Jira stops working after plugins upgrade.Any suggestions?

[Ivaylo Stanev]

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)

[Code 007 · Accepted solution]

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

[Nick Mancuso]

Thank you,

This worked like a charm for me!

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

[Michael Pfister]

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 :)

[DOT-COMmunications]

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.

[Evert Penninckx]

Thanks for sharing!

[Andy Brook [Plugin People]]

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.

[Jobin Kuruvilla [Adaptavist]]

Looks like some links in top navigation bar is broken!

[Farzad Panahi]

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

   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

[Intersel]

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.

[Saul Perdomo]

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.

[Nick Mancuso]

Thank you,

This worked like a charm for me!

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