#2304 closed defect (fixed)

The annotation import for files still can't use Path to identify files

Reported by: Nicklas Nordborg Owned by: everyone
Priority: major Milestone: BASE 3.19.9
Component: coreplugins Version:
Keywords: Cc:

Description

This should have been fixed in #2299, but the import fails with:

net.sf.basedb.core.BaseException: Cannot invoke "net.sf.basedb.util.parser.Mapper.getString(net.sf.basedb.util.parser.FlatFileParser$Data)" 
  because "this.itemMapper" is null on line 2 in file 'test_annotate_file.txt': /home/SCANB/Secon...
  at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:735)
  at net.sf.basedb.plugins.AnnotationFlatFileImporter.doImport(AnnotationFlatFileImporter.java:658)
  at net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:468)
  at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:117)
  at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:574)
  at java.base/java.lang.Thread.run(Thread.java:1623)
Caused by: java.lang.NullPointerException: Cannot invoke "net.sf.basedb.util.parser.Mapper.getString(net.sf.basedb.util.parser.FlatFileParser$Data)" 
  because "this.itemMapper" is null
  at net.sf.basedb.plugins.AnnotationFlatFileImporter.handleData(AnnotationFlatFileImporter.java:779)
  at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:700)
  ... 5 more

The problem seems to be that while a column mapping for "Path" can be selected it was never saved as a parameter to the job and we get a NullPointerException.

Change History (1)

comment:1 by Nicklas Nordborg, 19 months ago

Resolution: fixed
Status: newclosed

In 8147:

Fixes #2304: The annotation import for files still can't use Path to identify files

This time it should work!

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