CONTRABASS RESTful API

CONTRABASS RESTful API is a python asynchronous-tasks-based RESTful API intended for the computation and analysis of vulnerabilities in genome-scale metabolic models. These webservices are just a backend of CONTRABASS python tool.

Table of Contents

• License
• Requirements
• Install dependencies
• Run
• Run with docker-compose
• Test
• Deployment
  • Run
  • Run with supervisor
• Deployment with docker
• Maintainers

License

CONTRABASS-webservice is released under GPLv3 license.

Requirements

• Python>=3.7
• Redis
• MySQL
• GLPK (recommended)

Install dependencies

pip install -r requirements.txt

or

python3 -m pip install -r requirements.txt

Run

1. Change Redis and MySQL params on .env.
2. Run celery worker

   celery -A src.restapi.celery_app.celery_app worker --loglevel=debug
   

3. Run flower

   celery flower -A src.restapi.celery_app.celery_app -port=5555
   

4. Run Flask application

   python -m src.restapi.app
   

See:

• Swagger-UI API interface

  • http://127.0.0.1:5000/apidocs

• Flower management page

  • http://localhost:5555

Run with docker-compose

First setup variables on .docker.env. Assuming you have Docker and docker-compose installed, run on terminal:

docker-compose up

In order to bring it down run:

docker-compose down

Test

pytest -v

Deployment

Requirements

• Python>=3.7
• Redis
• MySQL
• GLPK (recommended)
• Gunicorn (recommended).
  • See Deploying Flask applications
• Nginx (recommended).
  • See Nginx gunicorn config
• Supervisor (optional, recommended)

Run

1. Change Redis and MySQL params on .env.
2. Run celery worker

   celery -A src.restapi.celery_app.celery_app worker --loglevel=info --concurrency=1 &> logs/celery.out
   

3. Run flower

   celery flower -A src.restapi.celery_app.celery_app -port=5555
   

4. Run Gunicorn app with unix socket bind and eventlet workers (See Flask-socketIO Deploy)

   gunicorn --worker-class eventlet -w 1 --bind unix:/tmp/gunicorn.sock src.restapi.wsgi:app
   

5. Setup and run Nginx according to:
   1. Gunicorn Nginx deployment
   2. Flask-SocketIO deployment
   3. Flask-SocketIO Using nginx as a Websocket Reverse Proxy

Run with supervisor (recommended)

"Supervisor is a client/server system that allows its users to monitor and control a number of processes on UNIX-like operating systems."

"The server piece of supervisor is named supervisord. It is responsible for starting child programs at its own invocation, responding to commands from clients, restarting crashed or exited subprocesseses, logging its subprocess stdout and stderr output, and generating and handling 'events' ". [Source]

To run CONTRABASS-webservice with Supervisor:

1. Change Redis and MySQL params on .env.
   1. Note: Redis can also be run with Supervisor.
2. Change the parameters on supervisor/dev/* config files accordingly.
3. Run celery, flower and Gunicorn with supervisor:

   cd supervisor/dev/
   supervisord -c supervisor.conf

   supervisorctl can be executed with:

   supervisorctl -s unix:///tmp/supervisor.sock
   

4. Setup and run Nginx as described previously.

For more info see:

• Supervisor Configuration file.
• Celery GitHub page: Supervisor example config file.

Deployment with docker

Requirements

• Docker
• docker-compose

Run

See section Run with docker-compose

Maintainers

@alexOarga