aslett1 / midas

Front end for the HICF pathogen genome store

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