Developer documentation

This page contains information pertinent to employees of WormBase.

Navigating and Editing the Developer Documentation

Category Hierarchy (Under Construction)

New Employee Orientation

• New Employee Orientation -- Getting started at WormBase, for employees at any location. Read this first.
• Webdev team/OICR Orientation -- For new employees of the web development team at OICR.

Project Management

• Project Calendar (Google)

Conference call agendas/minutes

• Conference call agendas and minutes (All WormBase)
• Conference call agendas and minutes (WebDev team)
• Project meeting agendas and minutes
• InterMine Strategy Meetings

Source Code Repositories

We use the distributed source code management system git. Projects are hosted on Github.

• website - The WormBase web application (public)
• website-admin - Administrative code (private)

Recommended reading (learning git):

• try.gihub.io

General Documentation

• Co-op Documentation
• Internal documentation and standard operating procedures
• Feature WishList

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
• GFF Release Data and Changes

Development Guidelines

• Setting up your development environment -- How to set up your development environment on dev.wormbase.org
• Developer Resources at WormBase -- Available developer resources, including the shared development space
• WormBase Release Workflow -- Project-wide schedule that documents what is happening when and where. (original wiki version)
• Formal Development Strategy -- An overview of the development process at WormBase
• Documentation and Communication Standards
• Coding standards
• Developer notes -- Best practices, conventions, etc
• Browser Support Statement -- official graded browser support statement

Testing

• Unit Testing

Help us maintain the site

• Contribute from GitHub

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
• Genome Browsing
  • GBrowse Set-up on dev.wormbase.org -- "Updating/rolling-back GBrowse installations on a per user basis"
  • Genome Browser Survey -- "Community survey for evaluating use cases and required functionality of a WormBase genome browser"
• Visualization
  • Website:Visualization Library Assessment -- "Assessment of several visualization options for integration in the Website"
  • Website:Visualization with ggplot2 of the R-Project -- "Installation, set-up, and other information about the R-project based visualization"

• WormMine -- How to install, update, and maintain the InterMine instance at WormBase
  • Website:WormMine Builds -- Summary stats of WormMine builds
• Contribute from Github

The Mobile Website

• Mobile -- Overview of the mobile website
• Router -- A definition of the possible routes of the mobile website
• Models -- Details about the models
• Collections -- Details about the collections
• Views -- Details about the views
• Widgets Porting -- Details about the porting of widgets in the mobile website/app

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
• Installing WormMine - How to get a basic installation of WormMine 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

• Software Life Cycle: 1. Build -- Preparing a new release for the website
• 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
• Software Life Cycle: 4. Production -- Deploying a new release to production

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

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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.
• Monitoring services and servers - Keeping tabs on the production architecture

Frozen Releases

• Building Frozen Releases - The most current documentation on how to build a frozen release

Deprecated Documentation

The good word gone bad. Cruft. Lint. Maybe useful. Probably not.

Rearchitecture

• Development Milestones
• Requirements analysis / Design Specifications
• Rearchitecture Development Duties
• AceDB classes -> API progress matrix (index of classes; see official matrix)
• HOWTO migrate a CGI - quick overview of how to migrate an existing CGI into a Model, Controller, and View. Sparse

Load balancing and Failover

• Building Squid - How to build, install and configure Squid

Administration

• Formal development strategy - An overview of the development process at WormBase -- THE OLD VERSION
• 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
• Monitoring services and servers - Monitoring services and servers

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