Tomcat + JPA + MySQL : java.lang.NoClassDefFoundError: javax/persistence/Persistence

Question

as part of a school project, I must connect a java REST API to a MySql database.

Unfortunately, I can't seem to instantiate the EntityManagerFactory. I've already tried to find the solution online, but I couldn't fix my issues.

I have several classes that will need to be stored in the datacase, and I've used annotations to describe them (basically @Entity annotations, @ManyToOne and others, and of course @Id and @GeneratedValue

My custom EntityManager :

import javax.persistence.EntityManager;
import javax.persistence.EntityManagerFactory;
import javax.persistence.Persistence;

public class NatagoraEntityManager {
    private EntityManager manager;
    public NatagoraEntityManager(){
        EntityManagerFactory factory =  Persistence.createEntityManagerFactory("MyPersistenceUnit");
        manager = factory.createEntityManager();
    }
}

My RestController :

@Path("/helloworld")
public class HelloWorld {

    private NatagoraEntityManager manager;
    public HelloWorld(){
        //Without this line it works fine
        manager = new NatagoraEntityManager();
    }


    // The Java method will process HTTP GET requests
    @GET
    // The Java method will produce content identified by the MIME Media type "text/plain"
    @Produces("text/plain")
    public String getClichedMessage() {
        // Return some cliched textual content
        return "Hello World";
    }
}

My persistence.xml :

<?xml version="1.0" encoding="UTF-8"?>
<persistence xmlns="http://java.sun.com/xml/ns/persistence" version="2.0">

    <persistence-unit name="MyPersistenceUnit">
        <properties>

            <property name="openjpa.ConnectionURL" value="jdbc:mysql://111.111.111.111:3306/bdname/"/>
            <property name="openjpa.ConnectionDriverName" value="com.mysql.jdbc.Driver"/>
            <property name="openjpa.ConnectionUserName" value="login"/>
            <property name="openjpa.ConnectionPassword" value="password"/>
            <property name="openjpa.Log" value="DefaultLevel=TRACE, Tool=INFO"/>
            <property name="openjpa.jdbc.SynchronizeMappings" value="buildSchema(ForeignKeys=true)"/>
        </properties>
    </persistence-unit>
</persistence>

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>JAXRS-Example</groupId>
    <artifactId>JAXRS-Example</artifactId>
    <version>0.0.1-SNAPSHOT</version>
    <packaging>war</packaging>

    <dependencies>
        <dependency>
            <groupId>com.sun.jersey</groupId>
            <artifactId>jersey-server</artifactId>
            <version>1.19</version>
        </dependency>
        <dependency>
            <groupId>com.sun.jersey</groupId>
            <artifactId>jersey-servlet</artifactId>
            <version>1.19</version>
        </dependency>
        <dependency>
            <groupId>com.owlike</groupId>
            <artifactId>genson</artifactId>
            <version>0.99</version>
        </dependency>
        <dependency>
            <groupId>com.sun.jersey</groupId>
            <artifactId>jersey-client</artifactId>
            <version>1.19</version>
        </dependency>
        <dependency>
            <groupId>com.sun.jersey</groupId>
            <artifactId>jersey-json</artifactId>
            <version>1.9</version>
        </dependency>
        <dependency>
            <groupId>javax.persistence</groupId>
            <artifactId>persistence-api</artifactId>
            <version>[1.0.2,)</version>
        </dependency>
        <dependency>
            <groupId>org.apache.openjpa</groupId>
            <artifactId>openjpa-persistence-jdbc</artifactId>
            <version>[1.0.1,)</version>
        </dependency>
    </dependencies>

    <build>
        <sourceDirectory>src</sourceDirectory>
        <plugins>
            <plugin>
                <artifactId>maven-war-plugin</artifactId>
                <version>2.6</version>
                <configuration>
                    <warSourceDirectory>WebContent</warSourceDirectory>
                    <failOnMissingWebXml>false</failOnMissingWebXml>
                </configuration>
            </plugin>
            <plugin>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.3</version>
                <configuration>
                    <source>1.7</source>
                    <target>1.7</target>
                </configuration>
            </plugin>
        </plugins>
    </build>
</project>

And finally, here is the errors I receive :

 java.lang.NoClassDefFoundError: javax/persistence/Persistence
    at DAL.NatagoraEntityManager.<init>(NatagoraEntityManager.java:10)
    at main.java.HelloWorld.<init>(HelloWorld.java:20)
    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.sun.jersey.server.spi.component.ResourceComponentConstructor._construct(ResourceComponentConstructor.java:245)
    at com.sun.jersey.server.spi.component.ResourceComponentConstructor.construct(ResourceComponentConstructor.java:233)
    at com.sun.jersey.server.impl.resource.PerRequestFactory$PerRequest._getInstance(PerRequestFactory.java:182)
    at com.sun.jersey.server.impl.resource.PerRequestFactory$AbstractPerRequest.getInstance(PerRequestFactory.java:144)
    at com.sun.jersey.server.impl.application.WebApplicationContext.getResource(WebApplicationContext.java:239)
    at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:83)
    at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
    at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84)
    at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1542)
    at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1473)
    at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1419)
    at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1409)
    at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:409)
    at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:558)
    at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:733)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:292)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:212)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:94)
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:504)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:141)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
    at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:620)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:502)
    at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1132)
    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:684)
    at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1539)
    at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1495)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.ClassNotFoundException: javax.persistence.Persistence
    at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1339)
    at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1167)
    ... 43 more

If you find an answer somewhere, I'll be grateful, as I'm stuck since several hours on this problem. If you need more informations, I'll be happy to tell you what you need.

Thank you !

EDIT : Here is a part of my project.iml file where I choose the JPA provider :

<facet type="jpa" name="JPA">
      <configuration>
        <setting name="validation-enabled" value="true" />
        <setting name="provider-name" value="OpenJPA" />
        <datasource-mapping />
        <deploymentDescriptor name="persistence.xml" url="file://$MODULE_DIR$/src/META-INF/persistence.xml" />
      </configuration>
    </facet>

EDIT2 : changed the pom.xml

EDIT3 : Here are the jars included in my WAR file :

Answer 1

There was a lot of changes to make this project work.

Here is my pom.xml now :

<?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>JAXRS-Example</groupId>
    <artifactId>JAXRS-Example</artifactId>
    <version>0.0.1-SNAPSHOT</version>
    <packaging>war</packaging>
    <repositories>
        <repository>
            <id>eclipselink</id>
            <url>http://www.eclipse.org/downloads/download.php?r=1&amp;nf=1&amp;file=/rt/eclipselink/maven.repo/</url>
        </repository>
    </repositories>
    <dependencies>
        <dependency>
            <groupId>org.eclipse.persistence</groupId>
            <artifactId>eclipselink</artifactId>
            <version>2.7.0</version>
        </dependency>
        <dependency>
            <groupId>javax.persistence</groupId>
            <artifactId>javax.persistence-api</artifactId>
            <version>2.2</version>
        </dependency>
        <dependency>
            <groupId>org.eclipse.persistence</groupId>
            <artifactId>org.eclipse.persistence.jpa</artifactId>
            <version>2.7.0</version>
        </dependency>
        <dependency>
            <groupId>com.sun.jersey</groupId>
            <artifactId>jersey-server</artifactId>
            <version>1.19</version>
        </dependency>
        <dependency>
            <groupId>com.sun.jersey</groupId>
            <artifactId>jersey-servlet</artifactId>
            <version>1.19</version>
        </dependency>
        <dependency>
            <groupId>com.owlike</groupId>
            <artifactId>genson</artifactId>
            <version>0.99</version>
        </dependency>
        <dependency>
            <groupId>com.sun.jersey</groupId>
            <artifactId>jersey-client</artifactId>
            <version>1.19</version>
        </dependency>
        <dependency>
            <groupId>com.sun.jersey</groupId>
            <artifactId>jersey-json</artifactId>
            <version>1.9</version>
        </dependency>
        <dependency>
            <groupId>mysql</groupId>
            <artifactId>mysql-connector-java</artifactId>
            <version>5.1.44</version>
        </dependency>
    </dependencies>

    <build>
        <sourceDirectory>src</sourceDirectory>
        <plugins>
            <plugin>
                <artifactId>maven-war-plugin</artifactId>
                <version>2.6</version>
                <configuration>
                    <warSourceDirectory>WebContent</warSourceDirectory>
                    <failOnMissingWebXml>false</failOnMissingWebXml>
                </configuration>
            </plugin>
            <plugin>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.3</version>
                <configuration>
                    <source>1.7</source>
                    <target>1.7</target>
                </configuration>
            </plugin>
        </plugins>
    </build>
</project>

And my persistence.xml

<?xml version="1.0" encoding="UTF-8"?>
<persistence xmlns="http://java.sun.com/xml/ns/persistence" version="2.0">

    <persistence-unit name="MyPersistenceUnit">
        <provider>org.eclipse.persistence.jpa.PersistenceProvider</provider>
        <exclude-unlisted-classes>false</exclude-unlisted-classes>
        <properties>
            <property name="javax.persistence.jdbc.url" value="jdbc:mysql://localhost:3306/bdname"/>
            <property name="javax.persistence.jdbc.driver" value="com.mysql.jdbc.Driver"/>
            <property name="javax.persistence.jdbc.user" value="login"/>
            <property name="javax.persistence.jdbc.password" value="password"/>
            <property name="javax.persistence.schema-generation.database.action" value="create"/>
        </properties>
    </persistence-unit>
</persistence>

I also had to change the whole structure of my project, because I had several packages not included in main.java. Now, everything is organized in this package and not outside.