Problem

Database operations timeout after period of inactivity.

The following appears in the atlassian-fisheye-YYYY-MM-DD.log

The last packet successfully received from the server was XXX milliseconds ago.  The last packet sent successfully to the server was 0 milliseconds ago.
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

Cause

The MySQL server closes connections due to inactivity but Fisheye/Crucible doesn't know about this and tries to perform database operations on the closed connection.

Resolution

Fisheye/Crucible use a c3p0 configuration which will discard connections after 1800 seconds, so if the MySQL wait_timeout is set to 1800 the problem can be mitigated.

wait_timeout can be set on a per connection basis but the value is hard coded into the app and changing this value isn't possible via jdbc parameters.

The alternative method is to set the wait_timeout to 1800 on your MySQL server:

http://dev.mysql.com/doc/refman/5.0/en/server-system-variables.html#sysvar_wait_timeout

Hint: you should configure this value in your my.ini file.