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:
Can you please tell us which BASE version you are using. The stack trace is hard to follow unless I know which version to look at. > > 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. Are you sure that you are checking the same DbControl as you used to get the raw bioassays and files? Ie. the check you must do should correspond to: rawBioAssays[i].getDbControl().isClosed() Otherwise I recommend that you do: rawBioAssays[i] = RawBioAssay.getById(dc, rawBioAssays[i].getId()) where dc is an open DbControl. I don't recommend using the DbControl.reattachItem(). It doesn't reattach linked items and may cause problems if trying to access those. The Affymetrix.setCelFile will access to array design linked to the raw bioassay and this may or may not work depending on what you have done earlier. /Nicklas > > 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. 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