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Zero flow files in onTrigger() method of AbstractProcessor of Apache Nifi

I am developing a custom processor for Apache NiFi. I have created nar of my processor and put it in the lib folder of nifi and started the nifi. I have setup the remote debugger in eclipse and enabled breakpoint on first line of onTrigger(). While debugging I am running one processor at a time in my nifi pipeline. I can find single flow file in the input queue of my custom processor, however my custom processor is not receiving any flow file. When I start my custom processor, it hits breakpoint inside onTrigger() method. Inside thie method, when I do:
public class MyCustomProc extends AbstractProcessor {
#Override
public void onTrigger(final ProcessContext context, final ProcessSession session) throws ProcessException {
List<FlowFile> flowFiles = session.get(5000);
if (flowFiles == null || flowFiles.size() == 0) {
return;
}
//...
flowFiles turns out to be of size zero!!! I am not able to guess in which direction should I check to find why this is happening. Any hint how I can diagnose this?
Edit
Stacktrace
2019-05-02 18:08:09,456 ERROR [Timer-Driven Process Thread-10] c.c.product.module.submodule.MyCustomProcessor MyCustomProcessor[id=016a1008-8956-1dbf-bd66-993e0ce98668] MyCustomProcessor[id=016a1008-8956-1dbf-bd66-993e0ce98668] failed to process due to org.apache.nifi.processor.exception.FlowFileHandlingException: StandardFlowFileRecord[uuid=408fbb3d-7cc2-48bc-be8f-6d0afdbddaf2,claim=StandardContentClaim [resourceClaim=StandardResourceClaim[id=1556800468726-1, container=default, section=1], offset=261, length=591447],offset=0,name=188149730353200,size=591447] transfer relationship not specified; rolling back session: {}
org.apache.nifi.processor.exception.FlowFileHandlingException: StandardFlowFileRecord[uuid=408fbb3d-7cc2-48bc-be8f-6d0afdbddaf2,claim=StandardContentClaim [resourceClaim=StandardResourceClaim[id=1556800468726-1, container=default, section=1], offset=261, length=591447],offset=0,name=188149730353200,size=591447] transfer relationship not specified
at org.apache.nifi.controller.repository.StandardProcessSession.checkpoint(StandardProcessSession.java:251)
at org.apache.nifi.controller.repository.StandardProcessSession.commit(StandardProcessSession.java:321)
at org.apache.nifi.processor.AbstractProcessor.onTrigger(AbstractProcessor.java:28)
at org.apache.nifi.controller.StandardProcessorNode.onTrigger(StandardProcessorNode.java:1122)
at org.apache.nifi.controller.tasks.ContinuallyRunProcessorTask.call(ContinuallyRunProcessorTask.java:147)
at org.apache.nifi.controller.tasks.ContinuallyRunProcessorTask.call(ContinuallyRunProcessorTask.java:47)
at org.apache.nifi.controller.scheduling.TimerDrivenSchedulingAgent$1.run(TimerDrivenSchedulingAgent.java:128)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.runAndReset(Unknown Source)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(Unknown Source)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
PS1: This method returns immediately from inside if's body, which gives me following exception:
org.apache.nifi.processor.exception.FlowFileHandlingException: StandardFlowFileRecord transfer relationship not specified
This exceptions keeps recurring forever, since flow file in the input queue of my custom processor.
PS2: I am getting following error in the apps.log, though I am unsure if this is the source of the problem:
2019-05-02 18:17:32,394 ERROR [Timer-Driven Process Thread-4] o.a.nifi.groups.StandardProcessGroup Unable to synchronize StandardProcessGroup[identifier=d25747e6-719e-3ed9-c6c5-56794af6555c] with Flow Registry because Process Group was placed under Version Control using Flow Registry with identifier 80016ab0-bfab-152b-ffff-ffffc441867c but cannot find any Flow Registry with this identifier

It is normal behavior to sometimes get zero flow files, which is why processors have the check that you have at the beginning.
The FlowFileHandlingException means that a flow file was obtained from the session, either from get or create, and that flow file was not transferred anywhere and was not removed, so basically it is unaccounted for. This could not happen from just returning at the beginning in that if statement, so the rest of the processor code is executing and producing this error. You haven't provided the rest of the code so we can't see the problem.
The second issue is fairly self-explanatory. You have a process group under version control, but the registry client that was used to start version control somehow no longer exists. I don't know how you created this scenario because I believe the UI/API won't let you delete a registry client that has active flows under version control, but you should be able to stop version control on the process group.

javax.ejb.EJBTransactionRolledbackException: Transaction rolled back

(I didn't find proper answer from the existing questions that's why I posted this)
I have an application which processes quite big number of data. I am getting the below errors / exceptions and the process gets terminated. But increasing the ram size resolving the issue. (but we can't do it for some restriction)
2019-02-11 14:02:59,662 ERROR [net.xxx.RuleHandler] (Thread-185232 (HornetQ-client-global-threads-1521150484)) failed to get rules from db: org.hibernate.HibernateException: Transaction was rolled back in a different thread!
at org.hibernate.engine.transaction.synchronization.internal.SynchronizationCallbackCoordinatorTrackingImpl.processAnyDelayedAfterCompletion(SynchronizationCallbackCoordinatorTrackingImpl.java:105) [hibernate-core-4.2.27.Final-redhat-1.jar:4.2.27.Final-redhat-1]
2019-02-11 14:02:59,693 ERROR [net.xxx.ejb.SearchReqMDB] (Thread-185232 (HornetQ-client-global-threads-1521150484)) Something failed while search indexing: net.xxx.xxx.JMPException: javax.ejb.EJBTransactionRolledbackException: Transaction rolled back
How to resolve this issue? Do I need to increase the timeout value for ejb call? and if yes then where I need to change it.
Using JBOSS 6 EAP , EJB & JPA

org.h2.jdbc.JdbcSQLException: General error: "java.lang.StackOverflowError" [50000-176]

Stackoverflow error while using H2 database in Multi Threaded Environment
Our Application has service layer querying H2 database and retrieving the resultset.
The service layer connects to the h2 database using opensource clustering middleware "Sequoia" (that offers load balancing and
transparent failover) and also manages database connections .
https://sourceforge.net/projects/sequoiadb/
Our service layer has 50 service methods and we have exposed the service methods as EJB's . While Invoking the EJB's
we get the response from service (that includes H2 READ) with an average response time of 0.2 secs .
The DAO layer, query the database using Hibernate Criteria and we also use JPA2.0 entity manager to manage datasource.
For Load testing , We created a test class (with a main method) that invokes all the 50 EJB Methods .
50 threads were created and all the threads invoked the test class . The execution was Ok for first run and all the 50 threads succssfully completed
invoking 50 EJB methods .
When we triggered the test class again , we encountered "stackoverflowerror".The Detailed stacktrace is shown below
org.h2.jdbc.JdbcSQLException: General error: "java.lang.StackOverflowError" [50000-176]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:344)
at org.h2.message.DbException.get(DbException.java:167)
at org.h2.message.DbException.convert(DbException.java:290)
at org.h2.server.TcpServerThread.sendError(TcpServerThread.java:222)
at org.h2.server.TcpServerThread.run(TcpServerThread.java:155)
at java.lang.Thread.run(Thread.java:784)
Caused by: java.lang.StackOverflowError
at java.lang.Character.digit(Character.java:4505)
at java.lang.Integer.parseInt(Integer.java:458)
at java.lang.Integer.parseInt(Integer.java:510)
at java.text.MessageFormat.makeFormat(MessageFormat.java:1348)
at java.text.MessageFormat.applyPattern(MessageFormat.java:469)
at java.text.MessageFormat.<init>(MessageFormat.java:361)
at java.text.MessageFormat.format(MessageFormat.java:822)
at org.h2.message.DbException.translate(DbException.java:92)
at org.h2.message.DbException.getJdbcSQLException(DbException.java:343)
at org.h2.message.DbException.get(DbException.java:167)
at org.h2.message.DbException.convert(DbException.java:290)
at org.h2.command.Command.executeUpdate(Command.java:262)
at org.h2.jdbc.JdbcPreparedStatement.execute(JdbcPreparedStatement.java:199)
at org.h2.server.TcpServer.addConnection(TcpServer.java:140)
at org.h2.server.TcpServerThread.run(TcpServerThread.java:152)
... 1 more
at org.h2.engine.SessionRemote.done(SessionRemote.java:606)
at org.h2.engine.SessionRemote.initTransfer(SessionRemote.java:129)
at org.h2.engine.SessionRemote.connectServer(SessionRemote.java:430)
at org.h2.engine.SessionRemote.connectEmbeddedOrServer(SessionRemote.java:311)
at org.h2.jdbc.JdbcConnection.<init>(JdbcConnection.java:107)
at org.h2.jdbc.JdbcConnection.<init>(JdbcConnection.java:91)
at org.h2.Driver.connect(Driver.java:74)
at org.continuent.sequoia.controller.connection.DriverManager.getConnectionForDriver(DriverManager.java:266)
We then even added a random thread sleep(10-25 secs) between EJB Invocation . The execution was successful thrice (all 50 EJB Invocation)
and when we triggered for 4th time ,it failed with above error .
We get to see the above failure even with a thread count of 25 .
The Failure is random and there doesn't seems to be a pattern . Kindly let us know if we have missed any configuration .
Please let me know if you need any additional information . Thanks in Advance for any help .
Technology Stack :
1) Java 1.6
2) h2-1.3.176
3) Sequoia Middleware that manages DB Connection Open and Close.
-Variable Connection Pool Manager
-init pool size 250

Thanks Lance Java for your suggestions . Increasing stack size didnt help in our scenario for the following reasons (i.e additional stack helped only for few more executions).
In Our App , we are using Entity Manager (JPA) and the transaction attribute was not set . Hence each query to the database , created a thread carrying out execution . In JVisualVm , we observed the DB Threads, the Live Threads was equal to Total Threads Started .
Eventually our app created more than 30K threads and hence has resulted in Stackoverflow error .
Upon Setting the transaction attribute , the threads get killed after DB execution and all the transactions are then managed by only 25-30 threads.
The Issue is resolved now .

There's two main causes for a stack overflow error
A bug containing a non-terminating recursive call
The allocated stack size for the jvm isn't big enough
Looking at your stack trace it doesn't look recursive so I'm guessing you are running out of space. Have you set the -Xss flag for your JVM? You might need to increase this value.

odd SQLException - Could not retrieve transation read-only status server

I have a Quartz Job that executes a Stored Procedure in my MySQL database once every 5 minutes, and for some reason, 1 out of 3 executions fails and gives this weird exception. I have searched and searched for what this exception means, but I could not find a solution. Here is the full stack trace:
java.sql.SQLException: Could not retrieve transation read-only status server
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1078)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:989)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:975)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:920)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:951)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:941)
at com.mysql.jdbc.ConnectionImpl.isReadOnly(ConnectionImpl.java:3939)
at com.mysql.jdbc.ConnectionImpl.isReadOnly(ConnectionImpl.java:3910)
at com.mysql.jdbc.PreparedStatement.checkReadOnlySafeStatement(PreparedStatement.java:1258)
at com.mysql.jdbc.CallableStatement.checkReadOnlySafeStatement(CallableStatement.java:2656)
at com.mysql.jdbc.PreparedStatement.execute(PreparedStatement.java:1278)
at com.mysql.jdbc.CallableStatement.execute(CallableStatement.java:920)
at com.mchange.v2.c3p0.impl.NewProxyCallableStatement.execute(NewProxyCallableStatement.java:3044)
at org.deadmandungeons.website.tasks.RankUpdateTask.execute(RankUpdateTask.java:30)
at org.quartz.core.JobRunShell.run(JobRunShell.java:202)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:573)
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
The last packet successfully received from the server was 1,198,219 milliseconds ago. The last packet sent successfully to the server was 950,420 milliseconds ago.
at sun.reflect.GeneratedConstructorAccessor43.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1121)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3673)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3562)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4113)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2570)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2731)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2812)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2761)
at com.mysql.jdbc.StatementImpl.executeQuery(StatementImpl.java:1612)
at com.mysql.jdbc.ConnectionImpl.isReadOnly(ConnectionImpl.java:3933)
... 9 more
Caused by: java.net.SocketException: Connection timed out
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.read(SocketInputStream.java:150)
at java.net.SocketInputStream.read(SocketInputStream.java:121)
at com.mysql.jdbc.util.ReadAheadInputStream.fill(ReadAheadInputStream.java:114)
at com.mysql.jdbc.util.ReadAheadInputStream.readFromUnderlyingStreamIfNecessary(ReadAheadInputStream.java:161)
at com.mysql.jdbc.util.ReadAheadInputStream.read(ReadAheadInputStream.java:189)
at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:3116)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3573)
... 17 more
So I figured it is timing out because it thinks the MySQL server is in read-only status?
This only happens for this quartz job, and not any other time when I communicate with the database. This execution is of course happening in another thread, but I don't think that would have anything to do with it.
Why would it think the server was in read-only mode?
Also, I don't think "transation" is a word, so there's that...

Sorry for posting on old thread,
As stack trace says
com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
This implies the link between JDBC and DB is broken.As per your observation you say 1 out of 3 job invocations fails.
You have these jobs scheduled every 5 minutes and as per trace the last successful message sent to server is ~15 minutes before.
Hence I suspect either
You are procedure is not returning (waiting on something)
The JDBC connection has been invalidated by the firewall/ proxy
It will interesting to see the how connections are managed, As per logs I see you are using c3p0.
You can try setting unreturnedConnectionTimeout and debugUnreturnedConnectionStackTraces. This will give you more insight into connection leaks or db calls which are taking long.

Research takes nowhere, as you guys said, but the error shows what seems to be a Database being populated by two applications at the same time.
Do you have admin privileges on this MySQL server? If you do, you should try setting
FLUSH TABLES WITH READ LOCK;
SET GLOBAL READ_ONLY=ON;
as a test to reproduce the error. Just to warn you, this command makes your database unwritable, so you will not be able to add data in it until you revert this configuration, obviously with
SET GLOBAL READ_ONLY=0;
UNLOCK TABLES;
If the result of this test is positive (same error had been reproduced), you should try isolating applications that are storing data on your database, to find out which one is conflicting with Quartz.
I'm sorry for being vague, but I hope it gives you some help...

SQL Server / JDBC Connectivity Issues

I am experiencing some strange behaviour in my Java server application whereby database operations that usually take a few milliseconds are sporadically taking much longer (30s - 170s) to complete. This isn't isolated to a specific query as I've seen the delays occurring for both SQL update and select statements. Also, all of my select statements use the NOLOCK option so I've ruled out possible lock contention.
The last time I saw a delay I managed to capture the following stack trace from JConsole; the update in question typically takes 5ms to complete but this stack trace was accessible for at least 10 - 20 seconds. The trace suggests to me that the statement has been executed but there is some delay in retrieving the result although I could be wrong? Obviously as this was an update statement the only result I'd expect would be the row count (i.e. not a large result set of data).
I saw a "transport level error" in SQL Server Management Studio at around the time of the delay.
One suggestion I've had is that these problems are due to SQL Server resources being exhausted. Has anyone seen anything similar? Can anyone shed any light on this problem?
Thanks in advance.
Stack Trace:
Name: MessageRouterImplThread-2
State: RUNNABLE
Total blocked: 0 Total waited: 224
Stack trace:
java.net.SocketInputStream.socketRead0(Native Method)
java.net.SocketInputStream.read(SocketInputStream.java:129)
com.microsoft.util.UtilSocketDataProvider.getArrayOfBytes(Unknown Source)
com.microsoft.util.UtilBufferedDataProvider.cacheNextBlock(Unknown Source)
com.microsoft.util.UtilBufferedDataProvider.getArrayOfBytes(Unknown Source)
com.microsoft.jdbc.sqlserver.SQLServerDepacketizingDataProvider.signalStartOfPacket(Unknown Source)
com.microsoft.util.UtilDepacketizingDataProvider.getByte(Unknown Source)
com.microsoft.util.UtilByteOrderedDataReader.readInt8(Unknown Source)
com.microsoft.jdbc.sqlserver.tds.TDSRequest.getTokenType(Unknown Source)
com.microsoft.jdbc.sqlserver.tds.TDSRequest.processReply(Unknown Source)
com.microsoft.jdbc.sqlserver.SQLServerImplStatement.getNextResultType(Unknown Source)
com.microsoft.jdbc.base.BaseStatement.commonTransitionToState(Unknown Source)
com.microsoft.jdbc.base.BaseStatement.postImplExecute(Unknown Source)
com.microsoft.jdbc.base.BasePreparedStatement.postImplExecute(Unknown Source)
com.microsoft.jdbc.base.BaseStatement.commonExecute(Unknown Source)
com.microsoft.jdbc.base.BaseStatement.executeUpdateInternal(Unknown Source)
com.microsoft.jdbc.base.BasePreparedStatement.executeUpdate(Unknown Source)
- locked com.microsoft.jdbc.sqlserver.SQLServerConnection#c4b83f
org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:101)
org.springframework.jdbc.core.JdbcTemplate$2.doInPreparedStatement(JdbcTemplate.java:798)
org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:591)
org.springframework.jdbc.core.JdbcTemplate.update(JdbcTemplate.java:792)
org.springframework.jdbc.core.JdbcTemplate.update(JdbcTemplate.java:850)
org.springframework.jdbc.core.JdbcTemplate.update(JdbcTemplate.java:858)
org.springframework.jdbc.core.simple.SimpleJdbcTemplate.update(SimpleJdbcTemplate.java:237)

"...whereby database operations that
usually take a few milliseconds are
sporadically taking much longer (30s -
170s) to complete."
What you are describing sounds like an incorrectly cached query plan, due to out of date statistics (and/or indexes that need rebuilding), or incorrect parameter sniffing. The timeout could be occuring because the server is taking longer than the default connection timeout.
I would talk to your DBA and first get statistics updated, and if that doesn't work get the indexes of the tables involved in the query rebuilt.
Run this on your Database (with the usual caveat about not runninhg in Production without talking to your admin/DBA, and run at own risk etc.):
EXEC sp_updatestats
EXEC sp_refreshview
EXEC sp_msForEachTable 'EXEC sp_recompile ''?'''
Alternatively, you mention time of day being a factor. Could it be that a backup or scheduled job is occuring at that time?
Update: You could kick off a profiler trace: MS SQL Server 2008 - How Can I Log and Find the Most Expensive Queries? but don't restrict to your DB. Such a trace, as long as it is started from SSMS as per that post, is relatively low impact (3-5% ish).

The "transport level error" seems to indicate connectivity problems. Is the database on a separate machine?