Opened 19 months ago
Closed 19 months ago
#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.
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