VDJServer API

This project is a node.js middleware API for VDJServer clients and the Agave API.

It provides a variety of important services for clients including:

• authentication
• Agave webhook processing
• websocket notifications

Service Dependencies

The VDJServer API requires a redis database for notification queueing. There are two ways of handling this:

Installation & Setup via Docker

This project has been dockerized, and building it in via docker is straightforward:

git clone git@bitbucket.org:vdjserver/vdjserver-web-api.git

cd vdjserver-web-api

docker build -t vdjserver-web-api .

Edit the environment configuration file:

cp .env.defaults .env
vim .env
# NOTE: the POSTFIX_RELAYHOST value is available on TACC VMs by looking for the relayhost value in /etc/postfix/main.cf on the host.
# POSTFIX_HOSTNAME should just be the hostname of wherever you've deployed the VDJ API.

Now you can start the VDJServer API:

docker run --env-file .env vdjserver-web-api

Running VDJServer API Without Docker

It may be faster to do iterative development on a local instance of the VDJServer API without using docker. Node.js applications need to be restarted to read changes in their codebases, and this can often be done faster on a local machine than in a docker container.

git clone git@bitbucket.org:vdjserver/vdjserver-web-api.git

cd vdjserver-web-api/app/scripts

npm install

cp config/agaveSettings.js.defaults config/agaveSettings.js

# Add in values as needed
vim config/agaveSettings.js

cp config/config.js.defaults config/config.js

# Add in values as needed
vim config/config.js

####
#Install and start a local redis database on your machine using yum, apt-get, homebrew, etc.
# e.g. on a mac:
# brew install redis
# redis-server /usr/local/etc/redis.conf
####

# Set the correct environment vars to run as http instead of https
export NODE_ENV=development

# Start up the API
node app.js

Documentation:

Swagger 2 docs are available at: vdjserver-web-api/swagger/swagger.yml

Documentation on Agave v2 is available at: http://agaveapi.co/live-docs/.

Tests

Unit tests use the mocha testing framework. They can be run with the commands 'make' or 'npm test' in the app root directory.

Note: If you want to be able to run integration tests, then make sure that test internal user credentials have been added to app/config/agaveSettings.js.

TODO:

Project Tickets/Issues are available at: https://trello.com/b/xTS13xH7/vdj-server.