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[protege-owl] MySql JDBC Driver and Database problem

Congmin min marlonmin at gmail.com
Tue Sep 5 12:58:08 PDT 2006


Jeff: after you got the Jena database model, can you look at it in Protege
or somewhere? because I want to use protege as a visualization tool. I am
developing a plugin for protege owl for visualizing various relations more
than ISA, so I still have to use Protege as the platform.

On 9/5/06, Congmin min <marlonmin at gmail.com> wrote:
>
> 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
> >
> >
> >
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