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springboot Unable to acquire JDBC Connection when deployed with gitlab ci

My spring application is throwing this error, when I deploy it using gitlab ci.
Caused by: org.hibernate.exception.JDBCConnectionException: Unable to acquire JDBC Connection
It works fine when I deploy the same container manually. But the error occurs only when app is deployed via gitlab ci.
I've define pool size, in application.properites file.
spring.datasource.hikari.minimumIdle=20
spring.datasource.hikari.maximumPoolSize=30
spring.datasource.hikari.connectionTimeout=50000
I dont how else can I troubleshoot this issue.
more log.
20:00:47.418 [http-nio-8098-exec-10] WARN o.h.e.jdbc.spi.SqlExceptionHelper - SQL Error: 0, SQLState: null
20:00:47.419 [http-nio-8098-exec-10] ERROR o.h.e.jdbc.spi.SqlExceptionHelper - HikariPool-1 - Connection is not available, request timed out after 30481ms.
20:00:47.452 [http-nio-8098-exec-10] WARN g.e.SimpleDataFetcherExceptionHandler - Exception while fetching data (/getCodes) : Could not open JPA EntityManager for transaction; nested exception is org.hiberna
te.exception.JDBCConnectionException: Unable to acquire JDBC Connection org.springframework.transaction.CannotCreateTransactionException: Could not open JPA EntityManager for transaction; nested exception is org.hibernate.exception.JDBCConnectionException: Unable to acquire JDBC Conne
ction
at org.springframework.orm.jpa.JpaTransactionManager.doBegin(JpaTransactionManager.java:467) ~[spring-orm-5.3.7.jar!/:5.3.7]
at org.springframework.transaction.support.AbstractPlatformTransactionManager.startTransaction(AbstractPlatformTransactionManager.java:400) ~[spring-tx-5.3.7.jar!/:5.3.7]
at org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:373) ~[spring-tx-5.3.7.jar!/:5.3.7]
at org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:595) ~[spring-tx-5.3.7.jar!/:5.3.7]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:382) ~[spring-tx-5.3.7.jar!/:5.3.7]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119) ~[spring-tx-5.3.7.jar!/:5.3.7]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.3.7.jar!/:5.3.7]
at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:750) ~[spring-aop-5.3.7.jar!/:5.3.7]
at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:692) ~[spring-aop-5.3.7.jar!/:5.3.7]
at com.idg.idgcore.pricing.app.service.priceCode.PriceCodeApplicationService$$EnhancerBySpringCGLIB$$936d76c1.getAll(<generated>) ~[classes!/:na]
at jdk.internal.reflect.GeneratedMethodAccessor172.invoke(Unknown Source) ~[na:na]
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:na]
at java.base/java.lang.reflect.Method.invoke(Method.java:568) ~[na:na]
at io.leangen.graphql.metadata.execution.SingletonMethodInvoker.execute(SingletonMethodInvoker.java:21) ~[spqr-0.9.9.jar!/:na]

Spring boot, hibernate, hikariCP and mysql no communication after inactivity

We are facing a weird error. When we first srtart the server we can login etc. After a few hours of inactivity we cannot login anymore. We can solve the problem by restarting the application, but it will occur at least one time each day. To restart the application is only a shortterm solution and we need to find a more stable solution to this a critical problem.
I am using the following configuration:
Environment
Hibernate : 5.2.13
JPA : spring-boot-starter-data-jpa (1.5.10)
JDK version : 1.8.0_191
Database : Mysql (version 5.7.25)
JDBC Driver : 5.1.45
Spring Boot : 1.5.10
OS : Ubuntu 16.04.6
Hikari
HikariCP version: 2.7.7
datasource:
type: com.zaxxer.hikari.HikariDataSource
driver-class-name: com.mysql.jdbc.Driver
url: jdbc:mysql://localhost:3306/<database>?useUnicode=true&characterEncoding=utf8&useSSL=false
username: <username>
password: <secret password>
hikari:
data-source-properties:
cachePrepStmts: true
prepStmtCacheSize: 250
prepStmtCacheSqlLimit: 2048
useServerPrepStmts: true
From the application log:
AuthenticationServiceException[http-nio-18080-exec-9] UserJWTController: Authentication exception trace: {}
org.springframework.security.authentication.InternalAuthenticationServiceException: Could not open JPA EntityManager for transaction; nested exception is org.hibernate.TransactionException: JDBC begin transaction failed: uthentication.dao.DaoAuthenticationProvider.retrieveUser(DaoAuthenticationProvider.java:126)
at org.springframework.security.authentication.dao.AbstractUserDetailsAuthenticationProvider.authenticate(AbstractUserDetailsAuthenticationProvider.java:144)
at org.springframework.security.authentication.ProviderManager.authenticate(ProviderManager.java:174)
at com.example.web.rest.UserJWTController.authorize(UserJWTController.java:48)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:205)
at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:133)
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:97)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:827)
...
...
...
...
...
...
Caused by: org.springframework.transaction.CannotCreateTransactionException: Could not open JPA EntityManager for transaction; nested exception is 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:461)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:277)
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.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy159.loadUserByUsername(Unknown Source)
at org.springframework.security.authentication.dao.DaoAuthenticationProvider.retrieveUser(DaoAuthenticationProvider.java:114)
... 107 common frames omitted
Caused by: org.hibernate.TransactionException: JDBC begin transaction failed:
at org.hibernate.resource.jdbc.internal.AbstractLogicalConnectionImplementor.begin(AbstractLogicalConnectionImplementor.java:73)
at org.hibernate.resource.jdbc.internal.LogicalConnectionManagedImpl.begin(LogicalConnectionManagedImpl.java:263)
at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcResourceLocalTransactionCoordinatorImpl$TransactionDriverControlImpl.begin(JdbcResourceLocalTransactionCoordinatorImpl.java:214)
at org.hibernate.engine.transaction.internal.TransactionImpl.begin(TransactionImpl.java:56)
at org.springframework.orm.jpa.vendor.HibernateJpaDialect.beginTransaction(HibernateJpaDialect.java:189)
at org.springframework.orm.jpa.JpaTransactionManager.doBegin(JpaTransactionManager.java:380)
... 115 common frames omitted
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: No operations allowed after connection closed.
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:423)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
at com.mysql.jdbc.Util.getInstance(Util.java:408)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:919)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:898)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:887)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:861)
at com.mysql.jdbc.ConnectionImpl.throwConnectionClosedException(ConnectionImpl.java:1184)
at com.mysql.jdbc.ConnectionImpl.checkClosed(ConnectionImpl.java:1179)
at com.mysql.jdbc.ConnectionImpl.setAutoCommit(ConnectionImpl.java:4770)
at sun.reflect.GeneratedMethodAccessor325.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.tomcat.jdbc.pool.ProxyConnection.invoke(ProxyConnection.java:126)
at org.apache.tomcat.jdbc.pool.JdbcInterceptor.invoke(JdbcInterceptor.java:108)
at org.apache.tomcat.jdbc.pool.interceptor.AbstractCreateStatementInterceptor.invoke(AbstractCreateStatementInterceptor.java:79)
at org.apache.tomcat.jdbc.pool.JdbcInterceptor.invoke(JdbcInterceptor.java:108)
at org.apache.tomcat.jdbc.pool.DisposableConnectionFacade.invoke(DisposableConnectionFacade.java:81)
at com.sun.proxy.$Proxy98.setAutoCommit(Unknown Source)
at org.hibernate.resource.jdbc.internal.AbstractLogicalConnectionImplementor.begin(AbstractLogicalConnectionImplementor.java:67)
... 120 common frames omitted
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
The last packet successfully received from the server was 33,215,831 milliseconds ago. The last packet sent successfully to the server was 7 milliseconds ago.
I really don't know how to trigger this issue manually after a restart so we have to wait a few hours before this state kicks in.
It seems that we are not the only one having this issue, but after days without solving it, it's a bit frustrating.
We need to solve this soon, any ideas?

I found a solution to our problem. It seemed like the configuration we did in the yaml file didn't work properly so I had to configure the HikariCP programmatically.
I removed the configuration for hikari in the yaml file and afterwards the datasource looked like:
datasource:
type: com.zaxxer.hikari.HikariDataSource
And the datasource config looks the following:
#Configuration
public class DatasourceConfiguration {
private static final Logger log = LoggerFactory.getLogger(DatasourceConfiguration.class);
private final Environment env;
public DatasourceConfiguration(Environment env) {
this.env = env;
}
#Bean(name="primaryDatasource")
#Primary
#ConfigurationProperties(prefix="spring.datasource")
public DataSource dataSource() {
HikariConfig config = new HikariConfig();
config.setDriverClassName("com.mysql.jdbc.Driver");
config.setPoolName("JPAHikariCP");
config.setAutoCommit(false);
config.setConnectionTestQuery("SELECT 1");
String profile = env.getProperty("spring.profiles.active");
Optional<String> db = Optional.of("database");
Optional<String> username = Optional.of("user");
Optional<String> password = Optional.of("pass");
if("test".equals(profile) || "dev".equals(profile)) {
config.addDataSourceProperty("cachePrepStmts", true);
config.addDataSourceProperty("prepStmtCacheSize", 250);
config.addDataSourceProperty("prepStmtCacheSqlLimit", 2048);
config.addDataSourceProperty("useServerPrepStmts", true);
}
config.setJdbcUrl(String.format("jdbc:mysql://localhost:3306/%s?useUnicode=true&characterEncoding=utf8&useSSL=false", db.get()));
config.setUsername(username.get());
config.setPassword(password.get());
return new HikariDataSource(config);
}
}
And now it works.

Could not open Hibernate Session for transaction nested exception is java.lang.NoClassDefFoundError:

I recently upgraded the jar file from common-collections 3.2.1 to commons-collections4 4.2 because of the vulnerability in the previous version.
But after the upgrade I am seeing the exception:
ERROR :-
org.springframework.transaction.CannotCreateTransactionException:
Could not open Hibernate Session for transaction; nested exception is
java.lang.NoClassDefFoundError:
org/apache/commons/collections/map/ReferenceMap
org.springframework.transaction.CannotCreateTransactionException:
Could not open Hibernate Session for transaction; nested exception is
java.lang.NoClassDefFoundError:
org/apache/commons/collections/map/ReferenceMap
at org.springframework.orm.hibernate4.HibernateTransactionManager.doBegin(HibernateTransactionManager.java:544)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:377)
at org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:461)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:277)
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.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy24.getQueueManagerNames(Unknown Source)
at com.ge.portal.service.impl.QueueManagerServiceImpl.getQueueManagerNames(QueueManagerServiceImpl.java:223)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
I am seeing this error because they have the class ReferenceMap in different package in commons-collections4 and maybe hibernate jars are not able to resolve the actual path.
My question what version of hibernate should I use now?
Below are the hibernate jars that I am using in my application:
compile "org.hibernate:com.springsource.org.hibernate:4.1.0.Final"
compile "org.hibernate.common:hibernate-commons-annotations:4.0.5.Final"
compile "org.hibernate:hibernate-core:4.3.11.Final"
compile "org.hibernate:hibernate-ehcache:4.3.11.Final"
compile "org.hibernate:hibernate-tools:4.3.5.Final"
compile "org.hibernate:hibernate-validator:4.3.2.Final"
In case I am trying to update the hibernate jars to 5.0.0.7 then after the deployment I am seeing 404 error.

JPA Hibernate Persistence exception [PersistenceUnit: default] Unable to build Hibernate SessionFactory

I've been trying to sort out a connection to my DB with JPA Hibernate and mysql, but for some reason, no matter what i try, when launching the tomcat server i get the same exception:
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'localContainerEntityManagerFactoryBean' defined in class path resource [core/JPAConfig.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean]: Factory method 'localContainerEntityManagerFactoryBean' threw exception; nested exception is javax.persistence.PersistenceException: [PersistenceUnit: default] Unable to build Hibernate SessionFactory
This is my JPA config class:
#Configuration
#EnableJpaRepositories("core.repository")
#EnableTransactionManagement
#EnableCaching
public class JPAConfig {
#Value("${db.jdbcURL}")
private String jdbcURL;
#Value("${db.user}")
private String user;
#Value("${db.password}")
private String password;
#Value("${db.generateDDL}")
private Boolean generateDDL;
#SuppressWarnings("Duplicates")
#Bean
public DataSource dataSource() {
BasicDataSource dataSource = new BasicDataSource();
dataSource.setDriverClassName(Driver.class.getName());
dataSource.setUrl("jdbc:mysql://localhost:3306/movierentaldb");
dataSource.setUsername(System.getProperty("root"));
dataSource.setPassword(System.getProperty("mdie1767"));
dataSource.setInitialSize(2);
dataSource.setMaxActive(5);
return dataSource;
}
#Bean
public LocalContainerEntityManagerFactoryBean localContainerEntityManagerFactoryBean(){
HibernateJpaVendorAdapter vendorAdapter = new HibernateJpaVendorAdapter();
vendorAdapter.setDatabase(Database.MYSQL);
vendorAdapter.setGenerateDdl(generateDDL);
vendorAdapter.setShowSql(true);
LocalContainerEntityManagerFactoryBean factory = new LocalContainerEntityManagerFactoryBean();
factory.setJpaVendorAdapter(vendorAdapter);
factory.setPackagesToScan("core.model");
factory.setDataSource(dataSource());
factory.afterPropertiesSet();
return factory;
}
#Bean
public EntityManagerFactory entityManagerFactory(){
return localContainerEntityManagerFactoryBean().getObject();
}
#Bean
public EntityManager entityManager(){
return entityManagerFactory().createEntityManager();
}
#Bean
PlatformTransactionManager transactionManager(){
JpaTransactionManager manager = new JpaTransactionManager();
manager.setEntityManagerFactory(entityManagerFactory());
return manager;
}
#Bean
public HibernateExceptionTranslator hibernateExceptionTranslator(){
return new HibernateExceptionTranslator();
}
#Bean
public CacheManager cacheManager(){
GuavaCacheManager guavaCacheManager = new GuavaCacheManager();
guavaCacheManager.setCacheBuilder(CacheBuilder.newBuilder().expireAfterAccess(2, TimeUnit.HOURS));
return guavaCacheManager;
}
}
At this point i can't think of anything else to try..any help is much obliged
Edit: This is the entire stacktrace
23-May-2016 13:05:10.267 INFO [RMI TCP Connection(3)-127.0.0.1] org.apache.catalina.core.ApplicationContext.log No Spring WebApplicationInitializer types detected on classpath
23-May-2016 13:05:10.444 INFO [RMI TCP Connection(3)-127.0.0.1] org.apache.catalina.core.ApplicationContext.log Initializing Spring root WebApplicationContext
23-May-2016 13:05:15.333 SEVERE [RMI TCP Connection(3)-127.0.0.1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class org.springframework.web.context.ContextLoaderListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'localContainerEntityManagerFactoryBean' defined in class path resource [core/JPAConfig.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean]: Factory method 'localContainerEntityManagerFactoryBean' threw exception; nested exception is javax.persistence.PersistenceException: [PersistenceUnit: default] Unable to build Hibernate SessionFactory
at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:599)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1123)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1018)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:510)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:482)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1054)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:829)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:538)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:444)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:326)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4732)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5194)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:152)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:726)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:702)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
at org.apache.catalina.startup.HostConfig.manageApp(HostConfig.java:1702)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:483)
at org.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:300)
at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:819)
at com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:801)
at org.apache.catalina.mbeans.MBeanFactory.createStandardContext(MBeanFactory.java:482)
at org.apache.catalina.mbeans.MBeanFactory.createStandardContext(MBeanFactory.java:431)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:483)
at org.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:300)
at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:819)
at com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:801)
at javax.management.remote.rmi.RMIConnectionImpl.doOperation(RMIConnectionImpl.java:1466)
at javax.management.remote.rmi.RMIConnectionImpl.access$300(RMIConnectionImpl.java:76)
at javax.management.remote.rmi.RMIConnectionImpl$PrivilegedOperation.run(RMIConnectionImpl.java:1307)
at javax.management.remote.rmi.RMIConnectionImpl.doPrivilegedOperation(RMIConnectionImpl.java:1399)
at javax.management.remote.rmi.RMIConnectionImpl.invoke(RMIConnectionImpl.java:828)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:483)
at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:323)
at sun.rmi.transport.Transport$1.run(Transport.java:200)
at sun.rmi.transport.Transport$1.run(Transport.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at sun.rmi.transport.Transport.serviceCall(Transport.java:196)
at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:568)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:826)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.lambda$run$240(TCPTransport.java:683)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler$$Lambda$1/108265094.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:682)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean]: Factory method 'localContainerEntityManagerFactoryBean' threw exception; nested exception is javax.persistence.PersistenceException: [PersistenceUnit: default] Unable to build Hibernate SessionFactory
at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:189)
at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:588)
... 60 more
Caused by: javax.persistence.PersistenceException: [PersistenceUnit: default] Unable to build Hibernate SessionFactory
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.persistenceException(EntityManagerFactoryBuilderImpl.java:954)
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.build(EntityManagerFactoryBuilderImpl.java:884)
at org.springframework.orm.jpa.vendor.SpringHibernateJpaPersistenceProvider.createContainerEntityManagerFactory(SpringHibernateJpaPersistenceProvider.java:60)
at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:343)
at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:319)
at core.JPAConfig.localContainerEntityManagerFactoryBean(JPAConfig.java:94)
at core.JPAConfig$$EnhancerBySpringCGLIB$$c2bcf261.CGLIB$localContainerEntityManagerFactoryBean$1(<generated>)
at core.JPAConfig$$EnhancerBySpringCGLIB$$c2bcf261$$FastClassBySpringCGLIB$$901863a2.invoke(<generated>)
at org.springframework.cglib.proxy.MethodProxy.invokeSuper(MethodProxy.java:228)
at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.intercept(ConfigurationClassEnhancer.java:355)
at core.JPAConfig$$EnhancerBySpringCGLIB$$c2bcf261.localContainerEntityManagerFactoryBean(<generated>)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:483)
at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:162)
... 61 more
Caused by: org.hibernate.tool.schema.spi.SchemaManagementException: Unable to obtain JDBC Connection
at org.hibernate.tool.schema.internal.exec.AbstractJdbcConnectionContextImpl.getConnection(AbstractJdbcConnectionContextImpl.java:46)
at org.hibernate.tool.schema.internal.exec.ImprovedExtractionContextImpl.getJdbcConnection(ImprovedExtractionContextImpl.java:59)
at org.hibernate.tool.schema.internal.exec.ImprovedExtractionContextImpl.getJdbcDatabaseMetaData(ImprovedExtractionContextImpl.java:66)
at org.hibernate.tool.schema.extract.internal.InformationExtractorJdbcDatabaseMetaDataImpl.getTable(InformationExtractorJdbcDatabaseMetaDataImpl.java:271)
at org.hibernate.tool.schema.internal.exec.ImprovedDatabaseInformationImpl.getTableInformation(ImprovedDatabaseInformationImpl.java:109)
at org.hibernate.tool.schema.internal.SchemaMigratorImpl.performMigration(SchemaMigratorImpl.java:252)
at org.hibernate.tool.schema.internal.SchemaMigratorImpl.doMigration(SchemaMigratorImpl.java:137)
at org.hibernate.tool.schema.internal.SchemaMigratorImpl.doMigration(SchemaMigratorImpl.java:110)
at org.hibernate.tool.schema.spi.SchemaManagementToolCoordinator.performDatabaseAction(SchemaManagementToolCoordinator.java:176)
at org.hibernate.tool.schema.spi.SchemaManagementToolCoordinator.process(SchemaManagementToolCoordinator.java:64)
at org.hibernate.internal.SessionFactoryImpl.<init>(SessionFactoryImpl.java:458)
at org.hibernate.boot.internal.SessionFactoryBuilderImpl.build(SessionFactoryBuilderImpl.java:465)
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.build(EntityManagerFactoryBuilderImpl.java:881)
... 75 more
Caused by: org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Access denied for user ''#'localhost' (using password: NO))
at org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1549)
at org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1388)
at org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
at org.hibernate.engine.jdbc.connections.internal.DatasourceConnectionProviderImpl.getConnection(DatasourceConnectionProviderImpl.java:122)
at org.hibernate.engine.jdbc.env.internal.JdbcEnvironmentInitiator$ConnectionProviderJdbcConnectionAccess.obtainConnection(JdbcEnvironmentInitiator.java:180)
at org.hibernate.tool.schema.internal.exec.AbstractJdbcConnectionContextImpl.getConnection(AbstractJdbcConnectionContextImpl.java:43)
... 87 more
Caused by: java.sql.SQLException: Access denied for user ''#'localhost' (using password: NO)
at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:695)
at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:663)
at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:653)
at com.mysql.cj.jdbc.exceptions.SQLExceptionsMapping.translateException(SQLExceptionsMapping.java:108)
at com.mysql.cj.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:1683)
at com.mysql.cj.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:656)
at com.mysql.cj.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:349)
at com.mysql.cj.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:221)
at org.apache.commons.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:38)
at org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:582)
at org.apache.commons.dbcp.BasicDataSource.validateConnectionFactory(BasicDataSource.java:1556)
at org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1545)
... 92 more
23-May-2016 13:05:15.379 INFO [RMI TCP Connection(3)-127.0.0.1] org.apache.catalina.core.ApplicationContext.log Closing Spring root WebApplicationContext
Error:(7, 24) java: package org.gjt.mm.mysql does not exist

The issue is that you are not able to get a connection to MYSQL database and hence it is throwing an error saying that cannot build a session factory.
Please see the error below:
Caused by: java.sql.SQLException: Access denied for user ''#'localhost' (using password: NO)
which points to username not getting populated.
Please recheck system properties
dataSource.setUsername(System.getProperty("root"));
some packages seems to be missing as well pointing to a dependency issue:
package org.gjt.mm.mysql does not exist
Please run a mvn dependency:tree command to check for dependencies

I was getting this error even when all the relevant dependencies were in place because I hadn't created the schema in MySQL.
I thought it would be created automatically but it wasn't. Although the table itself will be created, you have to create the schema.

I found some issue about that kind of error
Database username or password not match in the mysql or other other database. Please set application.properties like this
# ===============================
# = DATA SOURCE
# ===============================
# Set here configurations for the database connection
# Connection url for the database please let me know "mondolmislam#gmail.com"
spring.datasource.url = jdbc:mysql://localhost:3306/bookstoreapiabc
# Username and secret
spring.datasource.username = root
spring.datasource.password =
# Keep the connection alive if idle for a long time (needed in production)
spring.datasource.testWhileIdle = true
spring.datasource.validationQuery = SELECT 1
# ===============================
# = JPA / HIBERNATE
# ===============================
# Use spring.jpa.properties.* for Hibernate native properties (the prefix is
# stripped before adding them to the entity manager).
# Show or not log for each sql query
spring.jpa.show-sql = true
# Hibernate ddl auto (create, create-drop, update): with "update" the database
# schema will be automatically updated accordingly to java entities found in
# the project
spring.jpa.hibernate.ddl-auto = update
# Allows Hibernate to generate SQL optimized for a particular DBMS
spring.jpa.properties.hibernate.dialect = org.hibernate.dialect.MySQL5Dialect
Issue no 2.
Your local server has two database server and those database server conflict. this conflict like this mysql server & xampp or lampp or wamp server. Please one of the database like mysql server because xampp or lampp server automatically install mysql server on this machine

Got this error due to a mistake in a named query.

I had a semicolon at the end, and gave me this error.

On Login : java.sql.SQLException: The transaction is no longer active - status: 'Marked rollback

Our Application runs on web-logic 10. Application developed using java, spring framework, hibernae, jsp...
When try to login in tomcat, there is no error, but when deployed to weblogic server, whatever we do login or try to listen a message from MQ, gives the same exception, which is found by turning on the traces.
What can be causing the issue. Any suggestions are greatly helpful! Thanks in Advance
Stacktrace:
java.sql.SQLException: The transaction is no longer active - status: 'Marked rollback. [Reason=weblogic.transaction.internal.AppSetRollbackOnlyException: setRollbackOnly called on transaction]'. No further JDBC access is allowed within this transaction.
at weblogic.jdbc.wrapper.JTSConnection.checkIfRolledBack(JTSConnection.java:178)
at weblogic.jdbc.wrapper.JTSConnection.checkConnection(JTSConnection.java:188)
at weblogic.jdbc.wrapper.Connection.preInvocationHandler(Connection.java:93)
at weblogic.jdbc.wrapper.Connection.prepareStatement(Connection.java:480)
at weblogic.jdbc.wrapper.JTSConnection.prepareStatement(JTSConnection.java:486)
at org.hibernate.jdbc.AbstractBatcher.getPreparedStatement(AbstractBatcher.java:534)
at org.hibernate.jdbc.AbstractBatcher.prepareStatement(AbstractBatcher.java:116)
at org.hibernate.jdbc.AbstractBatcher.prepareStatement(AbstractBatcher.java:109)
at org.hibernate.jdbc.AbstractBatcher.prepareBatchStatement(AbstractBatcher.java:244)
at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2412)
at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2875)
at org.hibernate.action.EntityInsertAction.execute(EntityInsertAction.java:79)
at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:273)
at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:265)
at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:185)
at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:321)
at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:51)
at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1216)
at org.springframework.orm.hibernate3.SpringSessionSynchronization.beforeCommit(SpringSessionSynchronization.java:145)
at org.springframework.transaction.support.TransactionSynchronizationUtils.triggerBeforeCommit(TransactionSynchronizationUtils.java:95)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.triggerBeforeCommit(AbstractPlatformTransactionManager.java:925)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:738)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:725)
at org.springframework.transaction.interceptor.TransactionAspectSupport.commitTransactionAfterReturning(TransactionAspectSupport.java:475)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:270)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:94)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:631)
at pkg.add.send.msg.InterceptMessageListener$$EnhancerByCGLIB$$f327e73b.onMessage(<generated>)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:563)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:325)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:263)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1104)
... 3 more