mg-rest-3d

RESTful API for TADbit generated 3D coordinates

Requirements

• Mongo DB 3.2
• Python 2.7.10+
• pyenv
• pyenv virtualenv
• Python Modules:
  • h5py
  • numpy
  • DMP
  • Flask
  • Flask-Restful
  • Waitress

Installation

Cloneing from GitHub:

git clone https://github.com/Multiscale-Genomics/mg-rest-3d.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-3d.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
ftp_root = ftp://ftp.multiscalegenomics.eu/test

Setting up a server

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

cd mg-rest-3d
pyenv virtualenv 2.7.12 mg-rest-3d
pyenv activate mg-rest-3d
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-3d/bin/waitress-serve --listen=127.0.0.1:5003 rest.app:app &

Generating test data

Run the following script:

python scripts/GenerateSampleCoords.py

Testing the performance of the API

Run the test script:

 python -m scripts.test_regions_models