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So my first question is - should it be possible for the container to roll back the transaction without telling me it's going to do so through getRollbackOnly(), or is this a bug? And if it's not a bug, is there some other way for me to know whether my transaction will commit or not?getRollbackOnly is the right way to check.
You only catch a JMSException? If you don't want any roll backs due to exceptions then you must catch all possible exceptions.
Also, it could be that an exception is happening in the logRollbackValue method itself.
This is a good question, which isn't specific to JMS but applies to how transaction rollback is handled in EJBs generally.
Can I suggest you ask in the GlassFish forum, since that's where many EJB experts congregate?