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I want to be able to pull the data from a report, such as Cumulative Flow Diagram, and export it to Excel.
The "raw data" for the reports is just "the issues the report looks at", so if you run a search for the issues it is reporting on (often as simple as "project = XYZ" and updated > -30d"), then you'll be able to use the download option on the tools to get a spreadsheet-friendly dump of the raw data.
Is there a way to see the JQL or other source that drives the reports in order to create my own gadget with mods?
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The data used for the different reports is different, and so some may be accessible by JQL and others not so much...
The example report you noted, the "Cumulative Flow Diagram" (JIRA's version), uses issue change history, and that is not all accessible by JQL query.
Please see this other community post for ideas how to do this: JIRA add-ons for Excel or Google Sheets, the REST API, log extraction via webhook, or marketplace add-ons for purchase.
Best regards,
Bill
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