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[protege-owl] MySql JDBC Driver and Database problem

Schmitz, Jeffrey A Jeffrey.A.Schmitz at boeing.com
Wed Sep 6 07:00:41 PDT 2006


Note that the owl file referenced is just the file that is saved as part of your protégé project. 

-----Original Message-----
From: Roland Wallnöfer [mailto:roland.wallnoefer at i-med.ac.at] 
Sent: Wednesday, September 06, 2006 8:32 AM
To: User support for the Protege-OWL editor
Subject: Re: [protege-owl] MySql JDBC Driver and Database problem

Hi,

I also have a very big owl file. How can an owl file directly converted into a database ontology without first loading the owl file into Protégé. Can you give me a short instruction please? That would be very helpful.

Thanks and best regards

Roland

Congmin min schrieb:

> Thanks, I got it.
>
> On 9/5/06, *Schmitz, Jeffrey A* <Jeffrey.A.Schmitz at boeing.com 
> <mailto:Jeffrey.A.Schmitz at boeing.com>> wrote:
>
>     Just a quick note on the below snippet (because I've spent the day
>     debugging it), the FIRST time you run code to setup and use the
>     JENA database model, you must use:
>      
>     maker.createModel("MyPizzaClassModel");
>     After the database tables have been created in MySQL you will need
>     to use:
>      
>     maker.getModel("MyPizzaClassModel");
>     Jeff
>
>      
>     ------------------------------------------------------------------------
>     *From:* Schmitz, Jeffrey A
>     *Sent:* Tuesday, September 05, 2006 3:02 PM
>
>     *To:* User support for the Protege-OWL editor
>     *Subject:* Re: [protege-owl] MySql JDBC Driver and Database 
> problem
>
>     You would have to covert the database back into the file based
>     protege format first I think, going the other way of the example I
>     snippet in the previous message.  Should be a simple utility to
>     write, but I haven't tried it.
>      
>     btw, here's the definition of a few of the constants and variables
>     used in the snippet:
>      
>      public static final String inputClassFilename = "pizza.owl";
>      public static final String pizzaInstanceFilename =
>     "pizzaInstance.owl";
>      public static final String pizzaNamespaceURI =
>     "http://www.owl-ontologies.com/pizza.owl
>     <http://www.owl-ontologies.com/pizza.owl>#";
>         public static final String pizzaDataURI =
>     "http://www.owl-ontologies.com/pizzaInst.owl #";
>         public static final String amPizzaTypeURI = pizzaNamespaceURI
>     + "AmericanHot";
>         public static final String hasToppingURI = pizzaNamespaceURI +
>     "hasTopping";
>         public static final String isToppingURI = pizzaNamespaceURI +
>     "isToppingOf";
>         public static final String typeURI =
>     "http://www.w3.org/1999/02/22-rdf-syntax-ns#type ";
>         public static final String caperTopTypeURI = pizzaNamespaceURI
>     + "CaperTopping";
>         public static Model pizzaClassDBModel;
>         public static Model pizzaModel;
>      
>     Jeff
>
>     ------------------------------------------------------------------------
>     *From:* Congmin min [mailto:marlonmin at gmail.com
>     <mailto:marlonmin at gmail.com>]
>     *Sent:* Tuesday, September 05, 2006 2:58 PM
>     *To:* User support for the Protege-OWL editor
>     *Subject:* Re: [protege-owl] MySql JDBC Driver and Database 
> problem
>
>     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
>     <mailto: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
>         <mailto: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
>             <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
>             <mailto: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
>                 <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
>                 <mailto: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
>                     <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
>                     <mailto: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
>                         <mailto:marlonmin at gmail.com>]
>                         *Sent:* Thursday, August 31, 2006 12:16 PM
>                         *To:* protege-owl at lists.Stanford.EDU
>                         <mailto: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
>                         <mailto:protege-owl at lists.stanford.edu>
>                         
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>
>
>
>
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