Opened 14 years ago

Closed 14 years ago

Last modified 14 years ago

#589 closed defect (fixed)

BioAssaySetExporter tries to commit changes on a closed DbControl

Reported by: Nicklas Nordborg Owned by: Johan Enell
Priority: blocker Milestone: BASE 2.3
Component: coreplugins Version:
Keywords: Cc:

Description (last modified by 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.

Change History (6)

comment:1 Changed 14 years ago by Nicklas Nordborg

Description: modified (diff)

comment:2 Changed 14 years ago by Johan Enell

Resolution: fixed
Status: newclosed

(In [3335]) fixes #589

comment:3 Changed 14 years ago by Nicklas Nordborg

Milestone: BASE 2.3.1BASE 2.3

comment:4 Changed 14 years ago by base

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

BASE@LCB

comment:5 Changed 14 years ago by Jari Häkkinen

Milestone: BASE 2.3BASE 2.4

Milestone BASE 2.3 deleted

comment:6 Changed 14 years ago by Jari Häkkinen

Milestone: BASE 2.4BASE 2.3

Milestone BASE 2.4 deleted

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