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

Measuring Progress

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

July 14 - July 30th

• Coronate Czars
• 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

• 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
• UI features to address/develop
  • Enhanced, high-performance search
  • External URL handling
  • Error trapping and reporting
  • Authorization/Authentication
  • Customizability
  • Configurable two-panel selector
  • Incorporation of old site elements like BLAST/BLAT

September 1st

• Begin beta testing of new site to invited parties

October 1st - November 1st

• Begin public beta testing of new site
• Launch surveys on UI

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

• Keep configuration files neat, orderly, and documented
• Create new configuration for hard-coded variables and UI elements when needed.
• Enforce/evangelize configuration standards and formatting

CSS Czar -- Responsible for the maintenance of CSS files

• Develop and document CSS best practices
• Keep CSS files tidy and organized function
• Enforce/evangelize standard CSS markup in templates

Javascript Czar -- Javascript use and maintenance

• Develop and document Javascript best practices
• Explore and advise on javascript plugins
• Enforce/evangelize javascript standards and formatting

Template Czar -- Oversee template development

• Develop and document template standards
• Define and document shared template elements (ie tables, fields, widgets)
• Keep template directory organized
• Enforce/evangelize template standards

Controller Czar -- Maintain and develop new controllers as needed

• Document existing controllers
• Document logic flow through application
• Develop new controller actions as requested/needed

WormBase::API Czar -- Oversee development of the external Model

• Develop and document API coding standards and best practices
• Document shared API methods
• Enforce/evangelize coding standards

Testing Czar -- Oversee testing of the web app

• Develop and document test requirements
• Ensure adequate test coverage and performance
• Develop global View and API tests
• Stress Test app

Profiling Czar -- Track progress and performance of the web app

• Explore profiling options and discuss
• Add dynamically configurable profiling
• Identify and report bottlenecks

Coding standards and Best Practices

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

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

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

Administration

Routine Administration Tasks

• Testing - Testing guidelines for the web application and hardware platform
• 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