def node(self, id=None, **params):
"""
Get a node in a graph plus its metadata
Returns a BBOPGraph Node
"""
response = self.get_response("graph", q=id, format="json", **params)
if response.status_code == 404:
raise NoResultFoundException('SciGraph yields no result for {}'.format(id))
nodes = response.json()['nodes']
if len(nodes) == 0:
raise NoResultFoundException('SciGraph yields no result for {}'.format(id))
return self.make_NamedObject(**nodes[0])
def get(self, id):
"""
Returns edges emanating from a given node.
"""
args = self.parser.parse_args()
response = sg.get_response("dynamic/cliqueLeader",
q=id,
format="json",
depth=1)
nodes = response.json()['nodes']
if not nodes:
raise NoResultFoundException(
'SciGraph dynamic/cliqueLeader yields no result for {}'.format(
id))
clique_leader = nodes[0]['id']
final_graph = BBOPGraph({'nodes': [], 'edges': []})
if args.relationship_type:
for relationship in args.relationship_type:
graph = sg.neighbors(id=clique_leader,
relationshipType=relationship,
direction=args.direction,
depth=args.depth,
entail=args.entail)
final_graph.merge(graph)
else:
graph = sg.neighbors(id=clique_leader,
depth=args.depth,
entail=args.entail)
final_graph.merge(graph)
return final_graph
def get(self, id):
"""
Returns edges emanating from a given node.
"""
args = self.parser.parse_args()
if args['graph'] == 'data':
scigraph = sg_data
elif args['graph'] == 'ontology':
scigraph = sg_ont
else:
raise UnhandledException('{} not supported graph'.format(
args['graph']))
try:
node = scigraph.get_clique_leader(id)
except HTTPError:
raise NoResultFoundException(
'SciGraph yields no result for {}'.format(id))
if not node:
raise NoResultFoundException(
'SciGraph dynamic/cliqueLeader yields no result for {}'.format(
id))
clique_leader = node.id
final_graph = BBOPGraph({'nodes': [], 'edges': []})
if args.relationship_type:
for relationship in args.relationship_type:
graph = scigraph.neighbors(id=clique_leader,
relationshipType=relationship,
direction=args.direction,
depth=args.depth,
entail=args.entail)
final_graph.merge(graph)
else:
graph = scigraph.neighbors(id=clique_leader,
depth=args.depth,
entail=args.entail)
final_graph.merge(graph)
return final_graph.as_dict()
def get_clique_leader(self, id) -> BioObject:
"""
:raises NoResultFoundException
:return: BioObject
"""
response = self.get_response("dynamic/cliqueLeader", q=id, format="json")
nodes = response.json()['nodes']
if len(nodes) == 0:
raise NoResultFoundException('SciGraph dynamic/cliqueLeader yields no result for {}'.format(id))
return self.make_NamedObject(**nodes[0], class_name='BioObject')
def neighbors(self, id=None, **params):
"""
Get neighbors of a node
parameters are directly passed through to SciGraph: e.g. depth, relationshipType
Returns a BBOPGraph
"""
response = self.get_response("graph/neighbors", id, "json", **params)
if response.status_code == 404:
raise NoResultFoundException('SciGraph graph/neighbors yields no result for {}'.format(id))
return BBOPGraph(response.json())