EOFException thrown when exporting from database to file

[Maarten Menken]

Hello,

I am trying to export an ontology that is stored in a database to an
RDF(S) or OWL file. After a while I get the following exception:

java.io.EOFException
at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1842)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2341)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2784)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:750)
at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1251)
at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:2209)
at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:413)
at
com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:1899)
at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:1347)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1667)
at com.mysql.jdbc.Connection.execSQL(Connection.java:2376)
...

Browsing the ontology in Protégé works fine. I use the latest jdbc-mysql
driver (3.1.8a) and saved the jar to driver.jar in the Protégé
installation directory. The ontology is stored in a MySQL database on
the same machine.

This exception is thrown with the latest stable release of Protégé (3.0)
and as well as with the latest beta release (3.1 beta build 191).

Do you have any idea how I could solve this problem?

Thanks in advance,

Maarten Menken
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[Ray Fergerson]

This looks like a jdbc connection problem of some sort. Are you sure
that the driver is recommended for the version of the server that you
are using? Was the connection hung for a long time when this occurred?
Attaching the entire stack trace might help to diagnose the problem.

Is your project an "OWL database" project? If so then you should only
try to export to "OWL files". If it was a "Protege Database" then you
should try to export to "Protege files".

Ray

Post by Maarten Menken
Hello,
I am trying to export an ontology that is stored in a database to an
java.io.EOFException
at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1842)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2341)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2784)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:750)
at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1251)
at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:2209)
at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:413)
at
com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:1899)
at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:1347)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1667)
at com.mysql.jdbc.Connection.execSQL(Connection.java:2376)
...
Browsing the ontology in Protégé works fine. I use the latest jdbc-mysql
driver (3.1.8a) and saved the jar to driver.jar in the Protégé
installation directory. The ontology is stored in a MySQL database on
the same machine.
This exception is thrown with the latest stable release of Protégé (3.0)
and as well as with the latest beta release (3.1 beta build 191).
Do you have any idea how I could solve this problem?
Thanks in advance,
Maarten Menken
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