Ensembl Public REST API

The public RESTful API for the Ensembl Gene Autocomplete data table.

Tech

Ensembl Public REST API uses a number of open source projects to work properly:

• Flask
• flask_restful
• flask_script
• flask_migrate
• marshmallow
• flask_sqlalchemy
• flask_marshmallow
• marshmallow-sqlalchemy
• psycopg2
• pymysql

Installation

Clone this repository and enter the repository. You need to have python and pip installed in your working environment.

git clone https://github.com/chanakaDe/ensembl-public-rest.git
cd ensembl-public-rest

Then you have to creates a virtual environment.

python3.6 -m venv env

Or if you have python, use following command:

python -m venv env

Then you need to activate the virtual environment.

source env/bin/activate

Then you need to install all the dependencies.

pip install -r requirements.txt

Optional

If you need to change the database connection, use config.py file to change SQLALCHEMY_DATABASE_URI parameter.

SQLALCHEMY_DATABASE_URI = "mysql://anonymous@ensembldb.ensembl.org:3306/ensembl_website_97"

This is a public database and users don't need to enter any password.

Finally start the server.

python run.py

If you configured everything correctly, you will see following output in your terminal.

Running on http://127.0.0.1:5000/ (Press CTRL+C to quit)
Restarting with stat
Debugger is active!
Debugger PIN: xxx:xxx:xxx

For more information about the testing of Ensembl Public REST API : TESTING.md

For more information about the deployment of Ensembl Public REST API : DEPLOY.md