Annotation importer refuses to skip bad lines

[Jari Häkkinen]

I have a file (attached) that refuses to import. All lines with valid data is accepted by the importer but line 12 with obvious errors creates the below error. That is fine with me, the error occurs beyond my data, so I set default error handling to skip. Even with skip I get the burp below. Is there a problem with the importer?

net.sf.basedb.core.BaseException: Invalid use of null. The 'value' value cannot be set to null. on line 12 in file 'Labeledextract.txt': C02 ...
at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:731)
at net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:468)
at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:106)
at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:504)
at java.lang.Thread.run(Thread.java:619)
Caused by: net.sf.basedb.core.InvalidUseOfNullException: Invalid use of null. The 'value' value cannot be set to null.
at net.sf.basedb.core.AbstractQuery.setParameter(AbstractQuery.java:351)
at net.sf.basedb.core.AbstractQuery.setParameter(AbstractQuery.java:366)
at net.sf.basedb.core.ItemQuery.setParameter(ItemQuery.java:40)
at net.sf.basedb.plugins.AnnotationFlatFileImporter.handleData(AnnotationFlatFileImporter.java:750)
at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:699)
... 4 more

[Jari Häkkinen]

Sample file to import annotation to lableled extracts

[Nicklas Nordborg]

The error handling code is there, but it seems that it has not been properly initialized. In this case I would also consider this as a bug in the code that is looking up items in the database. I think it should be handled as an empty result and generate an ItemNotFoundException instead of an InvalidUseOfNullException (see line ​752-764 in AnnotationFlatFileImporter).

[Martin Svensson]

Tested Mylyn plugin for Eclipse but everything wasn't included in the submit.

[Martin Svensson]

(In [4800]) Fixes #1246 Annotation importer refuses to skip bad lines.
Annotationimporter is now handling lines, without a value in the identifier column, as an item not found.