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mg-rest-service

Service to monitor and list live REST services

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Requirements

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

Installation

Cloneing from GitHub:

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

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

pip install -e .

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-service.git

Configuration files

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

[rest]
host = localhost
port = 27017
user = mongo_user
pass = mongo_user_pwd
db = rest

For each REST service that is to be integrated into the MuG REST service should have the relevant URL and name stored within a registry.json file located in the mg-rest-service directory:

{"registry" : [{"name" : "DMP", "url" : "http://127.0.0.1:5001/api/dmp/ping"}, {"name" : "", "url" : ""}]}

Setting up a server

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

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

Starting the service:

nohup ${PATH_2_PYENV}/versions/2.7.12/envs/mg-rest-service/bin/waitress-serve --listen=127.0.0.1:5000 rest.app:app &

Apache Config

This is dependent on the version that you are running.

Apache 2.2 Config

In Apache 2.2 the <Location> tag for the /api server need to come last in the list of services so that it is not over written

<VirtualHost *:80>
  ServerName www.example.com
  ServerAlias rest-mug.example.com
  ServerAlias rest-mug
  <Proxy *>
    Order deny,allow
    Allow from all
  </Proxy>
  ProxyRequests Off
  ProxyPreserveHost On
  <Location /api/dmp>
    ProxyPass http://127.0.0.1:5001/api/dmp
    ProxyPassReverse http://127.0.0.1:5001/api/dmp
  </Location>
  <Location /api/adjacency>
    ProxyPass http://127.0.0.1:5002/api/adjacency
    ProxyPassReverse http://127.0.0.1:5002/api/adjacency
  </Location>
  <Location /api>
    ProxyPass http://127.0.0.1:5000/api
    ProxyPassReverse http://127.0.0.1:5000/api
  </Location>
  RequestHeader set X-Forwarded-Proto "http"
</VirtualHost>

RESTful API

List end points

Request:

wget http://127.0.0.1:5000/api

Returns:

{"_links": {"_self": "http://ves-ebi-64.ebi.ac.uk/api", "DMP" : "http://ves-ebi-64.ebi.ac.uk/api/dmp"}}

ping

Request:

wget http://127.0.0.1:5000/api

Returns:

{"status": "ready", "description": "Main process for checking REST APIs are available", "license": "Apache 2.0", "author": "Mark McDowall", "version": "v0.0", "name": "Service"}