Correct use of flush() in JPA/Hibernate

Probably the exact details of em.flush() are implementation-dependent. In general anyway, JPA providers like Hibernate can cache the SQL instructions they are supposed to send to the database, often until you actually commit the transaction. For example, you call em.persist(), Hibernate remembers it has to make a database INSERT, but does not actually execute the instruction until you commit the transaction. Afaik, this is mainly done for performance reasons.

In some cases anyway you want the SQL instructions to be executed immediately; generally when you need the result of some side effects, like an autogenerated key, or a database trigger.

What em.flush() does is to empty the internal SQL instructions cache, and execute it immediately to the database.

Bottom line: no harm is done, only you could have a (minor) performance hit since you are overriding the JPA provider decisions as regards the best timing to send SQL instructions to the database.

Can em.flush() cause any harm when using it within a transaction?

Yes, it may hold locks in the database for a longer duration than necessary.

Generally, When using JPA you delegates the transaction management to the container (a.k.a CMT - using @Transactional annotation on business methods) which means that a transaction is automatically started when entering the method and commited / rolled back at the end. If you let the EntityManager handle the database synchronization, sql statements execution will be only triggered just before the commit, leading to short lived locks in database. Otherwise your manually flushed write operations may retain locks between the manual flush and the automatic commit which can be long according to remaining method execution time.

Notes that some operation automatically triggers a flush : executing a native query against the same session (EM state must be flushed to be reachable by the SQL query), inserting entities using native generated id (generated by the database, so the insert statement must be triggered thus the EM is able to retrieve the generated id and properly manage relationships)

Actually, em.flush(), do more than just sends the cached SQL commands. It tries to synchronize the persistence context to the underlying database. It can cause a lot of time consumption on your processes if your cache contains collections to be synchronized.

Caution on using it.