Jira stops working after plugins upgrade.Any suggestions?

We have Jira v5.0.4 - downloadable version on Win machine. It was working fully fine for many months.

I have just updated the following plugins (using the UPM) to their latest versions: Atlassian Bonfire - JIRA Plugin, Atlassian GreenHopper, Balsamiq, Mockups, JIRA Importers Plugin (JIM), Tempo Plugin .

After the upgrade I see an error and almost nothing works. Any suggestions?

The error I see is here:

An error occurred whilst rendering this message. Please contact the administrators, and inform them of this bug. Details: ------- org.apache.velocity.exception.MethodInvocationException: Invocation of method 'getNotEmptySectionsForLocation' in class com.atlassian.jira.plugin.webfragment.DefaultSimpleLinkManager threw exception class java.lang.IllegalStateException : Method invoked on module descriptor after it was destroyed. This is only legal for some methods on AbstractModuleDescriptor. at org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:251) at org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:175) at org.apache.velocity.runtime.parser.node.ASTReference.value(ASTReference.java:327) at org.apache.velocity.runtime.parser.node.ASTExpression.value(ASTExpression.java:51) at org.apache.velocity.runtime.parser.node.ASTSetDirective.render(ASTSetDirective.java:95) at org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:230) at org.apache.velocity.Template.merge(Template.java:256) at org.apache.velocity.app.VelocityEngine.mergeTemplate(VelocityEngine.java:422) at com.atlassian.velocity.DefaultVelocityManager.getEncodedBody(DefaultVelocityManager.java:77) at com.atlassian.velocity.DefaultVelocityManager.getEncodedBody(DefaultVelocityManager.java:61) at com.atlassian.velocity.DefaultVelocityManager.getEncodedBody(DefaultVelocityManager.java:56) at com.atlassian.jira.web.component.AbstractWebComponent.getHtml(AbstractWebComponent.java:33) at com.atlassian.jira.web.component.webfragment.WebFragmentWebComponent.getHtml(WebFragmentWebComponent.java:48) at sun.reflect.GeneratedMethodAccessor3743.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.apache.velocity.util.introspection.UberspectImpl$VelMethodImpl.invoke(UberspectImpl.java:234) at org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:203) at org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:175) at org.apache.velocity.runtime.parser.node.ASTReference.render(ASTReference.java:220) at org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:55) at org.apache.velocity.runtime.parser.node.ASTIfStatement.render(ASTIfStatement.java:70) at org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:230) at org.apache.velocity.Template.merge(Template.java:256) at org.apache.velocity.app.VelocityEngine.mergeTemplate(VelocityEngine.java:422) at com.atlassian.velocity.DefaultVelocityManager.getEncodedBody(DefaultVelocityManager.java:77) at com.atlassian.velocity.DefaultVelocityManager.getEncodedBody(DefaultVelocityManager.java:61) at com.atlassian.velocity.DefaultVelocityManager.getEncodedBody(DefaultVelocityManager.java:56) at com.atlassian.jira.plugin.AbstractJiraModuleDescriptor.getHtml(AbstractJiraModuleDescriptor.java:109) at com.atlassian.jira.plugin.navigation.TopNavigationModuleDescriptorImpl.getTopNavigationHtml(TopNavigationModuleDescriptorImpl.java:84) at com.atlassian.jira.plugin.navigation.DefaultPluggableTopNavigation.getHtml(DefaultPluggableTopNavigation.java:23) at org.apache.jsp.decorators.admin_jsp._jspService(admin_jsp.java:550) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:386) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:646) at org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:551) at org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:488) at com.opensymphony.sitemesh.compatability.OldDecorator2NewDecorator.render(OldDecorator2NewDecorator.java:46) at com.opensymphony.sitemesh.webapp.decorator.BaseWebAppDecorator.render(BaseWebAppDecorator.java:33) at com.opensymphony.sitemesh.webapp.SiteMeshFilter.doFilter(SiteMeshFilter.java:84) at com.atlassian.jira.web.filters.SitemeshPageFilter.doFilter(SitemeshPageFilter.java:124) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.seraph.filter.SecurityFilter.doFilter(SecurityFilter.java:234) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.security.auth.trustedapps.filter.TrustedApplicationsFilter.doFilter(TrustedApplicationsFilter.java:98) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.seraph.filter.BaseLoginFilter.doFilter(BaseLoginFilter.java:157) at com.atlassian.jira.web.filters.JiraLoginFilter.doFilter(JiraLoginFilter.java:70) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66) at com.atlassian.oauth.serviceprovider.internal.servlet.OAuthFilter.doFilter(OAuthFilter.java:71) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66) at com.atlassian.bonfire.web.filters.BonfireP3PFilter.doFilter(BonfireP3PFilter.java:57) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.util.profiling.filters.ProfilingFilter.doFilter(ProfilingFilter.java:99) at com.atlassian.jira.web.filters.JIRAProfilingFilter.doFilter(JIRAProfilingFilter.java:19) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.johnson.filters.AbstractJohnsonFilter.doFilter(AbstractJohnsonFilter.java:71) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:350) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.gzipfilter.GzipFilter.doFilterInternal(GzipFilter.java:81) at com.atlassian.gzipfilter.GzipFilter.doFilter(GzipFilter.java:51) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66) at com.sysbliss.jira.plugins.workflow.servlet.JWDSendRedirectFilter.doFilter(JWDSendRedirectFilter.java:25) at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74) at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77) at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.jira.web.filters.steps.ChainedFilterStepRunner.doFilter(ChainedFilterStepRunner.java:78) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.core.filters.cache.AbstractCachingFilter.doFilter(AbstractCachingFilter.java:33) at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.core.filters.encoding.AbstractEncodingFilter.doFilter(AbstractEncodingFilter.java:41) at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31) at com.atlassian.jira.web.filters.PathMatchingEncodingFilter.doFilter(PathMatchingEncodingFilter.java:49) at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.jira.web.monitor.ActiveRequestsFilter$PassToChainFilterFunc.doFilter(ActiveRequestsFilter.java:346) at com.atlassian.jira.web.monitor.ActiveRequestsFilter$DebugLogFilterFunc.doFilter(ActiveRequestsFilter.java:463) at com.atlassian.jira.web.monitor.ActiveRequestsFilter.doFilter(ActiveRequestsFilter.java:173) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.jira.startup.JiraStartupChecklistFilter.doFilter(JiraStartupChecklistFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.multitenant.servlet.MultiTenantServletFilter.doFilter(MultiTenantServletFilter.java:91) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at com.atlassian.jira.web.filters.steps.ChainedFilterStepRunner.doFilter(ChainedFilterStepRunner.java:78) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:554) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298) at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:864) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:579) at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1665) at java.lang.Thread.run(Thread.java:662)

9 answers

1 accepted

Hi,

I filed a bug report and this is the response that I got back,

"Hi,

I am sorry to hear that you having issue with JIRA today.

Can you do the following and let me know how it goes with you :

  1. Shut down JIRA
  2. Delete JIRA.HOME/plugins/.osgi-plugins and .bundled-plugins
  3. Delete the index file inside JIRA_HOME\caches
  4. Restart JIRA
  5. Perform a re-index via _Administration -> System -> Indexing

Note : all deleted files will be re-created when you re-start.

Regards,
Abdullahi
Atlassian Support."

After following the instructions, my JIRA deployment seems to be up and running fine again. Hope it helps.

Cheers

Thank you,

This worked like a charm for me!

I'll buy you a beer if I ever run into you!

Disable plugins one at a time, locate the problem for starters, then I think it may be a support call to atlassian if its GH related.

Looks like some links in top navigation bar is broken!

Thanks for sharing!

I had this problem when i tried to update our plugins on JIRA 4.4.

It seems to be related to the Balsamiq Mockups plugin as when i tried i ended up with the old version and the new version both trying to start and that was what caused my problems.

I would suggest looking in the plugin files to see if you more than one of them and removing one of them.

Just ran into the same issue when trying to upgrade the following three plugins on Jira 5.0.6:

- Atlassian GreenHopper - 5.10.3
- JIRA Importers Plugin (JIM) - 4.3.1
- Support Tools Plugin - 3.0.5

Thanks for posting the solution code007 :)


Thank you,

This worked like a charm for me!

I'll buy you a beer if I ever run into you!

Thanks for sharing, code007.

We ran into the same issue when upgrading from JIRA 5.07 to 5.1.1 and Abdullahi's suggestion worked perfectly.

Hello guys, I experienced this problem updating iCalendar, JIRA importers and Bamboo plugins.

First thing I did was trying with a Re-index JIRA but it didn't work. Next I shut down JIRA and restarted again and voilá, it just worked fine.

Good Luck.

Just deleting the folders did the fix for me:

Run the following process to refresh caches.

  1. Shutdown JIRA.
  2. Remove the following folders:

    $JIRA_HOME/plugins/.bundled-plugins
    $JIRA_HOME/plugins/.osgi-plugins

    (info) These folders will be automatically rebuilt when JIRA is restarted.

  3. Start JIRA.

https://confluence.atlassian.com/display/JIRAKB/getLinksForSection+error+at+the+top+of+the+page?utm_source=STP&utm_medium=logScan

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