Upgrade Error Confluence 3.1.2 to 3.5.13

[Deleted user]

Hi,

I just tried to update confluence from 3.1.2 to 3.5.13 and the update does not run properly.

Before upgrading I added to my mysql setting:

transaction-isolation=READ-COMMITTED
default-storage-engine=innodb
default-character-set=utf8

like it was told in many fixes to do that.

the log file says:

2013-03-06 14:51:04,872 INFO [main] [com.atlassian.confluence.lifecycle] contextInitialized Starting Confluence 3.5.13 (build #2171)
2013-03-06 14:51:08,673 INFO [main] [atlassian.plugin.manager.DefaultPluginManager] init Initialising the plugin system
2013-03-06 14:51:09,088 INFO [main] [atlassian.plugin.manager.DefaultPluginManager] init Plugin system started in 0:00:00.412
2013-03-06 14:51:11,746 INFO [main] [springframework.web.context.ContextLoader] initWebApplicationContext Root WebApplicationContext: initialization started
2013-03-06 14:51:19,264 INFO [main] [com.atlassian.confluence.lifecycle] <init> Loading EhCache cache manager
2013-03-06 14:51:34,627 ERROR [main] [confluence.search.lucene.ConfluenceSearcherInitialisation] initialise Error encountered while warming up searcher - The index has not been upgraded. Please reindex.
2013-03-06 14:52:02,733 INFO [main] [springframework.web.context.ContextLoader] initWebApplicationContext Root WebApplicationContext: initialization completed in 50982 ms
2013-03-06 14:52:16,410 INFO [main] [confluence.upgrade.upgradetask.BandanaKeyUniqueConstraintCleaner] cleanUp Checking for invalid entries in the Bandana table
2013-03-06 14:52:16,440 INFO [main] [confluence.upgrade.upgradetask.AddBandanaConstraintsUpgradeTask] doUpgrade Adding not null and unique constraints on Bandana context and key columns
2013-03-06 14:52:16,671 INFO [main] [confluence.upgrade.upgradetask.ContentPermissionConstraintsUpgradeTask] doUpgrade Beginning task to add not null and unique constraints on Content Permissions and Content Permission Set columns
2013-03-06 14:52:16,795 INFO [main] [atlassian.confluence.upgrade.AbstractUpgradeManager] upgradeStarted Starting automatic upgrade of Confluence
2013-03-06 14:52:17,540 ERROR [main] [atlassian.confluence.upgrade.UpgradeLauncherServletContextListener] contextInitialized Upgrade failed, application will not start: Upgrade task com.atlassian.confluence.upgrade.upgradetask.PurgeThumbnailsUpgradeTask@19d839de failed during the UPGRADE phase
com.atlassian.confluence.upgrade.UpgradeException: Upgrade task com.atlassian.confluence.upgrade.upgradetask.PurgeThumbnailsUpgradeTask@19d839de failed during the UPGRADE phase
at com.atlassian.confluence.upgrade.AbstractUpgradeManager.executeUpgradeStep(AbstractUpgradeManager.java:205)
at com.atlassian.confluence.upgrade.AbstractUpgradeManager.runUpgradeTasks(AbstractUpgradeManager.java:146)
at com.atlassian.confluence.upgrade.AbstractUpgradeManager.upgrade(AbstractUpgradeManager.java:96)
at com.atlassian.confluence.upgrade.impl.DefaultUpgradeManager.upgrade(DefaultUpgradeManager.java:140)
at com.atlassian.confluence.upgrade.UpgradeLauncherServletContextListener.contextInitialized(UpgradeLauncherServletContextListener.java:28)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4205)
at org.apache.catalina.core.StandardContext.start(StandardContext.java:4704)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
at org.apache.catalina.core.StandardHost.start(StandardHost.java:840)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:463)
at org.apache.catalina.core.StandardService.start(StandardService.java:525)
at org.apache.catalina.core.StandardServer.start(StandardServer.java:754)
at org.apache.catalina.startup.Catalina.start(Catalina.java:595)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)
2013-03-06 14:52:17,553 ERROR [main] [atlassian.confluence.upgrade.UpgradeLauncherServletContextListener] contextInitialized 1 errors were encountered during upgrade:
2013-03-06 14:52:17,553 ERROR [main] [atlassian.confluence.upgrade.UpgradeLauncherServletContextListener] contextInitialized 1: Error removing thumbnails directory [/var/confluence/data/thumbnails] from confluence home
2013-03-06 14:52:20,149 INFO [main] [com.atlassian.confluence.lifecycle] init Confluence is ready to serve

has anybody an idea?

[William Zanchet [Atlassian] · Accepted solution]

Hi Andrea,

This error means, that Confluence tried to perform the re-index, but encountered an error. To fix this issue, we need to rebuild the content indexes from scratch, that way we'll let Confluence do it. To achieve it, you need to follow this steps:

1 - Shut down your Confluence server.
2 - Make a backup of your <confluence-home>/index/plugin directory if it exists. This is where the Usage Tracking plugin stores it's index for the usage statistics and it cannot be rebuilt.
3 - If you're in Confluence 4.2 onwards, make a backup of your <confluence-home>/index/edge directory if it exists. This is where the index of Likes and Popular Content are stored and cannot be rebuilt.
4 - Remove the <confluence-home>/index directory.
5 - If in step 2, you have the <confluence-home>/index/plugin directory, create the <confluence-home>/index directory and copy in the backup of <confluence-home>/index/plugin directory made in step 2.
6 - If in step 3, you have the <confluence-home>/index/edge directory, create the <confluence-home>/index directory and copy in the backup of <confluence-home>/index/edge directory made in step 3.
7 - Restart server.
A new index directory will be created upon restart of your application if it does not exist.
8 - Now perform the manual re-indexing of your site to build a brand new index from scratch.

This should do the trick.

Cheers,

WZ

[Deleted user]

thanks, re indexing solved the problem!

[Bruna Griebeler]

Hi Andrea!

Regarding the error below, seems like the user that is running Confluence (and the upgrade) has no rights on the folder /var/confluence/data/thumbnails, or one of the files inside it.

Please check if the user has read, write and execute permissions on the folder and read and write permissions on the files.

2013-03-06 14:52:17,553 ERROR [main] [atlassian.confluence.upgrade.UpgradeLauncherServletContextListener] contextInitialized 1: Error removing thumbnails directory [/var/confluence/data/thumbnails] from confluence home

Hope it helps!

[Deleted user]

Hi Bruna,

I granted read, write and execute rights on this folder and all subfolders, but the log file still says exactly the same.

other suggestions?

[Deleted user]

any clue what does this entry mean?

2013-03-06 14:51:34,627 ERROR [main] [confluence.search.lucene.ConfluenceSearcherInitialisation] initialise Error encountered while warming up searcher - The index has not been upgraded. Please reindex.

[RianA]

Looks like bruna was right in unable to purge the thumbnails directory. Please try to delete that directory manually and try to re do the upgrade. Make sure you reverted to unupgraded state.