mvn test

@Entity
@Table(name = "ITEM",
	indexes = @Index(columnList = "CODE", unique = true))
public class Item implements Serializable
{
	private static final long serialVersionUID = 1L;

	@Id
	@GeneratedValue
	protected Long id;

	@Column
	protected String code;

	@OneToMany(mappedBy = "parent", cascade = CascadeType.ALL, orphanRemoval = true)
	protected Set<ItemRelation> lowerItemRelations = new LinkedHashSet<>();

	@OneToMany(mappedBy = "child", cascade = CascadeType.ALL, orphanRemoval = true)
	protected Set<ItemRelation> higherItemRelations = new LinkedHashSet<>();

	...
}

@Entity
@Table(name = "ITEM_RELATION",
	indexes = @Index(columnList = "PARENT_ID, CHILD_ID", unique = true))
public class ItemRelation implements Serializable
{
	private static final long serialVersionUID = 1L;

	@Id
	@GeneratedValue
	protected Long id;

	@ManyToOne(optional = false)
	@JoinColumn(name = "PARENT_ID")
	private Item parent;

	@ManyToOne(optional = false)
	@JoinColumn(name = "CHILD_ID")
	private Item child;

	@Column(nullable = false, columnDefinition = "INT DEFAULT 0 NOT NULL")
	private int quantity = 1;

	...
}

EntityManager em = emf.createEntityManager();
EntityTransaction tx = em.getTransaction();

tx.begin();

Item item = em.createQuery("select x from Item x where x.code = 'first'", Item.class).getSingleResult();

Set<ItemRelation> lowerItemRelations = item.getLowerItemRelations();
Hibernate.initialize(lowerItemRelations);

// initializing higherItemRelations prevents orphanRemoval to work on lowerItemRelations
Set<ItemRelation> higherItemRelations = item.getHigherItemRelations();
Hibernate.initialize(higherItemRelations);

lowerItemRelations.clear();

tx.commit();
em.close();