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

• Internal documentation and standard operating procedures

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
• 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

Information for third party developers

• Linking To WormBase

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
• System Testing
• Validation (HTML/CSS/XML)
• Security Assessment
• Accessibility
• Usability
• Browser Compatibility Testing - browser support matrix and testing protocol
• Load Testing - Performance and load testing; historical benchmarks

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• Testing Overview - Overview of our testing strategy
• Code Testing and Profiling - Testing and profiling protocol for the web application
• Usability Testing - Validation, security assessments, usability, and compatibility

• Usability Testing - Validation, security assessments, usability, and compatibility

• 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 - Everything breaks. Here's how to fix it.
• 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

• NBC sign off documentation

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