Difference between revisions of "Developer documentation"

From WormBaseWiki
Jump to navigationJump to search
 
(37 intermediate revisions by 4 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 =
Line 9: Line 43:
 
*[[Conference call agendas and minutes| Conference call agendas and minutes (WebDev team)]]
 
*[[Conference call agendas and minutes| Conference call agendas and minutes (WebDev team)]]
 
*[[Project meeting agendas and minutes]]
 
*[[Project meeting agendas and minutes]]
*[[WormMine development status]]
 
 
*[[InterMine Strategy Meetings]]
 
*[[InterMine Strategy Meetings]]
  
Line 15: Line 48:
  
 
''We use the distributed source code management system git.  Projects are hosted on [http://github.org/WormBase Github].''
 
''We use the distributed source code management system git.  Projects are hosted on [http://github.org/WormBase Github].''
 
[[WormBase Source Code|How-To create, check out, and manage our repositories]]
 
  
 
*[http://github.org/WormBase/website website] - ''The WormBase web application (public)''
 
*[http://github.org/WormBase/website website] - ''The WormBase web application (public)''
Line 28: Line 59:
 
*[[SOPs|Internal documentation and standard operating procedures]]
 
*[[SOPs|Internal documentation and standard operating procedures]]
 
*[[Feature WishList]]
 
*[[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|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]]
 
 
= Web Site Development Guidelines =
 
 
*[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''
 
*[[WormBase Release Workflow|WormBase Release Workflow]] -- ''Project-wide schedule that documents what is happening when and where.''
 
*[[Development_workflow_-_webdev|Formal Development Strategy]] -- ''An overview of the development process at WormBase''
 
*[[Coding standards|Coding standards]]
 
*[[Developer_notes|Developer notes]] -- ''Best practices, conventions, etc''
 
*[[Browser Support Statement]] -- ''official graded browser support statement''
 
 
== Testing ==
 
*[[Unit Testing]]
 
 
== Help us maintain the site ==
 
*[[Website:Contribute from GitHub|Contribute from GitHub]]
 
  
 
= The Web Application =
 
= The Web Application =
Line 71: Line 76:
  
 
* [[Website:WormMine| WormMine]] -- ''How to install, update, and maintain the InterMine instance at WormBase''
 
* [[Website:WormMine| WormMine]] -- ''How to install, update, and maintain the InterMine instance at WormBase''
 +
** [[Website:WormMine Builds]] -- Summary stats of WormMine builds
 
*[[Website:Contribute_from_GitHub|Contribute from Github]]
 
*[[Website:Contribute_from_GitHub|Contribute from Github]]
  
Line 80: Line 86:
 
* [[Website:MobileViews| Views]] -- ''Details about the views''
 
* [[Website:MobileViews| Views]] -- ''Details about the views''
 
* [[Website:MobileWidgets| Widgets Porting]] -- ''Details about the porting of widgets in the mobile website/app''
 
* [[Website:MobileWidgets| 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|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]]
 +
 +
= Development Guidelines =
 +
* [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''
 +
 +
== Testing ==
 +
*[[Unit Testing]]
 +
 +
== Help us maintain the site ==
 +
*[[Website:Contribute from GitHub|Contribute from GitHub]]
  
 
= Information for third party developers =
 
= Information for third party developers =
Line 100: Line 132:
  
 
== Software Life Cycle ==
 
== Software Life Cycle ==
* [[Software Life Cycle: 1. Build https://docs.google.com/a/wormbase.org/document/d/1oPpj8d5gibUc-gpUZorl6ETT5baE6mp-v2bMedKauiA/]] -- ''Preparing a new release for the website''
+
* [https://docs.google.com/a/wormbase.org/document/d/1oPpj8d5gibUc-gpUZorl6ETT5baE6mp-v2bMedKauiA/ Software Life Cycle: 1. Build] -- ''Preparing a new release for the website''
* [[Software Life Cycle: 1. Updating The Development Server|Staging a new release]] - ''how to stage a new release of WormBase on the development server and cloud instances''
 
 
* [[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''
 
* [[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''
 
* [[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''
 
* [[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''
* [[Software Life Cycle: 4. Updating The Production Servers|Release to Production]] - ''Deploying the web app; updating to a new release of the database''
+
* [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''
  
 
== Measuring Application Performance ==
 
== Measuring Application Performance ==

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