Set up two clauses, like so:
# Important! Do not use "from java.lang import Exception", as that will
# hide access to jython's Exception class.
import java.lang.Exception
def something():
try:
# do something
pass
except java.lang.Exception, e:
# Handle java exceptions
# follow e.cause, e.cause.cause, .... to examine nested exceptions
pass
except Exception, e:
# Handle jython exceptions
pass