Upgraded Jira Apps & now server won't start

[James Hogbin]

Upgraded apps.

Server now won't start.

• Have tried Upgrading from 8.4.0 to 8.4.1
• Starting without any plugins using 
  sudo /opt/atlassian/jira/bin/start-jira.sh --disable-all-addons
• Removing all the plugins from the plugins directory
  mv /var/atlassian/application-data/jira/plugins/installed-plugins/ /var/atlassian/application-data/jira/plugins/old-installed-plugins/
• removing the .osgi directory cache with 
  rm -rf /var/atlassian/application-data/jira/plugins/.osgi-plugins

Nothing works.  

Help any suggestions?

I get to this entry in the logfile

2020-05-01 13:58:47,676+0000 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (38): [com.atlassian.plugins.jira-remote-link-aggregator-plugin, com.atlassian.jira.jira-admin-navigation-plugin, com.atlassian.upm.upm-application-plugin, com.atlassian.jira.jira-view-issue-plugin, com.atlassian.applinks.applinks-oauth-plugin, com.atlassian.applinks.applinks-trustedapps-plugin, com.atlassian.applinks.applinks-cors-plugin, com.atlassian.jira.diagnostics, com.atlassian.jirawallboard.atlassian-wallboard-plugin, com.atlassian.plugins.atlassian-whitelist-ui-plugin, com.atlassian.jira.plugins.jira-optimizer-plugin, com.atlassian.upm.atlassian-universal-plugin-manager-plugin, com.atlassian.plugins.atlassian-awareness-capability, com.atlassian.troubleshooting.plugin-jira, com.atlassian.plugins.atlassian-project-creation-plugin, com.atlassian.plugins.atlassian-whitelist-core-plugin, com.atlassian.jira.jira-issue-link-remote-jira-plugin, com.atlassian.applinks.applinks-plugin, com.atlassian.plugins.atlassian-nav-links-plugin, com.atlassian.plugins.base-hipchat-integration-plugin, com.atlassian.jira.plugins.jira-importers-trello-plugin, com.atlassian.cluster.monitoring.cluster-monitoring-plugin, com.atlassian.analytics.analytics-client, com.atlassian.jira.lookandfeel, com.atlassian.jira.jira-issue-link-confluence-plugin, com.atlassian.jira.project-templates-plugin, com.atlassian.jira.jira-soy-plugin, com.atlassian.mywork.mywork-common-plugin, com.atlassian.web.atlassian-servlet-plugin, com.atlassian.plugins.base-hipchat-integration-plugin-api, com.atlassian.jira.jira-core-reports-plugin, com.atlassian.mywork.mywork-jira-provider-plugin, com.atlassian.applinks.applinks-basicauth-plugin, com.atlassian.whisper.atlassian-whisper-plugin, com.atlassian.jira.jira-issue-link-applinks-common-plugin, com.atlassian.jira.gadgets, com.atlassian.jira.jira-header-plugin, com.atlassian.jira.mobile], 295 seconds remaining

2020-05-01 13:58:48,151+0000 ThreadPoolAsyncTaskExecutor::Thread 9 WARN [c.a.a.c.eventfilter.whitelist.AnalyticsWhitelistModuleDescriptor] No whitelist resource file found at [analytics-whitelist.json] in plugin [com.atlassian.jira.jira-core-reports-plugin] (bundle entry not found)

2020-05-01 13:58:48,154+0000 ThreadPoolAsyncTaskExecutor::Thread 9 WARN [c.a.a.c.eventfilter.whitelist.AnalyticsWhitelistModuleDescriptor] No whitelist resource file found at [analytics-whitelist.json] in plugin [com.atlassian.jira.jira-core-reports-plugin] (null InputStream)

2020-05-01 13:58:48,227+0000 ThreadPoolAsyncTaskExecutor::Thread 15 INFO [c.a.j.diagnostics.jql.JqlQueryMonitor] Initializing DatabaseMonitor

This then repeats until the 300 sec start-up period is complete

2020-05-01 13:58:48,676+0000 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (32): [com.atlassian.plugins.jira-remote-link-aggregator-plugin, com.atlassian.jira.jira-admin-navigation-plugin, com.atlassian.upm.upm-application-plugin, com.atlassian.jira.jira-view-issue-plugin, com.atlassian.applinks.applinks-oauth-plugin, com.atlassian.applinks.applinks-trustedapps-plugin, com.atlassian.applinks.applinks-cors-plugin, com.atlassian.jirawallboard.atlassian-wallboard-plugin, com.atlassian.plugins.atlassian-whitelist-ui-plugin, com.atlassian.plugins.atlassian-awareness-capability, com.atlassian.troubleshooting.plugin-jira, com.atlassian.plugins.atlassian-project-creation-plugin, com.atlassian.plugins.atlassian-whitelist-core-plugin, com.atlassian.jira.jira-issue-link-remote-jira-plugin, com.atlassian.applinks.applinks-plugin, com.atlassian.plugins.atlassian-nav-links-plugin, com.atlassian.plugins.base-hipchat-integration-plugin, com.atlassian.jira.plugins.jira-importers-trello-plugin, com.atlassian.cluster.monitoring.cluster-monitoring-plugin, com.atlassian.jira.lookandfeel, com.atlassian.jira.jira-issue-link-confluence-plugin, com.atlassian.jira.project-templates-plugin, com.atlassian.jira.jira-soy-plugin, com.atlassian.mywork.mywork-common-plugin, com.atlassian.web.atlassian-servlet-plugin, com.atlassian.jira.jira-core-reports-plugin, com.atlassian.mywork.mywork-jira-provider-plugin, com.atlassian.applinks.applinks-basicauth-plugin, com.atlassian.jira.jira-issue-link-applinks-common-plugin, com.atlassian.jira.gadgets, com.atlassian.jira.jira-header-plugin, com.atlassian.jira.mobile], 294 seconds remaining

....

2020-05-01 14:03:37,036+0000 Spring DM Context Creation Timer WARN [o.e.g.b.e.i.dependencies.startup.DependencyWaiterApplicationContextExecutor] Timeout occurred before finding service dependencies for [NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.applinks.applinks-basicauth-plugin, config=osgibundle:/META-INF/spring/*.xml)]

2020-05-01 14:03:37,039+0000 Spring DM Context Creation Timer ERROR [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-basicauth-plugin' never resolved service '&typeAccessor' with filter '(objectClass=com.atlassian.applinks.core.InternalTypeAccessor)'

2020-05-01 14:03:37,039+0000 Spring DM Context Creation Timer ERROR [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-basicauth-plugin' never resolved service '&authenticationConfigurationManager' with filter '(objectClass=com.atlassian.applinks.spi.auth.AuthenticationConfigurationManager)'

2020-05-01 14:03:37,039+0000 Spring DM Context Creation Timer ERROR [c.a.p.osgi.factory.OsgiPlugin] Plugin 'com.atlassian.applinks.applinks-basicauth-plugin' never resolved service '&applicationLinkService' with filter '(objectClass=com.atlassian.applinks.api.ApplicationLinkService)'

2020-05-01 14:03:37,042+0000 Spring DM Context Creation Timer ERROR [c.a.p.osgi.factory.OsgiPlugin] Unable to start the plugin container for plugin 'com.atlassian.applinks.applinks-basicauth-plugin'
org.springframework.context.ApplicationContextException: Application context initialization for 'com.atlassian.applinks.applinks-basicauth-plugin' has timed out waiting for (|(objectClass=com.atlassian.applinks.spi.auth.AuthenticationConfigurationManager)(objectClass=com.atlassian.applinks.api.ApplicationLinkService)(objectClass=com.atlassian.applinks.core.InternalTypeAccessor))
at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:489)
at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:54)
at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:109)
at java.util.TimerThread.mainLoop(Timer.java:555)
at java.util.TimerThread.run(Timer.java:505)

2020-05-01 14:03:37,074+0000 Spring DM Context Creation Timer ERROR [o.e.g.b.e.internal.support.ExtenderConfiguration] Application context refresh failed (NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.applinks.applinks-basicauth-plugin, config=osgibundle:/META-INF/spring/*.xml))
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