Opened 11 years ago

Last modified 7 years ago

#262 new defect

Tab2Mage exporter exception: Can't use an unsaved item in query: Annotation set[new]

Reported by: Nicklas Nordborg Owned by: Jari Häkkinen
Priority: major Milestone: ZZ Other tickets
Component: not classified Keywords:
Cc:

Description

I tried to use your plugin that exports an experiment to tab2mage formate, but it gave me the following error in the Stack trace tab:

net.sf.basedb.core.UnsavedItemException: Can't use an unsaved item in query: Annotation set[new]
at net.sf.basedb.core.query.Hql.entity(Hql.java:84)
at net.sf.basedb.core.AnnotationSet.getAnnotations(AnnotationSet.java:560)
at uk.ac.ebi.nugo.plugins.Tab2MageExporter.run(Tab2MageExporter.java:486)
at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:110)
at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:506)
at java.lang.Thread.run(Thread.java:636)

So please tell me how to solve it.

my name is Ahmed Ali and I'm a research assistant at the Nile University, Bioinformatics Research Group.

Change History (2)

comment:1 Changed 11 years ago by Nicklas Nordborg

It seems like the exporter is creating a new annotation on an item that doesn't have one. This is probably a bug in the exporter. To get around it you probably have to create an annotation where it is missing. Try to use the "Overview" and then "Validate" function in BASE for this.

comment:2 Changed 7 years ago by olle

Note: The stack trace in the Ticket description probably refers to rev. @449 of class/file uk/ac/ebi/nugo/plugins/Tab2MageExporter.java, where line 486 corresponds to:

ItemQuery<Annotation> query = bioSource.getAnnotationSet().getAnnotations();

in public method void run(Request request, Response response, ProgressReporter progress).

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