Pronto!

InterPro curation system

Pronto is a web application aiming to assist InterPro curators in creating/editing InterPro entries.

Getting started

Prerequisites

• Python>=3.11 with oracledb, Flask, mysqlclient, and psycopg.
• A public database link to the LITPUB database (literature service) must exist.
• Several PRONTO_* tables must exist in Oracle, see SCHEMA.md.

Installation

Deploy the code locally:

git clone https://github.com/ProteinsWebTeam/pronto.git
cd pronto
pip install .

Configuration

Create a copy of config.cfg (e.g. config.local.cfg), and set the following options:

• ORACLE_IP - Connection string for InterPro production Oracle database.
• ORACLE_GOA - Connection string for GOA production Oracle database.
• MYSQL - Connection string for InterPro7 MySQL database.
• POSTGRESQL - Connection string for Pronto PostgreSQL database.
• SECRET_KEY - key used to sign cookies (prevent forgery).

Format for connection strings: <user>/<password>@<host>:<port>/<schema>.

Generate secret key

Run the following command, then copy the printed string and paste it into the config file.

python -c "import os; print(os.urandom(16).hex())"

Usage

Pronto relies on the file the PRONTO_CONFIG environment variable points to. On Linux or OS X, you can set this environment variable with:

export PRONTO_CONFIG=/path/to/config/file

Built-in server

Easy to use and convenient for development, but not suitable for production.

export FLASK_APP=pronto
export FLASK_ENV=development
flask run

Gunicorn

After installing Gunicorn, run the command below to start Pronto with four worker processes:

gunicorn -w 4 -b 127.0.0.1:5000 pronto:app

To accept connections from all your network (i.e. not only your local machine), and detach the server from the terminal:

gunicorn --daemon -w 4 -b 0.0.0.0:5000 pronto:app
# To kill the process:
# kill `ps aux |grep gunicorn | grep pronto | awk '{print $2}'`