scREAD-backend

This is the API server for scREAD. Ther server builds on top of Koa.js and connects to a MYSQL database. The server is developed by Bioinformatics and Mathematical Biosciences Lab (BMBL)

For new users

You can directly use the scREAD backend api service from a public URL: https://bmbls.bmi.osumc.edu/api/scread.

Example APIs

# List all datasets
https://bmbls.bmi.osumc.edu/api/scread/dataset

# Search differentially expressed genes, e.g. GAD1 gene.
https://bmbls.bmi.osumc.edu/api/scread/de/gene/gad1

Install

git clone https://github.com/OSU-BMBL/scread-backend.git
cd scread-backend
npm install

Add configuration file

create a .env file and set the koa.js port, database username & password:

DB_USER=XXXX
DB_PASSWORD=YYYY
DB_URL=ZZZZ
PORT=8889

We use Sequelize to connect out MYSQL database, first export MYSQL table structure using sequelize-auto:

npm install -g sequelize-auto
npm install -g mysql

After installed [sequelize-auto] and [mysql],enter [./server] folder, run the following command:

sequelize-auto -o "./schema/scread" -d scread -h 127.0.0.1 -u root -p 3306 -x YOUR_PASSWORD -e mysql

Start the server

Node.js

Beacuse of using Koa2, Node.js >= v7.6.0 is needed.

Development:

npm run dev && npm run server

open browser: localhost:8889

Production:

Prerequisite: install PM2

Start the production server in PM2:

npm run serve

open browser: localhost:8890