Molgenis Python Auth Client

A lightweight Python client for performing OAuth 2.0 Device Authorization Flow with the Molgenis Authentication Server. This package allows you to authenticate users either:

• ✔ From the command line (CLI), or
• ✔ Programmatically in your own Python project

It opens the user's browser, waits for authorization, and returns the OAuth token payload when authentication is complete.

✨ Features

• 🔐 Implements OAuth 2.0 Device Flow
• 🌐 Automatic OpenID Connect discovery
• 🧭 Simple command-line interface (molgenis-auth)
• 🐍 Clean Python API for integration in your application
• 🕒 Handles authorization_pending, slow_down, and timeout conditions

📦 Installation

Install from source / local checkout

git clone https://github.com/YOURNAME/MolgenisPythonAuth.git
cd MolgenisPythonAuth
pip install -e .

The -e flag installs in editable mode for development.

🖥️ Command-Line Usage

After installation, the CLI tool molgenis-auth becomes available.

Authenticate using the Molgenis Auth Server

molgenis-auth \
    --auth-server https://auth.molgenis.org \
    --client-id YOUR_CLIENT_ID \
    --scopes "openid offline_access"

What the CLI does

1. Discovers OpenID configuration
2. Requests a device authorization code
3. Opens your browser
4. Waits until you authenticate
5. Prints the OAuth token response JSON

Example output:

{
    "access_token": "eyJhbGciOiJIUz...",
    "expires_in": 3600,
    "refresh_token": "def50200a4...",
    "scope": "openid offline_access",
    "token_type": "Bearer"
}

🐍 Python API Usage

Import the client and call device_flow_auth():

from molgenis_auth import MolgenisAuthClient

client = MolgenisAuthClient(
    auth_server="https://auth.molgenis.org",
    client_id="YOUR_CLIENT_ID",
    scopes="openid offline_access",
)

tokens = client.device_flow_auth()
print(tokens)

What the Python API does

1. Performs discovery via .well-known/openid-configuration
2. Requests the device code
3. Opens a browser window for login
4. Polls until authorization or timeout
5. Returns the final OAuth token JSON

All error conditions (timeouts, unsupported operations, invalid credentials) raise informative Python exceptions.

📁 Project Structure

molgenis_auth/
    cli.py
    client.py
    __init__.py
setup.py
README.md

🛠 Development Setup

Create a virtual environment:

python3 -m venv venv
source venv/bin/activate
pip install -e .

Run the CLI:

molgenis-auth --help

📄 License

GNU General Public License — Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.

🤝 Contributing

Pull requests are welcome! If you have feature ideas (saving tokens locally, adding a refresh endpoint, integrating with Molgenis APIs), open an issue.

💬 Support

If you have questions or run into issues, please open a GitHub issue in the repository.