Taverna Player Portal

An example application that implements Taverna Player.

Docker

The easiest way to get the portal up and running is to use Docker.

First, set up a taverna server container:

docker run --name taverna -p 8080:8080 -d taverna/taverna-server

Then set up the portal container:

docker run --name taverna-portal --link taverna:taverna -p 3000:3000 -d fbacall/taverna-player-portal

Manual Setup (for development)

Ubuntu 14.04 (or similar)

Install required packages

sudo apt-get install sqlite libsqlite3-dev libxml2-dev libxslt1-dev libtool libmagickwand-dev graphviz ImageMagick ghostscript nodejs git

Install Ruby 2.2.2

First, install RVM using the commands listed here: https://rvm.io/

Then run (you may need to restart your terminal first)

rvm install 2.2.2

Clone the portal

git clone https://github.com/myGrid/taverna-player-portal.git
cd taverna-player-portal

Install gems

gem install bundler

bundle install

Taverna Server configuration

cp config/initializers/taverna_server.rb.example config/initializers/taverna_server.rb

You will need to edit config/initializers/taverna_server.rb in your favourite text editor to include the location and credentials of the Taverna Server instance you wish to use.

Set up the database

bundle exec rake db:setup

Run the server

bin/rails s

This will start the application at http://localhost:3000/

Run the worker

To start the DelayedJob worker, which handles asynchronous tasks such as polling Taverna Server, run the following in a seperate terminal window:

rake jobs:work

Note: remember to restart the worker to reflect any back-end code changes

API

The portal has a basic API (provided by Rails) for listing and uploading workflows.

Authentication

The API uses HTTP Basic authentication, where the username is your email address, and the password is your password. Actions such as uploading a workflow require authentication. Other actions can be perform anonymously.

Workflows

Listing workflows

GET /workflows.json

Fetching a workflow's metadata

GET /workflows/1.json

Where the ID of the workflow is 1

Uploading a workflow

POST /workflows.json

Where the body of the POST is a JSON document, structured as follows:

{ "workflow" : { "document" : "data:application/octet-stream;base64,<<<workflow here>>>" } }

Where <<<workflow here>>> is a Base64 encoded T2Flow workflow.

Make sure to set the Content-Type of your request to application/json.

Example using curl

curl -u joebloggs@example.com -X POST -H "Content-Type: application/json" -d@my_post_body.json http://localhost:3000/workflows.json 

Runs

The workflow run API is provided by Taverna Player, and is documented here: https://github.com/myGrid/taverna-player/wiki/JSON-API-Documentation