XNat startup error : Application at context path [/xnat-web-1.8.8] could not be started

[Usman Bashir]

Hi,

I am trying to setup xnat on my PC. I am unable to get it up and running. I am using

Ubuntu 22.04

Postgresql 14.8

Java openjdk 1.8.0_302

tomcat 9.0.75

My default tomcat folder is /opt/tomcat. I have deployed the webapp inside the tomcat manager portal. But when I click start, I get message:

FAIL - Application at context path [/xnat-web-1.8.8] could not be started FAIL - Encountered exception [org.apache.catalina.LifecycleException: Failed to start component [org.apache.catalina.webresources.StandardRoot@35a50a4c]]

The log file says

28-May-2023 13:34:06.736 INFO [http-nio-8080-exec-1] org.apache.catalina.core.ApplicationContext.log HTMLManager: list: Listing contexts for virtual host 'localhost'
28-May-2023 13:34:07.953 INFO [http-nio-8080-exec-10] org.apache.catalina.core.ApplicationContext.log HTMLManager: start: Starting web application '/xnat-web-1.8.8'
28-May-2023 13:34:07.956 SEVERE [http-nio-8080-exec-10] org.apache.catalina.core.ApplicationContext.log HTMLManager: Error starting [/xnat-web-1.8.8]
org.apache.catalina.LifecycleException: Failed to start component [org.apache.catalina.webresources.StandardRoot@6dde5c8c]
at org.apache.catalina.util.LifecycleBase.handleSubClassException(LifecycleBase.java:440)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:198)
at org.apache.catalina.core.StandardContext.resourcesStart(StandardContext.java:4607)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:4740)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.manager.ManagerServlet.start(ManagerServlet.java:1438)
at org.apache.catalina.manager.HTMLManagerServlet.start(HTMLManagerServlet.java:702)
at org.apache.catalina.manager.HTMLManagerServlet.doPost(HTMLManagerServlet.java:220)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:555)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:623)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:209)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153)
at org.apache.catalina.filters.CsrfPreventionFilter.doFilter(CsrfPreventionFilter.java:190)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153)
at org.apache.catalina.filters.HttpHeaderSecurityFilter.doFilter(HttpHeaderSecurityFilter.java:126)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:178)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:153)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:167)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:90)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:596)
at org.apache.catalina.valves.RequestFilterValve.process(RequestFilterValve.java:355)
at org.apache.catalina.valves.RemoteAddrValve.invoke(RemoteAddrValve.java:54)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:130)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:93)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:673)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343)
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:390)
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:63)
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:926)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1791)
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:52)
at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191)
at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:750)
Caused by: java.lang.NullPointerException
at java.lang.String.startsWith(String.java:1405)
at java.lang.String.startsWith(String.java:1434)
at org.apache.catalina.webresources.AbstractFileResourceSet.file(AbstractFileResourceSet.java:98)
at org.apache.catalina.webresources.DirResourceSet.getResource(DirResourceSet.java:94)
at org.apache.catalina.webresources.StandardRoot.getResourceInternal(StandardRoot.java:272)
at org.apache.catalina.webresources.Cache.getResource(Cache.java:64)
at org.apache.catalina.webresources.StandardRoot.getResource(StandardRoot.java:211)
at org.apache.catalina.webresources.StandardRoot.listResources(StandardRoot.java:347)
at org.apache.catalina.webresources.StandardRoot.processWebInfLib(StandardRoot.java:585)
at org.apache.catalina.webresources.StandardRoot.startInternal(StandardRoot.java:722)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
... 38 more
28-May-2023 13:34:07.956 INFO [http-nio-8080-exec-10] org.apache.catalina.core.ApplicationContext.log HTMLManager: list: Listing contexts for virtual host 'localhost'

My tomcat unit file is :

[Unit]
Description=Apache Tomcat Web Application Container
After=network.target
[Service]
Type=forking
User=xnat
Group=xnat
PrivateTmp=yes
Environment="JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-amd64"
Environment="JAVA_OPTS=-Djava.security.egd=file:///dev/urandom -Djava.awt.headless=true"
Environment="CATALINA_BASE=/opt/tomcat"
Environment="CATALINA_HOME=/opt/tomcat"
Environment="CATALINA_PID=/opt/tomcat/temp/tomcat.pid"
Environment="CATALINA_OPTS="-Xms512M -Xmx1024M -server -XX:+UseParallelGC -Dxnat.home=/data/xnat/home"
ExecStart=/opt/tomcat/bin/startup.sh
ExecStop=/opt/tomcat/bin/shutdown.sh
AmbientCapabilities=CAP_NET_BIND_SERVICE
NoNewPrivileges=true
CacheDirectory=tomcat
CacheDirectoryMode=750
#ProtectSystem=strict
ReadWritePaths=/etc/tomcat/Catalina/
ReadWritePaths=/opt/tomcat/webapps/
ReadWritePaths=/var/lib/tomcat/webapps/
ReadWritePaths=/var/log/tomcat/
ReadWritePaths=/s/xnat/
ReadWritePaths=/data/xnat/
ReadWritePaths=/home/xnat/
[Install]
WantedBy=multi-user.target

Note, I have commented out #ProjectSystem=strict. This property won't let tomcat to start at all.

I put the issue in ChatGP :D . This is what it thinks:

Based on the provided log file, it appears that there is an error during the deployment of the web application '/xnat-web-1.8.8' in Tomcat. The error message indicates a NullPointerException and a LifecycleException related to the StandardRoot component.

The root cause of the issue seems to be the NullPointerException occurring within the AbstractFileResourceSet class. It specifically fails when attempting to access a file resource, likely due to a missing or invalid file path.

To troubleshoot this issue, you can follow these steps:

1. Verify that the web application package (xnat-web-1.8.8.war) is present and accessible in the appropriate location within the Tomcat deployment directory (e.g., webapps or a custom appBase directory).

2. Check if there are any missing or invalid dependencies required by the web application. Ensure that all necessary JAR files and libraries are present in the correct locations.

3. Review any configuration files related to the web application, such as context.xml or web.xml, to ensure they are properly configured and do not contain any errors.

Thanking in advance.

Usman.

[Usman Bashir]

Problem solved - thanks to a stackoverflow member. There was a typo in my environment variable:

Environment="CATALINA_OPTS="-Xms512M -Xmx1024M -server -XX:+UseParallelGC -Dxnat.home=/data/xnat/home"

I removed the extra " after the = sign and it runs now.

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