After upgrading bamboo form 5.6.1 to 5.14, While starting bamboo getting mysql db issue.

[vijay_kumar]

Logs

2020-05-21 15:38:24,673 INFO [localhost-startStop-1] [BootstrapLoaderListener] Starting BootstrapLoaderListener
2020-05-21 15:38:24,673 INFO [localhost-startStop-1] [lifecycle] *******************************
2020-05-21 15:38:24,673 INFO [localhost-startStop-1] [lifecycle] * Bamboo is starting up *
2020-05-21 15:38:24,673 INFO [localhost-startStop-1] [lifecycle] *******************************
2020-05-21 15:38:24,674 INFO [localhost-startStop-1] [ServletContextHolder] Setting servlet context: Bamboo
2020-05-21 15:38:24,714 INFO [localhost-startStop-1] [lifecycle] atlassian.org.osgi.framework.bootdelegation set to javax.servlet,javax.servlet.*,sun.*,com.sun.*,org.w3c.dom.*,org.apache.xerces.*
2020-05-21 15:38:24,842 INFO [localhost-startStop-1] [BootstrapLoaderListener] App classloader is the same as web app classloader
2020-05-21 15:38:25,863 INFO [localhost-startStop-1] [lifecycle] Starting Bamboo 5.14.1 (build #51413 Fri Nov 04 10:05:38 GMT 2016) using Java 1.8.0_241 from Oracle Corporation
2020-05-21 15:38:25,863 INFO [localhost-startStop-1] [lifecycle] Real path of servlet context: /opt/atlassian-bamboo-5.14.1/atlassian-bamboo/
2020-05-21 15:38:26,060 INFO [localhost-startStop-1] [DefaultBootstrapManager] Running pre-bootstrap validation tasks
2020-05-21 15:38:26,167 INFO [localhost-startStop-1] [AbstractUpgradeManager] -----------------------------------------------------------------
2020-05-21 15:38:26,167 INFO [localhost-startStop-1] [AbstractUpgradeManager] 4300 : Make sure there's single row in HIBERNATE_UNIQUE_KEY table
2020-05-21 15:38:26,167 INFO [localhost-startStop-1] [AbstractUpgradeManager] -----------------------------------------------------------------
2020-05-21 15:38:26,396 INFO [MLog-Init-Reporter] [MLog] MLog clients using slf4j logging.
2020-05-21 15:38:26,515 INFO [localhost-startStop-1] [C3P0Registry] Initializing c3p0-0.9.5.2 [built 08-December-2015 22:06:04 -0800; debug? true; trace: 10]
2020-05-21 15:38:26,607 INFO [localhost-startStop-1] [AbstractPoolBackedDataSource] Initializing c3p0 pool... com.mchange.v2.c3p0.PoolBackedDataSource@880da778 [ connectionPoolDataSource -> com.mchange.v2.c3p0.WrapperConnectionPoolDataSource@23fda7af [ acquireIncrement -> 1, acquireRetryAttempts -> 30, acquireRetryDelay -> 1000, autoCommitOnClose -> false, automaticTestTable -> null, breakAfterAcquireFailure -> false, checkoutTimeout -> 0, connectionCustomizerClassName -> null, connectionTesterClassName -> com.mchange.v2.c3p0.impl.DefaultConnectionTester, contextClassLoaderSource -> caller, debugUnreturnedConnectionStackTraces -> false, factoryClassLocation -> null, forceIgnoreUnresolvedTransactions -> false, forceSynchronousCheckins -> false, identityToken -> 1br9xikaafg30dg182y0sn|11f4da58, idleConnectionTestPeriod -> 100, initialPoolSize -> 0, maxAdministrativeTaskTime -> 0, maxConnectionAge -> 0, maxIdleTime -> 30, maxIdleTimeExcessConnections -> 0, maxPoolSize -> 25, maxStatements -> 0, maxStatementsPerConnection -> 0, minPoolSize -> 0, nestedDataSource -> com.mchange.v2.c3p0.DriverManagerDataSource@b3cee514 [ description -> null, driverClass -> null, factoryClassLocation -> null, forceUseNamedDriverClass -> false, identityToken -> 1br9xikaafg30dg182y0sn|71ee58d0, jdbcUrl -> jdbc:mysql://localhost/bamboo?autoReconnect=true&useUnicode=true&characterEncoding=utf8&sessionVariables=storage_engine=InnoDB, properties -> {user=******, password=******} ], preferredTestQuery -> null, privilegeSpawnedThreads -> false, propertyCycle -> 0, statementCacheNumDeferredCloseThreads -> 0, testConnectionOnCheckin -> false, testConnectionOnCheckout -> false, unreturnedConnectionTimeout -> 0, usesTraditionalReflectiveProxies -> false; userOverrides: {} ], dataSourceName -> null, extensions -> {}, factoryClassLocation -> null, identityToken -> 1br9xikaafg30dg182y0sn|5c292a01, numHelperThreads -> 3 ]
2020-05-21 15:38:26,885 INFO [localhost-startStop-1] [AbstractUpgradeManager] Completed task 4300 successfully.
2020-05-21 15:38:26,885 INFO [localhost-startStop-1] [AbstractUpgradeManager] -------------------------------------------------------------------------
2020-05-21 15:38:26,885 INFO [localhost-startStop-1] [AbstractUpgradeManager] 4410 : Make sure that all branch keys start with their master's chain key
2020-05-21 15:38:26,885 INFO [localhost-startStop-1] [AbstractUpgradeManager] -------------------------------------------------------------------------
2020-05-21 15:38:26,891 ERROR [localhost-startStop-1] [AbstractUpgradeManager] com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'BRANCH.MASTER_ID' in 'on clause'
com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'BRANCH.MASTER_ID' in 'on clause'
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:403)
at com.mysql.jdbc.Util.getInstance(Util.java:386)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:944)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3933)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3869)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2524)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2675)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2465)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2439)
at com.mysql.jdbc.StatementImpl.executeQuery(StatementImpl.java:1365)
at com.mchange.v2.c3p0.impl.NewProxyStatement.executeQuery(NewProxyStatement.java:327)
at com.atlassian.bamboo.upgrade.tasks.validation.BranchKeyStartsWithMastersChainKey$1.doInHibernateTransaction(BranchKeyStartsWithMastersChainKey.java:55)
at com.atlassian.bamboo.upgrade.AbstractBootstrapUpgradeTask.withDatabaseConnection(AbstractBootstrapUpgradeTask.java:83)
at com.atlassian.bamboo.upgrade.tasks.validation.BranchKeyStartsWithMastersChainKey.doUpgrade(BranchKeyStartsWithMastersChainKey.java:45)
at com.atlassian.bamboo.upgrade.AbstractUpgradeManager.runUpgradeTask(AbstractUpgradeManager.java:206)
at com.atlassian.bamboo.upgrade.BootstrapUpgradeManagerImpl.runValidationTests(BootstrapUpgradeManagerImpl.java:84)
at com.atlassian.bamboo.setup.DefaultBootstrapManager.runValidationTasks(DefaultBootstrapManager.java:473)
at com.atlassian.bamboo.setup.DefaultBootstrapManager.performPersistenceUpgrade(DefaultBootstrapManager.java:340)
at com.atlassian.config.bootstrap.DefaultAtlassianBootstra

[Daniel Ebers]

Hi Vijay,

it looks that, for some reason, the database is lacking (at least) the column which the error message is referring to.

Please check if the database is in a consistent state after/during upgrade.

If it shouldn't help please reach out to Bamboo support.

Cheers,
Daniel