<set name="zones" table="ApprovalZone">
      <key>
         <column name="ApprovalID" />
      </key>
      <element column="ZoneID" type="int" />
   </set>

select
...
zones2_.ApprovalID as ApprovalID1__,
zones2_.ZoneID as ZoneID1__,
...
zones2_.ApprovalID as ApprovalID1__,
zones2_.ZoneID as ZoneID1__,
...

from
  blah.Approval approval0_
  left outer join blah.ApprovalZone zones2_ on approval0_.ApprovalID=zones2_.ApprovalID

package test.mdlandon;

import java.util.Set;

public class ZonesContainer {
   private Long id;
   private Set zones;
   public Long getId() {
      return id;
   }
   public void setId(Long id) {
      this.id = id;
   }
   public Set getZones() {
      return zones;
   }
   public void setZones(Set zones) {
      this.zones = zones;
   }
   
}

<?xml version="1.0"?>
<!DOCTYPE hibernate-mapping PUBLIC
   "-//Hibernate/Hibernate Mapping DTD//EN"
   "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd" >

<hibernate-mapping package="test.mdlandon">
   <class name="ZonesContainer" table="mdlandon_zones_container">

      <id name="id" column="id">
         <generator class="increment" />
      </id>

      <set name="zones" table="mdlandon_approval_zone">
         <key column="approval_id" />
         <element column="zone_id" type="int"/>
      </set>

   </class>
</hibernate-mapping>

package test.mdlandon;

import java.util.HashSet;
import java.util.List;
import java.util.Set;

import junit.framework.TestCase;

import org.hibernate.Query;
import org.hibernate.Session;

public class TestIt extends TestCase {
   
   public void testIt() {
      Long id = createZonesContainerInDatabase();
      
      Session s = HibernateUtil.getSession();
      Query q = s.createQuery("from ZonesContainer as zc left join fetch zc.zones");
      List result = q.list();
      System.out.println("result size="+result.size());
      ZonesContainer zc = (ZonesContainer)result.get(0);
      System.out.println(""+zc.getZones());
      s.close();
   }

   private Long createZonesContainerInDatabase() {
      Session s = HibernateUtil.getSession();
      s.beginTransaction();
      
      Set<Integer> zones = new HashSet<Integer>();
      zones.add(new Integer(1));
      zones.add(new Integer(2));
      
      ZonesContainer zc = new ZonesContainer();
      zc.setZones(zones);
      Long id = (Long)s.save(zc);
      
      s.getTransaction().commit();
      s.close();
      return id;
   }

}

Hibernate: select max(id) from mdlandon_zones_container
Hibernate: insert into mdlandon_zones_container (id) values (?)
Hibernate: insert into mdlandon_approval_zone (approval_id, zone_id) values (?, ?)
Hibernate: insert into mdlandon_approval_zone (approval_id, zone_id) values (?, ?)
Hibernate: select zonesconta0_.id as id0_, zones1_.approval_id as approval1_0__, zones1_.zone_id as zone2_0__ from mdlandon_zones_container zonesconta0_ left outer join mdlandon_approval_zone zones1_ on zonesconta0_.id=zones1_.approval_id
result size=2
[1, 2]

create table mdlandon_zones_container
(
    ZoneID               integer                        not null default autoincrement,
    ZoneName             varchar(64)                    not null,
    primary key (ZoneID)
);

create table mdlandon_approval_zone
(
    ZoneID               integer                        not null,
    ApprovalID           integer                        not null,
    primary key (ZoneID, ApprovalID)
);

alter table mdlandon_approval_zone
   add foreign key FK_1 (ZoneID)
      references mdlandon_zones_container (ZoneID)
      on update restrict
      on delete restrict;

create table mdlandon_other_container
(
    OtherID              integer                        not null default autoincrement,
    ZoneID               integer                        not null,
    OtherName            varchar(64)                    not null,
    primary key (OtherID)
);

alter table mdlandon_other_container
   add foreign key FK_2 (ZoneID)
      references mdlandon_zones_container (ZoneID)
      on update restrict
      on delete restrict;

insert into mdlandon_zones_container(ZoneID, ZoneName) values (1, 'testing');
insert into mdlandon_zones_container(ZoneID, ZoneName) values (2, 'testing2');

insert into mdlandon_approval_zone(ZoneID, ApprovalID) values (1, 33);
insert into mdlandon_approval_zone(ZoneID, ApprovalID) values (1, 34);
insert into mdlandon_approval_zone(ZoneID, ApprovalID) values (1, 35);
insert into mdlandon_approval_zone(ZoneID, ApprovalID) values (2, 133);
insert into mdlandon_approval_zone(ZoneID, ApprovalID) values (2, 234);
insert into mdlandon_approval_zone(ZoneID, ApprovalID) values (2, 335);

insert into mdlandon_other_container(OtherID, ZoneID, OtherName) values (1, 1, 'other1-1');
insert into mdlandon_other_container(OtherID, ZoneID, OtherName) values (2, 1, 'other1-2');
insert into mdlandon_other_container(OtherID, ZoneID, OtherName) values (3, 1, 'other1-3');
insert into mdlandon_other_container(OtherID, ZoneID, OtherName) values (4, 2, 'other2-1');
insert into mdlandon_other_container(OtherID, ZoneID, OtherName) values (5, 2, 'other2-2');
insert into mdlandon_other_container(OtherID, ZoneID, OtherName) values (6, 2, 'other2-3');

package test.mdlandon;

import java.util.Set;

public class ZonesContainer {
   private Long zoneId;
   private String name;
   private Set zones;
   private Set others;
   public Long getZoneId() {
      return zoneId;
   }
   public void setZoneId(Long zoneId) {
      this.zoneId = zoneId;
   }
   public String getName() {
      return name;
   }
   public void setName(String name) {
      this.name = name;
   }
   public Set getZones() {
      return zones;
   }
   public void setZones(Set zones) {
      this.zones = zones;
   }
   public Set getOthers() {
      return others;
   }
   public void setOthers(Set others) {
      this.others = others;
   }
   
}

<?xml version="1.0"?>
<!DOCTYPE hibernate-mapping PUBLIC
   "-//Hibernate/Hibernate Mapping DTD//EN"
   "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd" >

<hibernate-mapping package="test.mdlandon">
   <class name="ZonesContainer" table="mdlandon_zones_container">
 
      <id name="zoneId" column="ZoneID">
         <generator class="native" />
      </id>

      <property name="name" type="string">
         <column name="ZoneName" length="64" not-null="true" />
      </property>

      <set name="zones" table="mdlandon_approval_zone">
         <key column="ApprovalID" />
         <element column="ZoneID" type="int"/>
      </set>

      <set name="others" inverse="true" cascade="save-update" fetch="subselect">
         <key>
            <column name="OtherID" not-null="true" />
         </key>
         <one-to-many class="test.mdlandon.OtherContainer" />
      </set>
   </class>
</hibernate-mapping>

package test.mdlandon;

public class OtherContainer {
   private Long otherId;
   private String name;
   private ZonesContainer zone;
   public Long getOtherId() {
      return otherId;
   }
   public void setOtherId(Long otherId) {
      this.otherId = otherId;
   }
   public String getName() {
      return name;
   }
   public void setName(String name) {
      this.name = name;
   }
   public ZonesContainer getZone() {
      return zone;
   }
   public void setZone(ZonesContainer zone) {
      this.zone = zone;
   }
   
}

<?xml version="1.0"?>
<!DOCTYPE hibernate-mapping PUBLIC
   "-//Hibernate/Hibernate Mapping DTD//EN"
   "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd" >

<hibernate-mapping package="test.mdlandon">
   <class name="OtherContainer" table="mdlandon_other_container">
 
      <id name="otherId" column="OtherID">
         <generator class="native" />
      </id>

      <many-to-one name="zone" class="test.mdlandon.ZonesContainer">
         <column name="ZoneID" />
      </many-to-one>

      <property name="name" type="string">
         <column name="OtherName" length="64" not-null="true" />
      </property>

   </class>
</hibernate-mapping>

package test.mdlandon;

import java.util.HashSet;
import java.util.List;
import java.util.Set;

import org.hibernate.Query;
import org.hibernate.Session;

public class TestIt {
   
   public void testIt() throws Exception {
      Session s = HibernateUtil.getSession();
      Query q = s.createQuery("from ZonesContainer as zc left join fetch zc.others left join fetch zc.zones");
      List result = q.list();
      System.out.println("result size="+result.size());
      ZonesContainer zc = (ZonesContainer)result.get(0);
      System.out.println(""+zc.getZones());
      System.out.println(""+zc.getOthers());
      s.close();
   }

   public static void main (String args[]) throws Exception {
       TestIt it = new TestIt();
       it.testIt();
   }

}

Hibernate: select zonesconta0_.ZoneID as ZoneID0_0_, others1_.OtherID as OtherID2_1_, zonesconta0_.ZoneName as ZoneName0_0_, zones2_.ApprovalID as ApprovalID1__, zones2_.ZoneID as ZoneID1__, others1_.ZoneID as ZoneID2_1_, others1_.OtherName as OtherName2_1_, others1_.OtherID as OtherID0__, zones2_.ApprovalID as ApprovalID1__, zones2_.ZoneID as ZoneID1__ from mdlandon_zones_container zonesconta0_ left outer join mdlandon_other_container others1_ on zonesconta0_.ZoneID=others1_.OtherID left outer join mdlandon_approval_zone zones2_ on zonesconta0_.ZoneID=zones2_.ApprovalID

SEVERE: ASA Error -830: Alias 'ApprovalID1__' is not unique
org.hibernate.exception.SQLGrammarException: could not execute query
   at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:67)
   at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)
   at org.hibernate.loader.Loader.doList(Loader.java:2223)
   at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2104)
   at org.hibernate.loader.Loader.list(Loader.java:2099)
   at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:378)
   at org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:338)
   at org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:172)
   at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1121)
   at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79)
   at test.mdlandon.TestIt.testIt(Unknown Source)
   at test.mdlandon.TestIt.main(Unknown Source)

Hibernate: select zonesconta0_.ZoneID as ZoneID0_0_, others1_.OtherID as OtherID2_1_, zonesconta0_.ZoneName as ZoneName0_0_, zones2_.ZoneID as ZoneID1__, zones2_.ApprovalID as ApprovalID1__, others1_.ZoneID as ZoneID2_1_, others1_.OtherName as OtherName2_1_, others1_.ZoneID as ZoneID0__, others1_.OtherID as OtherID0__, zones2_.ZoneID as ZoneID1__, zones2_.ApprovalID as ApprovalID1__ from mdlandon_zones_container zonesconta0_ left outer join mdlandon_other_container others1_ on zonesconta0_.ZoneID=others1_.ZoneID left outer join mdlandon_approval_zone zones2_ on zonesconta0_.ZoneID=zones2_.ZoneID

Hibernate: select zonesconta0_.ZoneID as ZoneID0_0_, others2_.OtherID as OtherID2_1_, zonesconta0_.ZoneName as ZoneName0_0_, zones1_.ZoneID as ZoneID0__, zones1_.ApprovalID as ApprovalID0__, others2_.ZoneID as ZoneID2_1_, others2_.OtherName as OtherName2_1_, others2_.ZoneID as ZoneID1__, others2_.OtherID as OtherID1__ from mdlandon_zones_container zonesconta0_ left outer join mdlandon_approval_zone zones1_ on zonesconta0_.ZoneID=zones1_.ZoneID left outer join mdlandon_other_container others2_ on zonesconta0_.ZoneID=others2_.ZoneID

<set name="others" inverse="true" cascade="save-update" fetch="subselect">
  <key>
    <column name="OtherID" not-null="true" />
  </key>
  <one-to-many class="test.mdlandon.OtherContainer" />
</set>

<key>
  <column name="ZoneID" not-null="true" />
</key>

<set name="zones" table="mdlandon_approval_zone">
  <key column="ApprovalID" />
  <element column="ZoneID" type="int"/>
</set>

<key column="ZoneID" />
  <element column="ApprovalID" type="int"/>
</set>

...
The underlying cause of this behaviour is that the link (the foreign key parent_id) from p to c is not considered part of the state of the Child object and is therefore not created in the INSERT. So the solution is to make the link part of the Child mapping.

<many-to-one name="parent" column="parent_id" not-null="true"/>
(We also need to add the parent property to the Child class.)

Now that the Child entity is managing the state of the link, we tell the collection not to update the link. We use the inverse attribute.

<set name="children" inverse="true">
    <key column="parent_id"/>
    <one-to-many class="Child"/>
</set>