having trouble with OWLViz

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having trouble with OWLViz

Elisabeth A. Immer
having trouble with OWLViz
all,

I'm running Protege beta 3.2 (build 311) with the default OWLViz tab.  Thanks to previous questions on the list, I successfully installed and configured my path to the GraphViz DOT application, but when I try to graph any OWL ontology, all the class ovals appear on top of each other and jammed almost beyond the top left corner of the display area.  Here's a tiny bit of a screen capture (assuming the list server will permit the image to go through) to show the effect:


  


I cannot grab or move the graph objects into the display area, and the exported image is (as you might expect) useless.  Any ideas on how to solve this problem?

many thanks for any info.
Lis Immer
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Trouble saving to owl file

JMiller

I am trying to save my data, loaded using the API, via the JenaOWLModel.save() method.  I am getting the error below.  I looked at the Protege-OWL source code, and it appears that it is trying to get a character at position 0, but I'm assuming that the input field is empty.  (Is there a legitimate case where this could happen?)

It is very possible that I have improperly saved something.  Can someone point me to an easy way to see the contents of my data model, while still in memory?  (The data model, viewed in a debugger, was not intuitive to me).

I am using Protege 3.2 beta build 318, OWL plugin version 2.2 build 311 (according to the GUI).


java.lang.StringIndexOutOfBoundsException: String index out of range: 0
        at java.lang.String.charAt(String.java:558)
        at edu.stanford.smi.protegex.owl.model.impl.AbstractOWLModel.isAnonymousResourceName(Unknown Source)
        at edu.stanford.smi.protegex.owl.model.impl.DefaultRDFIndividual.isAnonymous(Unknown Source)
        at edu.stanford.smi.protegex.owl.jena.protege2jena.Protege2Jena.getResource(Unknown Source)
        at edu.stanford.smi.protegex.owl.jena.protege2jena.Protege2Jena.createStatement(Unknown Source)
        at edu.stanford.smi.protegex.owl.jena.protege2jena.Protege2Jena.copyTriples(Unknown Source)
        at edu.stanford.smi.protegex.owl.jena.protege2jena.Protege2Jena.fillModels(Unknown Source)
        at edu.stanford.smi.protegex.owl.jena.protege2jena.Protege2Jena.<init>(Unknown Source)
        at edu.stanford.smi.protegex.owl.jena.protege2jena.Protege2Jena.createOntModel(Unknown Source)
        at edu.stanford.smi.protegex.owl.jena.protege2jena.Protege2Jena.createOntModel(Unknown Source)
        at edu.stanford.smi.protegex.owl.jena.protege2jena.Protege2Jena.saveAll(Unknown Source)
        at edu.stanford.smi.protegex.owl.jena.JenaOWLModel.save(Unknown Source)
        at com.rtn.dhs.km.protege.wrapper.DataModel.save(DataModel.java:51)
        at com.rtn.dhs.rpt.HtmlParser.updateKM(HtmlParser.java:307)
        at com.rtn.dhs.rpt.HtmlParser.<init>(HtmlParser.java:89)
        at com.rtn.dhs.rpt.HtmlParserTest.testParser(HtmlParserTest.java:15)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at junit.framework.TestCase.runTest(TestCase.java:154)
        at junit.framework.TestCase.runBare(TestCase.java:127)
        at junit.framework.TestResult$1.protect(TestResult.java:106)
        at junit.framework.TestResult.runProtected(TestResult.java:124)
        at junit.framework.TestResult.run(TestResult.java:109)
        at junit.framework.TestCase.run(TestCase.java:118)
        at junit.framework.TestSuite.runTest(TestSuite.java:208)
        at junit.framework.TestSuite.run(TestSuite.java:203)
        at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:478)
        at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:344)
        at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:196)
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Re: Trouble saving to owl file

Nick Drummond
James,

Did you create the model initially using the GUI or programmatically?
Does it save using the GUI? DON'T save over the top of it just in case.

Could you send me a copy of your ontology??

Nick

James A Miller wrote:

>
> I am trying to save my data, loaded using the API, via the
> JenaOWLModel.save() method.  I am getting the error below.  I looked
> at the Protege-OWL source code, and it appears that it is trying to
> get a character at position 0, but I'm assuming that the input field
> is empty.  (Is there a legitimate case where this could happen?)
>
> It is very possible that I have improperly saved something.  Can
> someone point me to an easy way to see the contents of my data model,
> while still in memory?  (The data model, viewed in a debugger, was not
> intuitive to me).
>
> I am using Protege 3.2 beta build 318, OWL plugin version 2.2 build
> 311 (according to the GUI).
>
>
> _java.lang.StringIndexOutOfBoundsException_: String index out of range: 0
>         at java.lang.String.charAt(_String.java:558_)
>         at
> edu.stanford.smi.protegex.owl.model.impl.AbstractOWLModel.isAnonymousResourceName(Unknown
> Source)
>         at
> edu.stanford.smi.protegex.owl.model.impl.DefaultRDFIndividual.isAnonymous(Unknown
> Source)
>         at
> edu.stanford.smi.protegex.owl.jena.protege2jena.Protege2Jena.getResource(Unknown
> Source)
>         at
> edu.stanford.smi.protegex.owl.jena.protege2jena.Protege2Jena.createStatement(Unknown
> Source)
>         at
> edu.stanford.smi.protegex.owl.jena.protege2jena.Protege2Jena.copyTriples(Unknown
> Source)
>         at
> edu.stanford.smi.protegex.owl.jena.protege2jena.Protege2Jena.fillModels(Unknown
> Source)
>         at
> edu.stanford.smi.protegex.owl.jena.protege2jena.Protege2Jena.<init>(Unknown
> Source)
>         at
> edu.stanford.smi.protegex.owl.jena.protege2jena.Protege2Jena.createOntModel(Unknown
> Source)
>         at
> edu.stanford.smi.protegex.owl.jena.protege2jena.Protege2Jena.createOntModel(Unknown
> Source)
>         at
> edu.stanford.smi.protegex.owl.jena.protege2jena.Protege2Jena.saveAll(Unknown
> Source)
>         at
> edu.stanford.smi.protegex.owl.jena.JenaOWLModel.save(Unknown Source)
>         at
> com.rtn.dhs.km.protege.wrapper.DataModel.save(_DataModel.java:51_)
>         at com.rtn.dhs.rpt.HtmlParser.updateKM(_HtmlParser.java:307_)
>         at com.rtn.dhs.rpt.HtmlParser.<init>(_HtmlParser.java:89_)
>         at
> com.rtn.dhs.rpt.HtmlParserTest.testParser(_HtmlParserTest.java:15_)
>         at sun.reflect.NativeMethodAccessorImpl.invoke0(_Native Method_)
>         at
> sun.reflect.NativeMethodAccessorImpl.invoke(_NativeMethodAccessorImpl.java:39_)
>
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(_DelegatingMethodAccessorImpl.java:25_)
>
>         at java.lang.reflect.Method.invoke(_Method.java:585_)
>         at junit.framework.TestCase.runTest(_TestCase.java:154_)
>         at junit.framework.TestCase.runBare(_TestCase.java:127_)
>         at junit.framework.TestResult$1.protect(_TestResult.java:106_)
>         at junit.framework.TestResult.runProtected(_TestResult.java:124_)
>         at junit.framework.TestResult.run(_TestResult.java:109_)
>         at junit.framework.TestCase.run(_TestCase.java:118_)
>         at junit.framework.TestSuite.runTest(_TestSuite.java:208_)
>         at junit.framework.TestSuite.run(_TestSuite.java:203_)
>         at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(_RemoteTestRunner.java:478_)
>
>         at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(_RemoteTestRunner.java:344_)
>
>         at
> org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(_RemoteTestRunner.java:196_)


--

Nick Drummond

http://www.cs.man.ac.uk/~drummond/ <http://www.cs.man.ac.uk/%7Edrummond/>
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Re: having trouble with OWLViz

Nick Drummond
In reply to this post by Elisabeth A. Immer
Lis,

Is this still a problem?

Nick

Elisabeth A. Immer wrote:

> all,
>
> I'm running Protege beta 3.2 (build 311) with the default OWLViz tab.  
> Thanks to previous questions on the list, I successfully installed and
> configured my path to the GraphViz DOT application, but when I try to
> graph any OWL ontology, all the class ovals appear on top of each
> other and jammed almost beyond the top left corner of the display
> area.  Here's a tiny bit of a screen capture (assuming the list server
> will permit the image to go through) to show the effect:
>
>
>  
>
>
> I cannot grab or move the graph objects into the display area, and the
> exported image is (as you might expect) useless.  Any ideas on how to
> solve this problem?
>
> many thanks for any info.
> Lis Immer

--

Nick Drummond

http://www.cs.man.ac.uk/~drummond/ <http://www.cs.man.ac.uk/%7Edrummond/>
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[protege-owl] Re: having trouble with OWLViz

Elisabeth A. Immer
yes it is.  Since posting that message, I've tried:

1. upgrading to Protege beta 3.2 build 318
2. upgrading to the latest Java (J2SE 5.0 Release 4 on Mac OS X 10.4)
3. displaying some known ontologies (e.g. pizza)

no joy.  I'm still guessing it's a configuration/version issue, but
haven't had the time to pursue it further.

>Lis,
>
>Is this still a problem?
>
>Nick
>
>Elisabeth A. Immer wrote:
>>all,
>>
>>I'm running Protege beta 3.2 (build 311) with the default OWLViz
>>tab.  Thanks to previous questions on the list, I successfully
>>installed and configured my path to the GraphViz DOT application,
>>but when I try to graph any OWL ontology, all the class ovals
>>appear on top of each other and jammed almost beyond the top left
>>corner of the display area.  Here's a tiny bit of a screen capture
>>(assuming the list server will permit the image to go through) to
>>show the effect:
>>
>>
>>
>>
>>I cannot grab or move the graph objects into the display area, and
>>the exported image is (as you might expect) useless.  Any ideas on
>>how to solve this problem?
>>
>>many thanks for any info.
>>Lis Immer
>
>--
>
>Nick Drummond
>
>http://www.cs.man.ac.uk/~drummond/ <http://www.cs.man.ac.uk/%7Edrummond/>
>-------------------------------------------------------------------------
>To unsubscribe go to http://protege.stanford.edu/community/subscribe.html


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[protege-owl] Re: having trouble with OWLViz

Doug Holmes
Elisabeth,
        This behavior is almost certainly a class path error.  On a Mac, the  
dot file is "within" the Graphviz.app file; the following works for  
me: DotApplicationPath=/Applications/ATT/Graphviz.app/Contents/MacOS/
dot [you may have to type that in, rather than navigating to it...
Doug
On May 24, 2006, at 9:22 AM, Elisabeth A. Immer wrote:

> yes it is.  Since posting that message, I've tried:
>
> 1. upgrading to Protege beta 3.2 build 318
> 2. upgrading to the latest Java (J2SE 5.0 Release 4 on Mac OS X 10.4)
> 3. displaying some known ontologies (e.g. pizza)
>
> no joy.  I'm still guessing it's a configuration/version issue, but  
> haven't had the time to pursue it further.
>
>> Lis,
>>
>> Is this still a problem?
>>
>> Nick
>>
>> Elisabeth A. Immer wrote:
>>> all,
>>>
>>> I'm running Protege beta 3.2 (build 311) with the default OWLViz  
>>> tab.  Thanks to previous questions on the list, I successfully  
>>> installed and configured my path to the GraphViz DOT application,  
>>> but when I try to graph any OWL ontology, all the class ovals  
>>> appear on top of each other and jammed almost beyond the top left  
>>> corner of the display area.  Here's a tiny bit of a screen  
>>> capture (assuming the list server will permit the image to go  
>>> through) to show the effect:
>>>
>>>
>>>
>>>
>>> I cannot grab or move the graph objects into the display area,  
>>> and the exported image is (as you might expect) useless.  Any  
>>> ideas on how to solve this problem?
>>>
>>> many thanks for any info.
>>> Lis Immer
>>
>> --
>>
>> Nick Drummond
>>
>> http://www.cs.man.ac.uk/~drummond/ <<a href="http://www.cs.man.ac.uk/%">http://www.cs.man.ac.uk/% 
>> 7Edrummond/>
>> ---------------------------------------------------------------------
>> ----
>> To unsubscribe go to http://protege.stanford.edu/community/ 
>> subscribe.html
>
>
> ----------------------------------------------------------------------
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> To unsubscribe go to http://protege.stanford.edu/community/ 
> subscribe.html
>
>

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