def get_digraph(ont, relations=None, writecache=False):
"""
Creates a basic graph object corresponding to a remote ontology
"""
digraph = networkx.MultiDiGraph()
logger.info("Getting edges (may be cached)")
for (s, p, o) in get_edges(ont):
p = map_legacy_pred(p)
if relations is None or p in relations:
digraph.add_edge(o, s, pred=p)
logger.info("Getting labels (may be cached)")
for (n, label) in fetchall_labels(ont):
digraph.add_node(n, **{'label': label})
return digraph
def add_obograph_digraph(
self,
og,
node_type=None,
predicates=None,
xref_graph=None,
logical_definitions=None,
property_chain_axioms=None,
parse_meta=True,
reverse_edges=True,
**args):
"""
Converts a single obograph to Digraph edges and adds to an existing networkx DiGraph
"""
digraph = self.digraph
logging.info("NODES: {}".format(len(og['nodes'])))
# if client passes an xref_graph we must parse metadata
if xref_graph is not None:
parse_meta = True
for node in og['nodes']:
is_obsolete = 'is_obsolete' in node and node['is_obsolete'] == 'true'
if is_obsolete:
continue
if node_type is not None and ('type' not in node or node['type'] != node_type):
continue
id = self.contract_uri(node['id'])
digraph.add_node(id, **node)
if 'lbl' in node:
digraph.node[id]['label'] = node['lbl']
if parse_meta and 'meta' in node:
if node['meta'] is None:
node['meta'] = {}
meta = self.transform_meta(node['meta'])
if xref_graph is not None and 'xrefs' in meta:
for x in meta['xrefs']:
xref_graph.add_edge(self.contract_uri(x['val']), id, source=id)
logging.info("EDGES: {}".format(len(og['edges'])))
for edge in og['edges']:
sub = self.contract_uri(edge['sub'])
obj = self.contract_uri(edge['obj'])
pred = self.contract_uri(edge['pred'])
pred = map_legacy_pred(pred)
if pred == 'is_a':
pred = 'subClassOf'
if predicates is None or pred in predicates:
meta = edge['meta'] if 'meta' in edge else {}
if reverse_edges:
digraph.add_edge(obj, sub, pred=pred, **meta)
else:
digraph.add_edge(sub, obj, pred=pred, **meta)
if 'equivalentNodesSets' in og:
nslist = og['equivalentNodesSets']
logging.info("CLIQUES: {}".format(len(nslist)))
for ns in nslist:
equivNodeIds = ns['nodeIds']
for i in ns['nodeIds']:
ix = self.contract_uri(i)
for j in ns['nodeIds']:
if i != j:
jx = self.contract_uri(j)
digraph.add_edge(ix, jx, pred='equivalentTo')
if logical_definitions is not None and 'logicalDefinitionAxioms' in og:
for a in og['logicalDefinitionAxioms']:
ld = LogicalDefinition(self.contract_uri(a['definedClassId']),
[self.contract_uri(x) for x in a['genusIds']],
[(self.contract_uri(x['propertyId']),
self.contract_uri(x['fillerId'])) for x in a['restrictions'] if x is not None])
logical_definitions.append(ld)
if property_chain_axioms is not None and 'propertyChainAxioms' in og:
for a in og['propertyChainAxioms']:
pca = PropertyChainAxiom(predicate_id=self.contract_uri(a['predicateId']),
chain_predicate_ids=[self.contract_uri(x) for x in a['chainPredicateIds']])
property_chain_axioms.append(pca)
