Terry : Troubleshooting Confluence Upgrade

This page last changed on Mar 17, 2011 by terry.

Upgrade Confluence from 3.4.9 to 3.5. Two major issues encountered, workaround provided.

Environment

  • Ubuntu 10.10 x86
  • Kernel 2.6.35-27-generic-pae
  • Sun JVM 1.6.0_24
  • Tomcat 6.0.20
  • MySQL 5.1.49

Issue 1

On accessing the Dashboard page, the error below will be encountered.

Error

Icon

MySQL isolation level 'REPEATABLE-READ' is no longer supported. Isolation level must be 'READ-COMMITTED'.

Use phpMyAdmin or mysql command line tool to connect to the database, run the SQL query below:

SELECT @@GLOBAL.tx_isolation, @@tx_isolation;

Change isolation level by editing your MySQL config file (usually /etc/my.cnf), add the following:

[mysqld]
transaction-isolation=READ-COMMITTED

Restart MySQL and Confluence/application server (Tomcat in this case).

Reference Database Setup For MySQL

Issue 2

Cannot access Dashboard page after starting application server. Error below were seen in confluence log (/opt/wiki/data/log)

2011-03-17 11:26:58,455 ERROR [main] [atlassian.confluence.upgrade.UpgradeLauncherServletContextListener] contextInitialized Upgrade failed, application will not start: com.atlassian.config.ConfigurationException: Cannot update schema
com.atlassian.confluence.upgrade.UpgradeException: com.atlassian.config.ConfigurationException: Cannot update schema
	at com.atlassian.confluence.upgrade.AbstractUpgradeManager.upgrade(AbstractUpgradeManager.java:84)
	at com.atlassian.confluence.upgrade.impl.DefaultUpgradeManager.upgrade(DefaultUpgradeManager.java:139)
	at com.atlassian.confluence.upgrade.UpgradeLauncherServletContextListener.contextInitialized(UpgradeLauncherServletContextListener.java:28)
	at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:3934)
	at org.apache.catalina.core.StandardContext.start(StandardContext.java:4429)
	at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:791)
	at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:771)
	at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:526)
	at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:630)
	at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:556)
	at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:491)
	at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1206)
	at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:314)
	at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
	at org.apache.catalina.core.StandardHost.start(StandardHost.java:722)
	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
	at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
	at org.apache.catalina.core.StandardService.start(StandardService.java:516)
	at org.apache.catalina.core.StandardServer.start(StandardServer.java:710)
	at org.apache.catalina.startup.Catalina.start(Catalina.java:583)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:288)
	at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:413)
Caused by: com.atlassian.config.ConfigurationException: Cannot update schema
	at bucket.core.persistence.hibernate.schema.SchemaHelper.updateSchemaIfNeeded(SchemaHelper.java:151)
	at bucket.core.persistence.hibernate.schema.SchemaHelper.updateSchemaIfNeeded(SchemaHelper.java:134)
	at com.atlassian.confluence.upgrade.AbstractUpgradeManager.upgradeSchema(AbstractUpgradeManager.java:158)
	at com.atlassian.confluence.upgrade.AbstractUpgradeManager.upgrade(AbstractUpgradeManager.java:62)
	... 26 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Specified key was too long; max key length is 1000 bytes
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:407)
	at com.mysql.jdbc.Util.getInstance(Util.java:382)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1052)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3603)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3535)
	at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1989)
	at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2150)
	at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2620)
	at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1664)
	at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1583)
	at org.apache.tomcat.dbcp.dbcp.DelegatingStatement.executeUpdate(DelegatingStatement.java:228)
	at net.sf.hibernate.tool.hbm2ddl.SchemaUpdate.execute(SchemaUpdate.java:167)
	at bucket.core.persistence.hibernate.schema.SchemaHelper.updateSchemaIfNeeded(SchemaHelper.java:147)
	... 29 more
2011-03-17 11:26:58,460 ERROR [main] [atlassian.confluence.upgrade.UpgradeLauncherServletContextListener] contextInitialized 1 errors were encountered during upgrade:
2011-03-17 11:26:58,460 ERROR [main] [atlassian.confluence.upgrade.UpgradeLauncherServletContextListener] contextInitialized 1: Cannot update schema

It's a MySQL Bug.

Workaround is to change storage engine for all existing tables from MyISAM to InnoDB, restart mysql and tomcat.

mysql command line tool example:

mysql -u root -p //log in

show databases; //list database instances (schema)

use confluence; //use database instance

show tables; //list tables

show table status; //show table status (storage engine)

Change the storage engine for specified table, this needs to be done to all existing tables (looking for automated way to do this).

alter table table_name ENGINE=INNODB;

Alternatively, a fast way to alter all tables is to use mysqldump to make a backup of your db, then use something like sed or a text editor with search and replace to replace all instances of "MyISAM" with "InnoDB". Then reimport the backup you made.

sed -e 's/MyISAM/InnoDB/g' wiki.sql

Upgrade to Confluence 3.0 or higher with MySQL Database Fails Due to 'specified key was too long'