[esip-semantictech] [EXTERNAL] Re: Importing SWEET into Protege

Tue Jul 16 05:45:10 EDT 2019

It appears a handful of the ttl files are munted.  I've created an issue [1]
explaining my findings.  I'm working on it now and hope to have it resolved
before the sessions start today.
/Brandon

[1] https://github.com/ESIPFed/sweet/issues/122

On Mon, 2019-07-15 at 23:23 +0000, Mcgibbney, Lewis J (398M) wrote:
> CC'ing esip-semtech mailing list
> 
> I built Protégé from source at https://github.com/protegeproject/protege.git
> 
> Once I load data from URL, this leads to the following stack trace
> 
> org.semanticweb.owlapi.io.OWLOntologyCreationIOException: Server returned
> HTTP response code: 403 for URL: http://sweetontology.net/sweetAll
> 	at
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOnt
> ologyFactoryImpl.java:231) ~[na:na]
> 	at
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntolog
> yManagerImpl.java:1293) ~[na:na]
> 	at
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntolo
> gyManagerImpl.java:1233) ~[na:na]
> 	at
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntolo
> gyDocument(OWLOntologyManagerImpl.java:1190) ~[na:na]
> 	at
> org.protege.editor.owl.model.io.OntologyLoader.loadOntologyInternal(Ontology
> Loader.java:116) ~[na:na]
> 	at
> org.protege.editor.owl.model.io.OntologyLoader.lambda$loadOntologyInOtherThr
> ead$0(OntologyLoader.java:68) ~[na:na]
> 	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> ~[na:1.8.0_191]
> 	at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:11
> 49) ~[na:1.8.0_191]
> 	at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:6
> 24) ~[na:1.8.0_191]
> 	at java.lang.Thread.run(Thread.java:748) ~[na:1.8.0_191]
> Caused by: java.io.IOException: Server returned HTTP response code: 403 for
> URL: http://sweetontology.net/sweetAll
> 	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> Method) ~[na:1.8.0_191]
> 	at
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAcces
> sorImpl.java:62) ~[na:1.8.0_191]
> 	at
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstruc
> torAccessorImpl.java:45) ~[na:1.8.0_191]
> 	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
> ~[na:1.8.0_191]
> 	at sun.net.
> www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1944)
> ~[na:1.8.0_191]
> 	at sun.net.
> www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1939)
> ~[na:1.8.0_191]
> 	at java.security.AccessController.doPrivileged(Native Method)
> ~[na:1.8.0_191]
> 	at sun.net.
> www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1938
> ) ~[na:1.8.0_191]
> 	at sun.net.
> www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1508
> ) ~[na:1.8.0_191]
> 	at sun.net.
> www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492
> ) ~[na:1.8.0_191]
> 	at
> org.semanticweb.owlapi.io.AbstractOWLParser.getInputStreamFromContentEncodin
> g(AbstractOWLParser.java:176) ~[na:na]
> 	at
> org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser
> .java:138) ~[na:na]
> 	at
> org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser
> .java:273) ~[na:na]
> 	at
> org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.jav
> a:72) ~[na:na]
> 	at
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOnt
> ologyFactoryImpl.java:221) ~[na:na]
> 	... 9 common frames omitted
> Caused by: java.io.IOException: Server returned HTTP response code: 403 for
> URL: http://sweetontology.net/sweetAll
> 	at sun.net.
> www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1894
> ) ~[na:1.8.0_191]
> 	at sun.net.
> www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492
> ) ~[na:1.8.0_191]
> 	at
> java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480)
> ~[na:1.8.0_191]
> 	at
> org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser
> .java:112) ~[na:na]
> 	... 12 common frames omitted
> 
> Once I navigate to OntologyLoader.java I can see that the
> OWLOntologyLoaderConfiguration provides an .setFollowRedirects(boolean)
> method. Once I set this to true as follows
> 
>         OWLOntologyLoaderConfiguration configuration = new
> OWLOntologyLoaderConfiguration();
>         configuration = configuration
>                 .setMissingImportHandlingStrategy(MissingImportHandlingStrat
> egy.SILENT)
>                 .setFollowRedirects(true);
>         IRIDocumentSource documentSource = new
> IRIDocumentSource(IRI.create(documentURI));
>         ontology =
> loadingManager.loadOntologyFromOntologyDocument(documentSource,
> configuration);
> 
> ... I still get the same error. I stepped through the source right down to
> the owlapi level but I am not yet able to see the source of the issue.
> 
> In short, I *think* that Protégé definitely has issues following redirects
> within input IRI's. I'm going to work this with the protégé users community
> in a bid to get to the bottom of this.
> Lewis
> 
> 
> On 7/15/19, 4:12 PM, "Carlos Rueda" <carueda at mbari.org> wrote:
> 
>     Ditto, thanks Simon for the tests!
>     
>     Carlos
>     
>     
>     ----- Original Message -----
>     > From: "brandon whitehead" <brandonnodnarb at gmail.com>
>     > To: "Simon Cox" <Simon.Cox at csiro.au>, "Carlos Rueda" <
> carueda at mbari.org>
>     > Sent: Monday, July 15, 2019 4:03:08 PM
>     > Subject: Re: [esip-semantictech] Importing SWEET into Protege
>     
>     > Interesting.  Thanks for testing, Simon.
>     > /Brandon
>     > 
>     > On 15/07/19 10:54 PM, Cox, Simon (L&W, Clayton) wrote:
>     >> I have just loaded in TopBraid 6.2 from the URI
>     >> http://sweetontology.net/sweetAll as a straight web-import.
>     >> But I also can't load in Protégé.
>     >> 
>     >> -----Original Message-----
>     >> From: esip-semanticweb <esip-semanticweb-bounces at lists.esipfed.org>
> On Behalf Of
>     >> brandon whitehead via esip-semanticweb
>     >> Sent: Monday, 15 July, 2019 14:44
>     >> To: Carlos Rueda <carueda at mbari.org>; esip-semanticweb
>     >> <esip-semanticweb at lists.esipfed.org>
>     >> Subject: Re: [esip-semantictech] Importing SWEET into Protege
>     >> 
>     >> Hi Carlos,
>     >> 
>     >> Many thanks for the reply.  More below.
>     >> 
>     >> On 15/07/19 10:05 PM, Carlos Rueda wrote:
>     >>>      [Fatal Error] :1:50: White spaces are required between publicID
> and
>     >>>      systemID.
>     >>>
>     >>>      I've been digging around in my protege log file, but it doesn't
>     >>>      actually show up there (the previous output is from the command
> line).
>     >>>
>     >>>      For further context, the page successfully redirects if I hit
> it in a
>     >>>      browser.  If I try to load one of the ontology files, for
> example
>     >>>      http://sweetontology.net/humanAgriculture, in a browser it
> pushes me to
>     >>>      the COR page as expected.  I can curl the URL and get a valid
> response
>     >>>      (full turtle file), but if I try the same thing via Protege
> (loading
>     >>>      that specific ttl file via URL instead of a local copy) I get a
> 403
>     >>>      error --- the same issue Lewis described.
>     >>>
>     >>>
>     >>> Same here.  I just did a few tests using HTTPie with variations of
> the
>     >>> basic http://sweetontology.net/sweetAll request, and all responded
> as
>     >>> expected, except when trying the relevant ones in Protege (resulting
>     >>> in 403), eg:
>     >>>
>     >>> http://sweetontology.net/sweetAll  --Protege should prefer an RDF
>     >>> representation via content negotiation)
>     >>>
>     >>> http://sweetontology.net/sweetAll.rdf  -- explicit preference for
> RDF
>     >>> via filename extension
>     >>>
>     >>> My HTTPie based tests suggest that the 403 error is not being
>     >>> generated from the sweetontology.net proxy-pass nor from the COR
>     >>> service.  So perhaps worth re-trying all of this with a newer
> Protege
>     >>> version(?).
>     >> 
>     >> Interesting.  Protege 5.5 is the newest stable version.  I've not
> tried buidling
>     >> from source via git and testing.  However, the response/error is the
> same in
>     >> TopBraid Composer (5.3) as was described in Protege so it's a bigger
> issue.
>     >> Perhaps OWLAPI?
>     >> 
>     >> Cheers,
>     >> /Brandon
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