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[protege-discussion] Error converting Ontology to DataBase format

Timothy Redmond tredmond at stanford.edu
Wed Aug 4 14:43:54 PDT 2010


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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