Spring and Hibernate project throws JDBC exception every day

Question

I'm using Spring and Hibernate for my project and my database is MySql. I'm using annotation instead of xml. Every day, When I make the first request for login, I get this exception, then after refresh it works.

18-Feb-2016 10:59:20.990 SEVERE [http-nio-443-exec-9] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [dispatcher] in context with path [/ATS] threw exception
 org.springframework.transaction.CannotCreateTransactionException: Could not open JPA EntityManager for transaction; nested exception is javax.persistence.PersistenceException: org.hibernate.TransactionException: JDBC begin transaction failed: 
    at org.springframework.orm.jpa.JpaTransactionManager.doBegin(JpaTransactionManager.java:431)
    at org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:373)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:427)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:276)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:653)
    at com.services.MyAuthoritiesPopulator$$EnhancerBySpringCGLIB$$9580eab6.getGrantedAuthorities(<generated>)
    at org.springframework.security.ldap.authentication.LdapAuthenticationProvider.loadUserAuthorities(LdapAuthenticationProvider.java:215)
    at org.springframework.security.ldap.authentication.AbstractLdapAuthenticationProvider.authenticate(AbstractLdapAuthenticationProvider.java:84)
    at org.springframework.security.authentication.ProviderManager.authenticate(ProviderManager.java:167)
    at org.springframework.security.authentication.ProviderManager.authenticate(ProviderManager.java:192)
    at org.springframework.security.web.authentication.UsernamePasswordAuthenticationFilter.attemptAuthentication(UsernamePasswordAuthenticationFilter.java:93)
    at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:217)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:120)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.csrf.CsrfFilter.doFilterInternal(CsrfFilter.java:120)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:64)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:91)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:53)
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:213)
    at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:176)
    at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:346)
    at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:262)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
    at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:616)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:518)
    at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1091)
    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:673)
    at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1526)
    at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1482)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
    at java.lang.Thread.run(Thread.java:745)
Caused by: javax.persistence.PersistenceException: org.hibernate.TransactionException: JDBC begin transaction failed: 
    at org.hibernate.jpa.spi.AbstractEntityManagerImpl.convert(AbstractEntityManagerImpl.java:1763)
    at org.hibernate.jpa.spi.AbstractEntityManagerImpl.convert(AbstractEntityManagerImpl.java:1677)
    at org.hibernate.jpa.spi.AbstractEntityManagerImpl.throwPersistenceException(AbstractEntityManagerImpl.java:1771)
    at org.hibernate.jpa.internal.TransactionImpl.begin(TransactionImpl.java:64)
    at org.springframework.orm.jpa.DefaultJpaDialect.beginTransaction(DefaultJpaDialect.java:67)
    at org.springframework.orm.jpa.JpaTransactionManager.doBegin(JpaTransactionManager.java:380)
    ... 49 more
Caused by: org.hibernate.TransactionException: JDBC begin transaction failed: 
    at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.doBegin(JdbcTransaction.java:76)
    at org.hibernate.engine.transaction.spi.AbstractTransactionImpl.begin(AbstractTransactionImpl.java:162)
    at org.hibernate.internal.SessionImpl.beginTransaction(SessionImpl.java:1471)
    at org.hibernate.jpa.internal.TransactionImpl.begin(TransactionImpl.java:61)
    ... 51 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: The last packet successfully received from the server was 65,266,256 milliseconds ago.  The last packet sent successfully to the server was 65,266,256 milliseconds ago. is longer than the server configured value of 'wait_timeout'. You should consider either expiring and/or testing connection validity before use in your application, increasing the server configured values for client timeouts, or using the Connector/J connection property 'autoReconnect=true' to avoid this problem.
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
    at com.mysql.jdbc.Util.handleNewInstance(Util.java:400)
    at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1038)
    at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3621)
    at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2429)
    at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2594)
    at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2541)
    at com.mysql.jdbc.ConnectionImpl.setAutoCommit(ConnectionImpl.java:4882)
    at org.apache.commons.dbcp.DelegatingConnection.setAutoCommit(DelegatingConnection.java:371)
    at org.apache.commons.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.setAutoCommit(PoolingDataSource.java:328)
    at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.doBegin(JdbcTransaction.java:72)
    ... 54 more
Caused by: java.net.SocketException: Broken pipe
    at java.net.SocketOutputStream.socketWrite0(Native Method)
    at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:109)
    at java.net.SocketOutputStream.write(SocketOutputStream.java:153)
    at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
    at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140)
    at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3603)
    ... 61 more

It seems that the server close connection with MySql, my application server is Tomcat, it may be a problem with code or Tomcat? This is my spring configuration class:

@EnableWebMvc
@Configuration
@PropertySource(value = { "classpath:application.properties" })
@ComponentScan({ "com.*" })
@EnableTransactionManagement
@Import({ SecurityConfig.class, SpringMvcInitializer.class})
@EnableJpaRepositories("com.repository")
public class AppConfig extends WebMvcConfigurerAdapter{
    @Autowired
    private Environment env;

    private static final String PROPERTY_NAME_DATABASE_DRIVER = "db.driver";
    private static final String PROPERTY_NAME_DATABASE_PASSWORD = "db.password";
    private static final String PROPERTY_NAME_DATABASE_URL = "db.url";
    private static final String PROPERTY_NAME_DATABASE_USERNAME = "db.username";

    private static final String PROPERTY_NAME_HIBERNATE_DIALECT = "hibernate.dialect";
    //  private static final String PROPERTY_NAME_HIBERNATE_SHOW_SQL = "hibernate.show_sql";
    private static final String PROPERTY_NAME_ENTITYMANAGER_PACKAGES_TO_SCAN = "entitymanager.packages.to.scan";
    private static final String PROPERTY_NAME_HIBERNATE_FORMAT_SQL = "hibernate.format_sql";


    /**
     * This and the next methods are used to avoid exception while jackson mapping the entity, so fields are setted with null value
     * unless use Hibernate.initialize
     * @return
     */
    public MappingJackson2HttpMessageConverter jacksonMessageConverter(){
        MappingJackson2HttpMessageConverter messageConverter = new MappingJackson2HttpMessageConverter();

        ObjectMapper mapper = new ObjectMapper();
        //Registering Hibernate4Module to support lazy objects
        mapper.registerModule(new Hibernate4Module());

        messageConverter.setObjectMapper(mapper);
        return messageConverter;

    }
    /**
     * Used for spring security
     * @return
     */
    @Bean
    public SpringSecurityDialect springSecurityDialect() {
        SpringSecurityDialect dialect = new SpringSecurityDialect();
        return dialect;
    }

    @Override
    public void configureMessageConverters(List<HttpMessageConverter<?>> converters) {
        //Here we add our custom-configured HttpMessageConverter
        converters.add(jacksonMessageConverter());
        super.configureMessageConverters(converters);
    }

    private Properties getHibernateProperties() {
        Properties properties = new Properties();
        properties.put(PROPERTY_NAME_HIBERNATE_DIALECT, env.getRequiredProperty(PROPERTY_NAME_HIBERNATE_DIALECT));
        //      properties.put(PROPERTY_NAME_HIBERNATE_SHOW_SQL, env.getRequiredProperty(PROPERTY_NAME_HIBERNATE_SHOW_SQL));
        properties.put(PROPERTY_NAME_HIBERNATE_FORMAT_SQL, env.getRequiredProperty(PROPERTY_NAME_HIBERNATE_FORMAT_SQL));
        properties.put("hibernate.enable_lazy_load_no_trans",true);
        return properties;
    }

    @Bean(name = "dataSource")
    public BasicDataSource dataSource() {
        BasicDataSource ds = new BasicDataSource();
        ds.setDriverClassName(env.getRequiredProperty(PROPERTY_NAME_DATABASE_DRIVER));
        ds.setUrl(env.getRequiredProperty(PROPERTY_NAME_DATABASE_URL));
        ds.setUsername(env.getRequiredProperty(PROPERTY_NAME_DATABASE_USERNAME));
        ds.setPassword(env.getRequiredProperty(PROPERTY_NAME_DATABASE_PASSWORD));
        return ds;
    }

    @Bean
    public ServletContextTemplateResolver TemplateResolver(){
        ServletContextTemplateResolver resolver = new ServletContextTemplateResolver();
        resolver.setPrefix("/WEB-INF/templates/pages/");
        resolver.setSuffix(".html");
        resolver.setTemplateMode("LEGACYHTML5");
        resolver.setCacheable(false);
        return resolver;
        /*ServletContextTemplateResolver resolver = new ServletContextTemplateResolver();
        resolver.setPrefix("/WEB-INF/pages/");
        resolver.setSuffix(".html");
        resolver.setTemplateMode("HTML5");
        return resolver;*/
    }

    @Bean
    public SpringTemplateEngine templateEngine(){
        SpringTemplateEngine templateEngine = new SpringTemplateEngine();
        templateEngine.setTemplateResolver(TemplateResolver());
        templateEngine.addDialect(springSecurityDialect());
        return templateEngine;
    }


    @Bean
    public ThymeleafViewResolver viewResolver() {
        ThymeleafViewResolver resolver = new ThymeleafViewResolver();
        resolver.setTemplateEngine(templateEngine());
        resolver.setOrder(1);
        resolver.setViewNames(new String[]{"*", "js/*", "template/*"});
        return resolver;
    }

    /**
     * Register multipartResolver for file upload
     * @return
     */
    @Bean
    public CommonsMultipartResolver multipartResolver() {
        CommonsMultipartResolver resolver=new CommonsMultipartResolver();
        resolver.setDefaultEncoding("utf-8");
        return resolver;    
    }

    /**
     * Allow use of bootstrap
     */
    @Override
    public void addResourceHandlers(ResourceHandlerRegistry registry) {
        registry.addResourceHandler("/static/**")
        .addResourceLocations("/static/");
    }

    /**
     * Allow use of JPA
     */
    @Bean
    public JpaTransactionManager transactionManager() {
        JpaTransactionManager transactionManager = new JpaTransactionManager();
        transactionManager.setEntityManagerFactory(entityManagerFactory().getObject());
        return transactionManager;
    }
    @Bean
    public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
        LocalContainerEntityManagerFactoryBean entityManagerFactoryBean = new LocalContainerEntityManagerFactoryBean();
        entityManagerFactoryBean.setDataSource(dataSource());
        entityManagerFactoryBean.setPersistenceProviderClass(HibernatePersistenceProvider.class);
        entityManagerFactoryBean.setPackagesToScan(env.
                getRequiredProperty(PROPERTY_NAME_ENTITYMANAGER_PACKAGES_TO_SCAN));
        entityManagerFactoryBean.setJpaProperties(getHibernateProperties());
        return entityManagerFactoryBean;

    }

}

UPDATE: I created this class

@Service
@EnableScheduling
public class wakeUpDatabase {

    @Autowired
    private DatabaseFleetsAndCarsServices databaseFleetsAndCarsServices;
    //This task is executing every 7h
    @Scheduled(fixedDelay = 25200000)
    public void smartQeury(){
        databaseFleetsAndCarsServices.getEcu();
    }

}

I test it and let you know if it works

Answer 1

I resolved with a query each 7 hours:

@Service
@EnableScheduling
public class wakeUpDatabase {

    @Autowired
    private DatabaseFleetsAndCarsServices databaseFleetsAndCarsServices;
    //This task is executing every 7h
    @Scheduled(fixedDelay = 25200000)
    public void smartQeury(){
        databaseFleetsAndCarsServices.getEcu();
    }

}