We recently moved to the Server version of Jira and am trying to extract data to load into our Data warehouse and cannot find the values associated with the custom fields we have setup and populated. I am betting it is stored in XML somewhere but nothing obvious has been found yet.
In fact it's in the database but I would advise you to prioritize using the REST API as much as possible.
If you need to keep using SQL, the table where information is stored is customfieldvalue (in the corresponding type column, you can join jiraissue table on issue ID and customfield on customfield_id).
Please note that if you're referreing to plugin data, they might use a proprietary format for storage or an Active Object table which is slightly different.
Hope this helps!
Also, for some custom fields, you will probably need to join on the "options" tables - specifically, select type fields.
I can't recommend Micky's first line more - please, do not use the Jira database for anything, it's a nightmare for reporting. Use the REST API.
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