spring hibernate application context (commit)

mauroyb0 · **Joined:** Wed Mar 21, 2007 10:23 am **Posts:** 20

Dear all,

I have still a problem with my spring hibernate application. My application context is defined like that :

Code:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE beans PUBLIC "-//SPRING//DTD BEAN//EN"
    "http://www.springframework.org/dtd/spring-beans.dtd">

<beans>
<bean id="dataSource" class="org.springframework.jdbc.datasource.DriverManagerDataSource">
        <property name="driverClassName"><value>org.hsqldb.jdbcDriver</value></property>
         <property name="url"><value>jdbc:hsqldb:/home/yannmauron/toxico_db</value></property>
        <property name="username"><value>sa</value></property>
        <property name="password"><value></value></property>
    </bean>

 <!-- Hibernate SessionFactory -->
<bean id="sessionFactory" class="org.springframework.orm.hibernate3.LocalSessionFactoryBean">
     <property name="dataSource"><ref local="dataSource"/></property>
    <property name="mappingResources">
        <list>
            <value>com/genebio/toxico/compound/CompoundImpl.hbm.xml</value>
        </list>
    </property>
    <property name="hibernateProperties">
    <props>
        <prop key="hibernate.dialect">org.hibernate.dialect.HSQLDialect</prop>
        <prop key="hibernate.connection.autocommit">true</prop>
    </props>
    </property>
</bean>

    <!-- Transaction manager for a single Hibernate SessionFactory (alternative to JTA) -->
    <bean id="transactionManager" class="org.springframework.orm.hibernate3.HibernateTransactionManager">
        <property name="sessionFactory"><ref local="sessionFactory"/></property>
    </bean>
    <bean id="CompoundDAO" class="com.genebio.toxico.compound.CompoundDAOImpl">
        <property name="sessionFactory"><ref local="sessionFactory"/></property>
    </bean>
</beans>

My mapping file as :

Code:

<?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="com.genebio.toxico.compound" schema="PUBLIC">
   <class table="COMPOUND" name="CompoundImpl">
      <id name="id" type="int" column="COMPOUND_ID"></id>
      <property name="cid" type="string" column="COMPOUND_CID" />
      <property name="SMILE" type="string" column="COMPOUND_SMILE" />
   </class>
   
</hibernate-mapping>

My object :

Code:

package com.genebio.toxico.compound;

/**
 * Basic class for the compound object
 * 
 * @author Yann
 *
 */

import java.util.ArrayList;
import java.io.Serializable;

public class CompoundImpl extends CompoundImplBase implements Serializable{
   
   public CompoundImpl() {
   }
   
   protected String cid;
   protected int id;
   protected String SMILE;
   protected ArrayList<CompoundDescriptor> compoundDescriptors;
   protected ArrayList<CompoundName> compoundNames;
   protected ArrayList<CompoundClassification> compoundclassification;
   protected ArrayList<CompoundCorrelation> compoundcorrelations;
   protected ArrayList<CompoundXref> compoundXrefs;
   
   //minimum information for a compound
   public CompoundImpl(int id, String cid, String SMILE){
      this.id                = id;
      this.cid                = cid;
      this.SMILE                = SMILE;   
   }
   
   //primary information for a compound
   public CompoundImpl(int id, String cid, String SMILE, 
         ArrayList<CompoundDescriptor> compoundDescriptors, 
         ArrayList<CompoundName> compoundNames, 
         ArrayList<CompoundXref> compoundXrefs
         ){

      this.id                = id;
      this.cid                = cid;
      this.SMILE                = SMILE;
      this.compoundDescriptors   = compoundDescriptors;
      this.compoundNames         = compoundNames;
      this.compoundXrefs         = compoundXrefs;
}

   //future information for a compound (correlation and classification informations are added)
   public CompoundImpl(int id, String cid, String SMILE, 
               ArrayList<CompoundDescriptor> compoundDescriptors, 
               ArrayList<CompoundName> compoundNames, 
               ArrayList<CompoundXref> compoundXrefs,
               ArrayList<CompoundClassification> compoundclassification, 
               ArrayList<CompoundCorrelation> compoundcorrelations 
               ){
   
      this.id                = id;
      this.cid                = cid;
      this.SMILE                = SMILE;
      this.compoundclassification   = compoundclassification;
      this.compoundcorrelations   = compoundcorrelations;
      this.compoundDescriptors   = compoundDescriptors;
      this.compoundNames         = compoundNames;
      this.compoundXrefs         = compoundXrefs;
   }
   
   
   public String getSMILE(){
      return SMILE;
   }
   
   public void setSMILE(String SMILE){
      this.SMILE=SMILE;
   }

   public ArrayList<CompoundClassification> getCompoundclassification() {
      return compoundclassification;
   }

   public void setCompoundclassification(
         ArrayList<CompoundClassification> compoundclassification) {
      this.compoundclassification = compoundclassification;
   }

   public ArrayList<CompoundCorrelation> getCompoundcorrelations() {
      return compoundcorrelations;
   }

   public void setCompoundcorrelations(
         ArrayList<CompoundCorrelation> compoundcorrelations) {
      this.compoundcorrelations = compoundcorrelations;
   }

   public ArrayList<CompoundDescriptor> getCompoundDescriptors() {
      return compoundDescriptors;
   }

   public void setCompoundDescriptors(
         ArrayList<CompoundDescriptor> compoundDescriptors) {
      this.compoundDescriptors = compoundDescriptors;
   }

   public ArrayList<CompoundName> getCompoundNames() {
      return compoundNames;
   }

   public void setCompoundNames(ArrayList<CompoundName> compoundNames) {
      this.compoundNames = compoundNames;
   }

   public ArrayList<CompoundXref> getCompoundXrefs() {
      return compoundXrefs;
   }

   public void setCompoundXrefs(ArrayList<CompoundXref> compoundXrefs) {
      this.compoundXrefs = compoundXrefs;
   }

   public int getId() {
      return id;
   }
   
   public String getCid() {
      return cid;
   }
   
   public void setId(int id) {
      this.id=id;
   }
   
   public void setCid(String cid) {
      this.cid=cid;
   }


}

And finnaly, my dao :

Code:

package com.genebio.toxico.compound;

import java.util.List;
import com.genebio.toxico.compound.Compound;
import org.springframework.orm.hibernate3.support.HibernateDaoSupport;


public class CompoundDAOImpl extends HibernateDaoSupport implements CompoundDAO{

   public void saveCompound(CompoundImpl compound) {
      getHibernateTemplate().saveOrUpdate(compound);
   }

   public CompoundImpl getCompound(int id) {
      return (CompoundImpl) getHibernateTemplate().get(CompoundImpl.class, id);
   }

   public void removeCompound(int id) {
      Object compound = getHibernateTemplate().load(Compound.class, id);
      getHibernateTemplate().delete(compound);
   }

}

I've made a junit test like that :

Code:

package com.genebio.toxico.compound;

import static org.junit.Assert.assertEquals;

import org.hibernate.classic.Session;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import junit.framework.TestCase;
import org.springframework.context.ApplicationContext;
import org.springframework.context.support.ClassPathXmlApplicationContext;

public class CompoundImplDAOTest {

private CompoundImpl compoundImpl = null;
private CompoundDAOImpl compoundDAO = null;
private ApplicationContext ctx = null;
   
   @Before
    public void setUp() throws Exception {
       String[] paths = {"applicationContext.xml"};
        ctx = new ClassPathXmlApplicationContext(paths);
       compoundDAO = (CompoundDAOImpl)  ctx.getBean("CompoundDAO");
   }

   
   @Test
       public void testSaveRecord() throws Exception {
              compoundImpl = new CompoundImpl();
              compoundImpl.setId(3);
              compoundImpl.setCid("1234567");
              compoundImpl.setSMILE("lkjfdg");
              compoundDAO.saveCompound(compoundImpl);
              Assert.assertNotNull("primary key assigned", compoundImpl.getId());
          }
   
   @Test
    public void testloadRecord() throws Exception {
      CompoundImpl compound = compoundDAO.getCompound(2);
      System.out.println(compound.toString());
       }
   
}

Everything ok, I can read an entry in the database (I have enter this entry through another tool), but when I try to enter a new record with my dao (the testSaveRecord() test in my junit), nothing is enter in the database... Any idea ?

Thank you very much...

dharmendra.pandey · **Posted:** Mon Mar 26, 2007 1:47 am

hi mauroyb0,

Are you getting any exception. If not the is related to Transaction management problem. Set auto commit false. And use Transaction Interceptor and set transaction attribute. For junit you could use TransactionSynchronizer for bind session and transaction. That might help. Not sure.

mauroyb0 · **Joined:** Wed Mar 21, 2007 10:23 am **Posts:** 20

I got no exception. I tried to add :

Code:

<!-- Hibernate SessionFactory -->
<bean id="sessionFactory" class="org.springframework.orm.hibernate3.LocalSessionFactoryBean">
     <property name="dataSource"><ref local="dataSource"/></property>
    <property name="mappingResources">
        <list>
            <value>com/genebio/toxico/compound/CompoundImpl.hbm.xml</value>
        </list>
    </property>
    <property name="hibernateProperties">
    <props>
        <prop key="hibernate.dialect">org.hibernate.dialect.HSQLDialect</prop>
        <prop key="hibernate.show_sql">true</prop>
        <prop key="hibernate.hbm2ddl.auto">update</prop>
    </props>
    </property>
</bean>

<!-- Transaction manager for a single Hibernate SessionFactory (alternative to JTA) -->
<bean id="transactionManager" class="org.springframework.orm.hibernate3.HibernateTransactionManager">
<property name="sessionFactory"><ref local="sessionFactory"/></property>
</bean>

<bean id="CompoundDAO" class="com.genebio.toxico.compound.CompoundDAOImpl">
        <property name="sessionFactory"><ref local="sessionFactory"/></property>
    </bean>

In my application context, but still don't have any entry in my db...

mar · **Posted:** Mon Mar 26, 2007 9:02 am

hi,

1. How do you manage transations? i do not see any transaction proxy defined in spring, nor the programmatically managed transaction using neither spring nor hibernate.

i believe you should have at least (programmatically managed tx):

Code:

// get your app context
final ApplicationContext ctx = evilSingleton.getInstance().getCtx();
// define your callback (simple call to dao.save() for example)
HibernateCallback callback = new HibernateCallback() {
  public Object doInHibernate(Session session) {
    AnyDao dao = ctx.getBean("anyDao");
    Entity e = new Entity();
    dao.save(e);
  }
};
// warp your callback with transaction
final SessionFactory sf = (SessionFactory)
ctx.getBean("sessionFactory");
AbstractPlatformTransactionManager txMng =
    (HibernateTransactionManager) ctx.getBean("transactionManager");
TransactionTemplate txTmpl = new TransactionTemplate(txMng);
txTmpl.execute(new TransactionCallbackWithoutResult() {
   public void doInTransactionWithoutResult(TransactionStatus
                   status) {
       new HibernateTemplate(sf).execute(callback);
   }
    });
}

* enable logging of org.springframework and you should hopefully see how you transaction starts and ends

* allow printing out of sql statements to see what statements are really executed

* i encourage you to get and see the petclinic example. it shows you many usefull things.

2. not to the problem -- you can use spring support for junit (its easy and well documented -- just derive your class not directly from TestCase but from AbstractDependencyInjectionSpringContextTests (or other base class suitable for your needs)) -- me myself wrote something very simple -- that speeds up the tests:

Code:

/**
 * <p>You may use this class as a base class for your JUnit test cases.  It
 * supports some nice features for spring:
 *
 * <ol>
 *
 * <li>Caching of application context between test case executions.
 *
 * <li>Access to your application context via <code>applicationContext</code>
 * instance variable.
 *
 * <li>Dependency injection by type for spring beans declared as properties in
 * your test case -- or simply do not declare getters/setters, override
 * <code>onSetUp()</code> and obtain the beans there (using {@link getBean}).
 *
 * </ol>
 */
public class SpringTestCaseBase
    extends AbstractDependencyInjectionSpringContextTests {

    /**
     * If reflection is used, the <code>name</code> should be the same as the
     * test method to be run.
     */
    public SpringTestCaseBase(String name) {
   super(name);
    }

    protected String[] getConfigLocations() {
   return new String[] { Beans.CTX_CONFIG };
    }

    protected Object getBean(String name) {
   return applicationContext.getBean(name);
    }
    
};

mauroyb0 · **Joined:** Wed Mar 21, 2007 10:23 am **Posts:** 20

Thank you very much for yout explanation. I have tried to look at the petclinic example and tried to mimik it, but have still some trouble. I have the following configuration :

Application context :

Code:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE beans PUBLIC "-//SPRING//DTD BEAN//EN"
    "http://www.springframework.org/dtd/spring-beans.dtd">

<beans>

 <!-- Hibernate data source -->
<bean id="dataSource" class="org.springframework.jdbc.datasource.DriverManagerDataSource">
        <property name="driverClassName"><value>org.hsqldb.jdbcDriver</value></property>
         <property name="url"><value>jdbc:hsqldb:/home/yannmauron/toxico_db</value></property>
        <property name="username"><value>sa</value></property>
        <property name="password"><value></value></property>

    </bean>


 <!-- Hibernate SessionFactory -->
<bean id="sessionFactory" class="org.springframework.orm.hibernate3.LocalSessionFactoryBean">
     <property name="dataSource"><ref local="dataSource"/></property>
    <property name="mappingResources">
        <list>
            <value>com/genebio/toxico/compound/CompoundImpl.hbm.xml</value>
        </list>
    </property>
    <property name="hibernateProperties">
    <props>
        <prop key="hibernate.dialect">org.hibernate.dialect.HSQLDialect</prop>
        <prop key="hibernate.show_sql">true</prop>
        <prop key="hibernate.hbm2ddl.auto">update</prop>
    </props>
    </property>
          <property name="eventListeners">
         <map>
            <entry key="merge">
               <bean class="org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener"/>
            </entry>
         </map>
      </property>
</bean>

<!-- Transaction manager for a single Hibernate SessionFactory (alternative to JTA) -->
<bean id="transactionManager" class="org.springframework.orm.hibernate3.HibernateTransactionManager">
<property name="sessionFactory"><ref local="sessionFactory"/></property>
</bean>

<bean id="compoundDAO" class="com.genebio.toxico.compound.CompoundDAOImpl">
<property name="sessionFactory"><ref local="sessionFactory"/></property>
</bean>

   <bean id="compound" class="org.springframework.transaction.interceptor.TransactionProxyFactoryBean">
      <property name="transactionManager"><ref local="transactionManager"/></property>
      <property name="target" ref="compoundDAO"/>
      <property name="transactionAttributes">
         <props>
            <prop key="*">PROPAGATION_REQUIRED</prop>
         </props>
      </property>
   </bean>
    
</beans>

DAO object (CompoundDAOImpl) :

Code:

package com.genebio.toxico.compound;

import com.genebio.toxico.compound.Compound;
import org.springframework.dao.DataAccessException;
import org.springframework.orm.hibernate3.support.HibernateDaoSupport;


public class CompoundDAOImpl extends HibernateDaoSupport implements CompoundDAO{

   public void saveCompound(CompoundImpl compound) throws DataAccessException {
      getHibernateTemplate().merge(compound);
   }

   public CompoundImpl getCompound(int id) {
      return (CompoundImpl) getHibernateTemplate().get(CompoundImpl.class, id);
   }

   public void removeCompound(int id) {
      Object compound = getHibernateTemplate().load(Compound.class, id);
      getHibernateTemplate().delete(compound);
   }
}

My test file :

Code:

package com.genebio.toxico.compound;

import org.junit.Test;
import org.springframework.context.ApplicationContext;
import org.springframework.context.support.ClassPathXmlApplicationContext;


public class CompoundImplDAOTest {

private CompoundImpl compoundImpl = null;
private CompoundDAO compoundDAO = null;
private ApplicationContext ctx = null;

   
   @Test
       public void testSaveRecord() throws Exception {
      
        compoundImpl = new CompoundImpl();
        compoundImpl.setId(1);
        compoundImpl.setCid("1234567");
        compoundImpl.setSMILE("lkjfdg");
       String[] paths = {"applicationContext.xml"};
       ctx = new ClassPathXmlApplicationContext(paths);
        compoundDAO = (CompoundDAO) ctx.getBean("compound");
        compoundDAO.saveCompound(compoundImpl);
         }
   
   @Test
    public void testloadRecord() throws Exception {
       String[] paths = {"applicationContext.xml"};
       ctx = new ClassPathXmlApplicationContext(paths);
        compoundDAO = (CompoundDAO) ctx.getBean("compound");
      CompoundImpl compound = compoundDAO.getCompound(2);
      System.out.println(compound.toString());
       }
   

   
}

But nothing is populate in my database within my test... I've tried to declare a transaction manager for my dao, but have certainly made a mistake... :-( Any idea ?

mauroyb0 · **Joined:** Wed Mar 21, 2007 10:23 am **Posts:** 20

Excuse me, for the information, I haves a framework of Spring version 2, and hibernate 3. I try to connect a HSQL db

mar · **Posted:** Mon Mar 26, 2007 5:21 pm

hi again,

im used to spring 1.2, but that does no difference.

to manage your transaction via transaction proxy you are doing the right thing. The steps are:

1. init the session factory and transaction manager -- you have it.

2. declare a transaction proxy -- you have it, though my declaration is like that (more simillar to petclinic example):

Code:

  <!--
  base transactional proxy, use it as a base for your transactional proxies
  -->
  <bean id="baseTransactionalProxy"
    abstract="true"
    class="org.springframework.transaction.interceptor.TransactionProxyFactoryBean">
    <property name="transactionManager" ref="transactionManager"/>
    <property name="target"><null/></property> <!-- override -->
    <property name="transactionAttributes">
      <props>
   <!-- carefull about properties getters -->
   <prop key="get*">PROPAGATION_REQUIRED,readOnly</prop>
   <prop key="find*">PROPAGATION_REQUIRED,readOnly</prop>
   <prop key="load*">PROPAGATION_REQUIRED,readOnly</prop>
   <prop key="save*">PROPAGATION_REQUIRED</prop>
   <prop key="persist*">PROPAGATION_REQUIRED</prop>
   <prop key="merge*">PROPAGATION_REQUIRED</prop>
   <prop key="delete*">PROPAGATION_REQUIRED</prop>
      </props>
    </property>
  </bean>

  <!--
  same as above, just ensures it uses CGLIB instead of default (dynamic)
  proxies, which is usefull for proxying classes rather than interfaces and
  ignores 'get*' methods
  -->
  <bean id="baseTransactionalProxyCglib"
    parent="baseTransactionalProxy"
    abstract="true"
    class="org.springframework.transaction.interceptor.TransactionProxyFactoryBean">
    <property name="transactionAttributes">
      <props>
   <!-- ignore properties getters -->
   <!--
   <prop key="get*">PROPAGATION_REQUIRED,readOnly</prop>   
   <prop key="get">PROPAGATION_REQUIRED,readOnly</prop>
   -->
   <prop key="find*">PROPAGATION_REQUIRED,readOnly</prop>
   <prop key="load*">PROPAGATION_REQUIRED,readOnly</prop>
   <prop key="save*">PROPAGATION_REQUIRED</prop>
   <prop key="persist*">PROPAGATION_REQUIRED</prop>
   <prop key="merge*">PROPAGATION_REQUIRED</prop>
   <prop key="delete*">PROPAGATION_REQUIRED</prop>
      </props>
    </property>
    <property name="proxyTargetClass" value="true"/>
  </bean>

the 1st proxy is used to proxy interfaces, the 2nd one is used to proxy classes, the second one is more general, but requires cglib in classpath

There are many other proxies defined in my spring context for various purposes. Note they are just abstract definitions and so they can be used elsewhere just by reference -- see below.

3. deploy your dao into the bean factory -- you have it, though the anming confused me.

Almost always i deploy non-transaction and transaction (proxied) version, like that:

Code:

  <!-- account -->
  <bean id="accountDao"
    class="cz.facility.facicash.app.core.AccountDaoImpl">
    <property name="sessionFactory" ref="sessionFactory"/>
    <property name="clazz"
      value="cz.facility.facicash.app.core.Account"/>
  </bean>

  <bean id="accountDaoProxy" parent="baseTransactionalProxy">
    <property name="target" ref="accountDao"/>
  </bean>

a) note that i use the 1st version of my proxy -- so only interface methods are proxied (as defined by proxy, only those starting with (get, load, save, persist, merge, find, delete))

b) you may ignore the clazz attribute -- it has nothing to do with the proxy and/or transaction, just for my own purposes

c) i use the parent definitions to save some typing

4. use in code -- you have it.

5. so where is the problem? :-)

To be honest, by reading your post i have no idea, probably some xml mistake. Pls, try:

a) Is there not any exception? (strange there is none)

b) enable logging and see what spring does underneath, it should show you how it creates and commits the transactions

your loggers of interests are (loglevel DEBUG):

org.springframework.orm.hibernate3
org.springframework.aop

c) try to obtain the session factory by hand and try to use the plain hibernate code to save the instance (obtain session from session factory and use session.save()) -- if problem, you have a hibernate problem --you may normally obtain SessionFactory by sf = (SessionFactory) ctx.get("sessionFactory")

d) try to use the programmtic transaction management -- i use simple class like this

Code:

public class TransactionWrapper {

    private ApplicationContext ctx;

    public TransactionWrapper(ApplicationContext ctx) {
   this.ctx = ctx;
    }

    public ApplicationContext getCtx() {
   return this.ctx;
    }

    public void setCtx(ApplicationContext ctx) {
   this.ctx = ctx;
    }

    public void execute(final HibernateCallback callback) {
   final SessionFactory sf = (SessionFactory)
       ctx.getBean("sessionFactory");
   AbstractPlatformTransactionManager txMng =
       (HibernateTransactionManager) ctx.getBean("transactionManager");
   TransactionTemplate txTmpl = new TransactionTemplate(txMng);

   txTmpl.execute(new TransactionCallbackWithoutResult() {
      public void doInTransactionWithoutResult(TransactionStatus
                      status) {
          new HibernateTemplate(sf).execute(callback);
      }
       });
    }
    
};

and than very simple inline classes like this to run in a separate tx:

Code:

   TransactionWrapper tx =
       new TransactionWrapper(Beans.getInstance().getCtx());
   tx.execute(new HibernateCallback() {
      public Object doInHibernate(Session session) {
          testSqlConnectionPropertries(session.connection());
          return null;
      }
       });

martin

mauroyb0 · **Joined:** Wed Mar 21, 2007 10:23 am **Posts:** 20

Thanks for your long answer... A last question before the next, how can I activate the loggers ?

and could it be a problem with the right or the installation of hsqldb ? is there any trap ?

mauroyb0 · **Joined:** Wed Mar 21, 2007 10:23 am **Posts:** 20

some hours latter... I have activated some log features and obtains that :

[code]
14:54:32,806 INFO CollectionFactory:73 - JDK 1.4+ collections available
14:54:32,810 INFO CollectionFactory:76 - Commons Collections 3.x available
14:54:32,856 DEBUG PluggableSchemaResolver:95 - Loading schema mappings from [META-INF/spring.schemas]
14:54:32,860 DEBUG PluggableSchemaResolver:101 - Loaded schema mappings: {http://www.springframework.org/schema/aop/spring-aop-2.0.xsd=org/springframework/aop/config/spring-aop-2.0.xsd, http://www.springframework.org/schema/util/spring-util.xsd=org/springframework/beans/factory/xml/spring-util-2.0.xsd, http://www.springframework.org/schema/util/spring-util-2.0.xsd=org/springframework/beans/factory/xml/spring-util-2.0.xsd, http://www.springframework.org/schema/jee/spring-jee.xsd=org/springframework/ejb/config/spring-jee-2.0.xsd, http://www.springframework.org/schema/beans/spring-beans.xsd=org/springframework/beans/factory/xml/spring-beans-2.0.xsd, http://www.springframework.org/schema/lang/spring-lang-2.0.xsd=org/springframework/scripting/config/spring-lang-2.0.xsd, http://www.springframework.org/schema/tx/spring-tx-2.0.xsd=org/springframework/transaction/config/spring-tx-2.0.xsd, http://www.springframework.org/schema/lang/spring-lang.xsd=org/springframework/scripting/config/spring-lang-2.0.xsd, http://www.springframework.org/schema/tool/spring-tool.xsd=org/springframework/beans/factory/xml/spring-tool-2.0.xsd, http://www.springframework.org/schema/aop/spring-aop.xsd=org/springframework/aop/config/spring-aop-2.0.xsd, http://www.springframework.org/schema/tx/spring-tx.xsd=org/springframework/transaction/config/spring-tx-2.0.xsd, http://www.springframework.org/schema/tool/spring-tool-2.0.xsd=org/springframework/beans/factory/xml/spring-tool-2.0.xsd, http://www.springframework.org/schema/jee/spring-jee-2.0.xsd=org/springframework/ejb/config/spring-jee-2.0.xsd, http://www.springframework.org/schema/beans/spring-beans-2.0.xsd=org/springframework/beans/factory/xml/spring-beans-2.0.xsd}
14:54:32,861 DEBUG PluggableSchemaResolver:95 - Loading schema mappings from [META-INF/spring.schemas]
14:54:32,864 DEBUG PluggableSchemaResolver:101 - Loaded schema mappings: {http://www.springframework.org/schema/aop/spring-aop-2.0.xsd=org/springframework/aop/config/spring-aop-2.0.xsd, http://www.springframework.org/schema/util/spring-util.xsd=org/springframework/beans/factory/xml/spring-util-2.0.xsd, http://www.springframework.org/schema/util/spring-util-2.0.xsd=org/springframework/beans/factory/xml/spring-util-2.0.xsd, http://www.springframework.org/schema/jee/spring-jee.xsd=org/springframework/ejb/config/spring-jee-2.0.xsd, http://www.springframework.org/schema/beans/spring-beans.xsd=org/springframework/beans/factory/xml/spring-beans-2.0.xsd, http://www.springframework.org/schema/lang/spring-lang-2.0.xsd=org/springframework/scripting/config/spring-lang-2.0.xsd, http://www.springframework.org/schema/tx/spring-tx-2.0.xsd=org/springframework/transaction/config/spring-tx-2.0.xsd, http://www.springframework.org/schema/lang/spring-lang.xsd=org/springframework/scripting/config/spring-lang-2.0.xsd, http://www.springframework.org/schema/tool/spring-tool.xsd=org/springframework/beans/factory/xml/spring-tool-2.0.xsd, http://www.springframework.org/schema/aop/spring-aop.xsd=org/springframework/aop/config/spring-aop-2.0.xsd, http://www.springframework.org/schema/tx/spring-tx.xsd=org/springframework/transaction/config/spring-tx-2.0.xsd, http://www.springframework.org/schema/tool/spring-tool-2.0.xsd=org/springframework/beans/factory/xml/spring-tool-2.0.xsd, http://www.springframework.org/schema/jee/spring-jee-2.0.xsd=org/springframework/ejb/config/spring-jee-2.0.xsd, http://www.springframework.org/schema/beans/spring-beans-2.0.xsd=org/springframework/beans/factory/xml/spring-beans-2.0.xsd}
14:54:32,873 INFO XmlBeanDefinitionReader:330 - Loading XML bean definitions from class path resource [applicationContext.xml]
14:54:32,879 DEBUG DefaultDocumentLoader:73 - Using JAXP provider [com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderFactoryImpl]
14:54:32,964 DEBUG BeansDtdResolver:72 - Found beans DTD [http://www.springframework.org/dtd/spring-beans.dtd] in classpath: spring-beans.dtd
14:54:33,002 DEBUG DefaultNamespaceHandlerResolver:110 - Loaded mappings [{http://www.springframework.org/schema/p=org.springframework.beans.factory.xml.SimplePropertyNamespaceHandler, http://www.springframework.org/schema/lang=org.springframework.scripting.config.LangNamespaceHandler, http://www.springframework.org/schema/jee=org.springframework.ejb.config.JeeNamespaceHandler, http://www.springframework.org/schema/aop=org.springframework.aop.config.AopNamespaceHandler, http://www.springframework.org/schema/util=org.springframework.beans.factory.xml.UtilNamespaceHandler, http://www.springframework.org/schema/tx=org.springframework.transaction.config.TxNamespaceHandler}]
14:54:33,008 DEBUG ClassUtils:134 - Class [groovy.lang.GroovyObject] or one of its dependencies is not present: java.lang.ClassNotFoundException: groovy.lang.GroovyObject
14:54:33,012 DEBUG ClassUtils:134 - Class [org.jruby.IRuby] or one of its dependencies is not present: java.lang.ClassNotFoundException: org.jruby.IRuby
14:54:33,014 DEBUG ClassUtils:134 - Class [bsh.Interpreter] or one of its dependencies is not present: java.lang.ClassNotFoundException: bsh.Interpreter
14:54:33,060 DEBUG DefaultBeanDefinitionDocumentReader:84 - Loading bean definitions
14:54:33,109 DEBUG BeanDefinitionParserDelegate:350 - Neither XML 'id' nor 'name' specified - using generated bean name [org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener#388993]
14:54:33,114 DEBUG XmlBeanDefinitionReader:143 - Loaded 5 bean definitions from location pattern [applicationContext.xml]
14:54:33,115 INFO ClassPathXmlApplicationContext:100 - Bean factory for application context [org.springframework.context.support.ClassPathXmlApplicationContext;hashCode=29855319]: org.springframework.beans.factory.support.DefaultListableBeanFactory defining beans [dataSource,sessionFactory,transactionManager,compoundDAO,compound]; root of BeanFactory hierarchy
14:54:33,126 INFO ClassPathXmlApplicationContext:322 - 5 beans defined in application context [org.springframework.context.support.ClassPathXmlApplicationContext;hashCode=29855319]
14:54:33,168 INFO ClassPathXmlApplicationContext:473 - Unable to locate MessageSource with name 'messageSource': using default [org.springframework.context.support.DelegatingMessageSource@ef5502]
14:54:33,174 INFO ClassPathXmlApplicationContext:495 - Unable to locate ApplicationEventMulticaster with name 'applicationEventMulticaster': using default [org.springframework.context.event.SimpleApplicationEventMulticaster@1ce2dd4]
14:54:33,176 INFO DefaultListableBeanFactory:261 - Pre-instantiating singletons in factory [org.springframework.beans.factory.support.DefaultListableBeanFactory defining beans [dataSource,sessionFactory,transactionManager,compoundDAO,compound]; root of BeanFactory hierarchy]
14:54:33,180 DEBUG DefaultListableBeanFactory:137 - Creating shared instance of singleton bean 'dataSource'
14:54:33,181 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'dataSource' with merged definition [Root bean: class [org.springframework.jdbc.datasource.DriverManagerDataSource]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
14:54:33,230 DEBUG DefaultListableBeanFactory:397 - Eagerly caching bean 'dataSource' to allow for resolving potential circular references
14:54:33,257 INFO DriverManagerDataSource:155 - Loaded JDBC driver: org.hsqldb.jdbcDriver
14:54:33,265 DEBUG DefaultListableBeanFactory:137 - Creating shared instance of singleton bean 'sessionFactory'
14:54:33,266 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'sessionFactory' with merged definition [Root bean: class [org.springframework.orm.hibernate3.LocalSessionFactoryBean]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
14:54:33,307 DEBUG DefaultListableBeanFactory:397 - Eagerly caching bean 'sessionFactory' to allow for resolving potential circular references
14:54:33,308 DEBUG DefaultListableBeanFactory:202 - Returning cached instance of singleton bean 'dataSource'
14:54:33,309 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener#388993' with merged definition [Root bean: class [org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
14:54:33,352 DEBUG DefaultListableBeanFactory:1116 - Invoking afterPropertiesSet() on bean with name 'sessionFactory'
14:54:33,371 INFO Environment:500 - Hibernate 3.2.1
14:54:33,375 INFO Environment:533 - hibernate.properties not found
14:54:33,379 INFO Environment:667 - Bytecode provider name : cglib
14:54:33,400 INFO Environment:584 - using JDK 1.4 java.sql.Timestamp handling
14:54:33,530 DEBUG DTDEntityResolver:38 - trying to resolve system-id [http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd]
14:54:33,532 DEBUG DTDEntityResolver:40 - recognized hibernate namespace; attempting to resolve on classpath under org/hibernate/
14:54:33,535 DEBUG DTDEntityResolver:50 - located [http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd] in classpath
14:54:33,692 INFO HbmBinder:300 - Mapping class: com.genebio.toxico.compound.CompoundImpl -> COMPOUND
14:54:33,701 DEBUG HbmBinder:1270 - Mapped property: id -> COMPOUND_ID
14:54:33,714 DEBUG HbmBinder:1270 - Mapped property: cid -> COMPOUND_CID
14:54:33,715 DEBUG HbmBinder:1270 - Mapped property: SMILE -> COMPOUND_SMILE
14:54:33,715 INFO LocalSessionFactoryBean:742 - Building new Hibernate SessionFactory
14:54:33,716 DEBUG Configuration:1282 - Preparing to build session factory with filters : {}
14:54:33,716 DEBUG Configuration:1117 - processing extends queue
14:54:33,717 DEBUG Configuration:1121 - processing collection mappings
14:54:33,717 DEBUG Configuration:1132 - processing native query and ResultSetMapping mappings
14:54:33,720 DEBUG Configuration:1140 - processing association property references
14:54:33,720 DEBUG Configuration:1162 - processing foreign key constraints
14:54:33,807 INFO ConnectionProviderFactory:72 - Initializing connection provider: org.springframework.orm.hibernate3.LocalDataSourceConnectionProvider
14:54:33,819 DEBUG DriverManagerDataSource:289 - Creating new JDBC Connection to [jdbc:hsqldb:file:data/toxico]
14:54:34,109 INFO SettingsFactory:81 - RDBMS: HSQL Database Engine, version: 1.8.0
14:54:34,110 INFO SettingsFactory:82 - JDBC driver: HSQL Database Engine Driver, version: 1.8.0
14:54:34,134 INFO Dialect:151 - Using dialect: org.hibernate.dialect.HSQLDialect
14:54:34,141 INFO TransactionFactoryFactory:31 - Using default transaction strategy (direct JDBC transactions)
14:54:34,144 INFO TransactionManagerLookupFactory:33 - No TransactionManagerLookup configured (in JTA environment, use of read-write or transactional second-level cache is not recommended)
14:54:34,144 INFO SettingsFactory:134 - Automatic flush during beforeCompletion(): disabled
14:54:34,145 INFO SettingsFactory:138 - Automatic session close at end of transaction: disabled
14:54:34,145 INFO SettingsFactory:145 - JDBC batch size: 15
14:54:34,146 INFO SettingsFactory:148 - JDBC batch updates for versioned data: disabled
14:54:34,147 INFO SettingsFactory:153 - Scrollable result sets: enabled
14:54:34,150 DEBUG SettingsFactory:157 - Wrap result sets: disabled
14:54:34,150 INFO SettingsFactory:161 - JDBC3 getGeneratedKeys(): disabled
14:54:34,150 INFO SettingsFactory:169 - Connection release mode: on_close
14:54:34,151 INFO SettingsFactory:196 - Default batch fetch size: 1
14:54:34,151 INFO SettingsFactory:200 - Generate SQL with comments: disabled
14:54:34,152 INFO SettingsFactory:204 - Order SQL updates by primary key: disabled
14:54:34,152 INFO SettingsFactory:369 - Query translator: org.hibernate.hql.ast.ASTQueryTranslatorFactory
14:54:34,155 INFO ASTQueryTranslatorFactory:24 - Using ASTQueryTranslatorFactory
14:54:34,156 INFO SettingsFactory:212 - Query language substitutions: {}
14:54:34,156 INFO SettingsFactory:217 - JPA-QL strict compliance: disabled
14:54:34,158 INFO SettingsFactory:222 - Second-level cache: enabled
14:54:34,158 INFO SettingsFactory:226 - Query cache: disabled
14:54:34,159 INFO SettingsFactory:356 - Cache provider: org.hibernate.cache.NoCacheProvider
14:54:34,159 INFO SettingsFactory:241 - Optimize cache for minimal puts: disabled
14:54:34,160 INFO SettingsFactory:250 - Structured second-level cache entries: disabled
14:54:34,174 INFO SettingsFactory:270 - Echoing all SQL to stdout
14:54:34,174 INFO SettingsFactory:277 - Statistics: disabled
14:54:34,175 INFO SettingsFactory:281 - Deleted entity synthetic identifier rollback: disabled
14:54:34,175 INFO SettingsFactory:296 - Default entity-mode: pojo
14:54:34,210 INFO SessionFactoryImpl:161 - building session factory
14:54:34,211 DEBUG SessionFactoryImpl:173 - Session factory constructed with filter configurations : {}
14:54:34,212 DEBUG SessionFactoryImpl:177 - instantiating session factory with properties: {java.runtime.name=Java(TM) SE Runtime Environment, sun.boot.library.path=/usr/java/jdk1.6.0_01/jre/lib/i386, java.vm.version=1.6.0_01-ea-b03, java.vm.vendor=Sun Microsystems Inc., java.vendor.url=http://java.sun.com/, path.separator=:, java.vm.name=Java HotSpot(TM) Client VM, file.encoding.pkg=sun.io, user.country=US, sun.java.launcher=SUN_STANDARD, sun.os.patch.level=unknown, java.vm.specification.name=Java Virtual Machine Specification, user.dir=/home/yannmauron/Desktop/test/ToxicoMSJava2, java.runtime.version=1.6.0_01-ea-b03, java.awt.graphicsenv=sun.awt.X11GraphicsEnvironment, java.endorsed.dirs=/usr/java/jdk1.6.0_01/jre/lib/endorsed, os.arch=i386, java.io.tmpdir=/tmp, line.separator=
, java.vm.specification.vendor=Sun Microsystems Inc., os.name=Linux, sun.jnu.encoding=UTF-8, java.library.path=/usr/java/jdk1.6.0_01/jre/lib/i386/client:/usr/java/jdk1.6.0_01/jre/lib/i386:/usr/java/jdk1.6.0_01/jre/../lib/i386:/usr/lib/j2se/1.4/jre/lib/i386/client:/usr/lib/j2se/1.4/jre/lib/i386:/usr/lib/j2se/1.4/jre/../lib/i386:/usr/lib/firefox/:/usr/java/packages/lib/i386:/lib:/usr/lib, java.specification.name=Java Platform API Specification, java.class.version=50.0, sun.management.compiler=HotSpot Client Compiler, os.version=2.6.17-11-generic, user.home=/home/yannmauron, user.timezone=Europe/Zurich, hibernate.connection.release_mode=on_close, java.awt.printerjob=sun.print.PSPrinterJob, file.encoding=UTF-8, java.specification.version=1.6, user.name=yannmauron, java.class.path=/home/yannmauron/Desktop/test/ToxicoMSJava2/bin:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/cdk-0.99.1.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/commons-logging-1.1.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/dom4j-1.6.1.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/jaxen-1.1-beta-6.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/junit-4.2.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/log4j-1.2.14.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/ProteomeCommons.org-IO.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/ProteomeCommons.org-IO-T2D.jar:/home/yannmauron/java/hsqldb.jar:/home/yannmauron/java/spring-framework-2.0.2/dist/spring.jar:/home/yannmauron/java/spring-framework-2.0.2/dist/spring-aspects.jar:/home/yannmauron/java/spring-framework-2.0.2/dist/spring-mock.jar:/home/yannmauron/java/spring-framework-2.0.2/dist/spring-src.zip:/home/yannmauron/java/spring-framework-2.0.2/lib/j2ee/jta.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/cglib/cglib-nodep-2.1_3.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/hibernate/jboss-archive-browsing.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/hibernate/hibernate3.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/jakarta-commons/commons-collections.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/log4j/log4j-1.2.14.jar:/home/yannmauron/Desktop/eclipse conf/eclipse/configuration/org.eclipse.osgi/bundles/228/1/.cp/:/home/yannmauron/Desktop/eclipse conf/eclipse/plugins/org.eclipse.jdt.junit_3.2.1.r321_v20060810/junitsupport.jar:/home/yannmauron/Desktop/eclipse conf/eclipse/plugins/org.eclipse.jdt.junit.runtime_3.2.1.r321_v20060721/junitruntime.jar, hibernate.bytecode.use_reflection_optimizer=false, hibernate.show_sql=true, java.vm.specification.version=1.0, sun.arch.data.model=32, java.home=/usr/java/jdk1.6.0_01/jre, hibernate.dialect=org.hibernate.dialect.HSQLDialect, java.specification.vendor=Sun Microsystems Inc., user.language=en, java.vm.info=mixed mode, sharing, java.version=1.6.0_01-ea, java.ext.dirs=/usr/java/jdk1.6.0_01/jre/lib/ext:/usr/java/packages/lib/ext, sun.boot.class.path=/usr/java/jdk1.6.0_01/jre/lib/resources.jar:/usr/java/jdk1.6.0_01/jre/lib/rt.jar:/usr/java/jdk1.6.0_01/jre/lib/sunrsasign.jar:/usr/java/jdk1.6.0_01/jre/lib/jsse.jar:/usr/java/jdk1.6.0_01/jre/lib/jce.jar:/usr/java/jdk1.6.0_01/jre/lib/charsets.jar:/usr/java/jdk1.6.0_01/jre/classes, java.vendor=Sun Microsystems Inc., file.separator=/, java.vendor.url.bug=http://java.sun.com/cgi-bin/bugreport.cgi, hibernate.connection.provider_class=org.springframework.orm.hibernate3.LocalDataSourceConnectionProvider, sun.cpu.endian=little, sun.io.unicode.encoding=UnicodeLittle, sun.desktop=gnome, sun.cpu.isalist=}
14:54:34,543 DEBUG AbstractEntityPersister:2688 - Static SQL for entity: com.genebio.toxico.compound.CompoundImpl
14:54:34,544 DEBUG AbstractEntityPersister:2693 - Version select: select COMPOUND_ID from COMPOUND where COMPOUND_ID =?
14:54:34,544 DEBUG AbstractEntityPersister:2696 - Snapshot select: select compoundim_.COMPOUND_ID, compoundim_.COMPOUND_CID as COMPOUND2_0_, compoundim_.COMPOUND_SMILE as COMPOUND3_0_ from COMPOUND compoundim_ where compoundim_.COMPOUND_ID=?
14:54:34,547 DEBUG AbstractEntityPersister:2699 - Insert 0: insert into COMPOUND (COMPOUND_CID, COMPOUND_SMILE, COMPOUND_ID) values (?, ?, ?)
14:54:34,547 DEBUG AbstractEntityPersister:2700 - Update 0: update COMPOUND set COMPOUND_CID=?, COMPOUND_SMILE=? where COMPOUND_ID=?
14:54:34,548 DEBUG AbstractEntityPersister:2701 - Delete 0: delete from COMPOUND where COMPOUND_ID=?
14:54:34,574 DEBUG EntityLoader:79 - Static select for entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_0_0_, compoundim0_.COMPOUND_CID as COMPOUND2_0_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_0_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
14:54:34,575 DEBUG EntityLoader:79 - Static select for entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_0_0_, compoundim0_.COMPOUND_CID as COMPOUND2_0_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_0_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
14:54:34,575 DEBUG EntityLoader:79 - Static select for entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_0_0_, compoundim0_.COMPOUND_CID as COMPOUND2_0_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_0_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
14:54:34,578 DEBUG EntityLoader:79 - Static select for entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_0_0_, compoundim0_.COMPOUND_CID as COMPOUND2_0_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_0_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
14:54:34,578 DEBUG EntityLoader:79 - Static select for entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_0_0_, compoundim0_.COMPOUND_CID as COMPOUND2_0_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_0_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
14:54:34,588 DEBUG EntityLoader:34 - Static select for action ACTION_MERGE on entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_0_0_, compoundim0_.COMPOUND_CID as COMPOUND2_0_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_0_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
14:54:34,589 DEBUG EntityLoader:34 - Static select for action ACTION_REFRESH on entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_0_0_, compoundim0_.COMPOUND_CID as COMPOUND2_0_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_0_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
14:54:34,592 DEBUG SessionFactoryObjectFactory:39 - initializing class SessionFactoryObjectFactory
14:54:34,595 DEBUG SessionFactoryObjectFactory:76 - registered: ff8081811193764701119376495e0000 (unnamed)
14:54:34,596 INFO SessionFactoryObjectFactory:82 - Not binding factory to JNDI, no JNDI name configured
14:54:34,603 DEBUG SessionFactoryImpl:308 - instantiated session factory
14:54:34,603 DEBUG SessionFactoryImpl:390 - Checking 0 named HQL queries
14:54:34,604 DEBUG SessionFactoryImpl:410 - Checking 0 named SQL queries
14:54:34,636 DEBUG DefaultListableBeanFactory:137 - Creating shared instance of singleton bean 'transactionManager'
14:54:34,636 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'transactionManager' with merged definition [Root bean: class [org.springframework.orm.hibernate3.HibernateTransactionManager]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
14:54:34,665 DEBUG DefaultListableBeanFactory:397 - Eagerly caching bean 'transactionManager' to allow for resolving potential circular references
14:54:34,666 DEBUG DefaultListableBeanFactory:202 - Returning cached instance of singleton bean 'sessionFactory'
14:54:34,668 DEBUG DefaultListableBeanFactory:1116 - Invoking afterPropertiesSet() on bean with name 'transactionManager'
14:54:34,695 INFO HibernateTransactionManager:373 - Using DataSource [org.springframework.jdbc.datasource.DriverManagerDataSource@edf389] of Hibernate SessionFactory for HibernateTransactionManager
14:54:34,706 DEBUG DefaultListableBeanFactory:137 - Creating shared instance of singleton bean 'compoundDAO'
14:54:34,706 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'compoundDAO' with merged definition [Root bean: class [com.genebio.toxico.compound.CompoundDAOImpl]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
14:54:34,715 DEBUG DefaultListableBeanFactory:397 - Eagerly caching bean 'compoundDAO' to allow for resolving potential circular references
14:54:34,715 DEBUG DefaultListableBeanFactory:202 - Returning cached instance of singleton bean 'sessionFactory'
14:54:34,719 DEBUG DefaultListableBeanFactory:1116 - Invoking afterPropertiesSet() on bean with name 'compoundDAO'
14:54:34,719 DEBUG DefaultListableBeanFactory:137 - Creating shared instance of singleton bean 'compound'
14:54:34,720 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'compound' with merged definition [Root bean: class [org.springframework.transaction.interceptor.TransactionProxyFactoryBean]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
14:54:34,729 INFO DefaultAopProxyFactory:61 - CGLIB2 available: proxyTargetClass feature enabled
14:54:34,764 DEBUG DefaultListableBeanFactory:397 - Eagerly caching bean 'compound' to allow for resolving potential circular references
14:54:34,765 DEBUG DefaultListableBeanFactory:202 - Returning cached instance of singleton bean 'transactionManager'
14:54:34,766 DEBUG DefaultListableBeanFactory:202 - Returning cached instance of singleton bean 'compoundDAO'
14:54:34,779 DEBUG NameMatchTransactionAttributeSource:108 - Adding transactional method [*] with attribute [PROPAGATION_REQUIRED,ISOLATION_DEFAULT]
14:54:34,782 DEBUG NameMatchTransactionAttributeSource:108 - Adding transactional method [find*] with attribute [PROPAGATION_REQUIRED,ISOLATION_DEFAULT,readOnly]
14:54:34,783 DEBUG NameMatchTransactionAttributeSource:108 - Adding transactional method [merge*] with attribute [PROPAGATION_REQUIRED,ISOLATION_DEFAULT]
14:54:34,784 DEBUG NameMatchTransactionAttributeSource:108 - Adding transactional method [delete*] with attribute [PROPAGATION_REQUIRED,ISOLATION_DEFAULT]
14:54:34,785 DEBUG NameMatchTransactionAttributeSource:108 - Adding transactional method [persist*] with attribute [PROPAGATION_REQUIRED,ISOLATION_DEFAULT]
14:54:34,786 DEBUG NameMatchTransactionAttributeSource:108 - Adding transactional method [load*] with attribute [PROPAGATION_REQUIRED,ISOLATION_DEFAULT,readOnly]
14:54:34,787 DEBUG NameMatchTransactionAttributeSource:108 - Adding transactional method [save*] with attribute [PROPAGATION_REQUIRED,ISOLATION_DEFAULT]
14:54:34,788 DEBUG DefaultListableBeanFactory:1116 - Invoking afterPropertiesSet() on bean with name 'compound'
14:54:34,815 DEBUG ProxyFactory:217 - Added new aspect interface: com.genebio.toxico.compound.CompoundDAO
14:54:34,816 DEBUG ProxyFactory:217 - Added new aspect interface: org.springframework.beans.factory.InitializingBean
14:54:34,823 DEBUG JdkDynamicAopProxy:110 - Creating JDK dynamic proxy for [com.genebio.toxico.compound.CompoundDAOImpl]
14:54:34,843 DEBUG ClassPathXmlApplicationContext:239 - Publishing event in context [org.springframework.context.support.ClassPathXmlApplicationContext;hashCode=29855319]: org.springframework.context.event.ContextRefreshedEvent[source=org.springframework.context.support.ClassPathXmlApplicationContext: display name [org.springframework.context.support.ClassPathXmlApplicationContext;hashCode=29855319]; startup date [Tue Mar 27 14:54:32 CEST 2007]; root of context hierarchy]
14:54:34,844 DEBUG DefaultListableBeanFactory:202 - Returning cached instance of singleton bean 'compound'
14:54:34,869 DEBUG HibernateTransactionManager:319 - Using transaction object [org.springframework.orm.hibernate3.HibernateTransactionManager$HibernateTransactionObject@1f4e571]
14:54:34,870 DEBUG HibernateTransactionManager:347 - Creating new transaction with name [com.genebio.toxico.compound.CompoundDAO.saveCompound]: PROPAGATION_REQUIRED,ISOLATION_DEFAULT
14:54:34,910 DEBUG SessionImpl:220 - opened session at timestamp: 11750000748
14:54:34,910 DEBUG HibernateTransactionManager:428 - Opened new Session [org.hibernate.impl.SessionImpl@1e1be92] for Hibernate transaction
14:54:34,919 DEBUG HibernateTransactionManager:440 - Preparing JDBC Connection of Hibernate Session [org.hibernate.impl.SessionImpl@1e1be92]
14:54:34,952 DEBUG JDBCTransaction:54 - begin
14:54:34,954 DEBUG ConnectionManager:415 - opening JDBC connection
14:54:34,954 DEBUG DriverManagerDataSource:289 - Creating new JDBC Connection to [jdbc:hsqldb:file:data/toxico]
14:54:34,955 DEBUG JDBCTransaction:59 - current autocommit status: true
14:54:34,955 DEBUG JDBCTransaction:62 - disabling autocommit
14:54:34,958 DEBUG HibernateTransactionManager:511 - Exposing Hibernate transaction as JDBC transaction [org.hsqldb.jdbc.jdbcConnection@1989b5]
14:54:34,960 DEBUG TransactionSynchronizationManager:166 - Bound value [org.springframework.jdbc.datasource.ConnectionHolder@c3c315] for key [org.springframework.jdbc.datasource.DriverManagerDataSource@edf389] to thread [main]
14:54:34,960 DEBUG TransactionSynchronizationManager:166 - Bound value [org.springframework.orm.hibernate3.SessionHolder@1328c7a] for key [org.hibernate.impl.SessionFactoryImpl@1a4ded3] to thread [main]
14:54:34,961 DEBUG TransactionSynchronizationManager:219 - Initializing transaction synchronization
14:54:34,963 DEBUG TransactionInterceptor:275 - Getting transaction for [com.genebio.toxico.compound.CompoundDAO.saveCompound]
14:54:34,964 DEBUG TransactionSynchronizationManager:139 - Retrieved value [org.springframework.orm.hibernate3.SessionHolder@1328c7a] for key [org.hibernate.impl.SessionFactoryImpl@1a4ded3] bound to thread [main]
14:54:34,965 DEBUG TransactionSynchronizationManager:139 - Retrieved value [org.springframework.orm.hibernate3.SessionHolder@1328c7a] for key [org.hibernate.impl.SessionFactoryImpl@1a4ded3] bound to thread [main]
14:54:34,965 DEBUG HibernateTemplate:359 - Found thread-bound Session for HibernateTemplate
14:54:34,971 DEBUG AbstractBatcher:358 - about to open PreparedStatement (open PreparedStatements: 0, globally: 0)
14:54:34,972 DEBUG SQL:393 - select compoundim_.COMPOUND_ID, compoundim_.COMPOUND_CID as COMPOUND2_0_, compoundim_.COMPOUND_SMILE as COMPOUND3_0_ from COMPOUND compoundim_ where compoundim_.COMPOUND_ID=?
Hibernate: select compoundim_.COMPOUND_ID, compoundim_.COMPOUND_CID as COMPOUND2_0_, compoundim_.COMPOUND_SMILE as COMPOUND3_0_ from COMPOUND compoundim_ where compoundim_.COMPOUND_ID=?
14:54:34,986 DEBUG AbstractBatcher:366 - about to close PreparedStatement (open PreparedStatements: 1, globally: 1)
14:54:34,987 DEBUG AbstractSaveEventListener:113 - generated identifier: 3, using strategy: org.hibernate.id.Assigned
14:54:35,005 DEBUG HibernateTemplate:383 - Not closing pre-bound Hibernate Session after HibernateTemplate
14:54:35,007 DEBUG TransactionSynchronizationManager:139 - Retrieved value [org.springframework.orm.hibernate3.SessionHolder@1328c7a] for key [org.hibernate.impl.SessionFactoryImpl@1a4ded3] bound to thread [main]
14:54:35,008 DEBUG TransactionSynchronizationManager:139 - Retrieved value [org.springframework.orm.hibernate3.SessionHolder@1328c7a] for key [org.hibernate.impl.SessionFactoryImpl@1a4ded3] bound to thread [main]
14:54:35,008 DEBUG HibernateTemplate:359 - Found thread-bound Session for HibernateTemplate
14:54:35,011 DEBUG AbstractFlushingEventListener:111 - processing flush-time cascades
14:54:35,013 DEBUG AbstractFlushingEventListener:154 - dirty checking collections
14:54:35,022 DEBUG AbstractFlushingEventListener:85 - Flushed: 1 insertions, 0 updates, 0 deletions to 1 objects
14:54:35,024 DEBUG AbstractFlushingEventListener:91 - Flushed: 0 (re)creations, 0 updates, 0 removals to 0 collections
14:54:35,027 DEBUG Printer:83 - listing entities:
14:54:35,028 DEBUG Printer:90 - com.genebio.toxico.compound.CompoundImpl{id=3, SMILE=lkjfdg, cid=1234567}
14:54:35,034 DEBUG AbstractBatcher:358 - about to open PreparedStatement (open PreparedStatements: 0, globally: 0)
14:54:35,034 DEBUG SQL:393 - insert into COMPOUND (COMPOUND_CID, COMPOUND_SMILE, COMPOUND_ID) values (?, ?, ?)
Hibernate: insert into COMPOUND (COMPOUND_CID, COMPOUND_SMILE, COMPOUND_ID) values (?, ?, ?)
14:54:35,036 DEBUG AbstractBatcher:44 - Executing batch size: 1
14:54:35,037 DEBUG AbstractBatcher:366 - about to close PreparedStatement (open PreparedStatements: 1, globally: 1)
14:54:35,038 DEBUG HibernateTemplate:383 - Not closing pre-bound Hibernate Session after HibernateTemplate
14:54:35,040 DEBUG TransactionInterceptor:305 - Completing transaction for [com.genebio.toxico.compound.CompoundDAO.saveCompound]
14:54:35,040 DEBUG HibernateTransactionManager:819 - Triggering beforeCommit synchronization
14:54:35,042 DEBUG HibernateTransactionManager:832 - Triggering beforeCompletion synchronization
14:54:35,042 DEBUG HibernateTransactionManager:652 - Initiating transaction commit
14:54:35,043 DEBUG HibernateTransactionManager:558 - Committing Hibernate transaction on Session [org.hibernate.impl.SessionImpl@1e1be92]
14:54:35,043 DEBUG JDBCTransaction:103 - commit
14:54:35,044 DEBUG AbstractFlushingEventListener:111 - processing flush-time cascades
14:54:35,044 DEBUG AbstractFlushingEventListener:154 - dirty checking collections
14:54:35,045 DEBUG AbstractFlushingEventListener:85 - Flushed: 0 insertions, 0 updates, 0 deletions to 1 objects
14:54:35,053 DEBUG AbstractFlushingEventListener:91 - Flushed: 0 (re)creations, 0 updates, 0 removals to 0 collections
14:54:35,054 DEBUG Printer:83 - listing entities:
14:54:35,055 DEBUG Printer:90 - com.genebio.toxico.compound.CompoundImpl{id=3, SMILE=lkjfdg, cid=1234567}
14:54:35,056 DEBUG JDBCTransaction:193 - re-enabling autocommit
14:54:35,059 DEBUG JDBCTransaction:116 - committed JDBC Connection
14:54:35,060 DEBUG ConnectionManager:296 - transaction completed on session with on_close connection release mode; be sure to close the session to release JDBC resources!
14:54:35,061 DEBUG HibernateTransactionManager:845 - Triggering afterCommit synchronization
14:54:35,062 DEBUG HibernateTransactionManager:861 - Triggering afterCompletion synchronization
14:54:35,062 DEBUG TransactionSynchronizationManager:272 - Clearing transaction synchronization
14:54:35,063 DEBUG TransactionSynchronizationManager:190 - Removed value [org.springframework.orm.hibernate3.SessionHolder@1328c7a] for key [org.hibernate.impl.SessionFactoryImpl@1a4ded3] from thread [main]
14:54:35,064 DEBUG TransactionSynchronizationManager:190 - Removed value [org.springframework.jdbc.datasource.ConnectionHolder@c3c315] for key [org.springframework.jdbc.datasource.DriverManagerDataSource@edf389] from thread [main]
14:54:35,065 DEBUG HibernateTransactionManager:637 - Closing Hibernate Session [org.hibernate.impl.SessionImpl@1e1be92] after transaction
14:54:35,066 DEBUG SessionFactoryUtils:781 - Closing Hibernate Session
14:54:35,066 DEBUG ConnectionManager:435 - releasing JDBC connection [ (open PreparedStatements: 0, globally: 0) (open ResultSets: 0, globally: 0)]
14:54:35,069 DEBUG ConnectionManager:296 - transaction completed on session with on_close connection release mode; be sure to close the session to release JDBC resources!
14:54:35,072 DEBUG PluggableSchemaResolver:95 - Loading schema mappings from [META-INF/spring.schemas]
14:54:35,076 DEBUG PluggableSchemaResolver:101 - Loaded schema mappings: {http://www.springframework.org/schema/aop/spring-aop-2.0.xsd=org/springframework/aop/config/spring-aop-2.0.xsd, http://www.springframework.org/schema/util/spring-util.xsd=org/springframework/beans/factory/xml/spring-util-2.0.xsd, http://www.springframework.org/schema/util/spring-util-2.0.xsd=org/springframework/beans/factory/xml/spring-util-2.0.xsd, http://www.springframework.org/schema/jee/spring-jee.xsd=org/springframework/ejb/config/spring-jee-2.0.xsd, http://www.springframework.org/schema/beans/spring-beans.xsd=org/springframework/beans/factory/xml/spring-beans-2.0.xsd, http://www.springframework.org/schema/lang/spring-lang-2.0.xsd=org/springframework/scripting/config/spring-lang-2.0.xsd, http://www.springframework.org/schema/tx/spring-tx-2.0.xsd=org/springframework/transaction/config/spring-tx-2.0.xsd, http://www.springframework.org/schema/lang/spring-lang.xsd=org/springframework/scripting/config/spring-lang-2.0.xsd, http://www.springframework.org/schema/tool/spring-tool.xsd=org/springframework/beans/factory/xml/spring-tool-2.0.xsd, http://www.springframework.org/schema/aop/spring-aop.xsd=org/springframework/aop/config/spring-aop-2.0.xsd, http://www.springframework.org/schema/tx/spring-tx.xsd=org/springframework/transaction/config/spring-tx-2.0.xsd, http://www.springframework.org/schema/tool/spring-tool-2.0.xsd=org/springframework/beans/factory/xml/spring-tool-2.0.xsd, http://www.springframework.org/schema/jee/spring-jee-2.0.xsd=org/springframework/ejb/config/spring-jee-2.0.xsd, http://www.springframework.org/schema/beans/spring-beans-2.0.xsd=org/springframework/beans/factory/xml/spring-beans-2.0.xsd}
14:54:35,076 DEBUG PluggableSchemaResolver:95 - Loading schema mappings from [META-INF/spring.schemas]
14:54:35,078 DEBUG PluggableSchemaResolver:101 - Loaded schema mappings: {http://www.springframework.org/schema/aop/spring-aop-2.0.xsd=org/springframework/aop/config/spring-aop-2.0.xsd, http://www.springframework.org/schema/util/spring-util.xsd=org/springframework/beans/factory/xml/spring-util-2.0.xsd, http://www.springframework.org/schema/util/spring-util-2.0.xsd=org/springframework/beans/factory/xml/spring-util-2.0.xsd, http://www.springframework.org/schema/jee/spring-jee.xsd=org/springframework/ejb/config/spring-jee-2.0.xsd, http://www.springframework.org/schema/beans/spring-beans.xsd=org/springframework/beans/factory/xml/spring-beans-2.0.xsd, http://www.springframework.org/schema/lang/spring-lang-2.0.xsd=org/springframework/scripting/config/spring-lang-2.0.xsd, http://www.springframework.org/schema/tx/spring-tx-2.0.xsd=org/springframework/transaction/config/spring-tx-2.0.xsd, http://www.springframework.org/schema/lang/spring-lang.xsd=org/springframework/scripting/config/spring-lang-2.0.xsd, http://www.springframework.org/schema/tool/spring-tool.xsd=org/springframework/beans/factory/xml/spring-tool-2.0.xsd, http://www.springframework.org/schema/aop/spring-aop.xsd=org/springframework/aop/config/spring-aop-2.0.xsd, http://www.springframework.org/schema/tx/spring-tx.xsd=org/springframework/transaction/config/spring-tx-2.0.xsd, http://www.springframework.org/schema/tool/spring-tool-2.0.xsd=org/springframework/beans/factory/xml/spring-tool-2.0.xsd, http://www.springframework.org/schema/jee/spring-jee-2.0.xsd=org/springframework/ejb/config/spring-jee-2.0.xsd, http://www.springframework.org/schema/beans/spring-beans-2.0.xsd=org/springframework/beans/factory/xml/spring-beans-2.0.xsd}
14:54:35,079 INFO XmlBeanDefinitionReader:330 - Loading XML bean definitions from class path resource [applicationContext.xml]
14:54:35,081 DEBUG DefaultDocumentLoader:73 - Using JAXP provider [com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderFactoryImpl]
14:54:35,087 DEBUG BeansDtdResolver:72 - Found beans DTD [http://www.springframework.org/dtd/spring-beans.dtd] in classpath: spring-beans.dtd
14:54:35,107 DEBUG DefaultNamespaceHandlerResolver:110 - Loaded mappings [{http://www.springframework.org/schema/p=org.springframework.beans.factory.xml.SimplePropertyNamespaceHandler, http://www.springframework.org/schema/lang=org.springframework.scripting.config.LangNamespaceHandler, http://www.springframework.org/schema/jee=org.springframework.ejb.config.JeeNamespaceHandler, http://www.springframework.org/schema/aop=org.springframework.aop.config.AopNamespaceHandler, http://www.springframework.org/schema/util=org.springframework.beans.factory.xml.UtilNamespaceHandler, http://www.springframework.org/schema/tx=org.springframework.transaction.config.TxNamespaceHandler}]
14:54:35,108 DEBUG ClassUtils:134 - Class [groovy.lang.GroovyObject] or one of its dependencies is not present: java.lang.ClassNotFoundException: groovy.lang.GroovyObject
14:54:35,110 DEBUG ClassUtils:134 - Class [org.jruby.IRuby] or one of its dependencies is not present: java.lang.ClassNotFoundException: org.jruby.IRuby
14:54:35,111 DEBUG ClassUtils:134 - Class [bsh.Interpreter] or one of its dependencies is not present: java.lang.ClassNotFoundException: bsh.Interpreter
14:54:35,112 DEBUG DefaultBeanDefinitionDocumentReader:84 - Loading bean definitions
14:54:35,117 DEBUG BeanDefinitionParserDelegate:350 - Neither XML 'id' nor 'name' specified - using generated bean name [org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener#82751]
14:54:35,121 DEBUG XmlBeanDefinitionReader:143 - Loaded 5 bean definitions from location pattern [applicationContext.xml]
14:54:35,122 INFO ClassPathXmlApplicationContext:100 - Bean factory for application context [org.springframework.context.support.ClassPathXmlApplicationContext;hashCode=22367538]: org.springframework.beans.factory.support.DefaultListableBeanFactory defining beans [dataSource,sessionFactory,transactionManager,compoundDAO,compound]; root of BeanFactory hierarchy
14:54:35,123 INFO ClassPathXmlApplicationContext:322 - 5 beans defined in application context [org.springframework.context.support.ClassPathXmlApplicationContext;hashCode=22367538]
14:54:35,129 INFO ClassPathXmlApplicationContext:473 - Unable to locate MessageSource with name 'messageSource': using default [org.springframework.context.support.DelegatingMessageSource@1d439fe]
14:54:35,135 INFO ClassPathXmlApplicationContext:495 - Unable to locate ApplicationEventMulticaster with name 'applicationEventMulticaster': using default [org.springframework.context.event.SimpleApplicationEventMulticaster@2b7db1]
14:54:35,137 INFO DefaultListableBeanFactory:261 - Pre-instantiating singletons in factory [org.springframework.beans.factory.support.DefaultListableBeanFactory defining beans [dataSource,sessionFactory,transactionManager,compoundDAO,compound]; root of BeanFactory hierarchy]
14:54:35,138 DEBUG DefaultListableBeanFactory:137 - Creating shared instance of singleton bean 'dataSource'
14:54:35,139 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'dataSource' with merged definition [Root bean: class [org.springframework.jdbc.datasource.DriverManagerDataSource]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
14:54:35,139 DEBUG DefaultListableBeanFactory:397 - Eagerly caching bean 'dataSource' to allow for resolving potential circular references
14:54:35,140 INFO DriverManagerDataSource:155 - Loaded JDBC driver: org.hsqldb.jdbcDriver
14:54:35,141 DEBUG DefaultListableBeanFactory:137 - Creating shared instance of singleton bean 'sessionFactory'
14:54:35,141 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'sessionFactory' with merged definition [Root bean: class [org.springframework.orm.hibernate3.LocalSessionFactoryBean]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
14:54:35,142 DEBUG DefaultListableBeanFactory:397 - Eagerly caching bean 'sessionFactory' to allow for resolving potential circular references
14:54:35,143 DEBUG DefaultListableBeanFactory:202 - Returning cached instance of singleton bean 'dataSource'
14:54:35,143 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener#82751' with merged definition [Root bean: class [org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
14:54:35,146 DEBUG DefaultListableBeanFactory:1116 - Invoking afterPropertiesSet() on bean with name 'sessionFactory'
14:54:35,148 DEBUG DTDEntityResolver:38 - trying to resolve system-id [http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd]
14:54:35,149 DEBUG DTDEntityResolver:40 - recognized hibernate namespace; attempting to resolve on classpath under org/hibernate/
14:54:35,151 DEBUG DTDEntityResolver:50 - located [http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd] in classpath
14:54:35,220 INFO HbmBinder:300 - Mapping class: com.genebio.toxico.compound.CompoundImpl -> COMPOUND
14:54:35,221 DEBUG HbmBinder:1270 - Mapped property: id -> COMPOUND_ID
14:54:35,222 DEBUG HbmBinder:1270 - Mapped property: cid -> COMPOUND_CID
14:54:35,223 DEBUG HbmBinder:1270 - Mapped property: SMILE -> COMPOUND_SMILE
14:54:35,224 INFO LocalSessionFactoryBean:742 - Building new Hibernate SessionFactory
14:54:35,225 DEBUG Configuration:1282 - Preparing to build session factory with filters : {}
14:54:35,226 DEBUG Configuration:1117 - processing extends queue
14:54:35,229 DEBUG Configuration:1121 - processing collection mappings
14:54:35,229 DEBUG Configuration:1132 - processing native query and ResultSetMapping mappings
14:54:35,230 DEBUG Configuration:1140 - processing association property references
14:54:35,231 DEBUG Configuration:1162 - processing foreign key constraints
14:54:35,232 INFO ConnectionProviderFactory:72 - Initializing connection provider: org.springframework.orm.hibernate3.LocalDataSourceConnectionProvider
14:54:35,233 DEBUG DriverManagerDataSource:289 - Creating new JDBC Connection to [jdbc:hsqldb:file:data/toxico]
14:54:35,235 INFO SettingsFactory:81 - RDBMS: HSQL Database Engine, version: 1.8.0
14:54:35,235 INFO SettingsFactory:82 - JDBC driver: HSQL Database Engine Driver, version: 1.8.0
14:54:35,236 INFO Dialect:151 - Using dialect: org.hibernate.dialect.HSQLDialect
14:54:35,238 INFO TransactionFactoryFactory:31 - Using default transaction strategy (direct JDBC transactions)
14:54:35,239 INFO TransactionManagerLookupFactory:33 - No TransactionManagerLookup configured (in JTA environment, use of read-write or transactional second-level cache is not recommended)
14:54:35,242 INFO SettingsFactory:134 - Automatic flush during beforeCompletion(): disabled
14:54:35,243 INFO SettingsFactory:138 - Automatic session close at end of transaction: disabled
14:54:35,243 INFO SettingsFactory:145 - JDBC batch size: 15
14:54:35,244 INFO SettingsFactory:148 - JDBC batch updates for versioned data: disabled
14:54:35,245 INFO SettingsFactory:153 - Scrollable result sets: enabled
14:54:35,246 DEBUG SettingsFactory:157 - Wrap result sets: disabled
14:54:35,246 INFO SettingsFactory:161 - JDBC3 getGeneratedKeys(): disabled
14:54:35,247 INFO SettingsFactory:169 - Connection release mode: on_close
14:54:35,248 INFO SettingsFactory:196 - Default batch fetch size: 1
14:54:35,248 INFO SettingsFactory:200 - Generate SQL with comments: disabled
14:54:35,249 INFO SettingsFactory:204 - Order SQL updates by primary key: disabled
14:54:35,251 INFO SettingsFactory:369 - Query translator: org.hibernate.hql.ast.ASTQueryTranslatorFactory
14:54:35,252 INFO ASTQueryTranslatorFactory:24 - Using ASTQueryTranslatorFactory
14:54:35,253 INFO SettingsFactory:212 - Query language substitutions: {}
14:54:35,254 INFO SettingsFactory:217 - JPA-QL strict compliance: disabled
14:54:35,255 INFO SettingsFactory:222 - Second-level cache: enabled
14:54:35,255 INFO SettingsFactory:226 - Query cache: disabled
14:54:35,256 INFO SettingsFactory:356 - Cache provider: org.hibernate.cache.NoCacheProvider
14:54:35,257 INFO SettingsFactory:241 - Optimize cache for minimal puts: disabled
14:54:35,258 INFO SettingsFactory:250 - Structured second-level cache entries: disabled
14:54:35,258 INFO SettingsFactory:270 - Echoing all SQL to stdout
14:54:35,259 INFO SettingsFactory:277 - Statistics: disabled
14:54:35,261 INFO SettingsFactory:281 - Deleted entity synthetic identifier rollback: disabled
14:54:35,262 INFO SettingsFactory:296 - Default entity-mode: pojo
14:54:35,269 INFO SessionFactoryImpl:161 - building session factory
14:54:35,271 DEBUG SessionFactoryImpl:173 - Session factory constructed with filter configurations : {}
14:54:35,272 DEBUG SessionFactoryImpl:177 - instantiating session factory with properties: {java.runtime.name=Java(TM) SE Runtime Environment, sun.boot.library.path=/usr/java/jdk1.6.0_01/jre/lib/i386, java.vm.version=1.6.0_01-ea-b03, java.vm.vendor=Sun Microsystems Inc., java.vendor.url=http://java.sun.com/, path.separator=:, java.vm.name=Java HotSpot(TM) Client VM, file.encoding.pkg=sun.io, user.country=US, sun.java.launcher=SUN_STANDARD, sun.os.patch.level=unknown, java.vm.specification.name=Java Virtual Machine Specification, user.dir=/home/yannmauron/Desktop/test/ToxicoMSJava2, java.runtime.version=1.6.0_01-ea-b03, java.awt.graphicsenv=sun.awt.X11GraphicsEnvironment, java.endorsed.dirs=/usr/java/jdk1.6.0_01/jre/lib/endorsed, os.arch=i386, java.io.tmpdir=/tmp, line.separator=
, java.vm.specification.vendor=Sun Microsystems Inc., os.name=Linux, sun.jnu.encoding=UTF-8, java.library.path=/usr/java/jdk1.6.0_01/jre/lib/i386/client:/usr/java/jdk1.6.0_01/jre/lib/i386:/usr/java/jdk1.6.0_01/jre/../lib/i386:/usr/lib/j2se/1.4/jre/lib/i386/client:/usr/lib/j2se/1.4/jre/lib/i386:/usr/lib/j2se/1.4/jre/../lib/i386:/usr/lib/firefox/:/usr/java/packages/lib/i386:/lib:/usr/lib, java.specification.name=Java Platform API Specification, java.class.version=50.0, sun.management.compiler=HotSpot Client Compiler, os.version=2.6.17-11-generic, user.home=/home/yannmauron, user.timezone=Europe/Zurich, hibernate.connection.release_mode=on_close, java.awt.printerjob=sun.print.PSPrinterJob, file.encoding=UTF-8, java.specification.version=1.6, user.name=yannmauron, java.class.path=/home/yannmauron/Desktop/test/ToxicoMSJava2/bin:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/cdk-0.99.1.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/commons-logging-1.1.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/dom4j-1.6.1.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/jaxen-1.1-beta-6.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/junit-4.2.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/log4j-1.2.14.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/ProteomeCommons.org-IO.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/ProteomeCommons.org-IO-T2D.jar:/home/yannmauron/java/hsqldb.jar:/home/yannmauron/java/spring-framework-2.0.2/dist/spring.jar:/home/yannmauron/java/spring-framework-2.0.2/dist/spring-aspects.jar:/home/yannmauron/java/spring-framework-2.0.2/dist/spring-mock.jar:/home/yannmauron/java/spring-framework-2.0.2/dist/spring-src.zip:/home/yannmauron/java/spring-framework-2.0.2/lib/j2ee/jta.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/cglib/cglib-nodep-2.1_3.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/hibernate/jboss-archive-browsing.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/hibernate/hibernate3.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/jakarta-commons/commons-collections.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/log4j/log4j-1.2.14.jar:/home/yannmauron/Desktop/eclipse conf/eclipse/configuration/org.eclipse.osgi/bundles/228/1/.cp/:/home/yannmauron/Desktop/eclipse conf/eclipse/plugins/org.eclipse.jdt.junit_3.2.1.r321_v20060810/junitsupport.jar:/home/yannmauron/Desktop/eclipse conf/eclipse/plugins/org.eclipse.jdt.junit.runtime_3.2.1.r321_v20060721/junitruntime.jar, hibernate.bytecode.use_reflection_optimizer=false, hibernate.show_sql=true, java.vm.specification.version=1.0, sun.arch.data.model=32, java.home=/usr/java/jdk1.6.0_01/jre, hibernate.dialect=org.hibernate.dialect.HSQLDialect, java.specification.vendor=Sun Microsystems Inc., user.language=en, java.vm.info=mixed mode, sharing, java.version=1.6.0_01-ea, java.ext.dirs=/usr/java/jdk1.6.0_01/jre/lib/ext:/usr/java/packages/lib/ext, sun.boot.class.path=/usr/java/jdk1.6.0_01/jre/lib/resources.jar:/usr/java/jdk1.6.0_01/jre/lib/rt.jar:/usr/java/jdk1.6.0_01/jre/lib/sunrsasign.jar:/usr/java/jdk1.6.0_01/jre/lib/jsse.jar:/usr/java/jdk1.6.0_01/jre/lib/jce.jar:/usr/java/jdk1.6.0_01/jre/lib/charsets.jar:/usr/java/jdk1.6.0_01/jre/classes, java.vendor=Sun Microsystems Inc., file.separator=/, java.vendor.url.bug=http://java.sun.com/cgi-bin/bugreport.cgi, hibernate.connection.provider_class=org.springframework.orm.hibernate3.LocalDataSourceConnectionProvider, sun.cpu.endian=little, sun.io.unicode.encoding=UnicodeLittle, sun.desktop=gnome, sun.cpu.isalist=}
14:54:35,278 DEBUG AbstractEntityPersister:2688 - Static SQL for entity: com.genebio.toxico.compound.CompoundImpl
14:54:35,279 DEBUG AbstractEntityPersister:2693 - Version select: select COMPOUND_ID from COMPOUND where COMPOUND_ID =?
14:54:35,282 DEBUG AbstractEntityPersister:2696 - Snapshot select: select compoundim_.COMPOUND_ID, compoundim_.COMPOUND_CID as COMPOUND2_2_, compoundim_.COMPOUND_SMILE as COMPOUND3_2_ from COMPOUND compoundim_ where compoundim_.COMPOUND_ID=?
14:54:35,282 DEBUG AbstractEntityPersister:2699 - Insert 0: insert into COMPOUND (COMPOUND_CID, COMPOUND_SMILE, COMPOUND_ID) values (?, ?, ?)
14:54:35,283 DEBUG AbstractEntityPersister:2700 - Update 0: update COMPOUND set COMPOUND_CID=?, COMPOUND_SMILE=? where COMPOUND_ID=?
14:54:35,284 DEBUG AbstractEntityPersister:2701 - Delete 0: delete from COMPOUND where COMPOUND_ID=?
14:54:35,286 DEBUG EntityLoader:79 - Static select for entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_2_0_, compoundim0_.COMPOUND_CID as COMPOUND2_2_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_2_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
14:54:35,287 DEBUG EntityLoader:79 - Static select for entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_2_0_, compoundim0_.COMPOUND_CID as COMPOUND2_2_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_2_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
14:54:35,288 DEBUG EntityLoader:79 - Static select for entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_2_0_, compoundim0_.COMPOUND_CID as COMPOUND2_2_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_2_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
14:54:35,289 DEBUG EntityLoader:79 - Static select for entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_2_0_, compoundim0_.COMPOUND_CID as COMPOUND2_2_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_2_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
14:54:35,290 DEBUG EntityLoader:79 - Static select for entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_2_0_, compoundim0_.COMPOUND_CID as COMPOUND2_2_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_2_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
14:54:35,293 DEBUG EntityLoader:34 - Static select for action ACTION_MERGE on entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_2_0_, compoundim0_.COMPOUND_CID as COMPOUND2_2_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_2_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
14:54:35,294 DEBUG EntityLoader:34 - Static select for action ACTION_REFRESH on entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_2_0_, compoundim0_.COMPOUND_CID as COMPOUND2_2_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_2_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
14:54:35,295 DEBUG SessionFactoryObjectFactory:76 - registered: ff80818111937647011193764c1f0001 (unnamed)
14:54:35,296 INFO SessionFactoryObjectFactory:82 - Not binding factory to JNDI, no JNDI name configured
14:54:35,297 DEBUG SessionFactoryImpl:308 - instantiated session factory
14:54:35,298 DEBUG SessionFactoryImpl:390 - Checking 0 named HQL queries
14:54:35,298 DEBUG SessionFactoryImpl:410 - Checking 0 named SQL queries
14:54:35,300 DEBUG DefaultListableBeanFactory:137 - Creating shared instance of singleton bean 'transactionManager'
14:54:35,300 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'transactionManager' with merged definition [Root bean: class [org.springframework.orm.hibernate3.HibernateTransactionManager]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
14:54:35,302 DEBUG DefaultListableBeanFactory:397 - Eagerly caching bean 'transactionManager' to allow for resolving potential circular references
14:54:35,302 DEBUG DefaultListableBeanFactory:202 - Returning cached instance of singleton bean 'sessionFactory'
14:54:35,305 DEBUG DefaultListableBeanFactory:1116 - Invoking afterPropertiesSet() on bean with name 'transactionManager'
14:54:35,306 INFO HibernateTransactionManager:373 - Using DataSource [org.springframework.jdbc.datasource.DriverManagerDataSource@2d189c] of Hibernate SessionFactory for HibernateTransactionManager
14:54:35,307 DEBUG DefaultListableBeanFactory:137 - Creating shared instance of singleton bean 'compoundDAO'
14:54:35,307 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'compoundDAO' with merged definition [Root bean: class [com.genebio.toxico.compound.CompoundDAOImpl]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
14:54:35,309 DEBUG DefaultListableBeanFactory:397 - Eagerly caching bean 'compoundDAO' to allow for resolving potential circular references
14:54:35,310 DEBUG DefaultListableBeanFactory:202 - Returning cached instance of singleton bean 'sessionFactory'
14:54:35,311 DEBUG DefaultListableBeanFactory:1116 - Invoking afterPropertiesSet() on bean with name 'compoundDAO'
14:54:35,312 DEBUG DefaultListableBeanFactory:137 - Creating shared instance of singleton bean 'compound'
14:54:35,315 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'compound' with merged definition [Root bean: class [org.springframework.transaction.interceptor.TransactionProxyFactoryBean]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
14:54:35,317 DEBUG DefaultListableBeanFactory:397 - Eagerly caching bean 'compound' to allow for resolving potential circular references
14:54:35,320 DEBUG DefaultListableBeanFactory:202 - Returning cached instance of singleton bean 'transactionManager'
14:54:35,321 DEBUG DefaultListableBeanFactory:202 - Returning cached instance of singleton bean 'compoundDAO'
14:54:35,325 DEBUG NameMatchTransactionAttributeSource:108 -

mar · **Posted:** Tue Mar 27, 2007 10:18 am

trully, i just dont get it

Code:

14:54:35,054 DEBUG Printer:83 - listing entities:
14:54:35,055 DEBUG Printer:90 com.genebio.toxico.compound.CompoundImpl{id=3, SMILE=lkjfdg, cid=1234567}

from this part i would say you have a compound record with id 3 in youir db, dont you?

are you able to run the petclinic example as is -- ie. compile the source, pack and try to save?

mauroyb0 · **Joined:** Wed Mar 21, 2007 10:23 am **Posts:** 20

Yes i am able to run petclinic, but no, there is no entry in my db... the complete trace is :

Code:

31:44,025  INFO CollectionFactory:73 - JDK 1.4+ collections available
31:44,028  INFO CollectionFactory:76 - Commons Collections 3.x available
31:44,077 DEBUG PluggableSchemaResolver:95 - Loading schema mappings from [META-INF/spring.schemas]
31:44,081 DEBUG PluggableSchemaResolver:101 - Loaded schema mappings: {http://www.springframework.org/schema/aop/spring-aop-2.0.xsd=org/springframework/aop/config/spring-aop-2.0.xsd, http://www.springframework.org/schema/util/spring-util.xsd=org/springframework/beans/factory/xml/spring-util-2.0.xsd, http://www.springframework.org/schema/util/spring-util-2.0.xsd=org/springframework/beans/factory/xml/spring-util-2.0.xsd, http://www.springframework.org/schema/jee/spring-jee.xsd=org/springframework/ejb/config/spring-jee-2.0.xsd, http://www.springframework.org/schema/beans/spring-beans.xsd=org/springframework/beans/factory/xml/spring-beans-2.0.xsd, http://www.springframework.org/schema/lang/spring-lang-2.0.xsd=org/springframework/scripting/config/spring-lang-2.0.xsd, http://www.springframework.org/schema/tx/spring-tx-2.0.xsd=org/springframework/transaction/config/spring-tx-2.0.xsd, http://www.springframework.org/schema/lang/spring-lang.xsd=org/springframework/scripting/config/spring-lang-2.0.xsd, http://www.springframework.org/schema/tool/spring-tool.xsd=org/springframework/beans/factory/xml/spring-tool-2.0.xsd, http://www.springframework.org/schema/aop/spring-aop.xsd=org/springframework/aop/config/spring-aop-2.0.xsd, http://www.springframework.org/schema/tx/spring-tx.xsd=org/springframework/transaction/config/spring-tx-2.0.xsd, http://www.springframework.org/schema/tool/spring-tool-2.0.xsd=org/springframework/beans/factory/xml/spring-tool-2.0.xsd, http://www.springframework.org/schema/jee/spring-jee-2.0.xsd=org/springframework/ejb/config/spring-jee-2.0.xsd, http://www.springframework.org/schema/beans/spring-beans-2.0.xsd=org/springframework/beans/factory/xml/spring-beans-2.0.xsd}
31:44,082 DEBUG PluggableSchemaResolver:95 - Loading schema mappings from [META-INF/spring.schemas]
31:44,085 DEBUG PluggableSchemaResolver:101 - Loaded schema mappings: {http://www.springframework.org/schema/aop/spring-aop-2.0.xsd=org/springframework/aop/config/spring-aop-2.0.xsd, http://www.springframework.org/schema/util/spring-util.xsd=org/springframework/beans/factory/xml/spring-util-2.0.xsd, http://www.springframework.org/schema/util/spring-util-2.0.xsd=org/springframework/beans/factory/xml/spring-util-2.0.xsd, http://www.springframework.org/schema/jee/spring-jee.xsd=org/springframework/ejb/config/spring-jee-2.0.xsd, http://www.springframework.org/schema/beans/spring-beans.xsd=org/springframework/beans/factory/xml/spring-beans-2.0.xsd, http://www.springframework.org/schema/lang/spring-lang-2.0.xsd=org/springframework/scripting/config/spring-lang-2.0.xsd, http://www.springframework.org/schema/tx/spring-tx-2.0.xsd=org/springframework/transaction/config/spring-tx-2.0.xsd, http://www.springframework.org/schema/lang/spring-lang.xsd=org/springframework/scripting/config/spring-lang-2.0.xsd, http://www.springframework.org/schema/tool/spring-tool.xsd=org/springframework/beans/factory/xml/spring-tool-2.0.xsd, http://www.springframework.org/schema/aop/spring-aop.xsd=org/springframework/aop/config/spring-aop-2.0.xsd, http://www.springframework.org/schema/tx/spring-tx.xsd=org/springframework/transaction/config/spring-tx-2.0.xsd, http://www.springframework.org/schema/tool/spring-tool-2.0.xsd=org/springframework/beans/factory/xml/spring-tool-2.0.xsd, http://www.springframework.org/schema/jee/spring-jee-2.0.xsd=org/springframework/ejb/config/spring-jee-2.0.xsd, http://www.springframework.org/schema/beans/spring-beans-2.0.xsd=org/springframework/beans/factory/xml/spring-beans-2.0.xsd}
31:44,094  INFO XmlBeanDefinitionReader:330 - Loading XML bean definitions from class path resource [applicationContext.xml]
31:44,106 DEBUG DefaultDocumentLoader:73 - Using JAXP provider [com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderFactoryImpl]
31:44,181 DEBUG BeansDtdResolver:72 - Found beans DTD [http://www.springframework.org/dtd/spring-beans.dtd] in classpath: spring-beans.dtd
31:44,228 DEBUG DefaultNamespaceHandlerResolver:110 - Loaded mappings [{http://www.springframework.org/schema/p=org.springframework.beans.factory.xml.SimplePropertyNamespaceHandler, http://www.springframework.org/schema/lang=org.springframework.scripting.config.LangNamespaceHandler, http://www.springframework.org/schema/jee=org.springframework.ejb.config.JeeNamespaceHandler, http://www.springframework.org/schema/aop=org.springframework.aop.config.AopNamespaceHandler, http://www.springframework.org/schema/util=org.springframework.beans.factory.xml.UtilNamespaceHandler, http://www.springframework.org/schema/tx=org.springframework.transaction.config.TxNamespaceHandler}]
31:44,235 DEBUG ClassUtils:134 - Class [groovy.lang.GroovyObject] or one of its dependencies is not present: java.lang.ClassNotFoundException: groovy.lang.GroovyObject
31:44,236 DEBUG ClassUtils:134 - Class [org.jruby.IRuby] or one of its dependencies is not present: java.lang.ClassNotFoundException: org.jruby.IRuby
31:44,241 DEBUG ClassUtils:134 - Class [bsh.Interpreter] or one of its dependencies is not present: java.lang.ClassNotFoundException: bsh.Interpreter
31:44,295 DEBUG DefaultBeanDefinitionDocumentReader:84 - Loading bean definitions
31:44,373 DEBUG BeanDefinitionParserDelegate:350 - Neither XML 'id' nor 'name' specified - using generated bean name [org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener#29428e]
31:44,378 DEBUG XmlBeanDefinitionReader:143 - Loaded 5 bean definitions from location pattern [applicationContext.xml]
31:44,380  INFO ClassPathXmlApplicationContext:100 - Bean factory for application context [org.springframework.context.support.ClassPathXmlApplicationContext;hashCode=26399554]: org.springframework.beans.factory.support.DefaultListableBeanFactory defining beans [dataSource,sessionFactory,transactionManager,compoundDAO,compound]; root of BeanFactory hierarchy
31:44,390  INFO ClassPathXmlApplicationContext:322 - 5 beans defined in application context [org.springframework.context.support.ClassPathXmlApplicationContext;hashCode=26399554]
31:44,428  INFO ClassPathXmlApplicationContext:473 - Unable to locate MessageSource with name 'messageSource': using default [org.springframework.context.support.DelegatingMessageSource@f7f540]
31:44,431  INFO ClassPathXmlApplicationContext:495 - Unable to locate ApplicationEventMulticaster with name 'applicationEventMulticaster': using default [org.springframework.context.event.SimpleApplicationEventMulticaster@19209ea]
31:44,433  INFO DefaultListableBeanFactory:261 - Pre-instantiating singletons in factory [org.springframework.beans.factory.support.DefaultListableBeanFactory defining beans [dataSource,sessionFactory,transactionManager,compoundDAO,compound]; root of BeanFactory hierarchy]
31:44,435 DEBUG DefaultListableBeanFactory:137 - Creating shared instance of singleton bean 'dataSource'
31:44,435 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'dataSource' with merged definition [Root bean: class [org.springframework.jdbc.datasource.DriverManagerDataSource]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
31:44,495 DEBUG DefaultListableBeanFactory:397 - Eagerly caching bean 'dataSource' to allow for resolving potential circular references
31:44,523  INFO DriverManagerDataSource:155 - Loaded JDBC driver: org.hsqldb.jdbcDriver
31:44,525 DEBUG DefaultListableBeanFactory:137 - Creating shared instance of singleton bean 'sessionFactory'
31:44,528 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'sessionFactory' with merged definition [Root bean: class [org.springframework.orm.hibernate3.LocalSessionFactoryBean]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
31:44,576 DEBUG DefaultListableBeanFactory:397 - Eagerly caching bean 'sessionFactory' to allow for resolving potential circular references
31:44,577 DEBUG DefaultListableBeanFactory:202 - Returning cached instance of singleton bean 'dataSource'
31:44,579 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener#29428e' with merged definition [Root bean: class [org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
31:44,632 DEBUG DefaultListableBeanFactory:1116 - Invoking afterPropertiesSet() on bean with name 'sessionFactory'
31:44,661  INFO Environment:500 - Hibernate 3.2.1
31:44,668  INFO Environment:533 - hibernate.properties not found
31:44,676  INFO Environment:667 - Bytecode provider name : cglib
31:44,682  INFO Environment:584 - using JDK 1.4 java.sql.Timestamp handling
31:44,797 DEBUG DTDEntityResolver:38 - trying to resolve system-id [http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd]
31:44,798 DEBUG DTDEntityResolver:40 - recognized hibernate namespace; attempting to resolve on classpath under org/hibernate/
31:44,799 DEBUG DTDEntityResolver:50 - located [http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd] in classpath
31:44,962  INFO HbmBinder:300 - Mapping class: com.genebio.toxico.compound.CompoundImpl -> COMPOUND
31:44,972 DEBUG HbmBinder:1270 - Mapped property: id -> COMPOUND_ID
31:44,984 DEBUG HbmBinder:1270 - Mapped property: cid -> COMPOUND_CID
31:44,984 DEBUG HbmBinder:1270 - Mapped property: SMILE -> COMPOUND_SMILE
31:44,985  INFO LocalSessionFactoryBean:742 - Building new Hibernate SessionFactory
31:44,986 DEBUG Configuration:1282 - Preparing to build session factory with filters : {}
31:44,986 DEBUG Configuration:1117 - processing extends queue
31:44,987 DEBUG Configuration:1121 - processing collection mappings
31:44,987 DEBUG Configuration:1132 - processing native query and ResultSetMapping mappings
31:44,987 DEBUG Configuration:1140 - processing association property references
31:44,990 DEBUG Configuration:1162 - processing foreign key constraints
31:45,076  INFO ConnectionProviderFactory:72 - Initializing connection provider: org.springframework.orm.hibernate3.LocalDataSourceConnectionProvider
31:45,087 DEBUG DriverManagerDataSource:289 - Creating new JDBC Connection to [jdbc:hsqldb:file:data/toxico]
31:45,386  INFO SettingsFactory:81 - RDBMS: HSQL Database Engine, version: 1.8.0
31:45,387  INFO SettingsFactory:82 - JDBC driver: HSQL Database Engine Driver, version: 1.8.0
31:45,410  INFO Dialect:151 - Using dialect: org.hibernate.dialect.HSQLDialect
31:45,417  INFO TransactionFactoryFactory:31 - Using default transaction strategy (direct JDBC transactions)
31:45,420  INFO TransactionManagerLookupFactory:33 - No TransactionManagerLookup configured (in JTA environment, use of read-write or transactional second-level cache is not recommended)
31:45,421  INFO SettingsFactory:134 - Automatic flush during beforeCompletion(): disabled
31:45,421  INFO SettingsFactory:138 - Automatic session close at end of transaction: disabled
31:45,422  INFO SettingsFactory:145 - JDBC batch size: 15
31:45,422  INFO SettingsFactory:148 - JDBC batch updates for versioned data: disabled
31:45,423  INFO SettingsFactory:153 - Scrollable result sets: enabled
31:45,426 DEBUG SettingsFactory:157 - Wrap result sets: disabled
31:45,426  INFO SettingsFactory:161 - JDBC3 getGeneratedKeys(): disabled
31:45,427  INFO SettingsFactory:169 - Connection release mode: on_close
31:45,427  INFO SettingsFactory:196 - Default batch fetch size: 1
31:45,428  INFO SettingsFactory:200 - Generate SQL with comments: disabled
31:45,428  INFO SettingsFactory:204 - Order SQL updates by primary key: disabled
31:45,429  INFO SettingsFactory:369 - Query translator: org.hibernate.hql.ast.ASTQueryTranslatorFactory
31:45,432  INFO ASTQueryTranslatorFactory:24 - Using ASTQueryTranslatorFactory
31:45,432  INFO SettingsFactory:212 - Query language substitutions: {}
31:45,433  INFO SettingsFactory:217 - JPA-QL strict compliance: disabled
31:45,433  INFO SettingsFactory:222 - Second-level cache: enabled
31:45,435  INFO SettingsFactory:226 - Query cache: disabled
31:45,435  INFO SettingsFactory:356 - Cache provider: org.hibernate.cache.NoCacheProvider
31:45,436  INFO SettingsFactory:241 - Optimize cache for minimal puts: disabled
31:45,436  INFO SettingsFactory:250 - Structured second-level cache entries: disabled
31:45,443  INFO SettingsFactory:270 - Echoing all SQL to stdout
31:45,444  INFO SettingsFactory:277 - Statistics: disabled
31:45,445  INFO SettingsFactory:281 - Deleted entity synthetic identifier rollback: disabled
31:45,446  INFO SettingsFactory:296 - Default entity-mode: pojo
31:45,487  INFO SessionFactoryImpl:161 - building session factory
31:45,488 DEBUG SessionFactoryImpl:173 - Session factory constructed with filter configurations : {}
31:45,489 DEBUG SessionFactoryImpl:177 - instantiating session factory with properties: {java.runtime.name=Java(TM) SE Runtime Environment, sun.boot.library.path=/usr/java/jdk1.6.0_01/jre/lib/i386, java.vm.version=1.6.0_01-ea-b03, java.vm.vendor=Sun Microsystems Inc., java.vendor.url=http://java.sun.com/, path.separator=:, java.vm.name=Java HotSpot(TM) Client VM, file.encoding.pkg=sun.io, user.country=US, sun.java.launcher=SUN_STANDARD, sun.os.patch.level=unknown, java.vm.specification.name=Java Virtual Machine Specification, user.dir=/home/yannmauron/Desktop/test/ToxicoMSJava2, java.runtime.version=1.6.0_01-ea-b03, java.awt.graphicsenv=sun.awt.X11GraphicsEnvironment, java.endorsed.dirs=/usr/java/jdk1.6.0_01/jre/lib/endorsed, os.arch=i386, java.io.tmpdir=/tmp, line.separator=
, java.vm.specification.vendor=Sun Microsystems Inc., os.name=Linux, sun.jnu.encoding=UTF-8, java.library.path=/usr/java/jdk1.6.0_01/jre/lib/i386/client:/usr/java/jdk1.6.0_01/jre/lib/i386:/usr/java/jdk1.6.0_01/jre/../lib/i386:/usr/lib/j2se/1.4/jre/lib/i386/client:/usr/lib/j2se/1.4/jre/lib/i386:/usr/lib/j2se/1.4/jre/../lib/i386:/usr/lib/firefox/:/usr/java/packages/lib/i386:/lib:/usr/lib, java.specification.name=Java Platform API Specification, java.class.version=50.0, sun.management.compiler=HotSpot Client Compiler, os.version=2.6.17-11-generic, user.home=/home/yannmauron, user.timezone=Europe/Zurich, hibernate.connection.release_mode=on_close, java.awt.printerjob=sun.print.PSPrinterJob, file.encoding=UTF-8, java.specification.version=1.6, user.name=yannmauron, java.class.path=/home/yannmauron/Desktop/test/ToxicoMSJava2/bin:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/cdk-0.99.1.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/commons-logging-1.1.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/dom4j-1.6.1.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/jaxen-1.1-beta-6.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/junit-4.2.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/log4j-1.2.14.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/ProteomeCommons.org-IO.jar:/home/yannmauron/Desktop/test/ToxicoMSJava2/lib/ProteomeCommons.org-IO-T2D.jar:/home/yannmauron/java/hsqldb.jar:/home/yannmauron/java/spring-framework-2.0.2/dist/spring.jar:/home/yannmauron/java/spring-framework-2.0.2/dist/spring-aspects.jar:/home/yannmauron/java/spring-framework-2.0.2/dist/spring-mock.jar:/home/yannmauron/java/spring-framework-2.0.2/dist/spring-src.zip:/home/yannmauron/java/spring-framework-2.0.2/lib/j2ee/jta.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/cglib/cglib-nodep-2.1_3.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/hibernate/jboss-archive-browsing.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/hibernate/hibernate3.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/jakarta-commons/commons-collections.jar:/home/yannmauron/java/spring-framework-2.0.2/lib/log4j/log4j-1.2.14.jar:/home/yannmauron/Desktop/eclipse conf/eclipse/configuration/org.eclipse.osgi/bundles/228/1/.cp/:/home/yannmauron/Desktop/eclipse conf/eclipse/plugins/org.eclipse.jdt.junit_3.2.1.r321_v20060810/junitsupport.jar:/home/yannmauron/Desktop/eclipse conf/eclipse/plugins/org.eclipse.jdt.junit.runtime_3.2.1.r321_v20060721/junitruntime.jar, hibernate.bytecode.use_reflection_optimizer=false, hibernate.show_sql=true, java.vm.specification.version=1.0, sun.arch.data.model=32, java.home=/usr/java/jdk1.6.0_01/jre, hibernate.dialect=org.hibernate.dialect.HSQLDialect, java.specification.vendor=Sun Microsystems Inc., user.language=en, java.vm.info=mixed mode, sharing, java.version=1.6.0_01-ea, java.ext.dirs=/usr/java/jdk1.6.0_01/jre/lib/ext:/usr/java/packages/lib/ext, sun.boot.class.path=/usr/java/jdk1.6.0_01/jre/lib/resources.jar:/usr/java/jdk1.6.0_01/jre/lib/rt.jar:/usr/java/jdk1.6.0_01/jre/lib/sunrsasign.jar:/usr/java/jdk1.6.0_01/jre/lib/jsse.jar:/usr/java/jdk1.6.0_01/jre/lib/jce.jar:/usr/java/jdk1.6.0_01/jre/lib/charsets.jar:/usr/java/jdk1.6.0_01/jre/classes, java.vendor=Sun Microsystems Inc., file.separator=/, java.vendor.url.bug=http://java.sun.com/cgi-bin/bugreport.cgi, hibernate.connection.provider_class=org.springframework.orm.hibernate3.LocalDataSourceConnectionProvider, sun.cpu.endian=little, sun.io.unicode.encoding=UnicodeLittle, sun.desktop=gnome, sun.cpu.isalist=}
31:45,839 DEBUG AbstractEntityPersister:2688 - Static SQL for entity: com.genebio.toxico.compound.CompoundImpl
31:45,839 DEBUG AbstractEntityPersister:2693 -  Version select: select COMPOUND_ID from COMPOUND where COMPOUND_ID =?
31:45,840 DEBUG AbstractEntityPersister:2696 -  Snapshot select: select compoundim_.COMPOUND_ID, compoundim_.COMPOUND_CID as COMPOUND2_0_, compoundim_.COMPOUND_SMILE as COMPOUND3_0_ from COMPOUND compoundim_ where compoundim_.COMPOUND_ID=?
31:45,840 DEBUG AbstractEntityPersister:2699 -  Insert 0: insert into COMPOUND (COMPOUND_CID, COMPOUND_SMILE, COMPOUND_ID) values (?, ?, ?)
31:45,843 DEBUG AbstractEntityPersister:2700 -  Update 0: update COMPOUND set COMPOUND_CID=?, COMPOUND_SMILE=? where COMPOUND_ID=?
31:45,843 DEBUG AbstractEntityPersister:2701 -  Delete 0: delete from COMPOUND where COMPOUND_ID=?
31:45,869 DEBUG EntityLoader:79 - Static select for entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_0_0_, compoundim0_.COMPOUND_CID as COMPOUND2_0_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_0_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
31:45,870 DEBUG EntityLoader:79 - Static select for entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_0_0_, compoundim0_.COMPOUND_CID as COMPOUND2_0_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_0_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
31:45,871 DEBUG EntityLoader:79 - Static select for entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_0_0_, compoundim0_.COMPOUND_CID as COMPOUND2_0_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_0_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
31:45,874 DEBUG EntityLoader:79 - Static select for entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_0_0_, compoundim0_.COMPOUND_CID as COMPOUND2_0_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_0_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
31:45,874 DEBUG EntityLoader:79 - Static select for entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_0_0_, compoundim0_.COMPOUND_CID as COMPOUND2_0_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_0_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
31:45,884 DEBUG EntityLoader:34 - Static select for action ACTION_MERGE on entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_0_0_, compoundim0_.COMPOUND_CID as COMPOUND2_0_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_0_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
31:45,886 DEBUG EntityLoader:34 - Static select for action ACTION_REFRESH on entity com.genebio.toxico.compound.CompoundImpl: select compoundim0_.COMPOUND_ID as COMPOUND1_0_0_, compoundim0_.COMPOUND_CID as COMPOUND2_0_0_, compoundim0_.COMPOUND_SMILE as COMPOUND3_0_0_ from COMPOUND compoundim0_ where compoundim0_.COMPOUND_ID=?
31:45,889 DEBUG SessionFactoryObjectFactory:39 - initializing class SessionFactoryObjectFactory
31:45,892 DEBUG SessionFactoryObjectFactory:76 - registered: ff8081811193985301119398555e0000 (unnamed)
31:45,892  INFO SessionFactoryObjectFactory:82 - Not binding factory to JNDI, no JNDI name configured
31:45,895 DEBUG SessionFactoryImpl:308 - instantiated session factory
31:45,895 DEBUG SessionFactoryImpl:390 - Checking 0 named HQL queries
31:45,896 DEBUG SessionFactoryImpl:410 - Checking 0 named SQL queries
31:45,935 DEBUG DefaultListableBeanFactory:137 - Creating shared instance of singleton bean 'transactionManager'
31:45,935 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'transactionManager' with merged definition [Root bean: class [org.springframework.orm.hibernate3.HibernateTransactionManager]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
31:45,956 DEBUG DefaultListableBeanFactory:397 - Eagerly caching bean 'transactionManager' to allow for resolving potential circular references
31:45,958 DEBUG DefaultListableBeanFactory:202 - Returning cached instance of singleton bean 'sessionFactory'
31:45,959 DEBUG DefaultListableBeanFactory:1116 - Invoking afterPropertiesSet() on bean with name 'transactionManager'
31:45,980  INFO HibernateTransactionManager:373 - Using DataSource [org.springframework.jdbc.datasource.DriverManagerDataSource@1556d12] of Hibernate SessionFactory for HibernateTransactionManager
31:45,981 DEBUG DefaultListableBeanFactory:137 - Creating shared instance of singleton bean 'compoundDAO'
31:45,984 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'compoundDAO' with merged definition [Root bean: class [com.genebio.toxico.compound.CompoundDAOImpl]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
31:46,000 DEBUG DefaultListableBeanFactory:397 - Eagerly caching bean 'compoundDAO' to allow for resolving potential circular references
31:46,001 DEBUG DefaultListableBeanFactory:202 - Returning cached instance of singleton bean 'sessionFactory'
31:46,006 DEBUG DefaultListableBeanFactory:1116 - Invoking afterPropertiesSet() on bean with name 'compoundDAO'
31:46,007 DEBUG DefaultListableBeanFactory:137 - Creating shared instance of singleton bean 'compound'
31:46,008 DEBUG DefaultListableBeanFactory:346 - Creating instance of bean 'compound' with merged definition [Root bean: class [org.springframework.transaction.interceptor.TransactionProxyFactoryBean]; scope=singleton; abstract=false; lazyInit=false; autowireCandidate=true; autowireMode=0; dependencyCheck=0; factoryBeanName=null; factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in class path resource [applicationContext.xml]]
31:46,016  INFO DefaultAopProxyFactory:61 - CGLIB2 available: proxyTargetClass feature enabled
31:46,049 DEBUG DefaultListableBeanFactory:397 - Eagerly caching bean 'compound' to allow for resolving potential circular references
31:46,050 DEBUG DefaultListableBeanFactory:202 - Returning cached instance of singleton bean 'transactionManager'
31:46,051 DEBUG DefaultListableBeanFactory:202 - Returning cached instance of singleton bean 'compoundDAO'
31:46,064 DEBUG NameMatchTransactionAttributeSource:108 - Adding transactional method[*] with attribute [PROPAGATION_REQUIRED,ISOLATION_DEFAULT]
31:46,065 DEBUG NameMatchTransactionAttributeSource:108 - Adding transactional method [find*] with attribute [PROPAGATION_REQUIRED,ISOLATION_DEFAULT,readOnly]
31:46,069 DEBUG NameMatchTransactionAttributeSource:108 - Adding transactional method [merge*] with attribute [PROPAGATION_REQUIRED,ISOLATION_DEFAULT]
31:46,070 DEBUG NameMatchTransactionAttributeSource:108 - Adding transactional method [delete*] with attribute [PROPAGATION_REQUIRED,ISOLATION_DEFAULT]
31:46,071 DEBUG NameMatchTransactionAttributeSource:108 - Adding transactional method [persist*] with attribute [PROPAGATION_REQUIRED,ISOLATION_DEFAULT]
31:46,072 DEBUG NameMatchTransactionAttributeSource:108 - Adding transactional method [load*] with attribute [PROPAGATION_REQUIRED,ISOLATION_DEFAULT,readOnly]
31:46,073 DEBUG NameMatchTransactionAttributeSource:108 - Adding transactional method [save*] with attribute [PROPAGATION_REQUIRED,ISOLATION_DEFAULT]
31:46,076 DEBUG DefaultListableBeanFactory:1116 - Invoking afterPropertiesSet() on bean with name 'compound'
31:46,095 DEBUG ProxyFactory:217 - Added new aspect interface: com.genebio.toxico.compound.CompoundDAO
31:46,095 DEBUG ProxyFactory:217 - Added new aspect interface: org.springframework.beans.factory.InitializingBean
31:46,100 DEBUG JdkDynamicAopProxy:110 - Creating JDK dynamic proxy for [com.genebio.toxico.compound.CompoundDAOImpl]
31:46,112 DEBUG ClassPathXmlApplicationContext:239 - Publishing event in context [org.springframework.context.support.ClassPathXmlApplicationContext;hashCode=26399554]: org.springframework.context.event.ContextRefreshedEvent[source=org.springframework.context.support.ClassPathXmlApplicationContext: display name [org.springframework.context.support.ClassPathXmlApplicationContext;hashCode=26399554]; startup date [Tue Mar 27 15:31:43 CEST 2007]; root of context hierarchy]
31:46,112 DEBUG DefaultListableBeanFactory:202 - Returning cached instance of singleton bean 'compound'
31:46,124 DEBUG HibernateTransactionManager:319 - Using transaction object [org.springframework.orm.hibernate3.HibernateTransactionManager$HibernateTransactionObject@77eaf8]
31:46,126 DEBUG HibernateTransactionManager:347 - Creating new transaction with name [com.genebio.toxico.compound.CompoundDAO.saveCompound]: PROPAGATION_REQUIRED,ISOLATION_DEFAULT
31:46,192 DEBUG SessionImpl:220 - opened session at timestamp: 11750023061
31:46,193 DEBUG HibernateTransactionManager:428 - Opened new Session [org.hibernate.impl.SessionImpl@19ec4ed] for Hibernate transaction
31:46,201 DEBUG HibernateTransactionManager:440 - Preparing JDBC Connection of Hibernate Session [org.hibernate.impl.SessionImpl@19ec4ed]
31:46,232 DEBUG JDBCTransaction:54 - begin
31:46,234 DEBUG ConnectionManager:415 - opening JDBC connection
31:46,235 DEBUG DriverManagerDataSource:289 - Creating new JDBC Connection to [jdbc:hsqldb:file:data/toxico]
31:46,237 DEBUG JDBCTransaction:59 - current autocommit status: true
31:46,237 DEBUG JDBCTransaction:62 - disabling autocommit
31:46,242 DEBUG HibernateTransactionManager:511 - Exposing Hibernate transaction as JDBC transaction [org.hsqldb.jdbc.jdbcConnection@10f41e9]
31:46,245 DEBUG TransactionSynchronizationManager:166 - Bound value [org.springframework.jdbc.datasource.ConnectionHolder@1989b5] for key [org.springframework.jdbc.datasource.DriverManagerDataSource@1556d12] to thread [main]
31:46,245 DEBUG TransactionSynchronizationManager:166 - Bound value [org.springframework.orm.hibernate3.SessionHolder@c3c315] for key [org.hibernate.impl.SessionFactoryImpl@3c9c31] to thread [main]
31:46,246 DEBUG TransactionSynchronizationManager:219 - Initializing transaction synchronization
31:46,250 DEBUG TransactionInterceptor:275 - Getting transaction for [com.genebio.toxico.compound.CompoundDAO.saveCompound]
31:46,252 DEBUG TransactionSynchronizationManager:139 - Retrieved value [org.springframework.orm.hibernate3.SessionHolder@c3c315] for key [org.hibernate.impl.SessionFactoryImpl@3c9c31] bound to thread [main]
31:46,253 DEBUG TransactionSynchronizationManager:139 - Retrieved value [org.springframework.orm.hibernate3.SessionHolder@c3c315] for key [org.hibernate.impl.SessionFactoryImpl@3c9c31] bound to thread [main]
31:46,254 DEBUG HibernateTemplate:359 - Found thread-bound Session for HibernateTemplate
31:46,264 DEBUG AbstractBatcher:358 - about to open PreparedStatement (open PreparedStatements: 0, globally: 0)
31:46,265 DEBUG SQL:393 - select compoundim_.COMPOUND_ID, compoundim_.COMPOUND_CID as COMPOUND2_0_, compoundim_.COMPOUND_SMILE as COMPOUND3_0_ from COMPOUND compoundim_ where compoundim_.COMPOUND_ID=?
Hibernate: select compoundim_.COMPOUND_ID, compoundim_.COMPOUND_CID as COMPOUND2_0_, compoundim_.COMPOUND_SMILE as COMPOUND3_0_ from COMPOUND compoundim_ where compoundim_.COMPOUND_ID=?
31:46,286 DEBUG AbstractBatcher:366 - about to close PreparedStatement (open PreparedStatements: 1, globally: 1)
31:46,287 DEBUG AbstractSaveEventListener:113 - generated identifier: 3, using strategy: org.hibernate.id.Assigned
31:46,310 DEBUG HibernateTemplate:383 - Not closing pre-bound Hibernate Session after HibernateTemplate
31:46,311 DEBUG TransactionSynchronizationManager:139 - Retrieved value [org.springframework.orm.hibernate3.SessionHolder@c3c315] for key [org.hibernate.impl.SessionFactoryImpl@3c9c31] bound to thread [main]
31:46,312 DEBUG TransactionSynchronizationManager:139 - Retrieved value [org.springframework.orm.hibernate3.SessionHolder@c3c315] for key [org.hibernate.impl.SessionFactoryImpl@3c9c31] bound to thread [main]
31:46,315 DEBUG HibernateTemplate:359 - Found thread-bound Session for HibernateTemplate
31:46,317 DEBUG AbstractFlushingEventListener:111 - processing flush-time cascades
31:46,319 DEBUG AbstractFlushingEventListener:154 - dirty checking collections
31:46,335 DEBUG AbstractFlushingEventListener:85 - Flushed: 1 insertions, 0 updates, 0 deletions to 1 objects
31:46,337 DEBUG AbstractFlushingEventListener:91 - Flushed: 0 (re)creations, 0 updates, 0 removals to 0 collections
31:46,340 DEBUG Printer:83 - listing entities:
31:46,341 DEBUG Printer:90 - com.genebio.toxico.compound.CompoundImpl{id=3, SMILE=lkjfdg, cid=1234567}
31:46,348 DEBUG AbstractBatcher:358 - about to open PreparedStatement (open PreparedStatements: 0, globally: 0)
31:46,348 DEBUG SQL:393 - insert into COMPOUND (COMPOUND_CID, COMPOUND_SMILE, COMPOUND_ID) values (?, ?, ?)
Hibernate: insert into COMPOUND (COMPOUND_CID, COMPOUND_SMILE, COMPOUND_ID) values (?, ?, ?)
31:46,350 DEBUG AbstractBatcher:44 - Executing batch size: 1
31:46,352 DEBUG AbstractBatcher:366 - about to close PreparedStatement (open PreparedStatements: 1, globally: 1)
31:46,352 DEBUG HibernateTemplate:383 - Not closing pre-bound Hibernate Session after HibernateTemplate
31:46,353 DEBUG TransactionInterceptor:305 - Completing transaction for [com.genebio.toxico.compound.CompoundDAO.saveCompound]
31:46,354 DEBUG HibernateTransactionManager:819 - Triggering beforeCommit synchronization
31:46,357 DEBUG HibernateTransactionManager:832 - Triggering beforeCompletion synchronization
31:46,358 DEBUG HibernateTransactionManager:652 - Initiating transaction commit
31:46,358 DEBUG HibernateTransactionManager:558 - Committing Hibernate transaction on Session [org.hibernate.impl.SessionImpl@19ec4ed]
31:46,358 DEBUG JDBCTransaction:103 - commit
31:46,359 DEBUG AbstractFlushingEventListener:111 - processing flush-time cascades
31:46,359 DEBUG AbstractFlushingEventListener:154 - dirty checking collections
31:46,360 DEBUG AbstractFlushingEventListener:85 - Flushed: 0 insertions, 0 updates, 0 deletions to 1 objects
31:46,360 DEBUG AbstractFlushingEventListener:91 - Flushed: 0 (re)creations, 0 updates, 0 removals to 0 collections
31:46,361 DEBUG Printer:83 - listing entities:
31:46,361 DEBUG Printer:90 - com.genebio.toxico.compound.CompoundImpl{id=3, SMILE=lkjfdg, cid=1234567}
31:46,362 DEBUG JDBCTransaction:193 - re-enabling autocommit
31:46,362 DEBUG JDBCTransaction:116 - committed JDBC Connection
31:46,364 DEBUG ConnectionManager:296 - transaction completed on session with on_close connection release mode; be sure to close the session to release JDBC resources!
31:46,364 DEBUG HibernateTransactionManager:845 - Triggering afterCommit synchronization
31:46,365 DEBUG HibernateTransactionManager:861 - Triggering afterCompletion synchronization
31:46,366 DEBUG TransactionSynchronizationManager:272 - Clearing transaction synchronization
31:46,366 DEBUG TransactionSynchronizationManager:190 - Removed value [org.springframework.orm.hibernate3.SessionHolder@c3c315] for key [org.hibernate.impl.SessionFactoryImpl@3c9c31] from thread [main]
31:46,367 DEBUG TransactionSynchronizationManager:190 - Removed value [org.springframework.jdbc.datasource.ConnectionHolder@1989b5] for key [org.springframework.jdbc.datasource.DriverManagerDataSource@1556d12] from thread [main]
31:46,377 DEBUG HibernateTransactionManager:637 - Closing Hibernate Session [org.hibernate.impl.SessionImpl@19ec4ed] after transaction
31:46,377 DEBUG SessionFactoryUtils:781 - Closing Hibernate Session
31:46,378 DEBUG ConnectionManager:435 - releasing JDBC connection [ (open PreparedStatements: 0, globally: 0) (open ResultSets: 0, globally: 0)]
31:46,383 DEBUG ConnectionManager:296 - transaction completed on session with on_close connection release mode; be sure to close the session to release JDBC resources!

mauroyb0 · **Joined:** Wed Mar 21, 2007 10:23 am **Posts:** 20

One more information, maybe usefull, if i insert and get the same element in the same session

Code:

package com.genebio.toxico.compound;

import org.hsqldb.Server;
import org.junit.Before;
import org.junit.Test;
import org.springframework.context.ApplicationContext;
import org.springframework.context.support.ClassPathXmlApplicationContext;


public class CompoundImplDAOTest {

private CompoundImpl compoundImpl = null;
private CompoundDAO compoundDAO = null;
private ApplicationContext ctx = null;


   @Test
       public void testSaveRecord() throws Exception {
           compoundImpl = new CompoundImpl();
          compoundImpl.setId(2);
           compoundImpl.setCid("1234567");
           compoundImpl.setSMILE("lkjfdg");
          String[] paths = {"applicationContext.xml"};
          ctx = new ClassPathXmlApplicationContext(paths);
           compoundDAO = (CompoundDAO) ctx.getBean("compound");
           compoundDAO.saveCompound(compoundImpl);
         }
   
   @Test
   public void testloadRecord() throws Exception {
          String[] paths = {"applicationContext.xml"};
          ctx = new ClassPathXmlApplicationContext(paths);
           compoundDAO = (CompoundDAO) ctx.getBean("compound");
           compoundImpl = compoundDAO.getCompound(2);
         System.out.println(compoundImpl.toString());
       }

   
}

I can retrieve the element. It is only when the session die that the element is not saved

mar · **Posted:** Tue Mar 27, 2007 12:17 pm

what about hsqldb log? you can see any sql really executed by running the hsql from console for example.

well, once i started talking with you, hard to quit :-), there is an email in my profile, you may check it and try me :-)

mauroyb0 · **Joined:** Wed Mar 21, 2007 10:23 am **Posts:** 20

Ok thank you... I sent you an e-mail...

mar · **Posted:** Fri Apr 13, 2007 3:32 am

i was away for some time, how about your problem?

if you are able to run and test the petclinic program (and assure yourself that it updates the database), you must be doing something wrong in the configuration files.

and, just an idea -- maybe completely wrong -- you use hsqldb -- are you sure you have persistent tables, not just in-memory tables?