+uv run poe dev
+```
+
+This will start the css-watcher as well as the django-development server,
+The application will be available at `http://localhost:8000`.
+
+**Note:** The development server automatically starts a CSS watcher (`pnpm run dev`) alongside the Django server to rebuild CSS files when changes are detected. This ensures your styles are always up-to-date during development.
+
+#### Other useful Poe commands
+
+You can list all available commands by running `uv run poe --help`.
+
+```bash
+uv run poe db-up         # Start PostgreSQL only
+uv run poe db-down       # Stop PostgreSQL
+uv run poe migrate       # Run migrations only
+uv run poe bootstrap     # Bootstrap data only
+uv run poe shell         # Open the Django shell
+uv run poe build         # Build frontend assets and collect static files
+uv run poe clean         # Remove database volumes (WARNING: destroys all data)
+```
+
+### Troubleshooting
+
+*   **Docker Connection Error:** If you see an error like `open //./pipe/dockerDesktopLinuxEngine: The system cannot find the file specified` (on Windows), it likely means your Docker Desktop application is not running. Please start Docker Desktop and try the command again.
+
+*   **SSH Keys for Git Dependencies:** Some dependencies are installed from private git repositories and require SSH authentication. Ensure your SSH keys are configured correctly for Git.
+    *   For a general guide, see [GitHub's official documentation](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent).
+    *   **Windows Users:** If `uv sync` hangs while fetching git dependencies, you may need to explicitly configure Git to use the Windows OpenSSH client and use the `ssh-agent` to manage your key's passphrase.
+
+        1.  **Point Git to the correct SSH executable:**
+            ```powershell
+            git config --global core.sshCommand "C:/Windows/System32/OpenSSH/ssh.exe"
+            ```
+        2.  **Enable and use the SSH agent:**
+            ```powershell
+            # Run these commands in an administrator PowerShell
+            Get-Service ssh-agent | Set-Service -StartupType Automatic -PassThru | Start-Service
+
+            # Add your key to the agent. It will prompt for the passphrase once.
+            ssh-add
+            ```

docker-compose.dev.yml

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

envipath/__init__.py

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

envipath/api.py

@@ -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 +21,96 @@ from sklearn.tree import DecisionTreeClassifier
 # Build paths inside the project like this: BASE_DIR / 'subdir'.
 BASE_DIR = Path(__file__).resolve().parent.parent
 
-load_dotenv(BASE_DIR / '.env', override=False)
+load_dotenv(BASE_DIR / ".env", override=False)
 
 # Quick-start development settings - unsuitable for production
 # See https://docs.djangoproject.com/en/4.2/howto/deployment/checklist/
 
 # SECURITY WARNING: keep the secret key used in production secret!
-SECRET_KEY = '7!VTW`aZqg/UBLsM.P=m)2]lWqg>{+:xUgG1"WO@bCyaHR2Up8XW&g<*3.F4l2gi9c.E3}dHyA0D`&z?u#U%^7HYbj],eP"g_MS|3BNMD[mI>s#<i/%2ngZ~Oy+/w&@]'
+SECRET_KEY = os.environ.get("SECRET_KEY", "secret-key")
 
 # SECURITY WARNING: don't run with debug turned on in production!
-DEBUG = os.environ.get('DEBUG', 'False') == 'True'
+DEBUG = os.environ.get("DEBUG", "False") == "True"
-ALLOWED_HOSTS = os.environ['ALLOWED_HOSTS'].split(',')
+
+ALLOWED_HOSTS = os.environ["ALLOWED_HOSTS"].split(",")
+
 
 # Application definition
 
 INSTALLED_APPS = [
-    'django.contrib.admin',
+    "django.contrib.admin",
-    'django.contrib.auth',
+    "django.contrib.auth",
-    'django.contrib.contenttypes',
+    "django.contrib.contenttypes",
-    'django.contrib.sessions',
+    "django.contrib.sessions",
-    'django.contrib.messages',
+    "django.contrib.messages",
-    'django.contrib.staticfiles',
+    "django.contrib.staticfiles",
     # 3rd party
-    'django_extensions',
+    "django_extensions",
-    'oauth2_provider',
+    "oauth2_provider",
     # Custom
-    'epdb',
+    "epapi",  # API endpoints (v1, etc.)
-    'migration',
+    "epdb",
-    'epauth',
+    # "migration",
 ]
 
+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.middleware.security.SecurityMiddleware",
-    'django.contrib.sessions.middleware.SessionMiddleware',
+    "django.contrib.sessions.middleware.SessionMiddleware",
-    'django.middleware.common.CommonMiddleware',
+    "django.middleware.common.CommonMiddleware",
-    'django.middleware.csrf.CsrfViewMiddleware',
+    "django.middleware.csrf.CsrfViewMiddleware",
-    'django.contrib.auth.middleware.AuthenticationMiddleware',
+    "django.contrib.auth.middleware.AuthenticationMiddleware",
-    'django.contrib.messages.middleware.MessageMiddleware',
+    "django.contrib.messages.middleware.MessageMiddleware",
-    'django.middleware.clickjacking.XFrameOptionsMiddleware',
+    "django.middleware.clickjacking.XFrameOptionsMiddleware",
-    'oauth2_provider.middleware.OAuth2TokenMiddleware',
+    "oauth2_provider.middleware.OAuth2TokenMiddleware",
 ]
 
 OAUTH2_PROVIDER = {
     "PKCE_REQUIRED": False,  # Accept PKCE requests but dont require them
 }
 
-if os.environ.get('REGISTRATION_MANDATORY', False) == 'True':
+if os.environ.get("REGISTRATION_MANDATORY", False) == "True":
-    MIDDLEWARE.append('epdb.middleware.login_required_middleware.LoginRequiredMiddleware')
+    MIDDLEWARE.append("epdb.middleware.login_required_middleware.LoginRequiredMiddleware")
 
-ROOT_URLCONF = 'envipath.urls'
+ROOT_URLCONF = "envipath.urls"
 
 TEMPLATES = [
     {
-        'BACKEND': 'django.template.backends.django.DjangoTemplates',
+        "BACKEND": "django.template.backends.django.DjangoTemplates",
-        'DIRS': (os.path.join(BASE_DIR, 'templates'),),
+        "DIRS": (os.path.join(BASE_DIR, "templates"),),
-        'APP_DIRS': True,
+        "APP_DIRS": True,
-        'OPTIONS': {
+        "OPTIONS": {
-            'context_processors': [
+            "context_processors": [
-                'django.template.context_processors.debug',
+                "django.template.context_processors.debug",
-                'django.template.context_processors.request',
+                "django.template.context_processors.request",
-                'django.contrib.auth.context_processors.auth',
+                "django.contrib.auth.context_processors.auth",
-                'django.contrib.messages.context_processors.messages',
+                "django.contrib.messages.context_processors.messages",
+                "epdb.context_processors.package_context",
             ],
         },
     },
 ]
 
-WSGI_APPLICATION = 'envipath.wsgi.application'
+ALLOWED_HTML_TAGS = {"b", "i", "u", "br", "em", "mark", "p", "s", "strong"}
+
+WSGI_APPLICATION = "envipath.wsgi.application"
 
 # Database
 # https://docs.djangoproject.com/en/4.2/ref/settings/#databases
@@ -98,11 +118,11 @@ WSGI_APPLICATION = 'envipath.wsgi.application'
 DATABASES = {
     "default": {
         "ENGINE": "django.db.backends.postgresql",
-        "USER": os.environ['POSTGRES_USER'],
+        "USER": os.environ["POSTGRES_USER"],
-        "NAME": os.environ['POSTGRES_DB'],
+        "NAME": os.environ["POSTGRES_DB"],
-        "PASSWORD": os.environ['POSTGRES_PASSWORD'],
+        "PASSWORD": os.environ["POSTGRES_PASSWORD"],
-        "HOST": os.environ['POSTGRES_SERVICE_NAME'],
+        "HOST": os.environ["POSTGRES_SERVICE_NAME"],
-        "PORT": os.environ['POSTGRES_PORT']
+        "PORT": os.environ["POSTGRES_PORT"],
     }
 }
 
@@ -110,96 +130,93 @@ 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.UserAttributeSimilarityValidator',
+    {"NAME": "django.contrib.auth.password_validation.MinimumLengthValidator"},
-    },
+    {"NAME": "django.contrib.auth.password_validation.CommonPasswordValidator"},
-    {
+    {"NAME": "django.contrib.auth.password_validation.NumericPasswordValidator"},
-        'NAME': 'django.contrib.auth.password_validation.MinimumLengthValidator',
-    },
-    {
-        'NAME': 'django.contrib.auth.password_validation.CommonPasswordValidator',
-    },
-    {
-        'NAME': 'django.contrib.auth.password_validation.NumericPasswordValidator',
-    },
 ]
 
 # Internationalization
 # https://docs.djangoproject.com/en/4.2/topics/i18n/
 
-LANGUAGE_CODE = 'en-us'
+LANGUAGE_CODE = "en-us"
 
-TIME_ZONE = 'UTC'
+TIME_ZONE = "UTC"
 
 USE_I18N = True
 
 USE_TZ = True
 
 
-
 # Default primary key field type
 # https://docs.djangoproject.com/en/4.2/ref/settings/#default-auto-field
 
-DEFAULT_AUTO_FIELD = 'django.db.models.BigAutoField'
+DEFAULT_AUTO_FIELD = "django.db.models.BigAutoField"
 
+EMAIL_SUBJECT_PREFIX = "[enviPath] "
 if DEBUG:
-    EMAIL_BACKEND = 'django.core.mail.backends.console.EmailBackend'
+    EMAIL_BACKEND = "django.core.mail.backends.console.EmailBackend"
 else:
-    EMAIL_BACKEND = 'django.core.mail.backends.smtp.EmailBackend'
+    EMAIL_BACKEND = "django.core.mail.backends.smtp.EmailBackend"
     EMAIL_USE_TLS = True
-    EMAIL_HOST = 'mail.gandi.net'
+    EMAIL_HOST = "mail.gandi.net"
-    EMAIL_HOST_USER = os.environ['EMAIL_HOST_USER']
+    EMAIL_HOST_USER = os.environ["EMAIL_HOST_USER"]
-    EMAIL_HOST_PASSWORD = os.environ['EMAIL_HOST_PASSWORD']
+    EMAIL_HOST_PASSWORD = os.environ["EMAIL_HOST_PASSWORD"]
     EMAIL_PORT = 587
+    DEFAULT_FROM_EMAIL = os.environ["DEFAULT_FROM_EMAIL"]
+    SERVER_EMAIL = os.environ["SERVER_EMAIL"]
 
 AUTH_USER_MODEL = "epdb.User"
-ADMIN_APPROVAL_REQUIRED = os.environ.get('ADMIN_APPROVAL_REQUIRED', 'False') == 'True'
+ADMIN_APPROVAL_REQUIRED = os.environ.get("ADMIN_APPROVAL_REQUIRED", "False") == "True"
 
 # # SESAME
 # SESAME_MAX_AGE = 300
 # # TODO set to "home"
 # LOGIN_REDIRECT_URL = "/"
-LOGIN_URL = '/login/'
+LOGIN_URL = "/login/"
 
-SERVER_URL = os.environ.get('SERVER_URL', 'http://localhost:8000')
+SERVER_URL = os.environ.get("SERVER_URL", "http://localhost:8000")
 
 CSRF_TRUSTED_ORIGINS = [SERVER_URL]
 
-AMBIT_URL = 'http://localhost:9001'
+AMBIT_URL = "http://localhost:9001"
-DEFAULT_VALUES = {
+DEFAULT_VALUES = {"description": "no description"}
-    'description': 'no description'
-}
 
-EP_DATA_DIR = os.environ['EP_DATA_DIR']
+EP_DATA_DIR = os.environ["EP_DATA_DIR"]
-MODEL_DIR = os.path.join(EP_DATA_DIR, 'models')
+if not os.path.exists(EP_DATA_DIR):
+    os.mkdir(EP_DATA_DIR)
+
+MODEL_DIR = os.path.join(EP_DATA_DIR, "models")
 if not os.path.exists(MODEL_DIR):
     os.mkdir(MODEL_DIR)
 
-STATIC_DIR = os.path.join(EP_DATA_DIR, 'static')
+STATIC_DIR = os.path.join(EP_DATA_DIR, "static")
 if not os.path.exists(STATIC_DIR):
     os.mkdir(STATIC_DIR)
 
-LOG_DIR = os.path.join(EP_DATA_DIR, 'log')
+LOG_DIR = os.path.join(EP_DATA_DIR, "log")
 if not os.path.exists(LOG_DIR):
     os.mkdir(LOG_DIR)
 
-PLUGIN_DIR = os.path.join(EP_DATA_DIR, 'plugins')
+PLUGIN_DIR = os.path.join(EP_DATA_DIR, "plugins")
+
+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 = (
+STATICFILES_DIRS = (BASE_DIR / "static",)
-    BASE_DIR / 'static',
-)
 
-FIXTURE_DIRS = (
+FIXTURE_DIRS = (BASE_DIR / "fixtures",)
-        BASE_DIR / 'fixtures',
-)
 
 # Logging
 LOGGING = {
@@ -207,8 +224,8 @@ LOGGING = {
     "disable_existing_loggers": True,
     "formatters": {
         "simple": {
-            'format': '[%(asctime)s] %(levelname)s %(module)s - %(message)s',
+            "format": "[%(asctime)s] %(levelname)s %(module)s - %(message)s",
-            'datefmt': '%Y-%m-%d %H:%M:%S',
+            "datefmt": "%Y-%m-%d %H:%M:%S",
         },
     },
     "handlers": {
@@ -221,7 +238,7 @@ LOGGING = {
             "level": "DEBUG",  # Or higher
             "class": "logging.FileHandler",
             "filename": os.path.join(LOG_DIR, "debug.log"),
-            "formatter": "simple"
+            "formatter": "simple",
         },
     },
     "loggers": {
@@ -229,72 +246,67 @@ LOGGING = {
         "epdb": {
             "handlers": ["file"],  # "console",
             "propagate": True,
-            "level": os.environ.get('LOG_LEVEL', 'INFO')
+            "level": os.environ.get("LOG_LEVEL", "INFO"),
         },
         # For everything under envipath/ loaded via getlogger(__name__)
-        'envipath': {
+        "envipath": {
-            'handlers': ['file', 'console'],
+            "handlers": ["file", "console"],
-            'propagate': True,
+            "propagate": True,
-            'level': os.environ.get('LOG_LEVEL', 'INFO')
+            "level": os.environ.get("LOG_LEVEL", "INFO"),
         },
         # For everything under utilities/ loaded via getlogger(__name__)
-        'utilities': {
+        "utilities": {
-            'handlers': ['file', 'console'],
+            "handlers": ["file", "console"],
-            'propagate': True,
+            "propagate": True,
-            'level': os.environ.get('LOG_LEVEL', 'INFO')
+            "level": os.environ.get("LOG_LEVEL", "INFO"),
         },
     },
 }
 
 # Flags
-ENVIFORMER_PRESENT = os.environ.get('ENVIFORMER_PRESENT', 'False') == 'True'
+ENVIFORMER_PRESENT = os.environ.get("ENVIFORMER_PRESENT", "False") == "True"
-if ENVIFORMER_PRESENT:
+ENVIFORMER_DEVICE = os.environ.get("ENVIFORMER_DEVICE", "cpu")
-    print("Loading enviFormer")
-    device = os.environ.get('ENVIFORMER_DEVICE', 'cpu')
-    from enviformer import load
-    ENVIFORMER_INSTANCE = load(device=device)
-    print("loaded")
 
 
 # If celery is not present set always eager to true which will cause delayed tasks to block until finished
-FLAG_CELERY_PRESENT = os.environ.get('FLAG_CELERY_PRESENT', 'False') == 'True'
+FLAG_CELERY_PRESENT = os.environ.get("FLAG_CELERY_PRESENT", "False") == "True"
 if not FLAG_CELERY_PRESENT:
     CELERY_TASK_ALWAYS_EAGER = True
 
 # Celery Configuration Options
 CELERY_TIMEZONE = "Europe/Berlin"
 # Celery Configuration
-CELERY_BROKER_URL = 'redis://localhost:6379/0'  # Use Redis as message broker
+CELERY_BROKER_URL = "redis://localhost:6379/0"  # Use Redis as message broker
-CELERY_RESULT_BACKEND = 'redis://localhost:6379/1'
+CELERY_RESULT_BACKEND = "redis://localhost:6379/1"
-CELERY_ACCEPT_CONTENT = ['json']
+CELERY_ACCEPT_CONTENT = ["json"]
-CELERY_TASK_SERIALIZER = 'json'
+CELERY_TASK_SERIALIZER = "json"
 
-MODEL_BUILDING_ENABLED = os.environ.get('MODEL_BUILDING_ENABLED', 'False') == 'True'
+MODEL_BUILDING_ENABLED = os.environ.get("MODEL_BUILDING_ENABLED", "False") == "True"
-APPLICABILITY_DOMAIN_ENABLED = os.environ.get('APPLICABILITY_DOMAIN_ENABLED', 'False') == 'True'
+APPLICABILITY_DOMAIN_ENABLED = os.environ.get("APPLICABILITY_DOMAIN_ENABLED", "False") == "True"
 DEFAULT_RF_MODEL_PARAMS = {
-    'base_clf': RandomForestClassifier(
+    "base_clf": RandomForestClassifier(
         n_estimators=100,
-        max_features='log2',
+        max_features="log2",
         random_state=42,
-        criterion='entropy',
+        criterion="entropy",
         ccp_alpha=0.0,
         max_depth=3,
-        min_samples_leaf=1
+        min_samples_leaf=1,
     ),
-    'num_chains': 10,
+    "num_chains": 10,
 }
 
 DEFAULT_MODEL_PARAMS = {
-    'base_clf': DecisionTreeClassifier(
+    "base_clf": DecisionTreeClassifier(
-        criterion='entropy',
+        criterion="entropy",
         max_depth=3,
         min_samples_split=5,
         # min_samples_leaf=5,
-        max_features='sqrt',
+        max_features="sqrt",
         # class_weight='balanced',
-        random_state=42
+        random_state=42,
     ),
-    'num_chains': 10,
+    "num_chains": 10,
 }
 
 DEFAULT_MAX_NUMBER_OF_NODES = 30
@@ -302,9 +314,10 @@ 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 +326,71 @@ 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'):
+        if event.get("logger"):
-            for log_path in LOGGING.get('loggers').keys():
+            for log_path in LOGGING.get("loggers").keys():
-                if event['logger'].startswith(log_path):
+                if event["logger"].startswith(log_path):
                     return None
 
         return event
 
     sentry_sdk.init(
-        dsn=os.environ.get('SENTRY_DSN'),
+        dsn=os.environ.get("SENTRY_DSN"),
         # Add data like request headers and IP for users,
         # see https://docs.sentry.io/platforms/python/data-management/data-collected/ for more info
         send_default_pii=True,
-        environment=os.environ.get('SENTRY_ENVIRONMENT', 'development'),
+        environment=os.environ.get("SENTRY_ENVIRONMENT", "development"),
         before_send=before_send,
     )
 
 # compile into digestible flags
 FLAGS = {
-    'MODEL_BUILDING': MODEL_BUILDING_ENABLED,
+    "MODEL_BUILDING": MODEL_BUILDING_ENABLED,
-    'CELERY': FLAG_CELERY_PRESENT,
+    "CELERY": FLAG_CELERY_PRESENT,
-    'PLUGINS': PLUGINS_ENABLED,
+    "PLUGINS": PLUGINS_ENABLED,
-    'SENTRY': SENTRY_ENABLED,
+    "SENTRY": SENTRY_ENABLED,
-    'ENVIFORMER': ENVIFORMER_PRESENT,
+    "ENVIFORMER": ENVIFORMER_PRESENT,
-    'APPLICABILITY_DOMAIN': APPLICABILITY_DOMAIN_ENABLED,
+    "APPLICABILITY_DOMAIN": APPLICABILITY_DOMAIN_ENABLED,
 }
 
 # path of the URL are checked via "startswith"
 # -> /password_reset/done is covered as well
 LOGIN_EXEMPT_URLS = [
-    '/register',
+    "/register",
-    '/api/legacy/',
+    "/api/v1/",  # Let API handle its own authentication
-    '/o/token/',
+    "/api/legacy/",
-    '/o/userinfo/',
+    "/o/token/",
-    '/password_reset/',
+    "/o/userinfo/",
-    '/reset/',
+    "/password_reset/",
-    '/microsoft/',
+    "/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']
+    # Add app to installed apps
-    MS_ENTRA_CLIENT_SECRET = os.environ['MS_CLIENT_SECRET']
+    INSTALLED_APPS.append("epauth")
-    MS_ENTRA_TENANT_ID = os.environ['MS_TENANT_ID']
+    # Set vars required by app
+    MS_ENTRA_CLIENT_ID = os.environ["MS_CLIENT_ID"]
+    MS_ENTRA_CLIENT_SECRET = os.environ["MS_CLIENT_SECRET"]
+    MS_ENTRA_TENANT_ID = os.environ["MS_TENANT_ID"]
     MS_ENTRA_AUTHORITY = f"https://login.microsoftonline.com/{MS_ENTRA_TENANT_ID}"
-    MS_ENTRA_REDIRECT_URI = os.environ['MS_REDIRECT_URI']
+    MS_ENTRA_REDIRECT_URI = os.environ["MS_REDIRECT_URI"]
-    MS_ENTRA_SCOPES = os.environ.get('MS_SCOPES', '').split(',')
+    MS_ENTRA_SCOPES = os.environ.get("MS_SCOPES", "").split(",")
+
+# Site ID 10 -> beta.envipath.org
+MATOMO_SITE_ID = os.environ.get("MATOMO_SITE_ID", "10")

envipath/urls.py

@@ -14,17 +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/v1/__init__.py

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

epapi/tests/v1/test_api_permissions.py

@@ -0,0 +1,532 @@
+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()
+
+        # user2 should see compounds from:
+        # - 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 compounds
+        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)
+
+    def test_read_permission_allows_viewing(self):
+        """READ permission allows viewing compounds."""
+        self.client.force_login(self.user2)
+        response = self.client.get(self.ENDPOINT)
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        # Check that read_compound is included
+        uuids = [item["uuid"] for item in payload["items"]]
+        self.assertIn(str(self.read_compound.uuid), uuids)
+
+    def test_write_permission_allows_viewing(self):
+        """WRITE permission also allows viewing compounds."""
+        self.client.force_login(self.user2)
+        response = self.client.get(self.ENDPOINT)
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        # Check that write_compound is included
+        uuids = [item["uuid"] for item in payload["items"]]
+        self.assertIn(str(self.write_compound.uuid), uuids)
+
+    def test_all_permission_allows_viewing(self):
+        """ALL permission allows viewing compounds."""
+        self.client.force_login(self.user2)
+        response = self.client.get(self.ENDPOINT)
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        # Check that all_compound is included
+        uuids = [item["uuid"] for item in payload["items"]]
+        self.assertIn(str(self.all_compound.uuid), uuids)
+
+    def test_group_permission_allows_viewing(self):
+        """Group membership grants access to group-permitted packages."""
+        self.client.force_login(self.user2)
+        response = self.client.get(self.ENDPOINT)
+
+        self.assertEqual(response.status_code, 200)
+        payload = response.json()
+
+        # Check that group_compound is included
+        uuids = [item["uuid"] for item in payload["items"]]
+        self.assertIn(str(self.group_compound.uuid), uuids)
+
+
+@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})
+        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/v1/auth.py

@@ -0,0 +1,8 @@
+from ninja.security import HttpBearer
+from ninja.errors import HttpError
+
+
+class BearerTokenAuth(HttpBearer):
+    def authenticate(self, request, token):
+        # FIXME: placeholder; implement it in O(1) time
+        raise HttpError(401, "Invalid or expired token")

epapi/v1/dal.py

@@ -0,0 +1,95 @@
+from django.db.models import Model
+from epdb.logic import PackageManager
+from epdb.models import CompoundStructure, User, Package, Compound
+from uuid import UUID
+
+from .errors import EPAPINotFoundError, EPAPIPermissionDeniedError
+
+
+def get_compound_or_error(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_or_error(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_user_packages_qs(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_qs(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_scoped_entities_qs(
+    model_class: Model, package_uuid: UUID, user: User | None = None
+):
+    """Build queryset for specific package entities."""
+    package = get_package_or_error(user, package_uuid)
+    qs = model_class.objects.filter(package=package).select_related("package")
+    return qs
+
+
+def get_user_structures_qs(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_scoped_structure_qs(
+    package_uuid: UUID, compound_uuid: UUID, user: User | None = None
+):
+    """Build queryset for specific package compound structures."""
+
+    get_package_or_error(user, package_uuid)
+    compound = get_compound_or_error(user, compound_uuid)
+
+    qs = CompoundStructure.objects.filter(compound=compound).select_related("compound__package")
+    return qs

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_qs, get_package_scoped_entities_qs
+
+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_qs(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_scoped_entities_qs(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_qs, get_package_scoped_entities_qs
+
+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_qs(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_scoped_entities_qs(EPModel, package_uuid, user).order_by("name").all()

epapi/v1/endpoints/packages.py

@@ -0,0 +1,27 @@
+from django.conf import settings as s
+from ninja import Router
+from ninja_extra.pagination import paginate
+import logging
+
+from ..dal import get_user_packages_qs
+from ..pagination import EnhancedPageNumberPagination
+from ..schemas import PackageOutSchema, SelfReviewStatusFilter
+
+router = Router()
+logger = logging.getLogger(__name__)
+
+
+@router.get("/packages/", response=EnhancedPageNumberPagination.Output[PackageOutSchema], auth=None)
+@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_qs(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_qs, get_package_scoped_entities_qs
+
+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_qs(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_scoped_entities_qs(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_qs, get_package_scoped_entities_qs
+
+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_qs(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_scoped_entities_qs(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_qs, get_package_scoped_entities_qs
+
+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_qs(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_scoped_entities_qs(Rule, package_uuid, user).order_by("name").all()

epapi/v1/endpoints/scenarios.py

@@ -0,0 +1,36 @@
+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 Scenario
+from ..pagination import EnhancedPageNumberPagination
+from ..schemas import ReviewStatusFilter, ScenarioOutSchema
+from ..dal import get_user_entities_qs, get_package_scoped_entities_qs
+
+router = Router()
+
+
+@router.get("/scenarios/", response=EnhancedPageNumberPagination.Output[ScenarioOutSchema])
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+    filter_schema=ReviewStatusFilter,
+)
+def list_all_scenarios(request):
+    user = request.user
+    return get_user_entities_qs(Scenario, user).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=ReviewStatusFilter,
+)
+def list_package_scenarios(request, package_uuid: UUID):
+    user = request.user
+    return get_package_scoped_entities_qs(Scenario, package_uuid, user).order_by("name").all()

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_structures_qs,
+    get_package_compound_scoped_structure_qs,
+)
+
+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_structures_qs(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_scoped_structure_qs(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 +1,22 @@
+from ninja import Router
+from ninja.security import SessionAuth
+from .auth import BearerTokenAuth
+from .endpoints import packages, scenarios, compounds, rules, reactions, pathways, models, structure
+
+# 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)

epapi/v1/schemas.py

@@ -0,0 +1,104 @@
+from ninja import FilterSchema, FilterLookup, Schema
+from typing import Annotated, Optional
+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
+
+
+# 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 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"

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"]
 
 
 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"]
+    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

@@ -21,7 +21,7 @@ class BearerTokenAuth(HttpBearer):
 def _anonymous_or_real(request):
     if request.user.is_authenticated and not request.user.is_anonymous:
         return request.user
-    return get_user_model().objects.get(username='anonymous')
+    return get_user_model().objects.get(username="anonymous")
 
 
 router = Router(auth=BearerTokenAuth())
@@ -85,7 +85,9 @@ def get_package(request, package_uuid):
     try:
         return PackageManager.get_package_by_id(request.auth, package_id=package_uuid)
     except ValueError:
-        return 403, {'message': f'Getting Package with id  {package_uuid} failed due to insufficient rights!'}
+        return 403, {
+            "message": f"Getting Package with id {package_uuid} failed due to insufficient rights!"
+        }
 
 
 @router.get("/compound", response={200: List[CompoundSchema], 403: Error})
@@ -97,7 +99,9 @@ def get_compounds(request):
     return qs
 
 
-@router.get("/package/{uuid:package_uuid}/compound", response={200: List[CompoundSchema], 403: Error})
+@router.get(
+    "/package/{uuid:package_uuid}/compound", response={200: List[CompoundSchema], 403: Error}
+)
 @paginate
 def get_package_compounds(request, package_uuid):
     try:
@@ -105,4 +109,5 @@ def get_package_compounds(request, package_uuid):
         return Compound.objects.filter(package=p)
     except ValueError:
         return 403, {
-            'message': f'Getting Compounds for Package with id  {package_uuid} failed due to insufficient rights!'}
+            "message": f"Getting Compounds for Package with id {package_uuid} failed due to insufficient rights!"
+        }

epdb/apps.py

@@ -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'
+    default_auto_field = "django.db.models.BigAutoField"
-    name = 'epdb'
+    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 +5,55 @@ from django.core.management.base import BaseCommand
 from django.db import transaction
 
 from epdb.logic import UserManager, GroupManager, PackageManager, SettingManager
-from epdb.models import UserSettingPermission, MLRelativeReasoning, EnviFormer, Permission, User, ExternalDatabase
+from epdb.models import (
+    UserSettingPermission,
+    MLRelativeReasoning,
+    EnviFormer,
+    Permission,
+    User,
+    ExternalDatabase,
+    License,
+)
 
 
 class Command(BaseCommand):
+    def add_arguments(self, parser):
+        parser.add_argument(
+            "-ol", "--only-licenses", action="store_true", help="Only create licenses."
+        )
 
     def create_users(self):
-
         # Anonymous User
-        if not User.objects.filter(email='anon@envipath.com').exists():
+        if not User.objects.filter(email="anon@envipath.com").exists():
-            anon = UserManager.create_user("anonymous", "anon@envipath.com", "SuperSafe",
+            anon = UserManager.create_user(
-                                           is_active=True, add_to_group=False, set_setting=False)
+                "anonymous",
+                "anon@envipath.com",
+                "SuperSafe",
+                is_active=True,
+                add_to_group=False,
+                set_setting=False,
+            )
         else:
-            anon = User.objects.get(email='anon@envipath.com')
+            anon = User.objects.get(email="anon@envipath.com")
 
         # Admin User
-        if not User.objects.filter(email='admin@envipath.com').exists():
+        if not User.objects.filter(email="admin@envipath.com").exists():
-            admin = UserManager.create_user("admin", "admin@envipath.com", "SuperSafe",
+            admin = UserManager.create_user(
-                                            is_active=True, add_to_group=False, set_setting=False)
+                "admin",
+                "admin@envipath.com",
+                "SuperSafe",
+                is_active=True,
+                add_to_group=False,
+                set_setting=False,
+            )
             admin.is_staff = True
             admin.is_superuser = True
             admin.save()
         else:
-            admin = User.objects.get(email='admin@envipath.com')
+            admin = User.objects.get(email="admin@envipath.com")
 
         # System Group
-        g = GroupManager.create_group(admin, 'enviPath Users', 'All enviPath Users')
+        g = GroupManager.create_group(admin, "enviPath Users", "All enviPath Users")
         g.public = True
         g.save()
 
@@ -43,14 +66,20 @@ class Command(BaseCommand):
         admin.default_group = g
         admin.save()
 
-        if not User.objects.filter(email='user0@envipath.com').exists():
+        if not User.objects.filter(email="user0@envipath.com").exists():
-            user0 = UserManager.create_user("user0", "user0@envipath.com", "SuperSafe",
+            user0 = UserManager.create_user(
-                                            is_active=True, add_to_group=False, set_setting=False)
+                "user0",
+                "user0@envipath.com",
+                "SuperSafe",
+                is_active=True,
+                add_to_group=False,
+                set_setting=False,
+            )
             user0.is_staff = True
             user0.is_superuser = True
             user0.save()
         else:
-            user0 = User.objects.get(email='user0@envipath.com')
+            user0 = User.objects.get(email="user0@envipath.com")
 
         g.user_member.add(user0)
         g.save()
@@ -60,19 +89,32 @@ class Command(BaseCommand):
 
         return anon, admin, g, user0
 
+    def create_licenses(self):
+        """Create the six default licenses supported by enviPath"""
+        cc_strings = ["by", "by-nc", "by-nc-nd", "by-nc-sa", "by-nd", "by-sa"]
+        for cc_string in cc_strings:
+            if not License.objects.filter(cc_string=cc_string).exists():
+                new_license = License()
+                new_license.cc_string = cc_string
+                new_license.link = f"https://creativecommons.org/licenses/{cc_string}/4.0/"
+                new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
+                new_license.save()
+
     def import_package(self, data, owner):
-        return PackageManager.import_legacy_package(data, owner, keep_ids=True, add_import_timestamp=False, trust_reviewed=True)
+        return PackageManager.import_legacy_package(
+            data, owner, keep_ids=True, add_import_timestamp=False, trust_reviewed=True
+        )
 
     def create_default_setting(self, owner, packages):
         s = SettingManager.create_setting(
             owner,
-            name='Global Default Setting',
+            name="Global Default Setting",
-            description='Global Default Setting containing BBD Rules and Max 30 Nodes and Max Depth of 8',
+            description="Global Default Setting containing BBD Rules and Max 30 Nodes and Max Depth of 8",
             max_nodes=30,
             max_depth=5,
             rule_packages=packages,
             model=None,
-            model_threshold=None
+            model_threshold=None,
         )
 
         return s
@@ -84,57 +126,58 @@ class Command(BaseCommand):
         """
         databases = [
             {
-                'name': 'PubChem Compound',
+                "name": "PubChem Compound",
-                'full_name': 'PubChem Compound Database',
+                "full_name": "PubChem Compound Database",
-                'description': 'Chemical database of small organic molecules',
+                "description": "Chemical database of small organic molecules",
-                'base_url': 'https://pubchem.ncbi.nlm.nih.gov',
+                "base_url": "https://pubchem.ncbi.nlm.nih.gov",
-                'url_pattern': 'https://pubchem.ncbi.nlm.nih.gov/compound/{id}'
+                "url_pattern": "https://pubchem.ncbi.nlm.nih.gov/compound/{id}",
             },
             {
-                'name': 'PubChem Substance',
+                "name": "PubChem Substance",
-                'full_name': 'PubChem Substance Database',
+                "full_name": "PubChem Substance Database",
-                'description': 'Database of chemical substances',
+                "description": "Database of chemical substances",
-                'base_url': 'https://pubchem.ncbi.nlm.nih.gov',
+                "base_url": "https://pubchem.ncbi.nlm.nih.gov",
-                'url_pattern': 'https://pubchem.ncbi.nlm.nih.gov/substance/{id}'
+                "url_pattern": "https://pubchem.ncbi.nlm.nih.gov/substance/{id}",
             },
             {
-                'name': 'ChEBI',
+                "name": "ChEBI",
-                'full_name': 'Chemical Entities of Biological Interest',
+                "full_name": "Chemical Entities of Biological Interest",
-                'description': 'Dictionary of molecular entities',
+                "description": "Dictionary of molecular entities",
-                'base_url': 'https://www.ebi.ac.uk/chebi',
+                "base_url": "https://www.ebi.ac.uk/chebi",
-                'url_pattern': 'https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:{id}'
+                "url_pattern": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:{id}",
             },
             {
-                'name': 'RHEA',
+                "name": "RHEA",
-                'full_name': 'RHEA Reaction Database',
+                "full_name": "RHEA Reaction Database",
-                'description': 'Comprehensive resource of biochemical reactions',
+                "description": "Comprehensive resource of biochemical reactions",
-                'base_url': 'https://www.rhea-db.org',
+                "base_url": "https://www.rhea-db.org",
-                'url_pattern': 'https://www.rhea-db.org/rhea/{id}'
+                "url_pattern": "https://www.rhea-db.org/rhea/{id}",
             },
             {
-                'name': 'KEGG Reaction',
+                "name": "KEGG Reaction",
-                'full_name': 'KEGG Reaction Database',
+                "full_name": "KEGG Reaction Database",
-                'description': 'Database of biochemical reactions',
+                "description": "Database of biochemical reactions",
-                'base_url': 'https://www.genome.jp',
+                "base_url": "https://www.genome.jp",
-                'url_pattern': 'https://www.genome.jp/entry/reaction+{id}'
+                "url_pattern": "https://www.genome.jp/entry/{id}",
             },
             {
-                'name': 'UniProt',
+                "name": "UniProt",
-                'full_name': 'MetaCyc Metabolic Pathway Database',
+                "full_name": "MetaCyc Metabolic Pathway Database",
-                'description': 'UniProt is a freely accessible database of protein sequence and functional information',
+                "description": "UniProt is a freely accessible database of protein sequence and functional information",
-                'base_url': 'https://www.uniprot.org',
+                "base_url": "https://www.uniprot.org",
-                'url_pattern': 'https://www.uniprot.org/uniprotkb?query="{id}"'
+                "url_pattern": 'https://www.uniprot.org/uniprotkb?query="{id}"',
-            }
+            },
         ]
 
         for db_info in databases:
-            ExternalDatabase.objects.get_or_create(
+            ExternalDatabase.objects.get_or_create(name=db_info["name"], defaults=db_info)
-                name=db_info['name'],
-                defaults=db_info
-            )
 
     @transaction.atomic
     def handle(self, *args, **options):
+        # Create licenses
+        self.create_licenses()
+        if options.get("only_licenses", False):
+            return
         # Create users
         anon, admin, g, user0 = self.create_users()
 
@@ -142,20 +185,24 @@ class Command(BaseCommand):
 
         # Import Packages
         packages = [
-            'EAWAG-BBD.json',
+            "EAWAG-BBD.json",
-            'EAWAG-SOIL.json',
+            "EAWAG-SOIL.json",
-            'EAWAG-SLUDGE.json',
+            "EAWAG-SLUDGE.json",
-            'EAWAG-SEDIMENT.json',
+            "EAWAG-SEDIMENT.json",
         ]
 
         mapping = {}
         for p in packages:
             print(f"Importing {p}...")
-            package_data = json.loads(open(s.BASE_DIR / 'fixtures' / 'packages' / '2025-07-18' / p).read())
+            package_data = json.loads(
+                open(
+                    s.BASE_DIR / "fixtures" / "packages" / "2025-07-18" / p, encoding="utf-8"
+                ).read()
+            )
             imported_package = self.import_package(package_data, admin)
-            mapping[p.replace('.json', '')] = imported_package
+            mapping[p.replace(".json", "")] = imported_package
 
-        setting = self.create_default_setting(admin, [mapping['EAWAG-BBD']])
+        setting = self.create_default_setting(admin, [mapping["EAWAG-BBD"]])
         setting.public = True
         setting.save()
         setting.make_global_default()
@@ -171,26 +218,28 @@ class Command(BaseCommand):
             usp.save()
 
         # Create Model Package
-        pack = PackageManager.create_package(admin, "Public Prediction Models",
+        pack = PackageManager.create_package(
-                                             "Package to make Prediction Models publicly available")
+            admin,
+            "Public Prediction Models",
+            "Package to make Prediction Models publicly available",
+        )
         pack.reviewed = True
         pack.save()
 
         # Create RR
         ml_model = MLRelativeReasoning.create(
             package=pack,
-            rule_packages=[mapping['EAWAG-BBD']],
+            rule_packages=[mapping["EAWAG-BBD"]],
-            data_packages=[mapping['EAWAG-BBD']],
+            data_packages=[mapping["EAWAG-BBD"]],
             eval_packages=[],
             threshold=0.5,
-            name='ECC - BBD - T0.5',
+            name="ECC - BBD - T0.5",
-            description='ML Relative Reasoning',
+            description="ML Relative Reasoning",
         )
 
         ml_model.build_dataset()
         ml_model.build_model()
-        # ml_model.evaluate_model()
 
         # If available, create EnviFormerModel
         if s.ENVIFORMER_PRESENT:
-            enviFormer_model = EnviFormer.create(pack, 'EnviFormer - T0.5', 'EnviFormer Model with Threshold 0.5', 0.5)
+            EnviFormer.create(pack, "EnviFormer - T0.5", "EnviFormer Model with Threshold 0.5", 0.5)

epdb/management/commands/create_ml_models.py

@@ -0,0 +1,121 @@
+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.data_packages.all()],
+            "threshold": model.threshold,
+            "eval_results": model.eval_results,
+            "multigen_eval": model.multigen_eval,
+            "model_status": model.model_status,
+        }
+
+        model_folder = os.path.join(s.MODEL_DIR, "enviformer", str(model.uuid))
+
+        self.package_dict_and_folder(data, model_folder, output)

epdb/management/commands/import_external_identifiers.py

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

epdb/management/commands/import_legacy_package.py

@@ -1,27 +1,29 @@
+import json
+
 from django.core.management.base import BaseCommand
+from django.db import transaction
 
 from epdb.logic import PackageManager
-from epdb.models import *
+from epdb.models import User
 
 
 class Command(BaseCommand):
-
     def add_arguments(self, parser):
         parser.add_argument(
-            '--data',
+            "--data",
             type=str,
-            help='Path of the Package to import.',
+            help="Path of the Package to import.",
             required=True,
         )
         parser.add_argument(
-            '--owner',
+            "--owner",
             type=str,
-            help='Username of the desired Owner.',
+            help="Username of the desired Owner.",
             required=True,
         )
 
     @transaction.atomic
     def handle(self, *args, **options):
-        owner = User.objects.get(username=options['owner'])
+        owner = User.objects.get(username=options["owner"])
-        package_data = json.load(open(options['data']))
+        package_data = json.load(open(options["data"]))
         PackageManager.import_legacy_package(package_data, owner)

epdb/management/commands/load_enviformer.py

@@ -0,0 +1,83 @@
+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 epdb.models import EnviPathModel
-from django.db.models.functions import Replace
 
 
 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',
+            "User",
-            'Group',
+            "Group",
-            'Package',
+            "Compound",
-            'Compound',
+            "CompoundStructure",
-            'CompoundStructure',
+            "Pathway",
-            'Pathway',
+            "Edge",
-            'Edge',
+            "Node",
-            'Node',
+            "Reaction",
-            'Reaction',
+            "SimpleAmbitRule",
-            'SimpleAmbitRule',
+            "SimpleRDKitRule",
-            'SimpleRDKitRule',
+            "ParallelRule",
-            'ParallelRule',
+            "SequentialRule",
-            'SequentialRule',
+            "Scenario",
-            'Scenario',
+            "Setting",
-            'Setting',
+            "MLRelativeReasoning",
-            'MLRelativeReasoning',
+            "RuleBasedRelativeReasoning",
-            'RuleBasedRelativeReasoning',
+            "EnviFormer",
-            'EnviFormer',
+            "ApplicabilityDomain",
-            'ApplicabilityDomain',
+            "EnzymeLink",
         ]
         for model in MODELS:
             obj_cls = apps.get_model("epdb", model)
-            print(f"Localizing urls for {model}")
             obj_cls.objects.update(
-                url=Replace(F('url'), Value(options['old']), Value(options['new']))
+                url=Replace(F("url"), Value(options["old"]), Value(options["new"]))
             )
+            if issubclass(obj_cls, EnviPathModel):
+                obj_cls.objects.update(
+                    kv=Cast(
+                        Replace(
+                            Cast(F("kv"), output_field=TextField()),
+                            Value(options["old"]),
+                            Value(options["new"]),
+                        ),
+                        output_field=JSONField(),
+                    )
+                )

epdb/management/commands/update_job_logs.py

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

epdb/middleware/login_required_middleware.py

@@ -3,22 +3,25 @@ from django.shortcuts import redirect
 from django.urls import reverse
 from urllib.parse import quote
 
+
 class LoginRequiredMiddleware:
     def __init__(self, get_response):
         self.get_response = get_response
         self.exempt_urls = [
-                               reverse('login'),
+            reverse("login"),
-                               reverse('logout'),
+            reverse("logout"),
-                               reverse('admin:login'),
+            reverse("admin:login"),
-                               reverse('admin:index'),
+            reverse("admin:index"),
-                           ] + getattr(settings, 'LOGIN_EXEMPT_URLS', [])
+        ] + getattr(settings, "LOGIN_EXEMPT_URLS", [])
 
     def __call__(self, request):
         if not request.user.is_authenticated:
             path = request.path_info
             if not any(path.startswith(url) for url in self.exempt_urls):
-                if request.method == 'GET':
+                if request.method == "GET":
-                    if request.get_full_path() and request.get_full_path() != '/':
+                    if request.get_full_path() and request.get_full_path() != "/":
-                        return redirect(f"{settings.LOGIN_URL}?next={quote(request.get_full_path())}")
+                        return redirect(
+                            f"{settings.LOGIN_URL}?next={quote(request.get_full_path())}"
+                        )
                 return redirect(settings.LOGIN_URL)
         return self.get_response(request)

epdb/migrations/0007_alter_enviformer_options_enviformer_app_domain_and_more.py

@@ -0,0 +1,53 @@
+# Generated by Django 5.2.1 on 2025-10-07 08:19
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('epdb', '0006_mlrelativereasoning_multigen_eval_and_more'),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name='enviformer',
+            options={},
+        ),
+        migrations.AddField(
+            model_name='enviformer',
+            name='app_domain',
+            field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.applicabilitydomain'),
+        ),
+        migrations.AddField(
+            model_name='enviformer',
+            name='data_packages',
+            field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_data_packages', to='epdb.package', verbose_name='Data Packages'),
+        ),
+        migrations.AddField(
+            model_name='enviformer',
+            name='eval_packages',
+            field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_eval_packages', to='epdb.package', verbose_name='Evaluation Packages'),
+        ),
+        migrations.AddField(
+            model_name='enviformer',
+            name='eval_results',
+            field=models.JSONField(blank=True, default=dict, null=True),
+        ),
+        migrations.AddField(
+            model_name='enviformer',
+            name='model_status',
+            field=models.CharField(choices=[('INITIAL', 'Initial'), ('INITIALIZING', 'Model is initializing.'), ('BUILDING', 'Model is building.'), ('BUILT_NOT_EVALUATED', 'Model is built and can be used for predictions, Model is not evaluated yet.'), ('EVALUATING', 'Model is evaluating'), ('FINISHED', 'Model has finished building and evaluation.'), ('ERROR', 'Model has failed.')], default='INITIAL'),
+        ),
+        migrations.AddField(
+            model_name='enviformer',
+            name='multigen_eval',
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AddField(
+            model_name='enviformer',
+            name='rule_packages',
+            field=models.ManyToManyField(related_name='%(app_label)s_%(class)s_rule_packages', to='epdb.package', verbose_name='Rule Packages'),
+        ),
+    ]

epdb/migrations/0008_enzymelink.py

@@ -0,0 +1,64 @@
+# Generated by Django 5.2.7 on 2025-10-10 06:58
+
+import django.db.models.deletion
+import django.utils.timezone
+import model_utils.fields
+import uuid
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0007_alter_enviformer_options_enviformer_app_domain_and_more"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="EnzymeLink",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                (
+                    "created",
+                    model_utils.fields.AutoCreatedField(
+                        default=django.utils.timezone.now, editable=False, verbose_name="created"
+                    ),
+                ),
+                (
+                    "modified",
+                    model_utils.fields.AutoLastModifiedField(
+                        default=django.utils.timezone.now, editable=False, verbose_name="modified"
+                    ),
+                ),
+                (
+                    "uuid",
+                    models.UUIDField(
+                        default=uuid.uuid4, unique=True, verbose_name="UUID of this object"
+                    ),
+                ),
+                ("name", models.TextField(default="no name", verbose_name="Name")),
+                (
+                    "description",
+                    models.TextField(default="no description", verbose_name="Descriptions"),
+                ),
+                ("url", models.TextField(null=True, unique=True, verbose_name="URL")),
+                ("kv", models.JSONField(blank=True, default=dict, null=True)),
+                ("ec_number", models.TextField(verbose_name="EC Number")),
+                ("classification_level", models.IntegerField(verbose_name="Classification Level")),
+                ("linking_method", models.TextField(verbose_name="Linking Method")),
+                ("edge_evidence", models.ManyToManyField(to="epdb.edge")),
+                ("reaction_evidence", models.ManyToManyField(to="epdb.reaction")),
+                (
+                    "rule",
+                    models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to="epdb.rule"),
+                ),
+            ],
+            options={
+                "abstract": False,
+            },
+        ),
+    ]

epdb/migrations/0009_joblog.py

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

epdb/migrations/0010_license_cc_string.py

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

epdb/migrations/0011_auto_20251111_1413.py

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

epdb/migrations/0012_node_stereo_removed_pathway_predicted.py

@@ -0,0 +1,22 @@
+# Generated by Django 5.2.7 on 2025-12-02 13:09
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0011_auto_20251111_1413"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="node",
+            name="stereo_removed",
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AddField(
+            model_name="pathway",
+            name="predicted",
+            field=models.BooleanField(default=False),
+        ),
+    ]

epdb/migrations/0013_setting_expansion_schema.py

@@ -0,0 +1,25 @@
+# Generated by Django 5.2.7 on 2025-12-14 11:30
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0012_node_stereo_removed_pathway_predicted"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="setting",
+            name="expansion_schema",
+            field=models.CharField(
+                choices=[
+                    ("BFS", "Breadth First Search"),
+                    ("DFS", "Depth First Search"),
+                    ("GREEDY", "Greedy"),
+                ],
+                default="BFS",
+                max_length=20,
+            ),
+        ),
+    ]

epdb/migrations/0014_rename_expansion_schema_setting_expansion_scheme.py

@@ -0,0 +1,17 @@
+# Generated by Django 5.2.7 on 2025-12-14 16:02
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0013_setting_expansion_schema"),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name="setting",
+            old_name="expansion_schema",
+            new_name="expansion_scheme",
+        ),
+    ]

epdb/tasks.py

@@ -1,58 +1,169 @@
+import csv
+import io
 import logging
-from typing import Optional
+from typing import Any, Callable, List, Optional
+from uuid import uuid4
 
 from celery import shared_task
-from epdb.models import Pathway, Node, Edge, EPModel, Setting
+from celery.utils.functional import LRUCache
-from epdb.logic import SPathway
+from django.conf import settings as s
+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
 
 
-@shared_task(queue='model')
+@shared_task(bind=True, queue="model")
-def build_model(model_pk: int):
+def build_model(self, model_pk: int):
     mod = EPModel.objects.get(id=model_pk)
-    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')
+@shared_task(bind=True, queue="model")
-def evaluate_model(model_pk: int):
+def evaluate_model(self, model_pk: int, multigen: bool, package_pks: Optional[list] = None):
+    packages = None
+
+    if package_pks:
+        packages = Package.objects.filter(pk__in=package_pks)
+
     mod = EPModel.objects.get(id=model_pk)
-    mod.evaluate_model()
+    if JobLog.objects.filter(task_id=self.request.id).exists():
+        JobLog.objects.filter(task_id=self.request.id).update(status="RUNNING", task_result=mod.url)
+
+    try:
+        mod.evaluate_model(multigen, eval_packages=packages)
+    except Exception as e:
+        if JobLog.objects.filter(task_id=self.request.id).exists():
+            JobLog.objects.filter(task_id=self.request.id).update(
+                status="FAILED", task_result=mod.url
+            )
+
+        raise e
+
+    if JobLog.objects.filter(task_id=self.request.id).exists():
+        JobLog.objects.filter(task_id=self.request.id).update(status="SUCCESS", task_result=mod.url)
+
+    return mod.url
 
 
-@shared_task(queue='model')
+@shared_task(queue="model")
 def retrain(model_pk: int):
     mod = EPModel.objects.get(id=model_pk)
     mod.retrain()
 
 
-@shared_task(queue='predict')
+@shared_task(bind=True, queue="predict")
-def predict(pw_pk: int, pred_setting_pk: int, limit: Optional[int] = None, node_pk: Optional[int] = None) -> Pathway:
+def predict(
+    self,
+    pw_pk: int,
+    pred_setting_pk: int,
+    limit: Optional[int] = None,
+    node_pk: Optional[int] = None,
+    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 +183,259 @@ 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.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__
+
+
+@register.filter
+def is_url(value):
+    try:
+        url_adapter.validate_python(value)
+        return True
+    except ValidationError:
+        return False

epdb/tests.py

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

epdb/urls.py

@@ -1,99 +1,213 @@
-from django.urls import path, re_path
 from django.contrib.auth import views as auth_views
+from django.urls import path, re_path
 
 from . import views as v
 
-UUID = '[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}'
+UUID = "[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}"
 
 urlpatterns = [
     # Home
-    re_path(r'^$', v.index, name='index'),
+    re_path(r"^$", v.index, name="index"),
-
     # Login
-    re_path(r'^login', v.login, name='login'),
+    re_path(r"^login", v.login, name="login"),
-    re_path(r'^logout', v.logout, name='logout'),
+    re_path(r"^logout", v.logout, name="logout"),
-    re_path(r'^register', v.register, name='register'),
+    re_path(r"^register", v.register, name="register"),
-
+    # Built-In views
-    # Built In views
+    path(
-    path('password_reset/', auth_views.PasswordResetView.as_view(
+        "password_reset/",
-        template_name='static/password_reset_form.html'
+        auth_views.PasswordResetView.as_view(template_name="static/password_reset_form.html"),
-    ), name='password_reset'),
+        name="password_reset",
-
+    ),
-    path('password_reset/done/', auth_views.PasswordResetDoneView.as_view(
+    path(
-        template_name='static/password_reset_done.html'
+        "password_reset/done/",
-    ), name='password_reset_done'),
+        auth_views.PasswordResetDoneView.as_view(template_name="static/password_reset_done.html"),
-
+        name="password_reset_done",
-    path('reset/<uidb64>/<token>/', auth_views.PasswordResetConfirmView.as_view(
+    ),
-        template_name='static/password_reset_confirm.html'
+    path(
-    ), name='password_reset_confirm'),
+        "reset/<uidb64>/<token>/",
-
+        auth_views.PasswordResetConfirmView.as_view(
-    path('reset/done/', auth_views.PasswordResetCompleteView.as_view(
+            template_name="static/password_reset_confirm.html"
-        template_name='static/password_reset_complete.html'
+        ),
-    ), name='password_reset_complete'),
+        name="password_reset_confirm",
-
+    ),
-
+    path(
+        "reset/done/",
+        auth_views.PasswordResetCompleteView.as_view(
+            template_name="static/password_reset_complete.html"
+        ),
+        name="password_reset_complete",
+    ),
     # Top level urls
-    re_path(r'^package$', v.packages, name='packages'),
+    re_path(r"^package$", v.packages, name="packages"),
-    re_path(r'^compound$', v.compounds, name='compounds'),
+    re_path(r"^compound$", v.compounds, name="compounds"),
-    re_path(r'^rule$', v.rules, name='rules'),
+    re_path(r"^rule$", v.rules, name="rules"),
-    re_path(r'^reaction$', v.reactions, name='reactions'),
+    re_path(r"^reaction$", v.reactions, name="reactions"),
-    re_path(r'^pathway$', v.pathways, name='pathways'),
+    re_path(r"^pathway$", v.pathways, name="pathways"),
-    re_path(r'^scenario$', v.scenarios, name='scenarios'),
+    re_path(r"^scenario$", v.scenarios, name="scenarios"),
-    re_path(r'^model$', v.models, name='model'),
+    re_path(r"^model$", v.models, name="model"),
-    re_path(r'^user$', v.users, name='users'),
+    re_path(r"^user$", v.users, name="users"),
-    re_path(r'^group$', v.groups, name='groups'),
+    re_path(r"^group$", v.groups, name="groups"),
-    re_path(r'^search$', v.search, name='search'),
+    re_path(r"^search$", v.search, name="search"),
-
+    re_path(r"^predict$", v.predict_pathway, name="predict_pathway"),
-
+    re_path(r"^batch-predict$", 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$', v.package_compounds, name='package compound list'),
+    re_path(
-    re_path(rf'^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})$', v.package_compound, name='package compound detail'),
+        rf"^package/(?P<package_uuid>{UUID})/compound$",
+        v.package_compounds,
+        name="package compound list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})$",
+        v.package_compound,
+        name="package compound detail",
+    ),
     # Compound Structure
-    re_path(rf'^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})/structure$', v.package_compound_structures, name='package compound structure list'),
+    re_path(
-    re_path(rf'^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})/structure/(?P<structure_uuid>{UUID})$', v.package_compound_structure, name='package compound structure detail'),
+        rf"^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})/structure$",
+        v.package_compound_structures,
+        name="package compound structure list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/compound/(?P<compound_uuid>{UUID})/structure/(?P<structure_uuid>{UUID})$",
+        v.package_compound_structure,
+        name="package compound structure detail",
+    ),
     # Rule
-    re_path(rf'^package/(?P<package_uuid>{UUID})/rule$', v.package_rules, name='package rule list'),
+    re_path(rf"^package/(?P<package_uuid>{UUID})/rule$", v.package_rules, name="package rule list"),
-    re_path(rf'^package/(?P<package_uuid>{UUID})/rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
+    re_path(
-    re_path(rf'^package/(?P<package_uuid>{UUID})/simple-ambit-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
+        rf"^package/(?P<package_uuid>{UUID})/rule/(?P<rule_uuid>{UUID})$",
-    re_path(rf'^package/(?P<package_uuid>{UUID})/simple-rdkit-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
+        v.package_rule,
-    re_path(rf'^package/(?P<package_uuid>{UUID})/parallel-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
+        name="package rule detail",
-    re_path(rf'^package/(?P<package_uuid>{UUID})/sequential-rule/(?P<rule_uuid>{UUID})$', v.package_rule, name='package rule detail'),
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/simple-ambit-rule/(?P<rule_uuid>{UUID})$",
+        v.package_rule,
+        name="package rule detail",
+    ),
+    # re_path(
+    #     rf"^package/(?P<package_uuid>{UUID})/simple-rdkit-rule/(?P<rule_uuid>{UUID})$",
+    #     v.package_rule,
+    #     name="package rule detail",
+    # ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/parallel-rule/(?P<rule_uuid>{UUID})$",
+        v.package_rule,
+        name="package rule detail",
+    ),
+    # re_path(
+    #     rf"^package/(?P<package_uuid>{UUID})/sequential-rule/(?P<rule_uuid>{UUID})$",
+    #     v.package_rule,
+    #     name="package rule detail",
+    # ),
+    # EnzymeLinks
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/rule/(?P<rule_uuid>{UUID})/enzymelink/(?P<enzymelink_uuid>{UUID})$",
+        v.package_rule_enzymelink,
+        name="package rule enzymelink detail",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/simple-ambit-rule/(?P<rule_uuid>{UUID})/enzymelink/(?P<enzymelink_uuid>{UUID})$",
+        v.package_rule_enzymelink,
+        name="package rule enzymelink detail",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/parallel-rule/(?P<rule_uuid>{UUID})/enzymelink/(?P<enzymelink_uuid>{UUID})$",
+        v.package_rule_enzymelink,
+        name="package rule enzymelink detail",
+    ),
     # Reaction
-    re_path(rf'^package/(?P<package_uuid>{UUID})/reaction$', v.package_reactions, name='package reaction list'),
+    re_path(
-    re_path(rf'^package/(?P<package_uuid>{UUID})/reaction/(?P<reaction_uuid>{UUID})$', v.package_reaction, name='package reaction detail'),
+        rf"^package/(?P<package_uuid>{UUID})/reaction$",
+        v.package_reactions,
+        name="package reaction list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/reaction/(?P<reaction_uuid>{UUID})$",
+        v.package_reaction,
+        name="package reaction detail",
+    ),
     # # Pathway
-    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway$', v.package_pathways, name='package pathway list'),
+    re_path(
-    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})$', v.package_pathway, name='package pathway detail'),
+        rf"^package/(?P<package_uuid>{UUID})/pathway$",
+        v.package_pathways,
+        name="package pathway list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})$",
+        v.package_pathway,
+        name="package pathway detail",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/predict$",
+        v.package_predict_pathway,
+        name="package predict pathway",
+    ),
     # Pathway Nodes
-    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node$', v.package_pathway_nodes, name='package pathway node list'),
+    re_path(
-    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node/(?P<node_uuid>{UUID})$', v.package_pathway_node, name='package pathway node detail'),
+        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node$",
+        v.package_pathway_nodes,
+        name="package pathway node list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/node/(?P<node_uuid>{UUID})$",
+        v.package_pathway_node,
+        name="package pathway node detail",
+    ),
     # Pathway Edges
-    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge$', v.package_pathway_edges, name='package pathway edge list'),
+    re_path(
-    re_path(rf'^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge/(?P<edge_uuid>{UUID})$', v.package_pathway_edge, name='package pathway edge detail'),
+        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge$",
+        v.package_pathway_edges,
+        name="package pathway edge list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/edge/(?P<edge_uuid>{UUID})$",
+        v.package_pathway_edge,
+        name="package pathway edge detail",
+    ),
     # Scenario
-    re_path(rf'^package/(?P<package_uuid>{UUID})/scenario$', v.package_scenarios, name='package scenario list'),
+    re_path(
-    re_path(rf'^package/(?P<package_uuid>{UUID})/scenario/(?P<scenario_uuid>{UUID})$', v.package_scenario, name='package scenario detail'),
+        rf"^package/(?P<package_uuid>{UUID})/scenario$",
+        v.package_scenarios,
+        name="package scenario list",
+    ),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/scenario/(?P<scenario_uuid>{UUID})$",
+        v.package_scenario,
+        name="package scenario detail",
+    ),
     # Model
-    re_path(rf'^package/(?P<package_uuid>{UUID})/model$', v.package_models, name='package model list'),
+    re_path(
-    re_path(rf'^package/(?P<package_uuid>{UUID})/model/(?P<model_uuid>{UUID})$', v.package_model,name='package model detail'),
+        rf"^package/(?P<package_uuid>{UUID})/model$", v.package_models, name="package model list"
-
+    ),
-    re_path(r'^setting$', v.settings, name='settings'),
+    re_path(
-    re_path(rf'^setting/(?P<setting_uuid>{UUID})', v.setting, name='setting'),
+        rf"^package/(?P<package_uuid>{UUID})/model/(?P<model_uuid>{UUID})$",
-
+        v.package_model,
-    re_path(r'^indigo/info$', v.indigo, name='indigo_info'),
+        name="package model detail",
-    re_path(r'^indigo/aromatize$', v.aromatize, name='indigo_aromatize'),
+    ),
-    re_path(r'^indigo/dearomatize$', v.dearomatize, name='indigo_dearomatize'),
+    re_path(r"^setting$", v.settings, name="settings"),
-    re_path(r'^indigo/layout$', v.layout, name='indigo_layout'),
+    re_path(rf"^setting/(?P<setting_uuid>{UUID})", v.setting, name="setting"),
-
+    re_path(r"^indigo/info$", v.indigo, name="indigo_info"),
-    re_path(r'^depict$', v.depict, name='depict'),
+    re_path(r"^indigo/aromatize$", v.aromatize, name="indigo_aromatize"),
-
+    re_path(r"^indigo/dearomatize$", v.dearomatize, name="indigo_dearomatize"),
+    re_path(r"^indigo/layout$", v.layout, name="indigo_layout"),
+    re_path(r"^depict$", v.depict, name="depict"),
+    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$", v.static_cite, name="cite"),
+    re_path(r"^legal$", v.static_legal, name="legal"),
 ]

migration/urls.py

@@ -12,4 +12,5 @@ urlpatterns = [
     re_path(rf'^migration/package/(?P<package_uuid>{UUID})/simple-rdkit-rule/(?P<rule_uuid>{UUID})$', v.migration_detail, name='migration detail'),
     re_path(rf'^migration/package/(?P<package_uuid>{UUID})/parallel-rule/(?P<rule_uuid>{UUID})$', v.migration_detail, name='migration detail'),
     re_path(rf'^migration/package/(?P<package_uuid>{UUID})/sequential-rule/(?P<rule_uuid>{UUID})$', v.migration_detail, name='migration detail'),
+    re_path(rf'^migration/compare$', v.compare, name='compare'),
 ]

migration/views.py

@@ -1,80 +1,117 @@
-import gzip
 import json
+import logging
 import os.path
 
 from django.conf import settings as s
+from django.http import HttpResponseNotAllowed
 from django.shortcuts import render
+from rdkit import Chem
+from rdkit.Chem.MolStandardize import rdMolStandardize
 
-from epdb.logic import PackageManager
+from epdb.models import CompoundStructure, Rule, SimpleAmbitRule
-from epdb.models import Rule
+from epdb.views import get_base_context
-from epdb.views import get_base_context, _anonymous_or_real
 from utilities.chem import FormatConverter
 
+logger = logging.getLogger(__name__)
+
+Package = s.GET_PACKAGE_MODEL()
+
+
+def normalize_smiles(smiles):
+    m1 = Chem.MolFromSmiles(smiles)
+    if m1 is None:
+        print("Couldnt read smi: ", smiles)
+        return smiles
+    Chem.RemoveStereochemistry(m1)
+    # Normalizer takes care of charge/tautomer/resonance standardization
+    normalizer = rdMolStandardize.Normalizer()
+    return Chem.MolToSmiles(normalizer.normalize(m1), canonical=True)
+
+
+def run_both_engines(SMILES, SMIRKS):
+    from envipy_ambit import apply
+
+    ambit_res = apply(SMIRKS, SMILES)
+    # ambit_res, ambit_errors = FormatConverter.sanitize_smiles([str(s) for s in ambit_res])
+
+    ambit_res = list(
+        set(
+            [
+                normalize_smiles(str(x))
+                for x in FormatConverter.sanitize_smiles([str(s) for s in ambit_res])[0]
+            ]
+        )
+    )
+
+    products = FormatConverter.apply(SMILES, SMIRKS)
+
+    all_rdkit_prods = []
+    for ps in products:
+        for p in ps:
+            all_rdkit_prods.append(p)
+
+    all_rdkit_prods = list(set(all_rdkit_prods))
+    # all_rdkit_res, rdkit_errors = FormatConverter.sanitize_smiles(all_rdkit_prods)
+    all_rdkit_res = list(
+        set(
+            [
+                normalize_smiles(str(x))
+                for x in FormatConverter.sanitize_smiles([str(s) for s in all_rdkit_prods])[0]
+            ]
+        )
+    )
+    # return ambit_res, ambit_errors, all_rdkit_res, rdkit_errors
+    return ambit_res, 0, all_rdkit_res, 0
+
 
 def migration(request):
-    if request.method == 'GET':
+    if request.method == "GET":
         context = get_base_context(request)
 
-        if os.path.exists(s.BASE_DIR / 'fixtures' / 'migration_status_per_rule.json') and request.GET.get(
+        if (
-                "force") is None:
+            os.path.exists(s.BASE_DIR / "fixtures" / "migration_status_per_rule.json")
-            migration_status = json.load(open(s.BASE_DIR / 'fixtures' / 'migration_status_per_rule.json'))
+            and request.GET.get("force") is None
+        ):
+            migration_status = json.load(
+                open(s.BASE_DIR / "fixtures" / "migration_status_per_rule.json")
+            )
         else:
-            data = json.load(gzip.open(s.BASE_DIR / 'fixtures' / 'ambit_rules.json.gz', 'rb'))
+            BBD = Package.objects.get(
-
+                url="http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1"
-            results = []
+            )
+            ALL_SMILES = [
+                cs.smiles for cs in CompoundStructure.objects.filter(compound__package=BBD)
+            ]
+            RULES = SimpleAmbitRule.objects.filter(package=BBD)
 
+            results = list()
+            num_rules = len(RULES)
             success = 0
             error = 0
             total = 0
 
-            num_keys = len(data.keys())
+            for i, r in enumerate(RULES):
-            for i, bt_rule_name in enumerate(data.keys()):
+                logger.debug(f"\r{i + 1:03d}/{num_rules}")
-                print(f"{i + 1}/{num_keys}")
-                bt_rule = data[bt_rule_name]
-                smirks = bt_rule['smirks']
-
-                all_prods = set()
-
                 res = True
+                for smiles in ALL_SMILES:
+                    try:
+                        ambit_res, _, rdkit_res, _ = run_both_engines(smiles, r.smirks)
 
-                for comp, ambit_prod in zip(bt_rule['compounds'], bt_rule['products']):
+                        res &= set(ambit_res) == set(rdkit_res)
-
+                    except Exception as e:
-                    products = FormatConverter.apply(comp['smiles'], smirks)
+                        logger.error(e)
-
-                    all_rdkit_prods = []
-                    for ps in products:
-                        for p in ps:
-                            all_rdkit_prods.append(p)
-
-                    all_rdkit_prods = list(set(all_rdkit_prods))
-
-                    ambit_smiles, ambit_errors = FormatConverter.sanitize_smiles(ambit_prod)
-                    rdkit_smiles, rdkit_errors = FormatConverter.sanitize_smiles(all_rdkit_prods)
-
-                    for x in ambit_smiles:
-                        all_prods.add(x)
-
-                    # TODO mode "intersection"
-                    # partial_res = (len(set(ambit_smiles).intersection(set(rdkit_smiles))) > 0) or (len(ambit_smiles) == 0)
-                    # FAILED (failures=37)
-
-                    # TODO mode = "full ambit"
-                    # partial_res = len(set(ambit_smiles).intersection(set(rdkit_smiles))) == len(ambit_smiles)
-                    # FAILED (failures=46)
-
-                    # TODO mode = "equality"
-                    partial_res = set(ambit_smiles) == set(rdkit_smiles)
-                    # FAILED (failures=69)
-
-                    res &= partial_res
 
                 results.append(
                     {
-                        'name': bt_rule_name,
+                        "name": r.name,
-                        'id': bt_rule['id'].split('/')[-1],
+                        "detail_url": s.SERVER_URL
-                        'url': bt_rule['id'],
+                        + "/migration/"
-                        'status': res,
+                        + r.url.replace("https://envipath.org/", "").replace(
-                        'detail_url': s.SERVER_URL + '/migration/' + bt_rule['id'].replace('https://envipath.org/', '')
+                            "http://localhost:8000/", ""
+                        ),
+                        "id": str(r.uuid),
+                        "url": r.url,
+                        "status": res,
                     }
                 )
 
@@ -84,95 +121,78 @@ def migration(request):
                     error += 1
 
                 total += 1
-
+            results = sorted(results, key=lambda x: (x["status"], x["name"]))
-            results = sorted(results, key=lambda x: (x['status'], x['name']))
 
             migration_status = {
-                'results': results,
+                "results": results,
-                'success': success,
+                "success": success,
-                'error': error,
+                "error": error,
-                'total': total
+                "total": total,
             }
 
-            json.dump(migration_status, open(s.BASE_DIR / 'fixtures' / 'migration_status_per_rule.json', 'w'))
+            json.dump(
+                migration_status,
+                open(s.BASE_DIR / "fixtures" / "migration_status_per_rule.json", "w"),
+            )
 
-        for r in migration_status['results']:
+        for r in migration_status["results"]:
-            r['detail_url'] = r['detail_url'].replace('http://localhost:8000', s.SERVER_URL)
+            r["detail_url"] = r["detail_url"].replace("http://localhost:8000", s.SERVER_URL)
 
         context.update(**migration_status)
 
-        return render(request, 'migration.html', context)
+        return render(request, "migration.html", context)
 
 
 def migration_detail(request, package_uuid, rule_uuid):
-    current_user = _anonymous_or_real(request)
+    if request.method == "GET":
-
-    if request.method == 'GET':
         context = get_base_context(request)
 
-        p = PackageManager.get_package_by_id(current_user, package_uuid)
+        BBD = Package.objects.get(name="EAWAG-BBD")
-        rule = Rule.objects.get(package=p, uuid=rule_uuid)
+        STRUCTURES = CompoundStructure.objects.filter(compound__package=BBD)
+        rule = Rule.objects.get(package=BBD, uuid=rule_uuid)
+
         bt_rule_name = rule.name
-
+        smirks = rule.smirks
-        data = json.load(gzip.open(s.BASE_DIR / 'fixtures' / 'ambit_rules.json.gz', 'rb'))
-
-        bt_rule = data[bt_rule_name]
-        smirks = bt_rule['smirks']
-
-        results = []
 
         res = True
+        results = []
 
         all_prods = set()
-        for comp, ambit_prod in zip(bt_rule['compounds'], bt_rule['products']):
+        for structure in STRUCTURES:
-            # if comp['smiles'] != 'CC1=C(C(=C(C=N1)CO)C=O)O':
+            ambit_smiles, ambit_errors, rdkit_smiles, rdkit_errors = run_both_engines(
-            #     continue
+                structure.smiles, smirks
-
+            )
-            products = FormatConverter.apply(comp['smiles'], smirks)
-
-            all_rdkit_prods = []
-            for ps in products:
-                for p in ps:
-                    all_rdkit_prods.append(p)
-
-            all_rdkit_prods = list(set(all_rdkit_prods))
-
-            ambit_smiles, ambit_errors = FormatConverter.sanitize_smiles(ambit_prod)
-            rdkit_smiles, rdkit_errors = FormatConverter.sanitize_smiles(all_rdkit_prods)
 
             for x in ambit_smiles:
                 all_prods.add(x)
 
             # TODO mode "intersection"
             # partial_res = (len(set(ambit_smiles).intersection(set(rdkit_smiles))) > 0) or (len(ambit_smiles) == 0)
-            # FAILED (failures=37)
+            # FAILED (failures=18)
 
             # TODO mode = "full ambit"
-            # partial_res = len(set(ambit_smiles).intersection(set(rdkit_smiles))) == len(ambit_smiles)
+            # partial_res = len(set(ambit_smiles).intersection(set(rdkit_smiles))) == len(set(ambit_smiles))
-            # FAILED (failures=46)
+            # FAILED (failures=34)
 
             # TODO mode = "equality"
             partial_res = set(ambit_smiles) == set(rdkit_smiles)
-            # FAILED (failures=69)
+            # FAILED (failures=30)
 
-            #
             if len(ambit_smiles) or len(rdkit_smiles):
                 temp = {
-                    'url': comp['id'],
+                    "url": structure.url,
-                    'id': comp['id'].split('/')[-1],
+                    "id": str(structure.uuid),
-                    'name': comp['name'],
+                    "name": structure.name,
-                    'initial_smiles': comp['smiles'],
+                    "initial_smiles": structure.smiles,
-                    'ambit_smiles': sorted(list(ambit_smiles)),
+                    "ambit_smiles": sorted(list(ambit_smiles)),
-                    'rdkit_smiles': sorted(list(rdkit_smiles)),
+                    "rdkit_smiles": sorted(list(rdkit_smiles)),
-                    'status': set(ambit_smiles) == set(rdkit_smiles),
+                    "status": set(ambit_smiles) == set(rdkit_smiles),
                 }
-
+                detail = f"""
-                if set(ambit_smiles) != set(rdkit_smiles):
-                    detail = f"""
                         BT: {bt_rule_name}
-                        SMIRKS: {bt_rule['smirks']}
+                        SMIRKS: {smirks}
-                        Compound: {comp['smiles']}
+                        Compound: {structure.smiles}
-                        Compound URL: {comp['id']}
+                        Compound URL: {structure.url}
                         Num ambit: {len(set(ambit_smiles))}
                         Num rdkit: {len(set(rdkit_smiles))}
                         Num Intersection A: {len(set(ambit_smiles).intersection(set(rdkit_smiles)))}
@@ -185,15 +205,61 @@ def migration_detail(request, package_uuid, rule_uuid):
                         rdkit_errors: {rdkit_errors}
                     """
 
-                    temp['detail'] = '\n'.join([x.strip() for x in detail.split('\n')])
+                temp["detail"] = "\n".join([x.strip() for x in detail.split("\n")])
-                    # print(detail.strip())
 
                 results.append(temp)
 
             res &= partial_res
 
-        results = sorted(results, key=lambda x: x['status'])
+        results = sorted(results, key=lambda x: x["status"])
-        context['results'] = results
+        context["results"] = results
-        context['res'] = res
+        context["res"] = res
-        context['bt_rule_name'] = bt_rule_name
+        context["bt_rule_name"] = bt_rule_name
-        return render(request, 'migration_detail.html', context)
+        return render(request, "migration_detail.html", context)
+
+
+def compare(request):
+    context = get_base_context(request)
+
+    if request.method == "GET":
+        context["smirks"] = (
+            "[#1,#6:6][#7;X3;!$(NC1CC1)!$([N][C]=O)!$([!#8]CNC=O):1]([#1,#6:7])[#6;A;X4:2][H:3]>>[#1,#6:6][#7;X3:1]([#1,#6:7])[H:3].[#6;A:2]=O"
+        )
+        context["smiles"] = "C(CC(=O)N[C@@H](CS[Se-])C(=O)NCC(=O)[O-])[C@@H](C(=O)[O-])N"
+        return render(request, "compare.html", context)
+
+    elif request.method == "POST":
+        smiles = request.POST.get("smiles")
+        smirks = request.POST.get("smirks")
+
+        from envipy_ambit import apply
+
+        ambit_res = apply(smirks, smiles)
+        ambit_res, _ = FormatConverter.sanitize_smiles([str(x) for x in ambit_res])
+
+        products = FormatConverter.apply(smiles, smirks)
+
+        all_rdkit_prods = []
+        for ps in products:
+            for p in ps:
+                all_rdkit_prods.append(p)
+
+        all_rdkit_prods = list(set(all_rdkit_prods))
+
+        rdkit_res, _ = FormatConverter.sanitize_smiles(all_rdkit_prods)
+        context["result"] = True
+        context["ambit_res"] = sorted(set(ambit_res))
+        context["rdkit_res"] = sorted(set(rdkit_res))
+        context["diff"] = sorted(set(ambit_res).difference(set(rdkit_res)))
+        context["smirks"] = smirks
+        context["smiles"] = smiles
+
+        r = SimpleAmbitRule.objects.filter(smirks=smirks)
+
+        if r.exists():
+            context["rule"] = r.first()
+
+        return render(request, "compare.html", context)
+
+    else:
+        return HttpResponseNotAllowed(["GET", "POST"])

package.json

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

pnpm-lock.yaml

@@ -0,0 +1,740 @@
+lockfileVersion: '9.0'
+
+settings:
+  autoInstallPeers: true
+  excludeLinksFromLockfile: false
+
+importers:
+
+  .:
+    devDependencies:
+      '@tailwindcss/cli':
+        specifier: ^4.1.16
+        version: 4.1.16
+      '@tailwindcss/postcss':
+        specifier: ^4.1.16
+        version: 4.1.16
+      daisyui:
+        specifier: ^5.4.3
+        version: 5.4.3
+      postcss:
+        specifier: ^8.5.6
+        version: 8.5.6
+      prettier:
+        specifier: ^3.6.2
+        version: 3.6.2
+      prettier-plugin-jinja-template:
+        specifier: ^2.1.0
+        version: 2.1.0(prettier@3.6.2)
+      prettier-plugin-tailwindcss:
+        specifier: ^0.7.1
+        version: 0.7.1(prettier@3.6.2)
+      tailwindcss:
+        specifier: ^4.1.16
+        version: 4.1.16
+
+packages:
+
+  '@alloc/quick-lru@5.2.0':
+    resolution: {integrity: sha512-UrcABB+4bUrFABwbluTIBErXwvbsU/V7TZWfmbgJfbkwiBuziS9gxdODUyuiecfdGQ85jglMW6juS3+z5TsKLw==}
+    engines: {node: '>=10'}
+
+  '@jridgewell/gen-mapping@0.3.13':
+    resolution: {integrity: sha512-2kkt/7niJ6MgEPxF0bYdQ6etZaA+fQvDcLKckhy1yIQOzaoKjBBjSj63/aLVjYE3qhRt5dvM+uUyfCg6UKCBbA==}
+
+  '@jridgewell/remapping@2.3.5':
+    resolution: {integrity: sha512-LI9u/+laYG4Ds1TDKSJW2YPrIlcVYOwi2fUC6xB43lueCjgxV4lffOCZCtYFiH6TNOX+tQKXx97T4IKHbhyHEQ==}
+
+  '@jridgewell/resolve-uri@3.1.2':
+    resolution: {integrity: sha512-bRISgCIjP20/tbWSPWMEi54QVPRZExkuD9lJL+UIxUKtwVJA8wW1Trb1jMs1RFXo1CBTNZ/5hpC9QvmKWdopKw==}
+    engines: {node: '>=6.0.0'}
+
+  '@jridgewell/sourcemap-codec@1.5.5':
+    resolution: {integrity: sha512-cYQ9310grqxueWbl+WuIUIaiUaDcj7WOq5fVhEljNVgRfOUhY9fy2zTvfoqWsnebh8Sl70VScFbICvJnLKB0Og==}
+
+  '@jridgewell/trace-mapping@0.3.31':
+    resolution: {integrity: sha512-zzNR+SdQSDJzc8joaeP8QQoCQr8NuYx2dIIytl1QeBEZHJ9uW6hebsrYgbz8hJwUQao3TWCMtmfV8Nu1twOLAw==}
+
+  '@parcel/watcher-android-arm64@2.5.1':
+    resolution: {integrity: sha512-KF8+j9nNbUN8vzOFDpRMsaKBHZ/mcjEjMToVMJOhTozkDonQFFrRcfdLWn6yWKCmJKmdVxSgHiYvTCef4/qcBA==}
+    engines: {node: '>= 10.0.0'}
+    cpu: [arm64]
+    os: [android]
+
+  '@parcel/watcher-darwin-arm64@2.5.1':
+    resolution: {integrity: sha512-eAzPv5osDmZyBhou8PoF4i6RQXAfeKL9tjb3QzYuccXFMQU0ruIc/POh30ePnaOyD1UXdlKguHBmsTs53tVoPw==}
+    engines: {node: '>= 10.0.0'}
+    cpu: [arm64]
+    os: [darwin]
+
+  '@parcel/watcher-darwin-x64@2.5.1':
+    resolution: {integrity: sha512-1ZXDthrnNmwv10A0/3AJNZ9JGlzrF82i3gNQcWOzd7nJ8aj+ILyW1MTxVk35Db0u91oD5Nlk9MBiujMlwmeXZg==}
+    engines: {node: '>= 10.0.0'}
+    cpu: [x64]
+    os: [darwin]
+
+  '@parcel/watcher-freebsd-x64@2.5.1':
+    resolution: {integrity: sha512-SI4eljM7Flp9yPuKi8W0ird8TI/JK6CSxju3NojVI6BjHsTyK7zxA9urjVjEKJ5MBYC+bLmMcbAWlZ+rFkLpJQ==}
+    engines: {node: '>= 10.0.0'}
+    cpu: [x64]
+    os: [freebsd]
+
+  '@parcel/watcher-linux-arm-glibc@2.5.1':
+    resolution: {integrity: sha512-RCdZlEyTs8geyBkkcnPWvtXLY44BCeZKmGYRtSgtwwnHR4dxfHRG3gR99XdMEdQ7KeiDdasJwwvNSF5jKtDwdA==}
+    engines: {node: '>= 10.0.0'}
+    cpu: [arm]
+    os: [linux]
+
+  '@parcel/watcher-linux-arm-musl@2.5.1':
+    resolution: {integrity: sha512-6E+m/Mm1t1yhB8X412stiKFG3XykmgdIOqhjWj+VL8oHkKABfu/gjFj8DvLrYVHSBNC+/u5PeNrujiSQ1zwd1Q==}
+    engines: {node: '>= 10.0.0'}
+    cpu: [arm]
+    os: [linux]
+
+  '@parcel/watcher-linux-arm64-glibc@2.5.1':
+    resolution: {integrity: sha512-LrGp+f02yU3BN9A+DGuY3v3bmnFUggAITBGriZHUREfNEzZh/GO06FF5u2kx8x+GBEUYfyTGamol4j3m9ANe8w==}
+    engines: {node: '>= 10.0.0'}
+    cpu: [arm64]
+    os: [linux]
+
+  '@parcel/watcher-linux-arm64-musl@2.5.1':
+    resolution: {integrity: sha512-cFOjABi92pMYRXS7AcQv9/M1YuKRw8SZniCDw0ssQb/noPkRzA+HBDkwmyOJYp5wXcsTrhxO0zq1U11cK9jsFg==}
+    engines: {node: '>= 10.0.0'}
+    cpu: [arm64]
+    os: [linux]
+
+  '@parcel/watcher-linux-x64-glibc@2.5.1':
+    resolution: {integrity: sha512-GcESn8NZySmfwlTsIur+49yDqSny2IhPeZfXunQi48DMugKeZ7uy1FX83pO0X22sHntJ4Ub+9k34XQCX+oHt2A==}
+    engines: {node: '>= 10.0.0'}
+    cpu: [x64]
+    os: [linux]
+
+  '@parcel/watcher-linux-x64-musl@2.5.1':
+    resolution: {integrity: sha512-n0E2EQbatQ3bXhcH2D1XIAANAcTZkQICBPVaxMeaCVBtOpBZpWJuf7LwyWPSBDITb7In8mqQgJ7gH8CILCURXg==}
+    engines: {node: '>= 10.0.0'}
+    cpu: [x64]
+    os: [linux]
+
+  '@parcel/watcher-win32-arm64@2.5.1':
+    resolution: {integrity: sha512-RFzklRvmc3PkjKjry3hLF9wD7ppR4AKcWNzH7kXR7GUe0Igb3Nz8fyPwtZCSquGrhU5HhUNDr/mKBqj7tqA2Vw==}
+    engines: {node: '>= 10.0.0'}
+    cpu: [arm64]
+    os: [win32]
+
+  '@parcel/watcher-win32-ia32@2.5.1':
+    resolution: {integrity: sha512-c2KkcVN+NJmuA7CGlaGD1qJh1cLfDnQsHjE89E60vUEMlqduHGCdCLJCID5geFVM0dOtA3ZiIO8BoEQmzQVfpQ==}
+    engines: {node: '>= 10.0.0'}
+    cpu: [ia32]
+    os: [win32]
+
+  '@parcel/watcher-win32-x64@2.5.1':
+    resolution: {integrity: sha512-9lHBdJITeNR++EvSQVUcaZoWupyHfXe1jZvGZ06O/5MflPcuPLtEphScIBL+AiCWBO46tDSHzWyD0uDmmZqsgA==}
+    engines: {node: '>= 10.0.0'}
+    cpu: [x64]
+    os: [win32]
+
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+    optional: true
+
+  '@parcel/watcher-win32-x64@2.5.1':
+    optional: true
+
+  '@parcel/watcher@2.5.1':
+    dependencies:
+      detect-libc: 1.0.3
+      is-glob: 4.0.3
+      micromatch: 4.0.8
+      node-addon-api: 7.1.1
+    optionalDependencies:
+      '@parcel/watcher-android-arm64': 2.5.1
+      '@parcel/watcher-darwin-arm64': 2.5.1
+      '@parcel/watcher-darwin-x64': 2.5.1
+      '@parcel/watcher-freebsd-x64': 2.5.1
+      '@parcel/watcher-linux-arm-glibc': 2.5.1
+      '@parcel/watcher-linux-arm-musl': 2.5.1
+      '@parcel/watcher-linux-arm64-glibc': 2.5.1
+      '@parcel/watcher-linux-arm64-musl': 2.5.1
+      '@parcel/watcher-linux-x64-glibc': 2.5.1
+      '@parcel/watcher-linux-x64-musl': 2.5.1
+      '@parcel/watcher-win32-arm64': 2.5.1
+      '@parcel/watcher-win32-ia32': 2.5.1
+      '@parcel/watcher-win32-x64': 2.5.1
+
+  '@tailwindcss/cli@4.1.16':
+    dependencies:
+      '@parcel/watcher': 2.5.1
+      '@tailwindcss/node': 4.1.16
+      '@tailwindcss/oxide': 4.1.16
+      enhanced-resolve: 5.18.3
+      mri: 1.2.0
+      picocolors: 1.1.1
+      tailwindcss: 4.1.16
+
+  '@tailwindcss/node@4.1.16':
+    dependencies:
+      '@jridgewell/remapping': 2.3.5
+      enhanced-resolve: 5.18.3
+      jiti: 2.6.1
+      lightningcss: 1.30.2
+      magic-string: 0.30.21
+      source-map-js: 1.2.1
+      tailwindcss: 4.1.16
+
+  '@tailwindcss/oxide-android-arm64@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-darwin-arm64@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-darwin-x64@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-freebsd-x64@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-linux-arm-gnueabihf@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-linux-arm64-gnu@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-linux-arm64-musl@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-linux-x64-gnu@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-linux-x64-musl@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-wasm32-wasi@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-win32-arm64-msvc@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide-win32-x64-msvc@4.1.16':
+    optional: true
+
+  '@tailwindcss/oxide@4.1.16':
+    optionalDependencies:
+      '@tailwindcss/oxide-android-arm64': 4.1.16
+      '@tailwindcss/oxide-darwin-arm64': 4.1.16
+      '@tailwindcss/oxide-darwin-x64': 4.1.16
+      '@tailwindcss/oxide-freebsd-x64': 4.1.16
+      '@tailwindcss/oxide-linux-arm-gnueabihf': 4.1.16
+      '@tailwindcss/oxide-linux-arm64-gnu': 4.1.16
+      '@tailwindcss/oxide-linux-arm64-musl': 4.1.16
+      '@tailwindcss/oxide-linux-x64-gnu': 4.1.16
+      '@tailwindcss/oxide-linux-x64-musl': 4.1.16
+      '@tailwindcss/oxide-wasm32-wasi': 4.1.16
+      '@tailwindcss/oxide-win32-arm64-msvc': 4.1.16
+      '@tailwindcss/oxide-win32-x64-msvc': 4.1.16
+
+  '@tailwindcss/postcss@4.1.16':
+    dependencies:
+      '@alloc/quick-lru': 5.2.0
+      '@tailwindcss/node': 4.1.16
+      '@tailwindcss/oxide': 4.1.16
+      postcss: 8.5.6
+      tailwindcss: 4.1.16
+
+  braces@3.0.3:
+    dependencies:
+      fill-range: 7.1.1
+
+  daisyui@5.4.3: {}
+
+  detect-libc@1.0.3: {}
+
+  detect-libc@2.1.2: {}
+
+  enhanced-resolve@5.18.3:
+    dependencies:
+      graceful-fs: 4.2.11
+      tapable: 2.3.0
+
+  fill-range@7.1.1:
+    dependencies:
+      to-regex-range: 5.0.1
+
+  graceful-fs@4.2.11: {}
+
+  is-extglob@2.1.1: {}
+
+  is-glob@4.0.3:
+    dependencies:
+      is-extglob: 2.1.1
+
+  is-number@7.0.0: {}
+
+  jiti@2.6.1: {}
+
+  lightningcss-android-arm64@1.30.2:
+    optional: true
+
+  lightningcss-darwin-arm64@1.30.2:
+    optional: true
+
+  lightningcss-darwin-x64@1.30.2:
+    optional: true
+
+  lightningcss-freebsd-x64@1.30.2:
+    optional: true
+
+  lightningcss-linux-arm-gnueabihf@1.30.2:
+    optional: true
+
+  lightningcss-linux-arm64-gnu@1.30.2:
+    optional: true
+
+  lightningcss-linux-arm64-musl@1.30.2:
+    optional: true
+
+  lightningcss-linux-x64-gnu@1.30.2:
+    optional: true
+
+  lightningcss-linux-x64-musl@1.30.2:
+    optional: true
+
+  lightningcss-win32-arm64-msvc@1.30.2:
+    optional: true
+
+  lightningcss-win32-x64-msvc@1.30.2:
+    optional: true
+
+  lightningcss@1.30.2:
+    dependencies:
+      detect-libc: 2.1.2
+    optionalDependencies:
+      lightningcss-android-arm64: 1.30.2
+      lightningcss-darwin-arm64: 1.30.2
+      lightningcss-darwin-x64: 1.30.2
+      lightningcss-freebsd-x64: 1.30.2
+      lightningcss-linux-arm-gnueabihf: 1.30.2
+      lightningcss-linux-arm64-gnu: 1.30.2
+      lightningcss-linux-arm64-musl: 1.30.2
+      lightningcss-linux-x64-gnu: 1.30.2
+      lightningcss-linux-x64-musl: 1.30.2
+      lightningcss-win32-arm64-msvc: 1.30.2
+      lightningcss-win32-x64-msvc: 1.30.2
+
+  magic-string@0.30.21:
+    dependencies:
+      '@jridgewell/sourcemap-codec': 1.5.5
+
+  micromatch@4.0.8:
+    dependencies:
+      braces: 3.0.3
+      picomatch: 2.3.1
+
+  mri@1.2.0: {}
+
+  nanoid@3.3.11: {}
+
+  node-addon-api@7.1.1: {}
+
+  picocolors@1.1.1: {}
+
+  picomatch@2.3.1: {}
+
+  postcss@8.5.6:
+    dependencies:
+      nanoid: 3.3.11
+      picocolors: 1.1.1
+      source-map-js: 1.2.1
+
+  prettier-plugin-jinja-template@2.1.0(prettier@3.6.2):
+    dependencies:
+      prettier: 3.6.2
+
+  prettier-plugin-tailwindcss@0.7.1(prettier@3.6.2):
+    dependencies:
+      prettier: 3.6.2
+
+  prettier@3.6.2: {}
+
+  source-map-js@1.2.1: {}
+
+  tailwindcss@4.1.16: {}
+
+  tapable@2.3.0: {}
+
+  to-regex-range@5.0.1:
+    dependencies:
+      is-number: 7.0.0

pyproject.toml

@@ -3,18 +3,19 @@ name = "envipy"
 version = "0.1.0"
 description = "Add your description here"
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.12"
 dependencies = [
     "celery>=5.5.2",
     "django>=5.2.1",
     "django-extensions>=4.1",
     "django-model-utils>=5.0.0",
-    "django-ninja>=1.4.1",
+    "django-ninja>=1.4.5",
+    "django-ninja-extra>=0.30.6",
     "django-oauth-toolkit>=3.0.1",
     "django-polymorphic>=4.1.0",
-    "django-stubs>=5.2.4",
     "enviformer",
     "envipy-additional-information",
+    "envipy-ambit>=0.1.0",
     "envipy-plugins",
     "epam-indigo>=1.30.1",
     "gunicorn>=23.0.0",
@@ -27,12 +28,117 @@ dependencies = [
     "scikit-learn>=1.6.1",
     "sentry-sdk[django]>=2.32.0",
     "setuptools>=80.8.0",
+    "nh3==0.3.2",
+    "polars==1.35.1",
 ]
 
 [tool.uv.sources]
-enviformer = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git", rev = "v0.1.0" }
+enviformer = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git", rev = "v0.1.4" }
 envipy-plugins = { git = "ssh://git@git.envipath.com/enviPath/enviPy-plugins.git", rev = "v0.1.0" }
-envipy-additional-information = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git", rev = "v0.1.4"}
+envipy-additional-information = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git", rev = "v0.1.7" }
+envipy-ambit = { git = "ssh://git@git.envipath.com/enviPath/enviPy-ambit.git" }
 
 [project.optional-dependencies]
 ms-login = ["msal>=1.33.0"]
+dev = [
+    "celery-stubs==0.1.3",
+    "django-stubs>=5.2.4",
+    "poethepoet>=0.37.0",
+    "pre-commit>=4.3.0",
+    "ruff>=0.13.3",
+    "pytest-playwright>=0.7.1",
+    "pytest-django>=4.11.1",
+    "pytest-cov>=7.0.0",
+]
+
+[tool.ruff]
+line-length = 100
+
+[tool.ruff.lint]
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[tool.ruff.format]
+docstring-code-format = true
+
+# 4. Ignore `E402` (import violations) in all `__init__.py` files, and in selected subdirectories.
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["E402"]
+"**/{tests,docs,tools}/*" = ["E402"]
+
+[tool.poe.tasks]
+# Main tasks
+setup = { sequence = [
+    "db-up",
+    "migrate",
+    "bootstrap",
+], help = "Complete setup: start database, run migrations, and bootstrap data" }
+dev = { cmd = "uv run python scripts/dev_server.py", help = "Start the development server with CSS watcher", deps = [
+    "db-up",
+    "js-deps",
+] }
+build = { sequence = [
+    "build-frontend",
+    "collectstatic",
+], help = "Build frontend assets and collect static files" }
+
+# Database tasks
+db-up = { cmd = "docker compose -f docker-compose.dev.yml up -d", help = "Start PostgreSQL database using Docker Compose" }
+db-down = { cmd = "docker compose -f docker-compose.dev.yml down", help = "Stop PostgreSQL database" }
+
+# Frontend tasks
+js-deps = { cmd = "uv run python scripts/pnpm_wrapper.py install", help = "Install frontend dependencies" }
+
+# Full cleanup tasks
+clean = { sequence = [
+    "clean-db",
+], help = "Remove model files and database volumes (WARNING: destroys all data!)" }
+clean-db = { cmd = "docker compose -f docker-compose.dev.yml down -v", help = "Removes the database container and volume." }
+
+# Django tasks
+migrate = { cmd = "uv run python manage.py migrate", help = "Run database migrations" }
+bootstrap = { shell = """
+echo "Bootstrapping initial data..."
+echo "This will take a bit ⏱️. Get yourself some coffee..."
+uv run python manage.py bootstrap
+echo "✓ Bootstrap complete"
+echo ""
+echo "Default admin credentials:"
+echo "  Username: admin"
+echo "  Email: admin@envipath.com"
+echo "  Password: SuperSafe"
+""", help = "Bootstrap initial data (anonymous user, packages, models)" }
+shell = { cmd = "uv run python manage.py shell", help = "Open Django shell" }
+
+
+build-frontend = { cmd = "uv run python scripts/pnpm_wrapper.py run build", help = "Build frontend assets using pnpm", deps = [
+    "js-deps",
+] } # Build tasks
+
+
+collectstatic = { cmd = "uv run python manage.py collectstatic --noinput", help = "Collect static files for production", deps = [
+    "build-frontend",
+] }
+
+frontend-test-setup = { cmd = "playwright install", help = "Install the browsers required for frontend testing" }
+
+[tool.pytest.ini_options]
+addopts = "--verbose --capture=no --durations=10"
+testpaths = ["tests", "*/tests"]
+pythonpath = ["."]
+norecursedirs = [
+    "env",
+    "venv",
+    "envipy-plugins",
+    "envipy-additional-information",
+    "envipy-ambit",
+    "enviformer",
+]
+markers = [
+    "api: API tests",
+    "frontend: Frontend tests",
+    "end2end: End-to-end tests",
+    "slow: Slow tests",
+]

scripts/dev_server.py

@@ -0,0 +1,201 @@
+#!/usr/bin/env python3
+"""
+Cross-platform development server script.
+Starts pnpm CSS watcher and Django dev server, handling cleanup on exit.
+Works on both Windows and Unix systems.
+"""
+
+import atexit
+import shutil
+import signal
+import subprocess
+import sys
+import time
+
+
+def find_pnpm():
+    """
+    Find pnpm executable on the system.
+    Returns the path to pnpm or None if not found.
+    """
+    # Try to find pnpm using shutil.which
+    # On Windows, this will find pnpm.cmd if it's in PATH
+    pnpm_path = shutil.which("pnpm")
+
+    if pnpm_path:
+        return pnpm_path
+
+    # On Windows, also try pnpm.cmd explicitly
+    if sys.platform == "win32":
+        pnpm_cmd = shutil.which("pnpm.cmd")
+        if pnpm_cmd:
+            return pnpm_cmd
+
+    return None
+
+
+class DevServerManager:
+    """Manages background processes for development server."""
+
+    def __init__(self):
+        self.processes = []
+        self._cleanup_registered = False
+
+    def start_process(self, command, description, shell=False):
+        """Start a background process and return the process object."""
+        print(f"Starting {description}...")
+        try:
+            if shell:
+                # Use shell=True for commands that need shell interpretation
+                process = subprocess.Popen(
+                    command,
+                    shell=True,
+                    stdout=subprocess.PIPE,
+                    stderr=subprocess.STDOUT,
+                    text=True,
+                    bufsize=1,
+                )
+            else:
+                # Split command into list for subprocess
+                process = subprocess.Popen(
+                    command,
+                    stdout=subprocess.PIPE,
+                    stderr=subprocess.STDOUT,
+                    text=True,
+                    bufsize=1,
+                )
+            self.processes.append((process, description))
+            print(f"✓ Started {description} (PID: {process.pid})")
+            return process
+        except Exception as e:
+            print(f"✗ Failed to start {description}: {e}", file=sys.stderr)
+            self.cleanup()
+            sys.exit(1)
+
+    def cleanup(self):
+        """Terminate all running processes."""
+        if not self.processes:
+            return
+
+        print("\nShutting down...")
+        for process, description in self.processes:
+            if process.poll() is None:  # Process is still running
+                try:
+                    # Try graceful termination first
+                    if sys.platform == "win32":
+                        process.terminate()
+                    else:
+                        process.send_signal(signal.SIGTERM)
+
+                    # Wait up to 5 seconds for graceful shutdown
+                    try:
+                        process.wait(timeout=5)
+                    except subprocess.TimeoutExpired:
+                        # Force kill if graceful shutdown failed
+                        if sys.platform == "win32":
+                            process.kill()
+                        else:
+                            process.send_signal(signal.SIGKILL)
+                        process.wait()
+
+                    print(f"✓ {description} stopped")
+                except Exception as e:
+                    print(f"✗ Error stopping {description}: {e}", file=sys.stderr)
+
+        self.processes.clear()
+
+    def register_cleanup(self):
+        """Register cleanup handlers for various exit scenarios."""
+        if self._cleanup_registered:
+            return
+
+        self._cleanup_registered = True
+
+        # Register atexit handler (works on all platforms)
+        atexit.register(self.cleanup)
+
+        # Register signal handlers (Unix only)
+        if sys.platform != "win32":
+            signal.signal(signal.SIGINT, self._signal_handler)
+            signal.signal(signal.SIGTERM, self._signal_handler)
+
+    def _signal_handler(self, signum, frame):
+        """Handle Unix signals."""
+        self.cleanup()
+        sys.exit(0)
+
+    def wait_for_process(self, process, description):
+        """Wait for a process to finish and handle its output."""
+        try:
+            # Stream output from the process
+            for line in iter(process.stdout.readline, ""):
+                if line:
+                    print(f"[{description}] {line.rstrip()}")
+
+            process.wait()
+            return process.returncode
+        except KeyboardInterrupt:
+            # Handle Ctrl+C
+            self.cleanup()
+            sys.exit(0)
+        except Exception as e:
+            print(f"Error waiting for {description}: {e}", file=sys.stderr)
+            self.cleanup()
+            sys.exit(1)
+
+
+def main():
+    """Main entry point."""
+    manager = DevServerManager()
+    manager.register_cleanup()
+
+    # Find pnpm executable
+    pnpm_path = find_pnpm()
+    if not pnpm_path:
+        print("Error: pnpm not found in PATH.", file=sys.stderr)
+        print("\nPlease install pnpm:", file=sys.stderr)
+        print("  Windows: https://pnpm.io/installation#on-windows", file=sys.stderr)
+        print("  Unix: https://pnpm.io/installation#on-posix-systems", file=sys.stderr)
+        sys.exit(1)
+
+    # Determine shell usage based on platform
+    use_shell = sys.platform == "win32"
+
+    # Start pnpm CSS watcher
+    # Use the found pnpm path to ensure it works on Windows
+    pnpm_command = f'"{pnpm_path}" run dev' if use_shell else [pnpm_path, "run", "dev"]
+    manager.start_process(
+        pnpm_command,
+        "CSS watcher",
+        shell=use_shell,
+    )
+
+    # Give pnpm a moment to start
+    time.sleep(1)
+
+    # Start Django dev server
+    django_process = manager.start_process(
+        ["uv", "run", "python", "manage.py", "runserver"],
+        "Django server",
+        shell=False,
+    )
+
+    print("\nDevelopment servers are running. Press Ctrl+C to stop.\n")
+
+    try:
+        # Wait for Django server (main process)
+        # If Django exits, we should clean up everything
+        return_code = manager.wait_for_process(django_process, "Django")
+
+        # If Django exited unexpectedly, clean up and exit
+        if return_code != 0:
+            manager.cleanup()
+            sys.exit(return_code)
+    except KeyboardInterrupt:
+        # Ctrl+C was pressed
+        manager.cleanup()
+        sys.exit(0)
+
+
+if __name__ == "__main__":
+    main()

scripts/pnpm_wrapper.py

@@ -0,0 +1,59 @@
+#!/usr/bin/env python3
+"""
+Cross-platform pnpm command wrapper.
+Finds pnpm correctly on Windows (handles pnpm.cmd) and Unix systems.
+"""
+
+import shutil
+import subprocess
+import sys
+
+
+def find_pnpm():
+    """
+    Find pnpm executable on the system.
+    Returns the path to pnpm or None if not found.
+    """
+    # Try to find pnpm using shutil.which
+    # On Windows, this will find pnpm.cmd if it's in PATH
+    pnpm_path = shutil.which("pnpm")
+
+    if pnpm_path:
+        return pnpm_path
+
+    # On Windows, also try pnpm.cmd explicitly
+    if sys.platform == "win32":
+        pnpm_cmd = shutil.which("pnpm.cmd")
+        if pnpm_cmd:
+            return pnpm_cmd
+
+    return None
+
+
+def main():
+    """Main entry point - execute pnpm with provided arguments."""
+    pnpm_path = find_pnpm()
+
+    if not pnpm_path:
+        print("Error: pnpm not found in PATH.", file=sys.stderr)
+        print("\nPlease install pnpm:", file=sys.stderr)
+        print("  Windows: https://pnpm.io/installation#on-windows", file=sys.stderr)
+        print("  Unix: https://pnpm.io/installation#on-posix-systems", file=sys.stderr)
+        sys.exit(1)
+
+    # Get all arguments passed to this script
+    args = sys.argv[1:]
+
+    # Execute pnpm with the provided arguments
+    try:
+        sys.exit(subprocess.call([pnpm_path] + args))
+    except KeyboardInterrupt:
+        # Handle Ctrl+C gracefully
+        sys.exit(130)
+    except Exception as e:
+        print(f"Error executing pnpm: {e}", file=sys.stderr)
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    main()

static/css/daisyui-theme.css

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

static/css/input.css

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

static/css/theme.css

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

static/images/logo-long.svg

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