The WormBase web application and external model
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README.md

WormBase Website Repository

This repository contains the WormBase Web application.

Installation

Execute the following commands in a BASH terminal:

git clone git://github.com/WormBase/website.git wormbase
cd wormbase
git submodule init
git submodule update
export approot=`pwd`
perl Makefile.PL
make installdeps

If you did not start off in /usr/local, then you can either change the preset paths in the application's configuration files, or alternatively, carry out these two steps:

sudo -E su
cd /usr/local
ln -s $approot

Dependencies

Most dependencies will be installed with make installdeps, but perl Makefile.PL itself is depending on some prerequisites:

  1. a development environment: Perl, make, gcc & co.
  2. sudo cpan Module::Install

On Mac OS X, Perl comes preinstalled. The C development tools are installed from within Xcode, which is free, and then selecting from the menu/dialogs: Xcode -> Preferences... -> Downloads -> Components -> "Command Line Tools" -> "Install".

Running the application

To run the app using the built-in Catalyst server:

script/wormbase_server.pl -p 8000

Running the application via Starman

starman --port 8000 --workers 10 wormbase.psgi

Unit Testing

We provide two sets of unit tests for the REST API and WormBase Perl API respectively. The tests are based on Test::More, they run on a fully populated WormBase database backend, they autonomously start and stop a Catalyst web server (random port between 28,000 and 31,999).

Running REST API tests:

perl t/rest.t

Running WormBase Perl API tests:

API_TESTS=1 perl t/api.t

Running WormBase Perl API tests for just the gene class:

API_TESTS=gene perl t/api.t

Comparative Testing

For testing GBrowse installations, we provide a test implementation that compares gbrowse_img images to a reference set.

Running comparative GBrowse tests:

perl t/gbrowse.t --base http://dev.wormbase.org:4466/cgi-bin/gb2/gbrowse_img

Creating a reference image set that is used for the comparative tests:

perl t/gbrowse.t --base http://dev.wormbase.org:4466/cgi-bin/gb2/gbrowse_img --reference

A summary log and a full disclosure of broken URLs is written to the logfile logs/gbrowse_test.log.

Contributing

Our development workflow can be found here:

http://wiki.wormbase.org/index.php/Development_workflow_-_webdev

Todd Harris (todd@wormbase.org)