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Entity Manager is null when trying to connect to Dockerised DB2 in Java using JPA, also using maven & Open Liberty

So I'm developing an API and I'm trying to connect to a local docker instance of DB2 from java using JPA entity manager. After running Apache Maven and getting build success, I try a GET request from Postman to test an endpoint and get a list of all users from DB2. I'm receiving the below error saying that entity manager is null. I've tried researching online and can't seem to find the solution.
The Dao class is virtually unchanged from a previous iteration that used Derby instead of DB2 and it worked fine.
I was wanting to know where I've gone wrong, what needs changing, and if anything is not needed. Provided below is the xml files and the DAO java class containing the entity manager. All properties for DB2 is correct as they're unchanged from a successful connection I was able to do from Eclipse's Database Development. The driver used then was db2jcc4 which I think is different to the driver said to use for the maven dependency so not sure if that's an issue.
Postman:
Error 500: java.lang.NullPointerException: Cannot invoke
"javax.persistence.EntityManager.createNamedQuery(String, java.lang.Class)" because
"this.em" is null
Maven:
[INFO] [ERROR ] CWWJP0015E: An error occurred in the org.eclipse.persistence.jpa.PersistenceProvider persistence provider when it attempted to create the container entity manager factory for the jpa-unit persistence unit. The following error occurred: Exception [EclipseLink-28018] (Eclipse Persistence Services - 2.7.9.v20210604-2c549e2208): org.eclipse.persistence.exceptions.EntityManagerSetupException
[INFO] Exception Description: Predeployment of PersistenceUnit [jpa-unit] failed.
[INFO] Internal Exception: javax.persistence.PersistenceException: CWWJP0013E: The server cannot locate the java:comp/DefaultDataSource data source for the jpa-unit persistence unit because it has encountered the following exception: javax.naming.NameNotFoundException: javax.naming.NameNotFoundException: java:comp/DefaultDataSource.
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 https://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.obdoblock</groupId>
<artifactId>hyperledger-api</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>war</packaging>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
<!-- Liberty configuration -->
<liberty.var.default.http.port>3500</liberty.var.default.http.port>
<liberty.var.default.https.port>9443</liberty.var.default.https.port>
<liberty.var.app.context.root>api</liberty.var.app.context.root>
<!-- TestDB Configuration -->
<version.ibm.db2>11.5.6.0</version.ibm.db2>
</properties>
<dependencies>
<!-- Provided dependencies -->
<dependency>
<groupId>jakarta.platform</groupId>
<artifactId>jakarta.jakartaee-api</artifactId>
<version>8.0.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.eclipse.microprofile</groupId>
<artifactId>microprofile</artifactId>
<version>3.3</version>
<type>pom</type>
<scope>provided</scope>
</dependency>
<!-- For tests -->
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
<version>5.6.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.cxf</groupId>
<artifactId>cxf-rt-rs-client</artifactId>
<version>3.3.6</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.cxf</groupId>
<artifactId>cxf-rt-rs-extension-providers</artifactId>
<version>3.3.6</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse</groupId>
<artifactId>yasson</artifactId>
<version>1.0.7</version>
<scope>test</scope>
</dependency>
<!-- DB2 connector -->
<dependency>
<groupId>com.ibm.db2</groupId>
<artifactId>jcc</artifactId>
<version>11.5.6.0</version>
</dependency>
<!-- Hyperledger Fabric Gateway for Blockchain -->
<dependency>
<groupId>org.hyperledger.fabric</groupId>
<artifactId>fabric-gateway-java</artifactId>
<version>2.2.0</version>
</dependency>
</dependencies>
<build>
<finalName>${project.artifactId}</finalName>
<plugins>
<!-- Enable liberty-maven plugin -->
<plugin>
<groupId>io.openliberty.tools</groupId>
<artifactId>liberty-maven-plugin</artifactId>
<version>3.3.4</version>
<configuration>
<copyDependencies>
<location>${project.build.directory}/liberty/wlp/usr/shared/resources</location>
<dependency>
<groupId>com.ibm.db2</groupId>
<artifactId>jcc</artifactId>
<version>11.5.6.0</version>
</dependency>
</copyDependencies>
</configuration>
</plugin>
<!-- Plugin to run functional tests -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>2.22.2</version>
<configuration>
<systemPropertyVariables>
<http.port>${liberty.var.default.http.port}</http.port>
<context.root>${liberty.var.app.context.root}</context.root>
</systemPropertyVariables>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>3.2.3</version>
</plugin>
<!-- Plugin to run unit tests -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.22.2</version>
</plugin>
</plugins>
</build>
</project>
server.xml
<server description="Obdoblock REST Server">
<featureManager>
<feature>jaxrs-2.1</feature>
<feature>openapi-3.1</feature>
<feature>jpa-2.2</feature>
<feature>cdi-2.0</feature>
</featureManager>
<httpEndpoint
httpPort="${default.http.port}"
httpsPort="${default.https.port}"
id="defaultHttpEndpoint"
host="*"
/>
<webApplication
location="hyperledger-api.war"
contextRoot="${app.context.root}"
/>
<!-- DB2 Library Configuration -->
<library id="DB2JCCLib">
<fileset dir="${shared.resource.dir}" includes="*.jar" />
</library>
<dataSource jndiName="jdbc/db2">
<jdbcDriver libraryRef="jdbcLib"/>
<properties
databaseName="testdb"
serverName="localhost"
portNumber="50000"
user="****" password="****"
/>
</dataSource>
</server>
persistence.xml
<?xml version="1.0" encoding="UTF-8"?>
<!-- TODO: This will have to be configured by ENV as well -->
<!-- https://www.eclipse.org/eclipselink/documentation/2.5/jpa/extensions/p_ddl_generation.htm -->
<persistence version="2.2"
xmlns="http://xmlns.jcp.org/xml/ns/persistence"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/persistence
http://xmlns.jcp.org/xml/ns/persistence/persistence_2_2.xsd">
<persistence-unit name="jpa-unit" transaction-type="JTA">
<properties>
<!-- Connection Specific -->
<property name="hibernate.dialect" value="org.hibernate.dialect.DB2Dialect"/>
<property name="javax.persistence.jdbc.driver" value="com.ibm.db2.jcc.DB2Driver" />
<property name="javax.persistence.jdbc.url" value="jdbc:db2://localhost:50000/testdb" />
<property name="javax.persistence.jdbc.user" value="****" />
<property name="javax.persistence.jdbc.password" value="****" />
<property name="show_sql" value="true"/>
<property name="hibernate.temp.use_jdbc_metadata_defaults" value="false"/>
</properties>
</persistence-unit>
</persistence>
UserDao.java
package dao;
import java.util.List;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.enterprise.context.RequestScoped;
import models.*;
#RequestScoped
public class UserDao {
#PersistenceContext(name = "jpa-unit")
private EntityManager em;
public void createUser(Users user){
em.persist(user);
}
public Users readUser(int userId){
return em.find(Users.class, userId);
}
public List<Users> readAllUsers(){
return em.createNamedQuery("Users.findAll", Users.class).getResultList();
}
public void updateUser(Users user){
em.merge(user);
}
public void deleteUser(Users userId){
em.remove(userId);
}
public List<Users> findUser(String email){
return em.createNamedQuery("Users.findUser", Users.class)
.setParameter("email", email)
.getResultList();
}
public void createHistory(History hist){
em.persist(hist);
}
//wait this doesnt do anything?
public Users readHistory(int id){
return em.find(Users.class, id);
}
public List<History> readAllHistory(){
return em.createNamedQuery("History.findAll", History.class).getResultList();
}
}
Versions:
Docker: 20.10.8, build 3967b7d
DB2: ibm/db2 docker image version 11.5.6
Maven: 3.8.3
Java: JDK 14.0.2
If needing any more details, I'm happy to provide them.
Thanks, Dylan

Your persistence.xml is incorrect. It should point to datasource configured in the server.xml, not specify driver properties.
Like this:
<?xml version="1.0" encoding="UTF-8"?>
<persistence version="2.2"
xmlns="http://xmlns.jcp.org/xml/ns/persistence"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/persistence
http://xmlns.jcp.org/xml/ns/persistence/persistence_2_2.xsd">
<persistence-unit name="jpa-unit" transaction-type="JTA">
<jta-data-source>jdbc/guestbookDS</jta-data-source>
<properties>
<property name="javax.persistence.schema-generation.database.action" value="create" />
<property name="javax.persistence.schema-generation.create-database-schemas" value="true" />
<property name="javax.persistence.schema-generation.scripts.action" value="create" />
<property name="javax.persistence.schema-generation.scripts.create-target" value="create.ddl"/>
<!--
<property name="eclipselink.ddl-generation" value="create-or-extend-tables"/>
<property name="eclipselink.ddl-generation.output-mode" value="both" />
-->
</properties>
</persistence-unit>
</persistence>
You can check this very simple Liberty project which uses JPA and database here https://github.com/stocktrader-ops/db-sat-demo (it is using PostgreSQL instead of DB2, but you should just use your datasource setup)

NoSuchMethod in hibernate-mysql connection

i'm facing a problem with connection to MySQL database by java. I've tried to change versions in pom.xml of hibernate-core/hibernate-entitymanager/hibernate-jpa and nothing worked.
It seems that it is a problem with hibernate-jpa duplication or it not working with mysql-connecot. After 2 hours of trying all these different versions i've decided to ask for help.
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>Pracownia</groupId>
<artifactId>PracowniaMain</artifactId>
<version>1.0-SNAPSHOT</version>
<properties>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
</properties>
<build>
<resources>
<resource>
<directory>src</directory>
<includes>
<include>META-INF/persistence.xml</include>
</includes>
</resource>
</resources>
<finalName>${project.artifactId}-${project.version}</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<attach>false</attach>
<appendAssemblyId>false</appendAssemblyId>
<archive>
<manifest>
<mainClass>
hibernate.Manager
</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.17</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
<scope>test</scope>
</dependency>
<!-- Hibernate resources -->
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>8.0.11</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>5.2.1.Final</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>5.2.0.Final</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-validator</artifactId>
<version>5.2.0.Final</version>
</dependency>
<dependency>
<groupId>org.hibernate.common</groupId>
<artifactId>hibernate-commons-annotations</artifactId>
<version>4.0.2.Final</version>
<classifier>tests</classifier>
</dependency>
<dependency>
<groupId>org.hibernate.javax.persistence</groupId>
<artifactId>hibernate-jpa-2.0-api</artifactId>
<version>1.0.1.Final</version>
</dependency>
<!-- Java Bind -->
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<version>2.2.11</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
<version>2.2.11</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.9.0</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-xml</artifactId>
<version>2.9.0</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-joda</artifactId>
<version>2.9.5</version>
</dependency>
<dependency>
<groupId>joda-time</groupId>
<artifactId>joda-time</artifactId>
<version>2.7</version>
</dependency>
</dependencies>
</project>
persistence.xml:
<!--<persistence xmlns="http://java.sun.com/xml/ns/persistence"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://java.sun.com/xml/ns/persistence http://java.sun.com/xml/ns/persistence/persistence_2_0.xsd"
version="2.0">-->
<persistence xmlns="http://xmlns.jcp.org/xml/ns/persistence"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/persistence
http://xmlns.jcp.org/xml/ns/persistence/persistence_2_1.xsd"
version="2.1">
<persistence-unit name="hibernate-dynamic" transaction-type="RESOURCE_LOCAL">
<provider>org.hibernate.jpa.HibernatePersistenceProvider</provider>
<!--<class>org.halyph.sessiondemo.Event</class>-->
<properties>
<property name="javax.persistence.jdbc.driver" value="com.mysql.cj.jdbc.Driver" />
<property name="javax.persistence.jdbc.url" value="jdbc:mysql://localhost/phpmyadmin?useSSL=false" />
<property name="javax.persistence.jdbc.user" value="root" />
<property name="javax.persistence.jdbc.password" value="" />
<property name="hibernate.connection.driver_class" value ="com.mysql.cj.jdbc.Driver" />
<property name="hibernate.dialect" value="org.hibernate.dialect.MySQL5Dialect" />
<property name="hibernate.show_sql" value="true" />
<property name="hibernate.hbm2ddl.auto" value="create" />
<property name="hibernate.format_sql" value="false"/>
</properties>
</persistence-unit>
</persistence>
Then after running this:
package hibernate;
import hibernate.model.artysci;
import javax.persistence.EntityManager;
import javax.persistence.EntityManagerFactory;
import javax.persistence.Persistence;
import javax.persistence.Query;
import java.util.List;
class Manager {
public static void main(String[] args) {
System.out.println("Start");
EntityManager entityManager = null;
EntityManagerFactory entityManagerFactory = null;
System.out.println("Start2");
try {
System.out.println("Start3");
//taka nazwa jak w persistence.xml
entityManagerFactory = Persistence.createEntityManagerFactory("hibernate-dynamic");
//utworz entityManagera
System.out.println("Start4");
entityManager = entityManagerFactory.createEntityManager();
//rozpocznij transakcje
entityManager.getTransaction().begin();
//System.out.println("dis");
/*
Employee emp = new Employee();
emp.setFirstName("Jan");
emp.setLastName("Polak");
emp.setSalary(100);
emp.setPesel(100);
entityManager.persist(emp);
Employee employee = entityManager.find(Employee.class, emp.getId());
entityManager.remove(emp);
System.out.println("Employee " + employee.getId() + " " + employee.getFirstName() + employee.getLastName());
*/
//zakoncz transakcje
entityManager.getTransaction().commit();
System.out.println("Done");
entityManager.close();
} catch (Throwable ex) {
System.err.println("Initial SessionFactory creation failed." + ex);
} finally {
entityManagerFactory.close();
}
}
}
Console:
Start
Start2
Start3
2021-01-06 18:52:56 DEBUG logging:38 - Logging Provider: org.jboss.logging.Log4jLoggerProvider
2021-01-06 18:52:56 INFO LogHelper:31 - HHH000204: Processing PersistenceUnitInfo [
name: hibernate-dynamic
...]
2021-01-06 18:52:57 INFO Version:37 - HHH000412: Hibernate Core {5.2.0.Final}
2021-01-06 18:52:57 INFO Environment:213 - HHH000206: hibernate.properties not found
2021-01-06 18:52:57 INFO Environment:318 - HHH000021: Bytecode provider name : javassist
2021-01-06 18:52:57 INFO Version:66 - HCANN000001: Hibernate Commons Annotations {5.0.1.Final}
2021-01-06 18:52:57 WARN connections:71 - HHH10001002: Using Hibernate built-in connection pool (not for production use!)
2021-01-06 18:52:57 INFO connections:127 - HHH10001005: using driver [com.mysql.cj.jdbc.Driver] at URL [jdbc:mysql://localhost/phpmyadmin?useSSL=false]
2021-01-06 18:52:57 INFO connections:136 - HHH10001001: Connection properties: {user=root}
2021-01-06 18:52:57 INFO connections:141 - HHH10001003: Autocommit mode: false
2021-01-06 18:52:57 INFO DriverManagerConnectionProviderImpl:39 - HHH000115: Hibernate connection pool size: 20 (min=1)
2021-01-06 18:52:57 INFO Dialect:152 - HHH000400: Using dialect: org.hibernate.dialect.MySQL5Dialect
Initial SessionFactory creation failed.java.lang.NoSuchMethodError: javax/persistence/Table.indexes()[Ljavax/persistence/Index; (loaded from file:/C:/Users/xxx/Desktop/PROJEKT%202/lib/javax.persistence.jar by sun.misc.Launcher$AppClassLoader#102dc1cf) called from class org.hibernate.cfg.annotations.EntityBinder (loaded from file:/C:/Users/xxx/.m2/repository/org/hibernate/hibernate-core/5.2.0.Final/hibernate-core-5.2.0.Final.jar by sun.misc.Launcher$AppClassLoader#102dc1cf).
Exception in thread "main" java.lang.NullPointerException
at hibernate.Manager.main(Manager.java:59)
Process finished with exit code -1
Thanks for help!

The problem is related to your dependencies, some of them in a transitive way load different versions of JPA so this produces the error.
In the case of your pom, you have 3 times the same dependency:
hibernate-entity-manager (in a transitive way load hibernate-jpa-2.0-api:1.0.0.Final)
hibernate-core (in a transitive way load hibernate-jpa-2.0-api:1.0.0.Final)
hibernate-jpa-2.0-api
All of them import "hibernate-jpa-2.0-api" but with a different version. I recommend removing hibernate-jpa-2.0-api
<dependency>
<groupId>org.hibernate.javax.persistence</groupId>
<artifactId>hibernate-jpa-2.0-api</artifactId>
<version>1.0.1.Final</version>
</dependency>
Another option is to exclude the dependency for the other dependencies.
A good plugin to check all the possible conflicts in your is Enforce

SessionFactory returning null in Hibernate

I am beginner in Hibernate and facing problem in creation of SessionFactory,
SessionFactoryProvider.java :
public class SessionFactoryProvider {
private static SessionFactory factory;
public static SessionFactory getFactory() {
try {
if (factory == null) {
Configuration cfg = new Configuration().configure("hibernate.cfg.xml");
factory = cfg.buildSessionFactory();
}
} catch (Exception e) {
try {
if (factory == null) {
Configuration configuration = new Configuration();
// Hibernate settings equivalent to hibernate.cfg.xml's properties
Properties property = new Properties();
property.put(Environment.DRIVER, "com.mysql.jdbc.Driver");
property.put(Environment.URL, "jdbc:mysql://localhost:3306/shopingsite");
property.put(Environment.USER, "root");
property.put(Environment.PASS, "");
property.put(Environment.DIALECT, "org.hibernate.dialect.MySQL5Dialect");
property.put(Environment.SHOW_SQL, "true");
property.put(Environment.HBM2DDL_AUTO, "update");
property.put(Environment.POOL_SIZE, 12);
configuration.setProperties(property);
configuration.addAnnotatedClass(Category.class);
configuration.addAnnotatedClass(User.class);
configuration.addAnnotatedClass(Product.class);
ServiceRegistry serviceRegistry = new StandardServiceRegistryBuilder()
.applySettings(configuration.getProperties()).build();
factory = configuration.buildSessionFactory(serviceRegistry);
}
} catch (HibernateException | NullPointerException he) {
System.out.println("Both factory code Fail");
}
}
return factory;
}
public static void shutdow() {
factory.close();
}
}
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>MavenShopping</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>war</packaging>
<name>MavenShopping</name>
<properties>
<endorsed.dir>${project.build.directory}/endorsed</endorsed.dir>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
<compilerArguments>
<endorseddirs>${endorsed.dir}</endorseddirs>
</compilerArguments>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.6</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>
<dependencies>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>5.4.6.Final</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>5.1.16</version>
</dependency>
<dependency>
<groupId>javax</groupId>
<artifactId>javaee-web-api</artifactId>
<version>8.0</version>
<type>jar</type>
</dependency>
</dependencies>
</project>
hibernate.cfg.xml
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE hibernate-configuration PUBLIC "-//Hibernate/Hibernate Configuration DTD 3.0//EN" "http://www.hibernate.org/dtd/hibernate-configuration-3.0.dtd">
<hibernate-configuration>
<session-factory>
<property name="hibernate.hbm2ddl.auto">update</property>
<property name="hibernate.dialect">org.hibernate.dialect.MySQL5Dialect</property>
<property name="hibernate.connection.url">jdbc:mysql://localhost:3306/shopingsite</property>
<property name="hibernate.connection.username">root</property>
<property name="hibernate.connection.password"/>
<property name="show_sql">true</property>
<property name="hibernate.connection.autocommit">true</property>
<property name="hibernate.connection.driver_class">com.mysql.jdbc.Driver</property>
<mapping class="BeanFile.Category"/>
<mapping class="BeanFile.Product"/>
<mapping class="BeanFile.User"/>
</session-factory>
</hibernate-configuration>
Error which was showing in the log is shown below
Info: MavenShopping was successfully deployed in 1,530 milliseconds.
Info: 1
Info: HHH000412: Hibernate Core {5.4.6.Final}
Info: ******************************************
Info: HCANN000001: Hibernate Commons Annotations {5.1.0.Final}
WARN: HHH10001002: Using Hibernate built-in connection pool (not for production use!)
Info: HHH10001005: using driver [com.mysql.jdbc.Driver] at URL [jdbc:mysql://localhost:3306/shopingsite]
Info: HHH10001001: Connection properties: {user=root, password=****, autocommit=true}
Info: HHH10001003: Autocommit mode: true
Warning: StandardWrapperValve[RegistrationServlet]: Servlet.service() for servlet RegistrationServlet threw exception
java.lang.NoSuchMethodError: org.hibernate.internal.CoreMessageLogger.debugf(Ljava/lang/String;I)V
How to solve this ?

The problem with your Hibernate SessionFactory has something to do with your environment. It would appear that your compile time libraries are not the same as your runtime libraries, as a method on one of the classes you use when coding isn't there when the server kicks off.
java.lang.NoSuchMethodError: org.hibernate.internal.CoreMessageLogger.debugf(Ljava/lang/String;I)V
That seems to be the big problem triggering issues with SessionFactory creation.

Why i can't run hibernate maven app from console?

I am trying to run a Hibernate application. I can do it from NetBeans IDE, when I am going to command line, with mvn install it builds successfully but when I am trying to run the jar file in target folder (java -jar hibernate-1.0-SNAPSHOT.jar) I am getting the following error:
Exception in thread "main" java.lang.NoClassDefFoundError: org/hibernate/cfg/Configuration
at hibernate.HibernateUtil.getSessionFactory(HibernateUtil.java:11)
at hibernate.SmartDevice.main(SmartDevice.java:13)
Caused by: java.lang.ClassNotFoundException: org.hibernate.cfg.Configuration
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
... 2 more
It doesn't find the Configuration class of Hibernate, but I added the hibernate-core dependency in my 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>hibernate</groupId>
<artifactId>hibernate</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>jar</packaging>
<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>
</properties>
<dependencies>
<!-- https://mvnrepository.com/artifact/org.hibernate/hibernate-core -->
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>5.4.1.Final</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.h2database/h2 -->
<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
<version>1.4.197</version>
</dependency>
<!-- https://mvnrepository.com/artifact/javax.persistence/persistence-api -->
<dependency>
<groupId>javax.persistence</groupId>
<artifactId>persistence-api</artifactId>
<version>1.0.2</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>1.2.1</version>
</plugin>
<plugin>
<!-- Build an executable JAR -->
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.1.0</version>
<configuration>
<archive>
<manifest>
<mainClass>hibernate.SmartDevice</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
<name>hibernate</name>
</project>
Here is my hibernate.cfg.xml:
<?xml version='1.0' encoding='utf-8'?>
<!DOCTYPE hibernate-configuration PUBLIC
"-//Hibernate/Hibernate Configuration DTD//EN"
"http://www.hibernate.org/hibernate-configuration-3.0.dtd">
<hibernate-configuration>
<session-factory>
<property name="connection.driver_class">org.h2.Driver</property>
<property name="connection.url">jdbc:h2:mem:test;DB_CLOSE_DELAY=-1</property>
<property name="dialect">org.hibernate.dialect.H2Dialect</property>
<property name="show_sql">true</property>
<property name="hbm2ddl.auto">create</property>
<mapping class="hibernate.User"/>
</session-factory>
</hibernate-configuration>
Should I add something else? Or why is this error? Thanks for the help!

ClassNotFoundException means that the org.hibernate.cfg.Configuration class in not included in your classpath. Looking for that class in the IDE, we see it is included in the hibernate-core-5.4.1-Final.jar file.
By running java -jar hibernate-1.0-SNAPSHOT.jar, the additional dependencies are missing.
There are some ways to package your jar with the required dependencies, one is by using the maven-assembly-plugin, or by using the shade plugin.
As a "manual" alternative, you can cd to your project root folder (containing the pom.xml file), and execute
mvn clean package
mvn dependency:copy-dependencies
java -cp target/*;target/dependency/* hibernate.SmartDevice
The dependency plugin copies all needed jars to the target\dependency folder, and the last command adds all jars to the classpath and runs your java class.
edit the above commands are for Windows; on Linux you would use ":" in place of ";"

load external config file in spring batch admin

I downloaded the spring batch admin application in the github repo and I imported it in eclipse. it works perfectly.
Then, I asked myself how to import an external config file into the application that I can use in my job definition class.
I tried this :
VM Arguments
-Dspring.config.location=C:/path/to/config/file/application.properties
Job configuration
src/main/java
org.springframework.batch.admin.sample.job
-------------------------------------------
#Configuration
public class JobConfiguration {
//I try to import this properties from an external config file.
#Value("${folder.input.files}")
private String pathToFiles;
#Autowired
public JobBuilderFactory jobBuilderFactory;
#Autowired
public StepBuilderFactory stepBuilderFactory;
#Bean
#JobScope
public ExampleItemReader itemReader() {
return new ExampleItemReader();
}
#Bean
#StepScope
public ExampleItemWriter itemWriter(#Value("#{jobParameters[fail]}") Boolean fail) {
ExampleItemWriter itemWriter = new ExampleItemWriter();
itemWriter.setFail(fail);
return itemWriter;
}
#Bean
public Step step1() {
return stepBuilderFactory.get("step1")
.<String, Object>chunk(5)
.reader(itemReader())
.writer(itemWriter(null))
.build();
}
#Bean
public Job javaJob() {
return jobBuilderFactory.get("javaJob")
.start(step1())
.build();
}
}
XML configuration
src/main/resources
launch-context.xml
-----------------------
<?xml version="1.0" encoding="UTF-8"?>
<beans xmlns="http://www.springframework.org/schema/beans"
xmlns:p="http://www.springframework.org/schema/p" 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.xsd">
<description><![CDATA[
A convenient aggregating config file for running the jobs in this project
from the command line instead of from the web application. E.g.
$ MAVEN_OPTS="-Dbatch.jdbc.url=jdbc:hsqldb:hsql://localhost:9005/samples -Dbatch.data.source.init=false" \
mvn exec:java -Dexec.classpathScope=runtime \
-Dexec.mainClass=org.springframework.batch.core.launch.support.CommandLineJobRunner \
-Dexec.args="classpath:launch-context.xml job1 fail=false run.id=1"
]]>
</description>
<import resource="classpath*:/META-INF/spring/batch/bootstrap/**/*.xml" />
<import resource="classpath*:/META-INF/spring/batch/override/**/*.xml" />
<bean id="jobLauncherTaskExecutor" class="org.springframework.core.task.SyncTaskExecutor"/>
<!-- Try to add my external config file -->
<bean class="org.springframework.beans.factory.config.PropertyPlaceholderConfigurer">
<property name="locations">
<list>
<value>classpath:file:///${spring.config.location}</value>
</list>
</property>
<property name="systemPropertiesModeName" value="SYSTEM_PROPERTIES_MODE_OVERRIDE" />
<property name="ignoreResourceNotFound" value="true" />
<property name="ignoreUnresolvablePlaceholders" value="false" />
<property name="order" value="1" />
</bean>
</beans>
Stack trace when I launch the app with tomcat 7
18:54:38,528 ERROR localhost-startStop-1 context.ContextLoader:331 - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'jobConfiguration': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private java.lang.String org.springframework.batch.admin.sample.job.JobConfiguration.pathToFiles; nested exception is java.lang.IllegalArgumentException: Could not resolve placeholder 'folder.input.files' in string value "${folder.input.files}"
at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessPropertyValues(AutowiredAnnotationBeanPostProcessor.java:334)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1204)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:538)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:302)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:229)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:298)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:762)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:757)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:480)
at org.springframework.batch.core.configuration.support.GenericApplicationContextFactory$ResourceAnnotationApplicationContext.<init>(GenericApplicationContextFactory.java:209)
at org.springframework.batch.core.configuration.support.GenericApplicationContextFactory.createApplicationContext(GenericApplicationContextFactory.java:70)
at org.springframework.batch.core.configuration.support.AbstractApplicationContextFactory.createApplicationContext(AbstractApplicationContextFactory.java:172)
at org.springframework.batch.core.configuration.support.DefaultJobLoader.doLoad(DefaultJobLoader.java:154)
at org.springframework.batch.core.configuration.support.DefaultJobLoader.load(DefaultJobLoader.java:147)
at org.springframework.batch.core.configuration.support.AutomaticJobRegistrar.start(AutomaticJobRegistrar.java:173)
at org.springframework.batch.core.configuration.support.AutomaticJobRegistrar.onApplicationEvent(AutomaticJobRegistrar.java:139)
at org.springframework.context.event.SimpleApplicationEventMulticaster.invokeListener(SimpleApplicationEventMulticaster.java:151)
at org.springframework.context.event.SimpleApplicationEventMulticaster.multicastEvent(SimpleApplicationEventMulticaster.java:128)
at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:331)
at org.springframework.context.support.AbstractApplicationContext.finishRefresh(AbstractApplicationContext.java:773)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:483)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:403)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:106)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4939)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5434)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1559)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1549)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.springframework.beans.factory.BeanCreationException: Could not autowire field: private java.lang.String org.springframework.batch.admin.sample.job.JobConfiguration.pathToFiles; nested exception is java.lang.IllegalArgumentException: Could not resolve placeholder 'folder.input.files' in string value "${folder.input.files}"
at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:555)
at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:87)
at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessPropertyValues(AutowiredAnnotationBeanPostProcessor.java:331)
... 34 more
Caused by: java.lang.IllegalArgumentException: Could not resolve placeholder 'folder.input.files' in string value "${folder.input.files}"
at org.springframework.util.PropertyPlaceholderHelper.parseStringValue(PropertyPlaceholderHelper.java:174)
at org.springframework.util.PropertyPlaceholderHelper.replacePlaceholders(PropertyPlaceholderHelper.java:126)
at org.springframework.beans.factory.config.PropertyPlaceholderConfigurer$PlaceholderResolvingStringValueResolver.resolveStringValue(PropertyPlaceholderConfigurer.java:259)
at org.springframework.beans.factory.support.AbstractBeanFactory.resolveEmbeddedValue(AbstractBeanFactory.java:800)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:962)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:949)
at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:527)
... 36 more
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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<artifactId>spring-batch-admin-sample</artifactId>
<description>A sample web application (WAR project) for Spring Batch Admin console.</description>
<parent>
<artifactId>spring-batch-admin-parent</artifactId>
<groupId>org.springframework.batch</groupId>
<version>2.0.0.BUILD-SNAPSHOT</version>
<relativePath>../spring-batch-admin-parent</relativePath>
</parent>
<packaging>war</packaging>
<name>Web Sample</name>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-test</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-aop</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-webmvc</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jdbc</artifactId>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
</dependency>
<dependency>
<groupId>commons-dbcp</groupId>
<artifactId>commons-dbcp</artifactId>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
</dependency>
<dependency>
<groupId>commons-collections</groupId>
<artifactId>commons-collections</artifactId>
</dependency>
<dependency>
<groupId>org.aspectj</groupId>
<artifactId>aspectjrt</artifactId>
</dependency>
<dependency>
<groupId>org.aspectj</groupId>
<artifactId>aspectjweaver</artifactId>
</dependency>
<dependency>
<groupId>org.hsqldb</groupId>
<artifactId>hsqldb</artifactId>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.freemarker</groupId>
<artifactId>freemarker</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.batch</groupId>
<artifactId>spring-batch-core</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.batch</groupId>
<artifactId>spring-batch-infrastructure</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.batch</groupId>
<artifactId>spring-batch-admin-manager</artifactId>
<version>2.0.0.BUILD-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.springframework.batch</groupId>
<artifactId>spring-batch-admin-resources</artifactId>
<version>2.0.0.BUILD-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-all</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.mortbay.jetty</groupId>
<artifactId>maven-jetty-plugin</artifactId>
<configuration>
<contextPath>/spring-batch-admin-sample</contextPath>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
</plugins>
</build>
<repositories>
<repository>
<id>spring-milestones</id>
<name>Spring Maven Milestone Repository</name>
<url>http://s3.amazonaws.com/maven.springframework.org/milestone</url>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
</repositories>
</project>
I tried this post and much more but without success.
I use exactly the same files and the same configuration than the spring batch admin github project.
Can someone tell me how to add the external configuration file to spring batch admin?

Spring batch admin searches configurations in specific paths.This page explains from which paths it loads resources:
<import resource="classpath*:/META-INF/spring/batch/bootstrap/**/*.xml"/>
<import resource="classpath*:/META-INF/spring/batch/override/**/*.xml"/>
Note that the "override" location has no files in it in Spring Batch
Admin distribution. This is a placeholder for users to add their own
content.
We managed to load external properties files placing xml configuration file under src/main/resources/META-INF/spring/batch/override/manager/env-context.xml which looks like this:
<?xml version="1.0" encoding="UTF-8"?>
<beans xmlns="http://www.springframework.org/schema/beans"
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.xsd">
<!-- Use this to set additional properties on beans at run time -->
<bean id="placeholderProperties"
class="org.springframework.beans.factory.config.PropertyPlaceholderConfigurer">
<property name="locations">
<list>
<value>classpath:/org/springframework/batch/admin/bootstrap/batch.properties</value>
<value>classpath:batch-default.properties</value>
<value>classpath:batch-${ENVIRONMENT:hsql}.properties</value>
<value>classpath:batch-${ENVIRONMENT:mysql}.properties</value>
<!-- here we load properties from external config folder -->
<value>file:${spring.file.location}</value>
</list>
</property>
<property name="systemPropertiesModeName" value="SYSTEM_PROPERTIES_MODE_OVERRIDE" />
<property name="ignoreResourceNotFound" value="false" />
<property name="ignoreUnresolvablePlaceholders" value="false" />
<property name="order" value="1" />
</bean>
</beans>

Under main folder of spring-batch-admin template, there are three folders - java, resources and webapp. Under resources there are some property files and META-INF folder. within META-INF there are two folders - batch and servlet.
Here If I want to add new property file "batch.properties" under resources and want to refer the property values from configuration (xml) files from "META-INF/batch/*.xml" in addition to the properties from spring-batch-admin-manager-1.0.0.M1.jar,
1. where to add below entries
Where to keep "env-context.xml". Under which folders, coz in "src/main/resources/META-INF" i can see only one folder batch.
I tried to create "spring/batch/override/manager/env-context.xml" under "src/main/resources/META-INF" but not able to read the property file entries.
If you provide your working application folder structure will help me a lot.

You can put your env-context.xml file on spring/batch/servlet/override/env-context.xml folder.