I want to create a query the will return all stories (regardless of status) and epic (if in progress) where the stories only belong to the epics returned.
JQL does not allow you do nested queries, like get all stories belonging to epics in specific status. You need an app like ScriptRunner or JQL Tricks, and there are other ones that can do it too.
If you use JQL Tricks the query would look like this:
issue in issuesWhereEpicIn("status = \"In Progress\"")
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This is as close I could get:
type = Epic AND status = "In Progress" OR type = Story
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Currently we do not use the concept of epic and stories, however I believe the JQL query would be, something like this:
"Story Points" = 1 AND "Epic Status" = "In Progress"
Change de "Story Points" to another issuetype.
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