[InterMine Dev] Getting started with InterMine?

Julie Sullivan julie at flymine.org
Tue Nov 24 09:52:24 GMT 2009


Hi Kalpana,

Which log files are you looking in?

Most of the error messages from the webapp I get are in 
$TOMCAT/logs/catalina.out but sometimes they are in the localhost file (eg. 
$TOMCAT/logs/localhost.2009-11-24.log).

Do you have those files in $TOMCAT/logs?  There should also be a log file in 
$TOMCAT, intermine.log.

Cheers,
Julie

Kalpana Karra wrote:
> Hi,
> 
> I am getting a blank page when I go to the /malariamine URL , after I 
> finished going through the Malaria Mine tutorial.
> 
> I have added the line-  webapp.logdir path, but I don't see any error 
> info in any of the log files.
> 
> # location of tomcat server and path of webapp - e.g. access 
> http://localhost:8080/malariamine
> 
> webapp.deploy.url=http://localhost:8080
> webapp.path=malariamine
> webapp.logdir=/usr/local/apache-tomcat-5.5.28/logs
> 
> 
> Earlier, last Friday when I had tried the same, I did see an error :
> 
> Nov 20, 2009 11:13:04 AM org.apache.catalina.startup.HostConfig deployWAR
> INFO: Deploying web application archive malariamine.war
> Nov 20, 2009 11:13:10 AM org.apache.catalina.loader.WebappClassLoader 
> loadClass
> INFO: Illegal access: this web application instance has been stopped 
> already.  Could not load org.postgresql.util.MessageTranslator.
> The eventual following stack trace is caused by an error thrown for 
> debugging purposes as well as to attempt to terminate the thread w
> hich caused the illegal access, and has no functional impact.
> java.lang.IllegalStateException
>         at 
> org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1272) 
> 
>         at 
> org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1232) 
> 
>         at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)
>         at 
> org.postgresql.util.PSQLException.translate(PSQLException.java:63)
>         at org.postgresql.util.PSQLException.<init>(PSQLException.java:30)
>         at org.postgresql.util.PSQLException.<init>(PSQLException.java:49)
>         at org.postgresql.core.PGStream.flush(PGStream.java:368)
>         at 
> org.postgresql.jdbc1.AbstractJdbc1Connection.closeV3(AbstractJdbc1Connection.java:1120) 
> 
>         at 
> org.postgresql.jdbc1.AbstractJdbc1Connection.close(AbstractJdbc1Connection.java:1106) 
> 
>         at 
> org.postgresql.jdbc1.AbstractJdbc1Connection.finalize(AbstractJdbc1Connection.java:1465) 
> 
>         at java.lang.ref.Finalizer.invokeFinalizeMethod(Native Method)
>         at java.lang.ref.Finalizer.runFinalizer(Finalizer.java:83)
>         at java.lang.ref.Finalizer.access$100(Finalizer.java:14)
>         at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:160)
> 
> 
> What could be the problem? Right now I don't see the above error, but I 
> still see a blank page.
> 
> 
> Thanks,
> -Kalpana
> 
> 
> 
>



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