> Dominic wrote:
> Quick question, are using the AnnotationTypeCvImporter plugin contained
> in the Tab2MageImporter.jar file?
No. I installed and tested the AnnotationTypeCvImporter with its own jar
file and assumed it was the same.
I now changed to use the Tab2MageImporter.jar and the plug-in finished
without errors reported to the plug-in window in BASE. Though there were a
bunch of error messages in the tomcat log. This is just the start:
Executing job: Importing data to raw bioassay: H_PropylParabenC1T1.gpr
13:19:29,197 ERROR jobqueue:435 - Exception while executing job: Job[id=78;
name=Importing data to raw bioassay: N_PropylParabenC1T2.gpr]
net.sf.basedb.core.BaseException: Permission denied: The item
RawBioAssay[id=102] was modified by another transaction.
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:429)
at java.lang.Thread.run(Thread.java:595)
Caused by: net.sf.basedb.core.ItemModifiedException: Permission denied: The
item RawBioAssay[id=102] was modified by another transaction.
at net.sf.basedb.core.HibernateUtil.commit(HibernateUtil.java:914)
at net.sf.basedb.core.DbControl.commit(DbControl.java:393)
at
net.sf.basedb.plugins.RawDataFlatFileImporter.end(RawDataFlatFileImporter.ja
va:521)
When I briefly inspected what was created in BASE it looked OK despite the
error messages in the log. The "overview" tab for the experiment crashed
though, but it has done that for me a lot and may not be caused by the
tab2mage importer. Anyways here is the error message
java.lang.NullPointerException
...at
net.sf.basedb.util.overview.ExperimentOverview.addProtocol(ExperimentOvervie
w.java:1502)
...at
net.sf.basedb.util.overview.ExperimentOverview.addSample(ExperimentOverview.
java:1145)
...at
net.sf.basedb.util.overview.ExperimentOverview.addExtract(ExperimentOverview
.java:1039)
...at
net.sf.basedb.util.overview.ExperimentOverview.addLabeledExtract(ExperimentO
verview.java:914)
...at
net.sf.basedb.util.overview.ExperimentOverview.addLabeledExtracts(Experiment
Overview.java:841)
...at
net.sf.basedb.util.overview.ExperimentOverview.addHybridization(ExperimentOv
erview.java:781)
...at
net.sf.basedb.util.overview.ExperimentOverview.addScan(ExperimentOverview.ja
va:748)
...at
net.sf.basedb.util.overview.ExperimentOverview.addRawBioAssay(ExperimentOver
view.java:604)
...at
net.sf.basedb.util.overview.ExperimentOverview.addRawBioAssays(ExperimentOve
rview.java:580)
...at
net.sf.basedb.util.overview.ExperimentOverview.generateOverview(ExperimentOv
erview.java:316)
...at
net.sf.basedb.util.overview.ExperimentOverview.<init>(ExperimentOverview.jav
a:257)
...at
net.sf.basedb.util.overview.ExperimentOverview.getOverview(ExperimentOvervie
w.java:188)
...at
org.apache.jsp.views.experiments.overview.index_jsp._jspService(index_jsp.ja
va:87)
... and more
I will now go on and test the tab2mage exporter and see if I get the same as
I started with. You will hear from me if I am stuck.
Vegard.
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