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[protege-discussion] Error converting Ontology to DataBase format

chaitanya guttula chaitanya.g86 at gmail.com
Sun Sep 5 22:19:07 PDT 2010


Hi Timothy,

Sorry for the late reply. I was waiting for our administrator to update the
MySQL server.
The problem is resolved. Thank you for helping out with this.

First I tried adding  the following line to our protege.properties file (in
the protege distribution)

Database.typename.frame.name.type=VARCHAR(310) COLLATE utf8_bin

But it did not work. We were using MySQL server version 4, so as you told we
updated the MySQL to 5.0.77 and then tried to convert the ontology into
database without adding the above line to the protege.properties file and it
worked. So, the update fixed the problems.

Thanks,
Chaitanya.



On Wed, Aug 4, 2010 at 5:43 PM, Timothy Redmond <tredmond at stanford.edu>wrote:

>
> I am sorry that we haven't responded to this yet.  The problem we have on
> this end is that while we see google hits about this type of problem we
> don't know how to replicate it.  I do have two ideas that you could try
> though.
>
> First you could try adding  the following line to your protege.properties
> file (in the protege distribution) when protege is not running:
>
>  Database.typename.frame.name.type=VARCHAR(310) COLLATE utf8_bin
>
>
> If this works we might put it in our source tree.
>
> Second maybe you are using an older version of mysql?  We are using 5.1.41
> here.  It is possible that an update might fix things.
>
> -Timothy
>
>
>
> On 07/30/2010 08:17 PM, chaitanya guttula wrote:
>
> Hi,
>
> I was trying to convert OBI ontology into Database back end and there was
> an error. I was using Protege 3.4.4 , MySQL Database for this purpose. I
> have checked the database after that error and I could find that the table
> for that ontology is created. The table was empty. The error that I got in
> Protege GUI is :
>
>  Errors at copying knowledgebase jdbc:mysql://localhost/itppr_protege
>     Exception class com.mysql.jdbc.exceptions.MySQLSyntaxErrorException.
> Message: BLOB/TEXT column 'frame' used in key specification without a key
> length
>
>
> The full trace of errors that were found in the console were :
>
>
> Creating database indicies:
> WARNING: Failed to create table on database MySQL with command 'CREATE
> TABLE TestTable3 (frame VARBINARY(310) NOT NULL, frame_type SMALLINT NOT
> NULL, slot VARBINARY(310) NOT NULL, facet VARBINARY(310) NOT NULL,
> is_template BIT NOT NULL, value_index INT NOT NULL, value_type SMALLINT NOT
> NULL, short_value VARCHAR(310) COLLATE utf8_general_ci, long_value
> MEDIUMTEXT)' :BLOB/TEXT column 'frame' used in key specification without a
> key length -- DefaultDatabaseFrameDb.createTable()
> WARNING: Errors at copying knowledgebase
> jdbc:mysql://localhost/itppr_protege --
> com.mysql.jdbc.exceptions.MySQLSyntaxErrorException: BLOB/TEXT column
> 'frame' used in key specification without a key length
>     at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1026)
>     at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:956)
>     at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3558)
>     at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3490)
>     at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1959)
>     at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2109)
>     at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2642)
>     at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1647)
>     at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1566)
>     at
> edu.stanford.smi.protege.storage.database.AbstractDatabaseFrameDb.executeUpdate(Unknown
> Source)
>     at
> edu.stanford.smi.protege.storage.database.DefaultDatabaseFrameDb.createIndices(Unknown
> Source)
>     at
> edu.stanford.smi.protege.storage.database.DefaultDatabaseFrameDb.createTable(Unknown
> Source)
>     at
> edu.stanford.smi.protege.storage.database.DefaultDatabaseFrameDb.ensureEmptyTableExists(Unknown
> Source)
>     at
> edu.stanford.smi.protege.storage.database.DefaultDatabaseFrameDb.overwriteKB(Unknown
> Source)
>     at
> edu.stanford.smi.protege.storage.database.DatabaseKnowledgeBaseFactory.copyKnowledgeBase(Unknown
> Source)
>     at
> edu.stanford.smi.protege.storage.database.DatabaseKnowledgeBaseFactory.copyKnowledgeBase(Unknown
> Source)
>     at
> edu.stanford.smi.protege.storage.database.DatabaseKnowledgeBaseFactory.saveKnowledgeBase(Unknown
> Source)
>     at
> edu.stanford.smi.protegex.owl.database.OWLDatabaseKnowledgeBaseFactory.saveKnowledgeBase(Unknown
> Source)
>     at edu.stanford.smi.protege.model.Project.saveDomainKB(Unknown Source)
>     at edu.stanford.smi.protege.model.Project.save(Unknown Source)
>     at edu.stanford.smi.protege.ui.ProjectManager.save(Unknown Source)
>     at
> edu.stanford.smi.protege.ui.ProjectManager.changeProjectStorageFormatRequest(Unknown
> Source)
>     at
> edu.stanford.smi.protege.action.ChangeProjectStorageFormat.actionPerformed(Unknown
> Source)
>     at
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1849)
>     at
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2169)
>     at
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
>     at
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
>     at javax.swing.AbstractButton.doClick(AbstractButton.java:302)
>     at
> javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1000)
>     at
> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1041)
>     at java.awt.Component.processMouseEvent(Component.java:5501)
>     at javax.swing.JComponent.processMouseEvent(JComponent.java:3135)
>     at java.awt.Component.processEvent(Component.java:5266)
>     at java.awt.Container.processEvent(Container.java:1966)
>     at java.awt.Component.dispatchEventImpl(Component.java:3968)
>     at java.awt.Container.dispatchEventImpl(Container.java:2024)
>     at java.awt.Component.dispatchEvent(Component.java:3803)
>     at
> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212)
>     at
> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3892)
>     at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)
>     at java.awt.Container.dispatchEventImpl(Container.java:2010)
>     at java.awt.Window.dispatchEventImpl(Window.java:1778)
>     at java.awt.Component.dispatchEvent(Component.java:3803)
>     at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
>     at
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242)
>     at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)
>     at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
>     at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
>     at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>
>
> Appreciate if someone can help me with this.
>
> Thanks,
> Chaitanya
>
>
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