def __new__(cls, something):
if '10.' in something:
if 'http' in something and 'doi.org' not in something:
pass # probably a publisher uri that uses the handle
else:
return idlib.Doi(something)
if 'orcid' in something:
return idlib.Orcid(something)
if '/ror.org/' in something or something.startswith('ror:'):
return idlib.Ror(something)
if 'protocols.io' in something:
return idlib.Pio(something)
return oq.OntId(something)
return OntTerm(something) # use the better local version of OntTerm
def test_ontid_curie_as_iri(self):
try:
oq.OntId(iri='BIRNLEX:796')
raise AssertionError('should have failed with ValueError')
except ValueError:
pass
def test_ontid_curie(self):
oq.OntId(curie='BIRNLEX:796')
def test_ontid_iri(self):
oq.OntId(iri='http://uri.neuinfo.org/nifa/nifstd/birnleex_796')
def test_ontid_curie_uriref(self):
c = oq.OntId(rdflib.URIRef(oq.OntId('RO:0000087')))
cl = oq.OntId('RO:0000087')
assert c.curie == cl.curie, f'{c!r} != {cl!r}'
def test_a_curies(self):
oq.OntCuries['new-prefix'] = 'https://my-prefixed-thing.org/'
oq.OntCuries['new-prefix'] = 'https://my-prefixed-thing.org/'
a = oq.OntCuries['new-prefix']
oq.OntId('new-prefix:working')
def test_id(self):
oq.OntId('UBERON:0000955')
oq.OntId('http://purl.obolibrary.org/obo/UBERON_0000955')
oq.OntId(prefix='UBERON', suffix='0000955')
SKIP_NETWORK, reason='Skipping due to network requirement')
oq.OntCuries(CURIE_MAP)
suffixes = (
'',
'hello',
'world',
'ev:il',
'1234567',
'1232/123123/asdfasdf',
'lol_this#is/even-worse/_/123',
)
test_graph = rdflib.Graph()
triples = (
('UBERON:0000955', 'rdf:type', 'owl:Class'),
('UBERON:0000955', 'rdfs:label', 'brain'),
('UBERON:0000955', 'rdfs:subClassOf', 'owl:Thing'),
('BIRNLEX:796', 'rdf:type', 'owl:Class'),
('BIRNLEX:796', 'rdfs:label', 'Brain'),
('BIRNLEX:796', 'definition:', 'Gray mushy thing in the nogin.'),
('BIRNLEX:796', 'NIFRID:synonym', 'biocpu'),
('BIRNLEX:796', 'NIFRID:synonym', 'thinkthink'),
)
for proto_t in triples:
test_graph.add(
rdflib.URIRef(oq.OntId(e)) if ':' in e else rdflib.Literal(e)
for e in proto_t)
# FIXME TODO per service ... + mismatch warning
oq.OntCuries({
'rdf': str(rdflib.RDF),
'rdfs': str(rdflib.RDFS),
'owl': str(rdflib.OWL),
'BFO': 'http://purl.obolibrary.org/obo/BFO_',
'UBERON': 'http://purl.obolibrary.org/obo/UBERON_',
'NLX': 'http://uri.neuinfo.org/nif/nifstd/nlx_',
'BIRNLEX': 'http://uri.neuinfo.org/nif/nifstd/birnlex_',
'ILX': 'http://uri.interlex.org/base/ilx_',
'RO': 'http://purl.obolibrary.org/obo/RO_',
'hasRole': 'http://purl.obolibrary.org/obo/RO_0000087',
})
oq.OntCuries({
'hasPart': oq.OntId('BFO:0000051'),
'partOf': oq.OntId('BFO:0000050'),
})
OntId = oq.OntId
class ServiceBase:
def setUp(self):
class OntTerm(oq.OntTerm):
pass
OntTerm.query_init(self.remote)
self.OntTerm = OntTerm
def test_ontid(self):
t = self.OntTerm(OntId('UBERON:0000955'))