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Why Eclipse dont generate complete persistence.xml?

I have Vaadin project with JPA 2.1 + EclipseLink + MySQL.
In eclipse in project settings I set connection to base and drivers correctly. Without problem I "generate Entities from Tables", but persistence.xml haven't info about driver, connection, login, pass to DB.
My auto generate persistence.xml
<?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="RadiologicalWarehouse">
<class>pl.intibs.rw.entitites.Message</class>
<class>pl.intibs.rw.entitites.Part</class>
<class>pl.intibs.rw.entitites.Role</class>
<class>pl.intibs.rw.entitites.Sample</class>
<class>pl.intibs.rw.entitites.SampleHistory</class>
<class>pl.intibs.rw.entitites.User</class>
</persistence-unit>
</persistence>
If I run my application with simple query, I get of course exception:
javax.servlet.ServletException: com.vaadin.server.ServiceException: javax.persistence.PersistenceException: Exception [EclipseLink-4021] (Eclipse Persistence Services - 2.5.0.v20130507-3faac2b): org.eclipse.persistence.exceptions.DatabaseException
Exception Description: Unable to acquire a connection from driver [null], user [null] and URL [null]. Verify that you have set the expected driver class and URL. Check your login, persistence.xml or sessions.xml resource. The jdbc.driver property should be set to a class that is compatible with your database platform
com.vaadin.server.VaadinServlet.service(VaadinServlet.java:239)
javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
If JPA has defined the connection in the project, why does not generate this persistence automatically?
Screenshot settings JPA: http://i.imgur.com/T2oEdHA.png

Based on what I understand you have set parameters for the Jpa plugin to eclipse and this is much different to set the parameters to persistence provider. Firstly you have to decide what persitent provide use and specify it in the persistence.xml together with the others paramenters.
This is an example of persistence.xml with eclipseLink:
<persistence>
<persistence-unit name="myUnit">
<provider>yourProvider</provider>
<class>it.myCompany.domain.MyFirstClass</class>
<class>it.myCompany.domain.MySecondClassClass</class>
<properties>
<property name="javax.persistence.jdbc.driver" value="${driverClass}" />
<property name="javax.persistence.jdbc.url" value="${connectionURL}" />
<property name="javax.persistence.jdbc.user" value="${username}" />
<property name="javax.persistence.jdbc.password" value="${password}" />
<property name="eclipselink.logging.level" value="info"/>
</properties>
<shared-cache-mode>NONE</shared-cache-mode>
</persistence-unit>
</persistence>

Why is there no transaction in my thread? JPA JTS/JTA Glassfish 4

I'm writing a small EJB3 application deployed on glassfish 4 and using the derbyDB that comes with glassfish.
To make testing easy I have declared one of my EJBs as #Webservice so I can trigger a method with the testers provided by glassfish. So far so good.
The callstack is like this:
DailyReportingJob( #Stateless and #WebService, EntryPoint for my test)
--> VerfahrensArchivService (#Stateless and #Transactional(value = TxType.REQUIRES_NEW) )
my persistence.xml is like this:
<?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="zvagent">
<jta-data-source>jdbc/zvagentdb</jta-data-source>
<class>de.kevinfleischer.zvagent.verfahren.Verfahren</class>
<properties>
<property name="eclipselink.logging.level" value="FINE"/>
<property name="javax.persistence.schema-generation.database.action" value="create"/>
<property name="eclipselink.deploy-on-startup" value="true"/>
</properties>
</persistence-unit>
</persistence>
I've configured a connection pool in glassfish of ressource type javax.sql.DataSource and a jdbc ressource with the name jdbc/zvagentdb that points to this pool.
When I trigger the webservice I see my app working. But when I try to call the VerfahrensArchivService - which should store data to the DB - the following warning shows up. In the webinterface of the webservice tester I see further an InvocationTargetException, telling me the call to "doPost" failed.
WARNING: javax.ejb.EJBException: java.lang.IllegalStateException: Transaction is not active in the current thread.
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2016)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:1979)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:220)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:88)
at com.sun.proxy.$Proxy455.storeAndUpdateVerfahren(Unknown Source)
at de.kevinfleischer.zvagent.archiv.__EJB31_Generated__VerfahrensArchivService__Intf____Bean__.storeAndUpdateVerfahren(Unknown Source)
at de.kevinfleischer.zvagent.job.DailyReportingJob.executeJob(DailyReportingJob.java:42)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
The DB is empty afterwards. No Data was stored.
(I have JUnit tests, that work completely local without appserver, that show, that the code would store data. So its a transaction problem, not a problem in the business code.)

I finally found that the configuration was no problem. The packaging was rubbish and the errors I got only follow up errors.

Class [org.apache.derby.jdbc.ClientDriver] not found. When trying to connect to db

I have set up a project in Netbeans, created a script, made a new database with javadb. I can connect to it by gui - display the tables contents etc, but when i run an application with:
EntityManager em = Persistence.createEntityManagerFactory("lab5PU").createEntityManager();
i get this quite long exception:
[EL Info]: 2013-04-05 21:40:45.554--ServerSession(1198260109)--EclipseLink, version: Eclipse Persistence Services - 2.3.0.v20110604-r9504
[EL Severe]: 2013-04-05 21:40:45.574--ServerSession(1198260109)--Local Exception Stack:
Exception [EclipseLink-4003] (Eclipse Persistence Services - 2.3.0.v20110604-r9504): org.eclipse.persistence.exceptions.DatabaseException
Exception in thread "AWT-EventQueue-0" javax.persistence.PersistenceException: Exception [EclipseLink-4003] (Eclipse Persistence Services - 2.3.0.v20110604-r9504): org.eclipse.persistence.exceptions.DatabaseException
Exception Description: Configuration error. Class [org.apache.derby.jdbc.ClientDriver] not found.
Exception Description: Configuration error. Class [org.apache.derby.jdbc.ClientDriver] not found.
at org.eclipse.persistence.exceptions.DatabaseException.configurationErrorClassNotFound(DatabaseException.java:82)
I can see the javadb drivers in the driver section in services, so i have no idea what the error might be.
EDIT: persistance.xml as requested:
<?xml version="1.0" encoding="UTF-8"?>
<persistence version="2.0" 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">
<persistence-unit name="lab5PU" transaction-type="RESOURCE_LOCAL">
<provider>org.eclipse.persistence.jpa.PersistenceProvider</provider>
<class>lab5.Colleagues</class>
<properties>
<property name="javax.persistence.jdbc.url" value="jdbc:derby://localhost:1527/lab5"/>
<property name="javax.persistence.jdbc.password" value="mypass"/>
<property name="javax.persistence.jdbc.driver" value="org.apache.derby.jdbc.ClientDriver"/>
<property name="javax.persistence.jdbc.user" value="admin"/>
<property name="eclipselink.ddl-generation" value="create-tables"/>
</properties>
</persistence-unit>
</persistence>

I think the problem you have is that you don't have the Derby driver in the classpath of the project.
You can easily achieve that adding the JavaDB library to your project:
Right-click on the project
Properties -> Libraries
Add Library -> JavaDB driver
This includes derby.jar, derbyclient.jar and derbynet.jar in your project's classpath.
The derbyclient.jar contains the class org.apache.derby.jdbc.ClientDriver your code is complaining about.

javax.persistence.PersistenceException: No Persistence provider for EntityManager named customerManager

I am new to JPA & Hibernate. After reading some online materials I now understand what Hibernate is and how it can be used with JPA.
Now, I am trying to run this JPA & Hibernate tutorial. I've done everything they mention in this tutorial.
I don't have Oracle DB, only MySQL. So I made some changes to persistence.xml using my understanding of JPA & Hibernate (I don't know if it's correct or not... Seems to me it is.)
Here is my 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_1_0.xsd" version="1.0">
<persistence-unit name="customerManager" transaction-type="RESOURCE_LOCAL">
<provider>org.hibernate.ejb.HibernatePersistence</provider>
<class>Customer</class>
<properties>
<property name="hibernate.dialect" value="org.hibernate.dialect.MySQLInnoDBDialect"/>
<property name="hibernate.connection.driver_class" value="com.mysql.jdbc.Driver"/>
<property name="hibernate.show_sql" value="true"/>
<property name="hibernate.connection.username" value="root"/>
<property name="hibernate.connection.password" value="1234"/>
<property name="hibernate.connection.url" value="jdbc:mysql://localhost:3306/general"/>
<property name="hibernate.max_fetch_depth" value="3"/>
</properties>
</persistence-unit>
</persistence>
But I don't seem to get the output they describe. It's giving me:
Customer id before creation:null
log4j:WARN No appenders could be found for logger (org.hibernate.cfg.annotations.Version).
log4j:WARN Please initialize the log4j system properly.
Exception in thread "main" javax.persistence.PersistenceException: No Persistence provider for EntityManager named customerManager
at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:55)
at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:33)
at CustomerDAO.create(CustomerDAO.java:8)
at CustomerDAO.main(CustomerDAO.java:22)
Any suggestions will be appreciated.
Update:
I have made the changes that are asked to done. But, still getting the asme error lines!!!
They didnt mentioned anything about orm.xml in that tutorial. may it be a problem causer!!!

Just for completeness. There is another situation causing this error:
missing META-INF/services/javax.persistence.spi.PersistenceProvider
file.
For Hibernate, it's located in hibernate-entitymanager-XXX.jar, so, if hibernate-entitymanager-XXX.jar is not in your classpath, you will got this error too.
This error message is so misleading, and it costs me hours to get it correct.
See JPA 2.0 using Hibernate as provider - Exception: No Persistence provider for EntityManager.

Your persistence.xml is not valid and the EntityManagerFactory can't get created. It should be:
<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_1_0.xsd" version="1.0">
<persistence-unit name="customerManager" transaction-type="RESOURCE_LOCAL">
<provider>org.hibernate.ejb.HibernatePersistence</provider>
<class>Customer</class>
<properties>
<property name="hibernate.dialect" value="org.hibernate.dialect.MySQLInnoDBDialect"/>
<property name="hibernate.connection.driver_class" value="com.mysql.jdbc.Driver"/>
<property name="hibernate.show_sql" value="true"/>
<property name="hibernate.connection.username" value="root"/>
<property name="hibernate.connection.password" value="1234"/>
<property name="hibernate.connection.url" value="jdbc:mysql://localhost:3306/general"/>
<property name="hibernate.max_fetch_depth" value="3"/>
</properties>
</persistence-unit>
</persistence>
(Note how the <property> elements are closed, they shouldn't be nested)
Update: I went through the tutorial and you will also have to change the Id generation strategy when using MySQL (as MySQL doesn't support sequences). I suggest using the AUTO strategy (defaults to IDENTITY with MySQL). To do so, remove the SequenceGenerator annotation and change the code like this:
#Entity
#Table(name="TAB_CUSTOMER")
public class Customer implements Serializable {
private static final long serialVersionUID = 1L;
#Id
#GeneratedValue(strategy=GenerationType.AUTO)
#Column(name="CUSTOMER_ID", precision=0)
private Long customerId = null;
...
}
This should help.
PS: you should also provide a log4j.properties as suggested.

I had the same problem today. My persistence.xml was in the wrong location. I had to put it in the following path:
project/src/main/resources/META-INF/persistence.xml

I was facing the same issue. I realised that I was using the Wrong provider class in persistence.xml
For Hibernate it should be
<provider>org.hibernate.ejb.HibernatePersistence</provider>
And for EclipseLink it should be
<provider>org.eclipse.persistence.jpa.PersistenceProvider</provider>

If you use Hibernate 5.2.10.Final, you should change
<provider>org.hibernate.ejb.HibernatePersistence</provider>
to
<provider>org.hibernate.jpa.HibernatePersistenceProvider</provider>
in your persistence.xml
According to Hibernate 5.2.2: No Persistence provider for EntityManager

If you are using Maven you may have both src/{main,test}/resources/META-INF/persistence.xml. This is a common setup: test your JPA code with h2 or Derby and deploy it with PostgreSQL or some other full DBMS. If you're using this pattern, do make sure the two files have different unit names, else some versions of the Persistence class will try to load BOTH (because of course your test-time CLASSPATH includes both classes and test-classes); this will cause conflicting definitions of the persistence unit, resulting in the dreaded annoying message that we all hate so much!
Worse: this may "work" with some older versions of e.g., Hibernate, but fail with current versions. Worth getting it right anyway...

A bit too late but I got the same issue and fixed it switching schemalocation into schemaLocation in the persistence.xml file (line 1).

I have seen this error , for me the issue was there was a space in the absolute path of the persistance.xml , removal of the same helped me.

I was also facing the same issue when I was trying to get JPA entity manager configured in Tomcat 8. First I has an issue with the SystemException class not being found and hence the entityManagerFactory was not being created. I removed the hibernate entity manager dependency and then my entityManagerFactory was not able to lookup for the persistence provider. After going thru a lot of research and time got to know that hibernate entity manager is must to lookup for some configuration. Then put back the entity manager jar and then added JTA Api as a dependency and it worked fine.

my experience tells me that missing persistence.xml,will generate the same exception too.
i caught the same error msg today when i tried to run a jar package packed by ant.
when i used jar tvf to check the content of the jar file, i realized that "ant" forgot to pack the persistnece.xml for me.
after I manually repacked the jar file ,the error msg disappered.
so i believe maybe you should try simplely putting META-INF under src directory and placing your persistence.xml there.

JPA Exception: No Persistence provider for EntityManager named MyJPAApplicationPU

I am newbie with JPA. I'm trying to run some sample code using JPA but I get the following exception:
javax.persistence.PersistenceException: No Persistence provider for EntityManager named MyJPAApplicationPU
I put my exception message here,
INFO: Could not find any META-INF/persistence.xml file in the classpath
javax.persistence.PersistenceException: No Persistence provider for EntityManager named MyJPAApplicationPU
at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:55)
at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:33)
at com.myJpa.TestJPA.setUp(TestJPA.java:30)
at com.myJpa.TestJPA.main(TestJPA.java:72)
Any help would be appreciated.

Well, the error is self explaining, you need to provide a META-INF/persistence.xml to use JPA. This file is used to define a "persistence unit". From the JPA 1.0 specification:
6.2.1 persistence.xml file
A persistence.xml file defines a
persistence unit. It may be used to
specify managed persistence classes
included in the persistence unit,
object/relational mapping information
for those classes, and other
configuration information for the
persistence unit and for the entity
manager(s) and entity manager factory
for the persistence unit. The
persistence.xml file is located in
the META-INF directory of the root
of the persistence unit. This
information may be defined by
containment or by reference, as
described below.
Here is a sample persistence.xml for a Java SE environment (using Hibernate as JPA provider):
<?xml version="1.0" encoding="UTF-8"?>
<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_1_0.xsd"
version="1.0">
<persistence-unit name="MyJPAApplicationPU" transaction-type="RESOURCE_LOCAL">
<provider>org.hibernate.ejb.HibernatePersistence</provider>
<class>com.mycompany.Foo</class>
<class>com.mycompany.Bar</class>
<exclude-unlisted-classes>true</exclude-unlisted-classes>
<properties>
<property name="hibernate.connection.provider_class" value="org.hibernate.connection.DriverManagerConnectionProvider" />
<property name="hibernate.connection.url" value="jdbc:hsqldb:mem:unit-testing-jpa"/>
<property name="hibernate.connection.driver_class" value="org.hsqldb.jdbcDriver"/>
<property name="hibernate.dialect" value="org.hibernate.dialect.HSQLDialect"/>
<property name="hibernate.connection.username" value="sa"/>
<property name="hibernate.connection.password" value=""/>
<property name="hibernate.show_sql" value="true"/>
</properties>
</persistence-unit>
</persistence>
Some comments about the above file:
when running in a Java SE environment, you cannot rely on JTA and the transaction type must be RESOURCE_LOCAL (which is actually the default in a Java SE environment but specifying it make it more clear).
when running in a Java SE environment, you cannot use a JDNI data source and the provider will obtain connections directly from the JDBC driver so you must pass the relevant informations to the provider (driver class name, connection url, user, password). With JPA 1.0 the properties used to pass these metadata are provider specific.
To insure the portability of a Java SE application, it is necessary to explicitly list the managed persistence classes that are included in the persistence unit.

For JPA to work, you need META-INF/persistence.xml. I will assume this is a web-app, so this folder has to be in WEB-INF/classes/.
The persistence.xml file would look like this:
<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_1_0.xsd"
version="1.0">
<persistence-unit name="MyJPAApplicationPU" transaction-type="RESOURCE_LOCAL">
</persistence-unit>
</persistence>

EntityManagerFactory emf = Persistence.createEntityManagerFactory("<JDBC connection>");
Check the correct JDBC Connection.