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I will be deploying a Web Application on a JBoss server and will using JPA/Hibernate for the persistence layer. I want to connect to a Remote MySQL database which I access through SSH with a certificate.

How can I do this programatically in combination with persistence.xml

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If you want connect to database via SSH tunnel I can recommend you Java implementation of SSH. Supports authorization with certificates, port-forwarding, the connection through a proxy, etc.

See

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