from here:

I can guarantee you that it's not using unix domain sockets. They're not supported by Java. Are you sure CocoaMySQL is Java-based, I assume it's Objective-C and uses libmysql, which can support unix domain sockets.

My guess is your server is started with --skip-networking (see the configuration files for the MySQL server), which means the JDBC driver won't be able to connect, since it requires TCP/IP on Unix.

Sure enough, if you're not able to get to MySQL with the default installation [of MySQL] on OS X Server, the problem is likely that it's not accepting network connections. Open up the "MySQL Manager" application and click "Allow network connections". Voila.

I've got to say, one great thing about using OS X Server is that you can pretty quickly Google up answers by adding "OS X Server" to your search terms. Just enough is kept constant from one Xserve to the next that your needle's haystack becomes much more managable. The joys of losing the battle on the server-side!