Hi.
This is for Dominic I guess.
The last error I reported yesterday was from my own shortcutting and is
fixed. (I had not yet made a design).
Today I got an error when the plug-in tried to use the
AnnotationTypeCvImporter.
BASE error message:
IMPORT FAILS: The tab2mage file supplied is not compliant with the tab2mage
specification
This was the error message from tomcat:
.
.
auto-detecting PluginConfiguration
net.sf.basedb.core.InvalidDataException: Plugin does not implement
uk.ac.ebi.nugo.plugins.AnnotationTypeCvImporter: Plugin definition[id=28;
name=Annotation Type and CV Loader]
at
net.sf.basedb.core.PluginDefinition.newInstance(PluginDefinition.java:944)
at
uk.ac.ebi.nugo.plugins.util.PluginConfigDetector.getConfigs(PluginConfigDete
ctor.java:179)
at
uk.ac.ebi.nugo.plugins.util.PluginConfigDetector.detectPluginConfig(PluginCo
nfigDetector.java:114)
at
uk.ac.ebi.nugo.plugins.tab2mageimport.io.AnnotationTypesWriter.write(Annotat
ionTypesWriter.java:84)
at
uk.ac.ebi.nugo.plugins.Tab2MageImporter.run(Tab2MageImporter.java:330)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java
:89)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:421)
at java.lang.Thread.run(Thread.java:595)
15:08:07,097 ERROR AnnotationTypesWriter:87 - No suitable plugin
configuration found for this plugin in NutriBase.
java.lang.NullPointerException
at
uk.ac.ebi.nugo.plugins.tab2mageimport.io.AnnotationTypesWriter.write(Annotat
ionTypesWriter.java:142)
at
uk.ac.ebi.nugo.plugins.Tab2MageImporter.run(Tab2MageImporter.java:330)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java
:89)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:421)
at java.lang.Thread.run(Thread.java:595)
15:08:07,191 ERROR jobqueue:435 - Exception while executing job: Job[id=73;
name=Run plugin: Tab2Mage Importer]
net.sf.basedb.core.BaseException
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:429)
at java.lang.Thread.run(Thread.java:595)
Caused by: java.lang.NullPointerException
at
uk.ac.ebi.nugo.plugins.tab2mageimport.io.AnnotationTypesWriter.write(Annotat
ionTypesWriter.java:142)
at
uk.ac.ebi.nugo.plugins.Tab2MageImporter.run(Tab2MageImporter.java:330)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java
:89)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:421)
... 1 more
I had installed the AnnotationTypeCvImporter with the
annotationtypecvimporter.xml config. I found the annotation file made by the
importer (anntype.txt) on BASE2's file system and successfully imported it
using only AnnotationTypeCvImporter. I did all this as the same user with
admin role. Somehow the importer plug-in was not able to find the
AnnotationTypeCvImporter I could manually find and use. When I tried to
debug in eclipse I found that the top java ref was not in my source code;
uk.ac.ebi.nugo.plugins.util.PluginConfigDetector.getConfigs. It was at
uk\ac\ebi\nugo\plugins\util\tab2mage\PluginConfigDetector.java in the source
code I downloaded from http://lev.thep.lu.se/trac/baseplugins/browser/trunk.
So I think the jar file is out of sync with the source code. This problem
might have been fixed but not included in the jar file. I hope this is the
case.
Best Regards
Vegard Nygaard
Software Engineer
Department of Tumor Biology (Montebello)
Rikshospitalet-Radiumhospitalet Medical Center 0310 Oslo
Bioinformatics user support (NMC)
Phone 0047 22935590
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