Developer documentation
This page contains information pertinent to employees of WormBase.
Contents
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
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 deployment strategy, 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
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 -- 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
- 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
- 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
- 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
Configuration
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
Model
Controller
- Caching -- a description of application level caching
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
- Testing - Testing guidelines for the web application and hardware platform
- Profiling - Profiling the web application (and historical benchmarks)
- 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