Upgrade from 1.8.5 build 12 to the latest posted version 1.8.6.1 failed
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Jasen Kloeppel
Jan 26, 2023, 10:52:41 AM1/26/23
to xnat_discussion
I followed the upgrade process stopping tomcat9 and removed the 1.8.5 .war file and /xnat directory from /var/lib/tomcat9/webapps and placed the updated .war file there. On restart of Tomcat9 I now have the following error. A
ny suggestions on what this issue might be?
26-Jan-2023 10:25:04.268 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name: Apache Tomcat/9.0.31 (Ubuntu)
26-Jan-2023 10:25:04.268 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Nov 18 2022 19:07:15 UTC
26-Jan-2023 10:25:04.268 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 9.0.31.0
26-Jan-2023 10:25:04.268 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
26-Jan-2023 10:25:04.268 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 5.4.0-135-generic
26-Jan-2023 10:25:04.268 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
26-Jan-2023 10:25:04.269 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /usr/lib/jvm/java-8-openjdk-amd64/jre
26-Jan-2023 10:25:04.269 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_352-8u352-ga-1~20.04-b08
26-Jan-2023 10:25:04.269 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Private Build
26-Jan-2023 10:25:04.269 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /var/lib/tomcat9
26-Jan-2023 10:25:04.269 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /usr/share/tomcat9
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.properties
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.awt.headless=true
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dxnat.home=/data/xnat/home
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dignore.endorsed.dirs=
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/var/lib/tomcat9
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/share/tomcat9
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/tmp
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent Loaded APR based Apache Tomcat Native library [1.2.23] using APR version [1.6.5].
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent APR capabilities: IPv6 [true], sendfile [true], accept filters [false], random [true].
26-Jan-2023 10:25:04.271 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent APR/OpenSSL configuration: useAprConnector [false], useOpenSSL [true]
26-Jan-2023 10:25:04.273 INFO [main] org.apache.catalina.core.AprLifecycleListener.initializeSSL OpenSSL successfully initialized [OpenSSL 1.1.1f 31 Mar 2020]
26-Jan-2023 10:25:04.432 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
26-Jan-2023 10:25:04.445 INFO [main] org.apache.catalina.startup.Catalina.load Server initialization in [291] milliseconds
26-Jan-2023 10:25:04.464 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
26-Jan-2023 10:25:04.464 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: [Apache Tomcat/9.0.31 (Ubuntu)]
26-Jan-2023 10:25:04.479 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive [/var/lib/tomcat9/webapps/xnat.war]
26-Jan-2023 10:25:14.209 INFO [main] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
26-Jan-2023 10:25:14.439 INFO [main] org.apache.catalina.core.ApplicationContext.log 2 Spring WebApplicationInitializers detected on classpath
26-Jan-2023 10:25:14.862 INFO [main] org.apache.catalina.core.ApplicationContext.log Initializing Spring root WebApplicationContext
26-Jan-2023 10:25:28.049 SEVERE [main] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class [org.springframework.web.context.ContextLoaderListener]
org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'updateSecurityFilterHandlerMethod' defined in file [/var/lib/tomcat9/webapps/xnat/WEB-INF/classes/org/nrg/xnat/event/listeners/methods/UpdateSecurityFilterHandlerMethod.class]: Unsatisfied dependency expressed through constructor parameter 1; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'appInfo' defined in org.nrg.xnat.initialization.RootConfig: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.nrg.xnat.services.XnatAppInfo]: Factory method 'appInfo' threw exception; nested exception is java.lang.NoSuchMethodError: com.fasterxml.jackson.dataformat.yaml.YAMLFactory._createContentReference(Ljava/lang/Object;)Lcom/fasterxml/jackson/core/io/ContentReference;
at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:749)
at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:189)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1196)
26-Jan-2023 10:25:04.268 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Nov 18 2022 19:07:15 UTC
26-Jan-2023 10:25:04.268 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 9.0.31.0
26-Jan-2023 10:25:04.268 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
26-Jan-2023 10:25:04.268 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 5.4.0-135-generic
26-Jan-2023 10:25:04.268 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
26-Jan-2023 10:25:04.269 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /usr/lib/jvm/java-8-openjdk-amd64/jre
26-Jan-2023 10:25:04.269 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_352-8u352-ga-1~20.04-b08
26-Jan-2023 10:25:04.269 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Private Build
26-Jan-2023 10:25:04.269 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /var/lib/tomcat9
26-Jan-2023 10:25:04.269 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /usr/share/tomcat9
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.properties
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.awt.headless=true
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dxnat.home=/data/xnat/home
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dignore.endorsed.dirs=
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/var/lib/tomcat9
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/share/tomcat9
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/tmp
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent Loaded APR based Apache Tomcat Native library [1.2.23] using APR version [1.6.5].
26-Jan-2023 10:25:04.270 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent APR capabilities: IPv6 [true], sendfile [true], accept filters [false], random [true].
26-Jan-2023 10:25:04.271 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent APR/OpenSSL configuration: useAprConnector [false], useOpenSSL [true]
26-Jan-2023 10:25:04.273 INFO [main] org.apache.catalina.core.AprLifecycleListener.initializeSSL OpenSSL successfully initialized [OpenSSL 1.1.1f 31 Mar 2020]
26-Jan-2023 10:25:04.432 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
26-Jan-2023 10:25:04.445 INFO [main] org.apache.catalina.startup.Catalina.load Server initialization in [291] milliseconds
26-Jan-2023 10:25:04.464 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
26-Jan-2023 10:25:04.464 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: [Apache Tomcat/9.0.31 (Ubuntu)]
26-Jan-2023 10:25:04.479 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive [/var/lib/tomcat9/webapps/xnat.war]
26-Jan-2023 10:25:14.209 INFO [main] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
26-Jan-2023 10:25:14.439 INFO [main] org.apache.catalina.core.ApplicationContext.log 2 Spring WebApplicationInitializers detected on classpath
26-Jan-2023 10:25:14.862 INFO [main] org.apache.catalina.core.ApplicationContext.log Initializing Spring root WebApplicationContext
26-Jan-2023 10:25:28.049 SEVERE [main] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class [org.springframework.web.context.ContextLoaderListener]
org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'updateSecurityFilterHandlerMethod' defined in file [/var/lib/tomcat9/webapps/xnat/WEB-INF/classes/org/nrg/xnat/event/listeners/methods/UpdateSecurityFilterHandlerMethod.class]: Unsatisfied dependency expressed through constructor parameter 1; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'appInfo' defined in org.nrg.xnat.initialization.RootConfig: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.nrg.xnat.services.XnatAppInfo]: Factory method 'appInfo' threw exception; nested exception is java.lang.NoSuchMethodError: com.fasterxml.jackson.dataformat.yaml.YAMLFactory._createContentReference(Ljava/lang/Object;)Lcom/fasterxml/jackson/core/io/ContentReference;
at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:749)
at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:189)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1196)
Charlie Moore
Jan 26, 2023, 10:54:35 AM1/26/23
to xnat_discussion
Hi there,
Take a look at the warning on the 1.8.6 release notes: https://wiki.xnat.org/display/XNAT18/XNAT+1.8.6+Release+Notes . That should explain how to deal with this.
Thanks,
Charlie Moore
Jasen Kloeppel
Jan 26, 2023, 11:27:24 AM1/26/23
to xnat_discussion
That was the issue, all is working now. Thanks,
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