I use Hibernate as my weapon of choice here. With Spring Data I often don't need to manually write queries at all. When I do, the JPQL is pretty good and eliminates a lot of the hassle of plain SQL. In rare cases (e.g. when I need to call native DB functions) I do write manual SQL, but this is a last resort.
In general, I use Graph Databases a lot. The mapping between objects and graphs is usually trivial.
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