RetroMol-GUI

Graphical user interface for trying out RetroMol.

This repository contains both a production-ready Docker setup and a developer-friendly local workflow.

Build and run with Docker

The default setup runs everything containerized:

• Builds and serves the frontend React app behind nginx
• Runs the Flask backend with gunicorn
• Runs PostgreSQL and initializes it from a dump file
• Exposes a read-only DB user for the backend

---

Start the full stack

First make sure to copy .env.example to .env and adjust any environment variables as needed.

Then run:

docker compose up -d --build

Access the application

• App UI: http://<server-ip>/**
• API endpoints: http://<server-ip>/api/...**

For local user, <server-ip> is typically localhost:4005.

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Database persistence

Postgres persists data inside the named Docker volume db_data.

Existing volumes can be listed with:

docker volume ls

To remove the volume (and all data inside), run:

docker volume rm <volume_name>

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Re-seed the database

Postgres will initialize once from the dump file specified in .env (make sure to copy .env.example to .env and edit before first build).

To re-seed the database:

docker compose down -v  # destroys db_data volume
docker compose up -d --build

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Check container health

Check that the backend and database are reachable through the API:

curl -i http://<server-ip>/api/health  # should return 200 OK (backend alive)
curl -i http://<server-ip>/api/ready  # should return 200 OK (DB connection OK)

For local runs, use:

curl -i http://localhost:4005/api/health  # should return 200 OK (backend alive)
curl -i http://localhost:4005/api/ready  # should return 200 OK (DB connection OK)

Make sure scripts in /db/init are executable before first build:

chmod +x db/init/*.sh

---

Local development mode

You can develop with hot-reloading for both backend and frontend, while still using the database from Docker.

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Start only the database (in Docker)

Expose Postgres to your host for local development:

docker compose -f docker-compose.yml -f docker-compose.dev.yml up -d db

This keeps the database running at:

Host: localhost
Port: 5432
User: app_ro
Password: apppass_ro
DB name: bionexus

---

Run the backend locally

First create a virtual environment and install backend dependencies listed in src/server/requirements.txt.

Then, run the helper script:

./scripts/dev_backend.sh

This script:

• Sets up DB connection variables
• Runs Flask in debug mode with auto-reload on port 4000

Verify health endpoint to check backend is running:

curl -i http://localhost:4000/api/health

---

Run the frontend locally

From the React client directory src/client, install dependencies and start the development server:

cd src/client
npm install
npm start

Ensure the package.json has the proxy set to the backend URL:

{
    "proxy": "http://localhost:4000"
}

Requests to /api/... will automatically proxy to Flask.