mg-rest-file

Data retrieval of files or sections of files

Requirements

• Python 2.7.10+
• pyenv
• pyenv virtualenv
• Python Modules:
  • mg-dm-api
  • mg-rest-util
  • Flask
  • Flask-Restful
  • Waitress

Installation

Cloneing from GitHub:

git clone https://github.com/Multiscale-Genomics/mg-rest-file.git

To get this to be picked up by pip if part of a webserver then:

pip install --editable .
pip install -r requirements.txt

This should install the required packages listed in the setup.py script.

Installation via pip:

pip install git+https://github.com/Multiscale-Genomics/mg-rest-file.git

Configuration files

Requires a file with the name mongodb.cnf with the following parameters to define the MongoDB server:

[dmp]
host = localhost
port = 27017
user = testuser
pass = test123
db = dmp

Customise the rest/auth_meta.json file to locate the authentication server

Setting up a server

git clone https://github.com/Multiscale-Genomics/mg-rest-file.git

cd mg-rest-dm
pyenv virtualenv 2.7.12 mg-rest-dm
pyenv activate mg-rest-dm
pip install git+https://github.com/Multiscale-Genomics/mg-dm-api.git
pip install -e .
pip deactivate

Starting the service:

nohup ${PATH_2_PYENV}/versions/2.7.12/envs/mg-rest-file/bin/waitress-serve --listen=127.0.0.1:5003 rest.app:app &