I have few .bqy which i am now running it manually using Hyperion client. Is there any java api to connect to Hyperion designer and run the brio queries(.bqy) and extract report out of that.
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It sounds like you are trying to run a bqy in SmartView (browser), but you want to run it in the desktop application. If the publisher has allowed it, and you have the desktop application, you can download the bqy and run it that way.
I think JOOLE is what you're describing, unless this is a pure Java question. And the object I think you're looking for is
BrioQuery.Application