Save ontology in RDF/XML syntax

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Save ontology in RDF/XML syntax

QHReul
As part of Protege 5.0.0 RC1 onward, I encounter issues trying to save an ontology in the RDF/XML syntax. More specifically, Protege returns a OWLOntologyStorageException when trying to save a modified ontology in the format; e.g.:
org.semanticweb.owlapi.model.OWLOntologyStorageException: java.io.IOException: XML literal is not self contained: ""
        at org.semanticweb.owlapi.rdf.rdfxml.renderer.RDFXMLStorer.storeOntology(RDFXMLStorer.java:61)
        at org.semanticweb.owlapi.util.AbstractOWLStorer.store(AbstractOWLStorer.java:99)
        at org.semanticweb.owlapi.util.AbstractOWLStorer.storeOntology(AbstractOWLStorer.java:64)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.saveOntology(OWLOntologyManagerImpl.java:1217)
        at org.stanford.ncbo.oapiwrapper.OntologyParser.serializeOntology(OntologyParser.java:673)
        at org.stanford.ncbo.oapiwrapper.OntologyParser.internalParse(OntologyParser.java:656)
        at org.stanford.ncbo.oapiwrapper.OntologyParser.parse(OntologyParser.java:624)

After looking on the web, it seems that the issue may be related to issue #495 [1] and #509 [2] in the OWLAPI, which has been addressed in version 4.2.1 of the API. Can you confirm that Protege is using the OWLAPI with the correct fix?

Kind regards,

Quentin Reul

[1] https://github.com/owlcs/owlapi/issues/495
[2] https://github.com/owlcs/owlapi/issues/509
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Re: Save ontology in RDF/XML syntax

Matthew Horridge-2
Administrator
Hi Quentin,

Protege 5.0.0 uses version 4.2.5 of the OWL API.

Cheers,

Matthew



> On 1 Jun 2016, at 10:21, QHReul <[hidden email]> wrote:
>
> As part of Protege 5.0.0 RC1 onward, I encounter issues trying to save an
> ontology in the RDF/XML syntax. More specifically, Protege returns a
> OWLOntologyStorageException when trying to save a modified ontology in the
> format; e.g.:
>
>
> After looking on the web, it seems that the issue may be related to issue
> #495 [1] and #509 [2] in the OWLAPI, which has been addressed in version
> 4.2.1 of the API. Can you confirm that Protege is using the OWLAPI with the
> correct fix?
>
> Kind regards,
>
> Quentin Reul
>
> [1] https://github.com/owlcs/owlapi/issues/495
> [2] https://github.com/owlcs/owlapi/issues/509
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Save-ontology-in-RDF-XML-syntax-tp4665482.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Save ontology in RDF/XML syntax

QHReul
Hi Matthew,

Thanks for the clarification. However, it seems that the issue is not resolved in Protege. Were you able to replicate the issue?

Kind regards,

Quentin Reul

On 1 June 2016 at 13:01, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

Protege 5.0.0 uses version 4.2.5 of the OWL API.

Cheers,

Matthew



> On 1 Jun 2016, at 10:21, QHReul <[hidden email]> wrote:
>
> As part of Protege 5.0.0 RC1 onward, I encounter issues trying to save an
> ontology in the RDF/XML syntax. More specifically, Protege returns a
> OWLOntologyStorageException when trying to save a modified ontology in the
> format; e.g.:
>
>
> After looking on the web, it seems that the issue may be related to issue
> #495 [1] and #509 [2] in the OWLAPI, which has been addressed in version
> 4.2.1 of the API. Can you confirm that Protege is using the OWLAPI with the
> correct fix?
>
> Kind regards,
>
> Quentin Reul
>
> [1] https://github.com/owlcs/owlapi/issues/495
> [2] https://github.com/owlcs/owlapi/issues/509
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Save-ontology-in-RDF-XML-syntax-tp4665482.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
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https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Save ontology in RDF/XML syntax

Matthew Horridge-2
Administrator
Hi Quentin,

It works for me.  I can save and reload.

What version of Protege are you using exactly?  Is it the release version?

Cheers,

Matthew



On 1 Jun 2016, at 11:07, Quentin Reul <[hidden email]> wrote:

Hi Matthew,

Thanks for the clarification. However, it seems that the issue is not resolved in Protege. Were you able to replicate the issue?

Kind regards,

Quentin Reul

On 1 June 2016 at 13:01, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

Protege 5.0.0 uses version 4.2.5 of the OWL API.

Cheers,

Matthew



> On 1 Jun 2016, at 10:21, QHReul <[hidden email]> wrote:
>
> As part of Protege 5.0.0 RC1 onward, I encounter issues trying to save an
> ontology in the RDF/XML syntax. More specifically, Protege returns a
> OWLOntologyStorageException when trying to save a modified ontology in the
> format; e.g.:
>
>
> After looking on the web, it seems that the issue may be related to issue
> #495 [1] and #509 [2] in the OWLAPI, which has been addressed in version
> 4.2.1 of the API. Can you confirm that Protege is using the OWLAPI with the
> correct fix?
>
> Kind regards,
>
> Quentin Reul
>
> [1] https://github.com/owlcs/owlapi/issues/495
> [2] https://github.com/owlcs/owlapi/issues/509
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Save-ontology-in-RDF-XML-syntax-tp4665482.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
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https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Save ontology in RDF/XML syntax

QHReul
Hi Matthew,

I have encountered the issue with Protege 5.0.0 RC1 and Protege 5.0.0. I had to revert to Protege 5.0.0 beta 17 to be able to save an existing RDF/XML ontology in that format.

Kind regards,

Quentin 

On 1 June 2016 at 13:10, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

It works for me.  I can save and reload.

What version of Protege are you using exactly?  Is it the release version?

Cheers,

Matthew



On 1 Jun 2016, at 11:07, Quentin Reul <[hidden email]> wrote:

Hi Matthew,

Thanks for the clarification. However, it seems that the issue is not resolved in Protege. Were you able to replicate the issue?

Kind regards,

Quentin Reul

On 1 June 2016 at 13:01, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

Protege 5.0.0 uses version 4.2.5 of the OWL API.

Cheers,

Matthew



> On 1 Jun 2016, at 10:21, QHReul <[hidden email]> wrote:
>
> As part of Protege 5.0.0 RC1 onward, I encounter issues trying to save an
> ontology in the RDF/XML syntax. More specifically, Protege returns a
> OWLOntologyStorageException when trying to save a modified ontology in the
> format; e.g.:
>
>
> After looking on the web, it seems that the issue may be related to issue
> #495 [1] and #509 [2] in the OWLAPI, which has been addressed in version
> 4.2.1 of the API. Can you confirm that Protege is using the OWLAPI with the
> correct fix?
>
> Kind regards,
>
> Quentin Reul
>
> [1] https://github.com/owlcs/owlapi/issues/495
> [2] https://github.com/owlcs/owlapi/issues/509
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Save-ontology-in-RDF-XML-syntax-tp4665482.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user



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Re: Save ontology in RDF/XML syntax

Matthew Horridge-2
Administrator
Hi Quentin,

Please could you post your ontology to the list (or a sample of it that exhibits the behaviour)?

Cheers,

Matthew



On 1 Jun 2016, at 11:28, Quentin Reul <[hidden email]> wrote:

Hi Matthew,

I have encountered the issue with Protege 5.0.0 RC1 and Protege 5.0.0. I had to revert to Protege 5.0.0 beta 17 to be able to save an existing RDF/XML ontology in that format.

Kind regards,

Quentin 

On 1 June 2016 at 13:10, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

It works for me.  I can save and reload.

What version of Protege are you using exactly?  Is it the release version?

Cheers,

Matthew



On 1 Jun 2016, at 11:07, Quentin Reul <[hidden email]> wrote:

Hi Matthew,

Thanks for the clarification. However, it seems that the issue is not resolved in Protege. Were you able to replicate the issue?

Kind regards,

Quentin Reul

On 1 June 2016 at 13:01, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

Protege 5.0.0 uses version 4.2.5 of the OWL API.

Cheers,

Matthew



> On 1 Jun 2016, at 10:21, QHReul <[hidden email]> wrote:
>
> As part of Protege 5.0.0 RC1 onward, I encounter issues trying to save an
> ontology in the RDF/XML syntax. More specifically, Protege returns a
> OWLOntologyStorageException when trying to save a modified ontology in the
> format; e.g.:
>
>
> After looking on the web, it seems that the issue may be related to issue
> #495 [1] and #509 [2] in the OWLAPI, which has been addressed in version
> 4.2.1 of the API. Can you confirm that Protege is using the OWLAPI with the
> correct fix?
>
> Kind regards,
>
> Quentin Reul
>
> [1] https://github.com/owlcs/owlapi/issues/495
> [2] https://github.com/owlcs/owlapi/issues/509
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Save-ontology-in-RDF-XML-syntax-tp4665482.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
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Re: Save ontology in RDF/XML syntax

QHReul
Hi Matthew,

I was able to reproduce the issue in Protege 5.0.0 by performing the following steps:
- Open Protege 5.0.0
- Add new rdfs:comment annotation with Type = rdf:XMLLiteral
- Save ontology in RDF/XML syntax
When performing these steps, I encounter a OWLOntologyStorageException (see attached stacktrace).

Kind regards,

Quentin

On 1 June 2016 at 14:59, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

Please could you post your ontology to the list (or a sample of it that exhibits the behaviour)?

Cheers,

Matthew



On 1 Jun 2016, at 11:28, Quentin Reul <[hidden email]> wrote:

Hi Matthew,

I have encountered the issue with Protege 5.0.0 RC1 and Protege 5.0.0. I had to revert to Protege 5.0.0 beta 17 to be able to save an existing RDF/XML ontology in that format.

Kind regards,

Quentin 

On 1 June 2016 at 13:10, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

It works for me.  I can save and reload.

What version of Protege are you using exactly?  Is it the release version?

Cheers,

Matthew



On 1 Jun 2016, at 11:07, Quentin Reul <[hidden email]> wrote:

Hi Matthew,

Thanks for the clarification. However, it seems that the issue is not resolved in Protege. Were you able to replicate the issue?

Kind regards,

Quentin Reul

On 1 June 2016 at 13:01, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

Protege 5.0.0 uses version 4.2.5 of the OWL API.

Cheers,

Matthew



> On 1 Jun 2016, at 10:21, QHReul <[hidden email]> wrote:
>
> As part of Protege 5.0.0 RC1 onward, I encounter issues trying to save an
> ontology in the RDF/XML syntax. More specifically, Protege returns a
> OWLOntologyStorageException when trying to save a modified ontology in the
> format; e.g.:
>
>
> After looking on the web, it seems that the issue may be related to issue
> #495 [1] and #509 [2] in the OWLAPI, which has been addressed in version
> 4.2.1 of the API. Can you confirm that Protege is using the OWLAPI with the
> correct fix?
>
> Kind regards,
>
> Quentin Reul
>
> [1] https://github.com/owlcs/owlapi/issues/495
> [2] https://github.com/owlcs/owlapi/issues/509
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Save-ontology-in-RDF-XML-syntax-tp4665482.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user



_______________________________________________
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Protege5_stacktrace.txt (10K) Download Attachment
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Re: Save ontology in RDF/XML syntax

Matthew Horridge-2
Administrator
Hi Quentin,

Thanks for this description.  

The value of the literal needs to be valid XML. i.e.

"<test>Hello World</test>"

works, but

“Hello World”

does not.

Cheers,

Matthew



On 1 Jun 2016, at 13:38, Quentin Reul <[hidden email]> wrote:

Hi Matthew,

I was able to reproduce the issue in Protege 5.0.0 by performing the following steps:
- Open Protege 5.0.0
- Add new rdfs:comment annotation with Type = rdf:XMLLiteral
- Save ontology in RDF/XML syntax
When performing these steps, I encounter a OWLOntologyStorageException (see attached stacktrace).

Kind regards,

Quentin

On 1 June 2016 at 14:59, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

Please could you post your ontology to the list (or a sample of it that exhibits the behaviour)?

Cheers,

Matthew



On 1 Jun 2016, at 11:28, Quentin Reul <[hidden email]> wrote:

Hi Matthew,

I have encountered the issue with Protege 5.0.0 RC1 and Protege 5.0.0. I had to revert to Protege 5.0.0 beta 17 to be able to save an existing RDF/XML ontology in that format.

Kind regards,

Quentin 

On 1 June 2016 at 13:10, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

It works for me.  I can save and reload.

What version of Protege are you using exactly?  Is it the release version?

Cheers,

Matthew



On 1 Jun 2016, at 11:07, Quentin Reul <[hidden email]> wrote:

Hi Matthew,

Thanks for the clarification. However, it seems that the issue is not resolved in Protege. Were you able to replicate the issue?

Kind regards,

Quentin Reul

On 1 June 2016 at 13:01, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

Protege 5.0.0 uses version 4.2.5 of the OWL API.

Cheers,

Matthew



> On 1 Jun 2016, at 10:21, QHReul <[hidden email]> wrote:
>
> As part of Protege 5.0.0 RC1 onward, I encounter issues trying to save an
> ontology in the RDF/XML syntax. More specifically, Protege returns a
> OWLOntologyStorageException when trying to save a modified ontology in the
> format; e.g.:
>
>
> After looking on the web, it seems that the issue may be related to issue
> #495 [1] and #509 [2] in the OWLAPI, which has been addressed in version
> 4.2.1 of the API. Can you confirm that Protege is using the OWLAPI with the
> correct fix?
>
> Kind regards,
>
> Quentin Reul
>
> [1] https://github.com/owlcs/owlapi/issues/495
> [2] https://github.com/owlcs/owlapi/issues/509
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Save-ontology-in-RDF-XML-syntax-tp4665482.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


<Protege5_stacktrace.txt>_______________________________________________
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Re: Save ontology in RDF/XML syntax

QHReul
Hi Matthew,

I have never had any issues with not including starting tags before the new release version. It seems to be a very strict constraint to implement...

Cheers,

Quentin

On 1 June 2016 at 15:53, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

Thanks for this description.  

The value of the literal needs to be valid XML. i.e.

"<test>Hello World</test>"

works, but

“Hello World”

does not.

Cheers,

Matthew



On 1 Jun 2016, at 13:38, Quentin Reul <[hidden email]> wrote:

Hi Matthew,

I was able to reproduce the issue in Protege 5.0.0 by performing the following steps:
- Open Protege 5.0.0
- Add new rdfs:comment annotation with Type = rdf:XMLLiteral
- Save ontology in RDF/XML syntax
When performing these steps, I encounter a OWLOntologyStorageException (see attached stacktrace).

Kind regards,

Quentin

On 1 June 2016 at 14:59, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

Please could you post your ontology to the list (or a sample of it that exhibits the behaviour)?

Cheers,

Matthew



On 1 Jun 2016, at 11:28, Quentin Reul <[hidden email]> wrote:

Hi Matthew,

I have encountered the issue with Protege 5.0.0 RC1 and Protege 5.0.0. I had to revert to Protege 5.0.0 beta 17 to be able to save an existing RDF/XML ontology in that format.

Kind regards,

Quentin 

On 1 June 2016 at 13:10, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

It works for me.  I can save and reload.

What version of Protege are you using exactly?  Is it the release version?

Cheers,

Matthew



On 1 Jun 2016, at 11:07, Quentin Reul <[hidden email]> wrote:

Hi Matthew,

Thanks for the clarification. However, it seems that the issue is not resolved in Protege. Were you able to replicate the issue?

Kind regards,

Quentin Reul

On 1 June 2016 at 13:01, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

Protege 5.0.0 uses version 4.2.5 of the OWL API.

Cheers,

Matthew



> On 1 Jun 2016, at 10:21, QHReul <[hidden email]> wrote:
>
> As part of Protege 5.0.0 RC1 onward, I encounter issues trying to save an
> ontology in the RDF/XML syntax. More specifically, Protege returns a
> OWLOntologyStorageException when trying to save a modified ontology in the
> format; e.g.:
>
>
> After looking on the web, it seems that the issue may be related to issue
> #495 [1] and #509 [2] in the OWLAPI, which has been addressed in version
> 4.2.1 of the API. Can you confirm that Protege is using the OWLAPI with the
> correct fix?
>
> Kind regards,
>
> Quentin Reul
>
> [1] https://github.com/owlcs/owlapi/issues/495
> [2] https://github.com/owlcs/owlapi/issues/509
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Save-ontology-in-RDF-XML-syntax-tp4665482.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


<Protege5_stacktrace.txt>_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user



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Re: Save ontology in RDF/XML syntax

Matthew Horridge-2
Administrator
Hi Quentin,

The change is due to recent changes in the OWL API.  It turns out that the OWL API was previously too lax about this.  Apparently, XML literals must be self contained XML fragments.

Cheers,

Matthew


On 1 Jun 2016, at 14:00, Quentin Reul <[hidden email]> wrote:

Hi Matthew,

I have never had any issues with not including starting tags before the new release version. It seems to be a very strict constraint to implement...

Cheers,

Quentin

On 1 June 2016 at 15:53, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

Thanks for this description.  

The value of the literal needs to be valid XML. i.e.

"<test>Hello World</test>"

works, but

“Hello World”

does not.

Cheers,

Matthew



On 1 Jun 2016, at 13:38, Quentin Reul <[hidden email]> wrote:

Hi Matthew,

I was able to reproduce the issue in Protege 5.0.0 by performing the following steps:
- Open Protege 5.0.0
- Add new rdfs:comment annotation with Type = rdf:XMLLiteral
- Save ontology in RDF/XML syntax
When performing these steps, I encounter a OWLOntologyStorageException (see attached stacktrace).

Kind regards,

Quentin

On 1 June 2016 at 14:59, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

Please could you post your ontology to the list (or a sample of it that exhibits the behaviour)?

Cheers,

Matthew



On 1 Jun 2016, at 11:28, Quentin Reul <[hidden email]> wrote:

Hi Matthew,

I have encountered the issue with Protege 5.0.0 RC1 and Protege 5.0.0. I had to revert to Protege 5.0.0 beta 17 to be able to save an existing RDF/XML ontology in that format.

Kind regards,

Quentin 

On 1 June 2016 at 13:10, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

It works for me.  I can save and reload.

What version of Protege are you using exactly?  Is it the release version?

Cheers,

Matthew



On 1 Jun 2016, at 11:07, Quentin Reul <[hidden email]> wrote:

Hi Matthew,

Thanks for the clarification. However, it seems that the issue is not resolved in Protege. Were you able to replicate the issue?

Kind regards,

Quentin Reul

On 1 June 2016 at 13:01, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

Protege 5.0.0 uses version 4.2.5 of the OWL API.

Cheers,

Matthew



> On 1 Jun 2016, at 10:21, QHReul <[hidden email]> wrote:
>
> As part of Protege 5.0.0 RC1 onward, I encounter issues trying to save an
> ontology in the RDF/XML syntax. More specifically, Protege returns a
> OWLOntologyStorageException when trying to save a modified ontology in the
> format; e.g.:
>
>
> After looking on the web, it seems that the issue may be related to issue
> #495 [1] and #509 [2] in the OWLAPI, which has been addressed in version
> 4.2.1 of the API. Can you confirm that Protege is using the OWLAPI with the
> correct fix?
>
> Kind regards,
>
> Quentin Reul
>
> [1] https://github.com/owlcs/owlapi/issues/495
> [2] https://github.com/owlcs/owlapi/issues/509
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Save-ontology-in-RDF-XML-syntax-tp4665482.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Save ontology in RDF/XML syntax

Steve Wartik
In reply to this post by QHReul

Quentin,

 

1.      I agree it’s strict.

2.      I’m not sure that’s a bad thing.

3.      I do wish the error message was a little better.

 

Best Regards,

 

Steve Wartik

 

From: protege-user [mailto:[hidden email]] On Behalf Of Quentin Reul
Sent: Wednesday, June 01, 2016 5:00 PM
To: User support for WebProtege and Protege Desktop <[hidden email]>
Subject: Re: [protege-user] Save ontology in RDF/XML syntax

 

Hi Matthew,

 

I have never had any issues with not including starting tags before the new release version. It seems to be a very strict constraint to implement...

 

Cheers,

 

Quentin

 

On 1 June 2016 at 15:53, Matthew Horridge <[hidden email]> wrote:

Hi Quentin,

 

Thanks for this description.  

 

The value of the literal needs to be valid XML. i.e.

 

"<test>Hello World</test>"

 

works, but

 

“Hello World”

 

does not.

 

Cheers,

 

Matthew

 

 

 

On 1 Jun 2016, at 13:38, Quentin Reul <[hidden email]> wrote:

 

Hi Matthew,

 

I was able to reproduce the issue in Protege 5.0.0 by performing the following steps:

- Open Protege 5.0.0

- Add new rdfs:comment annotation with Type = rdf:XMLLiteral

- Save ontology in RDF/XML syntax

When performing these steps, I encounter a OWLOntologyStorageException (see attached stacktrace).

 

Kind regards,

 

Quentin

 

On 1 June 2016 at 14:59, Matthew Horridge <[hidden email]> wrote:

Hi Quentin,

 

Please could you post your ontology to the list (or a sample of it that exhibits the behaviour)?

 

Cheers,

 

Matthew

 

 

 

On 1 Jun 2016, at 11:28, Quentin Reul <[hidden email]> wrote:

 

Hi Matthew,

 

I have encountered the issue with Protege 5.0.0 RC1 and Protege 5.0.0. I had to revert to Protege 5.0.0 beta 17 to be able to save an existing RDF/XML ontology in that format.

 

Kind regards,

 

Quentin 

 

On 1 June 2016 at 13:10, Matthew Horridge <[hidden email]> wrote:

Hi Quentin,

 

It works for me.  I can save and reload.

 

What version of Protege are you using exactly?  Is it the release version?

 

Cheers,

 

Matthew

 

 

 

On 1 Jun 2016, at 11:07, Quentin Reul <[hidden email]> wrote:

 

Hi Matthew,

 

Thanks for the clarification. However, it seems that the issue is not resolved in Protege. Were you able to replicate the issue?

 

Kind regards,

 

Quentin Reul

 

On 1 June 2016 at 13:01, Matthew Horridge <[hidden email]> wrote:

Hi Quentin,

Protege 5.0.0 uses version 4.2.5 of the OWL API.

Cheers,

Matthew



> On 1 Jun 2016, at 10:21, QHReul <[hidden email]> wrote:
>
> As part of Protege 5.0.0 RC1 onward, I encounter issues trying to save an
> ontology in the RDF/XML syntax. More specifically, Protege returns a
> OWLOntologyStorageException when trying to save a modified ontology in the
> format; e.g.:
>
>
> After looking on the web, it seems that the issue may be related to issue
> #495 [1] and #509 [2] in the OWLAPI, which has been addressed in version
> 4.2.1 of the API. Can you confirm that Protege is using the OWLAPI with the
> correct fix?
>
> Kind regards,
>
> Quentin Reul
>
> [1] https://github.com/owlcs/owlapi/issues/495
> [2] https://github.com/owlcs/owlapi/issues/509
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Save-ontology-in-RDF-XML-syntax-tp4665482.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Save ontology in RDF/XML syntax

Matthew Horridge-2
Administrator
I’ll file an issue for a better error message….

Cheers,

Matthew

On 1 Jun 2016, at 14:06, Wartik, Steven P Steve <[hidden email]> wrote:

Quentin,
 
1.      I agree it’s strict.
2.      I’m not sure that’s a bad thing.
3.      I do wish the error message was a little better.
 
Best Regards,
 
Steve Wartik
 
From: protege-user [[hidden email]] On Behalf Of Quentin Reul
Sent: Wednesday, June 01, 2016 5:00 PM
To: User support for WebProtege and Protege Desktop <[hidden email]>
Subject: Re: [protege-user] Save ontology in RDF/XML syntax
 
Hi Matthew,
 
I have never had any issues with not including starting tags before the new release version. It seems to be a very strict constraint to implement...
 
Cheers,
 
Quentin
 
On 1 June 2016 at 15:53, Matthew Horridge <[hidden email]> wrote:
Hi Quentin, 
 
Thanks for this description.  
 
The value of the literal needs to be valid XML. i.e.
 
"<test>Hello World</test>"
 
works, but
 
“Hello World”
 
does not.
 
Cheers,
 
Matthew
 
 
 
On 1 Jun 2016, at 13:38, Quentin Reul <[hidden email]> wrote:
 
Hi Matthew, 
 
I was able to reproduce the issue in Protege 5.0.0 by performing the following steps:
- Open Protege 5.0.0
- Add new rdfs:comment annotation with Type = rdf:XMLLiteral
- Save ontology in RDF/XML syntax
When performing these steps, I encounter a OWLOntologyStorageException (see attached stacktrace).
 
Kind regards,
 
Quentin
 
On 1 June 2016 at 14:59, Matthew Horridge <[hidden email]> wrote:
Hi Quentin, 
 
Please could you post your ontology to the list (or a sample of it that exhibits the behaviour)?
 
Cheers,
 
Matthew
 
 
 
On 1 Jun 2016, at 11:28, Quentin Reul <[hidden email]> wrote:
 
Hi Matthew, 
 
I have encountered the issue with Protege 5.0.0 RC1 and Protege 5.0.0. I had to revert to Protege 5.0.0 beta 17 to be able to save an existing RDF/XML ontology in that format.
 
Kind regards,
 
Quentin 
 
On 1 June 2016 at 13:10, Matthew Horridge <[hidden email]> wrote:
Hi Quentin, 
 
It works for me.  I can save and reload.
 
What version of Protege are you using exactly?  Is it the release version?
 
Cheers,
 
Matthew
 
 
 
On 1 Jun 2016, at 11:07, Quentin Reul <[hidden email]> wrote:
 
Hi Matthew, 
 
Thanks for the clarification. However, it seems that the issue is not resolved in Protege. Were you able to replicate the issue?
 
Kind regards,
 
Quentin Reul
 
On 1 June 2016 at 13:01, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

Protege 5.0.0 uses version 4.2.5 of the OWL API.

Cheers,

Matthew



> On 1 Jun 2016, at 10:21, QHReul <[hidden email]> wrote:
>
> As part of Protege 5.0.0 RC1 onward, I encounter issues trying to save an
> ontology in the RDF/XML syntax. More specifically, Protege returns a
> OWLOntologyStorageException when trying to save a modified ontology in the
> format; e.g.:
>
>
> After looking on the web, it seems that the issue may be related to issue
> #495 [1] and #509 [2] in the OWLAPI, which has been addressed in version
> 4.2.1 of the API. Can you confirm that Protege is using the OWLAPI with the
> correct fix?
>
> Kind regards,
>
> Quentin Reul
>
> [1] https://github.com/owlcs/owlapi/issues/495
> [2] https://github.com/owlcs/owlapi/issues/509
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Save-ontology-in-RDF-XML-syntax-tp4665482.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Save ontology in RDF/XML syntax

Matthew Horridge-2
Administrator
The relevant issue is here:


Cheers,

Matthew

On 1 Jun 2016, at 14:08, Matthew Horridge <[hidden email]> wrote:

I’ll file an issue for a better error message….

Cheers,

Matthew

On 1 Jun 2016, at 14:06, Wartik, Steven P Steve <[hidden email]> wrote:

Quentin,
 
1.      I agree it’s strict.
2.      I’m not sure that’s a bad thing.
3.      I do wish the error message was a little better.
 
Best Regards,
 
Steve Wartik
 
From: protege-user [[hidden email]] On Behalf Of Quentin Reul
Sent: Wednesday, June 01, 2016 5:00 PM
To: User support for WebProtege and Protege Desktop <[hidden email]>
Subject: Re: [protege-user] Save ontology in RDF/XML syntax
 
Hi Matthew,
 
I have never had any issues with not including starting tags before the new release version. It seems to be a very strict constraint to implement...
 
Cheers,
 
Quentin
 
On 1 June 2016 at 15:53, Matthew Horridge <[hidden email]> wrote:
Hi Quentin, 
 
Thanks for this description.  
 
The value of the literal needs to be valid XML. i.e.
 
"<test>Hello World</test>"
 
works, but
 
“Hello World”
 
does not.
 
Cheers,
 
Matthew
 
 
 
On 1 Jun 2016, at 13:38, Quentin Reul <[hidden email]> wrote:
 
Hi Matthew, 
 
I was able to reproduce the issue in Protege 5.0.0 by performing the following steps:
- Open Protege 5.0.0
- Add new rdfs:comment annotation with Type = rdf:XMLLiteral
- Save ontology in RDF/XML syntax
When performing these steps, I encounter a OWLOntologyStorageException (see attached stacktrace).
 
Kind regards,
 
Quentin
 
On 1 June 2016 at 14:59, Matthew Horridge <[hidden email]> wrote:
Hi Quentin, 
 
Please could you post your ontology to the list (or a sample of it that exhibits the behaviour)?
 
Cheers,
 
Matthew
 
 
 
On 1 Jun 2016, at 11:28, Quentin Reul <[hidden email]> wrote:
 
Hi Matthew, 
 
I have encountered the issue with Protege 5.0.0 RC1 and Protege 5.0.0. I had to revert to Protege 5.0.0 beta 17 to be able to save an existing RDF/XML ontology in that format.
 
Kind regards,
 
Quentin 
 
On 1 June 2016 at 13:10, Matthew Horridge <[hidden email]> wrote:
Hi Quentin, 
 
It works for me.  I can save and reload.
 
What version of Protege are you using exactly?  Is it the release version?
 
Cheers,
 
Matthew
 
 
 
On 1 Jun 2016, at 11:07, Quentin Reul <[hidden email]> wrote:
 
Hi Matthew, 
 
Thanks for the clarification. However, it seems that the issue is not resolved in Protege. Were you able to replicate the issue?
 
Kind regards,
 
Quentin Reul
 
On 1 June 2016 at 13:01, Matthew Horridge <[hidden email]> wrote:
Hi Quentin,

Protege 5.0.0 uses version 4.2.5 of the OWL API.

Cheers,

Matthew



> On 1 Jun 2016, at 10:21, QHReul <[hidden email]> wrote:
>
> As part of Protege 5.0.0 RC1 onward, I encounter issues trying to save an
> ontology in the RDF/XML syntax. More specifically, Protege returns a
> OWLOntologyStorageException when trying to save a modified ontology in the
> format; e.g.:
>
>
> After looking on the web, it seems that the issue may be related to issue
> #495 [1] and #509 [2] in the OWLAPI, which has been addressed in version
> 4.2.1 of the API. Can you confirm that Protege is using the OWLAPI with the
> correct fix?
>
> Kind regards,
>
> Quentin Reul
>
> [1] https://github.com/owlcs/owlapi/issues/495
> [2] https://github.com/owlcs/owlapi/issues/509
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Save-ontology-in-RDF-XML-syntax-tp4665482.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Save ontology in RDF/XML syntax

Steve Wartik

Thanks!

 

From: protege-user [mailto:[hidden email]] On Behalf Of Matthew Horridge
Sent: Wednesday, June 01, 2016 5:10 PM
To: User support for WebProtege and Protege Desktop <[hidden email]>
Subject: Re: [protege-user] Save ontology in RDF/XML syntax

 

The relevant issue is here:

 

 

Cheers,

 

Matthew

 


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