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[protege-owl] MySql JDBC Driver and Database problem

Schmitz, Jeffrey A Jeffrey.A.Schmitz at boeing.com
Tue Sep 5 13:02:25 PDT 2006


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#";
    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] 
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 > 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$EmptyList.get(Collections.java:2923)
		    at
edu.stanford.smi.protegex.owl.model.triplestore.impl.AbstractTripleStore
Model.setHomeTripleStore(Unknown Source)
		    at
edu.stanford.smi.protegex.owl.model.triplestore.impl.AddRDFTypePropertyH
andler.handleAdd(Unknown Source)
		    at
edu.stanford.smi.protegex.owl.model.triplestore.impl.AbstractTripleStore
.add(Unknown Source)
		    at
edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$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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