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Release Notes

ArkDB Web Application

Current Release: arkdb-webapp-2.20170907 (Fri, Sep 08, 2017)

Web Application to access data in the ArkDB database (a public repository for genome mapping data from farmed and other animal Species). Mapping Data can be explored textually through dynamically generated web pages, and maps can be drawn using ArkMAP, a desktop Java program downloadable using Web Start.

     
 

RELEASE HISTORY

 
 

arkdb-webapp-2.20170907 (Fri, Sep 08, 2017)

    Bug Fixes
   
  • Security patches for struts2.
  • Security patches for struts1.
  • Fixed broken jnlp file editing for ArkMAP display of selected files in ArkDB and GridQTL.
 
 

arkdb-webapp-2.20140508 (not known)

    Bug Fixes
   
  • Security patches.
 
 

arkdb-webapp-2.20131021 (Mon, Oct 21, 2013)

    Bug Fixes
   
  • Security patch.
 
 

arkdb-webapp-2.20130830 (Fri, Aug 30, 2013)

    Bug Fixes
   
  • Various Security patches.
 
 

arkdb-webapp-2.20130405 (Fri, Apr 05, 2013)

    New Features
   
  • Moved the ArkMAP help file to static pages at bioinformatics.roslin.ed.ac.uk/arkmap/help. Corrected all links in the web app to account for this, and created a redirect page from old http://www.thearkdb.org/webstarthelp/index.html to new location.
    Bug Fixes
   
  • fixed broken links to ArkMAP that appeared on several second level pages (search, find maps and release notes)
  • SVN command changed again (drop -r HEAD)
 
 

arkdb-webapp-2.20121205 (Wed, Dec 05, 2012)

    New Features
   
  • Moved the ArkMAP download information to static pages at bioinformatics.roslin.ed.ac.uk/arkmap. Corrected all links in the webapp to account for this, and changed the download.jsp page to redirect to the static pages (because ArkWS still refers to this page).
 
 

arkdb-webapp-2.20120716 (Mon, Jul 16, 2012)

    New Features
   
 
 

arkdb-webapp-2.20120522 (Tue, May 22, 2012)

    New Features
   
 
 

arkdb-webapp-2.20120411 (Wed, Apr 11, 2012)

    New Features
   
  • Production version, this app and webservices point at newarkdb on db-prod.thearkdb.org (new expanded schema). ArkDB database schema has been modified to allow GridQTL data to be saved. Many of the underlying arkdb code artifacts have been changed to use the new schema and provide further CRUD functionality.
  • The version of ArkMAP provided now uses JEnsembl API code to connect to Ensembl databases, and no longer uses the Biomart webservices. ArkMAP itself is downloaded not from within the web app, but deployed separately as a static resource at the url /webstart.
  • Removed Applet for drawing - now we only use the Web Start application ArkMAP
  • Removed links to and pages for Maven Code Site. /Code and artifacts jars temporarily taken away whilst site under redevelopment.
  • Added menu links and some explanation for the ArkDB:GridQTL system. But links to GridQTL application have been disrupted until this goes live.
  • Added links and page for Privacy/Cookie policy.
  • ArkDB webapp includes gff files for ensembl mappings of ark markers (at http://www.thearkdb.org/arkdb/AssemblyMaps)
  • ArkMAP updated to ENSEMBL release 66
  • ArkMAP now allows retrieval of maps from ArkDB by Accession ID
  • ArkMAP connections to Ensembl are now version aware
 
 

arkdb-webapp-2.020100823 (Mon, Aug 23, 2010)

    New Features
   
  • Separated the ArkMAP Web Start download site out of the ArkDB Web Application. This will allow the ArkMAP application to be updated without alterring the Web Application.
  • Updated ArkMAP to fix some bugs with Ensembl release 59. These arose because the Turkey assembly has been removed from Ensembl and Biomart.
 
 

arkdb-webapp-2.0.20100406 (Tue, Apr 06, 2010)

    Bug Fixes
   
  • RT4675 fixed ArkMAP/applet bug in loading projected copies of maps which have been loaded directly from the ArkDB website (prevents triggering lazy load).
 
 

arkdb-webapp-2.0.20100401 (Thu, Apr 01, 2010)

    New Features
   
  • All code modules were updated to include the GPLv3 licence.
    Bug Fixes
   
  • The code documentation sites which were to be made available at http://www.thearkdb.org/code were not activated in the previous release, now that they include licence details they will be.
  • RT4569 Problems with the hyperlinks out from the code sites were resolved.
  • RT4658 Deployed the code sites statically on Apache, with appropriate rewrites to alias to home domain (www.tharkdb.org)
  • added a robots.txt file to try and limit crawing by google bot etc.
 
 

arkdb-webapp-2.0.20100324 (Wed, Mar 24, 2010)

    New Features
   
  • New version (2.2) of ArkMAP included. Provides ability to find orthologues of Ensembl genes, to download regions of conserved synteny to an Ensembl map from other species in Ensembl, and displays various colour-coded orthology relationships between Ensembl genes on maps. Also has print function enabled. Fully featured Axis context menu now enables map zooming, projection, ensembl import and orthology searching. Connects to ENSEMBL v57.
  • Updated ArkMAP help documentation at http://www.thearkdb.org/webstarthelp/index.html.
  • Updated version of the ArkDB applet, to version 3.4.
  • Rebuilt whole ArkDB code base to provide mvn-sites documenting all code artifacts. These sites are available at http://www.thearkdb.org/code.
  • The code and source artifacts are available for download from these code sites.
  • Redesigned site navigation menus.
  • Refactored POM inheritance. Made a release version of the parent POM that provides greater inheritance to the modules, and no longer holds the dependency version numbers.
    Bug Fixes
   
  • RT4628, RT4630, RT4643 fixed ArkMAP bugs in loading user maps.
  • RT4631, RT4635 fixed ArkMAP bugs in coordinate selection on flipped maps, and slightly inaccurate coordinate labelling on axis.
  • RT4636, fixed ArkMAP bug in loading projected copies of maps (prevented triggering lazy load).
 
 

arkdb-webapp-2.0.20100106 (Wed, Jan 06, 2010)

    New Features
   
  • Code all recompiled to use the new shared Roslin genetic model
  • New version 3.0.5SIGN of the map drawing applet compiled and signed, uses the shared Roslin genetic model and is dependant on Java1.5 JVM (should work on legacy pre-Intel MACs).
  • New version 2.0 of ArkMAP included - with improved drawing configuration features (rescaling, resizing and dragging maps etc.). Dependant on Java1.6 JVM (not available for legacy pre-Intel MACs).
    Bug Fixes
   
  • Fixed Bug RT 4491: generates sensible error message for Ensembl datasources with no chromosome maps
 
 

arkdb-webapp-1.0.20091130 (Mon, Nov 30, 2009)

    New Features
   
  • Renamed the ArkDB Map Drawing application: ArkMAP
  • Changed the startup parameters for ArkMAP to give it more memory, so that multiple large maps can be loaded.
  • Added help pages on using ArkMAP ( www.thearkdb.org/webstarthelp)
  • Updated the desktop icons downloaded with ArkMAP
  • Added Release History Page ( www.thearkdb.org/Release.htm)
    Bug Fixes
   
  • Fixed Bug RT 4386: some markers were displaying the wrong species (when mapped on more than one species)
  • Fixed Bug RT 4422: ArkMAP : fixed bug when saving maps linked in from biomart which have ark markers superimposed
 
 

arkdb-webapp-1.0.20091005 (Mon, Oct 05, 2009)

    New Features
   
  • Added ability to search for Sequence (Assembly) Maps.
  • Webstart download for Map Drawing Application v1.4.
 
 

arkdb-webapp-1.0.20090902 (Wed, Sep 02, 2009)

    New Features
   
  • Reintroduced the ability to display Sequence (Assembly) Maps in ArkDB (previously hidden from users).
  • Added links to the ArkDB Web Services Application
  • Webstart download for Map Drawing Application v1.3.
 
 

arkdb-webapp-1.0.20090429 (Wed, Apr 29, 2009)

    New Features
   
  • First release to use stable release versions of all code dependencies
  • The embedded applet is now a permanently frozen Java1.5 version and digitally signed (1.0.20090305BJAVAsigned) The applet code is now frozen as Java1.5 compliant to allow use on older browsers and Macs.
  • Introduces webstart download for Map Drawing Application v1.0 (requires Java1.6).
  • Maps can now be drawn with either the embedded applet or by running the Map Drawing Application on the client machine. A user's preference is remembered throughout a session.
 
 

arkdb-webapp-1.0.20090115 (Thu, Jan 15, 2009)

 
 

arkdb-webapp-1.0.20081222 (Mon, Dec 22, 2008)

    New Features
   
  • Web App is now fully UTF8 enabled allowing display of and searching with extended character sets
  • Added the Roslin favicon to all pages on the Web App: will display in user's browser
 
 

arkdb-webapp-1.0.20081202 (Tue, Dec 02, 2008)

    Bug Fixes
   
  • Fixed bug RT3825: displaying duplicate maps erroneously
  • Fixed bug RT3859: bad hyperlinks created from missing publication records
 
 

arkdb-webapp-1.0.20081111 (Tue, Nov 11, 2008)

    New Features
   
  • First archived version of the ArkDB Web App
 
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