Difference between revisions of "Developer documentation"
From WormBaseWiki
Jump to navigationJump to searchLine 126: | Line 126: | ||
* [[Cronjobs|Cronjobs]] | * [[Cronjobs|Cronjobs]] | ||
* [[Creating_a_Google_Sitemap|Creating a Google Sitemap]] | * [[Creating_a_Google_Sitemap|Creating a Google Sitemap]] | ||
− | *[[Managing Perl Libraries]] - ''Managing Perl libraries across projects and architectures'' | + | * [[Managing Perl Libraries]] - ''Managing Perl libraries across projects and architectures'' |
− | *[[Managing GBrowse]] - ''Quick HowTo for managing GBrowse in development and production environments'' | + | * [[Managing GBrowse]] - ''Quick HowTo for managing GBrowse in development and production environments'' |
− | *[[Log file management and analysis|Log file management and analysis]] - ''rotating and analyzing logs.'' | + | * [[Log file management and analysis|Log file management and analysis]] - ''rotating and analyzing logs.'' |
* [[Site_statistics|Site statistics]] | * [[Site_statistics|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|Building WormMart]] - ''How to convert a WormBase AceDB database into WormMart'' | ||
=== Load balancing and Failover === | === Load balancing and Failover === | ||
Line 143: | Line 148: | ||
=== Frozen Releases === | === Frozen Releases === | ||
*[[Building Frozen Releases]] - ''The most current documentation on how to build a frozen release'' | *[[Building Frozen Releases]] - ''The most current documentation on how to build a frozen release'' | ||
− | |||
− | |||
− | |||
== Developer Tools == | == Developer Tools == |
Revision as of 16:17, 21 July 2010
This page contains information pertinent to employees of WormBase.
Contents
- 1 Project Management
- 2 Web Site Documentation
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
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
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
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