I am trying to automate the process of getting result of filters in PDF.
Can you please let me know if we there is a way by which we can go to database and write a query to extract issues and its attachments from database?
Reporting on JIRA by going to the database is horrid. Don't do it. And you can't get attachments that way at all, you'd have to write something else to serve them up on demand.
Write an external script to run your filter over REST and convert the results (including attachments) to your desired format.
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