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
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