Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[protege-owl] MySql JDBC Driver and Database problem

Congmin min marlonmin at gmail.com
Tue Sep 5 12:34:54 PDT 2006


Thank you, Jeff:
I will look into your solution.

Protege owl seems very inmature.

On 9/5/06, Schmitz, Jeffrey A <Jeffrey.A.Schmitz at boeing.com> wrote:
>
>  No, I haven't seen that one.  My database was pretty small.  Also, I've
> kind of punted on the Protege database for now and am using the Jena DB
> backend with MySQL which seems to work pretty well.  I'm using Jastor for
> generating and api to use the database instead of the Protege code
> generation tool.  Again, Jastor seems to be both easier and a little more
> stable than the Protege stuff.
>
> To get the protege ontology into the Jena/MySQL database I simply read in
> the Protege owl file into a memory based model and then add that model to my
> Jena database model:
>
>   IDBConnection conn = connectToDB(M_DB_URI, M_DB_USER, M_DB_PASSWD, M_DB,
> M_DBDRIVER_CLASS);
> //   create a model maker with the given connection parameters
>   ModelMaker maker = ModelFactory.createModelRDBMaker(conn);
> //   Create a named model
>   pizzaClassDBModel = maker.getModel("MyPizzaClassModel");
>
>   if (loadClasses) {
>    try {
>         pizzaClassIn = new FileInputStream("pizza.owl");
>                //Create the class database from the Protege OWL File based
> model.
>         pizzaClassOWLFileModel =
> ProtegeOWL.createJenaOWLModelFromInputStream(pizzaClassIn);
>         pizzaClassOntModel = pizzaClassOWLFileModel.getOntModel();
>          pizzaClassDBModel.add(pizzaClassOntModel);
>       } catch(Exception e) {
>     try {
>       FileOutputStream fileOut = new FileOutputStream(errFile);
>
>       err = new PrintStream(fileOut);
>       e.printStackTrace(err);
>       err.print("for input file: " + inputClassFilename + "\n");
>     } catch(Exception ex) {}
>          }
>
>
>   }
>
> Jeff
>
>  ------------------------------
> *From:* Congmin min [mailto:marlonmin at gmail.com]
> *Sent:* Tuesday, September 05, 2006 2:15 PM
>
> *To:* User support for the Protege-OWL editor
> *Subject:* Re: [protege-owl] MySql JDBC Driver and Database problem
>
> 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
> >
> >
> >
>
> _______________________________________________
> protege-owl mailing list
> protege-owl at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/protege-owl/attachments/20060905/510b7c8f/attachment.html>


More information about the protege-owl mailing list