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Hibernate connections remain open

We're facing huge versions upgrade of the codebase, in that codebase we're using hibernate and jdbi to connect to a postgres 12 db.
JDBI version is not changed in this upgrade, Hibernate version was 5.1.5.Final and has been updated to 5.3.10.Final.
Now I've a lot of trouble with connection that remain open, I report some tests that I've done (the problem are on reading).
In the previous version I do three query through hibernate (and for each one i use close method on entity manager after I get the result) and them all remain in idle in transaction, then I perform a jdbi query and all hibernate sessions will disappear.
With the new version, same test, I've to increase connection pool size through
<property name="hibernate.connection.pool_size" value="3"/></properties>
but connections remain always idle in transaction and never been closed.
I've noticed that adding commit method before closing the entity manager will leave a number of connection open equals to the number that I've placed as pool size.
Can someone explains how connection works in hibernate? Especially why in the previous version connections were closed automatically after doing a jdbi query.

How to check if you're still connected to the database with jpa

I'm trying to check the database connection with jpa using the EntitityManager/Session class.
To check both cases (connected/not connected), I simply start/deactivate the service mysql before running the code.
Asking simple sql queries to the database is out of mind since it doesn't cover all cases.
I already tried:
Session session = entityManager.unwrap(Session.class)
session.isConnected();
But that always returns true...
When I disable the mySQL service I want session.isConnected() to return false, but it always returns true;
Is there any other way to check for the database connection(using any other classes maybe)?

Short answer: don't
Long answer: if you're developing an application where this is important, you will probably be using some sort of database connection pooling framework, like the
Tomcat JDBC pool
Apache Commons DBCP
HikariCP
C3P0 Connection pool
This will manage many important aspects for you, including connection lifecycle. In tomcat jdbc for example you can specify:
testOnBorrow="true"
validationQuery="select 1 from sysibm.dual"
This on an IBM DB2 database will test whether a connection went stale every time you use it, and also swap it out for a fresh one if the select fails. Done this way, you will never have to worry about this on the level of you application code.

How to handle re-connects to the DB with ActiveJDBC

I've a Spring Boot Java application in production that uses ActiveJDBC to access a MariaDB database.
If at launch the application boots before the db server, of if the db server crashes and restarts, the apps doesn't re-estabilish the connection with the db.
ActiveJDBC is on version 1.4.13 and if possible I'd prefer not upgrading it, to avoid possible breakages. The db parameters are configured using the database.properties file and typically the usage pattern is:
try {
Base.open();
...
} finally {
Base.close();
}
Is there a way to circumvent this problem, without monitoring and relaunching the application? Maybe using connection pools? If this is the case, are there any docs or examples?

If you are using a direct JDBC connection in your database.properties file, a new connection will be open every time you execute Base.open(). This means that any old connection that is broken is not relevant anymore. If you use a JDNI pool such as:
production.jndi=java:comp/env/jdbc/acme
then you want to configure your containers' pool to ensure that every connection served from the pool is valid just before the pool serves the connection to your app. It is up to the implementation and documentation of your container/pool how to do that.
In any case, I do not think you are going to have issues.

How to configure connection timeout in hibernate?

I'm using Hibernate v4.1.4.final.jar using Java 1.7 to connect to Oracle 10g server. And this is a standalone java program.
Unfortunately, my query takes more than 30 minutes to run. I want to know where I can configure connection time out & read time out so that while running this standalone program, it will not time out and throw error?
Thanks!

There are a few options that you can try:
If the jdbc driver that you use support timeout function and can be configured through property, then you can pass on the property using: hibernate.connection.<propertyname>
Use external connection provider such as c3p0 or DBCP, and control the timeout as those external provider support.
Configure your hibernate to use DataSource instead of plain Connection and control timeout through that.
The closest property that I can find for Oracle driver is oracle.jdbc.ReadTimeout property. So in your hibernate configuration, the whole name will be hibernate.connection.oracle.jdbc.ReadTimeout..hope this works for you.

By default it won't throw any kind of error, FWIW...if you run a query, it'll just work, AFAIK.
In terms of connect timeout, you may be able to specify in your
hibernate.connection.url a particular option for your DB, ex: Postgres I'd add &connectTimeout=0

Efficient way to validate a DB connection

The DB driver I am working with (for a sybase DB) does not implement a Connection.isValid(). What is the most efficient way I can validate a db connection using a query (or otherwise) in Java?

Libraries such as C3P0 and DBCP allow you to provide a validation query which is typically something very simple such as "select 1". Hence, you could take the same approach or simply use either of these libraries (my recommendation would be C3P0).
However, rather than testing the connection prior to executing your query you could simply attempt to execute and then retry the operation if it fails because the connection is invalid. Alternatively you could consider a non-pooled connection approach where the connection is created on-the-fly each time (e.g. such as Spring's DriverManagerDataSource).

I mostly agree with Adamski's comment about using "select 1 from table" as an efficient way of checking connectivity and using connection pooling (e.g. commons-dbcp, C3PO).
Application servers (e.g. Websphere) allow you to configure this validation for you so your applciation code doesn't have to know about it. You have the choice of always having the connection checked prior to using it, or the connection pool being validated when a new connections is created. You can also purge connections periodically in case they get stale.
If you're not running in an application server you can use Common DBCP with the properties described here:
http://commons.apache.org/dbcp/configuration.html
Or C3PO and take a look at using the idleConnectionTestPeriod property. This link talks about use with Hibernate but its still relevant for C3PO generally
http://community.jboss.org/wiki/HowToConfigureTheC3P0ConnectionPool