def get_toolkit(schema: Optional[str] = None) -> Toolkit:
"""
Get an instance of bmt.Toolkit
If there no instance defined, then one is instantiated and returned.
"""
global toolkit
if toolkit is None:
if not schema:
config = get_config()
schema = config['biolink-model']
toolkit = Toolkit(schema=schema)
return toolkit
class CurieLookupService(object):
"""
A service to lookup label for a given CURIE.
"""
config = get_config()
ontologies = config['ontologies']
ontology_graph = None
def __init__(self, curie_map: dict = None):
if curie_map:
self.curie_map = CURIE_MAP
self.curie_map.update(curie_map)
else:
self.curie_map = CURIE_MAP
self.ontology_graph = nx.MultiDiGraph()
self.load_ontologies()
def load_ontologies(self):
"""
Load all required ontologies.
"""
for ontology in self.ontologies.values():
rdfgraph = rdflib.Graph()
input_format = rdflib.util.guess_format(ontology)
rdfgraph.parse(ontology, format=input_format)
# triples = rdfgraph.triples((None, rdflib.RDFS.subClassOf, None))
# for s,p,o in triples:
# subject_curie = contract(s)
# object_curie = contract(o)
# self.ontology_graph.add_node(subject_curie)
# self.ontology_graph.add_node(object_curie)
# key = generate_edge_key(subject_curie, 'subclass_of', object_curie)
# self.ontology_graph.add_edge(subject_curie, object_curie, key, **{'predicate': 'subclass_of', 'relation': 'rdfs:subClassOf'})
triples = rdfgraph.triples((None, rdflib.RDFS.label, None))
for s, p, o in triples:
key = contract(s)
value = o.value
value = value.replace(' ', '_')
self.curie_map[key] = value
self.ontology_graph.add_node(key, name=value)
from kgx.cli.cli_utils import (
get_input_file_types,
parse_source,
apply_operations,
graph_summary,
validate,
neo4j_download,
neo4j_upload,
transform,
merge,
summary_report_types,
get_report_format_types,
)
log = get_logger()
config = get_config()
def error(msg):
log.error(msg)
quit()
@click.group()
@click.version_option(version=kgx.__version__, prog_name=kgx.__name__)
def cli():
"""
Knowledge Graph Exchange CLI entrypoint.
\f
"""