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[protege-discussion] Error converting Ontology to DataBase format

Timothy Redmond tredmond at stanford.edu
Mon Sep 6 09:07:31 PDT 2010


Thanks for this  information - this is very useful feedback.

-Timothy


On Sep 5, 2010, at 10:19 PM, chaitanya guttula wrote:

> 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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