This is a known problem and has been fixed in 2.4.2 which was released yesterday.
If you don't want to upgrade you can manually give the Base1PluginExecuter more permissions. Go to Administrate -> Plugins -> Defninitions Open the edit dialog for the Base1PluginExecuter Switch to the 'Permissions' tab Find the 'Extra value types' entry in the list and then de-select the 'Use' checkbox in the 'Denied' column. /Nicklas Chad Matsalla wrote: > Greetings, > > I'm using base-2.4.1 (compiled from 2.4.2-src) on tomcat 6.0.14. > > I'm stumped on this one. My objective is to parse the output from a > base1 plugin. The output from the plugin is a basefile that looks like > this: > BASEfile > section spots > columns position reporter assayData > assayFields intensity1 intensity2 scaled ch1_sd_pmt_merged > ch2_sd_pmt_merged > assays 70 > setExtraFloats scaled ch1_sd_pmt_merged ch2_sd_pmt_merged > % > 1 25411 374 385 0 429 331 > 2 19204 524 583 0 478 343 > (much more data here) > > The exception I get is below[1]. > > I went to the 'Extra Value types' administration screen and I see > 'ch1_sd_pmt_merged','ch2_sd_pmt_merged', and 'scaled'. When I click on > 'scaled' I see 'Permissions on this item: Read, Use, Write, Delete'. > > Can anybody offer me some advice on a fix for this? > > Thank you! > > Chad Matsalla > > > > > > [1] > net.sf.basedb.core.BaseException: Permission denied: Not allowed to use > Extra value type[id=1; name=scaled] > at > net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:429) > at java.lang.Thread.run(Thread.java:595) > Caused by: net.sf.basedb.core.PermissionDeniedException: Permission > denied: Not allowed to use Extra value type[id=1; name=scaled] > at > net.sf.basedb.core.BasicItem.checkPermission(BasicItem.java:110) > at > net.sf.basedb.core.ExtraValue.setExtraValueType(ExtraValue.java:229) > at net.sf.basedb.core.ExtraValue.getNew(ExtraValue.java:83) > at > net.sf.basedb.core.BioAssaySet.getSpotExtraValueBatcher(BioAssaySet.java:924) > at > net.sf.basedb.plugins.Base1PluginExecuter.importData(Base1PluginExecuter.java:1424) > at > net.sf.basedb.plugins.Base1PluginExecuter.run(Base1PluginExecuter.java:698) > at > net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:89) > at > net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:421) > ... 1 more > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
