Co-op Documentation

Current Tasks

Tasks to be completed

• Refining Interactions widget:
  • Details:
    • If the number of interactions is too high, only show the minimal table (hide Cytoscape) and add "Show More" option(AJAX).
    • Otherwise, show all interactions(nearby interactions included) and Cytoscape plugin
  • Progress:
    • Looking into BLASTP field in Homology Widget on Protein page that uses similar mechanism
• Gene page alterations
  • Details:
    • Make corrections to Gene page interface
  • Progress:
    • Pending consultation from curators. Teleconference: 11:30 am EST Wednesday, January 18th, 2012

Possible Tasks: Additional tasks that require further investigation

• Loading/processing large amounts of data
  • Details:
    • Likely approach will be to change the database used from ACeDB to NoSQL/CouchDB
    • Sample Issue
  • Progress:
    • Ace2Couch Scripts for migrating data
    • AceCouch Perl API

Getting Started

Members/Contacts

• Abigail Cabunoc - abigail.cabunoc@oicr.on.ca
• Todd Harris - todd@wormbase.org
• Lincoln Stein - lincoln.stein@gmail.com
• Quang Trinh

Meetings

• WormBase OICR Developers Teleconference
  • Mondays, 3:00PM
  • Phone-in 1-800-747-5150 id: 6738514
• WormBase OICR Developers Teleconference with Lincoln
  • Wednesdays, 4:00PM EST
  • Lincoln's office
• WormBase International Groups Teleconference
  • Every other Thursday, 11:30AM
  • Lincoln's Office
• Group Meeting
  • Fridays, 3:00PM

Tools

The following are some of the tools with which many major aspects of WormBase are developed.

Perl

There is significant documentation on getting started with Perl. One starting point is PerlMonks.

Catalyst

Catalyst is the web development framework used to develop WormBase. To get started, read

• The Definitive Guide to Catalyst (should be available on bookshelf)
• CPAN - About Catalyst

Git

Git is a version control system used for collaboration and backup in the development process.

• WormBase repository located at https://github.com/organizations/WormBase
• Common commands
  • status, add, checkout, commit, push, pull, log, fetch, merge
• Usage example:

Given that we have modified two files a.txt and b.txt but do not wish to keep the changes made to b.txt

git status
git checkout b.txt
git add a.txt
git commit -m “Added change1 and change2 to a.txt”
git push

If we have did not have the most recent version, then we will run into an issue when trying to push. In this case we can:

git fetch
git merge
git push

Note: pull is similar to using fetch + merge

Other

Some other tools that you should be aware of but may not be required to know/interact with include:

• JavaScript
• ACeDB
• MySQL
• Xapian
• GFF
• Cytoscape Web
  • Cytoscape Tutorial
  • Plugin generally used for pathway analysis
  • This plugin is used in the Interactions widget on the Gene page ([WormBase dir]/root/templates/classes/gene/interactions.tt2)
  • Installed in [WormBase dir]/root/js/jquery/plugins/

General Concepts

Widget Data Loading

Widget Loading

REST Controller:

1. Catches internal url (/rest/widget/...)
2. Determines the class and widget from the url
3. From class and widget, determines which fields are required from the configuration file (wormbase.conf)
4. Retrieves data for corresponding fields from API methods (/lib/WormBase/API/Object/[Class].pm)
5. Sends data to the template to be used in rendering the widget (/root/templates/classes/[Class]/[Widget].tt2)

Other Notes

• [WormBase dir]/root/templates/config/main contains useful macros such as get_url that may be used in templates