Developer documentation
From WormBaseWiki
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
- 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
- Requirements analysis / Design Specifications
- Rearchitecture Development Duties
Development Milestones
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 22nd, 2010
- Begin private review of new site
- Launch surveys on UI
February 1st, 2011
- Preview new site to SAB
May 1st, 2011
- Public preview
June 1st, 2011
- Public launch of new site at International Worm Meeting
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
- NFS at WormBase
Hardware platform
- WormBase Infrastructure - A complete accounting of WormBase compute resources.
- Production Environment - Building, Configuring, and Maintaining the WormBase production environment
- Development Environment - Building, Configuring, and Maintaining the WormBase development server
Administration
Updates
- Updating The Development Server - Staging a new release of the database on the development server
- Updating The Production Servers - Testing, staging, and deploying the web app; updating to 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
- GBrowse Administration -- building, configuring, and maintaining production GBrowse nodes.
- Webserver Administration -- building, configuring, and maintaining non-GBrowse production nodes.
- 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
- Crises Recovery Plan - Everything breaks. Here's how to fix it.
- General administration and monitoring notes - Partially redundant, sorry
- Monitoring services and servers
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.
Rearchitecture
- HOWTO migrate a CGI - quick overview of how to migrate an existing CGI into a Model, Controller, and View. Sparse
- MySQL database replication - Mirroring mysql databases across production nodes
- 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