BioAssaySetExporter tries to commit changes on a closed DbControl

[Nicklas Nordborg]

Trying to export a bioassayset in serial BASEfile format. After navigating through workarounds for tickets #586, #587, #588 I still get an error:

net.sf.basedb.core.ConnectionClosedException: The connection has been closed.
at net.sf.basedb.core.DbControl.commit(DbControl.java:323)
at net.sf.basedb.plugins.BioAssaySetExporter.run(BioAssaySetExporter.java:949)
at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:88)
at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:420)
at java.lang.Thread.run(Thread.java:595)

It looks like exportBaseFileSerial() method closes the DbControl but the run() method expects it to be open and calls commit() later. I think the DbControl shouldn't be closes in the exportBaseFileSerial() method at all since it is not opened in this method.

Exporting in normal (matrix) formats works.

[Johan Enell]

(In [3335]) fixes #589

[base]

This also fixes a problem with B1PE and serial format export, so thanks for addressing the issue quickly!

BASE@LCB

[Jari Häkkinen]

Milestone BASE 2.3 deleted

[Jari Häkkinen]

Milestone BASE 2.4 deleted