Mobility Web App – Flask Backend API

This is the backend Flask API for the DOM Mobility project developed by Ulysses Echeverria. It enables users to query and visualize data stored in a PostgreSQL database (domdb). The application provides a search interface to filter mobility-related chemical compound records and allows viewing corresponding fragment data via hyperlinks.

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🚀 Features

• Filter mobility data by:
  • mz_exp (experimental m/z value)
  • mz_calc (calculated m/z value)
  • mz_error_ppm (parts-per-million error)
  • chem_formula
  • origin
• Clickable mz_exp values that link to matching fragment records
• Clean tabular HTML display for both mobility and fragment data
• Structured Python code with inline documentation
• Flask-based web server running locally

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🧐 Author Notes

This code is written with clarity and future collaboration in mind. Each component of the code is documented to ensure maintainability. The application is designed to be easily integrated with a frontend component or extended for research workflows.

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🛠️ Setup Instructions

🔧 Step 1: Clone the Repository

Open a terminal and clone the GitHub repository:

git clone https://github.com/pcdslab/mobility-web-app.git
cd mobility-web-app

🐍 Step 2: Create and Activate a Virtual Environment (Optional but Recommended)

python3 -m venv venv
source venv/bin/activate

If you're using Windows:

venv\Scripts\activate

📦 Step 3: Install Python Dependencies

Install the required libraries:

pip install -r requirements.txt

If requirements.txt is missing, you can create it manually:

pip install Flask psycopg2
pip freeze > requirements.txt

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🗄️ PostgreSQL Configuration

Ensure your PostgreSQL database is accessible with the following settings:

• Host: localhost
• Port: 5433
• Database: domdb
• User: domuser
• Password: Password

These values are defined in app.py:

DB_CONFIG = {
    'host': 'localhost',
    'port': 5433,
    'dbname': 'domdb',
    'user': 'domuser',
    'password': 'Password'
}

Ensure PostgreSQL is running and listening on port 5433, and the mobility_data and fragments_data tables are properly loaded.

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▶️ Running the Flask App

From the root of the repository:

python app.py

You should see an output like:

Running on http://127.0.0.1:8000

Now open your browser to:

http://127.0.0.1:8000/filter

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🔗 Example Usage

1. Access /filter endpoint.
2. Provide values for mz_exp, chem_formula, and/or other filters.
3. Submit the form to see matching mobility records.
4. Click on a mz_exp value to view corresponding fragment records.

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🤝 Contributing

This backend is part of a collaborative project. The frontend integration is managed by other team members. If you're extending the backend, feel free to open an issue or pull request.

To contribute:

git checkout -b feature-name
# Make your changes
# Commit and push

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📚 License

MIT License.

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