Hi Micha, in writing a plugin to batch import genepix and nimblegen files i have come across the following:
you can only call dc.commit(); once.. after that, the connection is closed.. maybe check if anything gets committed inbetween method calls. sometimes you have to call dc.reattachItem(Item); before you can start using it. try to reattach the arrayDesign and cdfFile before running any methods on them. -keith Micha Bayer wrote: > Hi, > > I am trying to add Affymetrix support for the batch import plugin I have > been working on, and I am having trouble getting things to work with the > Affymetrix class. Is there a unit test for this class that I could look > at for finding out about proper use of this class? I may just not be > doing things right here. > > I get exceptions from two of the method calls -- setCdfFile(ArrayDesign > design, File file) and setCelFile(RawBioAssay rawBioAssay, File file). > > setCdfFile(ArrayDesign design, File file) throws a NullPointerException > which is not related to my own code: > > Affymetrix.setCdfFile(arrayDesign, cdfFile); > > I have double checked and both the arrayDesign and cdfFile objects are > not null. The stacktrace looks like this: > > java.lang.NullPointerException > at > net.sf.basedb.core.HibernateUtil.createQuery(HibernateUtil.java:1238) > at > net.sf.basedb.core.HibernateUtil.getPredefinedQuery(HibernateUtil.java:1 > 387) > at net.sf.basedb.core.AnyToAny.getByName(AnyToAny.java:129) > at > net.sf.basedb.core.AnyToAny.getNewOrExisting(AnyToAny.java:169) > at net.sf.basedb.core.Affymetrix.setCdfFile(Affymetrix.java:86) > at > sbrn.base.BatchDataImport.importData(BatchDataImport.java:350) > at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:137) > at > net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest. > java:82) > at > net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java: > 420) > at java.lang.Thread.run(Thread.java:595) > > > Further down the line in my code I then try to attach the cel files to > my raw bioassays (I have tested this independently from the above > problem with a array design that already has a cdf file associated with > it): > > Affymetrix.setCelFile(rawBioAssays[i], dataFiles[i]); > > ...and this gives me the following exception: > > > net.sf.basedb.core.ConnectionClosedException: The connection has been > closed. > at net.sf.basedb.core.DbControl.getItem(DbControl.java:696) > at > net.sf.basedb.core.RawBioAssay.getArrayDesign(RawBioAssay.java:382) > at net.sf.basedb.core.Affymetrix.setCelFile(Affymetrix.java:169) > at > sbrn.base.BatchDataImport.importData(BatchDataImport.java:371) > at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:137) > at > net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest. > java:82) > at > net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java: > 420) > at java.lang.Thread.run(Thread.java:595) > > This is despite the fact that I have a check for a closed connection > immediately preceding my method call, so the connection is definitely > open before Affymetrix.setCelFile is called. > > Any help would be much appreciated. > > 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 > ============================= > > > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > > SCRI, Invergowrie, Dundee, DD2 5DA. > The Scottish Crop Research Institute is a charitable company limited by > guarantee. > Registered in Scotland No: SC 29367. > Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. > > > DISCLAIMER: > > This email is from the Scottish Crop Research Institute, but the views > expressed by the sender are not necessarily the views of SCRI and its > subsidiaries. This email and any files transmitted with it are confidential > to the intended recipient at the e-mail address to which it has been > addressed. It may not be disclosed or used by any other than that addressee. > If you are not the intended recipient you are requested to preserve this > confidentiality and you must not use, disclose, copy, print or rely on this > e-mail in any way. Please notify [EMAIL PROTECTED] quoting the > name of the sender and delete the email from your system. > > Although SCRI has taken reasonable precautions to ensure no viruses are > present in this email, neither the Institute nor the sender accepts any > responsibility for any viruses, and it is your responsibility to scan the > email > and the attachments (if any). > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? 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