Developer documentation

This page contains information pertinent to employees of WormBase.

Navigating and Editing the Developer Documentation

Web Dev Category Hierarchy (Under Construction)

You will be able to navigate the Developer Documentation by browsing through the Web Dev Category Hierarchy (Under Construction) above, which is under construction right now. In the mean time, please browse through this page or search for information that you need.

<categorytree mode=pages showcount="on" hideroot="on" depth=4 >Web Dev</categorytree>

How to Contribute to the Documentation

If you'd like to help out adding to the documentation, that's great! Here is some general good practice that will help keeping the documentation organized, navigable and up to date.

• Ensure a page is tagged with a category, when you add or edit a page. You can browse through our high level categories and locate the most specific category that describes your page.

For example, include the following code at the bottom of a page will make the page appear under the category Category: Getting Started (Web Dev) :

[[Category: Getting Started (Web Dev)]]

• Update, deprecate or remove old documentation when appropriate.

• Any documents that contain potentially sensitive information belong on Google Docs (Contact Todd for details). This might reasonably include anything that reveals information about our systems or architecture.

• Additional guidelines on Documentation and Communication Standards

• Other ideas? Please update the wiki here!

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.
• Co-op Documentation

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

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

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

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