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[protege-discussion] Help creating a server project

Timothy Redmond tredmond at
Thu Mar 1 11:20:21 PST 2012

On 02/28/2012 01:32 PM, Barrett, Michael wrote:
> Thank you very much for your reply, Timothy.  I will investigate making the changes suggested with our dba.

It occurred to me later that we could just treat the symptoms and ignore 
the cause.  If you set your transaction isolation level to read 
committed it is possible that your problem would go away.  You can do 
this by adding the jvm argument:


> However, I don't see how this could be the problem.  I am able to edit the ontology if I use the unix client and open the project with the "open recent" button.  Using the same client, I have a problem if I try to edit after opening the project via "open other / server"

This is a bit hard to understand.  I just checked and both cases use 
REPEATABLE_READ transaction level by default.  I don't have your full 
stack trace but I am guessing that the exception occurs when you make a 
change to the ontology.


> I'm using the same database in both cases, changes I make when I open via the "open recent" method are visible when I open by the "open other / server" method.
>   - Mike
> ----------------------------------------------------------------------
> Date: Mon, 27 Feb 2012 14:33:26 -0800
> From: Timothy Redmond<tredmond at>
> To: protege-discussion at
> Subject: Re: [protege-discussion] Help creating a server project
> 	stored in a database
> Message-ID:<4F4C04B6.8030803 at>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> Sorry for the late reply.
>> What am I doing wrong?
> I suspect that the answer is nothing.  Your exception:
>> Amongst the java output when I attempt to create a new class is the
>> statemet:
>>          at Source)
>> Caused by: java.sql.SQLException: Binary logging not possible.
>> Message: Transaction level 'READ-COMMITTED' in InnoDB is not safe for
>> binlog mode 'STATEMENT'
> is a database error that I have never seen before.  It is not clear how
> it can be connected to a misconfiguration of Protege.  It could be a
> Protege bug but I am guessing it is connected to the database and its
> configuration.
> I did a search on google and found some immediate hits.  One was a mysql
> bug [1] but this message [2] was also interesting indicating a
> configuration of my.cnf.
> -Timothy
> [1]
> [2]
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