def curie_lookup(curie: str) -> Optional[str]:
"""
Given a CURIE, find its label.
This method first does a lookup in predefined maps. If none found,
it makes use of CurieLookupService to look for the CURIE in a set
of preloaded ontologies.
Parameters
----------
curie: str
A CURIE
Returns
-------
Optional[str]
The label corresponding to the given CURIE
"""
cls = get_curie_lookup_service()
name: Optional[str] = None
prefix = PrefixManager.get_prefix(curie)
if prefix in ['OIO', 'OWL', 'owl', 'OBO', 'rdfs']:
name = stringcase.snakecase(curie.split(':', 1)[1])
elif curie in cls.curie_map:
name = cls.curie_map[curie]
elif curie in cls.ontology_graph:
name = cls.ontology_graph.nodes()[curie]['name']
return name
def infer_category(iri: URIRef, rdfgraph:rdflib.Graph) -> List[str]:
"""
Infer category for a given iri by traversing rdfgraph.
Parameters
----------
iri: rdflib.term.URIRef
IRI
rdfgraph: rdflib.Graph
A graph to traverse
Returns
-------
List[str]
A list of category corresponding to the given IRI
"""
category = None
subj = None
closure = list(rdfgraph.transitive_objects(iri, URIRef(RDFS.subClassOf)))
category = [top_level_terms[x] for x in closure if x in top_level_terms.keys()]
if category:
logging.debug("Inferred category as {} based on transitive closure over 'subClassOf' relation".format(category))
else:
subj = closure[-1]
if subj == iri:
return category
subject_curie = contract(subj)
if '_' in subject_curie:
fixed_curie = subject_curie.split(':', 1)[1].split('_', 1)[1]
logging.warning("Malformed CURIE {} will be fixed to {}".format(subject_curie, fixed_curie))
subject_curie = fixed_curie
cls = get_curie_lookup_service()
category = get_category_via_superclass(cls.ontology_graph, subject_curie)
return category
def get_category_via_superclass(graph: BaseGraph,
curie: str,
load_ontology: bool = True) -> Set[str]:
"""
Get category for a given CURIE by tracing its superclass, via ``subclass_of`` hierarchy,
and getting the most appropriate category based on the superclass.
Parameters
----------
graph: kgx.graph.base_graph.BaseGraph
Graph to traverse
curie: str
Input CURIE
load_ontology: bool
Determines whether to load ontology, based on CURIE prefix, or to simply
rely on ``subclass_of`` hierarchy from graph
Returns
-------
Set[str]
A set containing one (or more) category for the given CURIE
"""
log.debug("curie: {}".format(curie))
new_categories = []
toolkit = get_toolkit()
if PrefixManager.is_curie(curie):
ancestors = get_ancestors(graph, curie, relations=['subclass_of'])
if len(ancestors) == 0 and load_ontology:
cls = get_curie_lookup_service()
ontology_graph = cls.ontology_graph
new_categories += [
x for x in get_category_via_superclass(ontology_graph, curie,
False)
]
log.debug("Ancestors for CURIE {} via subClassOf: {}".format(
curie, ancestors))
seen = []
for anc in ancestors:
mapping = toolkit.get_by_mapping(anc)
seen.append(anc)
if mapping:
# there is direct mapping to BioLink Model
log.debug("Ancestor {} mapped to {}".format(anc, mapping))
seen_labels = [
graph.nodes()[x]['name'] for x in seen
if 'name' in graph.nodes()[x]
]
new_categories += [x for x in seen_labels]
new_categories += [x for x in toolkit.ancestors(mapping)]
break
return set(new_categories)
def test_get_curie_lookup_service():
cls = get_curie_lookup_service()
assert isinstance(cls, CurieLookupService)
def test_get_curie_lookup_service():
"""
Test to get an instance of CurieLookupService via get_curie_lookup_service.
"""
cls = get_curie_lookup_service()
assert isinstance(cls, CurieLookupService)