First, brute version of GIDS converter

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7694 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Adding images for DesignGG

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7695 42de9c89-b41c-0410-9fa9-f33e7b6bda7a


git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7696 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Adding designGG as a new app, with first versions of properties, db and ui files.

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7697 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Reworked xQTL Panacea GUI to also have the user groups, like the standalone version. Some components have been moved around as well.

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7698 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Removed file handler from LocalComputationResource because it was unused, and adjusted using classes accordingly.

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7699 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Parsing family relations from UliDb now works with lists too, so it is much faster

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7700 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Greatly slimmed down helper functions for special system tables. Adjusted storage dir plugin accordingly. In next phases this should be moved to a single admin panel for everyone (part of any application?) and smarter file storage management moved to the JDBCDatabase, to work seamlessly with the current path you can specificy in the properties file. (will need common functions such as getPath, setPath, validatePath)

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7701 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Used getExon_Id() instead of getExon() to be compliant with JPA.

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7705 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Rewrote query in order to be compliant with JPA.

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7706 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Removed JDBCDatabase in order to be compliant with JPA.

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7707 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
UliDb Converter now correctly parses parent relations. Original data is very messy, using different fields and different separators all the time...

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7708 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
In Matrix, filtering broke when you switched target type. Fixed this.

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7709 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Updates to the BOT

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7711 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Bot to web.xml for apache

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7712 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Option to true for me

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7713 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Improved and cleaned UliDb converter, so it can serve as an example for others.
Ran into trouble with measurement names "Gene" and "GeneState", which caused order of filter rules in ObservedValueMapper's resolveForeignKeys() to go awry. Similar issue to bug I filed yesterday. Solved it for now by renaming "Gene" to "GeneName".

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7714 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Removed JDBCDatabase in order to be compliant with JPA.

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7718 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Used constructor w/o arguments.

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7719 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Removed JDBCDatabase in order to be compliant with JPA.

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@7720 42de9c89-b41c-0410-9fa9-f33e7b6bda7a