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Why can't you just use asadmin? It can configure everything for you and updates the domain.xml properly. It launches CLIMain which is a java class. If you must, you could just instantiate it directly from your java code or better yet, use the JMX interface.
do you mean JDBc pool login in as admin is better, glassfish is not like tomcat, we did not direct chage something in xml, , but you can do that!