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[protege-discussion] protege-discussion Digest, Vol 64, Issue 40

Khánh Linh linhkid91 at gmail.com
Wed Nov 30 20:23:45 PST 2011


Dear Matthew

I changed it into a new query with prefixes added:

*SELECT ?p *
*WHERE*
*{*
*?p rdfs:subClassOf ?t .*
*?t rdf:type owl:Restriction .*
*?t owl:onProperty <
http://www.co-ode.org/ontologies/pizza/2005/10/18/pizza.owl#hasTopping>.*
*?t owl:someValuesFrom <
http://www.co-ode.org/ontologies/pizza/2005/10/18/pizza.owl#TomatoTopping> *
*}*

It runs on Protege and returns all classes which have TomatoTopping, It
also run on my Jena but returns null (here is the output on my Netbean):

-----
| p |
=====
-----

It getting me confused. Am I wrong in something ?

Regrads,

Linh Nguyen

On Wed, Nov 30, 2011 at 11:35 PM, <
protege-discussion-request at lists.stanford.edu> wrote:

> Send protege-discussion mailing list submissions to
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>
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>
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of protege-discussion digest..."
>
>
> Today's Topics:
>
>   1. Re: protege-discussion Digest, Vol 64, Issue 38 (Matthew Horridge)
>   2. Re: 3.4.7 WebStart Client failing (Timothy Redmond)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 29 Nov 2011 22:12:18 -0800
> From: Matthew Horridge <matthew.horridge at stanford.edu>
> To: User support for Core Protege and the Protege-Frames editor
>        <protege-discussion at lists.stanford.edu>
> Subject: Re: [protege-discussion] protege-discussion Digest, Vol 64,
>        Issue 38
> Message-ID: <6F906F07-0F67-489F-A8D1-62948C13242B at stanford.edu>
> Content-Type: text/plain; charset=iso-8859-1
>
> 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, Kh?nh 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, <
> protege-discussion-request at lists.stanford.edu> wrote:
> > Send protege-discussion mailing list submissions to
> >        protege-discussion at lists.stanford.edu
> >
> > 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
> >        protege-discussion-request at lists.stanford.edu
> >
> > You can reach the person managing the list at
> >        protege-discussion-owner at lists.stanford.edu
> >
> > 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 <matthew.horridge at stanford.edu>
> > To: User support for Core Protege and the Protege-Frames editor
> >        <protege-discussion at lists.stanford.edu>
> > Subject: Re: [protege-discussion] Problem with SPARQL query
> > Message-ID: <043CF413-B4CC-4EC2-8DF3-9CF62E069D57 at stanford.edu>
> > 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, <
> protege-discussion-request at lists.stanford.edu> wrote:
> > > Send protege-discussion mailing list submissions to
> > >        protege-discussion at lists.stanford.edu
> > >
> > > 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
> > >        protege-discussion-request at lists.stanford.edu
> > >
> > > You can reach the person managing the list at
> > >        protege-discussion-owner at lists.stanford.edu
> > >
> > > 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 <brice.sommacal at gmail.com>
> > > To: User support for Core Protege and the Protege-Frames editor
> > >        <protege-discussion at lists.stanford.edu>
> > > Subject: Re: [protege-discussion] Problem with SPARQL query
> > > Message-ID:
> > >        <CAKf=
> qYvT+BOkCFu973Aj03qK7DE87+se3GJrAyzLxGYBZmUbww at mail.gmail.com>
> > > 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 <linhkid91 at gmail.com>
> > >
> > > > 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
> > > >
> > > > _______________________________________________
> > > > protege-discussion mailing list
> > > > protege-discussion at lists.stanford.edu
> > > > https://mailman.stanford.edu/mailman/listinfo/protege-discussion
> > > >
> > > > Instructions for unsubscribing:
> > > > http://protege.stanford.edu/doc/faq.html#01a.03
> > > >
> > > >
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
> > > URL: <
> http://mailman.stanford.edu/pipermail/protege-discussion/attachments/20111129/b8e8f11b/attachment-0001.html
> >
> > >
> > > ------------------------------
> > >
> > > Message: 2
> > > Date: Tue, 29 Nov 2011 10:51:09 +0000
> > > From: Dennis Pierson <Dennis.Pierson at mphasis.com>
> > > To: User support for Core Protege and the Protege-Frames editor
> > >        <protege-discussion at lists.stanford.edu>
> > > Subject: Re: [protege-discussion] 3.4.7 WebStart Client failing
> > > Message-ID:
> > >        <
> 268F58C065D67D48853D7F4337BAFB4D01FACA at MPDAMBX01.corp.mphasis.com>
> > > Content-Type: text/plain; charset="iso-8859-1"
> > >
> > > I think this slipped by. Please take a look.
> > >
> > > From: protege-discussion-bounces at lists.stanford.edu [mailto:
> protege-discussion-bounces at lists.stanford.edu] On Behalf Of Dennis Pierson
> > > Sent: Sunday, November 27, 2011 3:39 PM
> > > To: protege-discussion at lists.stanford.edu
> > > 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
> mailmaster at mphasis.com 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
> mailmaster at mphasis.com and delete this mail from your records.
> > > -------------- next part --------------
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> > > URL: <
> http://mailman.stanford.edu/pipermail/protege-discussion/attachments/20111129/18d7707a/attachment.html
> >
> > >
> > > ------------------------------
> > >
> > > _______________________________________________
> > > protege-discussion mailing list
> > > protege-discussion at lists.stanford.edu
> > > https://mailman.stanford.edu/mailman/listinfo/protege-discussion
> > >
> > >
> > > End of protege-discussion Digest, Vol 64, Issue 36
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> ------------------------------
>
> Message: 2
> Date: Wed, 30 Nov 2011 08:35:16 -0800
> From: Timothy Redmond <tredmond at stanford.edu>
> To: protege-discussion at lists.stanford.edu
> Subject: Re: [protege-discussion] 3.4.7 WebStart Client failing
> Message-ID: <4ED65B44.1090400 at stanford.edu>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
>
> Hi -
>
> I am sorry about that.  One of the problems with this message is that it
> is a more difficult issue to debug and we need to spend some time with
> it. Web apps are tricky to develop because they tend to get a lot of
> these types of Permission denied errors.
>
> I just wanted to check one thing.  Is this issue occurring in the
> context of WebProtege?  If so I will add a GForge to the WebProtege
> project.
>
> -Timothy
>
>
> On 11/29/2011 02:51 AM, Dennis Pierson wrote:
> >
> > I think this slipped by. Please take a look.
> >
> > *From:*protege-discussion-bounces at lists.stanford.edu
> > [mailto:protege-discussion-bounces at lists.stanford.edu] *On Behalf Of
> > *Dennis Pierson
> > *Sent:* Sunday, November 27, 2011 3:39 PM
> > *To:* protege-discussion at lists.stanford.edu
> > *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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> > 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 mailmaster at mphasis.com 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
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> > information in any manner is strictly prohibited. In such cases,
> > please notify us immediately at mailmaster at mphasis.com and delete this
> > mail from your records.
> >
> >
> > _______________________________________________
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> > protege-discussion at lists.stanford.edu
> > https://mailman.stanford.edu/mailman/listinfo/protege-discussion
> >
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