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Using #Transactional with hibernate

I am using hibernate for the REST API. Right now all the transactions are handled by explicitly calling beginTransaction and transaction.commit. The transaction is rolled back in case of a failure. I am looking to use #Transactional instead of all the beginTransactions and commit transactions. Could someone tell me how can I integrate #Transactional in my hibernate. I am using mysql for querying the database.

You can annotate your query method with #Transactional so you get your transaction opened, commited and closed when your method ends.
Be careful about isolation levels (https://docs.spring.io/spring-framework/docs/current/javadoc-api/org/springframework/transaction/annotation/Transactional.html#isolation--) because it indicates when Spring will create a new session for your transaction, or simply use already opened one.
When you thrown an exception on your method, transaction gets an automatic rollback and you're good :)

You can use Spring Framework with Hibernate Integration. The advantage is spring manages the Hibernate session's and all the low level things that we have to manage manually in hibernate like granular commit etc. Here is the example of this. this is older repository so uses older version of Spring and Hibernate but you can upgrade it here

Integration of hibernate transaction in jta transaction manager

In my standalone java application, jms and hibernate are used for fulfilling my requirements. I used the JTA transaction manager for the transaction management purposes. Can i enlist the XAResource for the hibernate and jms in the jta transaction to ensure the atomicity of my application.

Yes, it's possible. Called sometimes two-phase commit, it synchronises transactions between multiple resources.
First of all make sure you're RDBMS supports and has the feature turned on. In PostgreSQL, for example, this means setting the max_prepared_transactions configuration parameter from postgresql.conf to something above 0.
Also, make sure the JMS queue you're using support this transaction method. In Wildfly this means adding transaction="xa" on pooled-connection-factory.

Exception thrown when using non-XA datasource in two-phase commit transaction

My Websphere application has 3 datsources. Two of them are XA and the other is non-XA.
I have made a Java method transactional by annotating the method with #transactional annotation.
Within the method, 3 tasks are performed. The first one is using one XA datasource to do some update, then the second one uses the non-XA datasource to select a few records and the final task uses another XA datasource to do some update again.
However, an exception is thrown with the following error:
An illegal attempt to commit a one phase capable resource with existing two phase capable resources
I want to know why the above error occurs even my application just uses the non-XA to select some data and no commit is required and how I can get rid of the problem if I am not allowed to change the non-XA datasource to XA.

The non-XA resource cannot by default participate in a distributed transaction. So you have the following options:
Change datasource to XA - you wrote that you cannot do that
Try to enable Last Participant Support - Last participant support is an extension to the transaction service that enables a single one-phase resource to participate in a two-phase transaction with one or more two-phase resources.
Set this (nonXA) datasource to be non transactional, if you don't need transactions for it. It will not be enlisted in the transaction:
Select Resources > JDBC > Data sources
Select the name of the data source that you want to configure.
Select WebSphere Application Server data source properties from the Additional Properties heading.
Select Non-transactional data source.
Click OK.
wrap that nonXA call in EJB, and mark it as not supporting transactions.
Manually manage transaction - don't use container managed transaction, but handle transaction inside your method manually using Transaction API.

when starting the second task, the previous task which does updates on a XA datasource need to be commit or rolled back while you are using #Transaction annotation the whole tasks automatically go through one transaction so don't use #Transaction annotation and instead of it put each task inside separate transaction

Transaction Management outside Data Access Layer

Data Access Layer is not responsible for transaction management am I correct? I have these DAO implementations: HibernateDAO and SqlDAO. If I will choose Hibernate and handle its transaction management at above layer, when I switch to SQL then I will change every single transaction management made by the Hibernate to SQL? This is bad right? What strategy will I gonna use in this case? TIA.

I've never worked on transactions outside of spring and JTA. Spring offers a transactions across several different platforms using transactions. You may want to check that out.
Also, I've seen JTA transactions work on ejb, Hibernate and Jms messages, but not sure if it will work for jdbc and hibernate, more on hibernate transactions here.

how the Transaction concept is implemented in EJB

I wan to know how the transaction is internally implemented in EJB. I want to know the logic they use to create a transaction. if you could point out some articles that would be helpful

Hibernate doesn't implement transactions, it relies on and wraps JDBC transactions or JTA transactions (either container managed or application managed).
Regarding EJBs, if you want to understand the details of a JTA Transaction Manager, you'll need to be fluent with the JTA interfaces UserTransaction, TransactionManager, and XAResource which are described in the JTA specification. The JDBC API Tutorial and Reference, Third Edition will also be useful to understand the XA part of a JDBC driver.
Then, get the sources of an EJB container (like JBoss) or of a standalone JTA Transaction Manager (like Atomikos) to analyze the TM part. And good luck.

This question could have answers at many levels.
A general discussion of what's going on can be found here
My summary goes like this ... First, somewhere there must be a transaction coordinator, the EJB container will know about the coordinator - typically that's part of the application server. So all the EJB container has to do is to call
someobject.BeginTransaction()
that's it. The actual API the EJB container uses is JTA. EJBs can actually use Bean Managed transaction transaction or Container managed transactions. In the Bean Managed case the implementer nhas to make the JTA calls. More usually we use Container Managed transactions (CMT). In which case the container has logic which is run before the implementation is reached. For example:
if ( we're not already in a transaction )
begin transaction
call the EJB implementation
and later the container has logic
if ( finished processing request )
commit transaction
with other paths to abort the transaction if errors have happened.
Now that logic is more complex because CMT EJBs are annotated with transaction control statements. For example you can say things "if we already have a transaction, use it" So if one EJB calls another only a single transaction is used. Read up the EJB spec for that.
However all that's pretty obvious in any write-up of Java EE EJBs. So I suspect that you're asking moe about what happens inside the JTA calls, how the transaction manager is implemented and its relationship to the transactional resource managers (eg. Databases). That's a huge topic. You've actually go implementations of the XA distributed transaction protocol down there. Frankly I doubt that you really need to need to know this. At some point you have trust the APIs you're using. However there is one key detail: your Transaction Manager (typically the App Server itself) must be able to tell the REsource Managers the fate of any given transaction, and that information must survive restart of the App Server, hence some persistent store of transaction information must be kept. You will find transaction logs somewhere, and in setting up the App Server you need to make sure those logs are well looked after.

From EJB in Action book
The protocol commonly used to achieve multiple resource is the two-phase commit. The two-phase commit protocol performs an additional preparatory step before the final commit. Each resource manager involved is asked if the current transaction can be successfully committed. If any of the resource managers indicate that the transaction cannot be committed if attempted, the entire transaction is abandoned (rolled back). Otherwise, the transaction is allowed to proceed and all resource managers are asked to commit.
A resource manager can be a database, for instance. Others examples includes a Message Service. The component which coordinates transactions is called Transaction manager.
Suppose you have an application which involves two distincts databases. How does Transaction manager performs its work by using Two phase commit protocol ?
Transaction Manager ask database 1 if it can commit the current transaction
If so, ask database 2 if it can commit the current transaction
Transaction Manager ask database 1 to commit
Transaction Manager ask database 2 to commit
Hibernate is built on top of the JDBC API. It just coordinates one database. So if you call
session.commit();
Behind the scenes, it call
connection.commit();
If you really want to study Transaction internals, my advice is Java Transaction Processing book.

Hibernate has TransactionFactory:
An abstract factory for Transaction instances. Concrete implementations are specified by hibernate.transaction.factory_class.
It has implementations: JDBCTransactionFactory, JTATransactionFactory, CMTTransactionFactory. These factories create an instance of Transaction - for example JDBCTransaction.
Then I can't tell you what happens for JTA and CMT, but for JDBC it's as simple as setting the auto-commit to false (when you call begin a transaction):
connection.setAutoCommit(false);
And respectively on transaction.commit(): connection.commit()
If any exception occurs when operating with the session, it invokes connection.rollback()

Another good read would be the JTS articles by Brian Goetz; links:
http://www.ibm.com/developerworks/java/library/j-jtp0305.html
http://www.ibm.com/developerworks/java/library/j-jtp0410/index.html
http://www.ibm.com/developerworks/java/library/j-jtp0514.html