Deployment

Using In built Sanic server (for development)

Sanic provides a default asynchronous web server to run the API. As a working example, checkout the Roadmap project from the Usecases section.

app = setup_app(mMgr)
app.run("0.0.0.0", port=8000)

Deploy using gunicorn + supervisor (for production)

Setup virtualenv and API

This process assumes the root API directory is /var/www/epiviz-api

Setup virtualenv either through pip or conda

cd /var/www/epiviz-api
virtualenv env
source env/bin/activate
pip install epivizfileserver

A generic version of the API script would look something like this (add this to /var/www/epiviz-api/epiviz.py)

from epivizfileserver import setup_app, create_fileHandler, MeasurementManager
from epivizfileserver.trackhub import TrackHub

# create measurements to load multiple trackhubs or configuration files
mMgr = MeasurementManager()

# create file handler, enables parallel processing of multiple requests
mHandler = create_fileHandler()

# add genome. - for supported genomes
# check https://obj.umiacs.umd.edu/genomes/index.html
genome = mMgr.add_genome("mm10")
genome = mMgr.add_genome("hg19")

# load measurements/files through config or TrackHub

# setup the app from the measurements manager
# and run the app
app = setup_app(mMgr)

# only if this file is run directly!
if __name__ == "__main__":
    app.run(host="127.0.0.1", port=8000)

Install dependencies

1. Supervisor (system wide) - http://supervisord.org/
2. Gunicorn (to the virtual environment) - https://gunicorn.org/

# if using ubuntu
sudo apt install supervisor

# activate virtualenv that runs the API
source /var/www/epiviz-api/env/bin/activate
pip install gunicorn

Configure supervisor

Add this configuration to /etc/supervisor/conf.d/epiviz.conf

This snippet also assumes epiviz-api repo is in /var/www/epiviz-api

[program:gunicorn]
directory=/var/www/epiviz-api
environment=PYTHONPATH=/var/www/epiviz-api/bin/python
command=/var/www/epiviz-api/env/bin/gunicorn epiviz:app --log-level debug --bind 0.0.0.0:8000 --worker-class sanic.worker.GunicornWorker
autostart=true
autorestart=true
stderr_logfile=/var/log/gunicorn/gunicorn.err.log
stdout_logfile=/var/log/gunicorn/gunicorn.out.log

Enable Supervisor configuration

sudo supervisorctl reread
sudo supervisorctl update

service supervisor restart

Note

check status of supervisor to make sure there are no errors

Add Proxypass to nginx/Apache

(the port number here should match the binding port from supervisor configuration

for Apache

sudo a2enmod proxy
sudo a2enmod proxy-http

# add this to the apache site config
ProxyPreserveHost On
<Location "/api">
    ProxyPass "http://127.0.0.1:8000/"
    ProxyPassReverse "http://127.0.0.1:8000/"
</Location>

for nginx

# add this to nginx site config

upstream epiviz_api_server {
    server 127.0.0.1:8000 fail_timeout=0;
}

location /api/ {
    proxy_pass http://epiviz_api_server/;
    proxy_set_header Host $host;
    proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
    proxy_set_header X-Forwarded-Proto $scheme;
    proxy_redirect off;
}