The basic rule is - follow the hierarchy
DB Adapter - QueryTimeout is the attribute you set here. This you can set at design time in JDev, or via em.
Ok, once you have set all of these, see Mark Foster's excellent article for screenshots etc. You can then
configure an appropriatefault policy bound to the reference(s) with various retry models optimized for the resource (e.g. accounts for different restart times etc.). This policy can then revert to human intervention if the retry does not succeed