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Error in application (Hibernate 5 + Spring MVC 5)

There is an application on Hibernate 5 + Spring MVC 5. GlassFish server 4.1.1 is used.
When you start the logs says:
Severe: java.lang.NoSuchMethodError:
org.jboss.logging.Logger.debugf(Ljava/lang/String;I)V
On the Internet write that it's dependencies, but I tried to no avail.
pom.xml
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.mycompany</groupId>
<artifactId>mawenWebTest</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>war</packaging>
<name>mawenWebTest</name>
<properties>
<endorsed.dir>${project.build.directory}/endorsed</endorsed.dir>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<!-- JAVA -->
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>4.3.1.Final</version>
</dependency>
<dependency>
<groupId>javax</groupId>
<artifactId>javaee-web-api</artifactId>
<version>7.0</version>
<scope>provided</scope>
</dependency>
<!-- SPRING -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>5.0.3.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-webmvc</artifactId>
<version>5.0.3.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-webmvc-portlet</artifactId>
<version>4.3.14.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-orm</artifactId>
<version>5.0.3.RELEASE</version>
</dependency>
<!-- HIBERNATE -->
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>5.2.12.Final</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>5.2.12.Final</version>
<exclusions>
<exclusion>
<artifactId>jboss-logging</artifactId>
<groupId>org.jboss.logging</groupId>
</exclusion>
</exclusions>
</dependency>
<!-- OTHER -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.9.4</version>
</dependency>
<dependency>
<groupId>com.microsoft.sqlserver</groupId>
<artifactId>mssql-jdbc</artifactId>
<version>6.3.6.jre8-preview</version>
<scope>test</scope>
</dependency>
<!-- <dependency>
<groupId>org.jboss.logging</groupId>
<artifactId>jboss-logging</artifactId>
<version>3.3.0.Final</version>
</dependency>-->
<dependency>
<groupId>org.glassfish.jersey.ext</groupId>
<artifactId>jersey-spring3</artifactId>
<version>2.25.1</version>
<exclusions>
<exclusion>
<groupId>org.glassfish.hk2.external</groupId>
<artifactId>bean-validator</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.ext</groupId>
<artifactId>jersey-bean-validation</artifactId>
<version>2.25.1</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
<compilerArguments>
<endorseddirs>${endorsed.dir}</endorseddirs>
</compilerArguments>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.3</version>
<configuration>
<failOnMissingWebXml>false</failOnMissingWebXml>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.6</version>
<executions>
<execution>
<phase>validate</phase>
<goals>
<goal>copy</goal>
</goals>
<configuration>
<outputDirectory>${endorsed.dir}</outputDirectory>
<silent>true</silent>
<artifactItems>
<artifactItem>
<groupId>javax</groupId>
<artifactId>javaee-endorsed-api</artifactId>
<version>7.0</version>
<type>jar</type>
</artifactItem>
</artifactItems>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
application-context.xml
<?xml version='1.0' encoding='UTF-8' ?>
<beans xmlns="http://www.springframework.org/schema/beans"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:p="http://www.springframework.org/schema/p"
xmlns:aop="http://www.springframework.org/schema/aop"
xmlns:tx="http://www.springframework.org/schema/tx"
xmlns:context="http://www.springframework.org/schema/context"
xmlns:mvc="http://www.springframework.org/schema/mvc"
xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-4.0.xsd
http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop-4.0.xsd
http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx-4.0.xsd
http://www.springframework.org/schema/context
http://www.springframework.org/schema/context/spring-context.xsd
http://www.springframework.org/schema/mvc
http://www.springframework.org/schema/mvc/spring-mvc-4.0.xsd">
<context:component-scan base-package="com.mycompany"/>
<mvc:annotation-driven/>
<!--#Transaction annotation support -->
<bean id="dataSource"
class="org.springframework.jdbc.datasource.DriverManagerDataSource"
p:driverClassName="com.microsoft.sqlserver.jdbc.SQLServerDriver"
p:url="java:app/MSSQL_TestDB"
p:username="sa"
p:password="123" />
<tx:annotation-driven transaction-manager="transactionManager"/>
<bean id="transactionManager" class="org.springframework.orm.jpa.JpaTransactionManager">
<property name="entityManagerFactory" ref="emf"/>
</bean>
<bean id="emf"
class="org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean" >
<!--packagesToScan - search Entity and mapping them -->
<property name="packagesToScan" value="com.mycompany.mawenwebtest" />
<property name="dataSource" ref="dataSource" />
<property name="jpaVendorAdapter">
<bean class="org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter" >
<property name="generateDdl" value="true" />
<property name="showSql" value="true" />
</bean>
</property>
<property name="jpaProperties">
<props>
<prop key="hibernate.dialect">org.hibernate.dialect.HSQLDialect</prop>
<prop key="hibernate.show_sql">true</prop>
<prop key="hibernate.format_sql">false</prop>
<prop key="hibernate.hbm2ddl.auto">update</prop>
</props>
</property>
</bean>
<bean id="mansDao" class="com.mycompany.mawenwebtest.dao.MansDao">
</bean>
</beans>

I suspect this dependency :
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>4.3.1.Final</version>
</dependency>
You are using hibernate 5.2.12.Final version why are you using 4.3.1.Final for this one. And as you can see here : https://mvnrepository.com/artifact/org.hibernate/hibernate-entitymanager this dependency is depricated and they suggest using hibernate-core instead.

NoClassDefFoundError: org/hibernate/ejb/HibernatePersistence

I met the NoClassDefFoundError when initiating the HibernateJPAVendorAdapter
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'jpaVendorAdapter' defined in class path resource [META-INF/applicationContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter]: Constructor threw exception; nested exception is java.lang.NoClassDefFoundError: org/hibernate/ejb/HibernatePersistence
I checked several threads on this exception but failed to find out the root cause of this. I think the initialization of JPAVendorAdapter has failed but not sure why. Maybe incompatibilities among my package dependencies, or in my applicationContext.xml. Here they are;
pom.xml(only related sections included)
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.canreef</groupId>
<artifactId>Calendar</artifactId>
<version>1.0</version>
<packaging>war</packaging>
<name>Calendar</name>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>1.7</maven.compiler.source>
<maven.compiler.target>1.7</maven.compiler.target>
<endorsed.dir>${project.build.directory}/endorsed</endorsed.dir>
<org.springframework.version>4.0.1.RELEASE</org.springframework.version>
<org.springframework.data.version>1.7.0.RELEASE</org.springframework.data.version>
<org.springframework.instrument.version>4.1.1.RELEASE</org.springframework.instrument.version>
<org.hibernate.version>4.1.7.Final</org.hibernate.version>
<jackson.version>2.4.4</jackson.version>
<external.resources>${project.basedir}/src/main/lib</external.resources>
</properties>
<dependencies>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>4.3.1.Final</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>4.3.0.Final</version>
</dependency>
<dependency>
<groupId>javax</groupId>
<artifactId>javaee-web-api</artifactId>
<version>7.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-webmvc</artifactId>
<version>${org.springframework.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-orm</artifactId>
<version>${org.springframework.version}</version>
</dependency>
<!-- Added-->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>${org.springframework.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-jpa</artifactId>
<version>${org.springframework.data.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-instrument</artifactId>
<version>${org.springframework.instrument.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbyclient</artifactId>
<version>10.11.1.1</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
<compilerArguments>
<endorseddirs>${endorsed.dir}</endorseddirs>
</compilerArguments>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.3</version>
<configuration>
<failOnMissingWebXml>false</failOnMissingWebXml>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.6</version>
<executions>
<execution>
<phase>validate</phase>
<goals>
<goal>copy</goal>
</goals>
<configuration>
<outputDirectory>${external.resources}</outputDirectory>
<silent>true</silent>
<artifactItems>
<artifactItem>
<groupId>javax</groupId>
<artifactId>javaee-endorsed-api</artifactId>
<version>7.0</version>
<type>jar</type>
</artifactItem>
</artifactItems>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<repositories>
<repository>
<id>unknown-jars-temp-repo</id>
<name>A temporary repository created by NetBeans for libraries and jars it could not identify. Please replace the dependencies in this repository with correct ones and delete this repository.</name>
<url>file:${project.basedir}/lib</url>
</repository>
</repositories>
</project>
applicationContext.xml
<?xml version='1.0' encoding='UTF-8' ?>
<!-- was: <?xml version="1.0" encoding="UTF-8"?> -->
<beans xmlns="http://www.springframework.org/schema/beans"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:p="http://www.springframework.org/schema/p"
xmlns:aop="http://www.springframework.org/schema/aop"
xmlns:tx="http://www.springframework.org/schema/tx"
xmlns:jpa="http://www.springframework.org/schema/data/jpa"
xmlns:context="http://www.springframework.org/schema/context"
xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd
http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop.xsd
http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx.xsd
http://www.springframework.org/schema/data/jpa http://www.springframework.org/schema/data/jpa/spring-jpa.xsd
http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context.xsd
http://www.springframework.org/schema/data/repository http://www.springframework.org/schema/data/repository/spring-repository.xsd">
<jpa:repositories base-package="com.canreef.calendar"/>
<context:component-scan base-package="com.canreef.calendar"/>
<!-- ADD PERSISTENCE SUPPORT HERE (jpa, hibernate, etc) -->
<bean id="dataSource" class="org.springframework.jdbc.datasource.DriverManagerDataSource">
<property name="driverClassName" value="org.apache.derby.jdbc.ClientDriver"/>
<property name="url" value="jdbc:derby://localhost:1527/GEAH"/>
<property name="username" value="xxx"/>
<property name="password" value="xxx"/>
</bean>
<bean id="jpaVendorAdapter" class="org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter">
<property name="showSql" value="true" />
<property name="generateDdl" value="true" />
</bean>
<bean id="entityManagerFactory" class="org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean">
<property name="dataSource" ref="dataSource"/>
<property name="persistenceUnitName" value="Test_PU"/>
<property name="jpaVendorAdapter" ref="jpaVendorAdapter"/>
<property name="packagesToScan" value="com.canreef.calendar"/>
</bean>
<bean id="transactionManager" class="org.springframework.orm.jpa.JpaTransactionManager">
<property name="entityManagerFactory" ref="entityManagerFactory"/>
</bean>
</beans>
Really appreciate it if anybody can point out what is wrong in my code.

Please make sure your compiled war file contains only ONE org.hibernate.javax.persistencejar, it should be 2.1. Spring-data-jpa drags hibernate-jpa 2.0 along with it, you should exclude that specifically in your pom.xml.
On top of that, you really need to remove hibernate-core and ONLY have hibernate-entitymanager on your class path. Make sure, nothing else drags along hibernate-core either. The class you're looking for is only contained within hibernate-entitymanager.
These 2 things are DEFINITELY your culprit. Compile and check for the correct JARs. If you're starting Tomcat from within Eclipse, make sure your Deployment Assemblyhas all the correct classpath files in it. Doing mvn eclipse:eclipsemight also help.
Basically, before the server starts, make sure all jars/classes are exactly where they should be. Doing as I said should fix it already, but if it doesn't, it should definitely help identity the culprit.

Same question as NoClassDefFoundError with Spring maven hibernate org/hibernate/ejb/HibernatePersistence ?
You miss a dependency:
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>${hibernate.version}</version>
</dependency>
If you have a NoClassDefFound exception a good starting point is to look if the missing class is in one of your dependency jars. If not, add the missing dependency.
The springframework-orm POM refers to hibernate-entitymanager 4.2.8.Final (see http://central.maven.org/maven2/org/springframework/spring-orm/4.0.1.RELEASE/spring-orm-4.0.1.RELEASE.pom) You depend on 4.1.*.

Facing UTF-8 issue after updating hibernate version

I know this question is somehow repetitive and boring but I didn't manage to solve it and it's been 3 hours I'm stuck in it. My webapp was working like a charm with hibernate 4.2.2.Final version and I didn't have any problem but after adding hibernate search (5.0.1.Final version) I had to update hibernate version because it wasn't compatible with it. And now when I do update or insert into database, all the UTF-8 characters are saved incorrectly. Here's my config files:
pom.xml (missing dependencies are in the parent project's pom.xml)
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<artifactId>myproject</artifactId>
<groupId>com.mycompany</groupId>
<version>1.0-SNAPSHOT</version>
</parent>
<groupId>com.mycompany.myproject.web</groupId>
<artifactId>web</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>war</packaging>
<name>web</name>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<jstl.version>1.2</jstl.version>
<log4j.version>1.2.17</log4j.version>
<servlet.version>2.5</servlet.version>
<commons-codec.version>1.10</commons-codec.version>
<spring-security.version>3.1.4.RELEASE</spring-security.version>
<endorsed.dir>${project.build.directory}/endorsed</endorsed.dir>
<hibernate.version>4.3.8.Final</hibernate.version>
<jpa.version>2.0.Beta-20090815</jpa.version>
<hibernate-search.version>5.0.1.Final</hibernate-search.version>
<hibernate-entitymanager.version>4.3.8.Final</hibernate-entitymanager.version>
<hibernate-search-infinispan.version>5.0.1.Final</hibernate-search-infinispan.version>
<kaptcha.version>2.3</kaptcha.version>
</properties>
<dependencies>
<dependency>
<groupId>javax</groupId>
<artifactId>javaee-web-api</artifactId>
<version>7.0</version>
<scope>provided</scope>
</dependency>
<!-- Servlet, JSP, JSTL -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>jstl</artifactId>
<version>${jstl.version}</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
<version>${servlet.version}</version>
</dependency>
<!--My Project Core-->
<dependency>
<groupId>${project.parent.groupId}.myproject.core</groupId>
<artifactId>core</artifactId>
<version>${project.parent.version}</version>
<type>jar</type>
</dependency>
<!--Spring MVC-->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-webmvc</artifactId>
<version>${spring.version}</version>
</dependency>
<!--Spring Security-->
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-core</artifactId>
<version>${spring-security.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-web</artifactId>
<version>${spring-security.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-config</artifactId>
<version>${spring-security.version}</version>
</dependency>
<!--log4j-->
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>${log4j.version}</version>
</dependency>
<!--Apache Commons-->
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>${commons-codec.version}</version>
</dependency>
<!--KAPTCHA-->
<dependency>
<groupId>kaptcha</groupId>
<artifactId>kaptcha</artifactId>
<version>2.3.2</version>
</dependency>
<!--Hibernate-->
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>${hibernate.version}</version>
</dependency>
<dependency>
<groupId>org.hibernate.java-persistence</groupId>
<artifactId>jpa-api</artifactId>
<version>${jpa.version}</version>
</dependency>
<!--Hibernate Search-->
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-search-orm</artifactId>
<version>${hibernate-search.version}</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>${hibernate-entitymanager.version}</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-search-infinispan</artifactId>
<version>${hibernate-search-infinispan.version}</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
<compilerArguments>
<endorseddirs>${endorsed.dir}</endorseddirs>
</compilerArguments>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>${kaptcha.version}</version>
<configuration>
<failOnMissingWebXml>false</failOnMissingWebXml>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.6</version>
<executions>
<execution>
<phase>validate</phase>
<goals>
<goal>copy</goal>
</goals>
<configuration>
<outputDirectory>${endorsed.dir}</outputDirectory>
<silent>true</silent>
<artifactItems>
<artifactItem>
<groupId>javax</groupId>
<artifactId>javaee-endorsed-api</artifactId>
<version>7.0</version>
<type>jar</type>
</artifactItem>
</artifactItems>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
spring-beans.xml
<?xml version="1.0" encoding="UTF-8"?>
<beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns="http://www.springframework.org/schema/beans"
xmlns:context="http://www.springframework.org/schema/context"
xmlns:p="http://www.springframework.org/schema/p"
xmlns:aop="http://www.springframework.org/schema/aop"
xmlns:tx="http://www.springframework.org/schema/tx"
xsi:schemaLocation="
http://www.springframework.org/schema/beans
http://www.springframework.org/schema/beans/spring-beans.xsd
http://www.springframework.org/schema/tx
http://www.springframework.org/schema/tx/spring-tx.xsd
http://www.springframework.org/schema/aop
http://www.springframework.org/schema/aop/spring-aop.xsd
http://www.springframework.org/schema/context
http://www.springframework.org/schema/context/spring-context.xsd">
<context:component-scan base-package="com.mycompany.myproject.web" />
<context:annotation-config/>
<!-- Model Beans Declaration -->
<bean id="User" class="com.mycompany.myproject.core.dataaccess.model.User"/>
<!-- Service Declaration -->
<bean id="UserBoImpl" class="com.mycompany.myproject.core.business.bo.impl.UserBoImpl">
<property name="userDao" ref="UserDaoImpl" />
</bean>
<!-- DAO Declaration -->
<bean id="UserDaoImpl" class="com.mycompany.myproject.core.dataaccess.dao.impl.UserDaoImpl">
<property name="sessionFactory" ref="SessionFactory" />
</bean>
<!--HIBERNATE-->
<bean id="dataSource"
class="org.springframework.jdbc.datasource.DriverManagerDataSource">
<property name="url" value="jdbc:mysql://localhost:3306/mydb?autoReconnect=true&useUnicode=true&characterEncoding=utf-8"></property>
<property name="username" value="root"></property>
<property name="password" value="password"></property>
<property name="driverClassName" value="com.mysql.jdbc.Driver"></property>
</bean>
<bean id="SessionFactory" class="org.springframework.orm.hibernate4.LocalSessionFactoryBean">
<property name="annotatedClasses">
<list>
<value>com.mycompany.myproject.core.dataaccess.model.User</value>
</list>
</property>
<property name="dataSource" ref="dataSource"></property>
<property name="hibernateProperties">
<props>
<prop key="hibernate.connection.useUnicode">true</prop>
<prop key="hibernate.connection.characterEncoding">UTF-8</prop>
<prop key="hibernate.connection.charSet">UTF-8</prop>
<prop key="hibernate.dialect">org.hibernate.dialect.MySQL5InnoDBDialect</prop>
<prop key="hibernate.show_sql">true</prop>
</props>
</property>
</bean>
<tx:annotation-driven transaction-manager="transactionManager" />
<bean id="transactionManager" class="org.springframework.orm.hibernate4.HibernateTransactionManager">
<property name="sessionFactory" ref="SessionFactory" />
</bean>
</beans>
web.xml
<?xml version="1.0" encoding="UTF-8"?>
<web-app version="3.0" xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_3_0.xsd">
...
<!--SPRING ENCODING FILTER-->
<filter>
<filter-name>SetCharacterEncodingFilter</filter-name>
<filter-class>org.springframework.web.filter.CharacterEncodingFilter</filter-class>
<init-param>
<param-name>encoding</param-name>
<param-value>UTF-8</param-value>
</init-param>
<init-param>
<param-name>forceEncoding</param-name>
<param-value>true</param-value>
</init-param>
</filter>
<filter-mapping>
<filter-name>SetCharacterEncodingFilter</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>
...
</web-app>
Tomcat server.xml
...
<Connector URIEncoding="utf-8" connectionTimeout="20000" port="8084" protocol="HTTP/1.1" redirectPort="8443"/>
...
I appreciate your comments.

Autowiring seems to fail

I know this question is asked multiple times, but I'm looking at it a couple of nights now and I can't seem to find out why the heck the Autowired fields keep null. I'm staring blind against it, so maybe somebody of you guys sees what is wrong.
I have the following code:
ApplicationContext.xml
<beans xmlns="http://www.springframework.org/schema/beans" xmlns:context="http://www.springframework.org/schema/context" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-4.0.xsd http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context-4.0.xsd ">
<context:component-scan base-package="com.skoerkamp"/>
<import resource="ApplicationContext-persistence.xml"/>
</beans>
ApplicationContext-persistence.xml
<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:jdbc="http://www.springframework.org/schema/jdbc" xmlns:tx="http://www.springframework.org/schema/tx" xsi:schemaLocation=" http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-4.0.xsd http://www.springframework.org/schema/jdbc http://www.springframework.org/schema/jdbc/spring-jdbc-4.0.xsd http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx-4.0.xsd">
<tx:annotation-driven transaction-manager="transactionManager"/>
<bean id="transactionManager" class="org.springframework.orm.jpa.JpaTransactionManager">
<property name="entityManagerFactory" ref="entityManagerFactory"/>
</bean>
<bean id="entityManagerFactory" class="org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean">
<property name="packagesToScan" value="com.skoerkamp.model"/>
<property name="dataSource" ref="dataSource"/>
<property name="persistenceUnitName" value="GP_UNIT"/>
<property name="jpaProperties">
<props>
<prop key="hibernate.dialect">org.hibernate.dialect.MySQL5InnoDBDialect</prop>
<!--
<prop key="hibernate.hbm2ddl.auto">create-drop</prop>
-->
</props>
</property>
<property name="jpaVendorAdapter">
<bean class="org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter">
<property name="showSql" value="false"/>
<property name="generateDdl" value="false"/>
</bean>
</property>
</bean>
<!-- DB configuration -->
<bean name="dataSource" class="org.springframework.jdbc.datasource.DriverManagerDataSource">
<property name="driverClassName" value="com.mysql.jdbc.Driver"/>
<property name="url" value="<connection-url>"/>
<property name="username" value="<user>"/>
<property name="password" value="<pw>"/>
</bean>
</beans>
pom.xml
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.skoerkamp</groupId>
<artifactId>groupplanner</artifactId>
<packaging>war</packaging>
<version>1.0-SNAPSHOT</version>
<name>Group Planner Server</name>
<url>http://maven.apache.org</url>
<repositories>
<repository>
<id>maven2-repository.java.net</id>
<name>Java.net Repository for Maven</name>
<url>http://download.java.net/maven/2/</url>
<layout>default</layout>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.8.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.sun.jersey</groupId>
<artifactId>jersey-server</artifactId>
<version>1.8</version>
</dependency>
<dependency>
<groupId>org.json</groupId>
<artifactId>json</artifactId>
<version>20141113</version>
</dependency>
<dependency>
<groupId>javax.ws.rs</groupId>
<artifactId>jsr311-api</artifactId>
<version>1.1.1</version>
</dependency>
<!-- Spring -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<version>4.1.3.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>4.1.3.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>3.0.4.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-beans</artifactId>
<version>4.1.3.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-tx</artifactId>
<version>4.0.5.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-orm</artifactId>
<version>4.1.3.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jdbc</artifactId>
<version>4.1.3.RELEASE</version>
</dependency>
<!--Database-->
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>5.1.24</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-validator</artifactId>
<version>5.1.3.Final</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>4.3.7.Final</version>
</dependency>
</dependencies>
<build>
<finalName>groupplanner</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.2</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-failsafe-plugin</artifactId>
<version>2.6</version>
<executions>
<execution>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.mortbay.jetty</groupId>
<artifactId>maven-jetty-plugin</artifactId>
<version>6.1.16</version>
<configuration>
<scanIntervalSeconds>10</scanIntervalSeconds>
<stopPort>8005</stopPort>
<stopKey>STOP</stopKey>
<webApp>
<contextPath>/groupplanner</contextPath>
</webApp>
</configuration>
<executions>
<execution>
<id>start-jetty</id>
<phase>pre-integration-test</phase>
<goals>
<goal>run</goal>
</goals>
<configuration>
<scanIntervalSeconds>0</scanIntervalSeconds>
<daemon>true</daemon>
</configuration>
</execution>
<execution>
<id>stop-jetty</id>
<phase>post-integration-test</phase>
<goals>
<goal>stop</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
For test purposes only a simple call to my service.
package com.skoerkamp.rest;
import com.skoerkamp.service.CalendarService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import javax.ws.rs.GET;
import javax.ws.rs.Path;
#Path("/calendar")
#Service
public class CalendarEndpoint {
#Autowired
private CalendarService calendarService;
#GET
public String getCalendarItems() {
calendarService.create();
return "";
}
}
Service:
package com.skoerkamp.service;
import com.skoerkamp.model.CalendarItem;
import com.skoerkamp.repository.CalendarRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import org.springframework.stereotype.Service;
#Service
public class CalendarService {
#Autowired
private CalendarRepository calendarRepository;
public void create() {
calendarRepository.create(new CalendarItem("TEST"));
}
}
This is a part of the stacktrace i get:
java.lang.NullPointerException
at com.skoerkamp.rest.CalendarEndpoint.getCalendarItems(CalendarEndpoint.java:23)
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 com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60)
at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatch
Line 23 is the call to calendarService.
Sorry for the long wall of text, but I wanted to show my problem as clear as possible. Any input or suggestions are appreciated! Thanks in advance:)

With Spring, Autowire will always wire the bean or it will fail unless you specifically mark it as #autowired(required = false) If you get a null pointer and it isn't autowiring that means you aren't using Spring to manage your beans.
You need to use Spring MVC (the Spring DispatcherServlet) to instantiate your objects. Take a look at 17.2 in http://docs.spring.io/spring/docs/current/spring-framework-reference/html/mvc.html. That shows you how to configure your project (either in XML or using Annotation only) so that Spring will manage your beans and properly autowire everything.

In order to load your beans and autowiring them, you need to configure the ContextLoaderListener in your web.xml and specify where is your main master context which is your case is "ApplicationContext.xml", by default the ContextLoaderListener loads the following file context "/WEB-INF/applicationContext.xml", so please rename your file appropriately. Here are some links that can help you to setup and understand the context loader mechanism:
http://www.springbyexample.org/examples/simple-spring-mvc-form-annotation-config-webapp.html#simple-spring-mvc-form-annotation-config-webapp-web-config
http://docs.spring.io/spring/docs/current/spring-framework-reference/html/beans.html#context-create
and a tutorial that explains how to create a restful api with Spring 3 step by step: http://www.ibm.com/developerworks/web/library/wa-spring3webserv/index.html?ca=drs-

you need to use #Autowired annotation on interface not a class.
so, create an interface, make CalendarService class implements it, then autowire the interface.
hope it works!

Unable to locate Spring Namespace Handler for XML schema namespace (JMS)

I am trying to build an executable jar and get the following error when I run it:
INFO: Loading XML bean definitions from class path resource [spring-app.xml]
Exception in thread "main" org.springframework.beans.factory.parsing.BeanDefinitionParsingException: Configuration problem: Unable to locate Spring NamespaceHandler for XML schema namespace [http://www.springframework.org/schema/jms]
Offending resource: class path resource [spring-app.xml]
My spring-app.xml is as below:
<?xml version="1.0" encoding="UTF-8"?>
<beans xmlns="http://www.springframework.org/schema/beans"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:jms="http://www.springframework.org/schema/jms"
xmlns:tx="http://www.springframework.org/schema/tx"
xsi:schemaLocation="http://www.springframework.org/schema/beans
http://www.springframework.org/schema/beans/spring-beans.xsd
http://www.springframework.org/schema/tx
http://www.springframework.org/schema/tx/spring-tx.xsd
http://www.springframework.org/schema/context
http://www.springframework.org/schema/context/spring-context.xsd
http://www.springframework.org/schema/jms
http://www.springframework.org/schema/jms/spring-jms.xsd">
<bean class="org.springframework.beans.factory.config.PropertyPlaceholderConfigurer">
<property name="locations">
<list>
<value>/etc/vtb/jndi.properties</value>
</list>
</property>
</bean>
<bean id="jndiTemplate" class="org.springframework.jndi.JndiTemplate">
<property name="environment">
<props>
<!-- prop key="java.naming.provider.url">jnp://ossprovesbjms01.gmtl.viasat.com:1099</prop-->
<prop key="java.naming.provider.url">${java.naming.provider.url}</prop>
<prop key="java.naming.factory.initial">${java.naming.factory.initial}</prop>
<prop key="java.naming.factory.url.pkgs">${java.naming.factory.url.pkgs}</prop>
</props>
</property>
</bean>
<bean id="connectionFactory" class="org.springframework.jndi.JndiObjectFactoryBean">
<property name="jndiTemplate" ref ="jndiTemplate"/>
<property name="jndiName" value="ConnectionFactory"/>
</bean>
<bean id="jmsTemplate" class="org.springframework.jms.core.JmsTemplate">
<property name="connectionFactory" ref="connectionFactory"/>
<property name="pubSubDomain" value="true"/>
<property name="deliveryPersistent" value="true"/>
<property name="deliveryMode" value="2"/>
</bean>
<!-- Listener Asynchronous -->
<bean id="beamBalanceListener" class="com.vtblistener.BeamBalanceListener"/>
<jms:listener-container concurrency="5-10">
<jms:listener destination="Beam_Balance" ref="beamBalanceListener"/>
</jms:listener-container>
And my pom is below:
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.viasat.nbn.nms</groupId>
<artifactId>vtb-hornetq-listener</artifactId>
<version>1.0.1</version>
<packaging>jar</packaging>
<name>vtb-hornetq-listener</name>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<hornetq.version>2.3.13.Final</hornetq.version>
<VTB_CONFIG_DIR>/etc/viasat/vtb/</VTB_CONFIG_DIR>
</properties>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>1.1.3</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-aop</artifactId>
<version>4.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-asm</artifactId>
<version>3.1.4.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-beans</artifactId>
<version>4.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>4.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<version>4.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-expression</artifactId>
<version>4.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jdbc</artifactId>
<version>4.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jms</artifactId>
<version>4.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-orm</artifactId>
<version>4.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-tx</artifactId>
<version>4.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>4.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-webmvc</artifactId>
<version>4.0.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.hornetq</groupId>
<artifactId>hornetq-commons</artifactId>
<version>${hornetq.version}</version>
</dependency>
<dependency>
<groupId>org.hornetq</groupId>
<artifactId>hornetq-core-client</artifactId>
<version>${hornetq.version}</version>
</dependency>
<dependency>
<groupId>org.hornetq</groupId>
<artifactId>hornetq-jms-client</artifactId>
<version>${hornetq.version}</version>
</dependency>
<dependency>
<groupId>org.jboss.naming</groupId>
<artifactId>jnpserver</artifactId>
<version>5.0.3.GA</version>
</dependency>
<!-- logback -->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
<version>1.0.13</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.0.13</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.5</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.6</source>
<target>1.6</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>com.vtblistener.VtbConsumer</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>com.vtblistener.VtbConsumer</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
<executions>
<execution>
<id>make-assembly</id> <!-- this is used for inheritance merges -->
<phase>package</phase> <!-- bind to the packaging phase -->
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
<finalName>vtb-hornetq-listener</finalName>
</build>

This is what I added to my maven-shade-plugin and it worked.The shade plugin provides options to append resources present in jar files like properties and xml files. AppendingTransformer is for normal files.XmlAppendingTransformer is for xml files.
<transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
<resource>META-INF/spring.handlers</resource>
</transformer>
<transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
<resource>META-INF/spring.schemas</resource>
</transformer>

Try to use the versioned xsd names of spring, like:
<beans xmlns="http://www.springframework.org/schema/beans"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:jms="http://www.springframework.org/schema/jms"
xmlns:tx="http://www.springframework.org/schema/tx"
xsi:schemaLocation="http://www.springframework.org/schema/beans
http://www.springframework.org/schema/beans/spring-beans.xsd
http://www.springframework.org/schema/tx
http://www.springframework.org/schema/tx/spring-tx.xsd
http://www.springframework.org/schema/context
http://www.springframework.org/schema/context/spring-context-4.0.xsd
http://www.springframework.org/schema/jms
http://www.springframework.org/schema/jms/spring-jms-4.0.xsd">