I find it hard to establish a link between jdbc and mysql. I think one of the reasons is the mysql port. I checked the port with the statement: \"show variables like \'port\';\"
You need to edit your mysql config file, my.cnf in /etc/my.cnf and change the port to 3306. Then restart mysql.
Source: http://www.cyberciti.biz/faq/change-default-mysql-port-under-linuxunix/
Edit:
This website might help you a bit more for your specific platform: https://wiki.archlinux.org/index.php/MySQL#Configuration
It has a portion talking about copying over your my.cnf file:
Copy your choice of config file:
# cp /usr/local/mysql/support-files/my-medium.cnf /usr/local/mysql/data/my.cnf