Try to remove the resource and then try again, I have deployed the WAR file several times with jdbc or jndi configured, and never had a problem with it
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The guide would be:
place the WAR in the webapps folder, let it explode, stop the server, edit the configs (as described in bugg_tb's email 5 mins ago), restart the server (maybe remove the WAR file before that so it doesn't overwrite the context probably)
you don't have to touch the hibernate.cfg.xml file... all you need to do is edit the pat-datasource.xml to use jndi (if thats not default) and then enter your JNDI in the context.xml .. and then open pat.properties and choose the right hibernate dialect and make sure you have something like : jndi.name=asdf in there
if something doesnt work you should see errors
what happens if you open the webapp?
so e.g: http://localhost:8080/pat-0.8/ ?
sh start_hypersonic.sh &
just remove it or put a # in front of it