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Java ORM and querying POJO's in memory or using other API's

I want to or need to (without the use of other databases) setup Entities(database tables) in memory that have relationships, like one-to-many or many-to-many etc.
I saw something related here on this forum:
Map SQL (not JPQL) to a collection of simple Java objects?
I need to query these Entities that have relationships and get the resultsets from this,
in order to push the resulting data into an Access database, I am using Jackcess and its not a JDBC driver.
So far I have looked at MetaModel and jOOQ.
Is there anything else out there. I have a little bit of exposure to ORM's, do they query the in-memory collections or only just pass the sql query to the database.
Any help or suggestions is greatly appreciated.

Apparently, you're looking for something like .NET's LINQ-to-Objects in the Java ecosystem. There's nothing as sophisticated as LINQ-to-Objects, but there are a couple of ways to "query" collections in Java as well. You might be interested in any of these libraries:
Quaere: http://quaere.codehaus.org
Coolection: https://github.com/wagnerandrade/coollection
Lambdaj: https://code.google.com/p/lambdaj
JXPath: http://commons.apache.org/proper/commons-jxpath
JoSQL: http://josql.sourceforge.net
All of the above projects are open source and may not be so actively maintained anymore, as Java 8 will introduce a much better collections API along with language-supported lambda expressions, which renders these non-SQL focused LINQesque Java APIs obsolete.
Note, you were asking specifically about MetaModel and jOOQ. These provide you with a querying API for querying databases. I think that will not help you much for your use-cases.

Hibernate will query the object cache, but only if you query using Criteria or HQL. If you query straight SQL, it'll get run directly against the database.
Your problem description sounds like it's more than Jackcess can handle natively, but what if at program startup you read the full Access DB into an in-memory database (one that has a JDBC driver), run Hibernate queries against that in-memory database, and then at program exit just flush all Hibernate changes to the in-memory database and then write the in-memory database's contents into the Access database? You get all the complicated querying capability of Hibernate, and all you have to do is write Jackcess-to-JDBC code to load the Access DB into an equivalent schema in the in-memory database and then the inverse code to copy it back, which is way easier than writing the full JDBC driver for Jackcess.

PlayFrameWork SQL tutorial?

i am new in playframework i know how to install playframework and connect it to the database . Is there is any tutorial for that like how to perform sql operation using java in playframework.

SQL is not dependent on the Play Framework; it's dependent on the database you choose to use as a store for your Play Framework application.
W3 Schools has a pretty good tutorial for basic SQL operations. You can also look up additional commands and functionality provided by your specific database provider in the docs for that database. e.g. look here if you've chosen to use a version of PostgreSQL
The problem is confused slightly in that what I think you need is a method for your application to map rich application objects to flat database tables. This task can be done using an Object-Relationship-Mapping or functional-mapping tool. Ebean is an example of an ORM and Slick is an example of a functional mapping tool, both of which can be used in Play applications by adding their drivers to your /project/build.scala file in the list of your project dependencies.
Setting up Ebean for your Java-based Play project is covered on the page of the Play 2.1 Java tutorial after the one linked to by bistros - Using the Ebean ORM

see playframework.com tutorial page.
http://www.playframework.com/documentation/2.1.x/Installing
http://www.playframework.com/documentation/2.1.x/JavaDatabase

You can start direct with examples from the website. I think this one is very nice to understand how to work with database.
play-java-ebean-example

Is it possible to save persistent objects to the file system

I'd like to save persistent objects to the file system using Hibernate without the need for a SQL database.
Is this possible?

Hibernate works on top of JDBC, so all you need is a JDBC driver and a matching Hibernate dialect.
However, JDBC is basically an abstraction of SQL, so whatever you use is going to look, walk and quack like an SQL database - you might as well use one and spare yourself a lot of headaches. Besides, any such solution is going to be comparable in size and complexity to lighweight Java DBs like Derby.
Of course if you don't insist absolutely on using Hibernate, there are many other options.

It appears that it might technically be possible if you use a JDBC plaintext driver; however I haven't seen any opensource ones which provide write access; the one I found on sourceforge is read-only.

You already have an entity model, I suppose you do not want to lose this nor the relationships contained within it. An entity model is directed to be translated to a relational database.
Hibernate and any other JPA provider (EclipseLink) translate this entity model to SQL. They use a JDBC driver to provide a connection to an SQL database. This, you need to keep as well.
The correct question to ask is: does anybody know an embedded Java SQL database, one that you can start from within Java? There are plenty of those, mentioned in this topic:
HyperSQL: stores the result in an SQL clear-text file, readily imported into any other database
H2: uses binary files, low JAR file size
Derby: uses binary files
Ashpool: stores data in an XML-structured file
I have used HyperSQL on one project for small data, and Apache Derby for a project with huge databases (2Gb and more). Apache Derby performs better on these huge databases.

I don't know exactaly your need, but maybe it's one of below:
1 - If your need is just run away from SQL, you can use a NoSQL database.
Hibernate suports it through Hibernate OGM ( http://www.hibernate.org/subprojects/ogm ).
There are some DBs like Cassandra, MongoDB, CouchDB, Hadoop... You have some suggestions Here
.
2 - Now, if you want not to use a database server (with a service process running always), you can use Apache Derby. It's a DB just like any other SQL, but no need of a server. It uses a singular file to keep data. You can easily transport all database with your program.
Take a look: http://db.apache.org/derby/
3 - If you really want some text plain file, you can do like Michael Borgwardt said. But I don't know if Hibernate would be a good idea in this case.

Both H2 and HyperSQL support embedded mode (running inside your JVM instead of in a separate server) and saving to local file(s); these are still SQL databases, but with Hibernate there's not many other options.

Well, since the question is still opened and the OP said he's opened to new approaches/suggestions, here's mine (a little late but ok).
Do you know Prevayler? It's a Java Prevalence implementation which keep all of your business objects in RAM and mantain Snapshots/Changelogs in the File System, this way it's extremely fast and reliable, since if there's any crash, it'll restore it's last state and reapply every change to it.
Also, it's really easy to setup and run in your app.

Ofcourse this is possible, You can simply use file io features of Java, following steps are required:-
Create a File Object
2.Create an object of FileInputStream (though there are ways which use other Classes)
Wrap this object in a Buffer object or simply inside a java.util.Scanner.
use specific write functions of the object created in previous step.
Note that your object must implement Serializable interface. See following link,

Migrating Data accross different DB Schema

I want to migrate my data from one DB to other using Java. Both DBs have different schema structure. I might also need to define some mapping / validation rule. Can anyone please guide me about any strategy, framework or any opensource project.
Thanks
Isn't in this case I have to create all the POJO to match the both schema (even by auto generating). Is there any way to avoid this thing i.e. giving schema mapping and generating POJO on fly in memory ?
Any idea?
Thanks

Yes, you need an Extract-Transform-Load (ETL) tool.
Here are some open source choices:
http://www.google.com/search?gcx=w&sourceid=chrome&ie=UTF-8&q=open+source+etl

ETL is generally used for this as in duffymo's answer.. you could also try ORM tools for this:
There is the Torque project.. http://db.apache.org/torque/
Read the data from your existing schema into java objects, then set them into the other objects for the other schema and then save them into the database. I am pretty sure hibernate also can be used, although I havent used hibernate per se. It works on the same way as torque..

easy object persistence strategy - hibernate?

I'm doing a Java software-project at my university that mainly is about storing data-sets (management of software tests).
The first thing I thought of was a simple SQL DB, however the necessary DB scheme is not available for now (let's say the project is stupid but there's no choice).
Is a persistency framework like Hibernate able to store data internally (for example in XML) and to convert this XML into decent SQL later?
My intention is to use the additional abstraction layer of a framework like Hibernate to save work, because it might have conversion functions. I know that Hibernate can generate class files from SQL, but I'm not too sure whether it needs a DB at every point during development. Using a XML Scheme for now and converting it into SQL later maybe an idea :)

You can persist XML with hibernate into a relational DB, but you cannot use XML directly as a storage engine. Why not simply store you're data into a relational db from the start - you'll create some schema yourself and you'll adapt it to the actual one when you receive it.

I would recommand using a lightweight DB such as HSQLDB instead.