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I have a little more information about this, but no solution yet; and, unfortunately, no reproducible test case that I can give you (yet). I attempted to put together a small example that would illustrate the problem, but was unsuccessful. I put together the simplest web app I could that opened an Oracle model, but unlike our full-fledged app, the test worked correctly, eliminating Tomcat by itself as the culprit.
I has since started trying to remove as much complexity I can little by little from the code in our webapp, and I am still seeing the issue. This leads me to believe that there is something about the way our WAR is packaged that is causing the problem, especially given that the attempt to open the model fails both when run as a REST request, as well as when run via a Quartz job (both in the same WAR with the same error).
All of the dependencies are the same, including the JDBC driver. Here are the versions of everything (relevant) we're using:
Oracle - 188.8.131.52.0
OJDBC6 - 184.108.40.206.0
Jena - 2.6.4
ARQ - 2.8.8
TDB - 0.8.10
Jena Oracle Adapter - 220.127.116.11.0
Tomcat - 7.0
I realize we have a mismatch between the Jena Adapter and the version of Oracle we're on, but since it works outside of Tomcat I don't suspect this is the problem. We're currently in the infancy of trying to upgrade our Oracle instances, but it could be quite some time before we complete that.
I'm going to continue to try and eliminate variables to see if I can figure out what about our WAR is causing the problem, but I wanted to post an update in case there was any advice you can provide.