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<dependencies>
    <dependency>
        <groupId>org.eclipse.persistence</groupId>
        <artifactId>eclipselink</artifactId>
        <version>2.6.1</version>
    </dependency>
    <dependency>
        <groupId>commons-dbcp</groupId>
        <artifactId>commons-dbcp</artifactId>
        <version>1.4</version>
    </dependency>
    <dependency>
        <groupId>org.apache.derby</groupId>
        <artifactId>derby</artifactId>
        <version>10.12.1.1</version>
        <scope>runtime</scope>
    </dependency>
    <dependency>
        <groupId>org.apache.tomcat</groupId>
        <artifactId>tomcat-catalina</artifactId>
        <version>8.0.28</version>
        <scope>runtime</scope>
    </dependency>
</dependencies>

<?xml version="1.0" encoding="UTF-8"?>
<persistence version="2.1" 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">
    <persistence-unit name="myPU" transaction-type="RESOURCE_LOCAL">
        <provider>org.eclipse.persistence.jpa.PersistenceProvider</provider>
        <non-jta-data-source>java:comp/env/jdbc/database</non-jta-data-source>
        <class>entity.Employee</class>
        <shared-cache-mode>NONE</shared-cache-mode>
        <properties>
            <property name="javax.persistence.schema-generation.database.action" value="create"/>
            <property name="eclipselink.logging.level" value="FINE"/>
            <property name="eclipselink.logging.parameters" value="true"/>
        </properties>
    </persistence-unit>
</persistence>

@Entity
public class Employee implements Serializable {
    @Id
    private Long id;
    private String firstName;
    private String lastName;

    // accessors omitted

public class Main {
    private static final String JNDI = "java:comp/env/jdbc/database";

    public static void main(String[] args) throws Exception {
        bind();
        lookup();
        final EntityManagerFactory emf = Persistence.createEntityManagerFactory("myPU");
        populate(emf);
        query(emf);
    }

    private static void bind() throws NamingException {
        System.setProperty(Context.INITIAL_CONTEXT_FACTORY, "org.apache.naming.java.javaURLContextFactory");
        System.setProperty(Context.URL_PKG_PREFIXES, "org.apache.naming");

        final BasicDataSource ds = new BasicDataSource();
        ds.setUrl("jdbc:derby:memory:myDB;create=true");

        final Context context = new InitialContext();
        try {
            context.createSubcontext("java:");
            context.createSubcontext("java:comp");
            context.createSubcontext("java:comp/env");
            context.createSubcontext("java:comp/env/jdbc");
            context.bind(JNDI, ds);
        } finally {
            context.close();
        }
    }

    private static void lookup() throws NamingException, SQLException {
        final Context context = new InitialContext();
        try {
            final DataSource ds = (DataSource) context.lookup(JNDI);
            try (final Connection cn = ds.getConnection();
                 final Statement st = cn.createStatement();
                 final ResultSet rs = st.executeQuery("SELECT CURRENT_TIMESTAMP FROM SYSIBM.SYSDUMMY1")) {
                while (rs.next()) {
                    System.out.println(rs.getTimestamp(1));
                }
            }
        } finally {
            context.close();
        }
    }

    private static void populate(final EntityManagerFactory emf) {
        final EntityManager em = emf.createEntityManager();
        try {
            final EntityTransaction tx = em.getTransaction();
            tx.begin();
            final Employee emp = new Employee();
            emp.setId(1l);
            emp.setFirstName("Jane");
            emp.setLastName("Doe");
            em.persist(emp);
            tx.commit();
        } finally {
            em.close();
        }
    }

    private static void query(final EntityManagerFactory emf) {
        final EntityManager em = emf.createEntityManager();
        try {
            System.out.println(em.find(Employee.class, 1l));
        } finally {
            em.close();
        }
    }
}

2015-10-25 10:33:24.235
[EL Fine]: server: 2015-10-25 10:33:24.478--Thread(Thread[main,5,main])--Configured server platform: org.eclipse.persistence.platform.server.NoServerPlatform
[EL Config]: metadata: 2015-10-25 10:33:24.633--ServerSession(1323434987)--Thread(Thread[main,5,main])--The access type for the persistent class [class entity.Employee] is set to [FIELD].
[EL Config]: metadata: 2015-10-25 10:33:24.654--ServerSession(1323434987)--Thread(Thread[main,5,main])--The alias name for the entity class [class entity.Employee] is being defaulted to: Employee.
[EL Config]: metadata: 2015-10-25 10:33:24.656--ServerSession(1323434987)--Thread(Thread[main,5,main])--The table name for entity [class entity.Employee] is being defaulted to: EMPLOYEE.
[EL Config]: metadata: 2015-10-25 10:33:24.666--ServerSession(1323434987)--Thread(Thread[main,5,main])--The column name for element [firstName] is being defaulted to: FIRSTNAME.
[EL Config]: metadata: 2015-10-25 10:33:24.668--ServerSession(1323434987)--Thread(Thread[main,5,main])--The column name for element [lastName] is being defaulted to: LASTNAME.
[EL Config]: metadata: 2015-10-25 10:33:24.668--ServerSession(1323434987)--Thread(Thread[main,5,main])--The column name for element [id] is being defaulted to: ID.
[EL Info]: 2015-10-25 10:33:24.7--ServerSession(1323434987)--Thread(Thread[main,5,main])--EclipseLink, version: Eclipse Persistence Services - 2.6.1.v20150916-55dc7c3
[EL Fine]: connection: 2015-10-25 10:33:24.706--Thread(Thread[main,5,main])--Detected database platform: org.eclipse.persistence.platform.database.JavaDBPlatform
[EL Config]: connection: 2015-10-25 10:33:24.714--ServerSession(1323434987)--Connection(1872973138)--Thread(Thread[main,5,main])--connecting(DatabaseLogin(
	platform=>JavaDBPlatform
	user name=> ""
	connector=>JNDIConnector datasource name=>java:comp/env/jdbc/database
))
[EL Config]: connection: 2015-10-25 10:33:24.715--ServerSession(1323434987)--Connection(1465346452)--Thread(Thread[main,5,main])--Connected: jdbc:derby:memory:myDB
	User: APP
	Database: Apache Derby  Version: 10.12.1.1 - (1704137)
	Driver: Apache Derby Embedded JDBC Driver  Version: 10.12.1.1 - (1704137)
[EL Config]: connection: 2015-10-25 10:33:24.715--ServerSession(1323434987)--Connection(1634387050)--Thread(Thread[main,5,main])--connecting(DatabaseLogin(
	platform=>JavaDBPlatform
	user name=> ""
	connector=>JNDIConnector datasource name=>java:comp/env/jdbc/database
))
[EL Config]: connection: 2015-10-25 10:33:24.716--ServerSession(1323434987)--Connection(1740223770)--Thread(Thread[main,5,main])--Connected: jdbc:derby:memory:myDB
	User: APP
	Database: Apache Derby  Version: 10.12.1.1 - (1704137)
	Driver: Apache Derby Embedded JDBC Driver  Version: 10.12.1.1 - (1704137)
[EL Info]: connection: 2015-10-25 10:33:24.747--ServerSession(1323434987)--Thread(Thread[main,5,main])--/file:/Users/kyle/src/jndi-se/target/classes/_myPU login successful
[EL Fine]: sql: 2015-10-25 10:33:24.784--ServerSession(1323434987)--Connection(762809053)--Thread(Thread[main,5,main])--CREATE TABLE EMPLOYEE (ID BIGINT NOT NULL, FIRSTNAME VARCHAR(255), LASTNAME VARCHAR(255), PRIMARY KEY (ID))
[EL Fine]: sql: 2015-10-25 10:33:24.85--ClientSession(1027495011)--Connection(1688470144)--Thread(Thread[main,5,main])--INSERT INTO EMPLOYEE (ID, FIRSTNAME, LASTNAME) VALUES (?, ?, ?)
	bind => [1, Jane, Doe]
[EL Fine]: sql: 2015-10-25 10:33:24.877--ServerSession(1323434987)--Connection(640808588)--Thread(Thread[main,5,main])--SELECT ID, FIRSTNAME, LASTNAME FROM EMPLOYEE WHERE (ID = ?)
	bind => [1]
Employee{id=1, firstName='Jane', lastName='Doe'}

<dependencies>
    <dependency>
        <groupId>javax.servlet</groupId>
        <artifactId>javax.servlet-api</artifactId>
        <version>3.1.0</version>
        <scope>provided</scope>
    </dependency>
    <dependency>
        <groupId>org.eclipse.persistence</groupId>
        <artifactId>eclipselink</artifactId>
        <version>2.6.0</version>
    </dependency>
    <dependency>
        <groupId>com.google.inject</groupId>
        <artifactId>guice</artifactId>
        <version>4.0</version>
    </dependency>
    <dependency>
        <groupId>com.google.inject.extensions</groupId>
        <artifactId>guice-servlet</artifactId>
        <version>4.0</version>
    </dependency>
    <dependency>
        <groupId>com.google.inject.extensions</groupId>
        <artifactId>guice-persist</artifactId>
        <version>4.0</version>
    </dependency>
</dependencies>

<web-app xmlns="http://xmlns.jcp.org/xml/ns/javaee"
         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
         xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee http://xmlns.jcp.org/xml/ns/javaee/web-app_3_1.xsd"
         version="3.1">

    <!-- taken from https://github.com/google/guice/wiki/Servlets -->

    <listener>
        <listener-class>guice.tomcat.MyGuiceServletConfig</listener-class>
    </listener>

    <filter>
        <filter-name>guiceFilter</filter-name>
        <filter-class>com.google.inject.servlet.GuiceFilter</filter-class>
    </filter>

    <filter-mapping>
        <filter-name>guiceFilter</filter-name>
        <url-pattern>/*</url-pattern>
    </filter-mapping>

    <resource-ref>
        <res-ref-name>jdbc/derby</res-ref-name>
        <res-type>javax.sql.DataSource</res-type>
        <res-auth>Container</res-auth>
    </resource-ref>

</web-app>

<?xml version="1.0" encoding="UTF-8"?>
<persistence version="2.1" 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">
    <persistence-unit name="myJpaUnit" transaction-type="RESOURCE_LOCAL">
        <provider>org.eclipse.persistence.jpa.PersistenceProvider</provider>
        <non-jta-data-source>java:comp/env/jdbc/derby</non-jta-data-source>
        <class>guice.tomcat.MyEntity</class>
        <properties>
            <property name="eclipselink.ddl-generation" value="drop-and-create-tables"/>
            <property name="eclipselink.logging.level" value="FINE"/>
            <property name="eclipselink.logging.level.sql" value="FINE"/>
        </properties>
    </persistence-unit>
</persistence>

public class MyGuiceServletConfig extends GuiceServletContextListener {
    @Override
    protected Injector getInjector() {
        return Guice.createInjector(new ServletModule() {
            @Override
            protected void configureServlets() {
                serve("/*").with(MyServlet.class);
                bind(MyService.class).to(MyServiceImpl.class);

                install(new JpaPersistModule("myJpaUnit"));
                filter("/*").through(PersistFilter.class);
            }
        });
    }
}

@Entity
@NamedQuery(name = "MyEntity.findAll", query = "SELECT e FROM MyEntity e ORDER BY e.id DESC")
public class MyEntity implements Serializable {

    @Id
    @GeneratedValue
    private Long id;
    @Column(nullable = false)
    @Temporal(TemporalType.TIMESTAMP)
    private Date ts;

... accessors are omitted

@javax.inject.Singleton
public class MyServlet extends HttpServlet {

    @javax.inject.Inject
    private MyService myService;

    @Override
    public void doGet(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
        MyEntity myEntity = new MyEntity();
        myEntity.setTs(new Date());
        myService.save(myEntity);

        PrintWriter writer = resp.getWriter();
        writer.write("<html><body><ul>");
        for(MyEntity e : myService.findAll()){
            writer.write("<li>");
            writer.write(e.toString());
            writer.write("</li>");
        }
        writer.write("</ul></body></html>");

    }
}