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JPA query not returning updated results in list

I have an issue with a webapp running in tomcat where I have an abstract DAO class with a method called all() which returns all entities from the database or JPA cache. It seems to correctly return the entities on the initial call but subsequent calls don't reflect updates happening from separate UI calls which will use the entity managers find method to find the specific entity from the list, update the relative fields and commit that. When I view that list via the same all() method later I still see the original values. If I make another update in the logs I can see the value changing from the correct value(not the original value) to the updated value and the logs shows those updates happening correctly each time.
I'm using guice for injection. I've played around with the logging and can see the same hashcode on the entity manager being used throughout a request but different for each request. I've played with the following the persistance.xml file which didn't seem to help either...
<property name="eclipselink.cache.shared.default" value="false" />
<shared-cache-mode>NONE</shared-cache-mode>
I can't see why my all() won't return updated results, I've also tried adding code to find the specific entity I'm updating in the list then replaced it by calling the following...
entity = em.find(Class.class, id)
This seemed to fix the issue on that particular entity so it appears my query is reusing old.
Here's a snippet from my DAO class
private final Provider<EntityManager> emP;
protected EntityManager em(boolean useTransaction) throws DaoException {
return useTransaction ? begin() : emP.get();
}
public List<T> all() throws DaoException {
EntityManager em = em(false);
CriteriaBuilder cb = em.getCriteriaBuilder();
CriteriaQuery<T> cq = cb.createQuery(eClass);
Root<T> from = cq.from(eClass);
return em.createQuery(cq.select(from)).getResultList();
}
public T save(T t) throws DaoException {
return save(t, em(true));
}
protected T save(T t, EntityManager em) throws DaoException {
if (Objects.isNull(t)) {
throw new DaoException("can't save null object: " + getDaoClass(), new NullPointerException());
}
T saved;
if (t.getId() > 0) {
saved = em.merge(t);
} else {
em.persist(t);
saved = t;
}
autoCommit();
return saved;
}
protected void autoCommit() throws DaoException {
if (autoCommit) {
commit();
}
}
public void commit() throws DaoException {
EntityManager em = emP.get();
if (!em.getTransaction().isActive()) {
throw new DaoException("transaction isn't active, unable to commit");
}
try {
em.getTransaction().commit();
} catch (IllegalStateException e) {
throw new DaoException("transaction not active", e);
} catch (RollbackException e) {
throw new DaoException("commit rolled back", e);
}
}
So I'm wondering if anyone has any insights on why this might be happening or have any suggestions on what else I can try to check?

So I found the cause of the issue I was having. I was using the ElementCollection annotation in my entities when referencing lists. I removed the annotation and replaced it with a JoinTable and OneToMany annotations and things are working correctly.
The issue I had was that the entity would be stored in the database fine and I was updating that entity as expected but JPA had embedded the list of entities where it was referenced.
So I was seeing the embedded list returned each time which was not the actual entity I had updated. My entities are now using proper join tables instead of embedded objects and everything is behaving as expected.

Spring refresh entity if db state has changed

I have got a Springboot Application and a Oracle DB with lots of PL/SQL Procedures and these change the state of the DB all the Time.
So now I want to change a loaded entity an want to save it. If the entitystate of the entitymanager and the state of the db is equal everything works fine. But in some cases they are not equal. So if I load an entity and make some changes an druring this a PL/SQL Procedure changes the DB Table. If I save the Entity I will get an Execption of course. So I tried to catch the Exception and then in the catch block I want to refresh the Entity before saving it. But I still get an Exception. Is the Transaction not jet finished? How can I handle this Problem?
I hope the example code explains a little bit.
#RestController
#RequestMapping("/*")
public class FacadeController {
...
#ResponseStatus(HttpStatus.OK)
#RequestMapping( value= "/test4" , method=RequestMethod.GET)
public String test4(){
Unit unit = unitSvice.loadUnit(346497519L);
List<UnitEntry> entries = unit.getEntries();
for (UnitEntry g : entries) {
if (g.getUnitEntryId == 993610345L) {
g.setTag("AA");
g.setVersion(g.getVersion() + 1);
g.setstatus("SaveOrUpdate");
}
}
//<-- DB Table changed entity managed by entitymanger and DB Table
// are no langer equal.
try {
unitSvice.updateUnit(unit , false);
}catch(DataAccessException | IllegalArgumentException e) {
unitSvice.updateUnit(unit , true);
}
...
}
}
#Service("unitSvice")
public class UnitSvice {
#Autowired
private UnitDao repoUnit;
#Transactional
public Unit loadUnit(Long _id) {
Unit unit = repoUnit.findOne(_id);
return unit;
}
#Transactional
public void updateUnit(Unit unit, boolean _withrefrsh ) {
if(_withrefrsh) {
getEntityManager().refresh(unit.getId());
}
repoUnit.save(unit);
}
}
I hope, anyone can help me.
Thanks

yes the problem is ..when you call load all method which is transactional method where entities became detached from session/entitymanager when you are returning from that method.. so,next you are trying to persist detached object. That's why you get exception.
so probably you can use session.update() or session.merge() to save the new update into database.

What Dropwizard-Hibernate doc is trying to say?

I have run into LazyInitializationException and then I ran into the following paragraph from the official doc. Unfortunately, it makes absolutely no sense to me. Please help.
(The code block above the paragraph in the doc.)
#GET
#Timed
#UnitOfWork
public Person findPerson(#PathParam("id") LongParam id) {
return dao.findById(id.get());
}
Important
The Hibernate session is closed before your resource method’s return
value (e.g., the Person from the database), which means your resource
method (or DAO) is responsible for initializing all lazily-loaded
collections, etc., before returning. Otherwise, you’ll get a
LazyInitializationException thrown in your template (or null values
produced by Jackson).
First The Hibernate session is closed before your resource method’s return value. How is this possible? This would have been possible had there been a try-finally block around my resource's return statement, but that is not the case here.
My resource should have been invoked by another method, which I am guessing would open the Hibernate session before my resource method is invoked and would then close the session after my resource method returns. How can it close it before my method returns. I don't get it.
The most important part - which means your resource method (or DAO) is responsible for initializing all lazily-loaded collections, etc., before returning. I have no Hibernate experience. I am using it for the first time now. How do I initialize, or rather what is exactly is meant by "initialize" in context of Hibernate? A code example will help a lot.
PS: This question might look odd, and someone at a cursory glance might even suggest to move it to "English Language and Usage", but please read it carefully. This is a technical question, not paragraph dissection.
Edit:
Added the code block from the doc else it won't make sense anyone. Also I removed one paragraph from my question, which became clear to me, immediately after posting the question.

First The Hibernate session is closed before your resource method’s
return value. How is this possible? This would have been possible had
there been a try-finally block around my resource's return statement,
but that is not the case here.
I know nothing about Dropwizard. So let's see the source (I change it a bit).
From UnitOfWorkAwareProxyFactory
class UnitOfWorkAwareProxyFactory {
public <T> T create(Class<T> clazz) {
final ProxyFactory factory = new ProxyFactory();
factory.setSuperclass(clazz);
final Proxy proxy = (Proxy) factory.createClass().newInstance();
proxy.setHandler(new MethodHandler() {
#Override
public Object invoke(Object self, Method overridden,
Method proceed, Object[] args) {
final UnitOfWork unitOfWork = overridden.getAnnotation(UnitOfWork.class);
final UnitOfWorkAspect unitOfWorkAspect = new UnitOfWorkAspect(sessionFactories);
try {
unitOfWorkAspect.beforeStart(unitOfWork);
Object result = proceed.invoke(self, args);
unitOfWorkAspect.afterEnd();
return result;
} catch (Exception e) {
unitOfWorkAspect.onError();
throw e;
}
}
});
return (T) proxy;
}
}
if you have a class
class PersonDao {
#UnitOfWork
public Person findPerson(LongParam id) {
return dao.findById(id.get());
}
}
You can do something like this
UnitOfWorkAwareProxyFactory factory = new UnitOfWorkAwareProxyFactory();
PersonDao proxy = factory.create(PersonDao.class);
when you do
Person person = proxy.findPerson(1L);
that line becomes
unitOfWorkAspect.beforeStart(unitOfWork);
Object result = findPerson.invoke(proxy, 1L);
unitOfWorkAspect.afterEnd();
return result;
Methods unitOfWorkAspect.beforeStart(unitOfWork) and unitOfWorkAspect.afterEnd() from the source UnitOfWorkAspect
class UnitOfWorkAspect {
public void beforeStart(UnitOfWork unitOfWork) {
session = sessionFactory.openSession();
configureSession();
beginTransaction();
}
public void afterEnd() {
try {
commitTransaction();
} catch (Exception e) {
rollbackTransaction();
throw e;
} finally {
session.close();
}
}
}
The most important part - which means your resource method (or DAO) is responsible for initializing all lazily-loaded collections, etc., before returning. I have no Hibernate experience. I am using it for the first time now. How do I initialize, or rather what is exactly is meant by "initialize" in context of Hibernate?
Initialize in this context means the collection data should be loaded from a database. Some methods of an initialization
1.Use an eager loading, for an example
class User {
#ManyToMany(fetch = FetchType.EAGER)
private List<Role> roles;
}
Hibernate will load roles via joins or subselects, when you get a User entity.
Use Hibernate.initialize(user.getRoles())
Use join fetch in HQL — from User user left join fetch user.roles
Use Criteria with setFetchMode()
Use fetch profiles, entity graphs. Don't know can entity graphs be used with a session, it is a JPA feature: http://docs.jboss.org/hibernate/orm/5.1/userguide/html_single/chapters/fetching/Fetching.html
If you don't need to fetch collections, you can use a partial objects loading with transforming to the root entity: How to transform a flat result set using Hibernate

Hibernate entity lifecycle

I'm getting in trouble trying to separate the business and the persistance in my project.
The skeleton does more or less something like:
private UsuarioBO findById(String idUsuario) {
Usuario dao = getUsuarioDao().findById(idUsuario);
return new UsuarioBO(dao);
}
private void save(UsuarioBO bo){
Usuario dao = bo.bo2dao();
getUsuarioDao().save(dao);
}
Some clarifications about the code above:
UsuarioBO is a business objet and Usuario is an entity mapped to a DB
table.
The new UsuarioBO(dao) is just a mapping method and the
bo.bo2dao() is also a mapping method, but it creates a new empty entity
Usuario.
As you can see, the entity created in both methods is erased of memory on method finish.
The problem goes when i try to do this:
UsuarioBO example = findById("whatever");
save(example);
When i do this, hibernate tells me "there's an existing entity with the same identifier", and thats true! (It's creating an entity on findById() and another on save() ).
The only solution i've found is to use the entity as "bo". I mean, bring the entity object to the service, do whatever modifications on the entity directly, and when i finish do the save sending the entity in spite of a BO.
I'm pretty sure there's a better way of doing so, but how?
EDIT:
this is the save(dao) method:
public void save(Usuario usuario) throws Exception {
try {
getSession().saveOrUpdate(usuario);
} catch (RuntimeException e) {
//error treatment
throw e;
}
}
this is the bo2dao() method (its inside the BO bean):
public Usuario bo2dao() throws Exception {
Usuario dao = new Usuario();
try {
dao.setId(this.id);
dao.setPassword(this.password);
//other similar fields...
dao.setLastLoginTime(this.lastLoginTime);
Role r = new Role();
r.setId(LoginHelper.getRoleId(this.role.getName()));
dao.setRole(r);
Status s = new Status();
s.setId(LoginHelper.getStatusId(this.status.getName()));
dao.setStatus(s);
} catch (Exception e) {
throw e;
}
return dao;
}
In this case, Role and Status are also entity beans connected with Usuario (one user can only have one role and one status).
getRoleId() and getStatusId() returns the correspondent id from the name (for example: "UNLOCKED" returns 1)

JPA ID Generation Strategy

I defined a generator for a JPA class:
<sequence-generator name="MY_SEQ" allocation-size="-1"
sequence-name="MY_SEQ"
initial-value="100000000" />
There are cases where I already have an ID for an entity but when I insert the Entity the Id gets generated using the generator.
Is it possible to define a generator that will only generate an Id when one does not exist?
I am using Hibernate as a JPA Provider.
Thank you

I couldn't find a way to do this in JPA so I used Hibernate EJB3 event listeners. I over rode the saveWithGeneratedId to use reflection to check the entity for an #Id annotation and then to check that field for a value. If it has a value then I call saveWithRequestedId instead. Other wise I let it generate the Id. This worked well because I can still use the sequence for Hibernate that is set up if I need an Id. The reflection might add overhead so I might change it a little. I was thinking of having a getId() or getPK() method in all entities so I don't have to search for which field is the #Id.
Before I used reflection I tried calling session.getIdentifier(entity) to check but I was getting TransientObjectException( "The instance was not associated with this session" ). I couldn;t figure out how to get the Entity into the session without saving it first so I gave up. Below is the listener code I wrote.
public class MergeListener extends org.hibernate.ejb.event.EJB3MergeEventListener
{
#Override
protected Serializable saveWithGeneratedId(Object entity, String entityName, Object anything, EventSource source, boolean requiresImmediateIdAccess) {
Integer id = null;
Field[] declaredFields = entity.getClass().getDeclaredFields();
for (Field field : declaredFields) {
Id annotation = field.getAnnotation(javax.persistence.Id.class);
if(annotation!=null) {
try {
Method method = entity.getClass().getMethod("get" + field.getName().substring(0, 1).toUpperCase() + field.getName().substring(1));
Object invoke = method.invoke(entity);
id = (Integer)invoke;
} catch (Exception ex) {
//something failed (method not found..etc) , keep going anyway
}
break;
}
}
if(id == null ||
id == 0) {
return super.saveWithGeneratedId(entity, entityName, anything, source, requiresImmediateIdAccess);
} else {
return super.saveWithRequestedId(entity, id, entityName, anything, source);
}
}
}
I then had to add the listener to my persistence.xml
<property name="hibernate.ejb.event.merge" value="my.package.MergeListener"/>

it's not a good Idea, sequences are used for surrogate keys, are meaningless in the business sense but assures you, there won't be duplicates thus no error at inserting time.