OARD (An acronym form of "oh alright"): an Open real-world based Annotation for Rare Diseases and its associated phenotypes

This is a Flask app to serve the backend API of OARD. Currently it is hosted on the NCATS AWS server (https://rare.cohd.io/). This repo currenly only have the Flask API part. The fron end React web app is hosted in another repo. We expect to merge two repos in the near future.

Columbia Open Health Data API (COHD)

The architecture of this web API is largely adopted from an exisitng project called COHD

Installation

To install

pip -r requirement.txt

Running the Application

The API is served using FLASK:

FLASK_APP=cohd.py flask run

Deploying and running OARD on AWS

OARD is served on an AWS EC2 instance using Nginx and uWSGI. For consistency, use the approach in the following blog post

Caveats:

• If using virtualenv, you either have to have the virtualenv directory in the same location as the cohd.py application, or specify the location of the virtualenv using the uWSGI -H parameter.

nsides back-end (drug effect database population)

Please see here

nsides middleware (on-demand job submission)

Please see here

On the EC2 server:

• /var/cohd-rare/ has the code
• /var/cohd-rare/cohd/cohd.ini – uwsgi configuration for running the app
• /var/cohd-rare/cohd/cohd_flask.conf – flask configuration
• /var/cohd-rare/cohd/database.cnf – mysql database configuration file. Currently using the main cohd database. Should be changed when you have the new database up
• /var/cohd-rare/cohd/venv – virtualenv location
• /var/log/uwsgi/cohd-rare.log – log file
• /etc/system/system/cohd-rare.service – system configuration (already set to automatically start on boot)
• sudo systemctl <start|stop|restart> cohd-rare restart after python code changes to app
• /etc/nginx/sites-available/cohd-rare – nginx configuration
• sudo systemctl restart nginx - restart nginx
• If you make changes Test configuration changes without applying: sudo nginx -t Apply configuration changes: sudo service nginx reload