HICF website

This is the web front end for the MIDAS sample metadata repository, funded by the Human Innovation Challenge Fund. The website is a Catalyst application, backed by a relational database (we use MySQL).

Installation

Clone the repo:

git clone https://github.com/sanger-pathogens/MIDAS.git

Install prerequisites

CPAN modules

The webapp requires, at a minimum, the following Perl modules:

• Catalyst::Runtime
• DBIx::Class
• Template
• Bio::Metadata::Validator
• Bio::HICF::Schema

For now there is no definitive list of lesser dependencies. Start the app and enjoy a game of whack-a-mole with CPAN.

Build tools

We use several nodejs-based build tools, coordinated by Grunt. You'll need to install several dependencies:

• node.js
• sass
• glue
• mocha-casperjs
• casper-chai

Start with node/npm and install the rest using

npm install -g grunt

and similar. For OS X, the easiest way to install way to install node is using Homebrew.

Install node packages

The checkout contains a package.json package list, which can be handed to npm:

cd MIDAS
npm install

(before running npm install you need to configure proxies:

export http_proxy=http://<proxy host>:<proxy port>
export https_proxy=http://<proxy host>:<proxy port>

otherwise downloading packages through the firewall fails.)

You may also need to install grunt-cli as a global package:

npm install -g grunt-cli

Testing

There are two sets of tests. There are Perl tests that exercise the webapp and its integration with the DB, and JS tests that test the front-end.

Perl tests

The perl tests check the page contents and API:

CATALYST_DEBUG=0 DBIC_TRACE=0 prove -lr t

You can turn on catalyst debugging and DBIC query logging by adding environment variables to the command line:

CATALYST_DEBUG=1 DBIC_TRACE=1 prove -lr t

The output will be significantly more verbose.

Front-end tests

The front-end tests use the Mocha testing framework and the ChaiJS assertion library. We use CasperJS, a headless WebKit browser, to test the front-end javascript. The interaction between Mocha and CasperJS is coordinated by mocha-casperjs.

The Perl tests start a headless server and use that, but the front-end tests need a server to be running already. Start it using the run_test_server.sh script:

cd MIDAS/app
sh run_test_server.sh

Run the tests themselves like:

cd MIDAS/test
mocha-casperjs 01_summary.js