BarleyNet REST-like API

BarleyNet API is processed under Flask (simple web framework) and Redis (in-memory data structure store).

Requirement

• Redis 4 or higher
• Python 3.x
  • Python packages : Flask, redis, scipy, statsmodels

Installation of API

1. Get API and data files

$ git clone https://github.com/netbiolab/BarleyNet
$ cd BarleyNet

2. Setup environment

You can use Anaconda (distribution of Python and R with simplifying managing their packages) or Python's virtualenv

2.1. Installation using conda (Anaconda or Miniconda)

Create an conda environment with installing packages

(base) $ conda create -n barleynet-env python=3 redis=4 flask redis-py scipy statsmodels -y
(base) $ conda activate barleynet-env

2.2. Installation using virtualenv

If you are not using conda, you may use virtualenv to create an environment and to install packages.

# for ubuntu linux
sudo apt install python3-virtualenv python3-dev

Run the commands below step-by-step or run install.sh file.

• Preparing an virtual environment

   $ virtualenv -p $(which python3) barleynet-env
  

• Installation of python packages from PyPI repository.

   $ source barleynet-env/bin/activate
   (barleynet-env) $ pip install Flask redis scipy statsmodels
  

• Installation of Redis
  • Compiling Redis

     (barleynet-env) $ wget http://download.redis.io/releases/redis-4.0.14.tar.gz
     (barleynet-env) $ tar xzf redis-4.0.14.tar.gz
     (barleynet-env) $ cd redis-4.0.14
     (barleynet-env) $ make
     (barleynet-env) $ cp src/redis-server src/redis-cli ${VIRTUAL_ENV}/bin
     (barleynet-env) $ cd ..

  • Or you can install Redis via package managers such as apt, yum, dnf.

     # for Ubuntu or Debian linux
     $ sudo apt install redis-server

Running Redis

(barleynet-env) $ cd data/redis
(barleynet-env) $ gunzip dump.rdb.gz
(barleynet-env) $ redis-server redis.conf

Redis server will run on the default port 6379. You can change the port number in redis.conf file.

Running API

Open the git directory in another shell prompt.

(barleynet-env) cd barleynet-api
(barleynet-env) export FLASK_ENV=development    # run the Flask app in development mode
(barleynet-env) python wsgi.py
 * Serving Flask app "api" (lazy loading)
 * Environment: development
 * Debug mode: on
 * Running on http://127.0.0.1:5000/ (Press CTRL+C to quit)
 * Restarting with stat
 * Debugger is active!
 * Debugger PIN: 118-953-618

Now API is running.

Check REDIS_SERVER variable on config.py if you changed the redis port number.

Using API

The API help page is available in http://127.0.0.1:5000/help. You can test it through API clients such as Postman.

Citation

Lee, S. , Lee, T. , Yang, S. , and Lee, I. (2019). BarleyNet: a network-based functional omics analysis server for cultivated barley, Hordeum vulgare L. Manuscript submitted for publication.