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How to solve "Using Hibernate built-in connection pool (not for production use!)" using JPA i.e. Hibernate EntityManager

I'm new to Hibernate and JPA in general.
I read a lot about this warning, but I still can't solve it.
The answers I read so far, said that it is necessary to have hibernate.cfg.xml in the project.
But I also read that:
If you are using JPA i.e. Hibernate EntityManager, you'll need the persistence.xml. So you generally don't need both as you use either Hibernate proprietary API or JPA.
(what is the purpose of two config files for Hibernate?)
Using persistence.xml I have this warning every time I use Hibernate.
This is my persistence.xml:
<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="integration"
transaction-type="RESOURCE_LOCAL">
<provider>org.hibernate.jpa.HibernatePersistenceProvider</provider>
<properties>
<property name="hibernate.dialect"
value="org.hibernate.dialect.MySQL5InnoDBDialect" />
<property name="hibernate.hbm2ddl.auto" value="update" />
<property name="hibernate.connection.url" value="jdbc:mysql://localhost:3306/db-name?autoReconnect=true"/>
<property name="hibernate.connection.username" value="root" />
<property name="hibernate.connection.password" value="root" />
<property name="hibernate.show_sql" value="false" />
<property name="hibernate.format_sql" value="true" />
<property name="hibernate.id.new_generator_mappings"
value="true" />
</properties>
</persistence-unit>
</persistence>
I can't figure out what I'm doing wrong.
Thanks in advances

It is just a warning stating that you are using a built_in connection pool which is not a suitable solution in the production environment, you should use the application server connection pool in the production environment. depending on your application server you can setup database connection inside your application server then configure hibernate to use that connection.
But if you want to solve this problem without configuring the application server you can see this.

how to index a database already created using lucene hibernate search

I have a database with existing data that I want to index using Lucene Hibernate. When I create new data, Hibernate indexes it but the question is: how can I index all the old data in my database?
This is my persistence.xml file:
<persistence xmlns="http://java.sun.com/xml/ns/persistence"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="2.0"
xsi:schemaLocation="http://java.sun.com/xml/ns/persistence http://java.sun.com/xml/ns/persistence/persistence_2_0.xsd">
<persistence-unit name="persistenceUnit"
transaction-type="RESOURCE_LOCAL">
<provider>org.hibernate.jpa.HibernatePersistenceProvider</provider>
<properties>
<property name="hibernate.dialect" value="com.zodiac.qtp.domain.MySQL5CustomInnoDBDialect"/>
<!-- value="create" to build a new database on each run; value="update"
to modify an existing database; value="create-drop" means the same as "create"
but also drops tables when Hibernate closes; value="validate" makes no changes
to the database -->
<property name="hibernate.format_sql" value="true"/>
<property name="hibernate.hbm2ddl.auto" value="update" />
<property name="hibernate.ejb.naming_strategy" value="org.hibernate.cfg.ImprovedNamingStrategy" />
<property name="hibernate.connection.charSet" value="UTF8" />
<property name="hibernate.connection.characterEncoding" value="UTF8"/>
<property name="hibernate.show_sql" value="false" />
<property name="hibernate.cache.provider_class" value="org.hibernate.cache.EhCacheProvider"/>
<property name="hibernate.cache.use_second_level_cache" value="true" />
<property name="hibernate.cache.use_query_cache" value="true" />
<property name="hibernate.generate_statistics" value="false" />
<property name="hibernate.cache.region.factory_class" value="org.hibernate.cache.ehcache.SingletonEhCacheRegionFactory" />
<!-- Uncomment the following two properties for JBoss only -->
<!-- property name="hibernate.validator.apply_to_ddl" value="false" / -->
<!-- property name="hibernate.validator.autoregister_listeners" value="false" / -->
<property name="hibernate.search.default.directory_provider" value="org.hibernate.search.store.impl.FSDirectoryProvider"/>
<property name="hibernate.search.default.indexBase" value="C:\ZAM_DEV\QTPGenerator-repository\lucene-indexes-v2"/>
</properties>
</persistence-unit>
</persistence>

The short answer is that indexing is automatic: Hibernate Search will transparently index every entity each time it’s persisted, updated or removed through Hibernate ORM. Its mission is to keep the index and your database in sync, allowing you to forget about this problem.
However, when introducing Hibernate Search in an existing application, you have to create an initial Lucene index for the data already present in your database.
Once you have added the above properties and annotations, if you have existing data in the database you will need to trigger an initial batch index of your books. This will rebuild your index to make sure your index and your database is in synch. You can achieve this by using one of the following code snippets (see also Rebuilding the whole index):
Using an Hibernate Session to rebuild an index
FullTextSession fullTextSession = Search.getFullTextSession(session);
fullTextSession.createIndexer().startAndWait();
Using an EntityManager (JPA) to rebuild an index
FullTextEntityManager fullTextEntityManager =
Search.getFullTextEntityManager(entityManager);
fullTextEntityManager.createIndexer().startAndWait();
After executing the above code, you should be able to see a Lucene index under /var/lucene/indexes/example.Book.
The root of the storage path depends on the configuration property hibernate.search.default.indexBase we specified in the configuration step.
You could now inspect this index with Luke. It will help you to understand how Hibernate Search works: Luke allows you to inspect the index contents and structure, similarly to how you would use a SQL console to inspect the working of Hibernate ORM on relational databases.

The purpose of the persistence.xml file is to access entities from your DB. It really doesn't say much about the underlying indices, and you can't create DB indices using this file. To create your indices, you must logon to your DB server as an admin and create the indices using the appropriate CREATE INDEX commands.

property tags in persistence.xml when using JPA

I am new to JPA and use Hibernate as the JPA provider. I came to know that we need META-INF/persistence.xml configuration file.
I successfully created a simple Java program to persist data in DB using JPA.
All fine, doubts started when I looked into the persistence.xml file to understand it better.
Sample below:
<persistence-unit name="test-jpa" transaction-type="RESOURCE_LOCAL">
<properties>
<property name="hibernate.connection.driver_class" value="org.h2.Driver"/>
<property name="hibernate.connection.url" value="jdbc:h2:tcp://localhost/~/test"/>
<property name="hibernate.connection.username" value="sa" />
<property name="hibernate.connection.password" value="" />
<property name="hibernate.dialect" value="org.hibernate.dialect.H2Dialect"/>
<property name="hibernate.hbm2ddl.auto" value="create" />
<property name="hibernate.show_sql" value="true" />
</properties>
</persistence-unit>
The following is the Java code for reading the configuration:
EntityManagerFactory entityManagerFactory = Persistence.createEntityManagerFactory("test-jpa");
The following are the doubts:
How do we know that Hibernate is the JPA provider? Is it inferred by seeing the property tags in the file?
In config file, there are many <property> tags, are they pre-defined which can appear in the file (for a given JPA provider) or can we randomly add any property? who reads those <property> tags?

A JPA provider would provide documentation that would tell you all of that. Doesn't yours? I'd be surprised.
You should either have a <provider> element in the persistence-unit to define which provider to use, or it would use the default for the environment that you are running in (in JavaSE you would need to have 1 and only one JPA provider in the CLASSPATH, in JavaEE the server would have its own default).
They are provider-specific. Any properties that are prefixed javax.persistence would be JPA STANDARD. The first 4 of those posted have javax.persistence variants that you should have used instead.

Using derby built-in glassfish4 through EclipseLink

I have been trying to learn how to connect to the embedded database Apache Derby that comes out of the box with glassfish4. What do I have to set in the src/META-INF/persistence.xml in my project? Is it somehow preconfigured? If not, how can I change its settings - through glassfish console?
Thanks in advance for your help.

You need to edit the persistence.xml to add the persistence-provider, the classes you want to manage, and some configuration for your database, in case you do not use JTA, in your IDE, and package it with the app. You can generally enter the following in the persistence.xml:
<persistence-unit name="call_it_as_you_want" transaction-type="RESOURCE_LOCAL">
<provider>org.eclipse.persistence.jpa.PersistenceProvider</provider>
<class>YourClass</class>
<properties>
<property name="javax.persistence.jdbc.driver" value="org.apache.derby.jdbc.ClientDriver" />
<property name="javax.persistence.jdbc.url" value="jdbc:derby://127.0.0.1:1527/yourDatabase;create=true" />
<property name="javax.persistence.jdbc.user" value="your_database_login" />
<property name="javax.persistence.jdbc.password" value="your_database_password" />
<property name="eclipselink.ddl-generation" value="drop-and-create-tables" />
</properties>
</persistence-unit>
Before that, check if derby runs on port 1527 - i think it should. If you are going to use JPA with EJBs you can use JTA configuration - in this case persistence.xml will only need to declare the pool you will create from the admin console of Glassfish.

How to generate table from entities

I am currently working on a seam project using eclipse jpa tools; is it possible to automatically generate sql tables from my entity definitions? If so, how do I achieve this?

It depends on the JPA implementation you are using.
With Hibernate you can specify 'create' or 'update' in the hibernate.hbm2ddl.auto properties in persistence.xml:
<persistence xmlns="http://java.sun.com/xml/ns/persistence" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="2.0">
<persistence-unit name="yourPersistenceUnit" transaction-type="JTA">
<description>Your Persistence Unit</description>
<jta-data-source>java:/DefaultDS</jta-data-source>
<provider>org.hibernate.ejb.HibernatePersistence</provider>
<properties>
<property name="hibernate.hbm2ddl.auto" value="create"/>
<property name="hibernate.show_sql" value="true"/>
<property name="hibernate.format_sql" value="true"/>
<property name="hibernate.transaction.flush_before_completion" value="true"/>
<property name="hibernate.dialect" value="org.hibernate.dialect.HSQLDialect"/>
</properties>
</persistence-unit>
</persistence>
Possible values for hibernate.hbm2ddl.auto property are:
create: create database tables and indexes at startup
create-drop: create database tables and indexes at startup and drop at shutdown
update: when the application starts, check the database schema and update as needed adding missing tables and columns
validate: when the application starts, check the database schema and fails if there is some missing table or column.