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Unable to install jira-software: error message "You have specified a database that is not empty"

Daniel Orton

I'm unable to install jira-software due to the error message "You have specified a database that is not empty, please specify an empty database."

I've tried a complete fresh install after deleting the directories /opt/atlassian/jira/ and /var/atlassian with a new database.

The server is running Ubuntu Linux 20.04

jira-software 8.13.0

MySQL 8.0.21

MySQL connector 8.0.21

Accepted answers

Andy Heinzer

Hi Daniel,

I can see that you are trying to install Jira server with a MySQL database. The error message would appear to indicate that the database selected might not be setup correctly for Jira to use.

I would want to make sure that you are following our version specific guide for both setting up MySQL and Jira over in Connecting Jira applications to MySQL 8.0. There are a couple of different ways in which that dbconfig.xml file can be properly filled out. My preferred method is to use the Jira Config tool to do this, after Jira has been installed, but before Jira has been started.

This is a setup utility that is also using Java. It has both a terminal interface for headless machines and a gui for other environments. But the thing I like best about this utility is that once you have your connection details filled out, there is also a 'Test Connection' button you can use to try to confirm that this other utility can also connect to your database as expected. Saving the changes here and then starting/restarting Jira will still launch the setup wizard for Jira, but at least this way you do not have to try to configure the database in the setup wizard.

Try these steps, if you're still running into problems here, I'd be interested to see any screenshots of errors you might get, or even any log entries you might find in the $JIRAINSTALL/logs/catalina.out file. These should help provide us additional clues here if we run into problems.

Andy

All comments

Nic Brough -Adaptavist-

This usually means what it has says - the installer expects an empty database and you have pointed it to one that has data in it.

I'd log into the database and do a "show tables" type thing to see what might be there. Does that list no tables, tables related to Atlassian stuff or unrelated tables?

Daniel Orton

The database set to be used by Jira returns "empty set", not sure if this is some kind of bug or if I have an incorrect setting somewhere

Nic Brough -Adaptavist-

I don't know what "returns empty set" means, you've not told us what you are doing to get that.

The problem here really is that there are tables in the target database and Jira won't try to insert itself into a database that is already there for something else.

Daniel Orton

Maybe should have been clearer, when logging into MySQL, using the database selected by Jira and carrying out the command "show tables", MySQL returns "empty set" stating that there are no tables in the database.

Andy Heinzer

Hi Daniel,

I can see that you are trying to install Jira server with a MySQL database. The error message would appear to indicate that the database selected might not be setup correctly for Jira to use.

Andy

Nic Brough -Adaptavist-

Thank you Andy, that's where I think I was heading, but I it would have taken some more steps for me to get there. So I'm glad you've jumped ahead to give us a better and faster answer.

Daniel Orton

Thankyou,

Using "config.sh" via the command line seemed to do the trick.

Nicholas Boughton

I am having an issue where the web setup interface incorrectly failed on DB setup telling me my database was not empty. I opened a mysql shell to the database (Mysql 8, Jira Software 8.16.0, mysql connector 8.0.23) and checked the database with the following output:

mysql> use jira_software 
Database changed 
mysql> show tables; 
Empty set (0.00 sec)

So after searching around for a bit online I found this thread. I tried doing a fresh install and used config.sh to configure the database before starting Jira and now Jira is unusable and showing the following error in the log output:

2021-04-16 10:24:52,825+0100 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /opt/atlassian/application-data/jira/dbconfig.xml 2021-04-16 10:24:52,855+0100 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigHandler] Trying to get encrypted password from xml and decrypt it 2021-04-16 10:24:52,857+0100 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigHandler] Database password decryption not performed. 16-Apr-2021 10:24:52.881 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 4110 ms 2021-04-16 10:24:53,404+0100 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger] Running Jira startup checks. 2021-04-16 10:24:53,404+0100 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger] Jira pre-database startup checks completed successfully. 2021-04-16 10:24:56,152+0100 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigurationManagerImpl] The database is configured. Now running Database Checklist Launcher 2021-04-16 10:24:56,154+0100 JIRA-Bootstrap INFO [c.a.jira.startup.DatabaseChecklistLauncher] Jira database startup checks completed successfully. 2021-04-16 10:24:56,155+0100 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigurationManagerImpl] The database is configured. Now running Post database-configuration launchers 2021-04-16 10:24:57,820+0100 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /opt/atlassian/application-data/jira/dbconfig.xml 2021-04-16 10:24:57,822+0100 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigHandler] Trying to get encrypted password from xml and decrypt it 2021-04-16 10:24:57,822+0100 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigHandler] Database password decryption not performed. 2021-04-16 10:24:58,145+0100 JIRA-Bootstrap ERROR [c.a.jira.startup.ComponentContainerLauncher] A fatal error occurred during initialisation. JIRA has been locked. com.opensymphony.module.propertyset.PropertyImplementationException: Unable to load values for CacheKey[entityName=jira.properties,entityId=1] at com.atlassian.jira.propertyset.CachingOfBizPropertyEntryStore.propEx(CachingOfBizPropertyEntryStore.java:374) at com.atlassian.jira.propertyset.CachingOfBizPropertyEntryStore.resolve(CachingOfBizPropertyEntryStore.java:128) at com.atlassian.jira.propertyset.CachingOfBizPropertyEntryStore.getEntry(CachingOfBizPropertyEntryStore.java:151) at com.atlassian.jira.propertyset.CachingOfBizPropertySet.get(CachingOfBizPropertySet.java:189)

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