http status 500 - no webapplicationcontext found no contextloaderlistener registered?
SIMON JONES
This has broken the XNAT install. Connecting to the website the response is
'http status 500 - no webapplicationcontext found no contextloaderlistener registered?'
In the file postgresql-9.5-main.log a number of errors are listed:
2019-10-02 17:44:12 BST [1006-1] LOG: database system is ready to accept connections
2019-10-02 17:44:12 BST [1085-1] LOG: autovacuum launcher started
2019-10-02 17:44:12 BST [1127-1] [unknown]@[unknown] LOG: incomplete startup packet
2019-10-02 17:53:21 BST [2945-1] xnat@xnat ERROR: column "xnat_projectData_resource_id" of relation "xnat_projectdata_resource" does not exist
2019-10-02 17:53:21 BST [2945-2] xnat@xnat STATEMENT: SELECT pg_get_serial_sequence('xnat_projectData_resource','xnat_projectData_resource_id') AS col_name
2019-10-02 17:53:21 BST [2945-3] xnat@xnat ERROR: column "xnat_projectData_investigator_id" of relation "xnat_projectdata_investigator" does not exist
2019-10-02 17:53:21 BST [2945-4] xnat@xnat STATEMENT: SELECT pg_get_serial_sequence('xnat_projectData_investigator','xnat_projectData_investigator_id') AS col_name
2019-10-02 17:53:21 BST [2945-5] xnat@xnat ERROR: relation "xnat_projectdata_investigator_xnat_projectdata_investigator_id_" does not exist at character 15
2019-10-02 17:53:21 BST [2945-6] xnat@xnat STATEMENT: SELECT * FROM xnat_projectData_investigator_xnat_projectData_investigator_id_seq
2019-10-02 17:53:21 BST [2945-7] xnat@xnat ERROR: relation "xnat_projectdata_investigator_xnat_projectdata_investigator__se" does not exist at character 15
2019-10-02 17:53:21 BST [2945-8] xnat@xnat STATEMENT: SELECT * FROM xnat_projectData_investigator_xnat_projectData_investigator__seq
2019-10-02 17:53:21 BST [2945-9] xnat@xnat ERROR: column "xnat_subjectData_resource_id" of relation "xnat_subjectdata_resource" does not exist
2019-10-02 17:53:21 BST [2945-10] xnat@xnat STATEMENT: SELECT pg_get_serial_sequence('xnat_subjectData_resource','xnat_subjectData_resource_id') AS col_name
2019-10-02 17:53:21 BST [2945-11] xnat@xnat ERROR: column "xnat_experimentData_resource_id" of relation "xnat_experimentdata_resource" does not exist
2019-10-02 17:53:21 BST [2945-12] xnat@xnat STATEMENT: SELECT pg_get_serial_sequence('xnat_experimentData_resource','xnat_experimentData_resource_id') AS col_name
2019-10-02 17:53:21 BST [2945-13] xnat@xnat ERROR: relation "xnat_experimentdata_resource_xnat_experimentdata_resource_id_se" does not exist at character 15
2019-10-02 17:53:21 BST [2945-14] xnat@xnat STATEMENT: SELECT * FROM xnat_experimentData_resource_xnat_experimentData_resource_id_seq
2019-10-02 17:53:21 BST [2945-15] xnat@xnat ERROR: column "xnat_datatypeProtocol_fieldGroups_id" of relation "xnat_datatypeprotocol_fieldgroups" does not exist
2019-10-02 17:53:21 BST [2945-16] xnat@xnat STATEMENT: SELECT pg_get_serial_sequence('xnat_datatypeProtocol_fieldGroups','xnat_datatypeProtocol_fieldGroups_id') AS col_name
2019-10-02 17:53:21 BST [2945-17] xnat@xnat ERROR: relation "xnat_datatypeprotocol_fieldgroups_xnat_datatypeprotocol_fieldgr" does not exist at character 15
2019-10-02 17:53:21 BST [2945-18] xnat@xnat STATEMENT: SELECT * FROM xnat_datatypeProtocol_fieldGroups_xnat_datatypeProtocol_fieldGroups_id_seq
2019-10-02 17:53:21 BST [2945-19] xnat@xnat ERROR: relation "xnat_datatypeprotocol_fieldgro_xnat_datatypeprotocol_fieldgro_s" does not exist at character 15
2019-10-02 17:53:21 BST [2945-20] xnat@xnat STATEMENT: SELECT * FROM xnat_datatypeProtocol_fieldGro_xnat_datatypeProtocol_fieldGro_seq
In tomcat7 logs
Oct 02, 2019 10:28:53 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring FrameworkServlet 'spring-mvc'
Oct 02, 2019 10:28:55 AM org.apache.catalina.core.ApplicationContext log
SEVERE: StandardWrapper.Throwable
java.lang.NoSuchMethodError: java.util.concurrent.ConcurrentHashMap.keySet()Ljava/util/concurrent/ConcurrentHashMap$KeySetView;
at org.apache.catalina.core.ApplicationContext.getInitParameterNames(ApplicationContext.java:368)
at org.apache.catalina.core.ApplicationContextFacade.getInitParameterNames(ApplicationContextFacade.java:367)
at org.springframework.web.context.support.WebApplicationContextUtils.registerEnvironmentBeans(WebApplicationContextUtils.java:195)
at org.springframework.web.context.support.AbstractRefreshableWebApplicationContext.postProcessBeanFactory(AbstractRefreshableWebApplicationContext.java:144)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:404)
at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:467)
at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:483)
at org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:358)
at org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:325)
at org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:127)
at javax.servlet.GenericServlet.init(GenericServlet.java:158)
at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1282)
at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1195)
at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1085)
at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:5318)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5610)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1572)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1562)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
And catalina
INFO: Stopping service Catalina
Oct 01, 2019 5:40:00 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesJdbc
SEVERE: The web application [] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Oct 01, 2019 5:40:00 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-1] but has failed to stop it. This is very likely to create a memory leak.
Oct 01, 2019 5:40:00 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-2] but has failed to stop it. This is very likely to create a memory leak.
Oct 01, 2019 5:40:00 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-3] but has failed to stop it. This is very likely to create a memory leak.
Oct 01, 2019 5:40:00 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-4] but has failed to stop it. This is very likely to create a memory leak.
Oct 01, 2019 5:40:00 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-5] but has failed to stop it. This is very likely to create a memory leak.
Oct 01, 2019 5:40:00 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-6] but has failed to stop it. This is very likely to create a memory leak.
Oct 01, 2019 5:40:00 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-7] but has failed to stop it. This is very likely to create a memory leak.
Oct 01, 2019 5:40:00 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-8] but has failed to stop it. This is very likely to create a memory leak.
Oct 01, 2019 5:40:00 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-9] but has failed to stop it. This is very likely to create a memory leak.
Oct 01, 2019 5:40:00 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-10] but has failed to stop it. This is very likely to create a memory leak.
Oct 01, 2019 5:40:00 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Oct 01, 2019 5:40:00 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_QuartzSchedulerThread] but has failed to stop it. This is very likely to create a memory leak.
Oct 01, 2019 5:40:00 PM org.apache.coyote.AbstractProtocol stop
velocity.log
2019-10-02 17:53:20,470 [localhost-startStop-1] ERROR velocity - VM #xdatStringBoxOnChange: error : too few arguments to macro. Wanted 6 got 0
2019-10-02 17:53:20,470 [localhost-startStop-1] ERROR velocity - VM #xdatStringBoxOnChange: error : too few arguments to macro. Wanted 6 got 0
2019-10-02 17:53:20,470 [localhost-startStop-1] ERROR velocity - VM #xdatStringBoxOnChange: error : too few arguments to macro. Wanted 6 got 0
2019-10-02 17:53:20,528 [localhost-startStop-1] ERROR velocity - VM #xdatSearchForm: error : too few arguments to macro. Wanted 2 got 0
2019-10-02 17:53:20,549 [localhost-startStop-1] ERROR velocity - VM #addCustomScreens: error : too few arguments to macro. Wanted 2 got 0
2019-10-02 17:53:20,597 [localhost-startStop-1] ERROR velocity - VM #displayFileSystem: error : too few arguments to macro. Wanted 1 got 0
2019-10-02 17:53:20,597 [localhost-startStop-1] ERROR velocity - VM #auditBoxes: error : too few arguments to macro. Wanted 4 got 0
Herrick, Rick
This is probably a Tomcat issue, as described here: https://groups.google.com/forum/#!msg/xnat_discussion/7AwtxVYYoDQ/GIIxN5gqBAAJ
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
Phone: +1 (314) 273-1645
--
You received this message because you are subscribed to the Google Groups "xnat_discussion" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
xnat_discussi...@googlegroups.com.
To view this discussion on the web visit
https://groups.google.com/d/msgid/xnat_discussion/cd814f04-f00f-4e16-b6a5-1c1325617aff%40googlegroups.com.
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
SIMON JONES
I did "Install Java 8 instead of Java 7 and set your JAVA_HOME variable to point to the new Java 8 installation" as you suggested. It is now java-8-openjdk-amd64
I am getting
'Horrible Exception: java.lang.Exception: Could not find screen for Login.vm'
Tomcat7 is Apache Tomcat/7.0.68 (Ubuntu)
psql (9.5.19)
Some errors I get now are,
catalina.out
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesJdbc
SEVERE: The web application [] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-1] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-2] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-3] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-4] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-5] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-6] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-7] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-8] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-9] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_Worker-10] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [org.springframework.scheduling.quartz.SchedulerFactoryBean#0_Worker-1] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [org.springframework.scheduling.quartz.SchedulerFactoryBean#0_Worker-2] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [org.springframework.scheduling.quartz.SchedulerFactoryBean#0_Worker-6] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [ActiveMQ Cleanup Timer] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [ActiveMQ Cleanup Timer] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [pool-1-thread-1] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [ActiveMQ Cleanup Timer] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [ActiveMQ Cleanup Timer] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [ActiveMQ Cleanup Timer] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [ActiveMQ BrokerService[activeMQBroker] Task-46] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase clearReferencesThreads
SEVERE: The web application [] appears to have started a thread named [DefaultQuartzScheduler_QuartzSchedulerThread] but has failed to stop it. This is very likely to create a memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase checkThreadLocalMapForLeaks
SEVERE: The web application [] created a ThreadLocal with key of type [org.apache.log4j.helpers.ThreadLocalMap] (value [org.apache.log4j.helpers.ThreadLocalMap@32958385]) and a value of type [java.util.Hashtable] (value [{activemq.broker=activeMQBroker}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase checkThreadLocalMapForLeaks
SEVERE: The web application [] created a ThreadLocal with key of type [org.apache.log4j.helpers.ThreadLocalMap] (value [org.apache.log4j.helpers.ThreadLocalMap@32958385]) and a value of type [java.util.Hashtable] (value [{activemq.broker=activeMQBroker}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase checkThreadLocalMapForLeaks
SEVERE: The web application [] created a ThreadLocal with key of type [org.apache.log4j.helpers.ThreadLocalMap] (value [org.apache.log4j.helpers.ThreadLocalMap@32958385]) and a value of type [java.util.Hashtable] (value [{activemq.broker=activeMQBroker}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase checkThreadLocalMapForLeaks
SEVERE: The web application [] created a ThreadLocal with key of type [org.apache.log4j.helpers.ThreadLocalMap] (value [org.apache.log4j.helpers.ThreadLocalMap@32958385]) and a value of type [java.util.Hashtable] (value [{activemq.broker=activeMQBroker}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase checkThreadLocalMapForLeaks
SEVERE: The web application [] created a ThreadLocal with key of type [org.apache.log4j.helpers.ThreadLocalMap] (value [org.apache.log4j.helpers.ThreadLocalMap@32958385]) and a value of type [java.util.Hashtable] (value [{activemq.broker=activeMQBroker}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Oct 11, 2019 3:23:06 PM org.apache.catalina.loader.WebappClassLoaderBase checkThreadLocalMapForLeaks
SEVERE: The web application [] created a ThreadLocal with key of type [org.apache.log4j.helpers.ThreadLocalMap] (value [org.apache.log4j.helpers.ThreadLocalMap@32958385]) and a value of type [java.util.Hashtable] (value [{activemq.connector=vm://localhost}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Oct 11, 2019 3:23:06 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
Oct 11, 2019 3:23:06 PM org.apache.coyote.AbstractProtocol stop
INFO: Stopping ProtocolHandler ["http-bio-8443"]
Oct 11, 2019 3:23:06 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8080"]
Oct 11, 2019 3:23:06 PM org.apache.coyote.AbstractProtocol destroy
INFO: Destroying ProtocolHandler ["http-bio-8443"]
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=512m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
Listening for transport dt_socket at address: 8000
Oct 11, 2019 3:23:14 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Oct 11, 2019 3:23:14 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8443"]
Oct 11, 2019 3:23:15 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 1519 ms
Oct 11, 2019 3:23:15 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Oct 11, 2019 3:23:15 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.68 (Ubuntu)
Oct 11, 2019 3:23:20 PM org.apache.catalina.startup.TldConfig execute
INFO: 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.
Oct 11, 2019 3:32:13 PM org.apache.catalina.util.SessionIdGeneratorBase createSecureRandom
INFO: Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [532,343] milliseconds.
[localhost-startStop-1] ERROR auto.AutoArcArchivespecification -
org.nrg.xft.exception.ElementNotFoundException: Element not found: 'arc:ArchiveSpecification'
at org.nrg.xft.meta.XFTMetaManager.FindElement(XFTMetaManager.java:219)
at org.nrg.xft.meta.XFTMetaManager.GetWrappedElementByName(XFTMetaManager.java:363)
at org.nrg.xft.schema.Wrappers.GenericWrapper.GenericWrapperElement.GetElement(GenericWrapperElement.java:163)
at org.nrg.xft.search.ItemSearch.GetAllItems(ItemSearch.java:853)
at org.nrg.xdat.om.base.auto.AutoArcArchivespecification.getAllArcArchivespecifications(AutoArcArchivespecification.java:860)
at org.nrg.xnat.turbine.utils.ArcSpecManager.GetFreshInstance(ArcSpecManager.java:51)
at org.nrg.xnat.turbine.utils.ArcSpecManager.GetInstance(ArcSpecManager.java:66)
at org.nrg.xnat.turbine.utils.ArcSpecManager.GetInstance(ArcSpecManager.java:60)
at org.nrg.xnat.security.FilterSecurityInterceptorBeanPostProcessor.initializeArcSpecInstance(FilterSecurityInterceptorBeanPostProcessor.java:103)
at org.nrg.xnat.security.FilterSecurityInterceptorBeanPostProcessor.isRequiredLogin(FilterSecurityInterceptorBeanPostProcessor.java:110)
at org.nrg.xnat.security.FilterSecurityInterceptorBeanPostProcessor.postProcessAfterInitialization(FilterSecurityInterceptorBeanPostProcessor.java:54)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsAfterInitialization(AbstractAutowireCapableBeanFactory.java:406)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1428)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:518)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:455)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:192)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:585)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:895)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:425)
at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:467)
at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:483)
at org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:358)
at org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:325)
at org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:127)
at javax.servlet.GenericServlet.init(GenericServlet.java:158)
at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1282)
at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1195)
at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1085)
at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:5318)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5610)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1572)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1562)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
[localhost-startStop-1] ERROR auto.AutoArcArchivespecification -
org.nrg.xft.exception.ElementNotFoundException: Element not found: 'arc:ArchiveSpecification'
at org.nrg.xft.meta.XFTMetaManager.FindElement(XFTMetaManager.java:219)
at org.nrg.xft.meta.XFTMetaManager.GetWrappedElementByName(XFTMetaManager.java:363)
at org.nrg.xft.schema.Wrappers.GenericWrapper.GenericWrapperElement.GetElement(GenericWrapperElement.java:163)
at org.nrg.xft.search.ItemSearch.GetAllItems(ItemSearch.java:853)
at org.nrg.xdat.om.base.auto.AutoArcArchivespecification.getAllArcArchivespecifications(AutoArcArchivespecification.java:860)
at org.nrg.xnat.turbine.utils.ArcSpecManager.GetFreshInstance(ArcSpecManager.java:51)
at org.nrg.xnat.turbine.utils.ArcSpecManager.GetInstance(ArcSpecManager.java:66)
at org.nrg.xnat.helpers.prearchive.PrearcDatabase.getPrearcPath(PrearcDatabase.java:140)
at org.nrg.xnat.helpers.prearchive.PrearcDatabase.initDatabase(PrearcDatabase.java:108)
at org.nrg.xnat.helpers.prearchive.PrearcDatabase.initDatabase(PrearcDatabase.java:67)
at org.nrg.xnat.turbine.utils.ArcSpecManager.GetInstance(ArcSpecManager.java:221)
at org.nrg.xnat.turbine.utils.ArcSpecManager.GetInstance(ArcSpecManager.java:60)
at org.nrg.xnat.security.FilterSecurityInterceptorBeanPostProcessor.initializeArcSpecInstance(FilterSecurityInterceptorBeanPostProcessor.java:103)
at org.nrg.xnat.security.FilterSecurityInterceptorBeanPostProcessor.isRequiredLogin(FilterSecurityInterceptorBeanPostProcessor.java:110)
at org.nrg.xnat.security.FilterSecurityInterceptorBeanPostProcessor.postProcessAfterInitialization(FilterSecurityInterceptorBeanPostProcessor.java:54)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsAfterInitialization(AbstractAutowireCapableBeanFactory.java:406)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1428)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:518)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:455)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:192)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:585)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:895)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:425)
at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:467)
at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:483)
at org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:358)
at org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:325)
at org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:127)
at javax.servlet.GenericServlet.init(GenericServlet.java:158)
at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1282)
at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1195)
at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1085)
at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:5318)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5610)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1572)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1562)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
[org.springframework.scheduling.quartz.SchedulerFactoryBean#0_Worker-2] ERROR core.JobRunShell - Job users-jobs.disable-inactive-users threw an unhandled Exception:
java.lang.ArrayIndexOutOfBoundsException: 0
at org.nrg.xft.db.PoolDBUtils.getDefaultDBName(PoolDBUtils.java:597)
at org.nrg.xft.db.PoolDBUtils.executeQuery(PoolDBUtils.java:879)
at org.nrg.xft.db.PoolDBUtils.executeSelectQuery(PoolDBUtils.java:409)
at org.nrg.xft.XFTTable.Execute(XFTTable.java:51)
at org.nrg.xnat.security.DisableInactiveUsersJob.execute(DisableInactiveUsersJob.java:46)
at org.nrg.schedule.DelegatingJobBean.executeInternal(DelegatingJobBean.java:55)
at org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86)
at org.quartz.core.JobRunShell.run(JobRunShell.java:216)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:549)
[org.springframework.scheduling.quartz.SchedulerFactoryBean#0_Worker-2] ERROR core.ErrorLogger - Job (users-jobs.disable-inactive-users threw an exception.
org.quartz.SchedulerException: Job threw an unhandled exception. [See nested exception: java.lang.ArrayIndexOutOfBoundsException: 0]
at org.quartz.core.JobRunShell.run(JobRunShell.java:227)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:549)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 0
at org.nrg.xft.db.PoolDBUtils.getDefaultDBName(PoolDBUtils.java:597)
at org.nrg.xft.db.PoolDBUtils.executeQuery(PoolDBUtils.java:879)
at org.nrg.xft.db.PoolDBUtils.executeSelectQuery(PoolDBUtils.java:409)
at org.nrg.xft.XFTTable.Execute(XFTTable.java:51)
at org.nrg.xnat.security.DisableInactiveUsersJob.execute(DisableInactiveUsersJob.java:46)
at org.nrg.schedule.DelegatingJobBean.executeInternal(DelegatingJobBean.java:55)
at org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86)
at org.quartz.core.JobRunShell.run(JobRunShell.java:216)
... 1 more
[org.springframework.scheduling.quartz.SchedulerFactoryBean#0_Worker-1] ERROR base.BaseElement -
org.nrg.xft.exception.ElementNotFoundException: Element not found: 'xdat:user'
at org.nrg.xft.meta.XFTMetaManager.FindElement(XFTMetaManager.java:219)
at org.nrg.xft.meta.XFTMetaManager.GetWrappedElementByName(XFTMetaManager.java:363)
at org.nrg.xft.schema.Wrappers.GenericWrapper.GenericWrapperElement.GetElement(GenericWrapperElement.java:163)
at org.nrg.xft.XFTItem.NewItem(XFTItem.java:203)
at org.nrg.xdat.base.BaseElement.<init>(BaseElement.java:86)
at org.nrg.xdat.om.base.auto.AutoXdatUser.<init>(AutoXdatUser.java:44)
at org.nrg.xdat.om.base.BaseXdatUser.<init>(BaseXdatUser.java:33)
at org.nrg.xdat.om.XdatUser.<init>(XdatUser.java:34)
at org.nrg.xdat.security.XDATUser.<init>(XDATUser.java:101)
at org.nrg.xnat.utils.XnatUserProvider.get(XnatUserProvider.java:35)
at org.nrg.xnat.utils.XnatUserProvider.get(XnatUserProvider.java:19)
at org.nrg.xnat.helpers.prearchive.SessionXMLRebuilderJob.execute(SessionXMLRebuilderJob.java:40)
at org.nrg.schedule.DelegatingJobBean.executeInternal(DelegatingJobBean.java:55)
at org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86)
at org.quartz.core.JobRunShell.run(JobRunShell.java:216)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:549)
[org.springframework.scheduling.quartz.SchedulerFactoryBean#0_Worker-1] ERROR utils.XnatUserProvider - Unable to retrieve user admin
org.nrg.xft.exception.ElementNotFoundException: Element not found: 'xdat:user'
at org.nrg.xft.meta.XFTMetaManager.FindElement(XFTMetaManager.java:219)
at org.nrg.xft.meta.XFTMetaManager.GetWrappedElementByName(XFTMetaManager.java:363)
at org.nrg.xft.schema.Wrappers.GenericWrapper.GenericWrapperElement.GetElement(GenericWrapperElement.java:163)
at org.nrg.xdat.schema.SchemaElement.GetElement(SchemaElement.java:118)
at org.nrg.xdat.security.XDATUser.<init>(XDATUser.java:102)
at org.nrg.xnat.utils.XnatUserProvider.get(XnatUserProvider.java:35)
at org.nrg.xnat.utils.XnatUserProvider.get(XnatUserProvider.java:19)
at org.nrg.xnat.helpers.prearchive.SessionXMLRebuilderJob.execute(SessionXMLRebuilderJob.java:40)
at org.nrg.schedule.DelegatingJobBean.executeInternal(DelegatingJobBean.java:55)
at org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86)
at org.quartz.core.JobRunShell.run(JobRunShell.java:216)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:549)
[org.springframework.scheduling.quartz.SchedulerFactoryBean#0_Worker-1] ERROR core.JobRunShell - Job prearchive-jobs.session-rebuilder threw an unhandled Exception:
java.lang.NullPointerException
at org.nrg.xnat.helpers.prearchive.SessionXMLRebuilderJob.execute(SessionXMLRebuilderJob.java:41)
at org.nrg.schedule.DelegatingJobBean.executeInternal(DelegatingJobBean.java:55)
at org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86)
at org.quartz.core.JobRunShell.run(JobRunShell.java:216)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:549)
[org.springframework.scheduling.quartz.SchedulerFactoryBean#0_Worker-1] ERROR core.ErrorLogger - Job (prearchive-jobs.session-rebuilder threw an exception.
org.quartz.SchedulerException: Job threw an unhandled exception. [See nested exception: java.lang.NullPointerException]
at org.quartz.core.JobRunShell.run(JobRunShell.java:227)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:549)
Caused by: java.lang.NullPointerException
at org.nrg.xnat.helpers.prearchive.SessionXMLRebuilderJob.execute(SessionXMLRebuilderJob.java:41)
at org.nrg.schedule.DelegatingJobBean.executeInternal(DelegatingJobBean.java:55)
at org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86)
at org.quartz.core.JobRunShell.run(JobRunShell.java:216)
... 1 more
WEBAPP:/xnat
SOURCE: /var/lib/tomcat7/webapps/xnat/
Oct 11, 2019 3:32:27 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Oct 11, 2019 3:32:27 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8443"]
Oct 11, 2019 3:32:27 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 552672 ms
localhost.log
Oct 11, 2019 1:56:48 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring FrameworkServlet 'spring-mvc'
Oct 11, 2019 3:22:50 PM org.apache.catalina.core.ApplicationContext log
INFO: Destroying Spring FrameworkServlet 'spring-mvc'
Oct 11, 2019 3:23:06 PM org.apache.catalina.core.ApplicationContext log
SEVERE: Servlet RestletServlet threw unload() exception
javax.servlet.ServletException: Servlet.destroy() for servlet RestletServlet threw exception
at org.apache.catalina.core.StandardWrapper.unload(StandardWrapper.java:1506)
at org.apache.catalina.core.StandardWrapper.stopInternal(StandardWrapper.java:1846)
at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:224)
at org.apache.catalina.core.StandardContext.stopInternal(StandardContext.java:5767)
at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:224)
at org.apache.catalina.core.ContainerBase$StopChild.call(ContainerBase.java:1588)
at org.apache.catalina.core.ContainerBase$StopChild.call(ContainerBase.java:1577)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.IllegalStateException: BeanFactory not initialized or already closed - call 'refresh' before accessing beans via the ApplicationContext
at org.springframework.context.support.AbstractRefreshableApplicationContext.getBeanFactory(AbstractRefreshableApplicationContext.java:171)
at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1083)
at org.nrg.framework.services.ContextService.getBean(ContextService.java:86)
at org.nrg.xnat.restlet.servlet.XNATRestletServlet.destroy(XNATRestletServlet.java:177)
at org.apache.catalina.core.StandardWrapper.unload(StandardWrapper.java:1484)
... 10 more
Oct 11, 2019 3:32:13 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring FrameworkServlet 'spring-mvc'
turbine.log
2019-10-11 15:32:28,241 [http-bio-8443-exec-4] ERROR org.apache.turbine.modules.screens.VelocityErrorScreen - Screen Error.vm not found!
2019-10-11 15:32:28,242 [http-bio-8443-exec-4] ERROR org.apache.turbine.Turbine - Could not find screen for Error.vm
java.lang.Exception: Could not find screen for Error.vm
at org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScreen.java:104)
at org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.java:101)
at org.apache.turbine.modules.Screen.build(Screen.java:57)
at org.apache.turbine.modules.ScreenLoader.eval(ScreenLoader.java:104)
at org.apache.turbine.modules.layouts.VelocityOnlyLayout.doBuild(VelocityOnlyLayout.java:92)
at org.apache.turbine.modules.Layout.build(Layout.java:53)
at org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:98)
at org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:146)
at org.apache.turbine.modules.Page.build(Page.java:53)
at org.apache.turbine.modules.PageLoader.exec(PageLoader.java:98)
at org.apache.turbine.Turbine.handleException(Turbine.java:963)
at org.apache.turbine.Turbine.doGet(Turbine.java:822)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
axis.log
9085 [localhost-startStop-1] ERROR org.apache.axis.configuration.EngineConfigurationFactoryServlet - Unable to find config file. Creating new servlet engine config file: /WEB-INF/server-config.wsdd
I notice the problem you describe here
https://groups.google.com/d/msg/xnat_discussion/Su4IYP731lo/ybmLOOHzAgAJ
is happening in this xnat instance.
I have tried this suggestion
"If you are running PostgreSQL 9.1 or later, you will need to set 'standard_conforming_strings = off' in your postgresql.conf."
Can you suggest any other changes?
Simon
To unsubscribe from this group and stop receiving emails from it, send an email to xnat_di...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/xnat_discussion/cd814f04-f00f-4e16-b6a5-1c1325617aff%40googlegroups.com.
Herrick, Rick
Hi Simon,
This looks like some kind of configuration issue, specifically around accessing the database:
[localhost-startStop-1] ERROR auto.AutoArcArchivespecification -
org.nrg.xft.exception.ElementNotFoundException: Element not found: 'arc:ArchiveSpecification'
at org.nrg.xft.meta.XFTMetaManager.FindElement(XFTMetaManager.java:219)
[org.springframework.scheduling.quartz.SchedulerFactoryBean#0_Worker-2] ERROR core.JobRunShell - Job users-jobs.disable-inactive-users threw an unhandled Exception:
java.lang.ArrayIndexOutOfBoundsException: 0
at org.nrg.xft.db.PoolDBUtils.getDefaultDBName(PoolDBUtils.java:597)
Messages like the arc:ArchiveSpecification one usually indicate that XNAT isn’t loading data-type definitions and relationships from the database. And not being able to retrieve the default database name (note that, if an array index of 0 is out of bounds, that means you have an empty array, i.e. no database names). Can you check that the database configuration in services.properties are properly configured and that you can reach the database using those values? This will look something like this:
datasource.name=xnat
datasource.driver=org.postgresql.Driver
datasource.url=jdbc:postgresql://localhost/xnat
datasource.username=xnat
datasource.password=xnat
You should be able to take these values and use them with psql like this:
$ psql -h localhost -U xnat -d xnat
Password for user xnat:
psql (10.10 (Ubuntu 10.10-1.pgdg18.04+1))
SSL connection (protocol: TLSv1.3, cipher: TLS_AES_256_GCM_SHA384, bits: 256, compression: off)
Type "help" for help.
xnat=>
One other thing I’ll mention: we strongly encourage users to upgrade from XNAT 1.6.x and earlier to the latest 1.7 release (currently 1.7.5.6). There are a number of practical reasons, e.g. future upgrades are much easier since you basically just swap the war file, compatibility with updated infrastructure (1.7.6 supports PostgreSQL up to the latest release of 11; I’ve tested with PostgreSQL 12 a little bit with no issue as well), and so on. It’s also much easier for the XNAT development team to support 1.7.x and analyze and fix user issues. I understand this isn’t always practical due to project requirements and dependencies on custom code (1.7 uses plugins rather than modules for extended functionality, so any modules need to be replaced or migrated), but your group should consider this if at all possible.
To unsubscribe from this group and stop receiving emails from it, send an email to
xnat_discussi...@googlegroups.com.
To view this discussion on the web visit
https://groups.google.com/d/msgid/xnat_discussion/3e4a6088-79b8-40a7-a0cd-32bf5376f53f%40googlegroups.com.
SIMON JONES
The command
psql -h localhost -U xnat -d xnat
works as you suggest. As I mentioned previously I see similar behaviour as described here,
https://groups.google.com/forum/#!msg/xnat_discussion/Su4IYP731lo/ybmLOOHzAgAJ
if you go into psql and try to run this query:
SELECT pg_get_serial_sequence('xnat_projectData_resource','xnat_projectData_resource_id') AS col_name ;
That will fail, but this will work:
SELECT pg_get_serial_sequence('xnat_projectdata_resource','xnat_projectdata_resource_id') AS col_name ;
There is no hyphen in the name of the web app.
I am not sure that the XNAT can be upgraded to XNAT 1.7 when it is not running at the moment.
Thanks
Herrick, Rick
If you dump your database:
$ pg_dump > xnat.sql
At the top you should find a number of SET and SELECT statements, e.g.:
SET statement_timeout = 0;
SET lock_timeout = 0;
SET idle_in_transaction_session_timeout = 0;
SET client_encoding = 'UTF8';
SET standard_conforming_strings = on;
SELECT pg_catalog.set_config('search_path', '', false);
SET check_function_bodies = false;
SET xmloption = content;
SET client_min_messages = warning;
SET row_security = off;
What’s in those statements?
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
Phone: +1 (314) 273-1645
From: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com> on behalf of SIMON JONES <psimo...@gmail.com>
Reply-To: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com>
Date: Tuesday, October 22, 2019 at 10:27 AM
To: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com>
Subject: Re: [XNAT Discussion] http status 500 - no webapplicationcontext found no contextloaderlistener registered?
The command
--
You received this message because you are subscribed to the Google Groups "xnat_discussion" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
xnat_discussi...@googlegroups.com.
To view this discussion on the web visit
https://groups.google.com/d/msgid/xnat_discussion/283d3612-311b-4d45-ac7f-ab7227e72823%40googlegroups.com.
SIMON JONES
SET statement_timeout = 0;
SET lock_timeout = 0;
SET idle_in_transaction_session_timeout = 0; MISSING
SET client_encoding = 'UTF8';
SET standard_conforming_strings = on;
SELECT pg_catalog.set_config('search_path', '', false);
SET check_function_bodies = false;
SET xmloption = content;
SET client_min_messages = warning;
SET row_security = off;
Simon
To unsubscribe from this group and stop receiving emails from it, send an email to xnat_di...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/xnat_discussion/283d3612-311b-4d45-ac7f-ab7227e72823%40googlegroups.com.
Herrick, Rick
I’m not sure how XNAT got into the state that it’s in where it’s providing a cased version of the column name. This is something that we’d run into occasionally with 1.6.x and I was never able to figure out why. The issue is that PostgreSQL makes all column names lower-case and, even if you use upper-case letters in a column name, interprets them as lower-case unless the column name is enclosed in quotations or provided as a variable, as in this case where the column name is passed into a function.
As of XNAT 1.7.3, this issue is fixed. Prior to that, XNAT composed that SQL query using the table and column name as they come from the database. Now it explicitly converts the column name to lower case.
That means one fix is to upgrade if possible.
Other possible fixes would be to figure out why you’re getting the cased value (i.e. xnat_projectData_resource_id) rather than a lower-cased version (as I said, I could never figure out why this would happen occasionally). Or possibly build a new version of the XDAT library that contains the two classes that generate these queries (DBAction and PoolDBUtils) with a code patch to add the lower-case call.
I’d recommend upgrading for a number of reasons, but try dumping your database, importing it into another database (e.g. on a Vagrant VM or test server), and running the latest version of XNAT against that. I’m sure that this problem at least would go away.
To unsubscribe from this group and stop receiving emails from it, send an email to
xnat_discussi...@googlegroups.com.
To view this discussion on the web visit
https://groups.google.com/d/msgid/xnat_discussion/e264c939-740f-43fa-a29e-211802d71797%40googlegroups.com.