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
• Genome Standards -- What criteria should a genome meet before we accept it for integration?
• WormBase Models
• Orthologs: use cases for searches
• Genome sequence changes
• WormBase Genomes

Web Site Documentation

• Installing the Web Application - Here's how to install the WormBase web application -- including Catalyst -- on your system DEPRECATED
• 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)
  • Variation, Protein, Sequence -- and maybe -- Gene
  • Todd to develop <strikethrough>deployment strategy</strikethrough>, hosting environment, and proxy configuration
  • Abby and Xiaoqi to work up templates and markup specific to the classic view
  • Norie to make requisite API changes as needed

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
  • Top-level species pages (/celegans, eg) and UI clues for distinguishing them

December 1st

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

February 1st

• Go Live with new site

Division of Labor

Duties, current as of July 2010.

Configuration Czar -- View and application configuration -- Norie

• 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 -- Norie

• 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 -- Todd

• 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 -- Todd

• See the Profiling documentation for additional details and progress.
• Explore profiling options and discuss
• Add dynamically configurable profiling
• Identify and report bottlenecks
• Develop caching mechanism of ajax-requested widgets

Coding standards and Best Practices

• Browser Support Statement -- official graded browser support statement
• Developer notes -- Best practices, conventions, etc
• Coding standards
• Formal development strategy - An overview of the development process at WormBase

Architecture

Software platform

• Application overview - A quick tour through the software platform, request flow, caching, etc
• Configuration -- Application and view configuration: formatting and standards
• WormBase::API -- The WormBase data model, maintained external to the web application
• View -- Templating system, commom template elements, javascript, and CSS
• Model -- The web application model; thin, glued to the external Model
• Controller -- Overview of controller files and actions
• Website:Software Platform -- The full software platform, including reverse proxy, webservers, and database node configuration

Hardware platform

• MySQL database replication - Mirroring mysql databases across production nodes
• WormBase Infrastructure - A complete accounting of WormBase compute resources.
• Development Environment - Building, Configuring, and Administering the WormBase development server
• Production Environment - Building, Configuring, and Maintaining the WormBase production environment

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

Administration

Updates

• Deployment - How to deploy the web app for production use
• 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

Routine Administration Tasks

• Testing - Testing guidelines for the web application and hardware platform
• Profiling - Profiling the web application, performance tuning, identifying memory and I/O bottlenecks, and historical benchmarks
• Cronjobs
• Creating a Google Sitemap
• Managing Perl Libraries - Managing Perl libraries across projects and architectures
• Log file management and analysis - rotating and analyzing logs.
• Site statistics

• 2010.12: Private Beta Notes -- Notes and documentation with respect to the private beta

• Building WormMart - How to convert a WormBase AceDB database into WormMart

Load balancing and Failover

• Building Squid - How to build, install and configure Squid

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

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
• Managing GBrowse - Quick HowTo for managing GBrowse in development and production environments

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