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I checked the below page for an idea of how to achieve OAuth based access.
https://developer.atlassian.com/cloud/jira/platform/jira-rest-api-oauth-authentication/
I even downloaded and tried it and it worked. But what I'm concerned with is that there are too many manual steps involved. Even if we automate the generation of the keys we still have to manually copy the key to the Applicaion Link creation page. Or maybe there is a REST API for this that I'm missing. Can you please point me to any such REST API if there is one. We are trying to avoid user intervention and automate the entire thing.