This is the obscure part. The creation of connection pool/datasource in EM is via the ascontrol application. So we need to let it know how to load mySQL jdbc driver. There are two steps. Firstly, copy mysql-connector-java-5.1.13-bin.jar to
C:\product\10.1.3.1\OracleAS_1\j2ee\home\applications\ascontrol\ascontrol\WEB-INF\lib. Secondly, edit C:\product\10.1.3.1\OracleAS_1\j2ee\home\applications\ascontrol\META-INF\orion-application.xml and comment out the "remove-inherited" section like below.
<imported-shared-libraries>
<!--
<remove-inherited name="global.libraries"/>
-->
<import-shared-library name="oracle.xml.security"/>
</imported-shared-libraries>
Everything is pretty straight forward after this. To create a connection pool, remember to use "com.mysql.jdbc.jdbc2.optional.MysqlConnectionPoolDataSource" for "Connection Factory Class" and similar to "jdbc:mysql://localhost:3306/test" for "JDBC URL". You can create a datasource the same way after a connection pool is created.
Reference:
http://forums.oracle.com/forums/thread.jspa?threadID=680574
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