Is there a way to extract more than 5000 rows of data from Jira. Right now they say it is restricted to 5000. I would like to know where this value is been set and where will I see. I am currently using Jira Ver. 5.2.11

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The default is 1000 max, not 5000, so you've already altered the limit and can do the same to increase it further - see https://confluence.atlassian.com/display/JIRAKB/Export+More+Than+1000+Results+to+Excel

Note, the limit is there for very good reasons - expect time-outs, failure and general non-responsiveness from Jira if you increase it. Seriously, question why you're doing it and think about reporting properly instead of bodging it through spreadsheets.

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