NullPointerException when using JEP mapping for column with string values

[Nicklas Nordborg]

This can for example be tested by using the reporter importer with a GenePix file. Change the reporter id mapping from \ID\ to =col('ID').

The parser return a null value instead of the value in the column. The error message is:

net.sf.basedb.core.BaseException: Invalid use of null. The 'externalId' value cannot be set to null. on line 33 in file 'genepix.mouse.v4.37k.00h.gpr': 1 1 1 "NULL" "M40...
at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:708)
at net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:445)
at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116)
at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:510)
at java.lang.Thread.run(Unknown Source)
Caused by: net.sf.basedb.core.InvalidUseOfNullException: Invalid use of null. The 'externalId' value cannot be set to null.
at net.sf.basedb.plugins.ReporterFlatFileImporter.handleData(ReporterFlatFileImporter.java:561)
at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:676)
... 4 more

After investigation it seems like the problem is a NullPointerException in the ColFunction that is happening for non-numerical values. The exception is swallowed by the JEP parser and null is returned.

[Nicklas Nordborg]

(In [5769]) Fixes #1632: NullPointerException when using JEP mapping for column with string values

The reason for the NullPointerException was that we tried to convert the string to a double. This is now fixed and I have also changed JEP to pass on exceptions instead of swallowing them. I hope that doesn't cause problems elsewhere.