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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 http://dev.mysql.com/doc/refman/5.6/en/connector-j-reference-using-ssl.html for details of how to do this using the keytool utility.

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