RESTful API providing adjacency data stored in hdf5 files that have been generated with the scripts in the mg-storage-hdf5 / mg-process-fastq repo
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README.md

mg-rest-adjacency

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Microservice RESTful API for the querying of Adjacency data stored in HDF5 files that have been generated using the code from the mg-storage-hdf5 / mg-process-fastq scripts

Requirements

  • Python 2.7+
  • pyenv
  • pyenv virtualenv
  • pip
  • Python Modules
    • h5py
    • NumPy
    • Flask
    • Flask-Restful
    • json
    • pytest
    • Waitress

Installation

Cloneing from GitHub:

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

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

pip install --editable .

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-adjacency.git

Setting up a server

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

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

Starting the service:

nohup ${PATH_2_PYENV}/versions/2.7.12/envs/mg-rest-adjacency/bin/waitress-serve --listen=127.0.0.1:5002 rest.app:app &

Testing

Test scripts are located in the test/ directory. Run pytest to from this directory to ensure that the API is working correctly.

The scripts require a valid hdf5 file generated using the scripts from mg-storage-hdf5 and a matching datasets.json file located in the rest/ directory