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[protege-discussion] [Dear Timothy] Re: C#, OWL & SAVE ISSUE!

Timothy Redmond tredmond at stanford.edu
Mon Aug 24 08:46:19 PDT 2009


>  don't want to use the "jenaOWLModel.save(…)" that ships with  
> Protégé 4 because it is causing problems. How to get around this?!

I don't understand what problems these are exactly.  You said before  
that

>  jenaOWLModel.save(…)
>
> Here when everything got worse, I needed to transfer the new library  
> ( protégé-owl )  which contains the JenaOWLModel so I get the save  
> command while I should still keep working with the old one (Jena  
> Ontology) because the JenaOWLModel.save takes the OntModel as one of  
> it argurments to save the ontology...
>

This I didn't understand at all.  First, the save method only requires  
a URI.  Second I didn't really understand the new and old library  
issue.  If you get the protege owl jars then you will see both the  
jena libraries and the protege owl libraries.

-TImothy


On Aug 22, 2009, at 1:07 AM, Alaa Tadmori wrote:

> Dear Timothy,
> thank you for replying back. Your message cleared out many issues  
> for me.
>
> When I used to work with the library that ships with Protégé 3  
> everything was working just fine, I only had a problem saving the  
> ontology. How can I save the ontology using this library? (There is  
> no "save" command on it; “write” command is only writing the  
> original model I read from a URL, it isn’t saving any of the new  
> classes & individuals I add). I don't want to use the  
> "jenaOWLModel.save(…)" that ships with Protégé 4 because it is  
> causing problems. How to get around this?!!
>
> Thank you in advance for your time & effort.
> Best regards
>
>
>
> From: Timothy Redmond <tredmond at stanford.edu>
> To: User support for Core Protege and the Protege-Frames editor <protege-discussion at lists.stanford.edu 
> >
> Sent: Friday, August 21, 2009 12:25:34 AM
> Subject: Re: [protege-discussion] C#, OWL & SAVE ISSUE!
>
>
> I am not expert on C#/Java integration but I do understand some  
> things about Protege and Java.
> > Here when everything got worse, I needed to transfer the new  
> library ( protégé-owl )  which contains the JenaOWLModel so I get  
> the save command while I should still keep working with the old one  
> (Jena Ontology) because the JenaOWLModel.save takes the OntModel as  
> one of it argurments to save the ontology...
> >
> If you get a Protege distribution then you should include the  
> protege.jar and all the jars found in the  
> edu.stanford.smi.protegex.owl plugin directory. In particular this  
> includes the jena library.
>
> > 2..      Import the Protégé-owl library and keep the old one; I am  
> getting coflict between the tow libraries.. (ex: Interface Statement  
> exists in both edu.stanford.smi.protegex.owl.jena  
> &com.hp.hpl.jena.ontology)
>
> This is not a conflict.  If the package is different then they are  
> different classes.  I don't know whether there will be any c#/Java  
> integration problems with this.
>
> > 3.      Work only with Protégé-owl library (this seems to be  
> perfect soultion, but unfortuantely I getting this error:
> >  
> org 
> .apache 
> .xerces 
> .parsers 
> .SAXParser 
> .<init>(Lorg.apache.xerces.xni.parser.XMLParserConfiguration;)V
> > Description: An unhandled exception occurred during the execution  
> of the current web request. Please review the stack trace for more  
> information about the error and where it originated in the code.
> >
>
> You are missing the xml-apis.jar and xerces.jar files that can be  
> found in the owl plugin directory of a distribution.
>
> >  (I also tried protégé 4 API found in this page http://protege.stanford.edu/download/protege/4.0/zip/?C=N;O=D 
>  Is this what i need?!). I do the transfer using “ikvm-0.34.0.2”.
> >
>
> Protege 4 uses an entirely different owl api than Protege 3.
>
> -Timothy
>
>
> On Aug 20, 2009, at 12:48 AM, Alaa Tadmori wrote:
>
> > Hello everyone,
> >
> > I am an asp.net developer; I have been trying to use the Jena  
> library to make a use of Semantic Web. As you know, Jena is Java  
> based (I don’t know much JavaL) so I tried to transfer the library  
> to C# to be able to work against it using asp.net. Everything was  
> going just fine, I was able to programmatically input the ontology,  
> add, edit & delete new classes & instances & query it. Almost in the  
> end, as expected, I needed a way to save the in-memory ontology I  
> have created or modified, I tried:
> >
> > ontModel.writeAll(outputStream, null, null) (with all its  
> vairations) But it didn’t work out.
> >
> > When I checked your mainling list I found that many people are  
> asking this question, like how to save the ontology or how to save  
> the inferred statements, the answer was to use
> >
> >  jenaOWLModel.save(…)
> >
> > Here when everything got worse, I needed to transfer the new  
> library ( protégé-owl )  which contains the JenaOWLModel so I get  
> the save command while I should still keep working with the old one  
> (Jena Ontology) because the JenaOWLModel..save takes the OntModel as  
> one of it argurments to save the ontology...
> >
> > The problem is that when I transfered both of the libraries and  
> imported them to Visual Studio they seem to conflict with each  
> other. To cut it short (I’m sorry that it is already long) these  
> were my unsuccessful solutions:
> >
> > 1.      Use ontModel.writeAll(…) Doesn’t save any new additions in  
> case I upload the ontology from a URI, it only writes the model  
> itself.
> > 2.      Import the Protégé-owl library and keep the old one; I am  
> getting coflict between the tow libraries.. (ex: Interface Statement  
> exists in both edu.stanford.smi.protegex.owl.jena  
> &com.hp.hpl.jena.ontology)
> >
> >
> > 3.      Work only with Protégé-owl library (this seems to be  
> perfect soultion, but unfortuantely I getting this error:
> >  
> org 
> .apache 
> .xerces 
> .parsers 
> .SAXParser 
> .<init>(Lorg.apache.xerces.xni.parser.XMLParserConfiguration;)V
> > Description: An unhandled exception occurred during the execution  
> of the current web request. Please review the stack trace for more  
> information about the error and where it originated in the code.
> >
> > Exception Details: java.lang.NoSuchMethodError:  
> org 
> .apache 
> .xerces 
> .parsers 
> .SAXParser 
> .<init>(Lorg.apache.xerces.xni.parser.XMLParserConfiguration;)V
> > Source Error:
> > Line 23:    public static void GetModel(string filePath)
> > Line 24:    {
> > Line 25:            model = ModelFactory.createOntologyModel();
> > Line 26:
> > Line 27:            inputstream = FileManager.get().open(filePath);
> > (This error drove me crazy, please Java foxes what is this:
> > java.lang.NoSuchMethodError:  
> org 
> .apache 
> .xerces 
> .parsers 
> .SAXParser 
> .<init>(Lorg.apache.xerces.xni.parser.XMLParserConfiguration;)V
> >
> >
> > An important thing to mention is that I’m transferring the library  
> of Jena Ontology using the zip file that contains all the jar files  
> of the API but for the protégé-owl I coun’t find such a thing, I  
> transferred the library using the jar files I found in the  
> Protege_3.3.1\plugins folder (I also tried protégé 4 API found in  
> this page http://protege.stanford.edu/download/protege/4.0/zip/?C=N;O=D 
>  Is this what i need?!). I do the transfer using “ikvm-0.34.0.2”.
> >
> > So this is my problem which I’m trying to solve for over than 3  
> weaks, more than 7 hours a day. I hope you have a solution or any  
> recommendation on how to solve this tricky problem.
> >
> > I appreciate your patience, thank you so much for your cooperation.
> >
> >
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