CREATE TABLE companies (
   company_id NUMBER NOT NULL PRIMARY KEY,
   company_name VARCHAR2(100) NOT NULL,
   data_version NUMBER NOT NULL
);
CREATE TABLE departments (
   department_id NUMBER NOT NULL PRIMARY KEY,
   company_id NUMBER REFERENCES companies (company_id),
   parent_department_id NUMBER REFERENCES departments (department_id),
   index_number NUMBER,
   department_name VARCHAR2(100) NOT NULL,
   data_version NUMBER NOT NULL
);
CREATE SEQUENCE company_id;
CREATE SEQUENCE department_id;

package test.bo;

import java.util.List;

public class Company {

   // attributes
   private Long companyId;
   private String companyName;
   private Long dataVersion;
   // associations
   private List<Department> departments;

   public Company() {
   }

   public List<Department> getDepartments() {
      return departments;
   }

   public void setDepartments(List<Department> departments) {
      this.departments = departments;
   }

   public Long getCompanyId() {
      return companyId;
   }

   public void setCompanyId(Long companyId) {
      this.companyId = companyId;
   }

   public String getCompanyName() {
      return companyName;
   }

   public void setCompanyName(String companyName) {
      this.companyName = companyName;
   }

   public Long getDataVersion() {
      return dataVersion;
   }

   public void setDataVersion(Long dataVersion) {
      this.dataVersion = dataVersion;
   }

}

package test.bo;

import java.util.List;

public class Department {

   // attributes
   private Long departmentId;
   private String departmentName;
   private Long dataVersion;
   // associations
   private Company company;
   private Department parentDepartment;
   private List<Department> childDepartments;

   public Department() {
   }

   public Long getDepartmentId() {
      return departmentId;
   }

   public void setDepartmentId(Long departmentId) {
      this.departmentId = departmentId;
   }

   public String getDepartmentName() {
      return departmentName;
   }

   public void setDepartmentName(String departmentName) {
      this.departmentName = departmentName;
   }

   public Long getDataVersion() {
      return dataVersion;
   }

   public void setDataVersion(Long dataVersion) {
      this.dataVersion = dataVersion;
   }

   public Company getCompany() {
      return company;
   }

   public void setCompany(Company company) {
      this.company = company;
   }

   public Department getParentDepartment() {
      return parentDepartment;
   }

   public void setParentDepartment(Department parentDepartment) {
      this.parentDepartment = parentDepartment;
   }

   public List<Department> getChildDepartments() {
      return childDepartments;
   }

   public void setChildDepartments(List<Department> childDepartments) {
      this.childDepartments = childDepartments;
   }

}

<?xml version="1.0"?>
<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
<hibernate-mapping package="test.bo">
   <class name="Company" table="companies" optimistic-lock="version">
      <id name="companyId" column="company_id" type="long" unsaved-value="null">
         <generator class="sequence">
            <param name="sequence">company_id</param>
         </generator>
      </id>
      <version name="dataVersion" column="data_version" type="long" />
      
      <property name="companyName" column="company_name" not-null="true" />
      
      <list name="departments" cascade="all">
         <key column="company_id" />
         <list-index column="index_number" base="1" />
         <one-to-many class="Department" />
      </list>
   </class>
</hibernate-mapping>

<?xml version="1.0"?>
<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
<hibernate-mapping package="test.bo">
   <class name="Department" table="departments" optimistic-lock="version">
      <id name="departmentId" column="department_id" type="long" unsaved-value="null">
         <generator class="sequence">
            <param name="sequence">department_id</param>
         </generator>
      </id>
      <version name="dataVersion" column="data_version" type="long" />
      
      <property name="departmentName" column="department_name" not-null="true" />
      
      <many-to-one name="company" column="company_id" class="Company" update="false" insert="false" />
      <many-to-one name="parentDepartment" column="parent_department_id" class="Department" update="false" insert="false" />
      
      <list name="childDepartments" cascade="all">
         <key column="parent_department_id" />
         <list-index column="index_number" base="1" />
         <one-to-many class="Department" />
      </list>
   </class>
</hibernate-mapping>

package test;

import java.sql.Connection;
import java.util.ArrayList;

import org.apache.log4j.Logger;
import org.hibernate.Criteria;
import org.hibernate.Session;
import org.hibernate.SessionFactory;
import org.hibernate.Transaction;
import org.hibernate.cfg.Configuration;
import org.hibernate.criterion.Restrictions;

import test.bo.Company;
import test.bo.Department;

public class Test {
   
   private static Logger logger = Logger.getLogger(Test.class);

   public static void main(String[] args) {
      Configuration configuration = (new Configuration()).configure();
      SessionFactory sessionFactory = configuration.buildSessionFactory();
      try {
         clean(sessionFactory);
         create(sessionFactory);
         update(sessionFactory);
         select(sessionFactory);
      } catch (RuntimeException e) {
         logger.error("Exception occurred", e);
      } finally {
         sessionFactory.close();
      }
   }
   
   @SuppressWarnings("deprecation")
   private static void clean(SessionFactory sessionFactory) {
      logger.debug("CLEAN:");
      Session session = sessionFactory.openSession();
      try {
         Connection connection = session.connection();
         connection.createStatement().executeUpdate("DELETE FROM departments");
         connection.createStatement().executeUpdate("DELETE FROM companies");
         connection.commit();
      } catch (Exception e) {
         throw new RuntimeException(e);
      } finally {
         session.close();
      }
   }
   
   private static void create(SessionFactory sessionFactory) {
      logger.debug("CREATE:");
      Session session = sessionFactory.openSession();
      Transaction transaction = session.beginTransaction();
      try {
         Company testCompany = new Company();
         testCompany.setCompanyName("TestCompany");
         testCompany.setDepartments(new ArrayList<Department>());
         
         Department salesDepartment = new Department();
         salesDepartment.setDepartmentName("SalesDepartment");
         salesDepartment.setChildDepartments(new ArrayList<Department>());
         // association
         salesDepartment.setCompany(testCompany);
         testCompany.getDepartments().add(salesDepartment);
         
         Department internetSales = new Department();
         internetSales.setDepartmentName("InternetSales");
         internetSales.setChildDepartments(new ArrayList<Department>());
         // association
         internetSales.setParentDepartment(salesDepartment);
         salesDepartment.getChildDepartments().add(internetSales);
         
         session.save(testCompany);
         transaction.commit();
         printCompany(testCompany);
      } catch (RuntimeException e) {
         transaction.rollback();
         throw e;
      } finally {
         session.close();
      }
   }
   
   private static void update(SessionFactory sessionFactory) {
      logger.debug("UPDATE:");
      Session session = sessionFactory.openSession();
      Transaction transaction = session.beginTransaction();
      try {
         Criteria testCompanyCriteria = session.createCriteria(Company.class);
         testCompanyCriteria.add(Restrictions.eq("companyName", "TestCompany"));
         Company testCompany = (Company)testCompanyCriteria.uniqueResult();

         Criteria internetSalesCriteria = session.createCriteria(Department.class);
         internetSalesCriteria.add(Restrictions.eq("departmentName", "InternetSales"));
         Department internetSales = (Department)internetSalesCriteria.uniqueResult();
         
         // remove association
         internetSales.getParentDepartment().getChildDepartments().remove(internetSales);
         // new association
         internetSales.setCompany(testCompany);
         testCompany.getDepartments().add(internetSales);
         
         transaction.commit();
         printCompany(testCompany);
      } catch (RuntimeException e) {
         transaction.rollback();
         throw e;
      } finally {
         session.close();
      }
   }
   
   private static void select(SessionFactory sessionFactory) {
      logger.debug("SELECT:");
      Session session = sessionFactory.openSession();
      try {
         Criteria criteria = session.createCriteria(Company.class);
         criteria.add(Restrictions.eq("companyName", "TestCompany"));
         Company testCompany = (Company)criteria.uniqueResult();
         
         printCompany(testCompany);
      } finally {
         session.close();
      }
   }

   private static void printCompany(Company company) {
      logger.debug("<DATA>");
      logger.debug(String.format("[Company] id:%d, name:%s", company.getCompanyId(), company.getCompanyName()));
      for (Department department : company.getDepartments()) {
         printDepartment(department, 1);
      }
   }
   
   private static void printDepartment(Department department, int indentSize) {
      StringBuilder indent = new StringBuilder();
      for (int i = 0; i < indentSize; i++) indent.append(" ");
      logger.debug(String.format("%s[Department] id:%d, name:%s", indent, department.getDepartmentId(), department.getDepartmentName()));
      for (Department childDepartment : department.getChildDepartments()) {
         printDepartment(childDepartment, indentSize + 1);
      }
   }
   
}

23:25:10,046 DEBUG Test:56 - CLEAN:
23:25:10,203 DEBUG Test:71 - CREATE:
23:25:10,218 DEBUG SQL:111 - select company_id.nextval from dual
23:25:10,343 DEBUG SQL:111 - select department_id.nextval from dual
23:25:10,343 DEBUG SQL:111 - select department_id.nextval from dual
23:25:10,375 DEBUG SQL:111 - insert into companies (data_version, company_name, company_id) values (?, ?, ?)
23:25:10,375 DEBUG SQL:111 - insert into departments (data_version, department_name, department_id) values (?, ?, ?)
23:25:10,375 DEBUG SQL:111 - insert into departments (data_version, department_name, department_id) values (?, ?, ?)
23:25:10,375 DEBUG SQL:111 - update departments set company_id=?, index_number=? where department_id=?
23:25:10,375 DEBUG SQL:111 - update departments set parent_department_id=?, index_number=? where department_id=?
23:25:10,390 DEBUG Test:148 - <DATA>
23:25:10,390 DEBUG Test:149 - [Company] id:24, name:TestCompany
23:25:10,390 DEBUG Test:158 -  [Department] id:47, name:SalesDepartment
23:25:10,390 DEBUG Test:158 -   [Department] id:48, name:InternetSales
23:25:10,390 DEBUG Test:105 - UPDATE:
23:25:10,406 DEBUG SQL:111 - select this_.company_id as company1_0_0_, this_.data_version as data2_0_0_, this_.company_name as company3_0_0_ from companies this_ where this_.company_name=?
23:25:10,421 DEBUG SQL:111 - select this_.department_id as department1_1_0_, this_.data_version as data2_1_0_, this_.department_name as department3_1_0_, this_.company_id as company4_1_0_, this_.parent_department_id as parent5_1_0_ from departments this_ where this_.department_name=?
23:25:10,437 DEBUG SQL:111 - select department0_.department_id as department1_1_0_, department0_.data_version as data2_1_0_, department0_.department_name as department3_1_0_, department0_.company_id as company4_1_0_, department0_.parent_department_id as parent5_1_0_ from departments department0_ where department0_.department_id=?
23:25:10,437 DEBUG SQL:111 - select childdepar0_.parent_department_id as parent5_1_, childdepar0_.department_id as department1_1_, childdepar0_.index_number as index6_1_, childdepar0_.department_id as department1_1_0_, childdepar0_.data_version as data2_1_0_, childdepar0_.department_name as department3_1_0_, childdepar0_.company_id as company4_1_0_, childdepar0_.parent_department_id as parent5_1_0_ from departments childdepar0_ where childdepar0_.parent_department_id=?
23:25:10,453 DEBUG SQL:111 - select department0_.company_id as company4_1_, department0_.department_id as department1_1_, department0_.index_number as index6_1_, department0_.department_id as department1_1_0_, department0_.data_version as data2_1_0_, department0_.department_name as department3_1_0_, department0_.company_id as company4_1_0_, department0_.parent_department_id as parent5_1_0_ from departments department0_ where department0_.company_id=?
23:25:10,546 DEBUG SQL:111 - update companies set data_version=?, company_name=? where company_id=? and data_version=?
23:25:10,546 DEBUG SQL:111 - update departments set data_version=?, department_name=? where department_id=? and data_version=?
23:25:10,546 DEBUG SQL:111 - update departments set company_id=?, index_number=? where department_id=?
23:25:10,593 DEBUG SQL:111 - update departments set parent_department_id=null, index_number=null where parent_department_id=?
23:25:10,593 DEBUG Test:148 - <DATA>
23:25:10,593 DEBUG Test:149 - [Company] id:24, name:TestCompany
23:25:10,609 DEBUG Test:158 -  [Department] id:47, name:SalesDepartment
23:25:10,609 DEBUG Test:158 -  [Department] id:48, name:InternetSales
23:25:10,609 DEBUG SQL:111 - select childdepar0_.parent_department_id as parent5_1_, childdepar0_.department_id as department1_1_, childdepar0_.index_number as index6_1_, childdepar0_.department_id as department1_1_0_, childdepar0_.data_version as data2_1_0_, childdepar0_.department_name as department3_1_0_, childdepar0_.company_id as company4_1_0_, childdepar0_.parent_department_id as parent5_1_0_ from departments childdepar0_ where childdepar0_.parent_department_id=?
23:25:10,609 DEBUG Test:134 - SELECT:
23:25:10,609 DEBUG SQL:111 - select this_.company_id as company1_0_0_, this_.data_version as data2_0_0_, this_.company_name as company3_0_0_ from companies this_ where this_.company_name=?
23:25:10,609 DEBUG Test:148 - <DATA>
23:25:10,609 DEBUG Test:149 - [Company] id:24, name:TestCompany
23:25:10,609 DEBUG SQL:111 - select department0_.company_id as company4_1_, department0_.department_id as department1_1_, department0_.index_number as index6_1_, department0_.department_id as department1_1_0_, department0_.data_version as data2_1_0_, department0_.department_name as department3_1_0_, department0_.company_id as company4_1_0_, department0_.parent_department_id as parent5_1_0_ from departments department0_ where department0_.company_id=?
23:25:10,625  WARN LoadContexts:132 - fail-safe cleanup (collections) : org.hibernate.engine.loading.CollectionLoadContext@d3db51<rs=oracle.jdbc.driver.OracleResultSetImpl@11381e7>
23:25:10,625  WARN CollectionLoadContext:348 - On CollectionLoadContext#cleanup, localLoadingCollectionKeys contained [1] entries
23:25:10,625 ERROR Test:48 - Exception occurred
org.hibernate.HibernateException: null index column for collection: test.bo.Company.departments
   at org.hibernate.persister.collection.AbstractCollectionPersister.readIndex(AbstractCollectionPersister.java:732)
   at org.hibernate.collection.PersistentList.readFrom(PersistentList.java:402)
   at org.hibernate.loader.Loader.readCollectionElement(Loader.java:1031)
   at org.hibernate.loader.Loader.readCollectionElements(Loader.java:669)
   at org.hibernate.loader.Loader.getRowFromResultSet(Loader.java:614)
   at org.hibernate.loader.Loader.doQuery(Loader.java:724)
   at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:259)
   at org.hibernate.loader.Loader.loadCollection(Loader.java:2015)
   at org.hibernate.loader.collection.CollectionLoader.initialize(CollectionLoader.java:59)
   at org.hibernate.persister.collection.AbstractCollectionPersister.initialize(AbstractCollectionPersister.java:587)
   at org.hibernate.event.def.DefaultInitializeCollectionEventListener.onInitializeCollection(DefaultInitializeCollectionEventListener.java:83)
   at org.hibernate.impl.SessionImpl.initializeCollection(SessionImpl.java:1743)
   at org.hibernate.collection.AbstractPersistentCollection.initialize(AbstractPersistentCollection.java:366)
   at org.hibernate.collection.AbstractPersistentCollection.read(AbstractPersistentCollection.java:108)
   at org.hibernate.collection.PersistentList.iterator(PersistentList.java:138)
   at test.Test.printCompany(Test.java:150)
   at test.Test.select(Test.java:141)
   at test.Test.main(Test.java:46)