We have a trial version for now to test MySQL as DB for JIRA software. port 3306 not working as expected, then I cannot access the database, however the site running very well.
I wonder -
Ok when you say site running well, it is a bit confusing. Because if you connected the DB to JIRA then some issues your are mentioning above shouldn't happen.
What are the steps you took to connect the DB to your JIRA instance?
Did you configure you DbConfig.xml file?
DB access just by a DB tool, such as DBVisualizer.
the problem is the port 3306, we cannot see it active to respond, however, the site running as expected
JIRA instance is working as expected, no issues so far.
didn't touch DBConfig.xml , should I modify anything ?
the mysql folder on server containing some configuration files, which set 3306 as port.
Please, forget the database. You can't write to it safely, and "safely" is going to take you months, if not years, to work out and prove.
It's also designed (well, grown up as anyway) as a data store. SQL is the single worst possible way to report on issue data.
Use the API to do all writes and most reads. That means going through the front-end UI, the REST interface or add-ons.
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