start communicating with the database. Looking at your URL
it looks like the problem is that 3036 should be 3306. Also, in a
recreated. Otherwise if you create the table you need to be sure
that to create exactly the right columns. It is easier to let protege
> Dear Dr. Redmond,
>
> Thanks a lot for that; some progress:
> Now have:
> JDBC Driver (as suggested)
> JDBC URL: jdbc:mysql://localhost:3036/prot1 (as I have already
> created the table in the DB)
> Table: TEST1 (as above)
>
> and I get:
> (apologies for the length, see below).
>
> Any further ideas?
>
> Thanks,
>
> Matt
>
> STACKTRACE:
>
> The driver was found but it is not possible to create a connection
> with the driver URL.
> Perhaps the URL syntax is wrong or the username/password is invalid.
>
> Unable to connect to any hosts due to exception:
> java.net.SocketException: java.net.ConnectException: Connection
> refused
>
> ** BEGIN NESTED EXCEPTION **
>
> java.net.SocketException
> MESSAGE: java.net.ConnectException: Connection refused
>
> STACKTRACE:
>
> java.net.SocketException: java.net.ConnectException: Connection
> refused
> at com.mysql.jdbc.StandardSocketFactory.connect
> (StandardSocketFactory.java:143)
> at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:225)
> at com.mysql.jdbc.Connection.createNewIO(Connection.java:1805)
> at com.mysql.jdbc.Connection.<init>(Connection.java:452)
> at com.mysql.jdbc.NonRegisteringDriver.connect
> (NonRegisteringDriver.java:411)
> at java.sql.DriverManager.getConnection(DriverManager.java:525)
> at java.sql.DriverManager.getConnection(DriverManager.java:171)
> at
> edu.stanford.smi.protege.storage.database.DatabaseKnowledgeBaseSources
> Editor.validateContents(Unknown Source)
> at edu.stanford.smi.protege.util.ModalDialog.attemptClose(Unknown
> Source)
> at edu.stanford.smi.protege.util.ModalDialog$1.actionPerformed
> (Unknown Source)
> at javax.swing.AbstractButton.fireActionPerformed
> (AbstractButton.java:1849)
> at javax.swing.AbstractButton$Handler.actionPerformed
> (AbstractButton.java:2169)
> at javax.swing.DefaultButtonModel.fireActionPerformed
> (DefaultButtonModel.java:420)
> at javax.swing.DefaultButtonModel.setPressed
> (DefaultButtonModel.java:258)
> at javax.swing.plaf.basic.BasicButtonListener.mouseReleased
> (BasicButtonListener.java:234)
> at java.awt.Component.processMouseEvent(Component.java:5488)
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
> at java.awt.Component.processEvent(Component.java:5253)
> at java.awt.Container.processEvent(Container.java:1966)
> at java.awt.Component.dispatchEventImpl(Component.java:3955)
> 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:1774)
> 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.pumpEventsForHierarchy
> (EventDispatchThread.java:153)
> at java.awt.Dialog$1.run(Dialog.java:515)
> at java.awt.Dialog.show(Dialog.java:536)
> at java.awt.Component.show(Component.java:1300)
> at java.awt.Component.setVisible(Component.java:1253)
> at edu.stanford.smi.protege.util.ModalDialog.init(Unknown Source)
> at edu.stanford.smi.protege.util.ModalDialog.<init>(Unknown Source)
> at edu.stanford.smi.protege.util.ModalDialog.showDialog(Unknown
> Source)
> at edu.stanford.smi.protege.util.ModalDialog.showDialog(Unknown
> Source)
> at edu.stanford.smi.protege.util.ModalDialog.showDialog(Unknown
> Source)
> at edu.stanford.smi.protege.ui.ProjectManager.loadNewSources
> (Unknown Source)
> at
> edu.stanford.smi.protege.ui.ProjectManager.changeProjectStorageFormatR
> equest(Unknown Source)
> at
> edu.stanford.smi.protege.action.ChangeProjectStorageFormat.actionPerfo
> rmed(Unknown Source)
> at javax.swing.AbstractButton.fireActionPerformed
> (AbstractButton.java:1849)
>
>
>
> Timothy Redmond wrote:
>>
>> I suspect the problem is that you are using the wrong driver for
>> mysql. There is a sun.jdbc driver for mysql but
>> I would recommend that you use the mysql driver from the mysql web
>> page. Given that the settings you would
>> use are
>>
>> JDBC Driver: com.mysql.jdbc.Driver
>> JDBC URL: jdbc:mysql://localhost:3306/ProtegeDB
>> Table: ProtegeTable
>>
>> Another warning is that there is a bug in mysql 5.0 that causes
>> incorrect behavior in Protege until the latest Protege beta (just
>> out).
>> Mysql 4 and lower work.
>>
>> --------------------------------
>> Timothy Redmond, PhD
>> Research Staff
>> Stanford Medical Informatics
>> Medical School Office Building X-215
>> 251 Campus Drive
>> Stanford, CA 94305
>>
[hidden email]
>>
>>
>>
>> On Jan 24, 2006, at 5:04 AM, Matt Williams wrote:
>>
>>> Dear List,
>>>
>>> I'm trying to save an OWL Ontology as a DB (using MySQL).
>>>
>>> I follow File -> Convert Project to Format ... -> OWL/ RDF Database
>>>
>>> The dialog has the following values:
>>>
>>> Project:
>>> /usr/local/home/mw/tmp/nciOncology.pprj
>>>
>>> JDBC Driver class name:
>>> sun.jdbc.odbc.JdbcOdbcDriver
>>>
>>> JDBC URL:
>>> jdbc:odbc:ProtegeDB
>>>
>>> Table:ProtegeTable
>>>
>>> (u/name & p/word are ok).
>>>
>>>
>>> I get the following message:
>>> The driver was found but it is not possible to create a
>>> connection with
>>> the driver URL.
>>> Perhaps the URL syntax is wrong or the username/password is invalid.
>>>
>>> [unixODBC][Driver Manager]Data source name not found, and no default
>>> driver specified
>>>
>>> Now, am I just pointing at the wrong place (the server is at
>>> localhost:3036, but I've tried that and it didn't work), or do I
>>> need a
>>> new driver. There are some instructions on the Jambalya website
>>> about
>>> using PostgreSQL, but they seem to be for an older version.
>>>
>>> I'm using Protege 3.2b build 235.
>>>
>>> Thanks a lot,
>>>
>>> Matt
>>>
>>>
>>> --------------------------------------------------------------------
>>> -----
>>> To unsubscribe go to
http://protege.stanford.edu/community/
>>> subscribe.html
>>>
>>
>> ---------------------------------------------------------------------
>> ----
>> To unsubscribe go to
http://protege.stanford.edu/community/
>> subscribe.html
>>
>
> ----------------------------------------------------------------------
> ---
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>
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