Upgrading failes due to missing database field

[phpr]

Hi,

after Upgrading from JIRA Software 7.9 to either 7.13 or 8.0.2 I get the following error in catalina.out after the instance has startet:

Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'sharepermissions.rights' in 'where clause'

2019-03-30 15:50:17,073 Caesium-1-3 INFO [c.a.jira.upgrade.UpgradeScheduler] Running scheduled upgrades
2019-03-30 15:50:17,079 Caesium-1-3 INFO [c.a.jira.upgrade.LoggingUpgradeService] run upgrades has started
2019-03-30 15:50:17,356 Caesium-1-3 INFO [c.a.upgrade.core.DefaultUpgradeTaskFactoryProcessor] Upgrade task [factory=host,buildNumber=710001] completed in 48 milliseconds
2019-03-30 15:50:17,392 Caesium-1-3 INFO [c.a.upgrade.core.DefaultUpgradeTaskFactoryProcessor] Upgrade task [factory=host,buildNumber=711001] completed in 34 milliseconds
2019-03-30 15:50:17,400 Caesium-1-3 ERROR [c.a.upgrade.core.DefaultUpgradeTaskFactoryProcessor] Upgrade task [host,buildNumber=712001] failed
com.querydsl.core.QueryException: Caught MySQLSyntaxErrorException for update jiradb.sharepermissions
set rights = ?
where sharepermissions.rights is null or sharepermissions.rights = ?
at com.querydsl.sql.DefaultSQLExceptionTranslator.translate(DefaultSQLExceptionTranslator.java:50)
at com.querydsl.sql.Configuration.translate(Configuration.java:459)
at com.querydsl.sql.dml.SQLUpdateClause.execute(SQLUpdateClause.java:217)
at com.atlassian.jira.upgrade.tasks.UpgradeTask_Build712001.lambda$addDefaultRightsValueToSharePermissions$0(UpgradeTask_Build712001.java:52)
at com.atlassian.jira.database.DefaultQueryDslAccessor.lambda$execute$1(DefaultQueryDslAccessor.java:74)
at com.atlassian.jira.database.DatabaseAccessorImpl.lambda$runInTransaction$0(DatabaseAccessorImpl.java:99)
at com.atlassian.jira.database.DatabaseAccessorImpl.executeQuery(DatabaseAccessorImpl.java:68)
at com.atlassian.jira.database.DatabaseAccessorImpl.runInTransaction(DatabaseAccessorImpl.java:94)
at com.atlassian.jira.database.DefaultQueryDslAccessor.execute(DefaultQueryDslAccessor.java:73)
at com.atlassian.jira.upgrade.tasks.UpgradeTask_Build712001.addDefaultRightsValueToSharePermissions(UpgradeTask_Build712001.java:46)
at com.atlassian.jira.upgrade.tasks.UpgradeTask_Build712001.runUpgrade(UpgradeTask_Build712001.java:41)
at com.atlassian.upgrade.core.DefaultUpgradeTaskFactoryProcessor.runOneUpgradeTask(DefaultUpgradeTaskFactoryProcessor.java:109)
at com.atlassian.upgrade.core.DefaultUpgradeTaskFactoryProcessor.lambda$performUpgradesUnsafe$13(DefaultUpgradeTaskFactoryProcessor.java:80)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:174)
at java.util.stream.SortedOps$RefSortingSink.end(SortedOps.java:395)
at java.util.stream.Sink$ChainedReference.end(Sink.java:258)
at java.util.stream.AbstractPipeline.copyIntoWithCancel(AbstractPipeline.java:499)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:485)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.FindOps$FindOp.evaluateSequential(FindOps.java:152)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.findFirst(ReferencePipeline.java:464)
at com.atlassian.upgrade.core.DefaultUpgradeTaskFactoryProcessor.performUpgradesUnsafe(DefaultUpgradeTaskFactoryProcessor.java:81)
at com.atlassian.upgrade.core.DefaultUpgradeTaskFactoryProcessor.performUpgrades(DefaultUpgradeTaskFactoryProcessor.java:46)
at com.atlassian.upgrade.core.DefaultUpgradeTaskManager.upgradeHostApp(DefaultUpgradeTaskManager.java:41)
at com.atlassian.jira.upgrade.LicenseCheckingUpgradeService.executeUpgrades(LicenseCheckingUpgradeService.java:134)
at com.atlassian.jira.upgrade.LicenseCheckingUpgradeService.runUpgrades(LicenseCheckingUpgradeService.java:97)
at com.atlassian.jira.upgrade.ClusterLockingUpgradeService.runUpgrades(ClusterLockingUpgradeService.java:35)
at com.atlassian.jira.upgrade.LoggingUpgradeService.lambda$runUpgradesWithLogging$0(LoggingUpgradeService.java:28)
at com.atlassian.jira.upgrade.LoggingUpgradeService.runWithTaskLogging(LoggingUpgradeService.java:43)
at com.atlassian.jira.upgrade.LoggingUpgradeService.runUpgradesWithLogging(LoggingUpgradeService.java:28)
at com.atlassian.jira.upgrade.IndexingUpgradeService.runUpgrades(IndexingUpgradeService.java:19)
at com.atlassian.jira.upgrade.UpgradeScheduler.runHostUpgrades(UpgradeScheduler.java:95)
at com.atlassian.jira.upgrade.UpgradeScheduler.runUpgrades(UpgradeScheduler.java:76)
at com.atlassian.scheduler.core.JobLauncher.runJob(JobLauncher.java:153)
at com.atlassian.scheduler.core.JobLauncher.launchAndBuildResponse(JobLauncher.java:118)
at com.atlassian.scheduler.core.JobLauncher.launch(JobLauncher.java:97)
at com.atlassian.scheduler.caesium.impl.CaesiumSchedulerService.launchJob(CaesiumSchedulerService.java:443)
at com.atlassian.scheduler.caesium.impl.CaesiumSchedulerService.executeClusteredJob(CaesiumSchedulerService.java:438)
at com.atlassian.scheduler.caesium.impl.CaesiumSchedulerService.executeClusteredJobWithRecoveryGuard(CaesiumSchedulerService.java:462)
at com.atlassian.scheduler.caesium.impl.CaesiumSchedulerService.executeQueuedJob(CaesiumSchedulerService.java:390)
at com.atlassian.scheduler.caesium.impl.CaesiumSchedulerService$1.consume(CaesiumSchedulerService.java:285)
at com.atlassian.scheduler.caesium.impl.CaesiumSchedulerService$1.consume(CaesiumSchedulerService.java:282)
at com.atlassian.scheduler.caesium.impl.SchedulerQueueWorker.executeJob(SchedulerQueueWorker.java:65)
at com.atlassian.scheduler.caesium.impl.SchedulerQueueWorker.executeNextJob(SchedulerQueueWorker.java:59)
at com.atlassian.scheduler.caesium.impl.SchedulerQueueWorker.run(SchedulerQueueWorker.java:34)
at java.lang.Thread.run(Thread.java:748)
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'sharepermissions.rights' in 'where clause'
at sun.reflect.GeneratedConstructorAccessor15.newInstance(Unknown Source)
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:425)
at com.mysql.jdbc.Util.getInstance(Util.java:408)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2484)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1858)
at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(PreparedStatement.java:2079)
at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(PreparedStatement.java:2013)
at com.mysql.jdbc.PreparedStatement.executeLargeUpdate(PreparedStatement.java:5104)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1998)
at org.apache.commons.dbcp2.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:98)
at org.apache.commons.dbcp2.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:98)
at com.querydsl.sql.dml.SQLUpdateClause.execute(SQLUpdateClause.java:203)
... 44 more
2019-03-30 15:50:17,407 Caesium-1-3 WARN [c.a.upgrade.core.DefaultUpgradeTaskFactoryProcessor] Failed to complete upgrade task [factory=host,buildNumber=712001]
2019-03-30 15:50:17,407 Caesium-1-3 INFO [c.a.j.upgrade.util.BuildNumberDao] Setting current build number to 711001
2019-03-30 15:50:17,414 Caesium-1-3 ERROR [c.a.jira.upgrade.LicenseCheckingUpgradeService] There was an error running the upgrades
2019-03-30 15:50:17,414 Caesium-1-3 INFO [c.a.j.upgrade.util.BuildNumberDao] Setting current version to 7.13.2
2019-03-30 15:50:17,420 Caesium-1-3 INFO [c.a.j.upgrade.util.BuildNumberDao] Setting downgrade version to 7.1.2
2019-03-30 15:50:17,427 Caesium-1-3 INFO [c.a.jira.upgrade.LoggingUpgradeService] run upgrades has finished unsuccessfully, and took 348 milliseconds to process.
2019-03-30 15:50:17,428 Caesium-1-3 ERROR [c.a.jira.upgrade.UpgradeScheduler] Error occurred during execution of upgrades

 Is there anything I might do wrong in the upgrade procedure?

This is running on a Linux machine (Ubuntu 16.04)

[Andy Heinzer · Accepted solution]

Hi Philipp,

I found another case with a nearly identical error to yours in https://community.atlassian.com/t5/Jira-Software-questions/Creating-any-project-fails-after-linux-upgrade-from-7-3-5-to-7/qaq-p/955049

In that post, Shannon found that the KB https://confluence.atlassian.com/jirakb/jira-throws-table-already-exist-error-due-to-incorrect-mysql-schema-338364885.html was applying here.  I would recommend trying to see if your environment also has this extra line in your dbconfig.xml file.  If it does, please follow the steps in the kb to remove this line, save that file, and then restart Jira once more.   Once this is complete you should then be able to upgrade without getting this specific error.

If this is not the case, I would be interested to see if we can get a logs from your $JIRAHOME/log/atlassian-jira.log and $JIRAINSTALL/logs/catalina.out files.   With these two log files, we should be better able to understand why you are seeing these kinds of errors during the upgrade attempts.

Andy

[phpr]

Thank you very much, that worked. :-)

Sorry, I haven´t found this issue before, even though I tried a lot to find a solution on google.