Difference between revisions of "Developer documentation"

From WormBaseWiki
Jump to navigationJump to search
 
(317 intermediate revisions by 13 users not shown)
Line 1: Line 1:
 
This page contains information pertinent to employees of WormBase.  
 
This page contains information pertinent to employees of WormBase.  
 +
 +
= Navigating and Editing the Developer Documentation =
 +
 +
 +
 +
== [[:Category:Web Dev| Web Dev Category Hierarchy (Under Construction)]] ==
 +
 +
'''You will be able to navigate the Developer Documentation by browsing through the [[:Category:Web Dev| 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 [[:Category:Web Dev| high level categories]] and locate the '''most specific category''' that describes your page.
 +
<blockquote> 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)]] :
 +
 +
<code><nowiki>
 +
[[Category: Getting Started (Web Dev)]]
 +
</nowiki></code>
 +
 +
</blockquote>
 +
 +
* '''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 =
 +
* [https://docs.google.com/document/d/1E37IgK1gsaw6ZXa3cYFz2HPVPuB__KmNs5tErO6VXDY/pub New Employee Orientation] -- ''Getting started at WormBase, for employees at any location. Read this first.''
 +
* [https://docs.google.com/document/d/1Xm1aQTm7zXapfirgD1PP7KWNjPlXHNw_iaLLAVvZ-Gg/pub Webdev team/OICR Orientation] -- ''For new employees of the web development team at OICR.''
 +
*[[Co-op Documentation]]
  
 
= Project Management =
 
= Project Management =
−
*[[Project Calendar|Project Calendar]]  
+
*[[Project Calendar|Project Calendar (Google)]]
−
*[[Conference call agendas and minutes]]
+
 
 +
==== Conference call agendas/minutes ====
 +
 
 +
*[[Conference calls| Conference call agendas and minutes (All WormBase)]]
 +
*[[Conference call agendas and minutes| Conference call agendas and minutes (WebDev team)]]
 
*[[Project meeting agendas and minutes]]
 
*[[Project meeting agendas and minutes]]
−
*[[Doodle Polls for conference call scheduling]]
+
*[[InterMine Strategy Meetings]]
−
*[[Linking To WormBase|Linking To WormBase]]  
+
 
−
*[[Suggested pre-release data checks|Suggested pre-release data checks]]  
+
==== Source Code Repositories ====
 +
 
 +
''We use the distributed source code management system git.  Projects are hosted on [http://github.org/WormBase Github].''
 +
 
 +
*[http://github.org/WormBase/website website] - ''The WormBase web application (public)''
 +
*[http://github.org/WormBase/website-admin website-admin] - ''Administrative code (private)''
 +
 
 +
Recommended reading (learning git):
 +
* [http://try.github.io/levels/1/challenges/1 try.gihub.io]
 +
 
 +
= General Documentation =
 +
*[[Co-op Documentation]]
 
*[[SOPs|Internal documentation and standard operating procedures]]
 
*[[SOPs|Internal documentation and standard operating procedures]]
−
*[[modENCODE Analysis & metadata discussion|modENCODE Analysis & metadata discussion]]
+
*[[Feature WishList]]
−
*[[Genome Standards|What criteria should a genome meet before we accept it for integration?]]
 
−
*[[Orthologs: use cases for searches]]
 
−
*[[Genome sequence changes]]
 
  
−
= Web Site Documentation =
+
= The Web Application =
  
−
== Rearchitecture Design Stages==
+
* [[Website:Application overview|Application overview]] - ''An overview of the web application, including MVC structure, request flow, caching, etc''
 +
* [[Website:Configuration|Configuration]] -- ''Application and view configuration: formatting and standards''
 +
* [[Website:WormBase::API|WormBase::API]] -- ''The WormBase data model, maintained external to the web application''
 +
* [[Website:View| View]] -- ''Templating system, commom template elements, javascript, and CSS''
 +
* [[Website:Model| Model]] -- ''The web application model; thin, glued to the external Model''
 +
* [[Website:Controller| Controller]] -- ''Overview of controller files and actions''
 +
* Genome Browsing
 +
** [[Website:GBrowse Set-up on dev.wormbase.org|GBrowse Set-up on dev.wormbase.org]] -- "Updating/rolling-back GBrowse installations on a per user basis"
 +
** [[Website:Genome Browser Survey|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"
  
−
#[[Website:Design Specifications|Requirements analysis / Design Specifications]]
+
* [[Website:WormMine| WormMine]] -- ''How to install, update, and maintain the InterMine instance at WormBase''
−
# [[Website:Architecture outline|Architecture Outline]]
+
** [[Website:WormMine Builds]] -- Summary stats of WormMine builds
−
# [[Website:Prototyping|Prototyping]]
+
*[[Website:Contribute_from_GitHub|Contribute from Github]]
−
# Formal Development via established conventions
 
−
## [[Formal_development_strategy|Formal development strategy]] - ''An overview of the development process at WormBase''
 
−
## [[Developer_notes|Developer notes]] - ''Best practices, conventions, etc''
 
−
##[[Coding standards|Coding standards]]
 
−
# [[Website:Testing|Testing]]
 
−
# [[Website:Production Deployment|Deployment]]
 
  
−
== Coding standards ==
+
== The Mobile Website ==
−
*[[Website:Data Structure| Data structure documentation]]
+
* [[Website:Mobile| Mobile]] -- ''Overview of the mobile website''
−
*[[Website:Common Template Elements| Common template elements]] -- ''how to include common elements like references and species in a page''
+
* [[Website:MobileRouter| Router]] -- ''A definition of the possible routes of the mobile website''
 +
* [[Website:MobileModels| Models]] -- ''Details about the models''
 +
* [[Website:MobileCollections| Collections]] -- ''Details about the collections''
 +
* [[Website:MobileViews| Views]] -- ''Details about the views''
 +
* [[Website:MobileWidgets| Widgets Porting]] -- ''Details about the porting of widgets in the mobile website/app''
 +
= Data Model and Data Development =
  
−
== Software platform  ==
+
*[[WormBase Models]]
 +
*[[Genome Standards]] -- ''What criteria should a genome meet before we accept it for integration?''
 +
*[[Suggested pre-release data checks|Suggested pre-release data checks]]
 +
*[[modENCODE Analysis & metadata discussion|modENCODE Analysis & metadata discussion]]
 +
*[[modENCODE Integration status|modENCODE Integration status]]
 +
*[[Genome sequence changes]]
 +
*[[WormBase Genomes]]
 +
*[[GFF Release Data and Changes]]
  
−
*[[Application overview|Application overview]] - ''A quick tour through the software platform''  
+
= Development Guidelines =
−
*[http://spreadsheets.google.com/ccc?key=pHvlNLMCZIv1KBoy8ZhbZXA&hl=en Migration matrix (GoogleDoc)]  
+
* [https://docs.google.com/a/wormbase.org/document/d/1jps4_bTrsR-Km0QTKk3ENRckbKyK3y8jZwSvq3rh2lo/pub Setting up your development environment] -- ''How to set up your development environment on dev.wormbase.org''
 +
*[https://docs.google.com/a/wormbase.org/document/d/1ONNKWe82OL5oZoPBmQ3nOZ_EZuzDfjbVpYvMkjnfULc/edit#heading=h.3t2png3rdgj8 Developer Resources at WormBase] -- ''Available developer resources, including the shared development space''
 +
*[https://docs.google.com/document/d/1zIOm95tV9A14n9xnkPkMgiOTGcOIzx161y9UbDZvfW4/pub WormBase Release Workflow] -- ''Project-wide schedule that documents what is happening when and where. ([[WormBase Release Workflow|original wiki version)]]''
 +
*[[Development_workflow_-_webdev|Formal Development Strategy]] -- ''An overview of the development process at WormBase''
 +
*[[Documentation and Communication Standards|Documentation and Communication Standards]]
 +
*[[Coding standards|Coding standards]]
 +
*[[Developer_notes|Developer notes]] -- ''Best practices, conventions, etc''
 +
*[[Browser Support Statement]] -- ''official graded browser support statement''
  
−
* [[Using_private_development_sites|Installing the Web Application (legacy code) ]] - ''Here's how to install the classic WormBase web site for development purposes''
+
== Testing ==
−
*[[Installing the Web Application|Installing the Web Application]] - ''Here's how to install the WormBase web application -- including Catalyst -- on your system''
+
*[[Unit Testing]]
−
*[[Common Model elements|Common Model elements]] - ''reference list of common model elements handled generically''
 
−
*[[HOWTO migrate a CGI|HOWTO migrate a CGI]] - ''quick overview of how to migrate an existing CGI into a Model, Controller, and View. Sparse''
 
−
*[[Deployment|Deployment]] - ''How to deploy the web app for production use''
 
  
−
== Hardware platform  ==
+
== Help us maintain the site ==
 +
*[[Website:Contribute from GitHub|Contribute from GitHub]]
  
−
*[[Physical structure|Physical structure]]
+
= Information for third party developers =
−
*[[MySQL database replication|MySQL database replication]] - ''Mirroring mysql databases across production nodes''
 
−
*[[Performance optimization|Performance optimization]] - ''Memory, Disk, and Network I/O troubleshooting''
 
−
*[[WormBase_Infrastructure|WormBase Infrastructure]] - ''A complete accounting of WormBase compute resources and topology.
 
−
*[[WormBase Development Environment|WormBase Development Environment]] - ''Building, Configuring, and Administering the WormBase development server''
 
  
−
--
+
*[[Linking To WormBase|Linking To WormBase]]
  
−
* [[GBrowse Administration]] -- ''building, configuring, and maintaining production GBrowse nodes.''
+
= Administration =
−
* [[Webserver Administration]] -- ''building, configuring, and maintaining non-GBrowse production nodes.''
 
  
−
== Administration  ==
+
== Architecture ==
  
−
=== Routine Administration Tasks ===
+
'''Software Platform'''
−
*[[NFS at WormBase]]
+
*[[Administration:Installing WormBase|Installing WormBase]] - ''How to get a basic installation of WormBase up and running''
−
* [[Cronjobs|Cronjobs]]
+
*[[Administration:Installing WormMine|Installing WormMine]] - ''How to get a basic installation of  WormMine up and running''
−
* [[Creating_a_Google_Sitemap|Creating a Google Sitemap]]
+
*[[Administration:WormBase Production Environment|Production Environment]] - ''Building and Maintaining the WormBase production environment; extends the "Installing WormBase" document''
−
*[[Managing Perl Libraries]] - ''Managing Perl libraries across projects and architectures''
+
* [[GBrowse Administration]] -- ''building, configuring, and maintaining production GBrowse nodes.''
−
*[[Managing GBrowse]] - ''Quick HowTo for managing GBrowse in development and production environments''
+
* [[Building WormMart|Building WormMart]] - ''How to convert a WormBase AceDB database into WormMart''
−
*[[Log file management and analysis|Log file management and analysis]] - ''rotating and analyzing logs.''
 
−
* [[Site_statistics|Site statistics]]
 
  
−
=== Load balancing and Failover  ===
+
'''Hardware Platform'''
−
*[[Building Squid|Building Squid]] - ''How to build and install Squid''  
+
*[[WormBase_Infrastructure|Hardware Platform]] - ''A complete accounting of WormBase compute resources.
−
*[[Configuring Squid|Configuring Squid]] - ''basic squid configuration at WormBase''
 
  
−
=== Monitoring and Crises Management ===
+
== Software Life Cycle ==
−
*[[Development Server Administration]] - ''Monitoring and fixing the development server''
+
* [https://docs.google.com/a/wormbase.org/document/d/1oPpj8d5gibUc-gpUZorl6ETT5baE6mp-v2bMedKauiA/ Software Life Cycle: 1. Build] -- ''Preparing a new release for the website''
−
* [[General_administration|General administration and monitoring notes]] - ''Partially redundant, sorry''
+
* [[Software Life Cycle: 2. Software development period|Software development period]] - ''Once a new database has been staged, the development phase begins in earnest on private development sites''
−
*[[Monitoring services and servers|Monitoring services and servers]]  
+
* [[Software Life Cycle: 3. QA/QC and Performance Benchmarking|QA/QC and Performance Benchmarking]] - ''Integrating changes and staging the code for QA/QC and performance testing prior to deployment''
−
*[[Crises Recovery Plan|Crises Recovery Plan]] - ''Everything breaks. Here's how to fix it.''
+
* [https://docs.google.com/a/wormbase.org/document/d/1KlweWzfxc9-uKxR1dJwuPfR4NPJs-H1S8Yxg_V1Ha8U/edit#heading=h.e2m5ps3gnzcs Software Life Cycle: 4. Production] -- ''Deploying a new release to production''
  
−
=== Frozen Releases ===
+
== Measuring Application Performance ==
−
*[[Building Frozen Releases]] - ''The most current documentation on how to build a frozen release''
 
−
==== Frozen Releases as Virtual Machines ====
 
−
* [[How_to_build_a_WormBase_Virtual_Machine|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|Configuring a server to host virtual machines]] -- ''quick guide to setting up a frozen release server''
 
−
* [[Managing_servers_hosting_virtual_machines|Managing servers hosting virtual machines]]
 
−
* [[How_to_build_a_frozen_release|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''
 
  
−
== Updates ==
+
* [[Website:Testing_And_Profiling|Unit Testing and Profiling]] - ''Testing and profiling protocol for the web application''
−
*[[Updating The Development Server]] - ''Updating the development server with a new release of the database''
+
* System Testing
−
*[[Building WormMart|Building WormMart]] - ''How to convert a WormBase AceDB database into WormMart''  
+
* [[Website:Validation|Standards Validation]] - ''Validation of HTML, CSS, XML''
 +
* Security Assessment
 +
* Accessibility
 +
* [[Website:Usability Testing|Usability Testing]] - ''usability testing strategies and evaluation''
 +
* [[Website:Browser Compatibility Statement|Browser Compatibility Testing]] - ''browser support matrix and testing protocol''
 +
* [[Website:Load Testing|Load Testing]] - ''Performance and load testing; historical benchmarks''
 +
----
  
−
== Developer Tools ==
+
== Routine Administration Tasks ==
 +
* [[Cronjobs|Cronjobs]] - ''a full accounting of all cronjobs at WB''
 +
* [[Creating_a_Google_Sitemap|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|Log file management and analysis]] - ''rotating and analyzing logs.''
 +
* [[Site_statistics|Site statistics]]
  
−
*Twitter: [http://twitter.com/wormbase General announcements]
+
== Monitoring and Crises Management ==
−
*FriendFeed: [http://friendfeed.com/wormbase WormBase FF room]
+
*[https://docs.google.com/a/wormbase.org/document/d/18oRqTtC-q1P1bPyLAjo4XkqMGzepPi5Be1w7CfLuzg8/edit?hl=en_US Crises Recovery Plan] - ''How to diagnose and recover from service interruptions.''
−
*[http://www.wormbase.org/forums/index.php?board=326.0 WormBase Forum: Developer Forum]  
+
*[https://docs.google.com/a/wormbase.org/document/d/18G-lemZ0zKXraQlzXqNmsUCWwZmjuUHIipF6uRd0R0k/edit Monitoring services and servers] - ''Keeping tabs on the production architecture''
  
−
== All Hands Meeting Agendas and Notes ==
+
== Frozen Releases ==
−
* [[2010.05 OICR WebDev Meeting]]
+
*[[Building Frozen Releases]] - ''The most current documentation on how to build a frozen release''
−
* [[WebDev_2010.03.17-Agenda_and_Minutes]]
 
  
−
== Source Code Repositories ==
+
= Deprecated Documentation =
  
−
''We use the distributed source code management system Mercurial. Projects are hosted on [http://bitbucket.org BitBucket].''
+
''The good word gone bad. Cruft. Lint. Maybe useful. Probably not.''
  
−
[[WormBase Source Code|How-To create, check out, and manage our repositories]]
+
==== Rearchitecture ====
 +
*[[Website:Development Milestones|Development Milestones]]
 +
*[[Website:Design Specifications|Requirements analysis / Design Specifications]]
 +
*[[Website:Rearchitecture Development Duties|Rearchitecture Development Duties]]
 +
* AceDB classes -> API progress matrix (index of classes; see [https://spreadsheets.google.com/a/wormbase.org/ccc?key=tygSYCz49YW5hyCcYMHUZ1Q#gid=2 official matrix])
 +
*[[HOWTO migrate a CGI|HOWTO migrate a CGI]] - ''quick overview of how to migrate an existing CGI into a Model, Controller, and View. Sparse''
  
−
*[http://bitbucket.org/tharris/wormbase WormBase] - ''The WormBase web application (public)''
+
==== Load balancing and Failover  ====
−
*[http://bitbucket.org/tharris/wormbase-admin WormBase-admin] - ''Administrative code (private)''
+
*[[Building Squid|Building Squid]] - ''How to build, install and configure Squid''
  
−
== Deprecated Documentation ==
+
==== Administration ====
−
 
+
*[[Formal_development_strategy|Formal development strategy]] - ''An overview of the development process at WormBase'' -- THE OLD VERSION
−
''The good word gone bad. Cruft. Lint. Maybe useful but probably not.''
+
*[[MySQL database replication|MySQL database replication]] - ''Mirroring mysql databases across production nodes''  
 
*[[Trac installation notes|Trac installation notes]]
 
*[[Trac installation notes|Trac installation notes]]
 
*[http://dev.wormbase.org/trac Trac Feature Tracker / Subversion repository]
 
*[http://dev.wormbase.org/trac Trac Feature Tracker / Subversion repository]
 
* [[Establishing the SVN repository]] - ''Setting up the subversion repository''
 
* [[Establishing the SVN repository]] - ''Setting up the subversion repository''
 +
* [[Managing GBrowse]] - ''Quick HowTo for managing GBrowse in development and production environments''
 +
*[[Website:Monitoring services|Monitoring services and servers]] - ''Monitoring services and servers''
 +
 +
==== Frozen Releases as Virtual Machines ====
 +
* [[How_to_build_a_WormBase_Virtual_Machine|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|Configuring a server to host virtual machines]] -- ''quick guide to setting up a frozen release server''
 +
* [[Managing_servers_hosting_virtual_machines|Managing servers hosting virtual machines]]
 +
* [[How_to_build_a_frozen_release|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''
 +
 +
 +
[[Category:Developer documentation]]

Latest revision as of 18:25, 18 June 2014

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.
  • Other ideas? Please update the wiki here!

New Employee Orientation

Project Management

Conference call agendas/minutes

Source Code Repositories

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

Recommended reading (learning git):

General Documentation

The Web Application

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

Development Guidelines

Testing

Help us maintain the site

Information for third party developers

Administration

Architecture

Software Platform

Hardware Platform

Software Life Cycle

Measuring Application Performance

Routine Administration Tasks

Monitoring and Crises Management

Frozen Releases

Deprecated Documentation

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

Rearchitecture

Load balancing and Failover

Administration

Frozen Releases as Virtual Machines

Retrieved from "https://wiki.wormbase.org/index.php?title=Developer_documentation&oldid=23624"