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"database that is not empty" when trying to use azure managed postgres database

Trying to install a fresh jira 7.9 fails on database setup with

You have specified a database that is not empty, please specify an empty database. If you want to upgrade an existing installation, please follow these instructions instead.

if the database is an azure postgres managed database.

The database _is_ empty.

What could be the issue ? Could it be that jira is assuming I am installing the datacenter version of jira for some reason ?


10 answers

I found this error in the logs which lead me to

Loading class `com.mysql.jdbc.Driver'. This is deprecated. The new driver class is `com.mysql.cj.jdbc.Driver'. The driver is automatically registered via the SPI and manual loading of the driver class is generally unnecessary.

The long and short of it is you need an older mysql-connector-java-5.1.x.jar driver instead of the latest mysql-connector-java-8.0.x.jar that the documentation would lead you to install.

Reverting my driver to mysql-connector-java-5.1.47.jar fixed the issue for me.

My issue was fixed by changing mysql-connector-java to mysql-connector-java-5.1.48.jar

По английски не говорю, напишу на русском, 21 век всё таки, у всех есть онлайн переводчики =)

Проблема была с mysql-connector

Я скачал два коннетора 8.0.15 и 5.1.47

После удаления 8.0.15 и перезапуска jira всё заработало.

rm /opt/atlassian/jira/lib/mysql-connector-java-8.0.15.jar

да, есть такой косяк, не знаю чей или Oracle или Atlassian. Два jar-файла с разными именами, но одинаковые по назначению вместе не работают.

1 vote
KellyW Atlassian Team May 03, 2018

Hi Jean-Baptiste,


If there are tables found in the database instance, Jira will mark it as not empty.


If you confirm no other Jira instance(s) is referencing the same database instance, try dropping all the tables and restart the setup:


(assuming public is the schema) 



I had the same issue for a slightly different setup; I am using a MySQL 5.7.22 database in AWS RDS.

First, I made sure I had all the right parameters set (had to create a new parameters group based on the default one for MySQL 5.7, modified the values for the parameters as documented at and then applied the parameters group to my AWS RDS MySQL instance). However, I was still getting the message about the database not being empty. I was using the connector mysql-connector-java-8.0.23; as soon as I changed to use mysql-connector-java-5.1.49, the issue was gone and I was able to proceed with the setup of the instance.

OK, I got it!

So I had the same Problem. My solution was to delete the extensions (pg_buffercache, pg_stat_statements) in my Postgres managed by Azure. Hope i can help someone.

Greetings Felix.

Thanks for the suggestion. No luck for me unfortunately.

Using mysql-connector-java-5.1.48.jar with Mysql 5.7 can lead to this issue. I fixed this by rolling back to mysql-connector-java-5.1.48.jar

I had tables pg_buffercache and pg_stat_statements in my public schema.

So just created a new schema and give it a try.


Same here,

Keep hitting this problem when trying to setup a burner instance on Digital Ocean

  • Ubuntu 18.04.2 LTS
  • mysql Ver 14.14 Distrib 5.7.25, for Linux (x86_64)
  • Driver: mysql-connector-java-8.0.15.jar
  • Jira 7.13.1 installed from .bin installer

If I DROP DATABASE jiradb; then jira tells me that it can't find 'jiradb'

If I then CREATE DATABASE jiradb; then jira tells me the DB is not empty.

USE jiradb;

Returns empty set (0.0)seconds

Same here. Any news on that? Create a new DB in MySQL but when I try to run the wizard it tells me "DB is not empty". But it sure is.

Did you get this fixed?

Was there a resolution to this? I think I'm having the exact same issue, but it's jira 7.13, MySQL, and AWS.

Is there a document to manually set up the database schema to bypass this?

And to make it more interesting, I tried restoring my original dbconfig.xml (H2), restarted JIRA, and it still goes through setup... now it won't move forward because my H2 database is not empty.

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