Developer documentation

This page contains information pertinent to employees of WormBase.

Project Management

• Project Calendar
• Conference call agendas and minutes
• Project meeting agendas and minutes
• Linking To WormBase
• Suggested pre-release data checks
• Internal documentation and standard operating procedures
• modENCODE Analysis & metadata discussion
• What criteria should a genome meet before we accept it for integration?
• WormBase Models
• Orthologs: use cases for searches
• Genome sequence changes

Web Site Documentation

• Installing the Web Application (legacy code) - Here's how to install the classic WormBase web site for development purposes
• Installing the Web Application - Here's how to install the WormBase web application -- including Catalyst -- on your system
• HOWTO migrate a CGI - quick overview of how to migrate an existing CGI into a Model, Controller, and View. Sparse
• Requirements analysis / Design Specifications

Development Milestones

July 14 - July 30th

• Coding standards and best practices for CSS, Javascript, API in place
• Release new pages to production powered by the new architecture (classic view only)

July 30th - August 31st

• http://wiki.wormbase.org/index.php/AceOjbect_Redesign_Page
• Finish API development of critical classes
• Finish migration of prominent CGI-based pages to new architecture and release into production (classic view only)
• Solidify look-and-feel of new site: site map, browsing paths, design patterns, navigation

September 1st

• Begin beta testing of new site to invited parties

October 1st - November 1st

• Begin public beta testing of new site
• Launch UI and general surveys.

November 1st - December 1st

• Address survey issues
• Test, test, test

December 1st

• Go Live with new site

Division of Labor

Duties, current as of July 2010.

• Configuration Czar -- View and application configuration
• View
  • CSS Czar
  • Javascript Czar
  • Template Czar -- define and document shared elements, keep template directory organized, enforce standards
  • Searches Czar
  • External URLs
• Controller
• WormBase::API Czar -- document shared API methods; enforce coding standards
• Testing Czar (View)
• Testing Czar (API)
• Profiling Czar

Measuring Progress

• AceDB classes -> API progress matrix
• Migration matrix (GoogleDoc)

Coding standards and Best Practices

• Developer notes - Best practices, conventions, etc
• Coding standards
• Formal development strategy - An overview of the development process at WormBase

Testing

• Unit testing
• System Testing
• Validation (HTML/CSS/XML)
• Security
• Accessibility
• Usability
• Browser compatability
• Performance and stress testing

Software platform

• Application overview - A quick tour through the software platform

WormBase::API

• Common Model elements - reference list of common model elements like Species
• Data structure documentation - codified data structure that should be returned by API classes

View

• Template Overview -- a quick tutorial on the templating system
• Common template elements -- how to include common elements like references and species in a page
• Things to document: evidence handling, linking entities, external URLs, searches

Hardware platform

• MySQL database replication - Mirroring mysql databases across production nodes
• Performance optimization - Memory, Disk, and Network I/O troubleshooting
• WormBase Infrastructure - A complete accounting of WormBase compute resources and topology.
• WormBase Development Environment - Building, Configuring, and Administering the WormBase development server

--

• GBrowse Administration -- building, configuring, and maintaining production GBrowse nodes.
• Webserver Administration -- building, configuring, and maintaining non-GBrowse production nodes.

Administration

Routine Administration Tasks

• Deployment - How to deploy the web app for production use
• Cronjobs
• Creating a Google Sitemap
• Managing Perl Libraries - Managing Perl libraries across projects and architectures
• Managing GBrowse - Quick HowTo for managing GBrowse in development and production environments
• Log file management and analysis - rotating and analyzing logs.
• Site statistics

Updates

• Updating The Development Server - Updating the development server with a new release of the database
• Updating The Production Servers - Updating production environments with a new release of the database
• Building WormMart - How to convert a WormBase AceDB database into WormMart

Load balancing and Failover

• Building Squid - How to build and install Squid
• Configuring Squid - basic squid configuration at WormBase

Monitoring and Crises Management

• Development Server Administration - Monitoring and fixing the development server
• General administration and monitoring notes - Partially redundant, sorry
• Monitoring services and servers
• Crises Recovery Plan - Everything breaks. Here's how to fix it.

Frozen Releases

• Building Frozen Releases - The most current documentation on how to build a frozen release

Developer Tools

• Twitter: General announcements
• FriendFeed: WormBase FF room
• WormBase Forum: Developer Forum

Source Code Repositories

We use the distributed source code management system Mercurial. Projects are hosted on BitBucket.

How-To create, check out, and manage our repositories

• WormBase - The WormBase web application (public)
• WormBase-admin - Administrative code (private)

Deprecated Documentation

The good word gone bad. Cruft. Lint. Maybe useful. Probably not.

• NFS at WormBase
• Trac installation notes
• Trac Feature Tracker / Subversion repository
• Establishing the SVN repository - Setting up the subversion repository

Frozen Releases as Virtual Machines

• How to build a WormBase Virtual Machine -- also describes how to create a VMX for a frozen release
• Configuring a server to host virtual machines -- quick guide to setting up a frozen release server
• Managing servers hosting virtual machines
• How to build a frozen release -- how to configure a WormBase VM as a frozen release server
• Creating Virtual Disks - How to create VMDKs for unlimited portable storage