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[protege-owl] MySql JDBC Driver and Database problem

Congmin min marlonmin at gmail.com
Tue Sep 5 12:14:59 PDT 2006


Hi, Jeff:
  Last week I talked to you and now I can connect to mysql database. Thanks,

But I have another problem, I don't know if you had a similar problem.

I need to create a new project using exiting owl file to build a database
ontology, because my ontology in file format is so big that it can't be
loaded into protege and then be converted. I need to directly  create  an
ontology with database backend, but there is an exception:
Did you find this before?

java.lang.IndexOutOfBoundsException: Index: 0
    at java.util.Collections$EmptyList.get(Collections.java:2923)
    at
edu.stanford.smi.protegex.owl.model.triplestore.impl.AbstractTripleStoreModel.setHomeTripleStore(Unknown
Source)
    at
edu.stanford.smi.protegex.owl.model.triplestore.impl.AddRDFTypePropertyHandler.handleAdd(Unknown
Source)
    at
edu.stanford.smi.protegex.owl.model.triplestore.impl.AbstractTripleStore.add(Unknown
Source)
    at
edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$MyStatementHandler.statement(Unknown
Source)
    at com.hp.hpl.jena.rdf.arp.ARPResource.tripleRes(ARPResource.java:185)
    at com.hp.hpl.jena.rdf.arp.ARPResource.triple(ARPResource.java:170)
    at com.hp.hpl.jena.rdf.arp.ARPResource.setPredObject(ARPResource.java
:147)
    at com.hp.hpl.jena.rdf.arp.ARPResource.setType(ARPResource.java:142)
    at com.hp.hpl.jena.rdf.arp.RDFParser.typedNode(RDFParser.java:961)
    at com.hp.hpl.jena.rdf.arp.RDFParser.description(RDFParser.java:433)
    at com.hp.hpl.jena.rdf.arp.RDFParser.obj(RDFParser.java:346)
    at com.hp.hpl.jena.rdf.arp.RDFParser.rdf(RDFParser.java:326)
    at com.hp.hpl.jena.rdf.arp.RDFParser.rdfFileSub(RDFParser.java:107)
    at com.hp.hpl.jena.rdf.arp.RDFParser.rdfFile(RDFParser.java:99)
    at com.hp.hpl.jena.rdf.arp.SingleThreadedParser.parse(
SingleThreadedParser.java:146)
    at com.hp.hpl.jena.rdf.arp.ARP.load(ARP.java:136)
    at
edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$1.invokeARP(Unknown
Source)
    at
edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.loadTriples(Unknown
Source)
    at edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown
Source)
    at edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown
Source)
    at edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown
Source)
    at
edu.stanford.smi.protegex.owl.database.CreateOWLDatabaseFromFileProjectPlugin.buildNewProject(Unknown
Source)
    at
edu.stanford.smi.protege.plugin.AbstractCreateProjectPlugin.createProject(Unknown
Source)
    at edu.stanford.smi.protege.plugin.CreateProjectWizard.onFinish(Unknown
Source)
    at edu.stanford.smi.protege.util.Wizard$1.actionPerformed(Unknown
Source)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java
:1834)
    at javax.swing.AbstractButton$Handler.actionPerformed(
AbstractButton.java:2152)
    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:5463)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3052)
    at java.awt.Component.processEvent(Component.java:5228)
    at java.awt.Container.processEvent(Container.java:1961)
    at java.awt.Component.dispatchEventImpl(Component.java:3931)
    at java.awt.Container.dispatchEventImpl(Container.java:2019)
    at java.awt.Component.dispatchEvent(Component.java:3779)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java
:4203)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3883)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3813)
    at java.awt.Container.dispatchEventImpl(Container.java:2005)
    at java.awt.Window.dispatchEventImpl(Window.java:1757)
    at java.awt.Component.dispatchEvent(Component.java:3779)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
    at java.awt.EventDispatchThread.pumpOneEventForHierarchy(
EventDispatchThread.java:234)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(
EventDispatchThread.java:163)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(
EventDispatchThread.java:153)
    at java.awt.Dialog+1.run(Dialog.java:514)
    at java.awt.Dialog.show(Dialog.java:535)
    at java.awt.Component.show(Component.java:1292)
    at java.awt.Component.setVisible(Component.java:1247)
    at edu.stanford.smi.protege.util.Wizard.execute(Unknown Source)
    at edu.stanford.smi.protege.ui.ProjectManager.createNewProjectRequest(Unknown
Source)
    at edu.stanford.smi.protege.action.CreateProject.actionPerformed(Unknown
Source)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java
:1834)
    at javax.swing.AbstractButton$Handler.actionPerformed(
AbstractButton.java:2152)
    at javax.swing.DefaultButtonModel.fireActionPerformed(
DefaultButtonModel.java:420)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java
:258)
    at javax.swing.AbstractButton.doClick(AbstractButton.java:302)
    at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java
:1000)
    at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(
BasicMenuItemUI.java:1041)
    at java.awt.Component.processMouseEvent(Component.java:5463)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3052)
    at java.awt.Component.processEvent(Component.java:5228)
    at java.awt.Container.processEvent(Container.java:1961)
    at java.awt.Component.dispatchEventImpl(Component.java:3931)
    at java.awt.Container.dispatchEventImpl(Container.java:2019)
    at java.awt.Component.dispatchEvent(Component.java:3779)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java
:4203)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3883)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3813)
    at java.awt.Container.dispatchEventImpl(Container.java:2005)
    at java.awt.Window.dispatchEventImpl(Window.java:1757)
    at java.awt.Component.dispatchEvent(Component.java:3779)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
    at java.awt.EventDispatchThread.pumpOneEventForHierarchy(
EventDispatchThread.java:234)
    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)



On 8/31/06, Schmitz, Jeffrey A <Jeffrey.A.Schmitz at boeing.com> wrote:
>
>  No, just a database named pizzas.  Protege will create its own tables as
> needed.
>
> Did you see the message concerning the mysql database plugin (it just
> came).  That's probably something you want to get before trying anything
> else.
>
> Jeff
>
>
>  ------------------------------
> *From:* Congmin min [mailto:marlonmin at gmail.com]
> *Sent:* Thursday, August 31, 2006 3:34 PM
>
> *To:* User support for the Protege-OWL editor
> *Subject:* Re: [protege-owl] MySql JDBC Driver and Database problem
>
> I did almost the same as yours. but it still can't find the driver. when
> you use
> jdbc:mysql://localhost/pizzas
> do you create a table named 'pizzas' in your database?
>
> I don't know if I should first create a database or table.
>
> On 8/31/06, Schmitz, Jeffrey A <Jeffrey.A.Schmitz at boeing.com> wrote:
> >
> >  I use:
> >
> >  jdbc:mysql://localhost/pizzas
> >
> > for the driver class itself I use
> >
> > com.mysql.jdbc.Driver
> >
> > Also, I had to copy the driver jar file to the Protege installation
> > folder and rename it to driver.jar
> >
> > Once I created my Protege database project, I noticed that it had
> > created the following two tables:
> >
> > protegepizzatable
> > protegepizzatable_includes
> >
> > I should mention that, while I didn't get any errors, I never did get
> > the Protege editor to work with the database project.  All of the tabs were
> > just blank grey sheets.  That's when I gave up.
> >
> >
> > Hope this helps,
> > Jeff
> >
> >  ------------------------------
> >  *From:* Congmin min [mailto: marlonmin at gmail.com]
> > *Sent:* Thursday, August 31, 2006 1:09 PM
> > *To:* User support for the Protege-OWL editor
> > *Subject:* Re: [protege-owl] MySql JDBC Driver and Database problem
> >
> >  thanks for your message. Yes, I have an account on mySql, I log in
> > mysql by:
> >
> > mysql -u cmar -pxyz04,
> >
> > then 'cmar' is my  username, and password is 'xyz04' on the form.
> >
> > How do you specify the Driver URI?
> >
> >
> >
> >
> > On 8/31/06, Schmitz, Jeffrey A <Jeffrey.A.Schmitz at boeing.com> wrote:
> > >
> > >  I didn't use the port number when I specified the database URL.
> > > Also, did you create your MySQL accounts in MySQL?  These accounts have
> > > nothing to do with your computer accounts.  For example, use the following
> > > to create a PizzaMan MySQL account from the mysql command line as root user:
> > >
> > >
> > >
> > > mysql> CREATE USER PizzaMan at localhost;
> > >
> > > mysql> SET PASSWORD FOR PizzaMan at localhost = password('pizzaPW');
> > >
> > > mysql> GRANT ALL PRIVILEGES ON *.* TO PizzaMan at localhost WITH GRANT
> > > OPTION;
> > >
> > > Then specify PizzaMan as the user and pizzaPW as the password in the
> > > Protege setup form.
> > >
> > > Jeff
> > >
> > >  ------------------------------
> > > *From:* Congmin min [mailto:marlonmin at gmail.com]
> > > *Sent:* Thursday, August 31, 2006 12:16 PM
> > > *To:* protege-owl at lists.Stanford.EDU
> > > *Subject:* [protege-owl] MySql JDBC Driver and Database problem
> > >
> > >  Hi, I also I have a database backend problem. I specify my JDBC
> > > driver URI as:
> > >
> > > JDBC Driver URL : jdbc:mysql://localhost:3306/test_owl
> > >
> > > Error 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.
> > >
> > >     No suitable driver "
> > >
> > > Show I first create the 'test_owl' table in mySql database? I just
> > > want to convert an owl file to an owl database format.
> > >
> > > I highly appreciate your help for specifying the correct JDBC Driver
> > > URL.
> > >
> > > _______________________________________________
> > > protege-owl mailing list
> > > protege-owl at lists.stanford.edu
> > > https://mailman.stanford.edu/mailman/listinfo/protege-owl
> > >
> > >
> > >
> >
> > _______________________________________________
> > protege-owl mailing list
> > protege-owl at lists.stanford.edu
> > https://mailman.stanford.edu/mailman/listinfo/protege-owl
> >
> >
> >
>
> _______________________________________________
> protege-owl mailing list
> protege-owl at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
>
>
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