owlviz plugin error due to graphviz ?

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owlviz plugin error due to graphviz ?

Daniel Schober
Dear OwlViz and OwlPropviz zards.
Currently OwlViz and the OwlPropViz (which I need) don't work in P4 with
the latest GraphViz distribution.
I use win xp and the latest P4 download and the latest GraphViz download.
Is this due to non backwards compatibility of the most recent Graph Viz
changes? If so, where can I download an older GraphViz version that
works with OntoViz?
In OwlViz, after setting the correct path to dot.exe The tab does not
show any relations and crashes. The OwlPropViz does also not work.
The error message is attached.

Funny enough Ontoviz in P3.4 seems to work fine.

Any ideas how to make any Graph based visualisation of selected parts of
my owl ontology ?
Cheers,
        Daniel Schober.




cwd: C:\Programme\Protege_4.0_beta
cmd: "C:\Programme\Protege_4.0_beta\jre\bin\java.exe" -Xms209715200 -Xmx20971520
0 -classpath "C:\Programme\Protege_4.0_beta\org.eclipse.osgi.jar;C:\Programme\Pr
otege_4.0_beta\lax.jar;" com.zerog.lax.LAX "C:/Programme/Protege_4.0_beta/Proteg
e.lax" "C:/Dokumente und Einstellungen/schober/Lokale Einstellungen/Temp/laxE.tm
p"
Starting Protege 4 OWL Editor (Version 4.0.110)
Platform:
    Java: JVM 1.5.0_11-b03 Memory: 208M
    Language: de, Country: DE
    Framework: Eclipse (1.4.0)
    OS: WindowsXP (5.1)
    Processor: x86
Installed plugin Pellet Reasoner
Installed plugin DL Query Tab
Installed plugin Owlviz Plug-in
Installed plugin owleditor
Installed plugin The OWL API
Installed plugin Factplusplus Plug-in
Downloading FaCT++ reasoner
Using OWL API version 2.2.1.1090
Rebuilding entity indices...
... rebuilt in 0 ms
Copying FaCT++ reasoner
loading http://www.debugit.eu/ontology/1.0/dco.owl from file:/C:/Dokumente%20und
%20Einstellungen/schober/Desktop/dco.owl
No mapping for http://purl.org/biotop/1.0/biotop-dolce-ro.owl found.
loading http://purl.org/biotop/1.0/biotop-dolce-ro.owl from http://purl.org/biot
op/1.0/biotop-dolce-ro.owl
No mapping for http://purl.org/biotop/1.0/biotop.owl found.
loading http://purl.org/biotop/1.0/biotop.owl from http://purl.org/biotop/1.0/bi
otop.owl
No mapping for http://www.ifomis.org/obo/ro/1.0/light found.
loading http://www.ifomis.org/obo/ro/1.0/light from http://www.ifomis.org/obo/ro
/1.0/light
No mapping for http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl found.
loading http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl from http://pr
otege.stanford.edu/plugins/owl/dc/protege-dc.owl
No mapping for http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl found.
loading http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl from http://www.loa-cnr.
it/ontologies/DOLCE-Lite.owl
Setting active ontology to http://www.debugit.eu/ontology/1.0/dco.owl
Rebuilding entity indices...
... rebuilt in 0 ms
... active ontology changed
DOT Process Error:
CreateProcess: C:\Program Files\GraphViz\bin\Dot C:\DOKUME~1\schober\LOKALE~1\Te
mp\OWLVizScratch137.tmp -q -o C:\DOKUME~1\schober\LOKALE~1\Temp\OWLVizScratch137
.tmp error=2
An error related to DOT has occurred. This error was probably because OWLViz cou
ld not find the DOT application.  Please ensure that the path to the DOT applica
tion is set properly
DOT Process Error:
CreateProcess: C:\Program Files\GraphViz\bin\Dot C:\DOKUME~1\schober\LOKALE~1\Te
mp\OWLVizScratch138.tmp -q -o C:\DOKUME~1\schober\LOKALE~1\Temp\OWLVizScratch138
.tmp error=2
An error related to DOT has occurred. This error was probably because OWLViz cou
ld not find the DOT application.  Please ensure that the path to the DOT applica
tion is set properly
DOT Process Error:
CreateProcess: C:\Program Files\GraphViz\bin\Dot C:\DOKUME~1\schober\LOKALE~1\Te
mp\OWLVizScratch139.tmp -q -o C:\DOKUME~1\schober\LOKALE~1\Temp\OWLVizScratch139
.tmp error=2
An error related to DOT has occurred. This error was probably because OWLViz cou
ld not find the DOT application.  Please ensure that the path to the DOT applica
tion is set properly
DOT Process Error:
CreateProcess: C:\Program Files\GraphViz\bin\Dot C:\DOKUME~1\schober\LOKALE~1\Te
mp\OWLVizScratch140.tmp -q -o C:\DOKUME~1\schober\LOKALE~1\Temp\OWLVizScratch140
.tmp error=2
An error related to DOT has occurred. This error was probably because OWLViz cou
ld not find the DOT application.  Please ensure that the path to the DOT applica
tion is set properly
Using OWL API version 2.2.1.1090
Rebuilding entity indices...
... rebuilt in 0 ms
loading http://www.debugit.eu/ontology/1.0/dco.owl from file:/C:/Dokumente%20und
%20Einstellungen/schober/Desktop/dco.owl
No mapping for http://purl.org/biotop/1.0/biotop-dolce-ro.owl found.
loading http://purl.org/biotop/1.0/biotop-dolce-ro.owl from http://purl.org/biot
op/1.0/biotop-dolce-ro.owl
No mapping for http://purl.org/biotop/1.0/biotop.owl found.
loading http://purl.org/biotop/1.0/biotop.owl from http://purl.org/biotop/1.0/bi
otop.owl
No mapping for http://www.ifomis.org/obo/ro/1.0/light found.
loading http://www.ifomis.org/obo/ro/1.0/light from http://www.ifomis.org/obo/ro
/1.0/light
No mapping for http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl found.
loading http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl from http://pr
otege.stanford.edu/plugins/owl/dc/protege-dc.owl
No mapping for http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl found.
loading http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl from http://www.loa-cnr.
it/ontologies/DOLCE-Lite.owl
Setting active ontology to http://www.debugit.eu/ontology/1.0/dco.owl
Rebuilding entity indices...
... rebuilt in 15 ms
... active ontology changed
BAD LISTENER: ()
Error logged
java.lang.NumberFormatException: For input string: "160.35"
        at java.lang.NumberFormatException.forInputString(Unknown Source)
        at java.lang.Integer.parseInt(Unknown Source)
        at java.lang.Integer.parseInt(Unknown Source)
        at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParam
eterSetter.parsePoint(DotParameterSetter.java:329)
        at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParam
eterSetter.setEdgePath(DotParameterSetter.java:230)
        at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParam
eterSetter.setEdgeAttribute(DotParameterSetter.java:176)
        at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParse
r.setEdgeAttribute(DotParser.java:56)
        at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParse
r.node_or_edge_stmt(DotParser.java:198)
        at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParse
r.stmt(DotParser.java:127)
        at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParse
r.graph(DotParser.java:107)
        at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParse
r.start(DotParser.java:72)
        at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParse
r.parse(DotParser.java:25)
        at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.DotGraphLayoutEngi
ne.layoutGraph(DotGraphLayoutEngine.java:111)
        at uk.ac.man.cs.mig.util.graph.ui.GraphView.revalidateGraph(GraphView.ja
va:308)
        at uk.ac.man.cs.mig.util.graph.ui.GraphView$3.graphChanged(GraphView.jav
a:141)
        at uk.ac.man.cs.mig.util.graph.controller.impl.DefaultGraphGenerator.fir
eGraphChangedEvent(DefaultGraphGenerator.java:613)
        at uk.ac.man.cs.mig.util.graph.controller.impl.DefaultGraphGenerator$1.o
bjectsAdded(DefaultGraphGenerator.java:171)
        at uk.ac.man.cs.mig.util.graph.controller.impl.DefaultVisualisedObjectMa
nager.fireObjectAddedEvent(DefaultVisualisedObjectManager.java:731)
        at uk.ac.man.cs.mig.util.graph.controller.impl.DefaultVisualisedObjectMa
nager.showObject(DefaultVisualisedObjectManager.java:320)
        at uk.ac.man.cs.mig.coode.owlviz.ui.OWLVizGraphPanel$3.selectionChanged(
OWLVizGraphPanel.java:153)
        at uk.ac.man.cs.mig.coode.owlviz.ui.OWLVizSelectionModel.fireSelectionCh
anged(OWLVizSelectionModel.java:69)
        at uk.ac.man.cs.mig.coode.owlviz.ui.OWLVizSelectionModel.setSelectedClas
s(OWLVizSelectionModel.java:54)
        at uk.ac.man.cs.mig.coode.owlviz.ui.OWLVizView.updateView(OWLVizView.jav
a:85)
        at org.protege.editor.owl.ui.view.AbstractOWLClassViewComponent.updateVi
ew(AbstractOWLClassViewComponent.java:29)
        at org.protege.editor.owl.ui.view.AbstractOWLClassViewComponent.updateVi
ew(AbstractOWLClassViewComponent.java:18)
        at org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.upda
teViewContentAndHeader(AbstractOWLSelectionViewComponent.java:189)
        at org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent$1.se
lectionChanged(AbstractOWLSelectionViewComponent.java:67)
        at org.protege.editor.owl.model.selection.OWLSelectionModelImpl.fireSele
ctionChanged(OWLSelectionModelImpl.java:100)
        at org.protege.editor.owl.model.selection.OWLSelectionModelImpl.updateSe
lectedObject(OWLSelectionModelImpl.java:88)
        at org.protege.editor.owl.model.selection.OWLSelectionModelImpl.setSelec
tedObject(OWLSelectionModelImpl.java:76)
        at org.protege.editor.owl.model.selection.OWLSelectionModelImpl.setSelec
tedEntity(OWLSelectionModelImpl.java:111)
        at org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.setS
electedEntity(AbstractOWLSelectionViewComponent.java:122)
        at org.protege.editor.owl.ui.clshierarchy.AbstractOWLClassHierarchyViewC
omponent.transmitSelection(AbstractOWLClassHierarchyViewComponent.java:188)
        at org.protege.editor.owl.ui.clshierarchy.AbstractOWLClassHierarchyViewC
omponent$6.valueChanged(AbstractOWLClassHierarchyViewComponent.java:173)
        at javax.swing.JTree.fireValueChanged(Unknown Source)
        at javax.swing.JTree$TreeSelectionRedirector.valueChanged(Unknown Source
)
        at javax.swing.tree.DefaultTreeSelectionModel.fireValueChanged(Unknown S
ource)
        at javax.swing.tree.DefaultTreeSelectionModel.notifyPathChange(Unknown S
ource)
        at javax.swing.tree.DefaultTreeSelectionModel.setSelectionPaths(Unknown
Source)
        at javax.swing.tree.DefaultTreeSelectionModel.setSelectionPath(Unknown S
ource)
        at javax.swing.JTree.setSelectionPath(Unknown Source)
        at javax.swing.plaf.basic.BasicTreeUI.selectPathForEvent(Unknown Source)

        at javax.swing.plaf.basic.BasicTreeUI$Handler.handleSelectionImpl(Unknow
n Source)
        at javax.swing.plaf.basic.BasicTreeUI$Handler.handleSelection(Unknown So
urce)
        at javax.swing.plaf.basic.BasicTreeUI$Handler.mousePressed(Unknown Sourc
e)
        at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
        at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
        at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
        at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
        at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
        at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
        at java.awt.AWTEventMulticaster.mousePressed(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.dispatchEvent(Unknown Source)
        at java.awt.EventDispatchThread.pumpOneEventForHierarchy(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)



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Re: owlviz plug-in error due to graphviz ?

Pitonyak, Andrew D
Last I heard, the latest version of Graphiz did not work with the latest version of Protégé, try the previous version of Graphiz.


-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Daniel Schober
Sent: Thursday, April 30, 2009 7:20 AM
To: [hidden email]; User support for the Protege-OWL editor; [hidden email]
Subject: [protege-owl] owlviz plugin error due to graphviz ?

Dear OwlViz and OwlPropviz zards.
Currently OwlViz and the OwlPropViz (which I need) don't work in P4 with the latest GraphViz distribution.
I use win xp and the latest P4 download and the latest GraphViz download.
Is this due to non backwards compatibility of the most recent Graph Viz changes? If so, where can I download an older GraphViz version that works with OntoViz?
In OwlViz, after setting the correct path to dot.exe The tab does not show any relations and crashes. The OwlPropViz does also not work.
The error message is attached.

Funny enough Ontoviz in P3.4 seems to work fine.

Any ideas how to make any Graph based visualisation of selected parts of my owl ontology ?
Cheers,
        Daniel Schober.



_______________________________________________
protege-owl mailing list
[hidden email]
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Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 
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Re: owlviz plugin error due to graphviz ?

Nick Drummond
In reply to this post by Daniel Schober
Hi Daniel,

I'll add the bug to the buglist, but it may just be a graphviz bug in this version.

I can't seem to find an older version on their website. Have other windows users managed to find one?

Nick


2009/4/30 Daniel Schober <[hidden email]>
Dear OwlViz and OwlPropviz zards.
Currently OwlViz and the OwlPropViz (which I need) don't work in P4 with
the latest GraphViz distribution.
I use win xp and the latest P4 download and the latest GraphViz download.
Is this due to non backwards compatibility of the most recent Graph Viz
changes? If so, where can I download an older GraphViz version that
works with OntoViz?
In OwlViz, after setting the correct path to dot.exe The tab does not
show any relations and crashes. The OwlPropViz does also not work.
The error message is attached.

Funny enough Ontoviz in P3.4 seems to work fine.

Any ideas how to make any Graph based visualisation of selected parts of
my owl ontology ?
Cheers,
       Daniel Schober.




cwd: C:\Programme\Protege_4.0_beta
cmd: "C:\Programme\Protege_4.0_beta\jre\bin\java.exe" -Xms209715200 -Xmx20971520
0 -classpath "C:\Programme\Protege_4.0_beta\org.eclipse.osgi.jar;C:\Programme\Pr
otege_4.0_beta\lax.jar;" com.zerog.lax.LAX "C:/Programme/Protege_4.0_beta/Proteg
e.lax" "C:/Dokumente und Einstellungen/schober/Lokale Einstellungen/Temp/laxE.tm
p"
Starting Protege 4 OWL Editor (Version 4.0.110)
Platform:
   Java: JVM 1.5.0_11-b03 Memory: 208M
   Language: de, Country: DE
   Framework: Eclipse (1.4.0)
   OS: WindowsXP (5.1)
   Processor: x86
Installed plugin Pellet Reasoner
Installed plugin DL Query Tab
Installed plugin Owlviz Plug-in
Installed plugin owleditor
Installed plugin The OWL API
Installed plugin Factplusplus Plug-in
Downloading FaCT++ reasoner
Using OWL API version 2.2.1.1090
Rebuilding entity indices...
... rebuilt in 0 ms
Copying FaCT++ reasoner
loading http://www.debugit.eu/ontology/1.0/dco.owl from file:/C:/Dokumente%20und
%20Einstellungen/schober/Desktop/dco.owl
No mapping for http://purl.org/biotop/1.0/biotop-dolce-ro.owl found.
loading http://purl.org/biotop/1.0/biotop-dolce-ro.owl from http://purl.org/biot
op/1.0/biotop-dolce-ro.owl

No mapping for http://purl.org/biotop/1.0/biotop.owl found.
loading http://purl.org/biotop/1.0/biotop.owl from http://purl.org/biotop/1.0/bi
otop.owl
No mapping for http://www.ifomis.org/obo/ro/1.0/light found.
loading http://www.ifomis.org/obo/ro/1.0/light from http://www.ifomis.org/obo/ro
/1.0/light
No mapping for http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl found.
loading http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl from http://pr
otege.stanford.edu/plugins/owl/dc/protege-dc.owl
No mapping for http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl found.
loading http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl from http://www.loa-cnr.
it/ontologies/DOLCE-Lite.owl
Setting active ontology to http://www.debugit.eu/ontology/1.0/dco.owl
Rebuilding entity indices...
... rebuilt in 0 ms
... active ontology changed
DOT Process Error:
CreateProcess: C:\Program Files\GraphViz\bin\Dot C:\DOKUME~1\schober\LOKALE~1\Te
mp\OWLVizScratch137.tmp -q -o C:\DOKUME~1\schober\LOKALE~1\Temp\OWLVizScratch137
.tmp error=2
An error related to DOT has occurred. This error was probably because OWLViz cou
ld not find the DOT application.  Please ensure that the path to the DOT applica
tion is set properly
DOT Process Error:
CreateProcess: C:\Program Files\GraphViz\bin\Dot C:\DOKUME~1\schober\LOKALE~1\Te
mp\OWLVizScratch138.tmp -q -o C:\DOKUME~1\schober\LOKALE~1\Temp\OWLVizScratch138
.tmp error=2
An error related to DOT has occurred. This error was probably because OWLViz cou
ld not find the DOT application.  Please ensure that the path to the DOT applica
tion is set properly
DOT Process Error:
CreateProcess: C:\Program Files\GraphViz\bin\Dot C:\DOKUME~1\schober\LOKALE~1\Te
mp\OWLVizScratch139.tmp -q -o C:\DOKUME~1\schober\LOKALE~1\Temp\OWLVizScratch139
.tmp error=2
An error related to DOT has occurred. This error was probably because OWLViz cou
ld not find the DOT application.  Please ensure that the path to the DOT applica
tion is set properly
DOT Process Error:
CreateProcess: C:\Program Files\GraphViz\bin\Dot C:\DOKUME~1\schober\LOKALE~1\Te
mp\OWLVizScratch140.tmp -q -o C:\DOKUME~1\schober\LOKALE~1\Temp\OWLVizScratch140
.tmp error=2
An error related to DOT has occurred. This error was probably because OWLViz cou
ld not find the DOT application.  Please ensure that the path to the DOT applica
tion is set properly
Using OWL API version 2.2.1.1090
Rebuilding entity indices...
... rebuilt in 0 ms
loading http://www.debugit.eu/ontology/1.0/dco.owl from file:/C:/Dokumente%20und
%20Einstellungen/schober/Desktop/dco.owl
No mapping for http://purl.org/biotop/1.0/biotop-dolce-ro.owl found.
loading http://purl.org/biotop/1.0/biotop-dolce-ro.owl from http://purl.org/biot
op/1.0/biotop-dolce-ro.owl

No mapping for http://purl.org/biotop/1.0/biotop.owl found.
loading http://purl.org/biotop/1.0/biotop.owl from http://purl.org/biotop/1.0/bi
otop.owl
No mapping for http://www.ifomis.org/obo/ro/1.0/light found.
loading http://www.ifomis.org/obo/ro/1.0/light from http://www.ifomis.org/obo/ro
/1.0/light
No mapping for http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl found.
loading http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl from http://pr
otege.stanford.edu/plugins/owl/dc/protege-dc.owl
No mapping for http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl found.
loading http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl from http://www.loa-cnr.
it/ontologies/DOLCE-Lite.owl
Setting active ontology to http://www.debugit.eu/ontology/1.0/dco.owl
Rebuilding entity indices...
... rebuilt in 15 ms
... active ontology changed
BAD LISTENER: ()
Error logged
java.lang.NumberFormatException: For input string: "160.35"
       at java.lang.NumberFormatException.forInputString(Unknown Source)
       at java.lang.Integer.parseInt(Unknown Source)
       at java.lang.Integer.parseInt(Unknown Source)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParam
eterSetter.parsePoint(DotParameterSetter.java:329)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParam
eterSetter.setEdgePath(DotParameterSetter.java:230)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParam
eterSetter.setEdgeAttribute(DotParameterSetter.java:176)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParse
r.setEdgeAttribute(DotParser.java:56)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParse
r.node_or_edge_stmt(DotParser.java:198)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParse
r.stmt(DotParser.java:127)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParse
r.graph(DotParser.java:107)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParse
r.start(DotParser.java:72)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParse
r.parse(DotParser.java:25)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.DotGraphLayoutEngi
ne.layoutGraph(DotGraphLayoutEngine.java:111)
       at uk.ac.man.cs.mig.util.graph.ui.GraphView.revalidateGraph(GraphView.ja
va:308)
       at uk.ac.man.cs.mig.util.graph.ui.GraphView$3.graphChanged(GraphView.jav
a:141)
       at uk.ac.man.cs.mig.util.graph.controller.impl.DefaultGraphGenerator.fir
eGraphChangedEvent(DefaultGraphGenerator.java:613)
       at uk.ac.man.cs.mig.util.graph.controller.impl.DefaultGraphGenerator$1.o
bjectsAdded(DefaultGraphGenerator.java:171)
       at uk.ac.man.cs.mig.util.graph.controller.impl.DefaultVisualisedObjectMa
nager.fireObjectAddedEvent(DefaultVisualisedObjectManager.java:731)
       at uk.ac.man.cs.mig.util.graph.controller.impl.DefaultVisualisedObjectMa
nager.showObject(DefaultVisualisedObjectManager.java:320)
       at uk.ac.man.cs.mig.coode.owlviz.ui.OWLVizGraphPanel$3.selectionChanged(
OWLVizGraphPanel.java:153)
       at uk.ac.man.cs.mig.coode.owlviz.ui.OWLVizSelectionModel.fireSelectionCh
anged(OWLVizSelectionModel.java:69)
       at uk.ac.man.cs.mig.coode.owlviz.ui.OWLVizSelectionModel.setSelectedClas
s(OWLVizSelectionModel.java:54)
       at uk.ac.man.cs.mig.coode.owlviz.ui.OWLVizView.updateView(OWLVizView.jav
a:85)
       at org.protege.editor.owl.ui.view.AbstractOWLClassViewComponent.updateVi
ew(AbstractOWLClassViewComponent.java:29)
       at org.protege.editor.owl.ui.view.AbstractOWLClassViewComponent.updateVi
ew(AbstractOWLClassViewComponent.java:18)
       at org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.upda
teViewContentAndHeader(AbstractOWLSelectionViewComponent.java:189)
       at org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent$1.se
lectionChanged(AbstractOWLSelectionViewComponent.java:67)
       at org.protege.editor.owl.model.selection.OWLSelectionModelImpl.fireSele
ctionChanged(OWLSelectionModelImpl.java:100)
       at org.protege.editor.owl.model.selection.OWLSelectionModelImpl.updateSe
lectedObject(OWLSelectionModelImpl.java:88)
       at org.protege.editor.owl.model.selection.OWLSelectionModelImpl.setSelec
tedObject(OWLSelectionModelImpl.java:76)
       at org.protege.editor.owl.model.selection.OWLSelectionModelImpl.setSelec
tedEntity(OWLSelectionModelImpl.java:111)
       at org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.setS
electedEntity(AbstractOWLSelectionViewComponent.java:122)
       at org.protege.editor.owl.ui.clshierarchy.AbstractOWLClassHierarchyViewC
omponent.transmitSelection(AbstractOWLClassHierarchyViewComponent.java:188)
       at org.protege.editor.owl.ui.clshierarchy.AbstractOWLClassHierarchyViewC
omponent$6.valueChanged(AbstractOWLClassHierarchyViewComponent.java:173)
       at javax.swing.JTree.fireValueChanged(Unknown Source)
       at javax.swing.JTree$TreeSelectionRedirector.valueChanged(Unknown Source
)
       at javax.swing.tree.DefaultTreeSelectionModel.fireValueChanged(Unknown S
ource)
       at javax.swing.tree.DefaultTreeSelectionModel.notifyPathChange(Unknown S
ource)
       at javax.swing.tree.DefaultTreeSelectionModel.setSelectionPaths(Unknown
Source)
       at javax.swing.tree.DefaultTreeSelectionModel.setSelectionPath(Unknown S
ource)
       at javax.swing.JTree.setSelectionPath(Unknown Source)
       at javax.swing.plaf.basic.BasicTreeUI.selectPathForEvent(Unknown Source)

       at javax.swing.plaf.basic.BasicTreeUI$Handler.handleSelectionImpl(Unknow
n Source)
       at javax.swing.plaf.basic.BasicTreeUI$Handler.handleSelection(Unknown So
urce)
       at javax.swing.plaf.basic.BasicTreeUI$Handler.mousePressed(Unknown Sourc
e)
       at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
       at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
       at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
       at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
       at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
       at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
       at java.awt.AWTEventMulticaster.mousePressed(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.dispatchEvent(Unknown Source)
       at java.awt.EventDispatchThread.pumpOneEventForHierarchy(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)



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Re: owlviz plugin error due to graphviz ?

Jennifer Vendetti
Administrator
Hi Nick,

I looked around for older Windows distributions when we were conducting the short course.  I found a reference to this page:

http://www.graphviz.org/pub/graphviz/ARCHIVE/

... that is supposedly for older versions.  But, none of the versions I downloaded contained the "dot" executable file.

I'll try posting a message on the GraphViz developers mailing list to see if they have another location for older versions.

Jennifer


Nick Drummond wrote:
Hi Daniel,

I'll add the bug to the buglist, but it may just be a graphviz bug in this version.

I can't seem to find an older version on their website. Have other windows users managed to find one?

Nick


2009/4/30 Daniel Schober <[hidden email]>
Dear OwlViz and OwlPropviz zards.
Currently OwlViz and the OwlPropViz (which I need) don't work in P4 with
the latest GraphViz distribution.
I use win xp and the latest P4 download and the latest GraphViz download.
Is this due to non backwards compatibility of the most recent Graph Viz
changes? If so, where can I download an older GraphViz version that
works with OntoViz?
In OwlViz, after setting the correct path to dot.exe The tab does not
show any relations and crashes. The OwlPropViz does also not work.
The error message is attached.

Funny enough Ontoviz in P3.4 seems to work fine.

Any ideas how to make any Graph based visualisation of selected parts of
my owl ontology ?
Cheers,
       Daniel Schober.




cwd: C:\Programme\Protege_4.0_beta
cmd: "C:\Programme\Protege_4.0_beta\jre\bin\java.exe" -Xms209715200 -Xmx20971520
0 -classpath "C:\Programme\Protege_4.0_beta\org.eclipse.osgi.jar;C:\Programme\Pr
otege_4.0_beta\lax.jar;" com.zerog.lax.LAX "C:/Programme/Protege_4.0_beta/Proteg
e.lax" "C:/Dokumente und Einstellungen/schober/Lokale Einstellungen/Temp/laxE.tm
p"
Starting Protege 4 OWL Editor (Version 4.0.110)
Platform:
   Java: JVM 1.5.0_11-b03 Memory: 208M
   Language: de, Country: DE
   Framework: Eclipse (1.4.0)
   OS: WindowsXP (5.1)
   Processor: x86
Installed plugin Pellet Reasoner
Installed plugin DL Query Tab
Installed plugin Owlviz Plug-in
Installed plugin owleditor
Installed plugin The OWL API
Installed plugin Factplusplus Plug-in
Downloading FaCT++ reasoner
Using OWL API version 2.2.1.1090
Rebuilding entity indices...
... rebuilt in 0 ms
Copying FaCT++ reasoner
loading http://www.debugit.eu/ontology/1.0/dco.owl from file:/C:/Dokumente%20und
%20Einstellungen/schober/Desktop/dco.owl
No mapping for http://purl.org/biotop/1.0/biotop-dolce-ro.owl found.
loading http://purl.org/biotop/1.0/biotop-dolce-ro.owl from http://purl.org/biot
op/1.0/biotop-dolce-ro.owl

No mapping for http://purl.org/biotop/1.0/biotop.owl found.
loading http://purl.org/biotop/1.0/biotop.owl from http://purl.org/biotop/1.0/bi
otop.owl
No mapping for http://www.ifomis.org/obo/ro/1.0/light found.
loading http://www.ifomis.org/obo/ro/1.0/light from http://www.ifomis.org/obo/ro
/1.0/light
No mapping for http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl found.
loading http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl from http://pr
otege.stanford.edu/plugins/owl/dc/protege-dc.owl
No mapping for http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl found.
loading http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl from http://www.loa-cnr.
it/ontologies/DOLCE-Lite.owl
Setting active ontology to http://www.debugit.eu/ontology/1.0/dco.owl
Rebuilding entity indices...
... rebuilt in 0 ms
... active ontology changed
DOT Process Error:
CreateProcess: C:\Program Files\GraphViz\bin\Dot C:\DOKUME~1\schober\LOKALE~1\Te
mp\OWLVizScratch137.tmp -q -o C:\DOKUME~1\schober\LOKALE~1\Temp\OWLVizScratch137
.tmp error=2
An error related to DOT has occurred. This error was probably because OWLViz cou
ld not find the DOT application.  Please ensure that the path to the DOT applica
tion is set properly
DOT Process Error:
CreateProcess: C:\Program Files\GraphViz\bin\Dot C:\DOKUME~1\schober\LOKALE~1\Te
mp\OWLVizScratch138.tmp -q -o C:\DOKUME~1\schober\LOKALE~1\Temp\OWLVizScratch138
.tmp error=2
An error related to DOT has occurred. This error was probably because OWLViz cou
ld not find the DOT application.  Please ensure that the path to the DOT applica
tion is set properly
DOT Process Error:
CreateProcess: C:\Program Files\GraphViz\bin\Dot C:\DOKUME~1\schober\LOKALE~1\Te
mp\OWLVizScratch139.tmp -q -o C:\DOKUME~1\schober\LOKALE~1\Temp\OWLVizScratch139
.tmp error=2
An error related to DOT has occurred. This error was probably because OWLViz cou
ld not find the DOT application.  Please ensure that the path to the DOT applica
tion is set properly
DOT Process Error:
CreateProcess: C:\Program Files\GraphViz\bin\Dot C:\DOKUME~1\schober\LOKALE~1\Te
mp\OWLVizScratch140.tmp -q -o C:\DOKUME~1\schober\LOKALE~1\Temp\OWLVizScratch140
.tmp error=2
An error related to DOT has occurred. This error was probably because OWLViz cou
ld not find the DOT application.  Please ensure that the path to the DOT applica
tion is set properly
Using OWL API version 2.2.1.1090
Rebuilding entity indices...
... rebuilt in 0 ms
loading http://www.debugit.eu/ontology/1.0/dco.owl from file:/C:/Dokumente%20und
%20Einstellungen/schober/Desktop/dco.owl
No mapping for http://purl.org/biotop/1.0/biotop-dolce-ro.owl found.
loading http://purl.org/biotop/1.0/biotop-dolce-ro.owl from http://purl.org/biot
op/1.0/biotop-dolce-ro.owl

No mapping for http://purl.org/biotop/1.0/biotop.owl found.
loading http://purl.org/biotop/1.0/biotop.owl from http://purl.org/biotop/1.0/bi
otop.owl
No mapping for http://www.ifomis.org/obo/ro/1.0/light found.
loading http://www.ifomis.org/obo/ro/1.0/light from http://www.ifomis.org/obo/ro
/1.0/light
No mapping for http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl found.
loading http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl from http://pr
otege.stanford.edu/plugins/owl/dc/protege-dc.owl
No mapping for http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl found.
loading http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl from http://www.loa-cnr.
it/ontologies/DOLCE-Lite.owl
Setting active ontology to http://www.debugit.eu/ontology/1.0/dco.owl
Rebuilding entity indices...
... rebuilt in 15 ms
... active ontology changed
BAD LISTENER: ()
Error logged
java.lang.NumberFormatException: For input string: "160.35"
       at java.lang.NumberFormatException.forInputString(Unknown Source)
       at java.lang.Integer.parseInt(Unknown Source)
       at java.lang.Integer.parseInt(Unknown Source)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParam
eterSetter.parsePoint(DotParameterSetter.java:329)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParam
eterSetter.setEdgePath(DotParameterSetter.java:230)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParam
eterSetter.setEdgeAttribute(DotParameterSetter.java:176)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParse
r.setEdgeAttribute(DotParser.java:56)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParse
r.node_or_edge_stmt(DotParser.java:198)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParse
r.stmt(DotParser.java:127)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParse
r.graph(DotParser.java:107)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParse
r.start(DotParser.java:72)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.DotParse
r.parse(DotParser.java:25)
       at uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.DotGraphLayoutEngi
ne.layoutGraph(DotGraphLayoutEngine.java:111)
       at uk.ac.man.cs.mig.util.graph.ui.GraphView.revalidateGraph(GraphView.ja
va:308)
       at uk.ac.man.cs.mig.util.graph.ui.GraphView$3.graphChanged(GraphView.jav
a:141)
       at uk.ac.man.cs.mig.util.graph.controller.impl.DefaultGraphGenerator.fir
eGraphChangedEvent(DefaultGraphGenerator.java:613)
       at uk.ac.man.cs.mig.util.graph.controller.impl.DefaultGraphGenerator$1.o
bjectsAdded(DefaultGraphGenerator.java:171)
       at uk.ac.man.cs.mig.util.graph.controller.impl.DefaultVisualisedObjectMa
nager.fireObjectAddedEvent(DefaultVisualisedObjectManager.java:731)
       at uk.ac.man.cs.mig.util.graph.controller.impl.DefaultVisualisedObjectMa
nager.showObject(DefaultVisualisedObjectManager.java:320)
       at uk.ac.man.cs.mig.coode.owlviz.ui.OWLVizGraphPanel$3.selectionChanged(
OWLVizGraphPanel.java:153)
       at uk.ac.man.cs.mig.coode.owlviz.ui.OWLVizSelectionModel.fireSelectionCh
anged(OWLVizSelectionModel.java:69)
       at uk.ac.man.cs.mig.coode.owlviz.ui.OWLVizSelectionModel.setSelectedClas
s(OWLVizSelectionModel.java:54)
       at uk.ac.man.cs.mig.coode.owlviz.ui.OWLVizView.updateView(OWLVizView.jav
a:85)
       at org.protege.editor.owl.ui.view.AbstractOWLClassViewComponent.updateVi
ew(AbstractOWLClassViewComponent.java:29)
       at org.protege.editor.owl.ui.view.AbstractOWLClassViewComponent.updateVi
ew(AbstractOWLClassViewComponent.java:18)
       at org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.upda
teViewContentAndHeader(AbstractOWLSelectionViewComponent.java:189)
       at org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent$1.se
lectionChanged(AbstractOWLSelectionViewComponent.java:67)
       at org.protege.editor.owl.model.selection.OWLSelectionModelImpl.fireSele
ctionChanged(OWLSelectionModelImpl.java:100)
       at org.protege.editor.owl.model.selection.OWLSelectionModelImpl.updateSe
lectedObject(OWLSelectionModelImpl.java:88)
       at org.protege.editor.owl.model.selection.OWLSelectionModelImpl.setSelec
tedObject(OWLSelectionModelImpl.java:76)
       at org.protege.editor.owl.model.selection.OWLSelectionModelImpl.setSelec
tedEntity(OWLSelectionModelImpl.java:111)
       at org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.setS
electedEntity(AbstractOWLSelectionViewComponent.java:122)
       at org.protege.editor.owl.ui.clshierarchy.AbstractOWLClassHierarchyViewC
omponent.transmitSelection(AbstractOWLClassHierarchyViewComponent.java:188)
       at org.protege.editor.owl.ui.clshierarchy.AbstractOWLClassHierarchyViewC
omponent$6.valueChanged(AbstractOWLClassHierarchyViewComponent.java:173)
       at javax.swing.JTree.fireValueChanged(Unknown Source)
       at javax.swing.JTree$TreeSelectionRedirector.valueChanged(Unknown Source
)
       at javax.swing.tree.DefaultTreeSelectionModel.fireValueChanged(Unknown S
ource)
       at javax.swing.tree.DefaultTreeSelectionModel.notifyPathChange(Unknown S
ource)
       at javax.swing.tree.DefaultTreeSelectionModel.setSelectionPaths(Unknown
Source)
       at javax.swing.tree.DefaultTreeSelectionModel.setSelectionPath(Unknown S
ource)
       at javax.swing.JTree.setSelectionPath(Unknown Source)
       at javax.swing.plaf.basic.BasicTreeUI.selectPathForEvent(Unknown Source)

       at javax.swing.plaf.basic.BasicTreeUI$Handler.handleSelectionImpl(Unknow
n Source)
       at javax.swing.plaf.basic.BasicTreeUI$Handler.handleSelection(Unknown So
urce)
       at javax.swing.plaf.basic.BasicTreeUI$Handler.mousePressed(Unknown Sourc
e)
       at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
       at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
       at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
       at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
       at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
       at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)
       at java.awt.AWTEventMulticaster.mousePressed(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.dispatchEvent(Unknown Source)
       at java.awt.EventDispatchThread.pumpOneEventForHierarchy(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)



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Re: owlviz plugin error due to graphviz ?

BassMan123
In reply to this post by Daniel Schober
I see older versions of GraphViz at http://www.graphviz.org/pub/graphviz/stable/windows/

Can anybody comment on a version of GraphViz that works well with Protege 3.4?
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Re: owlviz plugin error due to graphviz ?

Jennifer Vendetti
Administrator
I have version 2.20 installed and it works fine.  I'm also fairly
certain that any version prior to 2.20 will work as well.

Jennifer

BassMan123 wrote:
> I see older versions of GraphViz at
> http://www.graphviz.org/pub/graphviz/stable/windows/
>
> Can anybody comment on a version of GraphViz that works well with Protege
> 3.4?
>
>  
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Re: owlviz plugin error due to graphviz ?

BassMan123
FYI, just installed "graphviz-2.20.3a.msi", which looks like the latest version just before Protege 3.4 was released 3/16/2009.  Got it here: http://www.graphviz.org/pub/graphviz/stable/windows/

Works great!


jvendetti wrote
I have version 2.20 installed and it works fine.  I'm also fairly
certain that any version prior to 2.20 will work as well.

Jennifer

BassMan123 wrote:
> I see older versions of GraphViz at
> http://www.graphviz.org/pub/graphviz/stable/windows/
>
> Can anybody comment on a version of GraphViz that works well with Protege
> 3.4?
>
>  
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Re: owlviz plugin error due to graphviz ?

Tania Tudorache
In reply to this post by Daniel Schober
Daniel,

There are fixed versions of OWLViz available that work with GraphViz 2.22:

Protege 3.4: http://protegewiki.stanford.edu/index.php/OWLViz_build_22
Protege 4: http://protege.stanford.edu/plugins/protege4/org.coode.owlviz.jar

Tania

Daniel Schober wrote:

> Dear OwlViz and OwlPropviz zards.
> Currently OwlViz and the OwlPropViz (which I need) don't work in P4 with
> the latest GraphViz distribution.
> I use win xp and the latest P4 download and the latest GraphViz download.
> Is this due to non backwards compatibility of the most recent Graph Viz
> changes? If so, where can I download an older GraphViz version that
> works with OntoViz?
> In OwlViz, after setting the correct path to dot.exe The tab does not
> show any relations and crashes. The OwlPropViz does also not work.
> The error message is attached.
>
> Funny enough Ontoviz in P3.4 seems to work fine.
>
> Any ideas how to make any Graph based visualisation of selected parts of
> my owl ontology ?
> Cheers,
>     Daniel Schober.
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 
>  

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Protege 3.4 Bug when importing ontologies that use content negotiation?

Leyla Jael García Castro

Hello there,

There seems to be a bug in Protégé 3.4, JVM 1.5, when importing ontologies that use content negotiation, 
i.e. GoodRelations (and other ontologies). The effect is that if you try to import GoodRelations into a
new OWL project using the official URI "http://purl.org/goodrelations/v1", you will get a Java exception
(please, see the screen shot attached).

The reason seems to be that Protégé does not explicitly request RDF/XML and then gets XHTML (the documentation).

There is an easy fix to that: Simply use the URI of the GoodRelations OWL file,
i.e. http://purl.org/goodrelations/v1.owl. That will do the trick.

Is that a bug or id the expected behavior?

Thanks in advanced for your cooperation.

Best,

Leyla Garcia



Windows Live™: Keep your life in sync. Check it out.
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Re: Protege 3.4 Bug when importing ontologies that use content negotiation?

Tania Tudorache
Leyla,

This is not a bug. If you import an ontology from a URL, you need to
specify the URL of the owl file. So in case of the GoodRelations
ontology, you need to specify:
http://www.heppnetz.de/ontologies/goodrelations/v1.owl

And that works fine in Protege 3.4.

Tania

Leyla Jael García Castro wrote:

>
> Hello there,
>
> There seems to be a bug in Protégé 3.4, JVM 1.5, when importing ontologies that use content negotiation,
> i.e. GoodRelations (and other ontologies). The effect is that if you try to import GoodRelations into a
> new OWL project using the official URI "http://purl.org/goodrelations/v1", you will get a Java exception
> (please, see the screen shot attached).
>
> The reason seems to be that Protégé does not explicitly request RDF/XML and then gets XHTML (the documentation).
>
> There is an easy fix to that: Simply use the URI of the GoodRelations OWL file,
> i.e. http://purl.org/goodrelations/v1.owl. That will do the trick.
>
> Is that a bug or id the expected behavior?
>
> Thanks in advanced for your cooperation.
>
> Best,
>
> Leyla Garcia
>  
>
>
> ------------------------------------------------------------------------
> Windows Live™: Keep your life in sync. Check it out.
> <http://windowslive.com/explore?ocid=TXT_TAGLM_BR_life_in_synch_052009>
> ------------------------------------------------------------------------
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 
>  

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Re: Protege 3.4 Bug when importing ontologies that use content negotiation?

Leyla Jael García Castro
Thanks a lot for this information Tania.

Best,

Leyla

> Date: Fri, 8 May 2009 16:21:04 -0700
> From: [hidden email]
> To: [hidden email]
> Subject: Re: [protege-owl] Protege 3.4 Bug when importing ontologies that use content negotiation?
>
> Leyla,
>
> This is not a bug. If you import an ontology from a URL, you need to
> specify the URL of the owl file. So in case of the GoodRelations
> ontology, you need to specify:
> http://www.heppnetz.de/ontologies/goodrelations/v1.owl
>
> And that works fine in Protege 3.4.
>
> Tania
>
> Leyla Jael García Castro wrote:
> >
> > Hello there,
> >
> > There seems to be a bug in Protégé 3.4, JVM 1.5, when importing ontologies that use content negotiation,
> > i.e. GoodRelations (and other ontologies). The effect is that if you try to import GoodRelations into a
> > new OWL project using the official URI "http://purl.org/goodrelations/v1", you will get a Java exception
> > (please, see the screen shot attached).
> >
> > The reason seems to be that Protégé does not explicitly request RDF/XML and then gets XHTML (the documentation).
> >
> > There is an easy fix to that: Simply use the URI of the GoodRelations OWL file,
> > i.e. http://purl.org/goodrelations/v1.owl. That will do the trick.
> >
> > Is that a bug or id the expected behavior?
> >
> > Thanks in advanced for your cooperation.
> >
> > Best,
> >
> > Leyla Garcia
> >
> >
> >
> > ------------------------------------------------------------------------
> > Windows Live™: Keep your life in sync. Check it out.
> > <http://windowslive.com/explore?ocid=TXT_TAGLM_BR_life_in_synch_052009>
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > protege-owl mailing list
> > [hidden email]
> > https://mailman.stanford.edu/mailman/listinfo/protege-owl
> >
> > Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
> >
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03


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Re: owlviz plugin error due to graphviz ?

Yu Lin-2
In reply to this post by Tania Tudorache
Dear Tania,

I have copied OWLViz build22 to Protege3.4 plugins' folder
in Vista.
However, I can not get the right graph from OWLViz.
No edges which link the nodes are shown, and the nodes are
located one upon another on the right top corner of the
graph window.

Anybody else met the same problem?
Could you please tell me how to solve it?

PS: as for protege4.0, I have copied
"http://protege.stanford.edu/plugins/protege4/org.coode.owlviz.jar"
and nothing shows in the OWLViz graph window. (with the
strange font)

Any solutions?

Thanks!

************
Lin Yu

Ph.D.,M.D.

Genome Resource and Analysis Unit
Genomics Laboratory
Center for Development Biology
RIKEN,JAPAN.

TEL&FAX 0081-78-3063048
Email: [hidden email]
************




--- Tania Tudorache <[hidden email]> wrote:

> Daniel,
>
> There are fixed versions of OWLViz available that
> work with GraphViz 2.22:
>
> Protege 3.4:
>
http://protegewiki.stanford.edu/index.php/OWLViz_build_22
> Protege 4:
>
http://protege.stanford.edu/plugins/protege4/org.coode.owlviz.jar

>
> Tania
>
> Daniel Schober wrote:
> > Dear OwlViz and OwlPropviz zards.
> > Currently OwlViz and the OwlPropViz (which I need)
> don't work in P4 with
> > the latest GraphViz distribution.
> > I use win xp and the latest P4 download and the
> latest GraphViz download.
> > Is this due to non backwards compatibility of the
> most recent Graph Viz
> > changes? If so, where can I download an older
> GraphViz version that
> > works with OntoViz?
> > In OwlViz, after setting the correct path to
> dot.exe The tab does not
> > show any relations and crashes. The OwlPropViz
> does also not work.
> > The error message is attached.
> >
> > Funny enough Ontoviz in P3.4 seems to work fine.
> >
> > Any ideas how to make any Graph based
> visualisation of selected parts of
> > my owl ontology ?
> > Cheers,
> >     Daniel Schober.
> >
> >
> >
> >
>
------------------------------------------------------------------------
> >
> > _______________________________________________
> > protege-owl mailing list
> > [hidden email]
> >
>
https://mailman.stanford.edu/mailman/listinfo/protege-owl
> >
> > Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03 
> >  
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
>
https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03 
>

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Re: owlviz plugin error due to graphviz ?

Tania Tudorache
I've just tested in Protege 3.4 OWLViz build 22 with GraphViz 2.22 on a
Vista machine and it worked fine.

In Protege 4, there is a problem with the fonts. If you get all the
nodes in top level corner, it means that OWLViz does not find the path
to GraphViz. You would see in the console a message like:

"An error related to DOT has occurred. This error was probably because
OWLViz could not find the DOT application. Please ensure that the path
to the DOT application is set properly"

To fix this, go in the OWLViz tab, click on the configuration button,
and select again the right path to dot.exe.

Also, make sure that you have GraphViz 2.22 installed on your machine,
and that the OWLViz configuration points to the 2.22 version of Graphviz.

If you still have problems, please post the exception that you get in
the console.

Tania

Yu Lin wrote:

> Dear Tania,
>
> I have copied OWLViz build22 to Protege3.4 plugins' folder
> in Vista.
> However, I can not get the right graph from OWLViz.
> No edges which link the nodes are shown, and the nodes are
> located one upon another on the right top corner of the
> graph window.
>
> Anybody else met the same problem?
> Could you please tell me how to solve it?
>
> PS: as for protege4.0, I have copied
> "http://protege.stanford.edu/plugins/protege4/org.coode.owlviz.jar"
> and nothing shows in the OWLViz graph window. (with the
> strange font)
>
> Any solutions?
>
> Thanks!
>
> ************
> Lin Yu
>
> Ph.D.,M.D.
>
> Genome Resource and Analysis Unit
> Genomics Laboratory
> Center for Development Biology
> RIKEN,JAPAN.
>
> TEL&FAX 0081-78-3063048
> Email: [hidden email]
> ************
>
>
>
>
> --- Tania Tudorache <[hidden email]> wrote:
>
>  
>> Daniel,
>>
>> There are fixed versions of OWLViz available that
>> work with GraphViz 2.22:
>>
>> Protege 3.4:
>>
>>    
> http://protegewiki.stanford.edu/index.php/OWLViz_build_22
>  
>> Protege 4:
>>
>>    
> http://protege.stanford.edu/plugins/protege4/org.coode.owlviz.jar
>  
>> Tania
>>
>> Daniel Schober wrote:
>>    
>>> Dear OwlViz and OwlPropviz zards.
>>> Currently OwlViz and the OwlPropViz (which I need)
>>>      
>> don't work in P4 with
>>    
>>> the latest GraphViz distribution.
>>> I use win xp and the latest P4 download and the
>>>      
>> latest GraphViz download.
>>    
>>> Is this due to non backwards compatibility of the
>>>      
>> most recent Graph Viz
>>    
>>> changes? If so, where can I download an older
>>>      
>> GraphViz version that
>>    
>>> works with OntoViz?
>>> In OwlViz, after setting the correct path to
>>>      
>> dot.exe The tab does not
>>    
>>> show any relations and crashes. The OwlPropViz
>>>      
>> does also not work.
>>    
>>> The error message is attached.
>>>
>>> Funny enough Ontoviz in P3.4 seems to work fine.
>>>
>>> Any ideas how to make any Graph based
>>>      
>> visualisation of selected parts of
>>    
>>> my owl ontology ?
>>> Cheers,
>>>     Daniel Schober.
>>>
>>>
>>>
>>>
>>>      
> ------------------------------------------------------------------------
>  
>>> _______________________________________________
>>> protege-owl mailing list
>>> [hidden email]
>>>
>>>      
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>  
>>> Instructions for unsubscribing:
>>>      
>> http://protege.stanford.edu/doc/faq.html#01a.03 
>>    
>>>  
>>>      
>> _______________________________________________
>> protege-owl mailing list
>> [hidden email]
>>
>>    
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>  
>> Instructions for unsubscribing:
>> http://protege.stanford.edu/doc/faq.html#01a.03 
>>
>>    
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
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>
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>
>  

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Re: owlviz plugin error due to graphviz ?

Yu Lin-2
Dear Tania,

I have tried on other OS. No problem.

I am using Windows Vista Business. That maybe the problem?


I don't know how to save the output from the console.
But I guess the following sentence maybe important:

--------
uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.ParseException:Encountered
"=" at line 1, colum 18.
Was expecting one of:
    "["...
    "->"...
--------------

for your convenience, I also made a screen print. Please
check out the attachment file.

Thank you very much!

Lin.

--- Tania Tudorache <[hidden email]> wrote:

> I've just tested in Protege 3.4 OWLViz build 22 with
> GraphViz 2.22 on a
> Vista machine and it worked fine.
>
> In Protege 4, there is a problem with the fonts. If
> you get all the
> nodes in top level corner, it means that OWLViz does
> not find the path
> to GraphViz. You would see in the console a message
> like:
>
> "An error related to DOT has occurred. This error
> was probably because
> OWLViz could not find the DOT application. Please
> ensure that the path
> to the DOT application is set properly"
>
> To fix this, go in the OWLViz tab, click on the
> configuration button,
> and select again the right path to dot.exe.
>
> Also, make sure that you have GraphViz 2.22
> installed on your machine,
> and that the OWLViz configuration points to the 2.22
> version of Graphviz.
>
> If you still have problems, please post the
> exception that you get in
> the console.
>
> Tania
>
> Yu Lin wrote:
> > Dear Tania,
> >
> > I have copied OWLViz build22 to Protege3.4
> plugins' folder
> > in Vista.
> > However, I can not get the right graph from
> OWLViz.
> > No edges which link the nodes are shown, and the
> nodes are
> > located one upon another on the right top corner
> of the
> > graph window.
> >
> > Anybody else met the same problem?
> > Could you please tell me how to solve it?
> >
> > PS: as for protege4.0, I have copied
> >
>
"http://protege.stanford.edu/plugins/protege4/org.coode.owlviz.jar"

> > and nothing shows in the OWLViz graph window.
> (with the
> > strange font)
> >
> > Any solutions?
> >
> > Thanks!
> >
> > ************
> > Lin Yu
> >
> > Ph.D.,M.D.
> >
> > Genome Resource and Analysis Unit
> > Genomics Laboratory
> > Center for Development Biology
> > RIKEN,JAPAN.
> >
> > TEL&FAX 0081-78-3063048
> > Email: [hidden email]
> > ************
> >
> >
> >
> >
> > --- Tania Tudorache <[hidden email]>
> wrote:
> >
> >  
> >> Daniel,
> >>
> >> There are fixed versions of OWLViz available that
> >> work with GraphViz 2.22:
> >>
> >> Protege 3.4:
> >>
> >>    
> >
>
http://protegewiki.stanford.edu/index.php/OWLViz_build_22
> >  
> >> Protege 4:
> >>
> >>    
> >
>
http://protege.stanford.edu/plugins/protege4/org.coode.owlviz.jar

> >  
> >> Tania
> >>
> >> Daniel Schober wrote:
> >>    
> >>> Dear OwlViz and OwlPropviz zards.
> >>> Currently OwlViz and the OwlPropViz (which I
> need)
> >>>      
> >> don't work in P4 with
> >>    
> >>> the latest GraphViz distribution.
> >>> I use win xp and the latest P4 download and the
> >>>      
> >> latest GraphViz download.
> >>    
> >>> Is this due to non backwards compatibility of
> the
> >>>      
> >> most recent Graph Viz
> >>    
> >>> changes? If so, where can I download an older
> >>>      
> >> GraphViz version that
> >>    
> >>> works with OntoViz?
> >>> In OwlViz, after setting the correct path to
> >>>      
> >> dot.exe The tab does not
> >>    
> >>> show any relations and crashes. The OwlPropViz
> >>>      
> >> does also not work.
> >>    
> >>> The error message is attached.
> >>>
> >>> Funny enough Ontoviz in P3.4 seems to work fine.
> >>>
> >>> Any ideas how to make any Graph based
> >>>      
> >> visualisation of selected parts of
> >>    
> >>> my owl ontology ?
> >>> Cheers,
> >>>     Daniel Schober.
> >>>
> >>>
> >>>
> >>>
> >>>      
> >
>
------------------------------------------------------------------------
> >  
> >>> _______________________________________________
> >>> protege-owl mailing list
> >>> [hidden email]
> >>>
> >>>      
> >
>
https://mailman.stanford.edu/mailman/listinfo/protege-owl

> >  
> >>> Instructions for unsubscribing:
> >>>      
> >> http://protege.stanford.edu/doc/faq.html#01a.03 
> >>    
> >>>  
> >>>      
> >> _______________________________________________
> >> protege-owl mailing list
> >> [hidden email]
> >>
> >>    
> >
>
https://mailman.stanford.edu/mailman/listinfo/protege-owl

> >  
> >> Instructions for unsubscribing:
> >> http://protege.stanford.edu/doc/faq.html#01a.03 
> >>
> >>    
> >
> > _______________________________________________
> > protege-owl mailing list
> > [hidden email]
> >
>
https://mailman.stanford.edu/mailman/listinfo/protege-owl

> >
> > Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03 
> >
> >  
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
>
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>
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Re: owlviz plugin error due to graphviz ?

Tania Tudorache
This error suggests that you do not have OWLViz configurated to use
GraphViz 2.22.

I know that there is a problem in Vista and possibly it is related to
the fonts. This is something that we'll need to investigate.

Are you sure you have downloaded GraphViz 2.22 from here:

http://www.graphviz.org/Download_windows.php

rather than the WinGraphviz from the same webpage, which does not work
with OWLViz?

Tania

Yu Lin wrote:

> Dear Tania,
>
> I have tried on other OS. No problem.
>
> I am using Windows Vista Business. That maybe the problem?
>
>
> I don't know how to save the output from the console.
> But I guess the following sentence maybe important:
>
> --------
> uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.ParseException:Encountered
> "=" at line 1, colum 18.
> Was expecting one of:
>     "["...
>     "->"...
> --------------
>
> for your convenience, I also made a screen print. Please
> check out the attachment file.
>
> Thank you very much!
>
> Lin.
>
> --- Tania Tudorache <[hidden email]> wrote:
>
>  
>> I've just tested in Protege 3.4 OWLViz build 22 with
>> GraphViz 2.22 on a
>> Vista machine and it worked fine.
>>
>> In Protege 4, there is a problem with the fonts. If
>> you get all the
>> nodes in top level corner, it means that OWLViz does
>> not find the path
>> to GraphViz. You would see in the console a message
>> like:
>>
>> "An error related to DOT has occurred. This error
>> was probably because
>> OWLViz could not find the DOT application. Please
>> ensure that the path
>> to the DOT application is set properly"
>>
>> To fix this, go in the OWLViz tab, click on the
>> configuration button,
>> and select again the right path to dot.exe.
>>
>> Also, make sure that you have GraphViz 2.22
>> installed on your machine,
>> and that the OWLViz configuration points to the 2.22
>> version of Graphviz.
>>
>> If you still have problems, please post the
>> exception that you get in
>> the console.
>>
>> Tania
>>
>> Yu Lin wrote:
>>    
>>> Dear Tania,
>>>
>>> I have copied OWLViz build22 to Protege3.4
>>>      
>> plugins' folder
>>    
>>> in Vista.
>>> However, I can not get the right graph from
>>>      
>> OWLViz.
>>    
>>> No edges which link the nodes are shown, and the
>>>      
>> nodes are
>>    
>>> located one upon another on the right top corner
>>>      
>> of the
>>    
>>> graph window.
>>>
>>> Anybody else met the same problem?
>>> Could you please tell me how to solve it?
>>>
>>> PS: as for protege4.0, I have copied
>>>
>>>      
> "http://protege.stanford.edu/plugins/protege4/org.coode.owlviz.jar"
>  
>>> and nothing shows in the OWLViz graph window.
>>>      
>> (with the
>>    
>>> strange font)
>>>
>>> Any solutions?
>>>
>>> Thanks!
>>>
>>> ************
>>> Lin Yu
>>>
>>> Ph.D.,M.D.
>>>
>>> Genome Resource and Analysis Unit
>>> Genomics Laboratory
>>> Center for Development Biology
>>> RIKEN,JAPAN.
>>>
>>> TEL&FAX 0081-78-3063048
>>> Email: [hidden email]
>>> ************
>>>
>>>
>>>
>>>
>>> --- Tania Tudorache <[hidden email]>
>>>      
>> wrote:
>>    
>>>  
>>>      
>>>> Daniel,
>>>>
>>>> There are fixed versions of OWLViz available that
>>>> work with GraphViz 2.22:
>>>>
>>>> Protege 3.4:
>>>>
>>>>    
>>>>        
> http://protegewiki.stanford.edu/index.php/OWLViz_build_22
>  
>>>  
>>>      
>>>> Protege 4:
>>>>
>>>>    
>>>>        
> http://protege.stanford.edu/plugins/protege4/org.coode.owlviz.jar
>  
>>>  
>>>      
>>>> Tania
>>>>
>>>> Daniel Schober wrote:
>>>>    
>>>>        
>>>>> Dear OwlViz and OwlPropviz zards.
>>>>> Currently OwlViz and the OwlPropViz (which I
>>>>>          
>> need)
>>    
>>>>>      
>>>>>          
>>>> don't work in P4 with
>>>>    
>>>>        
>>>>> the latest GraphViz distribution.
>>>>> I use win xp and the latest P4 download and the
>>>>>      
>>>>>          
>>>> latest GraphViz download.
>>>>    
>>>>        
>>>>> Is this due to non backwards compatibility of
>>>>>          
>> the
>>    
>>>>>      
>>>>>          
>>>> most recent Graph Viz
>>>>    
>>>>        
>>>>> changes? If so, where can I download an older
>>>>>      
>>>>>          
>>>> GraphViz version that
>>>>    
>>>>        
>>>>> works with OntoViz?
>>>>> In OwlViz, after setting the correct path to
>>>>>      
>>>>>          
>>>> dot.exe The tab does not
>>>>    
>>>>        
>>>>> show any relations and crashes. The OwlPropViz
>>>>>      
>>>>>          
>>>> does also not work.
>>>>    
>>>>        
>>>>> The error message is attached.
>>>>>
>>>>> Funny enough Ontoviz in P3.4 seems to work fine.
>>>>>
>>>>> Any ideas how to make any Graph based
>>>>>      
>>>>>          
>>>> visualisation of selected parts of
>>>>    
>>>>        
>>>>> my owl ontology ?
>>>>> Cheers,
>>>>>     Daniel Schober.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>      
>>>>>          
> ------------------------------------------------------------------------
>  
>>>  
>>>      
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Re: owlviz plugin error due to graphviz ?

Yu Lin-2
Dear Tania,

I downloaded the graphviz-2.22.2.msi from the webpage.

Lin.


--- Tania Tudorache <[hidden email]> wrote:

> This error suggests that you do not have OWLViz
> configurated to use
> GraphViz 2.22.
>
> I know that there is a problem in Vista and possibly
> it is related to
> the fonts. This is something that we'll need to
> investigate.
>
> Are you sure you have downloaded GraphViz 2.22 from
> here:
>
> http://www.graphviz.org/Download_windows.php
>
> rather than the WinGraphviz from the same webpage,
> which does not work
> with OWLViz?
>
> Tania
>
> Yu Lin wrote:
> > Dear Tania,
> >
> > I have tried on other OS. No problem.
> >
> > I am using Windows Vista Business. That maybe the
> problem?
> >
> >
> > I don't know how to save the output from the
> console.
> > But I guess the following sentence maybe
> important:
> >
> > --------
> >
>
uk.ac.man.cs.mig.util.graph.layout.dotlayoutengine.dotparser.ParseException:Encountered

> > "=" at line 1, colum 18.
> > Was expecting one of:
> >     "["...
> >     "->"...
> > --------------
> >
> > for your convenience, I also made a screen print.
> Please
> > check out the attachment file.
> >
> > Thank you very much!
> >
> > Lin.
> >
> > --- Tania Tudorache <[hidden email]>
> wrote:
> >
> >  
> >> I've just tested in Protege 3.4 OWLViz build 22
> with
> >> GraphViz 2.22 on a
> >> Vista machine and it worked fine.
> >>
> >> In Protege 4, there is a problem with the fonts.
> If
> >> you get all the
> >> nodes in top level corner, it means that OWLViz
> does
> >> not find the path
> >> to GraphViz. You would see in the console a
> message
> >> like:
> >>
> >> "An error related to DOT has occurred. This error
> >> was probably because
> >> OWLViz could not find the DOT application. Please
> >> ensure that the path
> >> to the DOT application is set properly"
> >>
> >> To fix this, go in the OWLViz tab, click on the
> >> configuration button,
> >> and select again the right path to dot.exe.
> >>
> >> Also, make sure that you have GraphViz 2.22
> >> installed on your machine,
> >> and that the OWLViz configuration points to the
> 2.22
> >> version of Graphviz.
> >>
> >> If you still have problems, please post the
> >> exception that you get in
> >> the console.
> >>
> >> Tania
> >>
> >> Yu Lin wrote:
> >>    
> >>> Dear Tania,
> >>>
> >>> I have copied OWLViz build22 to Protege3.4
> >>>      
> >> plugins' folder
> >>    
> >>> in Vista.
> >>> However, I can not get the right graph from
> >>>      
> >> OWLViz.
> >>    
> >>> No edges which link the nodes are shown, and the
> >>>      
> >> nodes are
> >>    
> >>> located one upon another on the right top corner
> >>>      
> >> of the
> >>    
> >>> graph window.
> >>>
> >>> Anybody else met the same problem?
> >>> Could you please tell me how to solve it?
> >>>
> >>> PS: as for protege4.0, I have copied
> >>>
> >>>      
> >
>
"http://protege.stanford.edu/plugins/protege4/org.coode.owlviz.jar"

> >  
> >>> and nothing shows in the OWLViz graph window.
> >>>      
> >> (with the
> >>    
> >>> strange font)
> >>>
> >>> Any solutions?
> >>>
> >>> Thanks!
> >>>
> >>> ************
> >>> Lin Yu
> >>>
> >>> Ph.D.,M.D.
> >>>
> >>> Genome Resource and Analysis Unit
> >>> Genomics Laboratory
> >>> Center for Development Biology
> >>> RIKEN,JAPAN.
> >>>
> >>> TEL&FAX 0081-78-3063048
> >>> Email: [hidden email]
> >>> ************
> >>>
> >>>
> >>>
> >>>
> >>> --- Tania Tudorache <[hidden email]>
> >>>      
> >> wrote:
> >>    
> >>>  
> >>>      
> >>>> Daniel,
> >>>>
> >>>> There are fixed versions of OWLViz available
> that
> >>>> work with GraphViz 2.22:
> >>>>
> >>>> Protege 3.4:
> >>>>
> >>>>    
> >>>>        
> >
>
http://protegewiki.stanford.edu/index.php/OWLViz_build_22
> >  
> >>>  
> >>>      
> >>>> Protege 4:
> >>>>
> >>>>    
> >>>>        
> >
>
http://protege.stanford.edu/plugins/protege4/org.coode.owlviz.jar

> >  
> >>>  
> >>>      
> >>>> Tania
> >>>>
> >>>> Daniel Schober wrote:
> >>>>    
> >>>>        
> >>>>> Dear OwlViz and OwlPropviz zards.
> >>>>> Currently OwlViz and the OwlPropViz (which I
> >>>>>          
> >> need)
> >>    
> >>>>>      
> >>>>>          
> >>>> don't work in P4 with
> >>>>    
> >>>>        
> >>>>> the latest GraphViz distribution.
> >>>>> I use win xp and the latest P4 download and
> the
> >>>>>      
> >>>>>          
>
=== 以下のメッセージは省略されました ===

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Re: owlviz plugin error due to graphviz ?

adborgman
In reply to this post by Tania Tudorache
Tania,

I downloaded and installed build 22 for Protege 3.4 (Win XP) and still encounter problems. Essentially, the UI seems unable to refresh the graph. To reproduce, open the example Pizza ontology included in the Protege install. Open the OWLViz tab using OWL->Preferences. Classify the taxonomy using the direct link to Pellet 1.5.2 reasoner. On the OWLViz tab, select the Inferred Model tab and the inferred hierarchy is missing. Select a class in the asserted hierarchy and the graph appears with links, but cannot be refreshed or modified. For example, I selected one of the subclasses in the graph and hit "Show Children" and got no response. Switched to view the Protege command window and there was no command shown after opening the OWLViz tab. When I switched back to the Protege window the UI did not refresh at all so I just had a gray box where the command window had been viewed. The only solution is to restart Protege (after ending it via Ctrl+C in the command window).

Any hints as to what might be wrong?

Thanks,
Alicia


Tania Tudorache wrote
Daniel,

There are fixed versions of OWLViz available that work with GraphViz 2.22:

Protege 3.4: http://protegewiki.stanford.edu/index.php/OWLViz_build_22
Protege 4: http://protege.stanford.edu/plugins/protege4/org.coode.owlviz.jar

Tania