Developer documentation
From WormBaseWiki
This page contains information pertinent to employees of WormBase.
Contents
Project Management
- Conference call agendas and minutes (All WormBase)
- Conference call agendas and minutes (WebDev team)
- Project meeting agendas and minutes
Data Model and Data Development
- WormBase Models
- Genome Standards -- What criteria should a genome meet before we accept it for integration?
- Suggested pre-release data checks
- modENCODE Analysis & metadata discussion
- modENCODE Integration status
- Genome sequence changes
- WormBase Genomes
Web Site Development Guidelines
Documents pertaining to WormBase 2.0
- Development Milestones
- Requirements analysis / Design Specifications
- Rearchitecture Development Duties
- AceDB classes -> API progress matrix (index of classes; see official matrix)
- Formal development strategy - An overview of the development process at WormBase
- Coding standards
- Developer notes -- Best practices, conventions, etc
- Browser Support Statement -- official graded browser support statement MIGRATED TO NEW SITE
The Web Application
- Application overview - An overview of the web application, including MVC structure, 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
- WormMine -- How to install, update, and maintain the InterMine instance at WormBase
- Curator Feature Requests -- Sample template for Feature Requirements Specification
Information for third party developers
Administration
Architecture
Software Platform
- Installing WormBase - How to get a basic installation of WormBase up and running
- Production Environment - Building and Maintaining the WormBase production environment; extends the "Installing WormBase" document
- GBrowse Administration -- building, configuring, and maintaining production GBrowse nodes.
- Building WormMart - How to convert a WormBase AceDB database into WormMart
Hardware Platform
- Hardware Platform - A complete accounting of WormBase compute resources.
Software Life Cycle
- Staging a new release - how to stage a new release of WormBase on the development server and cloud instances
- Software development period - Once a new database has been staged, the development phase begins in earnest on private development sites
- QA/QC and Performance Benchmarking - Integrating changes and staging the code for QA/QC and performance testing prior to deployment
- Release to Production - Deploying the web app; updating to a new release of the database
Measuring Application Performance
- Unit Testing and Profiling - Testing and profiling protocol for the web application
- System Testing
- Standards Validation - Validation of HTML, CSS, XML
- Security Assessment
- Accessibility
- Usability Testing - usability testing strategies and evaluation
- Browser Compatibility Testing - browser support matrix and testing protocol
- Load Testing - Performance and load testing; historical benchmarks
- Monitoring services and servers - Monitoring services and servers
Routine Administration Tasks
- Cronjobs - a full accounting of all cronjobs at WB
- Creating a Google Sitemap - how to tell Google which URLs to index
- Managing Perl Libraries - Managing Perl libraries across projects and architectures
- Log file management and analysis - rotating and analyzing logs.
- Site statistics
Monitoring and Crises Management
- Crises Recovery Plan - How to diagnose and recover from service interruptions.
- General administration and monitoring notes - Partially redundant, sorry
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)
Developer Notes
Deprecated Documentation
The good word gone bad. Cruft. Lint. Maybe useful. Probably not.
Load balancing and Failover
- Building Squid - How to build, install and configure Squid
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
