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Separate Web Section in Jira that uses Java classes and Javascript in velocity templates

Hello,

I have built a tool to visualize links between our issues and also find missing links based on some machine learning. I now would like to move the tool into Jira as a separate page / webwork action. Currently, the prototype uses java and javascript. Java mostly for accessing some microservices to get data and javascript to have some functionality and visualize the data. 

When I tried to do this as a jira plug-in I got stuck because I do not know how to use my existing classes in the velocity templates. Is it possible and if so how to use my .jsp files instead of velocity templates? If that does not work, how can I access my classes from velocity?

Some background information: 

Prototype is https://api.openreq.eu/openreq-issue-link-map/

Current Code is in https://github.com/OpenReqEU/qthulhu

Thanks for any help :)

Clara

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