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From "McGibbney, Lewis John" <Lewis.McGibb...@gcu.ac.uk>
Subject RE: HTTP Status 500 - Server Internal Error (continued!)
Date Mon, 20 Dec 2010 09:42:25 GMT
>I'm not sure the thread Tomcat points out wasn't
>stopped is related to Commons Logging. Could it be
>that you created the thread in your app?

I think that you are correct here although if I post more of the log for you to see then maybe
we can confirm whether it is a common issue or not

20-Dec-2010 08:52:46 org.apache.catalina.startup.Catalina start
INFO: Server startup in 8843 ms
20-Dec-2010 08:55:09 org.apache.coyote.http11.Http11AprProtocol pause
INFO: Pausing Coyote HTTP/1.1 on http-8080
20-Dec-2010 08:55:09 org.apache.coyote.ajp.AjpAprProtocol pause
INFO: Pausing Coyote AJP/1.3 on ajp-8009
20-Dec-2010 08:55:10 org.apache.catalina.core.StandardService stop
INFO: Stopping service Catalina
20-Dec-2010 08:55:11 org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: A web application appears to have started a thread named [Thread-4] but has failed
to stop it. This is very likely to create a memory leak.
20-Dec-2010 08:55:11 org.apache.coyote.http11.Http11AprProtocol destroy
INFO: Stopping Coyote HTTP/1.1 on http-8080
20-Dec-2010 08:55:11 org.apache.coyote.ajp.AjpAprProtocol destroy
INFO: Stopping Coyote AJP/1.3 on ajp-8009

>This one? This is about references held by a class
>in the container classloader to a class in the
>webapp classloader, which prevents *all* of the
>webapp classes from being unloaded on undeploy.
>The problem is not related to Tomcat's complaint
>about the thread that wasn't stopped.

The wiki entry I was referring to was this one (I should have included it in last post). It
has a direct link to the one you provided
http://wiki.apache.org/commons/Logging/FrequentlyAskedQuestions under subheading (towards
the bottom) "A memory leak occurs when undeploying/redeploying a webapp that uses Commons
Logging. How do I fix this?". This refers to commons-logging-1.0.5.jar, the jar version used
within the tika parser plugin in my webapp is version 1.1.1, this is why I am unsure as to
how accurate the code is in this wiki entry (although it was last edited on 2010-05-05) actually
is. It then goes on to mention that the deployment descriptor for the webapp would need to
be updated etc... this is what I was referring to when I mentioned the can of worms.

In reading about ClassLoader I have come full circle and have ended up running back into my
friend the Endorsed Standards Override Mechanism. I made Jena (which uses its own OWL parser,
therefore no need for xerces) available to Tomcat in an endorsed folder, this should override
the JAXP API's this seemed to solve the parser problem. If the error I am getting is not related
to commons logging, and instead as you mentioned (and as shown in logs) related to the WebappClassLoader
then I will pursue this route.

Sorry for long post
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