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From Clayton Turner <caturn...@g.cofc.edu>
Subject cTAKES CPE MySQL Exception
Date Thu, 24 Jul 2014 14:32:00 GMT
Hi, everyone.

First off, I'd like to say "awesome and thank you" for the cTAKES 3.2
release and information. I've been following those pages and it's been
really helpful for helping me move along in my own progress. Really cool

So I'm using the Collection Processing Engine (with ytex and umls) and I'm
trying to process ~1 million notes (as opposed to the about 30 in the given

I've tried this the past 2 days and when I come back in to check the
progress I see that I've received an error about 14000 notes into the

org.apache.uima.analysis_engine.AnalysisEngineProcessException: Annotator
processing failed.
CausedBy: org.springframework.transaction.CannotCreateTransactionException:
Could not open Hibernate Session for transaction; nested exception is
com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: The last packet
successfully received from the server was 53,888,249 milliseconds ago. The
last packet sent successfully to the server was 53,888,249 milliseconds
ago. is longer than the server configured value of 'wait_timeout'. You
should consider either expiring and/or testing connection validity before
use in your application, increasing the server configured values for client
timeouts, or using the Connector/J connection property 'autoReconnect=true'
to avoid this problem.

So, in my own debugging, I have ensured that autoReconnect true was on (it
always has been).

I looked at my CPE output in the command prompt and noticed a
"PacketTooBigException" so I increased the packet max size to 1G (the max
for sql server).

I increased the time allowed for timeouts.

I'm really unsure of what to do here. Should I find a way to see if there
is a problematic note that is giving me issues (though I can't understand
how 1 note would make a packet too large)? Should I try to do some
horizontal sharding and break the problem into smaller chunks (though I
would think this program could handle large datasets since it's using a
query language)? I'm just at a loss with this error, especially since it
takes so long to actually spit the error out at me.

Thanks in advance everyone,

Clayton Turner
email: caturner3@g.cofc.edu
phone: (843)-424-3784
web: claytonturner.blogspot.com
“When scientifically investigating the natural world, the only thing worse
than a blind believer is a seeing denier.”
- Neil deGrasse Tyson

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