Hi Abhishek, Sorry, I initially thought your message was about the new core batch importers.
Yes, Nicklas is right, it looks like your zip file is missing the cdf file. Currently this needs to be included for Affy imports. Try again with this included. Cheers Micha ================================== Dr Micha M Bayer Bioinformatics Specialist Genetics Programme The Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland, UK Telephone +44(0)1382 562731 ext. 2309 Fax +44(0)1382 562426 http://www.scri.ac.uk/staff/michabayer ================================== > -----Original Message----- > From: Abhishek Goel [mailto:abhishekspe...@gmail.com] > Sent: 12 May 2009 00:18 > To: basedb-users@lists.sourceforge.net > Subject: Re: [base] batch data importer > > Hello, > > The stacktrace for the issue is below. Thank you so much for taking the > time to help. > > Abhishek > > > > experiment: Experiment[id=102; name=groner] file selected: Groner.zip > zipFile is located in dir Directory[id=23; name=dhglab03] new subDir = > Groner110509_155651 quotaValue for user User[id=1; name=Root] = -1 > currentDiskUsage = 942474865 remainingSpace = -942474866 zipFileSize = > 170749391 unpacking May 11, 2009 3:56:58 PM > org.apache.catalina.startup.HostConfig deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml May > 11, 2009 3:57:08 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml May > 11, 2009 3:57:18 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml > numUnpackedFiles = 17 BatchDataImport importData dir = > Groner110509_155651 rawDataType = Affymetrix instantiating dataFiles > array of length 16 affy data -- iterating over file names file name = > 128238-128234.CEL, extension = CEL setting dataFiles[0] to file 128238- > 128234.CEL file name = 113177-108460.CEL, extension = CEL setting > dataFiles[1] to file 113177-108460.CEL file name = 113168-108451.CEL, > extension = CEL setting dataFiles[2] to file 113168-108451.CEL file > name = 113163-108446.CEL, extension = CEL setting dataFiles[3] to file > 113163-108446.CEL file name = 113162-108445.CEL, extension = CEL > setting dataFiles[4] to file 113162-108445.CEL file name = 113166- > 108449.CEL, extension = CEL setting dataFiles[5] to file 113166- > 108449.CEL file name = 113167-108450.CEL, extension = CEL setting > dataFiles[6] to file 113167-108450.CEL file name = 113169-108452.CEL, > extension = CEL setting dataFiles[7] to file 113169-108452.CEL file > name = 113172-108455.CEL, extension = CEL setting dataFiles[8] to file > 113172-108455.CEL file name = 113170-108453.CEL, extension = CEL > setting dataFiles[9] to file 113170-108453.CEL file name = 108461- > 108444.CEL, extension = CEL setting dataFiles[10] to file 108461- > 108444.CEL file name = 113171-108454.CEL, extension = CEL setting > dataFiles[11] to file 113171-108454.CEL file name = 113173-108456.CEL, > extension = CEL setting dataFiles[12] to file 113173-108456.CEL file > name = 113174-108457.CEL, extension = CEL setting dataFiles[13] to file > 113174-108457.CEL file name = 128235-128231.CEL, extension = CEL > setting dataFiles[14] to file 128235-128231.CEL file name = 128237- > 128233.CEL, extension = CEL setting dataFiles[15] to file 128237- > 128233.CEL file name = 128236-128232.CEL, extension = CEL setting > dataFiles[16] to file 128236-128232.CEL > java.lang.ArrayIndexOutOfBoundsException: 16 > at sbrn.base.BatchDataImport.importData(BatchDataImport.java:297) > at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:137) > at > net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest > .java:110) > at > net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java > :506) > at java.lang.Thread.run(Thread.java:619) > May 11, 2009 3:57:28 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml May > 11, 2009 3:57:38 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml May > 11, 2009 3:57:48 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml May > 11, 2009 3:57:58 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml May > 11, 2009 3:58:08 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml May > 11, 2009 3:58:18 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml May > 11, 2009 3:58:28 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml May > 11, 2009 3:58:38 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml May > 11, 2009 3:58:48 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml May > 11, 2009 3:58:59 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml May > 11, 2009 3:59:09 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml May > 11, 2009 3:59:19 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml May > 11, 2009 3:59:29 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml May > 11, 2009 3:59:39 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml May > 11, 2009 3:59:49 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml May > 11, 2009 3:59:59 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml May > 11, 2009 4:00:09 PM org.apache.catalina.startup.HostConfig > deployDescriptor > SEVERE: Error deploying configuration descriptor base-2.11.0.xml > > > Message: 4 > Date: Mon, 11 May 2009 07:53:13 +0200 > From: Nicklas Nordborg <nick...@thep.lu.se> > Subject: Re: [base] batch data importer > To: BASE ML <basedb-users@lists.sourceforge.net> > Message-ID: <4a07bd49.6090...@thep.lu.se> > Content-Type: text/plain; charset=ISO-8859-1 > > Abhishek Goel wrote: > > Hello, > > > > I'm a programmer with the Geschwind Lab at UCLA trying to fix some > > issues with our installation of BASE. I'm having a problem with the > > batch data importer plugin. When trying to import a zip file into > BASE > > using the batch data importer plugin, I receive the following error: > > > > Plugin failed: java.lang. > ArrayIndexOutOfBoundsException: 16 > > Can you submit the complete stacktrace? > > /Nicklas > > > > ------------------------------ > > > -- > Abhishek Goel > Programmer Analyst > Geschwind Laboratory, UCLA Neurology > Gonda Neuroscience and Genetics Research Center #2309 University of > California Los Angeles > 695 Charles E. 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