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Statement.setQueryTimeout doesn't work on Oracle 18c jdbc driver

We have a J2EE application on a payara 5.2020 server that executes a long running query (PL/SQL that executes for a couple of hours).
To avoid a timeout exception, we use this sentence at StatementLevel:
statement.setQueryTimeout(0);
This works using Oracle jdbc drivers version 12c, but when we have migrated to Oracle 18c, and we changed the driver to the version 18c, the query execution stops after 15 minutes with this exception. The code works with Oracle 12 and Oracle 18 is the change in the driver's jar what brings up the problem.
The problem has been reproduced in Linux and Windows machines:
2021-06-14T07:50:01.762+0200|SEVERE: java.sql.SQLRecoverableException: Error de E/S: Socket read interrupted
at oracle.jdbc.driver.T4CCallableStatement.executeForRows(T4CCallableStatement.java:946)
at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1136)
at oracle.jdbc.driver.OraclePreparedStatement.executeInternal(OraclePreparedStatement.java:3640)
at oracle.jdbc.driver.T4CCallableStatement.executeInternal(T4CCallableStatement.java:1318)
at oracle.jdbc.driver.OraclePreparedStatement.execute(OraclePreparedStatement.java:3752)
at oracle.jdbc.driver.OracleCallableStatement.execute(OracleCallableStatement.java:4242)
at oracle.jdbc.driver.OraclePreparedStatementWrapper.execute(OraclePreparedStatementWrapper.java:1079)
at com.sun.gjc.spi.base.PreparedStatementWrapper.execute(PreparedStatementWrapper.java:532)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at com.sun.gjc.spi.jdbc40.ProfiledConnectionWrapper40$1.invoke(ProfiledConnectionWrapper40.java:437)
at com.sun.proxy.$Proxy324.execute(Unknown Source)
at org.apache.jsp.index_jsp.callPL(index_jsp.java:49)
at org.apache.jsp.index_jsp._jspService(index_jsp.java:108)
at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:111)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:750)
at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:411)
at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:473)
at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:377)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:750)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1636)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:259)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:161)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:757)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:577)
at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:158)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:371)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:238)
at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:520)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:217)
at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:182)
at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:156)
at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:218)
at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:95)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:260)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:177)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:109)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:88)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:53)
at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:524)
at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:89)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:94)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:33)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:114)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:569)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:549)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.io.InterruptedIOException: Socket read interrupted
at oracle.net.nt.TimeoutSocketChannel.handleInterrupt(TimeoutSocketChannel.java:262)
at oracle.net.nt.TimeoutSocketChannel.read(TimeoutSocketChannel.java:184)
at oracle.net.ns.NSProtocolNIO.doSocketRead(NSProtocolNIO.java:544)
at oracle.net.ns.NIOPacket.readHeader(NIOPacket.java:234)
at oracle.net.ns.NIOPacket.readPacketFromSocketChannel(NIOPacket.java:174)
at oracle.net.ns.NIOPacket.readFromSocketChannel(NIOPacket.java:122)
at oracle.net.ns.NIOPacket.readFromSocketChannel(NIOPacket.java:100)
at oracle.net.ns.NIONSDataChannel.readDataFromSocketChannel(NIONSDataChannel.java:86)
at oracle.jdbc.driver.T4CMAREngineNIO.prepareForUnmarshall(T4CMAREngineNIO.java:762)
at oracle.jdbc.driver.T4CMAREngineNIO.unmarshalUB1(T4CMAREngineNIO.java:427)
at oracle.jdbc.driver.T4CTTIfun.receive(T4CTTIfun.java:394)
at oracle.jdbc.driver.T4CTTIfun.doRPC(T4CTTIfun.java:255)
at oracle.jdbc.driver.T4C8Oall.doOALL(T4C8Oall.java:610)
at oracle.jdbc.driver.T4CCallableStatement.doOall8(T4CCallableStatement.java:249)
at oracle.jdbc.driver.T4CCallableStatement.doOall8(T4CCallableStatement.java:82)
at oracle.jdbc.driver.T4CCallableStatement.executeForRows(T4CCallableStatement.java:924)
It seems the transport layer has been migrated to java.nio and the method setQueryTimeout is no longer
Things We've tried:
Setting the default Statement timeout to -1 in the JDBC Connection Pool Advanced Attributes screen in payara console.
Trying to set the time directly in the connection with conn.setNetworkTimeout(Executors.newFixedThreadPool(1), 0) didn't make any effect.
In different sources we have found that these properties below should affect the network timeout evaluation. We set them as JVM properties for payara startup (-Doracle.net.CONNECT_TIMEOUT=xxx) and as JDBC Connection Pool Properties, both cases with values 0 and -1. Didn't work in any case.
oracle.net.CONNECT_TIMEOUT
oracle.net.READ_TIMEOUT
oracle.jdbc.ReadTimeout
Sources:
Oracle 18c Net services best practices
Oracle 18c java jdbc reference. E.1.5 Using JDBC with Firewalls
4.- As we are accessing the DataSource through payara DataSource pool, we cannot cast the com.sun.gjc.spi.jdbc40.DataSource40 (class provided by payara) to an OracleDataSource, but we created the DataSorce programatically to set the connection properties as shown here and setting the properties seen in the image above but it doesn't work:
public static Properties oracleProperties() {
// Already tried -1 and 0
Properties properties = new Properties();
properties.put("Oracle.net.CONNECT_TIMEOUT", 0);
properties.put("Oracle.net.READ_TIMEOUT", 0);
properties.put("Oracle.jdbc.ReadTimeout", 0);
return properties;
}
public static OracleDataSource createDataSource() throws Exception {
OracleDataSource ods = new OracleDataSource();
ods.setURL("jdbc:oracle:thin:#itauc4602x:1521/BDExp");
ods.setUser("enevac");
ods.setPassword("enevac");
ods.setDataSourceName("OracleXADataSource");
ods.setLoginTimeout(0);
// default connection properties to avoid timeoutException
ods.setConnectionProperties(oracleProperties());
return ods;
}
Has anyone faced this problem, any idea on how to avoid the timeOut restriction?
Why 15 minutes?, according to the reference, the default value for oracle.net.ReadTimeout is 10 minutes.
Update:
To explain in more detail why I think the problem is in the driver and why I discard other possible origins of the exception, I assume the timeout can be raised from three sources:
Network timeout: I discard it cause I'm testing a payara server in my local machine against the development database, with no firewall in between.
Database server: the DBA has checked the Oracle net services configuration and there's no limit set that explains the 15 minutes cut. Besides, in these case, an SQLException would be expected with some kind of ORA-xxx error code.
JDBC: this can be set at connection level, statement level and transaction level. As I said at the beginning, the code works with oracle 12c drivers against Oracle 12 and Oracle 18 servers, it was the change of the driver's jar what make the code stop working.

Finally the problem was fixed configuring in the payara pool the "connectionProperties" custom property of the OracleDataSource. As #ibre5041 pointed, setting the property oracle.jdbc.javaNetNio=false changes the transport layer used by the driver and it starts working as the oracle 12c previous version.
According to Oracle reference, the OracleDataSource implementors can receive the connection properties as a java.util.Properties object.
Table 8-2 Oracle Extended Data Source Properties
Name: connectionProperties
Type: java.util.Properties
Description: Specifies the connection properties.
To set a multivalued property to the jdbc pool in the Payara Admin Console, you have to set the properties as (prop1=value1,prop2=value2), (Thank you again Ondro Mihályi). So in our case we set:
connectionProperties = (oracle.jdbc.ReadTimeout=0, oracle.jdbc.javaNetNio=false)
As a summary of what works and doesn't using Oracle 18c jdbc driver (every step tested separately)::
Setting timeout at statement level doesn't work:
statement.setQueryTimeout(0)
Setting timeout at connection level, with -1 or 0, doesn't work:
conn.setNetworkTimeout(Executors.newFixedThreadPool(1), timeout in ms)
Setting timeout properties programmatically in the java.util.connection using the OracleDataSource makes it work as indicated in the question.
Setting timeout properties as JVM properties makes it work if the limit is below 15min, but if you set a value > 15 minutes the exceptions is thrown, so setting to 0 or -1 has no effect:
So this makes the query stop after 10 secs:
-Doracle.net.CONNECT_TIMEOUT=10000 -Doracle.net.READ_TIMEOUT=10000 -Doracle.jdbc.ReadTimeout=10000
But with this stops after 15 minutes:
-Doracle.net.CONNECT_TIMEOUT=-1 -Doracle.net.READ_TIMEOUT=-1 -Doracle.jdbc.ReadTimeout=-1
Setting oracle.net.keepAlive=true as JVM property as #Nirmala suggested doesn’t work.
Setting oracle.jdbc.javaNetNio=false as JVM property as #ibre5041 makes it work. So it points to some problem with the java.nio transport layer.
Anyway, we opened a support issue to Oracle, cause the jdbc api statement.setQueryTimeout(0) should work without having to configure the datasource, I'll put the response when the case is closed.

The query execution could be stopped because of default tcp connection timeout. Can you set keepalive property "oracle.net.keepAlive" to “true” and verify?

Not able to connect oracle Database while using Cluster type HOST

I'm facing the following errors while connecting oracle DB, I'm using spring boot JDBC template to connect to database. The errors are below,
Exception in thread "main" java.lang.Exception: java.sql.SQLRecoverableException: IO Error: The Network Adapter could not establish the connection
at com.falabella.util.OracleDB.main(OracleDB.java:70)
Caused by: java.sql.SQLRecoverableException: IO Error: The Network Adapter could not establish the connection
Caused by: oracle.net.ns.NetException: The Network Adapter could not establish the connection
at oracle.net.nt.ConnStrategy.execute(ConnStrategy.java:392)
Caused by: java.net.UnknownHostException: NODE-01: nodename nor servname provided, or not known
Below are my finding, My database server host having the cluster and it has two nodes, like below,
Cluster (wood.clsuter.com)
| NODE01 (wood-01)
| NODE02 (wood-02)
My connection string is like this, jdbc:oracle:thin:#wood-clsuter.com:1531/service_name
When I'm using the cluster name in the connection string, I'm facing the below error
Caused by: java.net.UnknownHostException: wood-01: nodename nor servname provided, or not known
Whereas if I use any of the node name in the connection string , able to connect Data base without any issue, the working connection string is like below,
jdbc:oracle:thin:#wood-01.com:1531/service_name or
jdbc:oracle:thin:#wood-02.com:1531/service_name
Since I need to use my DB requests as load balancing, I need to use the cluster name instead of slave nodes,
I would like to know the root cause of this issue, such kind of production environment issues,
Could you please help me out with this?

You need to change connect string to:
"jdbc:oracle:thin:#(DESCRIPTION=(FAILOVER=ON)(LOAD_BALANCE=ON)(ADDRESS_LIST=(ADDRESS=(PROTOCOL=TCP)(HOST=wood-01.com)(PORT = 1531))(ADDRESS = (PROTOCOL = TCP)(HOST = wood-02.com)(PORT = 1531)))(CONNECT_DATA=(SERVICE_NAME =service_name)(FAILOVER_MODE=(TYPE=select)(METHOD=basic))))"

Local and Remote connection pools, Java DBCP

I have the following use-case:
I have a system that needs to use two different connection pools, One is for 'local' database (Meaning a database running on the local machine) and the other one is a 'remote' database. (Meaning a database that is running on a remote different server)
The remote database is a configuration sharing database, while the local one is has different kinds of data.
I've created two classes in order to connect to those datababase:
public class ConnectionPool {
private static BasicDataSource ds = createNewDatasource();
private static BasicDataSource createNewDatasource() {
BasicDataSource ds = new BasicDataSource();
String url = "jdbc:mysql://127.0.0.1:3306/SOME_DB"
ds.setUrl(url);
ds.setUsername(...);
ds.setPassword(...);
return ds;
}
public static Connection getConnection() throws SQLException {
return ds.getConnection();
}
}
The other class looks exactly the same, Only it's called RemoteConnection and the url is changed to:
String url = "jdbc:mysql://<REMOTE_IP>:3306/SOME_DB_2"
Running the above classes, I keep receiving the following message in my logs:
ERROR (RemoteConnection.java:40) - Failed on getConnection
java.sql.SQLException: Cannot create PoolableConnectionFactory (Access denied for user '...'#'<MACHINE_LOCAL_IP>' (using password: YES))
at org.apache.commons.dbcp2.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:2291)
at org.apache.commons.dbcp2.BasicDataSource.createDataSource(BasicDataSource.java:2038)
at org.apache.commons.dbcp2.BasicDataSource.getConnection(BasicDataSource.java:1533)
at Censored.RemoteConnection.getConnection(RemoteConnection.java:59)
...
Caused by: java.sql.SQLException: Access denied for user '...'#'<MACHINE_LOCAL_IP>' (using password: YES)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:965)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:873)
at com.mysql.jdbc.MysqlIO.proceedHandshakeWithPluggableAuthentication(MysqlIO.java:1710)
at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1226)
at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2188)
at com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2219)
at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2014)
at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:776)
at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
at sun.reflect.GeneratedConstructorAccessor31.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:57)
at java.lang.reflect.Constructor.newInstance(Constructor.java:437)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:386)
at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:330)
at org.apache.commons.dbcp2.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:39)
at org.apache.commons.dbcp2.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:256)
at org.apache.commons.dbcp2.BasicDataSource.validateConnectionFactory(BasicDataSource.java:2301)
at org.apache.commons.dbcp2.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:2287)
...
Firstly, The error above is weird. I've never used the machine local IP. So I don't understand where it came from. In addition, It doesn't seems like a privilege problem since I've tried logging into remote database through cli, using:
mysql -u'...' -p'...' -h <REMOTE_IP> SOME_DB_2
And it connected successfully. It smells to me like a JDBC Driver or connection definition problem but I can't seem to find the problematic spot.
Any idea what I'm doing wrong?

I've found the problem. It was an SSL issue.
The user I've used had to connect with SSL certificate.
That's also the reason why I've seen the local machine IP in the error.
A way to check is:
Select * from mysql.user where user='...';
What I've found was that:
ssl_type != ''
So I had to define:
jdbc:mysql://<REMOTE_IP>:3306/SOME_DB_2&useSSL=true
Configure the relevant certificates, and all was well.

trying to find db connection leak in my code, using Spring / JPA / Hikari

I've got a problem with a Spring web application that periodically runs into an error fetching a connection from my connection pool. Eventually in the logs I see entries like:
Caused by: javax.persistence.PersistenceException: org.hibernate.exception.JDBCConnectionException: Unable to acquire JDBC Connection
Caused by: java.sql.SQLTransientConnectionException: HikariPool-1 - Connection is not available, request timed out after 30000ms.
Only way to recover I've found once it hits this point is to restart Tomcat.
I think the most likely explanation is I have some code somewhere that is not properly cleaning up its connection - returning it to Hikari, leaving something open so Spring can't clean it up, etc.
To troubleshoot I've set my hikari config leakDetectionThreshold to 5000ms and enabled logging. After that, I see log entries like
2018-04-24 19:53:56 WARN ProxyLeakTask:87 - Connection leak detection
triggered for org.postgresql.jdbc.PgConnection#664ec666, stack trace
follows
java.lang.Exception: Apparent connection leak detected
at org.hibernate.engine.jdbc.connections.internal.DatasourceConnectionProviderImpl.getConnection(DatasourceConnectionProviderImpl.java:122)
at org.hibernate.internal.NonContextualJdbcConnectionAccess.obtainConnection(NonContextualJdbcConnectionAccess.java:35)
at org.hibernate.resource.jdbc.internal.LogicalConnectionManagedImpl.acquireConnectionIfNeeded(LogicalConnectionManagedImpl.java:99)
at org.hibernate.resource.jdbc.internal.LogicalConnectionManagedImpl.getPhysicalConnection(LogicalConnectionManagedImpl.java:129)
at org.hibernate.engine.jdbc.internal.StatementPreparerImpl.connection(StatementPreparerImpl.java:47)
at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$5.doPrepare(StatementPreparerImpl.java:146)
at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:172)
at org.hibernate.engine.jdbc.internal.StatementPreparerImpl.prepareQueryStatement(StatementPreparerImpl.java:148)
at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1940)
at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1909)
at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1887)
at org.hibernate.loader.Loader.doQuery(Loader.java:932)
at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:349)
at org.hibernate.loader.Loader.doList(Loader.java:2615)
at org.hibernate.loader.Loader.doList(Loader.java:2598)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2430)
at org.hibernate.loader.Loader.list(Loader.java:2425)
at org.hibernate.loader.custom.CustomLoader.list(CustomLoader.java:335)
at org.hibernate.internal.SessionImpl.listCustomQuery(SessionImpl.java:2129)
at org.hibernate.internal.AbstractSharedSessionContract.list(AbstractSharedSessionContract.java:981)
at org.hibernate.query.internal.NativeQueryImpl.doList(NativeQueryImpl.java:147)
at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1398)
at org.hibernate.query.internal.AbstractProducedQuery.getSingleResult(AbstractProducedQuery.java:1444)
at sun.reflect.GeneratedMethodAccessor191.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.orm.jpa.SharedEntityManagerCreator$DeferredQueryInvocationHandler.invoke(SharedEntityManagerCreator.java:379)
at com.sun.proxy.$Proxy163.getSingleResult(Unknown Source)
at com.mycompany.web.jpa.util.DBHelper.getPagedMappedDbResults(DBHelper.java:76)
at com.mycompany.web.jpa.repository.TaskRepositoryImpl.findTaskDetailsByStepIdAndIdIn(TaskRepositoryImpl.java:245)
......
So it is detecting a possible leak. Could be a false positive I suppose? But this is also the only class in my app that is doing database access outside of the standard service/repository pattern often used in Spring apps, so it seems like a likely culprit, and it's my best lead at the moment.
Anyway, the last piece of non library code I see in the trace (ie stuff I wrote, so most likely to be the cause of the leak!) is my DBHelper::getPagedMappedDbResults method, relevant bit included here:
Query q = entityManager.createNativeQuery(countQueryText);
setQueryParameters(q, parameters);
long numActualResults = 0;
try {
numActualResults = ((Number)q.getSingleResult()).longValue(); // line 76
} catch (Exception e) {
System.out.println("just in case: " + e);
}
So basically I create a Query object from my EntityManager instance, set some parameters, and run it to get some results.
Is there something I need to be doing with a Query object when I'm done with it? q.cleanup()? I don't see anything like this from reading the docs, but am I not doing good housekeeping on this resource?
The entityManager itself is created from an #Autowired annotation. My understanding is if I didn't "new" it to instantiate it and instead let the Spring framework autowire it, then Spring will do whatever cleanup is necessary. Is that right? Or do I need to be doing some cleanup after I use the entityManager?
Version details:
Tomcat 8 / Java 8
Spring 5.0.0.RELEASE
Spring Data Kay-RELEASE
Hibernate 5.2.3.Final
Hikari 2.4.5
Any advice or suggestions would be greatly appreciated, thanks!

What is the query? Is it heavy? Maybe you have deadlock here? Connection management looks fine. You do not acquire connection explicitly, so no need to release it. The query might be long running so Hibernate is not able to complete it and release the connection.
Also, you can check the number of open connections on the DB side. Do some analysis on that side as well.

How to connect to Azure SQL database with jTDS

I try to connect to Azure SQL with:
import java.sql.*;
public class ExampleJTDS {
public static void main(String[] args) {
// Setting.
String connectionUrl = "jdbc:jtds:sqlserver://SERVER.database.windows.net:1433/DATABASE;ssl=off";
String user = "USER#SERVER";
String pass = "PASSWORD";
// Declare the JDBC object.
Connection conn = null;
try {
// Establish the connection.
Class.forName("net.sourceforge.jtds.jdbc.Driver");
conn = DriverManager.getConnection(connectionUrl, user, pass);
}
catch (Exception e) {
e.printStackTrace();
}
}
}
But I am getting:
java.sql.SQLException: I/O Error: DB server closed connection.
at net.sourceforge.jtds.jdbc.TdsCore.nextToken(TdsCore.java:2481)
at net.sourceforge.jtds.jdbc.TdsCore.login(TdsCore.java:632)
at net.sourceforge.jtds.jdbc.JtdsConnection.<init>(JtdsConnection.java:371)
at net.sourceforge.jtds.jdbc.Driver.connect(Driver.java:184)
at java.sql.DriverManager.getConnection(DriverManager.java:664)
at java.sql.DriverManager.getConnection(DriverManager.java:247)
at run.ExampleJTDS.main(ExampleJTDS.java:21)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.intellij.rt.execution.application.AppMain.main(AppMain.java:144)
If I force the encryption by substituting ssl=off with ssl=require, I am getting:
java.sql.SQLException: Network error IOException: Connection reset
at net.sourceforge.jtds.jdbc.JtdsConnection.<init>(JtdsConnection.java:436)
at net.sourceforge.jtds.jdbc.Driver.connect(Driver.java:184)
at java.sql.DriverManager.getConnection(DriverManager.java:664)
at java.sql.DriverManager.getConnection(DriverManager.java:247)
at run.ExampleJTDS.main(ExampleJTDS.java:21)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.intellij.rt.execution.application.AppMain.main(AppMain.java:144)
Interestingly, I can connect to the database from the same computer and with the same JDBC driver with SQuirreL SQL (although without SSL - SQuirreL SQL manages to put the credentials into the first TDS packet and Azure accepts that). Hence, the problem should not be in the setting of firewalls.
Metadata:
Server: Azure V12
Driver: jtds-1.3.1
JRE: 1.8.0_72-b15 (from Oracle)
_JAVA_OPTIONS: -Djsse.enableCBCProtection=false
security.provider.1: sun.security.provider.Sun
OS: OS X 10.11.5
SQuirreL SQL: 3.7.1
How can I connect to Azure SQL from Java?

Per my experience, I think the issue was caused by the connection string which is the variable connectionUrl of your code. I have answered your similar question of the SO thread, please see How to connect to Azure SQL with JDBC.
However, using jTDS instead of Microsoft JDBC driver for SQL Server has a little difference, you can refer to a note in the step 3 of the tutorial to know it. As reference, I post the contento of the note here.
Note:
If you are using the JTDS JDBC driver, then you will need to add "ssl=require" to the URL of the connection string and you need to set the following option for the JVM "-Djsse.enableCBCProtection=false". This JVM option disables a fix for a security vulnerability, so make sure you understand what risk is involved before setting this option.
Hope it helps. Any concern, please feel free to let me know.