Thanks for the stacktrace. It seems to be a bug in the Base1PluginExecuter plug-in. It is trying to remap the raw data associations after the bioassays have been merged. Obviously, this is not possible if there is no raw data stored in the first place. The Base1PluginExecuter need to be fixed with a check for this case.
I have created a ticket for this fix to be included with the BASE 2.17.2 release. Unfortunately there is no workaround. http://base.thep.lu.se/ticket/1610 /Nicklas On 2011-05-20 10:12, Irina 264 wrote: > > > from "Stack trace" tab: > > > > View job -- Run plugin: Base1PluginExecuter > > <javascript:Main.openTabControlHelp('7a1ebdaa616cc46f',%20'main',%20'null')> > > Name Run plugin: Base1PluginExecuter > Description > Priority 5 (1 = highest, 10 = lowest) > Status Error: Raw data for raw data type: Affymetrix is not stored in > the database. > Percent complete > unknown > > 100% > > Created 2011-05-20 18:10:30 > Scheduled 2011-05-20 18:11:10 > Started 2011-05-20 18:11:28 > Ended 2011-05-20 18:11:42 > Running time 14 seconds > Server vera097.its.monash.edu.au > Job agent /- none -/ > User Irina Rusinova > Experiment E-GEOD-6257 > Plugin Base1PluginExecuter (version 2.16.0) > Configuration MergeBioAssay > > net.sf.basedb.core.BaseException: Raw data for raw data type: Affymetrix > is not stored in the database. > at > net.sf.basedb.core.DynamicSpotQuery.joinRawData(DynamicSpotQuery.java:261) > at > net.sf.basedb.util.importer.spotdata.BaseFileImporter.createChildRawDataMapping(BaseFileImporter.java:510) > at > net.sf.basedb.util.importer.spotdata.BaseFileImporter.doImport(BaseFileImporter.java:346) > at > net.sf.basedb.plugins.Base1PluginExecuter.importData(Base1PluginExecuter.java:1471) > at > net.sf.basedb.plugins.Base1PluginExecuter.run(Base1PluginExecuter.java:774) > at > net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116) > at > net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:510) > at java.lang.Thread.run(Thread.java:636) > > > > > > > Date: Fri, 20 May 2011 09:21:12 +0200 > > From: nick...@thep.lu.se > > To: basedb-users@lists.sourceforge.net > > Subject: Re: [base] reporters on MergeBioAssay plug-in > > > > On 2011-05-20 09:04, Irina 264 wrote: > > > Hi Nicklas, > > > > > > Thanks for the quick reply. > > > > > > I run RMAExpress with Affy data, then I done filtering with equal size > > > of arrays afterwards. > > > > > > Then I run MergeBioAssay (with Base1pluginExecuter) to find average > > > between replicates (grouping assays by control and treatment with > method > > > ‘arithmetic mean of intensity) and have this error message: “Error: Raw > > > data for raw data type: Affymetrix is not stored in the database.” > > > > > > When I use Agilent data, i have no problems. > > > > > > Did I explain better? > > > > Yes... but I still have no idea why the error about raw data is coming > > up... As far as I know the Merge BioAssay plug-in doesn't use raw data > > for the calculations. It would be useful to get a complete stacktrace of > > the error in order to locate the source of the problem. > > > > Do you get the error while you are configuring the job? If so you should > > be able to display more error information by clicking on the little [+] > > icon in the configuration wizard. > > > > Or, if you get the error while the plug-in is running, there is a "Stack > > trace" tab in the job dialog. > > > > > > /Nicklas > > > > > > > ------------------------------------------------------------------------------ > > What Every C/C++ and Fortran developer Should Know! > > Read this article and learn how Intel has extended the reach of its > > next-generation tools to help Windows* and Linux* C/C++ and Fortran > > developers boost performance applications - including clusters. > > http://p.sf.net/sfu/intel-dev2devmay > > _______________________________________________ > > The BASE general discussion mailing list > > basedb-users@lists.sourceforge.net > > unsubscribe: send a mail with subject "unsubscribe" to > > basedb-users-requ...@lists.sourceforge.net > > > > ------------------------------------------------------------------------------ > What Every C/C++ and Fortran developer Should Know! > Read this article and learn how Intel has extended the reach of its > next-generation tools to help Windows* and Linux* C/C++ and Fortran > developers boost performance applications - including clusters. > http://p.sf.net/sfu/intel-dev2devmay > > > > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > basedb-users-requ...@lists.sourceforge.net ------------------------------------------------------------------------------ What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
