[esip-semantictech] Importing SWEET into Protege

[Carlos Rueda]

Hi Lewis / Brandon: 

Just giving this a quick review (also after a long time) ... 
Please see inline. 

> From: "esip-semanticweb" <esip-semanticweb at lists.esipfed.org>
> To: "esip-semanticweb" <esip-semanticweb at lists.esipfed.org>
> Sent: Monday, July 15, 2019 11:21:03 AM
> Subject: Re: [esip-semantictech] Importing SWEET into Protege

> Hi All,

> Thanks for following up, Lewis.

> I have been getting the following error when trying to load
> 'http://sweetontology.net':
http://sweetontology.net is not the SWEET ontology IRI. The one I used for testing (again, a while ago) is http://sweetontology.net/sweetAll (see https://github.com/ESIPFed/sweet/issues/57 ), which can be used to bring the whole set of SWEET ontologies into Protege via corresponding imports. 

However, I'm just also getting a 403 error message right now in Protege (5.2.0) 

> [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(?). 

Carlos 

> These results are identical using using protege 5.5, protege 5.2, and
> potege 5.2 'platform independent version'.

> Also, the ontologies load from a local copy in protege (all versions
> listed previously) as well as TopBraid Composer 5.3. However, in TBC
> the base class name for the file (i.e. humanAgriculture.ttl) shows up
> as an openrdf error link, which I have not seen before. ( i.e.
> org.openrdf.RDFParse.../error#(n) )

> I'm not sure what to test next. I would assume the 403 error needs to
> be addressed before the parser can be tested.

> Thoughts?

> Cheers,
> /Brandon

> On Mon, 2019-07-15 at 17:58 +0000, Mcgibbney, Lewis J (398M) wrote:

>> Hi Folks,
>> Does anyone have advice or is anyone actually able to import SWEET
>> into Protégé? I have not used Protégé in quite a while and recently
>> encountered issues.
>> With Protégé 5.5.0 I am getting 403 errors when attempting to do the
>> following

>> File > Open from URL > this results in a HTTP 403 error

>> We do ofcourse have the redirection setup between all
>> sweetontology.net resources to the actual resource within COR.

>> Any suggestions? Surely someone has been able to do this recently.
>> I’m also going to head over to the Protégé mailing list and ask over
>> there.
>> Thanks

>> Dr. Lewis John McGibbney Ph.D., B.Sc.(Hons)
>> Data Scientist III
>> Computer Science for Data Intensive Applications Group (398M)
>> Instrument Software and Science Data Systems Section (398)
>> Jet Propulsion Laboratory
>> California Institute of Technology
>> 4800 Oak Grove Drive
>> Pasadena, California 91109-8099
>> Mail Stop : 158-256C
>> Tel: (+1) (818)-393-7402
>> Cell: (+1) (626)-487-3476
>> Fax: (+1) (818)-393-1190
>> Email: lewis.j.mcgibbney at jpl.nasa.gov
>> ORCID: orcid.org/0000-0003-2185-928X

>> Dare Mighty Things
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-- 
Carlos A. Rueda, PhD 
Sr Software Engineer 
Monterey Bay Aquarium Research Institute - mbari.org 
carueda at mbari.org - 831-775-1929 
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