Difference between revisions of "Developer documentation"

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This page contains information pertinent to employees of WormBase.  
 
This page contains information pertinent to employees of WormBase.  
  
−
= Project Management =
+
= Navigating and Editing the Developer Documentation =
−
*[[Project Calendar|Project Calendar]]
 
−
*[[Conference call agendas and minutes]]
 
−
*[[Project meeting agendas and minutes]]
 
−
*[[Linking To WormBase|Linking To WormBase]]
 
−
*[[Suggested pre-release data checks|Suggested pre-release data checks]]
 
−
*[[SOPs|Internal documentation and standard operating procedures]]
 
−
*[[modENCODE Analysis & metadata discussion|modENCODE Analysis & metadata discussion]]
 
−
*[[Genome Standards|What criteria should a genome meet before we accept it for integration?]]
 
−
*[[WormBase Models]]
 
−
*[[Orthologs: use cases for searches]]
 
−
*[[Genome sequence changes]]
 
  
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= Web Site Documentation =
 
  
−
* [[Using_private_development_sites|Installing the Web Application (legacy code) ]] - ''Here's how to install the classic WormBase web site for development purposes''
 
−
*[[Installing the Web Application|Installing the Web Application]] - ''Here's how to install the WormBase web application -- including Catalyst -- on your system''
 
−
*[[HOWTO migrate a CGI|HOWTO migrate a CGI]] - ''quick overview of how to migrate an existing CGI into a Model, Controller, and View. Sparse''
 
−
*[[Website:Design Specifications|Requirements analysis / Design Specifications]]
 
  
−
== Development Milestones ==
+
== [[:Category:Web Dev| Web Dev Category Hierarchy (Under Construction)]] ==
  
−
=== July 14 - July 30th ===
+
'''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.'''
−
* Coronate Czars
 
−
* Coding standards and best practices for CSS, Javascript, API in place
 
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* Release new pages to production powered by the new architecture (classic view only)
 
  
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=== July 30th - August 31st ===
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<categorytree mode=pages showcount="on" hideroot="on" depth=4 >Web Dev</categorytree>
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* http://wiki.wormbase.org/index.php/AceOjbect_Redesign_Page
 
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* Finish API development of critical classes
 
−
* Finish migration of prominent CGI-based pages to new architecture and release into production (classic view only)
 
−
* Solidify look-and-feel of new site: site map, browsing paths, design patterns, navigation
 
  
−
=== September 1st ===
+
== 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)]] :
  
−
* Begin beta testing of new site to invited parties
+
<code><nowiki>
 +
[[Category: Getting Started (Web Dev)]]
 +
</nowiki></code>
  
−
=== October 1st - November 1st ===
+
</blockquote>
  
−
* Begin public beta testing of new site
+
* '''Update''', deprecate or remove old documentation when appropriate.
−
* Launch UI and general surveys.
 
  
−
=== November 1st - December 1st ===
+
* 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'''.
  
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* Address survey issues
+
* Additional guidelines on [[Documentation and Communication Standards]]
−
* Test, test, test
 
  
−
=== December 1st ===
+
* '''Other ideas?''' Please update the wiki here!
  
−
* Go Live with new site
+
= 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]]
  
−
== Division of Labor ==
+
= Project Management =
 +
*[[Project Calendar|Project Calendar (Google)]]
  
−
''Duties, current as of July 2010.''
+
==== Conference call agendas/minutes ====
  
−
=== Configuration Czar ===
+
*[[Conference calls| Conference call agendas and minutes (All WormBase)]]
−
''View and application configuration''
+
*[[Conference call agendas and minutes| Conference call agendas and minutes (WebDev team)]]
−
* Keep configuration files neat, orderly, and documented
+
*[[Project meeting agendas and minutes]]
−
* Create new configuration for hard-coded variables and UI elements when needed.
+
*[[InterMine Strategy Meetings]]
−
* Evangelize configuration standards and formatting to dev group
 
  
−
=== CSS Czar ===
+
==== Source Code Repositories ====
−
''Responsible for the maintenance of CSS files''
 
−
* Develop CSS best practices for the dev group
 
−
* Keep CSS files tidy and organized  function
 
−
* Help enforce standard CSS markup in templates
 
  
−
=== Javascript Czar ===
+
''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)''
  
−
=== Template Czar ===
+
Recommended reading (learning git):
−
''Define and document shared elements, keep template directory organized, enforce standards''
+
* [http://try.github.io/levels/1/challenges/1 try.gihub.io]
  
 +
= General Documentation =
 +
*[[Co-op Documentation]]
 +
*[[SOPs|Internal documentation and standard operating procedures]]
 +
*[[Feature WishList]]
  
 +
= The Web Application =
  
−
Major UI features
+
* [[Website:Application overview|Application overview]] - ''An overview of the web application, including MVC structure, request flow, caching, etc''
−
** Searches Czar
+
* [[Website:Configuration|Configuration]] -- ''Application and view configuration: formatting and standards''
−
** External URLs
+
* [[Website:WormBase::API|WormBase::API]] -- ''The WormBase data model, maintained external to the web application''
−
=== Controller ===
+
* [[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"
  
−
=== WormBase::API Czar ===
+
* [[Website:WormMine| WormMine]] -- ''How to install, update, and maintain the InterMine instance at WormBase''
−
''document shared API methods; enforce coding standards''
+
** [[Website:WormMine Builds]] -- Summary stats of WormMine builds
 +
*[[Website:Contribute_from_GitHub|Contribute from Github]]
  
−
=== Testing Czar ===
+
== The Mobile Website ==
−
* Develop and document test requirements for the dev group
+
* [[Website:Mobile| Mobile]] -- ''Overview of the mobile website''
−
* Ensure adequate test coverage and performance
+
* [[Website:MobileRouter| Router]] -- ''A definition of the possible routes of the mobile website''
−
* Develop global View and API tests
+
* [[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 =
  
 +
*[[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]]
  
−
* Profiling Czar
+
= 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''
−
== Measuring Progress ==
+
*[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''
−
* [[AceOjbect_Redesign_Page|AceDB classes -> API progress matrix]]
+
*[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)]]''
−
*[http://spreadsheets.google.com/ccc?key=pHvlNLMCZIv1KBoy8ZhbZXA&hl=en Migration matrix (GoogleDoc)]
+
*[[Development_workflow_-_webdev|Formal Development Strategy]] -- ''An overview of the development process at WormBase''
−
 
+
*[[Documentation and Communication Standards|Documentation and Communication Standards]]
−
== Coding standards and Best Practices ==
 
−
*[[Developer_notes|Developer notes]] - ''Best practices, conventions, etc''
 
 
*[[Coding standards|Coding standards]]  
 
*[[Coding standards|Coding standards]]  
−
*[[Formal_development_strategy|Formal development strategy]] - ''An overview of the development process at WormBase''
+
*[[Developer_notes|Developer notes]] -- ''Best practices, conventions, etc''
 +
*[[Browser Support Statement]] -- ''official graded browser support statement''
  
 
== Testing ==
 
== Testing ==
 +
*[[Unit Testing]]
  
−
* Unit testing
+
== Help us maintain the site ==
−
* System Testing
+
*[[Website:Contribute from GitHub|Contribute from GitHub]]
−
* Validation (HTML/CSS/XML)
 
−
* Security
 
−
* Accessibility
 
−
* Usability
 
−
* Browser compatability
 
−
* Performance and stress testing
 
  
−
== Software platform  ==
+
= Information for third party developers =
  
−
*[[Application overview|Application overview]] - ''A quick tour through the software platform''
+
*[[Linking To WormBase|Linking To WormBase]]  
  
−
=== Configuration ===
+
= Administration  =
  
−
=== WormBase::API ===
+
== Architecture ==
−
*[[Common Model elements|Common Model elements]] - ''reference list of common model elements like Species''
 
−
*[[Website:Data Structure| Data structure documentation]] - ''codified data structure that should be returned by API classes''
 
  
−
=== View ===
+
'''Software Platform'''
−
*[[Website:Template Overview| Template Overview]] -- ''a quick tutorial on the templating system''
+
*[[Administration:Installing WormBase|Installing WormBase]] - ''How to get a basic installation of WormBase up and running''
−
*[[Website:Common Template Elements| Common template elements]] -- ''how to include common elements like references and species in a page''
+
*[[Administration:Installing WormMine|Installing WormMine]] - ''How to get a basic installation of  WormMine up and running''
−
* Things to document: evidence handling, linking entities, external URLs, searches
+
*[[Administration:WormBase Production Environment|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|Building WormMart]] - ''How to convert a WormBase AceDB database into WormMart''
  
−
=== Model ===
+
'''Hardware Platform'''
 +
*[[WormBase_Infrastructure|Hardware Platform]] - ''A complete accounting of WormBase compute resources.
  
−
=== Controller ===
+
== Software Life Cycle ==
 +
* [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: 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''
 +
* [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''
  
−
== Hardware platform  ==
+
== Measuring Application Performance ==
  
−
*[[MySQL database replication|MySQL database replication]] - ''Mirroring mysql databases across production nodes''  
+
* [[Website:Testing_And_Profiling|Unit Testing and Profiling]] - ''Testing and profiling protocol for the web application''
−
*[[Performance optimization|Performance optimization]] - ''Memory, Disk, and Network I/O troubleshooting''  
+
* System Testing
−
*[[WormBase_Infrastructure|WormBase Infrastructure]] - ''A complete accounting of WormBase compute resources and topology.
+
* [[Website:Validation|Standards Validation]] - ''Validation of HTML, CSS, XML''
−
*[[WormBase Development Environment|WormBase Development Environment]] - ''Building, Configuring, and Administering the WormBase development server''
+
* 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''
 +
----
  
−
* [[GBrowse Administration]] -- ''building, configuring, and maintaining production GBrowse nodes.''
+
== Routine Administration Tasks ==
−
* [[Webserver Administration]] -- ''building, configuring, and maintaining non-GBrowse production nodes.''
+
* [[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''
−
== Administration  ==
 
−
 
 
−
=== Routine Administration Tasks ===
 
−
* [[Deployment|Deployment]] - ''How to deploy the web app for production use''
 
−
* [[Cronjobs|Cronjobs]]
 
−
* [[Creating_a_Google_Sitemap|Creating a Google Sitemap]]
 
 
* [[Managing Perl Libraries]] - ''Managing Perl libraries across projects and architectures''
 
* [[Managing Perl Libraries]] - ''Managing Perl libraries across projects and architectures''
−
* [[Managing GBrowse]] - ''Quick HowTo for managing GBrowse in development and production environments''
 
 
* [[Log file management and analysis|Log file management and analysis]] - ''rotating and analyzing logs.''
 
* [[Log file management and analysis|Log file management and analysis]] - ''rotating and analyzing logs.''
 
* [[Site_statistics|Site statistics]]
 
* [[Site_statistics|Site statistics]]
  
−
=== Updates ===
+
== Monitoring and Crises Management ==
−
* [[Updating The Development Server]] - ''Updating the development server with a new release of the database''
+
*[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.''
−
* [[Updating The Production Servers]] - ''Updating production environments with a new release of the database''
+
*[https://docs.google.com/a/wormbase.org/document/d/18G-lemZ0zKXraQlzXqNmsUCWwZmjuUHIipF6uRd0R0k/edit Monitoring services and servers] - ''Keeping tabs on the production architecture''
−
* [[Building WormMart|Building WormMart]] - ''How to convert a WormBase AceDB database into WormMart''  
 
  
−
=== Load balancing and Failover  ===
+
== Frozen Releases ==
−
*[[Building Squid|Building Squid]] - ''How to build and install Squid''
 
−
*[[Configuring Squid|Configuring Squid]] - ''basic squid configuration at WormBase''
 
−
 
 
−
=== Monitoring and Crises Management ===
 
−
*[[Development Server Administration]] - ''Monitoring and fixing the development server''
 
−
* [[General_administration|General administration and monitoring notes]] - ''Partially redundant, sorry''
 
−
*[[Monitoring services and servers|Monitoring services and servers]]
 
−
*[[Crises Recovery Plan|Crises Recovery Plan]] - ''Everything breaks. Here's how to fix it.''
 
−
 
 
−
=== Frozen Releases ===
 
 
*[[Building Frozen Releases]] - ''The most current documentation on how to build a frozen release''
 
*[[Building Frozen Releases]] - ''The most current documentation on how to build a frozen release''
  
−
== Developer Tools ==
+
= Deprecated Documentation =
  
−
*Twitter: [http://twitter.com/wormbase General announcements]
+
''The good word gone bad. Cruft. Lint. Maybe useful. Probably not.''
−
*FriendFeed: [http://friendfeed.com/wormbase WormBase FF room]
 
−
*[http://www.wormbase.org/forums/index.php?board=326.0 WormBase Forum: Developer Forum]
 
  
 +
==== 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''
  
−
== Source Code Repositories ==
+
==== Load balancing and Failover  ====
 +
*[[Building Squid|Building Squid]] - ''How to build, install and configure Squid''
  
−
''We use the distributed source code management system Mercurial.  Projects are hosted on [http://bitbucket.org BitBucket].''
+
==== Administration ====
−
 
+
*[[Formal_development_strategy|Formal development strategy]] - ''An overview of the development process at WormBase'' -- THE OLD VERSION
−
[[WormBase Source Code|How-To create, check out, and manage our repositories]]
+
*[[MySQL database replication|MySQL database replication]] - ''Mirroring mysql databases across production nodes''  
−
 
 
−
*[http://bitbucket.org/tharris/wormbase WormBase] - ''The WormBase web application (public)''
 
−
*[http://bitbucket.org/tharris/wormbase-admin WormBase-admin] - ''Administrative code (private)''
 
−
 
 
−
== Deprecated Documentation ==
 
−
 
 
−
''The good word gone bad. Cruft. Lint. Maybe useful. Probably not.''
 
−
*[[NFS at WormBase]]
 
 
*[[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 ====
 
==== Frozen Releases as Virtual Machines ====
Line 203: Line 192:
 
* [[How_to_build_a_frozen_release|How to build a frozen release]] -- ''how to configure a WormBase VM as a frozen release server''
 
* [[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''
 
* [[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"