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[b]Hibernate version:[/b]
3.2.0 GA
[b]Mapping documents:[/b]

<hibernate-mapping>
<class name="user.model.User" table="user" catalog="fuel">
<comment>
</comment>

<id name="id" type="java.lang.Integer">
<column name="id" />

<generator class="native">
</generator>
</id>


<set name="sites" lazy="true" table="site" cascade="all-delete-orphan" >
<key>
<column name="user_id"/>
</key>
<one-to-many class="site.model.Site" />
</set>

</class>
</hibernate-mapping>


<hibernate-mapping>
<class name="site.model.Site" table="site" catalog="fuel">
<comment></comment>
<id name="id" type="java.lang.Integer">
<column name="id" />
<generator class="native" />
</id>

<property name="userId" type="integer">
<column name="user_id" not-null="true">
</column>
</property>

</class>
</hibernate-mapping>

[b]Code between sessionFactory.openSession() and session.close():[/b]
I am using Spring 2.0+Hibernate, related entity are,

public class User implements Serializable, UserDetails {

// Fields

private Integer id;
private Set<Site> sites = new HashSet<Site>(0);

// Constructors

/** default constructor */
public User() {
}
// Property accessors
public Integer getId() {
return this.id;
}

public void setId(Integer id) {
this.id = id;
}

public Site getSite() {
Iterator iterator = this.sites.iterator();
if (iterator.hasNext())
return (Site) iterator.next();
else
return null;

}

public Set<Site> getSites() {
return this.sites;
}

public void setSites(Set<Site> sites) {
this.sites = sites;
}

public void addSite(Site site) {
getSites().add(site);
}

}

public class Site implements java.io.Serializable {

// Fields

private Integer id;

private Integer userId;

private String siteName;
// Constructors

/** default constructor */
public Site() {
}


// Property accessors
public Integer getId() {
return this.id;
}

public void setId(Integer id) {
this.id = id;
}

public String getSiteName() {
return this.siteName;
}

public void setSiteName(String siteName) {
this.siteName = siteName;
}

public int hashCode() {
return (siteName != null ? siteName.hashCode() : 0);
}

public boolean equals(Object o) {
if (this == o)
return true;
if (!(o instanceof Site))
return false;

final Site site = (Site) o;

return !(siteName != null ? !siteName.equals(site.siteName) : site.siteName != null);

}

public Integer getUserId() {
return userId;
}

public void setUserId(Integer userId) {
this.userId = userId;
}

}

[b]Full stack trace of any exception that occurs:[/b]
[appfuse] DEBUG [http-8080-Processor24] SQL.log(393) | update fuel.user set username=?, password=?, password_hint=?, first_name=?, last_name=?, address=?, city=?, county=?, province=?, postal_code=?, email=?, phone_number=?, ip=?, account_enabled=?, account_locked=?, last_update_date=?, attempt_login=? where id=?
[appfuse] DEBUG [http-8080-Processor24] SQL.log(393) | update fuel.site set user_id=null where user_id=?
[appfuse] WARN [http-8080-Processor24] JDBCExceptionReporter.logExceptions(71) | SQL Error: 0, SQLState: 01004
[appfuse] ERROR [http-8080-Processor24] JDBCExceptionReporter.logExceptions(72) | Data truncation: Column set to default value; NULL supplied to NOT NULL column 'user_id' at row 1
[appfuse] ERROR [http-8080-Processor24] AbstractFlushingEventListener.performExecutions(301) | Could not synchronize database state with session
org.hibernate.exception.GenericJDBCException: Could not execute JDBC batch update
at org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:103)
at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:91)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)
at org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:249)
at org.hibernate.jdbc.AbstractBatcher.prepareStatement(AbstractBatcher.java:92)
at org.hibernate.jdbc.AbstractBatcher.prepareStatement(AbstractBatcher.java:87)
at org.hibernate.jdbc.AbstractBatcher.prepareBatchStatement(AbstractBatcher.java:218)
at org.hibernate.persister.collection.AbstractCollectionPersister.remove(AbstractCollectionPersister.java:1030)
at org.hibernate.action.CollectionRemoveAction.execute(CollectionRemoveAction.java:28)
at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:248)
at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:232)
at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:141)
at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298)
at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
at org.springframework.orm.hibernate3.HibernateTemplate$27.doInHibernate(HibernateTemplate.java:801)
at org.springframework.orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java:362)
at org.springframework.orm.hibernate3.HibernateTemplate.flush(HibernateTemplate.java:799)
at common.dao.hibernate.BaseDaoHibernate.saveObject(BaseDaoHibernate.java:95)
at common.mgr.impl.BaseManagerImpl.saveObject(BaseManagerImpl.java:129)
at common.mgr.impl.BaseManagerImpl.saveObject(BaseManagerImpl.java:114)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:318)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:203)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:162)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:107)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:209)
at $Proxy1.saveObject(Unknown Source)
at common.action.EditFormController.saveObject(EditFormController.java:112)
at common.action.EditFormController.onSubmit(EditFormController.java:55)
at user.web.action.SignupController.onSubmit(SignupController.java:88)
at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:258)
at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:250)
at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:45)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:806)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:736)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:396)
at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:360)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:118)
at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:375)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at org.appfuse.webapp.filter.GZIPFilter.doFilterInternal(GZIPFilter.java:42)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:77)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at org.appfuse.webapp.filter.LocaleFilter.doFilterInternal(LocaleFilter.java:55)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:77)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.opensymphony.clickstream.ClickstreamFilter.doFilter(ClickstreamFilter.java:42)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:174)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:77)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264)
at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107)
at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72)
at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110)
at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
at org.acegisecurity.providers.anonymous.AnonymousProcessingFilter.doFilter(AnonymousProcessingFilter.java:125)
at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
at org.acegisecurity.ui.rememberme.RememberMeProcessingFilter.doFilter(RememberMeProcessingFilter.java:142)
at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81)
at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217)
at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
at org.acegisecurity.ui.logout.LogoutFilter.doFilter(LogoutFilter.java:108)
at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:193)
at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148)
at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:98)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:78)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:77)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)
at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664)
at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
at java.lang.Thread.run(Thread.java:595)
[b]Name and version of the database you are using:[/b]
MySQL 5.0.24-community
[b]The generated SQL (show_sql=true):[/b]
appfuse] DEBUG [http-8080-Processor24] SQL.log(393) | update fuel.user set username=?, password=?, password_hint=?, first_name=?, last_name=?, address=?, city=?, county=?, province=?, postal_code=?, email=?, phone_number=?, ip=?, account_enabled=?, account_locked=?, last_update_date=?, attempt_login=? where id=?
[appfuse] DEBUG [http-8080-Processor24] SQL.log(393) | update fuel.site set user_id=null where user_id=?

[b]Debug level Hibernate log excerpt:[/b]

There is FK between user(id) and site(user_id) tables. For an existing entity, there is no problem in first update, but in second update in site table it tries to set user_id=null which causes exception. user_id should be the same id used in first update. Does anyone know why? Thanks!