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[protege-owl] MySql JDBC Driver and Database problem

Schmitz, Jeffrey A Jeffrey.A.Schmitz at boeing.com
Tue Sep 5 12:22:01 PDT 2006


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$EmptyList.get(Collections.java:2923)
    at
edu.stanford.smi.protegex.owl.model.triplestore.impl.AbstractTripleStore
Model.setHomeTripleStore(Unknown Source)
    at
edu.stanford.smi.protegex.owl.model.triplestore.impl.AddRDFTypePropertyH
andler.handleAdd(Unknown Source)
    at
edu.stanford.smi.protegex.owl.model.triplestore.impl.AbstractTripleStore
.add(Unknown Source)
    at
edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$MyStatementHa
ndler.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(U
nknown Source)
    at
edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.loadTriples(U
nknown 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.CreateOWLDatabaseFromFileProjectP
lugin.buildNewProject(Unknown Source)
    at
edu.stanford.smi.protege.plugin.AbstractCreateProjectPlugin.createProjec
t(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:2
152)
    at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.ja
va:420)
    at
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
    at
javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonList
ener.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(EventDispatchThrea
d.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(Unkno
wn Source)
    at
edu.stanford.smi.protege.action.CreateProject.actionPerformed(Unknown
Source)
    at
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1834)
    at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2
152)
    at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.ja
va:420)
    at
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
    at javax.swing.AbstractButton.doClick(AbstractButton.java:302)
    at
javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1000
)
    at
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuIt
emUI.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(EventDispatchThrea
d.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
<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
<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.

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