I'm not sure exactly how I solved it. But I have pasted for you the parts in my 
code which are different from my original post.

web.xml:
<resource-ref>
  |     <res-ref-name>jdbc/MySqlDS</res-ref-name>
  |     <jndi-name>jdbc/MySqlDS</jndi-name>
  | </resource-ref>

DS lookup:
Context ctx = new InitialContext();
  | this.dataSource = (DataSource) ctx.lookup("java:comp/env/jdbc/MySqlDS");

The rest of the files remain the same. Try it, and it should work. Good luck!

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