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I want to encrypt a connection to an Amazon RDS MySQL server. I have the .pem and can connect to the server using mysql --ssl_ca=file.pem in bash, but I need to connect to the server in a web app with the JNDI DataSource. Is it possible to do that?

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The MySQL Reference Manual indicates that it's possible, provided you've registered your client certificate in the keystore of the JVM under which your Tomcat server is running. See for details of how to do this using the keytool utility.

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