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[protege-owl] MySql JDBC Driver and Database problem

Congmin min marlonmin at gmail.com
Wed Sep 6 07:28:15 PDT 2006


Jeff:
I compiled the code and then it can't find a symbol. Should i also include
"import com.hp.hpl.jena.util.ModelLoader;"
Thanks,

cannot find symbol
symbol  : method connectToDB(java.lang.String,java.lang.String,
java.lang.String,java.lang.String,java.lang.String)
location: class jena
        IDBConnection conn = connectToDB(M_DB_URI, M_DB_USER, M_DB_PASSWD,
M_DB, M_DBDRIVER_CLASS);
                             ^
jena.java:54: cannot find symbol
symbol  : variable err
location: class jena
            e.printStackTrace(err);
                              ^
2 errors


On 9/6/06, Schmitz, Jeffrey A <Jeffrey.A.Schmitz at boeing.com> wrote:
>
> 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>
> >
> > https://mailman.stanford.edu/mailman/listinfo/protege-owl
> >
> >
> >
> >
> >                     _______________________________________________
> >                     protege-owl mailing list
> >                     protege-owl at lists.stanford.edu
> >                     <mailto:protege-owl at lists.stanford.edu>
> >
> > https://mailman.stanford.edu/mailman/listinfo/protege-owl
> >
> >
> >
> >
> >                 _______________________________________________
> >                 protege-owl mailing list
> >                 protege-owl at lists.stanford.edu
> >                 <mailto:protege-owl at lists.stanford.edu>
> >
> > https://mailman.stanford.edu/mailman/listinfo/protege-owl
> >
> >
> >
> >
> >             _______________________________________________
> >             protege-owl mailing list
> >             protege-owl at lists.stanford.edu
> >             <mailto:protege-owl at lists.stanford.edu>
> >             https://mailman.stanford.edu/mailman/listinfo/protege-owl
> >
> >
> >
> >
> >
> >     _______________________________________________
> >     protege-owl mailing list
> >     protege-owl at lists.stanford.edu <mailto:
> 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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