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[protege-discussion] Help creating a server project stored in a database

Timothy Redmond tredmond at stanford.edu
Mon Feb 27 14:33:26 PST 2012


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 java.awt.EventDispatchThread.run(Unknown 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] http://bugs.mysql.com/bug.php?id=40360
[2] http://help.hannonhill.com/discussions/installation/56-database-error-on-upgrade-to-673



On 2/23/12 3:41 PM, Barrett, Michael wrote:
>
> Here's what I did (as near as I can remember):
>
> 1)  edited run_protege_server.sh
>
>     A) added
>
> RMI_REG_PORT=1099
>
> RMI_SERV_PORT=5200
>
>     B) replaced
>
> HOSTNAME_PARAM=-Djava.rmi.server.hostname=`hostname`
>
>     with
>
> HOSTNAME_PARAM=-Djava.rmi.server.hostname=dgdlcdcpvm001.nyumc.org
>
>    C) replaced
>
> #PORTOPTS="-Dprotege.rmi.server.port=5200 
> -Dprotege.rmi.registry.port=5100"
>
>     with
>
> PORTOPTS="-Dprotege.rmi.server.port=$RMI_SERV_PORT 
> -Dprotege.rmi.registry.port=$RMI_REG_PORT"
>
>     D) replaced
>
> $JAVA_PATH/rmiregistry &
>
>     with
>
> $JAVA_PATH/rmiregistry $RMI_REG_PORT &
>
> 2) I installed the mysql driver in the protege directory as driver.jar
>
> 3) I started up the server with ./run_protege_server.sh
>
> 4) I started up the client with ./run_protege.sh
>
> 5) I created a database "PROTEGE" on my mysql server.
>
> 6) I created a subdirectory on the server "projects"
>
> 7) I created a new project via the protege client using the "Protege 
> Database" Project Type
>
> 8) I saved the project "Dogs" to the server's "projects" subdirectory.
>
> 9) I edited the server's server metaproject in server's "example" 
> subdirectory
>
> 10) I added a new instance of the project class with the location of 
> the project file in the "projects" subdirectory
>
> 11) I saved the metaproject
>
> 12) I attempted to "Open Other/Server" to connect to the Dogs project 
> on the server.
>
> The "Dogs" project was not listed.
>
> 13) I stopped and started the protege server using the 
> shutdown_protege_server.sh and the run_protege_server.sh scripts.
>
> 14) I attempted to "Open Other/Server" to connect to the "Dogs" 
> project on the server.
>
> This time the "Dogs" project was an option, but I was not able to 
> create new classes in the project.
>
> 15) I opened the "Dogs" project using the file method  and created new 
> classes
>
> 16) I opened the "Dogs" project using the "Open Other/Server" method.  
> The new clases I had created in step 15 were there, but I could not 
> edit them or create new classes.
>
> Amongst the java output when I attempt to create a new class is the 
> statemet:
>
>         at java.awt.EventDispatchThread.run(Unknown Source)
>
> Caused by: java.sql.SQLException: Binary logging not possible. 
> Message: Transaction level 'READ-COMMITTED' in InnoDB is not safe for 
> binlog mode 'STATEMENT'
>
> What am I doing wrong?
>
> Thanks,
>
> -Mike
>
>
>
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