How quickly do the waters become muddy. This thread now has multiple issues posted to it, which renders it pretty much useless to anyone trying to actually track down and fix a bug in Glassfish.
The original issue that this thread was about has nothing whatever to do with database connections or deadlocked threads. My application doesn't even hit a database. The symptoms, and hints as to the source of the problem are to be found in my original post at the top of this thread. I wish the Glassfish team luck fixing that issue, because I very much believe it to be a bug in Glassfish, unlike deadlocked threads which is more likely to be application code.
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