Error with module when starting jira after upgrading jira 6.4 to jira 7.0.11 to version 7.12.3

[Jonatan Bouillon]

When I start jira 7.12.3 after the in-place update from 7.0.11 I get an error that said the server.xml file is missing parameters needed by Jira to handle requests that contain special characters.

Setup: Tomcat is misconfigured

The update from 6.4 to jira 7.0.11 worked fine.

But when I look at the jira log I see errors with 3 plugins that fails.

• AutowatchJiraListener :
  • Could not find class: org.openmrs.jira.listeners.AutowatchJiraListener
• Subversion plugin :
  • Could not find class: com.atlassian.jira.plugin.ext.subversion.revisions.RevisionIndexService
• Git plugin : 
  • Could not find class: com.xiplink.jira.git.revisions.RevisionIndexService

I have updated each plugin in jira home plugin folder but I still get thoses errors. I have also clear the indexes caches and modify to be use more memory. I can't find the solution.

So, I'm wondering if there is a way to disable those plugin so I can still load jira?

---

2018-11-03 19:39:28,347 JIRA-Bootstrap ERROR [c.a.jira.event.DefaultListenerManager] Could not configure listener: Autowatch Jira Listener className:org.openmrs.jira.listeners.AutowatchJiraListener
com.atlassian.jira.event.ListenerException: Could not find class: org.openmrs.jira.listeners.AutowatchJiraListener
at com.atlassian.jira.event.ListenerFactory.getListener(ListenerFactory.java:29)
at com.atlassian.jira.event.DefaultListenerManager$Listeners.loadListeners(DefaultListenerManager.java:150)
at com.atlassian.jira.event.DefaultListenerManager$Listeners.create(DefaultListenerManager.java:108)
at com.atlassian.jira.event.DefaultListenerManager$Listeners.create(DefaultListenerManager.java:105)
at com.atlassian.util.concurrent.ResettableLazyReference$InternalReference.create(ResettableLazyReference.java:182)
at com.atlassian.util.concurrent.LazyReference$Sync.run(LazyReference.java:325)
at com.atlassian.util.concurrent.LazyReference.getInterruptibly(LazyReference.java:143)
at com.atlassian.util.concurrent.LazyReference.get(LazyReference.java:112)
at com.atlassian.util.concurrent.ResettableLazyReference.get(ResettableLazyReference.java:92)
at com.atlassian.jira.event.DefaultListenerManager$Listeners.start(DefaultListenerManager.java:127)
at com.atlassian.jira.event.DefaultListenerManager.start(DefaultListenerManager.java:50)
at com.atlassian.jira.component.pico.ComponentManager.runStartable(ComponentManager.java:325)
at com.atlassian.jira.component.pico.ComponentManager.quickStart(ComponentManager.java:241)
at com.atlassian.jira.component.pico.ComponentManager.start(ComponentManager.java:182)
at com.atlassian.jira.upgrade.PluginSystemLauncher.start(PluginSystemLauncher.java:45)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$2(DefaultJiraLauncher.java:143)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:304)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:199)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:135)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$0(DefaultJiraLauncher.java:102)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:100)
at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:154)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ClassNotFoundException: Class 'org.openmrs.jira.listeners.AutowatchJiraListener' not found.
at com.atlassian.jira.plugin.DefaultComponentClassManager.constructEvenIfNotEnabled(DefaultComponentClassManager.java:122)
at com.atlassian.jira.plugin.DefaultComponentClassManager.newInstance(DefaultComponentClassManager.java:57)
at com.atlassian.jira.event.ListenerFactory.getListener(ListenerFactory.java:24)
... 23 more
2018-11-03 19:39:28,472 JIRA-Bootstrap ERROR [c.a.jira.service.OfBizServiceConfigStore] Unable to create a service config for service with the name : Subversion Revision Indexing Service
com.atlassian.jira.service.OfBizServiceConfigStore$ClassNotFoundServiceException: Could not find class: com.atlassian.jira.plugin.ext.subversion.revisions.RevisionIndexService
at com.atlassian.jira.service.OfBizServiceConfigStore.instantiateServiceContainer(OfBizServiceConfigStore.java:216)
at com.atlassian.jira.service.OfBizServiceConfigStore.getServiceContainer(OfBizServiceConfigStore.java:186)
at com.atlassian.jira.service.OfBizServiceConfigStore.getAllServiceConfigs(OfBizServiceConfigStore.java:174)
at com.atlassian.jira.service.DefaultServiceManager.loadServiceCache(DefaultServiceManager.java:573)
at com.atlassian.cache.memory.MemoryCacheManager$1$1.load(MemoryCacheManager.java:125)
at com.atlassian.cache.memory.MemoryCacheManager$1$1.load(MemoryCacheManager.java:101)
at com.google.common.cache.LocalCache$LoadingValueReference.loadFuture(LocalCache.java:3527)
at com.google.common.cache.LocalCache$Segment.loadSync(LocalCache.java:2319)
at com.google.common.cache.LocalCache$Segment.lockedGetOrLoad(LocalCache.java:2282)
at com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2197)
at com.google.common.cache.LocalCache.get(LocalCache.java:3937)
at com.google.common.cache.LocalCache.getOrLoad(LocalCache.java:3941)
at com.google.common.cache.LocalCache$LocalLoadingCache.get(LocalCache.java:4824)
at com.google.common.cache.LocalCache$LocalLoadingCache.getUnchecked(LocalCache.java:4830)
at com.atlassian.cache.memory.DelegatingCachedReference.getUnderLock(DelegatingCachedReference.java:101)
at com.atlassian.cache.memory.DelegatingCachedReference.get(DelegatingCachedReference.java:86)
at com.atlassian.jira.service.DefaultServiceManager.getServiceCache(DefaultServiceManager.java:517)
at com.atlassian.jira.service.DefaultServiceManager.getServices(DefaultServiceManager.java:115)
at com.atlassian.jira.service.DefaultServiceManager.ensureServicesScheduled(DefaultServiceManager.java:521)
at com.atlassian.jira.service.DefaultServiceManager.start(DefaultServiceManager.java:104)
at com.atlassian.jira.component.pico.ComponentManager.runStartable(ComponentManager.java:325)
at com.atlassian.jira.component.pico.ComponentManager.quickStart(ComponentManager.java:241)
at com.atlassian.jira.component.pico.ComponentManager.start(ComponentManager.java:182)
at com.atlassian.jira.upgrade.PluginSystemLauncher.start(PluginSystemLauncher.java:45)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$2(DefaultJiraLauncher.java:143)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:304)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:199)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:135)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$0(DefaultJiraLauncher.java:102)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:100)
at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:154)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ClassNotFoundException: Class 'com.atlassian.jira.plugin.ext.subversion.revisions.RevisionIndexService' not found.
at com.atlassian.jira.plugin.DefaultComponentClassManager.constructEvenIfNotEnabled(DefaultComponentClassManager.java:122)
at com.atlassian.jira.plugin.DefaultComponentClassManager.newInstance(DefaultComponentClassManager.java:57)
at com.atlassian.jira.service.OfBizServiceConfigStore.loadServiceClass(OfBizServiceConfigStore.java:322)
at com.atlassian.jira.service.OfBizServiceConfigStore.instantiateServiceContainer(OfBizServiceConfigStore.java:213)
... 32 more
2018-11-03 19:39:28,474 JIRA-Bootstrap ERROR [c.a.jira.service.OfBizServiceConfigStore] The class 'com.atlassian.jira.plugin.ext.subversion.revisions.RevisionIndexService' could not be found. This can happen when a plugin is uninstalled or disabled
2018-11-03 19:39:28,474 JIRA-Bootstrap ERROR [c.a.jira.service.OfBizServiceConfigStore] A NoOp Service has been returned and hence 'Subversion Revision Indexing Service' will not do anything until fixed.
2018-11-03 19:39:28,577 JIRA-Bootstrap ERROR [c.a.jira.service.OfBizServiceConfigStore] Unable to create a service config for service with the name : Git Revision Indexing Service
com.atlassian.jira.service.OfBizServiceConfigStore$ClassNotFoundServiceException: Could not find class: com.xiplink.jira.git.revisions.RevisionIndexService
at com.atlassian.jira.service.OfBizServiceConfigStore.instantiateServiceContainer(OfBizServiceConfigStore.java:216)
at com.atlassian.jira.service.OfBizServiceConfigStore.getServiceContainer(OfBizServiceConfigStore.java:186)
at com.atlassian.jira.service.OfBizServiceConfigStore.getAllServiceConfigs(OfBizServiceConfigStore.java:174)
at com.atlassian.jira.service.DefaultServiceManager.loadServiceCache(DefaultServiceManager.java:573)
at com.atlassian.cache.memory.MemoryCacheManager$1$1.load(MemoryCacheManager.java:125)
at com.atlassian.cache.memory.MemoryCacheManager$1$1.load(MemoryCacheManager.java:101)
at com.google.common.cache.LocalCache$LoadingValueReference.loadFuture(LocalCache.java:3527)
at com.google.common.cache.LocalCache$Segment.loadSync(LocalCache.java:2319)
at com.google.common.cache.LocalCache$Segment.lockedGetOrLoad(LocalCache.java:2282)
at com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2197)
at com.google.common.cache.LocalCache.get(LocalCache.java:3937)
at com.google.common.cache.LocalCache.getOrLoad(LocalCache.java:3941)
at com.google.common.cache.LocalCache$LocalLoadingCache.get(LocalCache.java:4824)
at com.google.common.cache.LocalCache$LocalLoadingCache.getUnchecked(LocalCache.java:4830)
at com.atlassian.cache.memory.DelegatingCachedReference.getUnderLock(DelegatingCachedReference.java:101)
at com.atlassian.cache.memory.DelegatingCachedReference.get(DelegatingCachedReference.java:86)
at com.atlassian.jira.service.DefaultServiceManager.getServiceCache(DefaultServiceManager.java:517)
at com.atlassian.jira.service.DefaultServiceManager.getServices(DefaultServiceManager.java:115)
at com.atlassian.jira.service.DefaultServiceManager.ensureServicesScheduled(DefaultServiceManager.java:521)
at com.atlassian.jira.service.DefaultServiceManager.start(DefaultServiceManager.java:104)
at com.atlassian.jira.component.pico.ComponentManager.runStartable(ComponentManager.java:325)
at com.atlassian.jira.component.pico.ComponentManager.quickStart(ComponentManager.java:241)
at com.atlassian.jira.component.pico.ComponentManager.start(ComponentManager.java:182)
at com.atlassian.jira.upgrade.PluginSystemLauncher.start(PluginSystemLauncher.java:45)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$2(DefaultJiraLauncher.java:143)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:304)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:199)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:135)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$0(DefaultJiraLauncher.java:102)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:100)
at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:154)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ClassNotFoundException: Class 'com.xiplink.jira.git.revisions.RevisionIndexService' not found.
at com.atlassian.jira.plugin.DefaultComponentClassManager.constructEvenIfNotEnabled(DefaultComponentClassManager.java:122)
at com.atlassian.jira.plugin.DefaultComponentClassManager.newInstance(DefaultComponentClassManager.java:57)
at com.atlassian.jira.service.OfBizServiceConfigStore.loadServiceClass(OfBizServiceConfigStore.java:322)
at com.atlassian.jira.service.OfBizServiceConfigStore.instantiateServiceContainer(OfBizServiceConfigStore.java:213)
... 32 more
2018-11-03 19:39:28,580 JIRA-Bootstrap ERROR [c.a.jira.service.OfBizServiceConfigStore] The class 'com.xiplink.jira.git.revisions.RevisionIndexService' could not be found. This can happen when a plugin is uninstalled or disabled
2018-11-03 19:39:28,580 JIRA-Bootstrap ERROR [c.a.jira.service.OfBizServiceConfigStore] A NoOp Service has been returned and hence 'Git Revision Indexing Service' will not do anything until fixed.
2018-11-03 19:39:28,798 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from C:\Program Files (x86)\Atlassian\Application Data\JIRA\dbconfig.xml
2018-11-03 19:39:28,816 JIRA-Bootstrap INFO [c.a.j.instrumentation.external.DatabaseExternalGauges] Installing DBCP monitoring instruments: DatabaseExternalGauges.JiraDbcpInstruments[instruments=[DBCP_MAX, DBCP_ACTIVE, DBCP_IDLE],objectName=com.atlassian.jira:name=BasicDataSource]
2018-11-03 19:39:29,458 JIRA-Bootstrap ERROR [c.a.j.health.checks.TomcatConfigurationHealthCheck]
Required path chars: [ ] |
Configured path chars: null
Required query chars: [ ] | { } ^ \ ` " < >
Configured query chars: null

2018-11-03 19:39:29,466 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] Tomcat is misconfigured
2018-11-03 19:39:29,466 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] The server.xml file is missing parameters needed by Jira to handle requests that contain special characters.

2018-11-03 19:39:29,466 JIRA-Bootstrap ERROR [c.a.jira.startup.DefaultJiraLauncher] JIRA has failed to start because of the following errors: [(Event: Level = (EventLevel: error) , Key = (EventType: setup) , Desc = Tomcat is misconfigured , Exception = The server.xml file is missing parameters needed by Jira to handle requests that contain special characters.<br/>)]
2018-11-03 19:39:29,473 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Memory Usage:
---------------------------------------------------------------------------------
Heap memory : Used: 352 MiB. Committed: 674 MiB. Max: 997 MiB
Non-heap memory : Used: 148 MiB. Committed: 154 MiB. Max: 240 MiB
---------------------------------------------------------------------------------
TOTAL : Used: 500 MiB. Committed: 828 MiB. Max: 1237 MiB
---------------------------------------------------------------------------------

[Andy Heinzer · Accepted solution]

In regards to the plugins, some of these are no longer supported in the latest version of Jira, while others might just require an update.   In the process of doing the upgrade, it might just be best to temporarily remove these from the $JIRAHOME/plugins/installed-plugins/ folder so that you can at least get Jira started and upgraded first.  After Jira itself is working I'd then recommend trying to use the UPM in Jira in order to update/reinstall compatible versions of any plugins you might need for Jira.

As for the other major problem with Tomcat, this is a known problem when upgrading any version such as 7.12.1 or earlier versions to a higher version.  This is mentioned in the upgrade notes at https://confluence.atlassian.com/jiracore/jira-core-7-12-x-upgrade-notes-955179470.html

as well as the bug ticket https://jira.atlassian.com/browse/JRASERVER-67974

Both documents indicate the steps needed in order to make this work.  They involve making changes to your server.xml file for all the connectors you have there:

Workaround

1. Open configuration file server.xml (should be in conf directory)
2. Find all connectors your application is using
3. Add ** relaxedPathChars="[]|" relaxedQueryChars="[]|{}^\`"<>" to properties for example: 

   <Connector port="8080" relaxedPathChars="[]|" relaxedQueryChars="[]|{}^&#x5c;&#x60;&quot;&lt;&gt;" maxThreads="150" minSpareThreads="25" connectionTimeout="20000" enableLookups="false" maxHttpHeaderSize="8192" protocol="HTTP/1.1" useBodyEncodingForURI="true" redirectPort="8443" acceptCount="100" disableUploadTimeout="true" bindOnInit="false"/>

4. Restart Jira
   See KB for full details: changing server.xml to handle requests with special characters

Note: If you have more than one connector in that server.xml file, you will need to repeat step #3 for each of them.

[Jonatan Bouillon]

Thanks for the answer, I have tried to remove the plugin from the folder but it didn't work, maybe I didn't remove correctly.

To fix my problem, I ended up installing a new Jira in another folder without any existing pluging and it worked.

I realize that is not a good idea to inplace-upgrade with unsupported plugin.

It would have been a better idea to review each plugin and remove or disable those plugin before upgrade like suggested in the installation documentation.

I didn't needed the SVN, Autowatcher plugin with the new jira version anyway.

The problem was not related to the server.xml config and relaxed chars.