Tomcat error using war file
Neil Thackeray
Herrick, Rick
I think you haven’t defined xnat.home in your Tomcat configuration. XNAT has a custom context definition that configures that VirtualWebappLoader class:
<Loader className="org.apache.catalina.loader.VirtualWebappLoader" searchVirtualFirst="true" virtualClasspath="${xnat.home}/plugins/*.jar"/>
I think the null is coming because it’s trying to expand that ${xnat.home} reference but it doesn’t have anything to expand it with.
You can check whether Tomcat is getting xnat.home set by looking at the process:
$ ps ax | fgrep tomcat
30064 ? Sl 1:34 /usr/lib/jvm/java-8-openjdk-amd64/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djava.awt.headless=true -Xms512m -Xmx1g -XX:+UseConcMarkSweepGC -XX:-OmitStackTraceInFastThrow -XX:+CMSIncrementalMode -XX:+CMSClassUnloadingEnabled -Dxnat.home=/data/xnat/home -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=8000 -agentpath:/opt/yourkit/bin/linux-x86-64/libyjpagent.so -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start
For Debian/Ubuntu servers, you can set this in /etc/default/tomcat7, while on Fedora/RHEL/CentOS servers you can set it in /etc/sysconfig/tomcat7 (or sometimes it’s just tomcat). On my current development server, I have this in /etc/default/tomcat7:
# Set CATALINA_OPTS for Tomcat-specific operations, mainly service start and run.
CATALINA_OPTS="-Xms512m -Xmx1g -XX:+UseConcMarkSweepGC -XX:-OmitStackTraceInFastThrow"
CATALINA_OPTS="${CATALINA_OPTS} -XX:+CMSIncrementalMode -XX:+CMSClassUnloadingEnabled"
CATALINA_OPTS="${CATALINA_OPTS} -Dxnat.home=/data/xnat/home"
CATALINA_OPTS="${CATALINA_OPTS} -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=8000"
CATALINA_OPTS="${CATALINA_OPTS} -agentpath:/opt/yourkit/bin/linux-x86-64/libyjpagent.so"
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
Phone: +1 (314) 273-1645
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Neil Thackeray
Moore, Charlie
What version of tomcat do you have installed? I recall people having issues with the version of tomcat7 that CentOS7 wants to give you by default.
Thanks,
Charlie
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Neil Thackeray
tomcat.noarch 7.0.76-6.el7 @basetomcat-el-2.2-api.noarch 7.0.76-6.el7 @basetomcat-jsp-2.2-api.noarch 7.0.76-6.el7 @basetomcat-lib.noarch 7.0.76-6.el7 @basetomcat-native.x86_64 1.2.17-1.el7 @epeltomcat-servlet-3.0-api.noarch 7.0.76-6.el7 @base
Moore, Charlie
Yep, tomcat 7.0.76 was the version installed where an issue like this happened previously: https://groups.google.com/forum/#!searchin/xnat_discussion/saltstack%7Csort:date/xnat_discussion/nw7g5tjhDTo/m1mBIZ2VAgAJ . For some reason, the last message in this thread was deleted from the google group. I’m not really sure why that is, but I still have a copy of it in my email. I’d like to check with Rick to see why it was deleted though before I post it; that shouldn’t take long.
Thanks,
Charlie
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Moore, Charlie
In the meantime, here’s another related thread: https://groups.google.com/forum/#!searchin/xnat_discussion/xnat$20systemd%7Csort:date/xnat_discussion/5IysygSbaf0/PQwSwTiDAAAJ .
Thanks,
Charlie
Herrick, Rick
Neil,
Charlie and I were just going over this and came up with an idea that might work around the issue. The problem is that Tomcat gets a list of jar files from the folder specified in the VirtualWebappLoader configuration, but it doesn’t find any and so gets a null back. It then tries to sort the list without checking whether or not it’s null, which leads to the failure. To fix this, try the following:
$ cd /data/xnat/home/plugins
$ echo Hello > hello.txt
$ jar cf hello.jar hello.txt
$ rm hello.txt
Now try starting Tomcat. I think it should work just by virtue of giving it something to sort rather than a null.
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
Phone: +1 (314) 273-1645
Neil Thackeray
Marcel Koek
Marcel