Long running transactions might be killed by the App Server's Transaction Reaper. I have implemented a litte helper to programmatic handle such kinds of exceptions.
For long running transactions sometimes we wish to commit a kind of intermediate result to the database. This sounds pretty simple – however, if we do not want to commit the current transaction, you may run into deadlock situations. In my current project I implemented a nice solution using JPA and EJB.
When invoking a method of an EJB we get features like transactions, security or monitoring for free. However, this only works when the method call is intercepted by the container. So, method calls within the same bean do not enjoy this benefits. There is a nice hack to solve this problem.