If the database columns are created such that the serial id is not the first one, then the EntityManager.persist(Object) method sets the wrong value on the entity's @Id field (it sets it to the value of the first db column). For example:

Create the table:

CREATE TABLE info.rmbtest_course2
(
fee integer,
id bigserial NOT NULL,
starttime timestamp without time zone,
title character varying(100) NOT NULL,
CONSTRAINT rmbtest_course2_pkey PRIMARY KEY (id)
)

Note that the id column is the second column.

Create the entity:
package testhibernate.course;

import org.hibernate.annotations.GenericGenerator;
import org.hibernate.annotations.Type;
import org.joda.time.DateTime;

import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.IdClass;
import javax.persistence.NamedQueries;
import javax.persistence.NamedQuery;
import javax.persistence.Table;

@Entity(name = "course")
@Table(name = "rmbTest_course2", schema = "info")
@NamedQueries(@NamedQuery(name = "Course.findByTest", query = "from course"))
public class Course {

@Id
@GeneratedValue(strategy = GenerationType.IDENTITY)
@Column(name = "ID")
private final Long id;

@Column(name = "TITLE", length = 100, nullable = false)
private final String title;

@Column(name = "FEE")
private final int fee;

@Column(name = "startTime")
@Type(type="org.jadira.usertype.dateandtime.joda.PersistentDateTime")
private final DateTime startTime;

public Course(final String title, final int fee, final DateTime startTime) {

this.id = null;
this.title = title;
this.fee = fee;
this.startTime = startTime;
}

/**

• Required by JPA
  */
  public Course() {
  id = null;
  title = null;
  fee = 0;
  startTime = null;
  }

public CourseKey getKey() {

return new CourseKey(id);
}

public String getTitle() {

return title;
}

public int getFee() {

return fee;
}

public DateTime getStartTime() {

return startTime;
}

@Override
public String toString()
{
return "Course{" +
"id=" + id +
", title='" + title + '\'' +
", fee=" + fee +
", startTime=" + startTime +
'}';
}
}

Run this code:

Course course = new Course("Core Spring", 1000, new DateTime());

course = myRepository.save(course);

System.out.println("key = " + course.getKey());

In this case the returned course.getKey() should've been the auto allocated serial id, but it is 1000, i.e. the first column in the table.

The problem is that IdentifierGeneratorHelper.get(ResultSet rs, Type type) assumes that the id column is always the first column.

As a workaround I have set my entities @Id annotations to:

...
public class Course {

@Id
@GeneratedValue(generator = "myGenerator")
@GenericGenerator(name = "myGenerator", strategy = "testhibernate.MyGenerator")
@Column(name = "ID")
private final Long id;
...

and had the following Generator code:

package testhibernate;

import org.hibernate.HibernateException;
import org.hibernate.dialect.Dialect;
import org.hibernate.id.IdentifierGenerationException;
import org.hibernate.id.IdentifierGeneratorHelper;
import org.hibernate.id.IdentityGenerator;
import org.hibernate.id.PostInsertIdentityPersister;
import org.hibernate.id.ResultSetIdentifierConsumer;
import org.hibernate.id.insert.InsertGeneratedIdentifierDelegate;
import org.hibernate.persister.entity.SingleTableEntityPersister;
import org.hibernate.type.CustomType;
import org.hibernate.type.Type;

import java.io.Serializable;
import java.math.BigDecimal;
import java.math.BigInteger;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;

public class MyGenerator extends IdentityGenerator
{
@Override
public InsertGeneratedIdentifierDelegate getInsertGeneratedIdentifierDelegate(final PostInsertIdentityPersister persister,
final Dialect dialect,
final boolean isGetGeneratedKeysEnabled) throws HibernateException
{
final InsertGeneratedIdentifierDelegate result;

if(isGetGeneratedKeysEnabled)
{
result = new MyGetGeneratedKeysDelegate(persister, dialect);
}
else
{
result = super.getInsertGeneratedIdentifierDelegate(persister, dialect, isGetGeneratedKeysEnabled);
}

return result;
}

private static class MyGetGeneratedKeysDelegate extends GetGeneratedKeysDelegate
{
private final PostInsertIdentityPersister persister;

private MyGetGeneratedKeysDelegate(final PostInsertIdentityPersister persister, final Dialect dialect)
{
super(persister, dialect);

assert persister != null;

this.persister = persister;
}

private Serializable getGeneratedIdentityByColumnName(ResultSet rs,
Type type,
String columnName) throws SQLException, HibernateException {
if ( !rs.next() ) {
throw new HibernateException( "The database returned no natively generated identity value" );
}

final Serializable id = get(rs, type, columnName);
// todo log.debug( "Natively generated identity: " + id );
return id;
}

private Serializable get(ResultSet rs, Type type, String columnName) throws SQLException, IdentifierGenerationException
{
if ( ResultSetIdentifierConsumer.class.isInstance( type ) )
{
return ( ( ResultSetIdentifierConsumer ) type ).consumeIdentifier( rs );
}

if ( CustomType.class.isInstance( type ) )
{
final CustomType customType = (CustomType) type;
if ( ResultSetIdentifierConsumer.class.isInstance( customType.getUserType() ) ) {
return ( (ResultSetIdentifierConsumer) customType.getUserType() ).consumeIdentifier( rs );
}
}

Class<?> clazz = type.getReturnedClass();
if ( clazz == Long.class )
{
return rs.getLong(columnName);
}
else if ( clazz == Integer.class )
{
return rs.getInt(columnName);
}
else if ( clazz == Short.class )
{
return rs.getShort(columnName);
}
else if ( clazz == String.class )
{
return rs.getString( columnName );
}
else if ( clazz == BigInteger.class )
{
return rs.getBigDecimal( columnName ).setScale( 0, BigDecimal.ROUND_UNNECESSARY ).toBigInteger();
}
else if ( clazz == BigDecimal.class )
{
return rs.getBigDecimal( columnName ).setScale( 0, BigDecimal.ROUND_UNNECESSARY );
}
else
{
throw new IdentifierGenerationException("unrecognised id type : " + type.getName() + " -> " + clazz.getName());
}
}

@Override
public Serializable executeAndExtract(final PreparedStatement insert) throws SQLException
{
insert.executeUpdate();

ResultSet rs = insert.getGeneratedKeys();
try
{
final Type identifierType = persister.getIdentifierType();

Serializable result = null;
boolean useDefaultTechnique = true;

if(persister instanceof SingleTableEntityPersister)
{
final String[] idColumnNames = ((SingleTableEntityPersister)persister).getIdentifierColumnNames();
if(idColumnNames.length == 1)
{
// do it by column name
result = getGeneratedIdentityByColumnName(rs, identifierType, idColumnNames[0] );

useDefaultTechnique = false;
}
else
{
// todo - log
}
}
else
{
// todo - log
}

if(useDefaultTechnique)
{
result = IdentifierGeneratorHelper.getGeneratedIdentity(rs, identifierType);
}

return result;
}
finally
{
rs.close();
}
}
}

}

This seems to do the trick but is obviously an ugly hack.