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Ontology for consent codes and data use requirements
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contains text but no `xsd:datatype` #33

Closed jimmyhli closed 4 years ago

jimmyhli commented 4 years ago

I was parsing the duo-basic.owl, and got these warnings

These are all minor, and doesn't really affect the terms to be read, most of these are just contains text but noxsd:datatype``, and i was wondering if maybe this is something that may not follow the specs too closely? Again, I'm not too sure about this part, so if they are alright please ignore this issue.

Thanks - 

`SyntaxWarning: <Element {http://www.geneontology.org/formats/oboInOwl#}shorthand at 0x7f1155abba08> contains text but no `xsd:datatype`
  self._extract_term(class_, aliases)
/home/jimli/2to3/test_server_190911/lib/python3.6/site-packages/pronto/ontology.py:167: SyntaxWarning: several names found for 'DUO:0000004', concatenating
  cls(self).parse_from(_handle)
SyntaxWarning: <Element {http://purl.obolibrary.org/obo/}DUO_0000041 at 0x7f1155ad2188> contains text but no `xsd:datatype`
  self._extract_term(class_, aliases)
SyntaxWarning: <Element {http://www.geneontology.org/formats/oboInOwl#}shorthand at 0x7f1155ad2188> contains text but no `xsd:datatype`
  self._extract_term(class_, aliases)
SyntaxWarning: <Element {http://www.geneontology.org/formats/oboInOwl#}shorthand at 0x7f1155ad2108> contains text but no `xsd:datatype`
  self._extract_term(class_, aliases)
SyntaxWarning: <Element {http://www.geneontology.org/formats/oboInOwl#}shorthand at 0x7f1155ad2508> contains text but no `xsd:datatype`
  self._extract_term(class_, aliases)
SyntaxWarning: <Element {http://www.geneontology.org/formats/oboInOwl#}shorthand at 0x7f1155ad2588> contains text but no `xsd:datatype`
  self._extract_term(class_, aliases)
SyntaxWarning: <Element {http://www.geneontology.org/formats/oboInOwl#}shorthand at 0x7f1155ad2848> contains text but no `xsd:datatype`
  self._extract_term(class_, aliases)
SyntaxWarning: <Element {http://purl.obolibrary.org/obo/}IAO_0000118 at 0x7f1155ad2a48> contains text but no `xsd:datatype`
  self._extract_term(class_, aliases)
SyntaxWarning: <Element {http://www.geneontology.org/formats/oboInOwl#}shorthand at 0x7f1155ad2ac8> contains text but no `xsd:datatype`
  self._extract_term(class_, aliases)
SyntaxWarning: <Element {http://www.geneontology.org/formats/oboInOwl#}shorthand at 0x7f1155ad2b48> contains text but no `xsd:datatype`
  self._extract_term(class_, aliases)
SyntaxWarning: <Element {http://www.geneontology.org/formats/oboInOwl#}shorthand at 0x7f1155ad2d08> contains text but no `xsd:datatype`
  self._extract_term(class_, aliases)
SyntaxWarning: <Element {http://www.geneontology.org/formats/oboInOwl#}shorthand at 0x7f1155adc1c8> contains text but no `xsd:datatype`
  self._extract_term(class_, aliases)
SyntaxWarning: <Element {http://www.geneontology.org/formats/oboInOwl#}shorthand at 0x7f1155adc148> contains text but no `xsd:datatype`
  self._extract_term(class_, aliases)
SyntaxWarning: <Element {http://www.geneontology.org/formats/oboInOwl#}shorthand at 0x7f1155ae7148> contains text but no `xsd:datatype`
  self._extract_term(class_, aliases)
SyntaxWarning: <Element {http://purl.obolibrary.org/obo/}IAO_0000111 at 0x7f1155ab6a48> contains text but no `xsd:datatype`
  self._extract_term(class_, aliases)
mcourtot commented 4 years ago

Thanks for the feedback! Would you be ok making a PR for those?

jimmyhli commented 4 years ago

I'd be willing to take a look at the issue

mcourtot commented 4 years ago

It’s an easy fix - just adding the data type declaration as xsd:string. I’m away from the office at the moment; if it’s problematic on your side I’ll do it on a Thursday when back. Let me know what you prefer :)

jimmyhli commented 4 years ago

oh ok! that sounds easy haha. Thanks for the instructions.

Sorry I was busy with the implementation of our own dataset lookup API endpoints (powered by DUO) today and didn't see your response.

I will certainly try to fix this tomorrow and keep you posted of our progress.

jimmyhli commented 4 years ago

It’s an easy fix - just adding the data type declaration as xsd:string. I’m away from the office at the moment; if it’s problematic on your side I’ll do it on a Thursday when back. Let me know what you prefer :)

i made a PR, kindly lemme know if anything needs to be changed

thanks!

mcourtot commented 4 years ago

Thanks for the PR - just merged it in.