Develop Reference

Hibernate - after some time I am getting JDBCConnectionException in AWS -

I started to get this exception when I made SessionFactory as static property. I don't get this exception right away when I push code to AWS server. I get it after few days. And when I get it I keep on getting it. Exception goes away when I restart AWS server.
Here is my code...
public List<E> getAll(Class<E> c) {
if (busUtil.iSessionFactory == null)
busUtil.loadSessionFactory();
Session session = busUtil.iSessionFactory.openSession();
List<E> t = null;
try {
session.beginTransaction();
t = session.createCriteria(c).list();
session.getTransaction().commit();
} catch (Exception e) {
e.printStackTrace();
new AppLogger().log("Exception" + busUtil.getStackTrace(e) , busConstant.SeveritySevere, new Object() {
}.getClass().getEnclosingMethod().getName());
session.getTransaction().rollback();
} finally {
session.close();
}
return t;
}
This is what I found in my logs.
Jun 19, 2015 1:12:40 PM com.org.panthers.util.AppLogger log - SEVERE: selectFirstOrDefault - Exceptionorg.hibernate.exception.JDBCConnectionException: could not extract ResultSet
at org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQLStateConversionDelegate.java:132)
at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:49)
at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:126)
at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:112)
at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.extract(ResultSetReturnImpl.java:91)
at org.hibernate.loader.Loader.getResultSet(Loader.java:2065)
at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1862)
at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1838)
at org.hibernate.loader.Loader.doQuery(Loader.java:909)
at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:354)
at org.hibernate.loader.Loader.doList(Loader.java:2553)
at org.hibernate.loader.Loader.doList(Loader.java:2539)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2369)
at org.hibernate.loader.Loader.list(Loader.java:2364)
at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:496)
at org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:387)
at org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:231)
at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1264)
at org.hibernate.internal.QueryImpl.list(QueryImpl.java:103)
at com.org.panthers.util.BaseDAOImpl.selectFirstOrDefault(BaseDAOImpl.java:232)
at com.org.panthers.business.busQuestion.loadQuestionsByThread(busQuestion.java:109)
at com.org.panthers.service.QuestionService.loadQuestionsByThread(QuestionService.java:62)
at com.org.panthers.controller.QuestionController.getQuestionsByThread(QuestionController.java:49)
at sun.reflect.GeneratedMethodAccessor55.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60)
at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$ResponseOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:205)
at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75)
at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:302)
at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108)
at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84)
at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1480)
at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1411)
at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1360)
at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1350)
at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:416)
at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:538)
at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:716)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745) - Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure - The last packet successfully received from the server was 28,901,647 milliseconds ago. The last packet sent successfully to the server was 0 milliseconds ago.
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:377)
at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1036)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3427)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3327)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3814)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2435)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2582)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2530)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1907)
at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2030)
at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.extract(ResultSetReturnImpl.java:82)
... 56 more - Caused by: java.io.EOFException: Can not read response from server. Expected to read 4 bytes, read 0 bytes before connection was unexpectedly lost.
at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:2914)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3337)
... 64 more
Database configuration ..
<hibernate-configuration>
<session-factory>
<!-- Database connection settings -->
<property name="hibernate.connection.driver_class">com.mysql.jdbc.Driver</property>
<property name="hibernate.connection.password">root</property>
<property name="hibernate.connection.url">jdbc:mysql://localhost:3306/CURIOSITE</property>
<property name="hibernate.connection.username">root</property>
<property name="hibernate.dialect">org.hibernate.dialect.MySQL5Dialect</property>
<!-- JDBC connection pool (use the built-in) -->
<property name="connection.pool_size">10</property>
<!-- SQL dialect -->
<property name="dialect">org.hibernate.dialect.MySQL5Dialect</property>
<!-- Disable the second-level cache -->
<property name="cache.provider_class">org.hibernate.cache.NoCacheProvider</property>
<!-- Echo all executed SQL to stdout -->
<property name="show_sql">true</property>
<!-- Drop and re-create the database schema on startup -->
<property name="hbm2ddl.auto">update</property>
</session-factory>
Well one way to get rid this exception is to catch this exception and reload SessionFactory as this started happening when I made SessionFactory as static property.
But does anybody know why am I getting this exception?
Any help is appreciated. Thanks

As Hibernate's session-factory documentation states: "Hibernate's own connection pooling algorithm is, however, quite rudimentary. It is intended to help you get started and is not intended for use in a production system".
One of the reasons is that Hibernate doesn't test connection health. That means long-running connections on imperfect networks tend towards failure, as you are seeing.
c3p0 works well with Hibernate and allows you to easily configure max connection age and test connection health.

Tomcat - Mysql -Persistence... Cannot create resource

I have a webapp running in Glassfish + postgreSQl + JPA and I am supposed to migrate it to Tomcat + MySQL.
I have the data available in MYsql but I face issue with resource creation.
Maven Project --> META-INF --> context.xml
<Resource auth="Container"
driverClassName="com.mysql.jdbc.Driver"
maxActive="10" maxIdle="4"
name="jdbc/pool"
password="pwd"
type="javax.sql.DataSource"
factory="org.apache.tomcat.jdbc.pool.DataSourceFactory"
url="jdbc:mysql://xx.xx.xx.xx:3306/db"
username="user"/>
Project -- > src/main/resouces/META-INF --> persistence.xml
<persistence-unit name="testPU" transaction-type="JTA">
<provider>org.eclipse.persistence.jpa.PersistenceProvider</provider>
<jta-data-source>jdbc/Pool</jta-data-source>
<class> </class>
<properties>
<property name="javax.persistence.jdbc.url" value="jdbc:mysql://xx.xx.xx.xx:3306/db?zeroDateTimeBehavior=convertToNull"/>
<property name="javax.persistence.jdbc.password" value="pwd"/>
<property name="javax.persistence.jdbc.driver" value="com.mysql.jdbc.Driver"/>
<property name="javax.persistence.jdbc.user" value="test"/>
<property name="javax.persistence.schema-generation.database.action" value="create"/>
</properties>
</persistence-unit>
Maven Project --> WEB-INF --> web.xml
<resource-ref>
<description>DB Connection</description>
<res-ref-name>jdbc/Pool</res-ref-name>
<res-type>javax.sql.DataSource</res-type>
<res-auth>Container</res-auth>
</resource-ref>
I have the mysql-connector undet tomcat/lib
When deployed , tomcat logs has
INFO: Deploying configuration descriptor F:\Dev_Env\apache-tomcat-7.0.42\conf\Catalina\localhost\TestApp.xml
Jun 12, 2014 2:37:37 PM org.apache.tomcat.jdbc.pool.ConnectionPool init
but resource instance is not created
SEVERE: Servlet /TestApp threw load() exception
javax.naming.NamingException: Cannot create resource instance
at org.apache.naming.factory.ResourceEnvFactory.getObjectInstance(ResourceEnvFactory.java:117)
at javax.naming.spi.NamingManager.getObjectInstance(NamingManager.java:321)
at org.apache.naming.NamingContext.lookup(NamingContext.java:843)
at org.apache.naming.NamingContext.lookup(NamingContext.java:154)
at org.apache.naming.NamingContext.lookup(NamingContext.java:831)
at org.apache.naming.NamingContext.lookup(NamingContext.java:168)
at org.apache.catalina.core.DefaultInstanceManager.lookupFieldResource(DefaultInstanceManager.java:580)
at org.apache.catalina.core.DefaultInstanceManager.processAnnotations(DefaultInstanceManager.java:470)
at org.apache.catalina.core.DefaultInstanceManager.newInstance(DefaultInstanceManager.java:157)
at org.apache.catalina.core.DefaultInstanceManager.newInstance(DefaultInstanceManager.java:138)
at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1144)
at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1088)
at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:5176)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5460)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:633)
at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:656)
at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:535)
at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1461)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
at org.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:301)
at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:819)
at com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:791)
at org.apache.catalina.manager.ManagerServlet.check(ManagerServlet.java:1445)
at org.apache.catalina.manager.ManagerServlet.deploy(ManagerServlet.java:860)
at org.apache.catalina.manager.ManagerServlet.doGet(ManagerServlet.java:357)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:687)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:108)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:611)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1023)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:589)
at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:1852)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:722)

Tomcat does not completely supports Java EE, it is only a Servlet container (implements the Servlet and JSP specifications)
What is the difference between Tomcat, JBoss and Glassfish?)
If you application is using Java EE resources (e.g. EJB), you should not be able to run it using Tomcat.
I suggest the creation of a new application from scratch using TomCat and then check if it runs, after that you can compare the configuration files to make sure that nothing from the Glassfish configuration was left behind.

For tomcat you should use and transaction_type should be "RESOURCE_LOCAL"

Tomcat 7.0 Connection pooling - jdbc driver exception

I want to implement connection pooling on my Tomcat server. Here is my context.xml file (placed under WebContent/META-INF/context.xml:
<Context path="/evappserver" reloadable="true">
<Resource
name="jdbc/evapp"
auth="Container"
type="javax.sql.DataSource"
factory="org.apache.tomcat.jdbc.pool.DataSourceFactory"
initialSize="34"
maxActive="377"
maxIdle="233"
minIdle="89"
timeBetweenEvictionRunsMillis="34000"
minEvictableIdleTimeMillis="55000"
validationQuery="SELECT 1"
validationInterval="34"
testOnBorrow="true"
removeAbandoned="true"
removeAbandonedTimeout="55"
username="root"
password=""
driverClassName="com.mysql.jdbc.Driver"
url="jdbc:mysql://localhost:3306/evapp?allowMultiQueries=true"
/>
</Context>
I have a maven project so the mysql jdbc driver is imported via the pom.xml file, like this:
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>5.1.6</version>
</dependency>
Here is my java code which throws the exception:
Context initContext = new InitialContext();
Context envContext = (Context) initContext.lookup("java:/comp/env");
dataSource = (DataSource) envContext.lookup("jdbc/evapp"); //here is the exception
Here is the exception:
May 13, 2014 10:39:58 AM org.apache.naming.NamingContext lookup
WARNING: Unexpected exception resolving reference
java.sql.SQLException: com.mysql.jdbc.Driver
at org.apache.tomcat.jdbc.pool.PooledConnection.connectUsingDriver(PooledConnection.java:254)
at org.apache.tomcat.jdbc.pool.PooledConnection.connect(PooledConnection.java:182)
at org.apache.tomcat.jdbc.pool.ConnectionPool.createConnection(ConnectionPool.java:702)
at org.apache.tomcat.jdbc.pool.ConnectionPool.borrowConnection(ConnectionPool.java:634)
at org.apache.tomcat.jdbc.pool.ConnectionPool.init(ConnectionPool.java:488)
at org.apache.tomcat.jdbc.pool.ConnectionPool.<init>(ConnectionPool.java:144)
at org.apache.tomcat.jdbc.pool.DataSourceProxy.pCreatePool(DataSourceProxy.java:116)
at org.apache.tomcat.jdbc.pool.DataSourceProxy.createPool(DataSourceProxy.java:103)
at org.apache.tomcat.jdbc.pool.DataSourceFactory.createDataSource(DataSourceFactory.java:539)
at org.apache.tomcat.jdbc.pool.DataSourceFactory.getObjectInstance(DataSourceFactory.java:237)
at org.apache.naming.factory.ResourceFactory.getObjectInstance(ResourceFactory.java:143)
at javax.naming.spi.NamingManager.getObjectInstance(NamingManager.java:321)
at org.apache.naming.NamingContext.lookup(NamingContext.java:843)
at org.apache.naming.NamingContext.lookup(NamingContext.java:154)
at org.apache.naming.NamingContext.lookup(NamingContext.java:831)
at org.apache.naming.NamingContext.lookup(NamingContext.java:168)
at com.evappserver.dblayer.DBType.<init>(DBType.java:62)
at com.evappserver.dblayer.MySqlDB.<init>(MySqlDB.java:16)
at com.evappserver.logiclayer.BaseLogic.getMainDbConnection(BaseLogic.java:19)
at com.evappserver.logiclayer.PasswordLoginLogic.doLogin(PasswordLoginLogic.java:27)
at com.evappserver.servlets.PasswordLoginServlet.doGet(PasswordLoginServlet.java:37)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1023)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:589)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:722)
Caused by: java.lang.ClassNotFoundException: com.mysql.jdbc.Driver
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:266)
at org.apache.tomcat.jdbc.pool.PooledConnection.connectUsingDriver(PooledConnection.java:246)
... 38 more
Is there something wrong with this configuration?

I think you should include the driver for MySQL in your tomcat /lib folder instead of deploying it along with your web application. This way the server will find the proper classes to instantiate your connection pool and everything should go fine.

check if the classpath of your project contains the file mysql-connector-java-5.1.6.jar. Did maven run without problems?

I had this same problem. For a reason unknown to me, putting the mysql-connector-java*.jar in WEB-INF/lib no longer works in Ubuntu LTS 14.04
I solved it by copying this file (and this file alone) to /usr/share/tomcat7/lib and restarted tomcat7 as a service service tomcat7 restart and everything sprang to life.
Best of luck

Hibernate, Postgresql on TomEE

I tried run my application on tomee 1.6.0 but I have problem with JPA and Hibernate. I'm using postgresql and driver 9.3-1100. I read more tutorials about this theme but my problem is still here. Something I read that my server and commpiler use differnet JVM, but no, I check this possibility. Also I copy jar files from tutorial to tomee/lib directory, but without change. I try hibernate jar files 4.3.0 and also 4.1.4 and same result. Can you tell me what I doing wrong?
I try
http://tomee.apache.org/tomee-and-hibernate.html
http://tomee.apache.org/examples-trunk/jpa-hibernate/README.html
Log from my TomEE:
Feb 10, 2014 11:05:55 PM org.apache.tomee.catalina.TomcatWebAppBuilder startInternal
SEVERE: Unable to deploy collapsed ear in war StandardEngine[Catalina].StandardHost[localhost].StandardContext[/]
org.apache.openejb.OpenEJBException: Creating application failed: /home/leaflock/3.Programovanie/Java/Intellij Projects/Avicularia/target/avicularia: org.apache.openejb.OpenEJBRuntimeException: java.lang.ClassNotFoundException: org.hibernate.jpa.HibernatePersistenceProvider: java.lang.ClassNotFoundException: org.hibernate.jpa.HibernatePersistenceProvider
at org.apache.openejb.assembler.classic.Assembler.createApplication(Assembler.java:897)
at org.apache.openejb.assembler.classic.Assembler.createApplication(Assembler.java:612)
at org.apache.tomee.catalina.TomcatWebAppBuilder.startInternal(TomcatWebAppBuilder.java:1205)
at org.apache.tomee.catalina.TomcatWebAppBuilder.configureStart(TomcatWebAppBuilder.java:1051)
at org.apache.tomee.catalina.GlobalListenerSupport.lifecycleEvent(GlobalListenerSupport.java:127)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:90)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5322)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:633)
at org.apache.tomee.catalina.TomcatWebAppBuilder.deployWar(TomcatWebAppBuilder.java:622)
at org.apache.tomee.catalina.TomcatWebAppBuilder.deployWebApps(TomcatWebAppBuilder.java:593)
at org.apache.tomee.catalina.deployment.TomcatWebappDeployer.deploy(TomcatWebappDeployer.java:44)
at org.apache.openejb.assembler.DeployerEjb.deploy(DeployerEjb.java:168)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.openejb.core.interceptor.ReflectionInvocationContext$Invocation.invoke(ReflectionInvocationContext.java:182)
at org.apache.openejb.core.interceptor.ReflectionInvocationContext.proceed(ReflectionInvocationContext.java:164)
at org.apache.openejb.security.internal.InternalSecurityInterceptor.invoke(InternalSecurityInterceptor.java:34)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.openejb.core.interceptor.ReflectionInvocationContext$Invocation.invoke(ReflectionInvocationContext.java:182)
at org.apache.openejb.core.interceptor.ReflectionInvocationContext.proceed(ReflectionInvocationContext.java:164)
at org.apache.openejb.monitoring.StatsInterceptor.record(StatsInterceptor.java:180)
at org.apache.openejb.monitoring.StatsInterceptor.invoke(StatsInterceptor.java:99)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.openejb.core.interceptor.ReflectionInvocationContext$Invocation.invoke(ReflectionInvocationContext.java:182)
at org.apache.openejb.core.interceptor.ReflectionInvocationContext.proceed(ReflectionInvocationContext.java:164)
at org.apache.openejb.core.interceptor.InterceptorStack.invoke(InterceptorStack.java:80)
at org.apache.openejb.core.stateless.StatelessContainer._invoke(StatelessContainer.java:212)
at org.apache.openejb.core.stateless.StatelessContainer.invoke(StatelessContainer.java:181)
at org.apache.openejb.server.ejbd.EjbRequestHandler.doEjbObject_BUSINESS_METHOD(EjbRequestHandler.java:370)
at org.apache.openejb.server.ejbd.EjbRequestHandler.processRequest(EjbRequestHandler.java:181)
at org.apache.openejb.server.ejbd.EjbDaemon.processEjbRequest(EjbDaemon.java:344)
at org.apache.openejb.server.ejbd.EjbDaemon.service(EjbDaemon.java:240)
at org.apache.openejb.server.ejbd.EjbServer.service(EjbServer.java:86)
at org.apache.openejb.server.httpd.ServerServlet.service(ServerServlet.java:58)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
at org.apache.tomee.catalina.OpenEJBValve.invoke(OpenEJBValve.java:45)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:312)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)
Caused by: org.apache.openejb.OpenEJBException: org.apache.openejb.OpenEJBRuntimeException: java.lang.ClassNotFoundException: org.hibernate.jpa.HibernatePersistenceProvider: java.lang.ClassNotFoundException: org.hibernate.jpa.HibernatePersistenceProvider
at org.apache.openejb.assembler.classic.Assembler.createApplication(Assembler.java:758)
... 62 more
Caused by: org.apache.openejb.OpenEJBRuntimeException: java.lang.ClassNotFoundException: org.hibernate.jpa.HibernatePersistenceProvider
at org.apache.openejb.assembler.classic.ReloadableEntityManagerFactory.createDelegate(ReloadableEntityManagerFactory.java:117)
at org.apache.openejb.assembler.classic.ReloadableEntityManagerFactory.(ReloadableEntityManagerFactory.java:101)
at org.apache.openejb.assembler.classic.PersistenceBuilder.createEntityManagerFactory(PersistenceBuilder.java:150)
at org.apache.openejb.assembler.classic.Assembler.createApplication(Assembler.java:752)
... 62 more
Caused by: java.lang.ClassNotFoundException: org.hibernate.jpa.HibernatePersistenceProvider
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1702)
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1547)
at org.apache.tomee.catalina.LazyStopWebappClassLoader.loadClass(LazyStopWebappClassLoader.java:109)
at org.apache.openejb.assembler.classic.EntityManagerFactoryCallable.call(EntityManagerFactoryCallable.java:47)
at org.apache.openejb.assembler.classic.ReloadableEntityManagerFactory.createDelegate(ReloadableEntityManagerFactory.java:115)
... 65 more
[2014-02-10 11:05:55,315] Artifact Avicularia:war: Error during artifact deployment. See server log for details.
[2014-02-10 11:05:55,317] Artifact Avicularia:war: javax.ejb.EJBException: The bean encountered a non-application exception; nested exception is:
org.apache.openejb.OpenEJBRuntimeException: java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/]]

Assuming your libs are OK, maybe is something wrong with your persistence.xml
It must look something like this:
<?xml version="1.0" encoding="UTF-8"?>
<persistence version="2.0" xmlns="http://java.sun.com/xml/ns/persistence" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://java.sun.com/xml/ns/persistence http://java.sun.com/xml/ns/persistence/persistence_2_0.xsd">
<persistence-unit name="NewFleetSystem" transaction-type="JTA">
<provider>org.hibernate.ejb.HibernatePersistence</provider>
<jta-data-source>java:openejb/Resource/YOUR_RESOURCE_NAME</jta-data-source>
<properties>
<property name="hibernate.show_sql" value="true"/>
<property name="hibernate.format_sql" value="true"/>
<property name="hibernate.use_sql_comments" value="true"/>
<property name="hibernate.generate_statistics" value="true"/>
<property name="hibernate.dialect" value="org.hibernate.dialect.Oracle10gDialect"/>
</properties>
</persistence-unit>
</persistence>
I guess the error you are facing is just wrong configuration.
Hope this helps.

Please doublecheck that you have the hibernate-entitymanager somewhere in your classpath.
You should have it defined as your WebApps's dependency, as you should try to keep it self-contained. the goal is to have it run on Tomcat, Jetty, Resin and alike.
Be advised that TomEE comes with openjpa installed. It is one of the main reasons to use TomEE over Tomcat because it provides a stack of technologies already integrated and tested for compatibility.

Not able to build session factory in servlet init method

I am trying to use hibernate with servlet. as SessionFactory took lots of time to initialise i decided to build session factory in init method. below is my servlet code.
public void init()throws ServletException
{
factory = new Configuration().configure().buildSessionFactory();
}
but i gets the error as follows.
Sep 10, 2013 4:27:12 PM org.apache.catalina.core.ApplicationContext log
INFO: Marking servlet cgi as unavailable
Sep 10, 2013 4:27:12 PM org.apache.catalina.core.StandardContext loadOnStartup
SEVERE: Servlet /school threw load() exception
java.lang.SecurityException: Restricted class org.apache.catalina.servlets.CGIServlet
at org.apache.catalina.core.DefaultInstanceManager.checkAccess(DefaultInstanceManager.java:432)
at org.apache.catalina.core.DefaultInstanceManager.checkAccess(DefaultInstanceManager.java:423)
at org.apache.catalina.core.DefaultInstanceManager.loadClassMaybePrivileged(DefaultInstanceManager.java:399)
at org.apache.catalina.core.DefaultInstanceManager.newInstance(DefaultInstanceManager.java:118)
at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1099)
at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1043)
at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4957)
at org.apache.catalina.core.StandardContext$3.call(StandardContext.java:5284)
at org.apache.catalina.core.StandardContext$3.call(StandardContext.java:5279)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:722)
Sep 10, 2013 4:27:52 PM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet [StaffAttendanceReport] in context with path [/school] threw exception [Servlet execution threw an exception] with root cause
java.lang.ClassNotFoundException: org.dom4j.DocumentException
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
at com.enext.security.base.BaseServlet.getSessionFactory(BaseServlet.java:45)
at com.enext.edu.school.attendance.servlet.StaffAttendanceReport.service(StaffAttendanceReport.java:56)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:304)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.smartware.antisql.AntiSQLFilter.doFilter(AntiSQLFilter.java:102)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at Filters.BlockSplChrFliter.doFilter(BlockSplChrFliter.java:46)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:224)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:185)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:151)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:929)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:405)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:269)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:515)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:302)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:722)
what is meaning of this exception.
SEVERE: Servlet /school threw load() exception
java.lang.SecurityException: Restricted class org.apache.catalina.servlets.CGIServlet
I changed the tomcat and tried the same i got below exception
log4j:WARN No appenders could be found for logger (org.hibernate.cfg.Environment).
log4j:WARN Please initialize the log4j system properly.
below is my hibernate.cfg.xml file
<hibernate-configuration>
<session-factory>
<property name="hibernate.dialect">org.hibernate.dialect.OracleDialect</property>
<property name="hibernate.connection.driver_class">oracle.jdbc.OracleDriver</property>
<property name="hibernate.connection.url">jdbc:oracle:thin:#ip:port:sid</property>
<property name="hibernate.connection.username">uname</property>
<property name="hibernate.connection.password">passwd</property>
<mapping resource="com/enext/edu/school/attendance/entity/EmployeeMaster.hbm.xml"/>
<mapping resource="com/enext/edu/school/attendance/entity/StudentHolidayMasterBean.hbm.xml"/>
<mapping resource="com/enext/edu/school/attendance/entity/EmployeeSignin.hbm.xml"/>
</session-factory>
</hibernate-configuration>
how can i solve the problem ?

seems some jar missing..dom4j-1.5.2.jar as u get Caused by: java.lang.ClassNotFoundException: org.dom4j.DocumentException

Seems you are missing with dom4j jars, Please make sure you have these dependacy
<dependency>
<groupId>dom4j</groupId>
<artifactId>dom4j</artifactId>
<version><version></version>
</dependency>