Hi again, That's these bugs all fixed (I hope):
- change handling of dirs and files so that file is unzipped in its current dir - unclosed DbControl -- now fixed - User Quota for files needs to be greater than the file size to be imported -- code now checks - misreporting of raw data type fixed - documentation updated as appropriate All files in SVN are up to date so you can download the new jar and try it. Ready for the next round of bugs.... :-) 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.sari.ac.uk/MichaBayer.htm ============================= > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:basedb-users- > [EMAIL PROTECTED] On Behalf Of Dominic Oyeniran > Sent: 20 February 2007 11:22 > To: BASE ML > Subject: Re: [base] batch importer plugin is available for testing now > > Hi Micha, > > I did another test run with a non-root user, as you suggested and the > import failed (see the exception). I have stated what I noticed below. > Please check them out in addition to the suggestion by Nicklas > ===================================== > ===========NEW BATCH IMPORT ========= > ===================================== > zn =HG-U133A.cdf > experiment: Experiment[id=6; name=New experiment] > file selected: affyMicher.zip > user = Dominic > net.sf.basedb.core.ItemNotFoundException: Item not found: > Directory[path=/home/d > ominic/raw data] > at net.sf.basedb.core.Directory.getIdFromPath(Directory.java:236) > at net.sf.basedb.core.Directory.getByPath(Directory.java:179) > at > sbrn.base.BatchDataImport.unpackZipFile(BatchDataImport.java:143) > at sbrn.base.BatchDataImport.importData(BatchDataImport.java:197) > at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:137) > at > net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionReque > st.java:88) > at > net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.ja > va:420) > at java.lang.Thread.run(Thread.java:595) > > 1. raw data sub directory must be created before hand for the import to > work. > > 2. User Quota for files needs to be greater than the file size to be > imported. If this is not done the import fails. > > These should either be specified in the documentation or better still > handled in the code with appropriate messages. > > Also, despite creating an affy experiment with raw data type correctly > specified, I got the ff exception: > > java.lang.Exception: Affymetrix data found but Experiment data type was > specified > as non-Affy > at sbrn.base.BatchDataImport.importData(BatchDataImport.java:294) > at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:137) > at > net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionReque > t.java:88) > at > net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.ja > a:420) > at java.lang.Thread.run(Thread.java:595) > > > Hope this helps. Thanks. Got to move on now. > > ¬Dominic > > > > > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. 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