Manual upgrade of Jira Server leads to Setup Wizard

[AMI IT]

Hi everyone,

I performed a manual upgrade of Jira Server based on Atlassian documentation and Atlassian support instruction. When I run Jira post-upgrade, I get the setup wizard (SetupMode!default.jspa) instead of the upgrade success page. I need to either get to the upgrade success page or revert back and run my old instance of Jira as it was, but whether I run the new or old version of Jira (via ./start-jira.sh), the result is the same: the setup wizard.

Any help would be appreciated.

[Peter-Dave Sheehan]

It would seem that perhaps Jira is not finding your jira-home directory.

How were you specifying that before? Using the JIRA_HOME environment variable?

If unsure, you can try to set it in the <jira_install_dir>/atlassian-jira/WEB-INF/classes/jira-application.properties

[AMI IT]

Hi Peter, and thank you. I have JIRA_HOME set in several places (all to the same path), including in jira-application.properties. I have checked directory permissions, dbconfig.xml file existence and permissions, etc. - but Jira just keeps showing me the setup screen when I stop and start it. I tried this, too: https://community.atlassian.com/t5/Jira-Software-questions/How-do-I-use-my-renewed-license-with-the-existing-server/qaq-p/1417671

Any other ideas?

[Peter-Dave Sheehan]

Review catalina.out, you might get some clues.

Also look for hidden files in jira-home. If you see an empty file called .jira-home.lock (and with a created date that matches your start time) that means that jira found the jira-home and is using it. Then you can further review the <jira-home>/log/atlassian-jira.log

If the file is not there, the startup didn't identify the jira-home directory or didn't have access to it.

[AMI IT]

The lock file is indeed present, so that rules out a pathing issue. The log shows that the dbconfig.xml file is being read, but then there's a message that "The database is not yet configured". I know the db is configured because we've been using it for a long time, and I've inspected the dbconfig.xml file and everything looks correct.

Here's the tail of the atlassian-jira.log file that shows the db issue:

2021-04-24 18:20:01,454-0600 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /srv/jira/jira-data/dbconfig.xml
2021-04-24 18:20:01,475-0600 JIRA-Bootstrap INFO [c.a.j.instrumentation.external.DatabaseExternalGauges] Installing DBCP monitoring instruments: DatabaseExternalGauges.JiraDbcpInstruments[instruments=[DBCP_MAX, DBCP_ACTIVE, DBCP_IDLE],objectName=com.atlassian.jira:name=BasicDataSource]
2021-04-24 18:20:01,556-0600 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger] Running Jira startup checks.
2021-04-24 18:20:01,557-0600 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger] Jira pre-database startup checks completed successfully.
2021-04-24 18:20:01,613-0600 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigurationManagerImpl] The database is not yet configured. Enqueuing Database Checklist Launcher on post-database-configured-but-pre-database-activated queue
2021-04-24 18:20:01,614-0600 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigurationManagerImpl] The database is not yet configured. Enqueuing Post database-configuration launchers on post-database-activated queue
2021-04-24 18:20:01,621-0600 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Startup is complete. Jira is ready to serve.

[Peter-Dave Sheehan]

Next thing to check is to make sure that the process has access to the dbconfig.xml file.

What user is your process running as? Who owns the dbconfig and what's the permission mask?
Can you confirm that the jira user can read the file?

[AMI IT]

This is what I see:

-rwxr-xr-x. 1 jira jira 739 Apr 22 10:32 dbconfig.xml

I'm currently running Jira from a command line while logged in as root.

[Peter-Dave Sheehan]

Depending on how it was setup before, it's possible there is some user impersonation set up.

After you star jira, can you confirm who owns the java process?

$ ps -ef |grep jira

[AMI IT]

jira 11639 1 99 19:13 ? 00:00:28 /srv/jira/jira-home/jre//bin/java -Djava.util.logging.config.file=/srv/jira/jira-home/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms1024m -Xmx2048m -Djava.awt.headless=true -Datlassian.standalone=JIRA -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true -Dmail.mime.decodeparameters=true -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory -XX:+PrintGCDateStamps -XX:-OmitStackTraceInFastThrow -Djira.home=/srv/jira/jira-data -Datlassian.plugins.startup.options= -Djdk.tls.ephemeralDHKeySize=2048 -Djava.protocol.handler.pkgs=org.apache.catalina.webresources -classpath /srv/jira/jira-home/bin/bootstrap.jar:/srv/jira/jira-home/bin/tomcat-juli.jar -Dcatalina.base=/srv/jira/jira-home -Dcatalina.home=/srv/jira/jira-home -Djava.io.tmpdir=/srv/jira/jira-home/temp org.apache.catalina.startup.Bootstrap start
root 11709 2945 0 19:13 pts/2 00:00:00 grep jira

[Peter-Dave Sheehan]

So while you are root while running, the startup routine changes the user to "jira" (the first column).

But that shouldn't matter since the dbconfig is owned by jira and the owner has read and write permission (the first rw in -rwxr-xr-x)

You can be sure by running: 

$ runuser jira -c 'cat /srv/jira/jira-data/dbconfig.xml'

[AMI IT]

That command shows the contents of the dbconfig.xml file successfully.

[Peter-Dave Sheehan]

I'm not sure what to try next.

Are you sure your DB is compatible with the newer version of jira?

Do you have the correct .jar file for the dbengine you are using? For example, jira doesn't ship with a mysql driver. You have to install that in <jira-install>/lib

[AMI IT]

It's a Postgres db and it was working a day or two ago.

The strange thing is that I'm seeing the setup wizard when I run the new OR the old version of Jira. I see in the console that the version I'm expecting is running actually is, but the end result appears to be the same.

Thank you for your help today. I really appreciate it.