Re: protege-discussion Digest, Vol 64, Issue 38

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Re: protege-discussion Digest, Vol 64, Issue 38

Khánh Linh
Dear Matthew,

Thank you for your enthusiastic and instant help for my issue. Your explanation is completely clear and that's all I need to understand it deeper. 

I run on my Protege, it works. But when I implement it on Jena, it returns "Line 1, column 752: Unresolved prefixed name: :hasTopping", although I added prefixes in the query.

By the way, can you tell me more about the differences between running query directly on Protege and running query from Jena. Why I run the query on Protege it works but not in Jena ? I think the query is absolutely right, but there might be something that I still do not understand.

Best regrads,

Linh Nguyen
On Wed, Nov 30, 2011 at 6:35 AM, <[hidden email]> wrote:
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Today's Topics:

  1. Re: Problem with SPARQL query (Matthew Horridge)


----------------------------------------------------------------------

Message: 1
Date: Tue, 29 Nov 2011 15:35:27 -0800
From: Matthew Horridge <[hidden email]>
To: User support for Core Protege and the Protege-Frames editor
       <[hidden email]>
Subject: Re: [protege-discussion] Problem with SPARQL query
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"

Hi Linh,

You need to know something about how toppings in this ontology are represented in OWL and how this OWL translates to RDF under the hood.  Take your example of Caprina pizza.  The fact that a Caprina pizza has a tomato topping is represented by the following axiom in OWL:

Class:  Caprina

SubClassOf:
        hasTopping some TomatoTopping

in other words Caprina is a subclass of the class of things that have at least one hasTopping relationship to an instance of TomatoTopping.  This gets translated to the following RDF triples:


:Caprina  rdfs:subClassOf _:x .
_:x rdf:type owl:Restriction .
_:x owl:onProperty :hasTopping .
_:x owl:someValuesFrom :TomatoTopping .

where the _:x represents a blank node that is used in RDF to encode the "hasTopping some TomatoTopping" class expression.  You would therefore need to ask the following query, which returns a table with two columns - one containing the pizza and one containing the topping.


SELECT ?p ?t

WHERE
{
?p rdfs:subClassOf _:x .
_:x rdf:type owl:Restriction .
_:x owl:onProperty :hasTopping .
_:x owl:someValuesFrom ?t .
}

This gives the results you seem to want (see screenshot below).  You should note that these results are based on asserted information as Protege 3 doesn't use any reasoning to answer sparql queries.  If you need reasoning to compute query answers then you'll need to use reasoners that support this such as Pellet or HermiT directly.

Cheers,

Matthew



On 29 Nov 2011, at 07:32, Kh?nh Linh wrote:

> Hi,
>
> I have added "SELECT ?p" instead of "SELECT *" but it still does not work (returns "No matches found").
>
> I think we will get rid of it and try to focus on thinking query for example: Find which pizzas has TomatoTopping or, which toppings that a Caprina pizza has ?
>
> Thanks a lot,
>
> Linh
> On Tue, Nov 29, 2011 at 5:51 PM, <[hidden email]> wrote:
> Send protege-discussion mailing list submissions to
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> Today's Topics:
>
>   1. Re: Problem with SPARQL query (Brice Sommacal)
>   2. Re: 3.4.7 WebStart Client failing (Dennis Pierson)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 29 Nov 2011 11:31:16 +0100
> From: Brice Sommacal <[hidden email]>
> To: User support for Core Protege and the Protege-Frames editor
>        <[hidden email]>
> Subject: Re: [protege-discussion] Problem with SPARQL query
> Message-ID:
>        <CAKf=[hidden email]>
> Content-Type: text/plain; charset="utf-8"
>
> Hello Linh,
>
> In your SELECT, you have to refer to a variable which is defined in your
> query.
> You can't use "*" in SELECT, but only a variable (?x).
>
> You should try:
> *"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> *
> *PREFIX pizza: <http://www.co-ode.org/ontologies/pizza/pizza.owl#> *
> *SELECT ?p WHERE { ?p rdf:type pizza:Pizza; pizza:hasTopping ?t. ?t
> rdf:type pizza:TomatoTopping }"*
>
> Regards,
>
> Brice
>
> 2011/11/29 Kh?nh Linh <[hidden email]>
>
> > Dear all,
> >
> > I know this maybe a stupid question but I will be very glad if someone
> > help me with this. I'm absolutely new with Ontology.
> >
> > Started with Pizza example. I want to list a Pizza that has Tomato
> > Topping. And I tried this in my Prote?ge? 3.4.7 in the SPARQL Query Panel:
> >
> > *"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> *
> > *PREFIX pizza: <http://www.co-ode.org/ontologies/pizza/pizza.owl#> *
> > *SELECT * WHERE { ?p rdf:type pizza:Pizza; pizza:hasTopping ?t. ?t
> > rdf:type pizza:TomatoTopping }"*
> >
> > It returns "No matches found".
> >
> > I don't know why the result is like that. Can you run this query and find
> > out why it returns null ?
> >
> > Beside, I also attach the Pizza.owl.pprj file if somebody doesn't have it.
> >
> > I'm looking forward to hearing from you,
> >
> > Best regrads,
> >
> > Linh Nguyen
> >
> > _______________________________________________
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> > http://protege.stanford.edu/doc/faq.html#01a.03
> >
> >
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> ------------------------------
>
> Message: 2
> Date: Tue, 29 Nov 2011 10:51:09 +0000
> From: Dennis Pierson <[hidden email]>
> To: User support for Core Protege and the Protege-Frames editor
>        <[hidden email]>
> Subject: Re: [protege-discussion] 3.4.7 WebStart Client failing
> Message-ID:
>        <[hidden email]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I think this slipped by. Please take a look.
>
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Dennis Pierson
> Sent: Sunday, November 27, 2011 3:39 PM
> To: [hidden email]
> Cc: Solomon Harsha
> Subject: [protege-discussion] 3.4.7 WebStart Client failing
>
> Hi,
>
> I believe the downloaded client is connecting across the internet ok. It stalls when I click the Open Other button. I can create a new one, but I'm not sure which file system it's looking at because I can't find it either locally or remotely after I save it.  The webapp is working fine.
>
> Here's the stack trace from the java console - the logger.access denied, bundle, and jgo NoClassDefFoundError warnings happen on load (where is that class?).
>
> The AccessControlException exceptions occur when I click the Open Other button. I tried cert-signing the prot?g?.jar in the webapps/WebProtege/lib folder, but that didn't help. If that really is the solution, I may have done it wrong
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> Exception configuring logger
> Could not set logger level
> Warning: IO exception getting logger. access denied (java.util.PropertyPermission protege.properties.in.user.home read)
> Nov 27, 2011 3:29:21 PM edu.stanford.smi.protege.plugin.PluginUtilities findPluginsDirectory
> WARNING: Application directory not specified
> Nov 27, 2011 3:29:22 PM edu.stanford.smi.protege.resource.BundleHelper <init>
> WARNING: missing bundle: standard_extensions_text
> Nov 27, 2011 3:29:22 PM edu.stanford.smi.protege.resource.BundleHelper internalGetText
> WARNING: no resource bundle: tab.queries
> Nov 27, 2011 3:29:22 PM edu.stanford.smi.protege.plugin.PluginUtilities isLoadableClass
> WARNING: java.lang.NoClassDefFoundError: com/nwoods/jgo/JGoViewListener
> JGoodies Looks: Can't read the System property Plastic.tabStyle.
> JGoodies Looks: Can't read the System property Plastic.highContrastFocus.
> JGoodies Looks: Can't read the System property Plastic.defaultTheme.
> JGoodies Looks: Can't read the System property jgoodies.useNarrowButtons.
> JGoodies Looks: Can't read the System property jgoodies.tabIconsEnabled.
> JGoodies Looks: Can't read the System property jgoodies.popupDropShadowEnabled.
> Nov 27, 2011 3:29:22 PM edu.stanford.smi.protege.resource.BundleHelper <init>
> WARNING: missing bundle: protege_text
> Exception occurred during event dispatching:
> java.security.AccessControlException: access denied (java.util.PropertyPermission user.dir read)
>                at java.security.AccessControlContext.checkPermission(Unknown Source)
>                at java.security.AccessController.checkPermission(Unknown Source)
>                at java.lang.SecurityManager.checkPermission(Unknown Source)
>                at java.lang.SecurityManager.checkPropertyAccess(Unknown Source)
>                at java.lang.System.getProperty(Unknown Source)
>                at java.io.Win32FileSystem.getUserPath(Unknown Source)
>                at java.io.Win32FileSystem.resolve(Unknown Source)
>                at java.io.File.getAbsolutePath(Unknown Source)
>                at javax.swing.filechooser.WindowsFileSystemView.isFloppyDrive(Unknown Source)
>                at javax.swing.plaf.basic.BasicFileChooserUI$BasicFileView.getIcon(Unknown Source)
>                at com.jgoodies.looks.plastic.PlasticFileChooserUI$SystemIconFileView.getIcon(PlasticFileChooserUI.java:95)
>                at javax.swing.JFileChooser.getIcon(Unknown Source)
>                at javax.swing.plaf.metal.MetalFileChooserUI$DirectoryComboBoxRenderer.getListCellRendererComponent(Unknown Source)
>                at javax.swing.plaf.basic.BasicListUI.updateLayoutState(Unknown Source)
>                at javax.swing.plaf.basic.BasicListUI.maybeUpdateLayoutState(Unknown Source)
>                at javax.swing.plaf.basic.BasicListUI$Handler.valueChanged(Unknown Source)
>                at javax.swing.DefaultListSelectionModel.fireValueChanged(Unknown Source)
>                at javax.swing.DefaultListSelectionModel.fireValueChanged(Unknown Source)
>                at javax.swing.DefaultListSelectionModel.fireValueChanged(Unknown Source)
>                at javax.swing.DefaultListSelectionModel.changeSelection(Unknown Source)
>                at javax.swing.DefaultListSelectionModel.changeSelection(Unknown Source)
>                at javax.swing.DefaultListSelectionModel.setSelectionInterval(Unknown Source)
>                at javax.swing.JList.setSelectedIndex(Unknown Source)
>                at javax.swing.plaf.basic.BasicComboPopup.setListSelection(Unknown Source)
>                at javax.swing.plaf.basic.BasicComboPopup.access$300(Unknown Source)
>                at javax.swing.plaf.basic.BasicComboPopup$Handler.itemStateChanged(Unknown Source)
>                at javax.swing.JComboBox.fireItemStateChanged(Unknown Source)
>                at javax.swing.JComboBox.selectedItemChanged(Unknown Source)
>                at javax.swing.JComboBox.contentsChanged(Unknown Source)
>                at javax.swing.AbstractListModel.fireContentsChanged(Unknown Source)
>                at javax.swing.plaf.metal.MetalFileChooserUI$DirectoryComboBoxModel.setSelectedItem(Unknown Source)
>                at javax.swing.plaf.metal.MetalFileChooserUI$DirectoryComboBoxModel.addItem(Unknown Source)
>                at javax.swing.plaf.metal.MetalFileChooserUI$DirectoryComboBoxModel.access$900(Unknown Source)
>                at javax.swing.plaf.metal.MetalFileChooserUI.doDirectoryChanged(Unknown Source)
>                at javax.swing.plaf.metal.MetalFileChooserUI.access$1200(Unknown Source)
>                at javax.swing.plaf.metal.MetalFileChooserUI$5.propertyChange(Unknown Source)
>                at java.beans.PropertyChangeSupport.firePropertyChange(Unknown Source)
>                at java.beans.PropertyChangeSupport.firePropertyChange(Unknown Source)
>                at java.awt.Component.firePropertyChange(Unknown Source)
>                at javax.swing.JFileChooser.setCurrentDirectory(Unknown Source)
>                at javax.swing.JFileChooser.<init>(Unknown Source)
>                at javax.swing.JFileChooser.<init>(Unknown Source)
>                at edu.stanford.smi.protege.util.ProjectChooser.<init>(Unknown Source)
>                at edu.stanford.smi.protege.ui.ProjectManager.getRequestedProject(Unknown Source)
>                at edu.stanford.smi.protege.ui.ProjectManager.openProjectRequest(Unknown Source)
>                at edu.stanford.smi.protege.ui.WelcomeDialog.openOtherButton_actionPerformed(Unknown Source)
>                at edu.stanford.smi.protege.ui.WelcomeDialog$3.actionPerformed(Unknown Source)
>                at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
>                at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
>                at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
>                at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
>                at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
>                at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
>                at java.awt.Component.processMouseEvent(Unknown Source)
>                at javax.swing.JComponent.processMouseEvent(Unknown Source)
>                at java.awt.Component.processEvent(Unknown Source)
>                at java.awt.Container.processEvent(Unknown Source)
>                at java.awt.Component.dispatchEventImpl(Unknown Source)
>                at java.awt.Container.dispatchEventImpl(Unknown Source)
>                at java.awt.Component.dispatchEvent(Unknown Source)
>                at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
>                at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
>                at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
>                at java.awt.Container.dispatchEventImpl(Unknown Source)
>                at java.awt.Window.dispatchEventImpl(Unknown Source)
>                at java.awt.Component.dispatchEvent(Unknown Source)
>                at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
>                at java.awt.EventQueue.access$000(Unknown Source)
>                at java.awt.EventQueue$1.run(Unknown Source)
>                at java.awt.EventQueue$1.run(Unknown Source)
>                at java.security.AccessController.doPrivileged(Native Method)
>                at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
>                at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
>                at java.awt.EventQueue$2.run(Unknown Source)
>                at java.awt.EventQueue$2.run(Unknown Source)
>                at java.security.AccessController.doPrivileged(Native Method)
>                at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
>                at java.awt.EventQueue.dispatchEvent(Unknown Source)
>                at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
>                at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
>                at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
>                at java.awt.Dialog$1.run(Unknown Source)
>                at java.awt.event.InvocationEvent.dispatch(Unknown Source)
>                at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
>                at java.awt.EventQueue.access$000(Unknown Source)
>                at java.awt.EventQueue$1.run(Unknown Source)
>                at java.awt.EventQueue$1.run(Unknown Source)
>                at java.security.AccessController.doPrivileged(Native Method)
>                at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
>                at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
>                at java.awt.EventQueue$2.run(Unknown Source)
>                at java.awt.EventQueue$2.run(Unknown Source)
>                at java.security.AccessController.doPrivileged(Native Method)
>                at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
>                at java.awt.EventQueue.dispatchEvent(Unknown Source)
>                at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
>                at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
>                at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
>                at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>                at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>                at java.awt.EventDispatchThread.run(Unknown Source)
>
> Dennis Pierson | Senior Architect, MDM and Semantics | M P H A S I S  an HP Company | 460 Park Avenue South, Suite 1101, New York, NY 10016  |  Fax:  (212) 686 2422 | Mobile: (215) 622 1650|  www.mphasis.com<https://usmail1.mphasis.com/owa/UrlBlockedError.aspx>
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Re: protege-discussion Digest, Vol 64, Issue 38

Matthew Horridge-2
Administrator
Hi Linh Nguyen,

How did you add the prefixes to the query?  I believe the syntax is (for the default prefix):

@prefix  :  <http://www.co-ode.org/ontologies/pizza/pizza.owl#>

If you use Jena you may need to declare both the rdf, rdfs and owl prefixes as well, but I'm not sure about this.  Protege 3.x will automatically add these standard prefixes and a prefix corresponding to the ontology IRI to the query.

Cheers,

Matthew



On 29 Nov 2011, at 20:06, Khánh Linh wrote:

> Dear Matthew,
>
> Thank you for your enthusiastic and instant help for my issue. Your explanation is completely clear and that's all I need to understand it deeper.
>
> I run on my Protege, it works. But when I implement it on Jena, it returns "Line 1, column 752: Unresolved prefixed name: :hasTopping", although I added prefixes in the query.
>
> By the way, can you tell me more about the differences between running query directly on Protege and running query from Jena. Why I run the query on Protege it works but not in Jena ? I think the query is absolutely right, but there might be something that I still do not understand.
>
> Best regrads,
>
> Linh Nguyen
> On Wed, Nov 30, 2011 at 6:35 AM, <[hidden email]> wrote:
> Send protege-discussion mailing list submissions to
>        [hidden email]
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        https://mailman.stanford.edu/mailman/listinfo/protege-discussion
> or, via email, send a message with subject or body 'help' to
>        [hidden email]
>
> You can reach the person managing the list at
>        [hidden email]
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of protege-discussion digest..."
>
>
> Today's Topics:
>
>   1. Re: Problem with SPARQL query (Matthew Horridge)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 29 Nov 2011 15:35:27 -0800
> From: Matthew Horridge <[hidden email]>
> To: User support for Core Protege and the Protege-Frames editor
>        <[hidden email]>
> Subject: Re: [protege-discussion] Problem with SPARQL query
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Linh,
>
> You need to know something about how toppings in this ontology are represented in OWL and how this OWL translates to RDF under the hood.  Take your example of Caprina pizza.  The fact that a Caprina pizza has a tomato topping is represented by the following axiom in OWL:
>
> Class:  Caprina
>
> SubClassOf:
>         hasTopping some TomatoTopping
>
> in other words Caprina is a subclass of the class of things that have at least one hasTopping relationship to an instance of TomatoTopping.  This gets translated to the following RDF triples:
>
>
> :Caprina  rdfs:subClassOf _:x .
> _:x rdf:type owl:Restriction .
> _:x owl:onProperty :hasTopping .
> _:x owl:someValuesFrom :TomatoTopping .
>
> where the _:x represents a blank node that is used in RDF to encode the "hasTopping some TomatoTopping" class expression.  You would therefore need to ask the following query, which returns a table with two columns - one containing the pizza and one containing the topping.
>
>
> SELECT ?p ?t
>
> WHERE
> {
> ?p rdfs:subClassOf _:x .
> _:x rdf:type owl:Restriction .
> _:x owl:onProperty :hasTopping .
> _:x owl:someValuesFrom ?t .
> }
>
> This gives the results you seem to want (see screenshot below).  You should note that these results are based on asserted information as Protege 3 doesn't use any reasoning to answer sparql queries.  If you need reasoning to compute query answers then you'll need to use reasoners that support this such as Pellet or HermiT directly.
>
> Cheers,
>
> Matthew
>
>
>
> On 29 Nov 2011, at 07:32, Kh?nh Linh wrote:
>
> > Hi,
> >
> > I have added "SELECT ?p" instead of "SELECT *" but it still does not work (returns "No matches found").
> >
> > I think we will get rid of it and try to focus on thinking query for example: Find which pizzas has TomatoTopping or, which toppings that a Caprina pizza has ?
> >
> > Thanks a lot,
> >
> > Linh
> > On Tue, Nov 29, 2011 at 5:51 PM, <[hidden email]> wrote:
> > Send protege-discussion mailing list submissions to
> >        [hidden email]
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >        https://mailman.stanford.edu/mailman/listinfo/protege-discussion
> > or, via email, send a message with subject or body 'help' to
> >        [hidden email]
> >
> > You can reach the person managing the list at
> >        [hidden email]
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of protege-discussion digest..."
> >
> >
> > Today's Topics:
> >
> >   1. Re: Problem with SPARQL query (Brice Sommacal)
> >   2. Re: 3.4.7 WebStart Client failing (Dennis Pierson)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Tue, 29 Nov 2011 11:31:16 +0100
> > From: Brice Sommacal <[hidden email]>
> > To: User support for Core Protege and the Protege-Frames editor
> >        <[hidden email]>
> > Subject: Re: [protege-discussion] Problem with SPARQL query
> > Message-ID:
> >        <CAKf=[hidden email]>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hello Linh,
> >
> > In your SELECT, you have to refer to a variable which is defined in your
> > query.
> > You can't use "*" in SELECT, but only a variable (?x).
> >
> > You should try:
> > *"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> *
> > *PREFIX pizza: <http://www.co-ode.org/ontologies/pizza/pizza.owl#> *
> > *SELECT ?p WHERE { ?p rdf:type pizza:Pizza; pizza:hasTopping ?t. ?t
> > rdf:type pizza:TomatoTopping }"*
> >
> > Regards,
> >
> > Brice
> >
> > 2011/11/29 Kh?nh Linh <[hidden email]>
> >
> > > Dear all,
> > >
> > > I know this maybe a stupid question but I will be very glad if someone
> > > help me with this. I'm absolutely new with Ontology.
> > >
> > > Started with Pizza example. I want to list a Pizza that has Tomato
> > > Topping. And I tried this in my Prote?ge? 3.4.7 in the SPARQL Query Panel:
> > >
> > > *"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> *
> > > *PREFIX pizza: <http://www.co-ode.org/ontologies/pizza/pizza.owl#> *
> > > *SELECT * WHERE { ?p rdf:type pizza:Pizza; pizza:hasTopping ?t. ?t
> > > rdf:type pizza:TomatoTopping }"*
> > >
> > > It returns "No matches found".
> > >
> > > I don't know why the result is like that. Can you run this query and find
> > > out why it returns null ?
> > >
> > > Beside, I also attach the Pizza.owl.pprj file if somebody doesn't have it.
> > >
> > > I'm looking forward to hearing from you,
> > >
> > > Best regrads,
> > >
> > > Linh Nguyen
> > >
> > > _______________________________________________
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> > > http://protege.stanford.edu/doc/faq.html#01a.03
> > >
> > >
> > -------------- next part --------------
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> >
> > ------------------------------
> >
> > Message: 2
> > Date: Tue, 29 Nov 2011 10:51:09 +0000
> > From: Dennis Pierson <[hidden email]>
> > To: User support for Core Protege and the Protege-Frames editor
> >        <[hidden email]>
> > Subject: Re: [protege-discussion] 3.4.7 WebStart Client failing
> > Message-ID:
> >        <[hidden email]>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > I think this slipped by. Please take a look.
> >
> > From: [hidden email] [mailto:[hidden email]] On Behalf Of Dennis Pierson
> > Sent: Sunday, November 27, 2011 3:39 PM
> > To: [hidden email]
> > Cc: Solomon Harsha
> > Subject: [protege-discussion] 3.4.7 WebStart Client failing
> >
> > Hi,
> >
> > I believe the downloaded client is connecting across the internet ok. It stalls when I click the Open Other button. I can create a new one, but I'm not sure which file system it's looking at because I can't find it either locally or remotely after I save it.  The webapp is working fine.
> >
> > Here's the stack trace from the java console - the logger.access denied, bundle, and jgo NoClassDefFoundError warnings happen on load (where is that class?).
> >
> > The AccessControlException exceptions occur when I click the Open Other button. I tried cert-signing the prot?g?.jar in the webapps/WebProtege/lib folder, but that didn't help. If that really is the solution, I may have done it wrong
> > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> > Exception configuring logger
> > Could not set logger level
> > Warning: IO exception getting logger. access denied (java.util.PropertyPermission protege.properties.in.user.home read)
> > Nov 27, 2011 3:29:21 PM edu.stanford.smi.protege.plugin.PluginUtilities findPluginsDirectory
> > WARNING: Application directory not specified
> > Nov 27, 2011 3:29:22 PM edu.stanford.smi.protege.resource.BundleHelper <init>
> > WARNING: missing bundle: standard_extensions_text
> > Nov 27, 2011 3:29:22 PM edu.stanford.smi.protege.resource.BundleHelper internalGetText
> > WARNING: no resource bundle: tab.queries
> > Nov 27, 2011 3:29:22 PM edu.stanford.smi.protege.plugin.PluginUtilities isLoadableClass
> > WARNING: java.lang.NoClassDefFoundError: com/nwoods/jgo/JGoViewListener
> > JGoodies Looks: Can't read the System property Plastic.tabStyle.
> > JGoodies Looks: Can't read the System property Plastic.highContrastFocus.
> > JGoodies Looks: Can't read the System property Plastic.defaultTheme.
> > JGoodies Looks: Can't read the System property jgoodies.useNarrowButtons.
> > JGoodies Looks: Can't read the System property jgoodies.tabIconsEnabled.
> > JGoodies Looks: Can't read the System property jgoodies.popupDropShadowEnabled.
> > Nov 27, 2011 3:29:22 PM edu.stanford.smi.protege.resource.BundleHelper <init>
> > WARNING: missing bundle: protege_text
> > Exception occurred during event dispatching:
> > java.security.AccessControlException: access denied (java.util.PropertyPermission user.dir read)
> >                at java.security.AccessControlContext.checkPermission(Unknown Source)
> >                at java.security.AccessController.checkPermission(Unknown Source)
> >                at java.lang.SecurityManager.checkPermission(Unknown Source)
> >                at java.lang.SecurityManager.checkPropertyAccess(Unknown Source)
> >                at java.lang.System.getProperty(Unknown Source)
> >                at java.io.Win32FileSystem.getUserPath(Unknown Source)
> >                at java.io.Win32FileSystem.resolve(Unknown Source)
> >                at java.io.File.getAbsolutePath(Unknown Source)
> >                at javax.swing.filechooser.WindowsFileSystemView.isFloppyDrive(Unknown Source)
> >                at javax.swing.plaf.basic.BasicFileChooserUI$BasicFileView.getIcon(Unknown Source)
> >                at com.jgoodies.looks.plastic.PlasticFileChooserUI$SystemIconFileView.getIcon(PlasticFileChooserUI.java:95)
> >                at javax.swing.JFileChooser.getIcon(Unknown Source)
> >                at javax.swing.plaf.metal.MetalFileChooserUI$DirectoryComboBoxRenderer.getListCellRendererComponent(Unknown Source)
> >                at javax.swing.plaf.basic.BasicListUI.updateLayoutState(Unknown Source)
> >                at javax.swing.plaf.basic.BasicListUI.maybeUpdateLayoutState(Unknown Source)
> >                at javax.swing.plaf.basic.BasicListUI$Handler.valueChanged(Unknown Source)
> >                at javax.swing.DefaultListSelectionModel.fireValueChanged(Unknown Source)
> >                at javax.swing.DefaultListSelectionModel.fireValueChanged(Unknown Source)
> >                at javax.swing.DefaultListSelectionModel.fireValueChanged(Unknown Source)
> >                at javax.swing.DefaultListSelectionModel.changeSelection(Unknown Source)
> >                at javax.swing.DefaultListSelectionModel.changeSelection(Unknown Source)
> >                at javax.swing.DefaultListSelectionModel.setSelectionInterval(Unknown Source)
> >                at javax.swing.JList.setSelectedIndex(Unknown Source)
> >                at javax.swing.plaf.basic.BasicComboPopup.setListSelection(Unknown Source)
> >                at javax.swing.plaf.basic.BasicComboPopup.access$300(Unknown Source)
> >                at javax.swing.plaf.basic.BasicComboPopup$Handler.itemStateChanged(Unknown Source)
> >                at javax.swing.JComboBox.fireItemStateChanged(Unknown Source)
> >                at javax.swing.JComboBox.selectedItemChanged(Unknown Source)
> >                at javax.swing.JComboBox.contentsChanged(Unknown Source)
> >                at javax.swing.AbstractListModel.fireContentsChanged(Unknown Source)
> >                at javax.swing.plaf.metal.MetalFileChooserUI$DirectoryComboBoxModel.setSelectedItem(Unknown Source)
> >                at javax.swing.plaf.metal.MetalFileChooserUI$DirectoryComboBoxModel.addItem(Unknown Source)
> >                at javax.swing.plaf.metal.MetalFileChooserUI$DirectoryComboBoxModel.access$900(Unknown Source)
> >                at javax.swing.plaf.metal.MetalFileChooserUI.doDirectoryChanged(Unknown Source)
> >                at javax.swing.plaf.metal.MetalFileChooserUI.access$1200(Unknown Source)
> >                at javax.swing.plaf.metal.MetalFileChooserUI$5.propertyChange(Unknown Source)
> >                at java.beans.PropertyChangeSupport.firePropertyChange(Unknown Source)
> >                at java.beans.PropertyChangeSupport.firePropertyChange(Unknown Source)
> >                at java.awt.Component.firePropertyChange(Unknown Source)
> >                at javax.swing.JFileChooser.setCurrentDirectory(Unknown Source)
> >                at javax.swing.JFileChooser.<init>(Unknown Source)
> >                at javax.swing.JFileChooser.<init>(Unknown Source)
> >                at edu.stanford.smi.protege.util.ProjectChooser.<init>(Unknown Source)
> >                at edu.stanford.smi.protege.ui.ProjectManager.getRequestedProject(Unknown Source)
> >                at edu.stanford.smi.protege.ui.ProjectManager.openProjectRequest(Unknown Source)
> >                at edu.stanford.smi.protege.ui.WelcomeDialog.openOtherButton_actionPerformed(Unknown Source)
> >                at edu.stanford.smi.protege.ui.WelcomeDialog$3.actionPerformed(Unknown Source)
> >                at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
> >                at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
> >                at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
> >                at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
> >                at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
> >                at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
> >                at java.awt.Component.processMouseEvent(Unknown Source)
> >                at javax.swing.JComponent.processMouseEvent(Unknown Source)
> >                at java.awt.Component.processEvent(Unknown Source)
> >                at java.awt.Container.processEvent(Unknown Source)
> >                at java.awt.Component.dispatchEventImpl(Unknown Source)
> >                at java.awt.Container.dispatchEventImpl(Unknown Source)
> >                at java.awt.Component.dispatchEvent(Unknown Source)
> >                at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
> >                at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
> >                at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
> >                at java.awt.Container.dispatchEventImpl(Unknown Source)
> >                at java.awt.Window.dispatchEventImpl(Unknown Source)
> >                at java.awt.Component.dispatchEvent(Unknown Source)
> >                at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
> >                at java.awt.EventQueue.access$000(Unknown Source)
> >                at java.awt.EventQueue$1.run(Unknown Source)
> >                at java.awt.EventQueue$1.run(Unknown Source)
> >                at java.security.AccessController.doPrivileged(Native Method)
> >                at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
> >                at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
> >                at java.awt.EventQueue$2.run(Unknown Source)
> >                at java.awt.EventQueue$2.run(Unknown Source)
> >                at java.security.AccessController.doPrivileged(Native Method)
> >                at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
> >                at java.awt.EventQueue.dispatchEvent(Unknown Source)
> >                at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
> >                at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
> >                at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
> >                at java.awt.Dialog$1.run(Unknown Source)
> >                at java.awt.event.InvocationEvent.dispatch(Unknown Source)
> >                at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
> >                at java.awt.EventQueue.access$000(Unknown Source)
> >                at java.awt.EventQueue$1.run(Unknown Source)
> >                at java.awt.EventQueue$1.run(Unknown Source)
> >                at java.security.AccessController.doPrivileged(Native Method)
> >                at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
> >                at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
> >                at java.awt.EventQueue$2.run(Unknown Source)
> >                at java.awt.EventQueue$2.run(Unknown Source)
> >                at java.security.AccessController.doPrivileged(Native Method)
> >                at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
> >                at java.awt.EventQueue.dispatchEvent(Unknown Source)
> >                at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
> >                at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
> >                at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
> >                at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> >                at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> >                at java.awt.EventDispatchThread.run(Unknown Source)
> >
> > Dennis Pierson | Senior Architect, MDM and Semantics | M P H A S I S  an HP Company | 460 Park Avenue South, Suite 1101, New York, NY 10016  |  Fax:  (212) 686 2422 | Mobile: (215) 622 1650|  www.mphasis.com<https://usmail1.mphasis.com/owa/UrlBlockedError.aspx>
> >
> >
> > ________________________________
> >
> > Information transmitted by this e-mail is proprietary to MphasiS, its associated companies and/ or its customers and is intended for use only by the individual or entity to which it is addressed, and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If you are not the intended recipient or it appears that this mail has been forwarded to you without proper authority, you are notified that any use or dissemination of this information in any manner is strictly prohibited. In such cases, please notify us immediately at [hidden email] and delete this mail from your records.
> >
> > ________________________________
> >
> > Information transmitted by this e-mail is proprietary to MphasiS, its associated companies and/ or its customers and is intended for use only by the individual or entity to which it is addressed, and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If you are not the intended recipient or it appears that this mail has been forwarded to you without proper authority, you are notified that any use or dissemination of this information in any manner is strictly prohibited. In such cases, please notify us immediately at [hidden email] and delete this mail from your records.
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