def get_label(self, identifier):
obo_id = Text.curie_to_obo(identifier)
text = """
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
select distinct ?label
from <http://reasoner.renci.org/ontology>
where {
$obo_id rdfs:label ?label .
}
"""
results = self.triplestore.query_template(inputs={'obo_id': obo_id},
outputs=['label'],
template_text=text)
if len(results) < 1:
return ''
return results[0]['label']
def test_obo_to_curie():
test_set = {
'http://purl.obolibrary.org/obo/prefix_suffix':
'prefix:suffix',
'http://purl.obolibrary.org/obo/prefix_suffix_suffix':
'prefix:suffix_suffix',
'http://purl.obolibrary.org/obo/path/prefix_suffix':
'path_prefix:suffix',
'http://purl.obolibrary.org/obo/path/prefix#suffix':
'path_prefix:suffix',
'http://purl.obolibrary.org/obo/path/prefix#suffix_more_suffix':
'path_prefix:suffix_more_suffix'
}
for obo, curie in test_set.items():
assert Text.obo_to_curie(obo) == curie
# could not find a way to smartly go back to urls containing # back
do = 3
for obo, curie in test_set.items():
if do == 1:
break
do -= 1
assert Text.curie_to_obo(curie) == f'<{obo}>'
