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[protege-discussion] Protege Server lost connection to MySQLdatabase
jonathan.carter at e-asolutions.com
Mon Feb 25 07:29:54 PST 2008
Good to know that you're on top of this.
I'll keep going with the MySQL timeout being high. A colleague has suggested
using a 3rd party connection pooling toolkit that appears to the client as a
JDBC driver but operates as an adapter layer between the client and the
_real_ JDBC driver. In this you can configure "keep alive" type statements
which periodically run simple queries against the database to keep the
However, I've just realised that if I use that, the Protégé code won't be
able to recognise the MySQL driver for any MySQL-specific coding.
Jonathan Carter - Head of Technical Architecture
From: protege-discussion-bounces at lists.stanford.edu
[mailto:protege-discussion-bounces at lists.stanford.edu] On Behalf Of Timothy
Sent: 22 February 2008 20:28
To: User support for Core Protege and the Protege-Frames editor
Subject: Re: [protege-discussion] Protege Server lost connection to
On Feb 21, 2008, at 2:54 AM, Jonathan Carter wrote:
> Has anyone else had a similar exception from Protege Server -
> connection lost to database?
> I'm using MySQL 5.051 Community edition and my server had been running
> for about 1.5 days with possibly more than 8 hours idle time over
> When the server received the database connection loss, it seemed to go
> into a funny state, locking up a Protege Client that was connected at
> the time. The only way forward was to restart the Protege server.
Yes this is a known bug. The database is closing the connection and the
client does not know. Sometimes there are ways to correct the problem which
a new session but it is awkward. For some time I was unclear on how to fix
The good news is that it is fixed in the release coming in March thanks to a
suggestion by Bob Dionne. I did not find a good way to determine that a
connection has been closed. So what the new version of Protege does is to
have a timeout on idle connections so that it can close the connection on
its side. Then when the user tries to access the knowledge base again
protege automatically sets up a new connection with the database. The idle
timeout can be set with a flag (and should be longer than any single
> I've done some digging and losing connections to MySQL 5 appears to
> be something that others (in the wider Java community) have seen and
> it sounds like when MySQL shuts down idle connections, any connection
> pools don't seem to get notified of this.
> Has anyone had a similar experience?
> Does the Protege Server attempt to reconnect explicitly (rather than
> relying on the connection pool) with MySQL?
> Are there any recommended settings on MySQL that have been used to
> avoid this? e.g. I've found a suggestion to up the wait-timeout in
> MySQL from default of 8 hours to much more to stop MySQL culling idle
> connections. I'm going to try putting this to 36 hours and see how
> that affects things.
NCI is using this setting and it is working for them. I believe that the
code has been fixed on their branch though.
> Jonathan Carter - Head of Technical Architecture Enterprise
> Architecture Solutions Ltd
> Mobile: +44 (0) 7904 198295
> Email: jonathan.carter at e-asolutions.com
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