def add_edge(self, subject_iri: URIRef, object_iri: URIRef, predicate_iri: URIRef) -> Tuple[str, str, str]:
"""
This method should be used by all derived classes when adding an edge to the networkx.MultiDiGraph.
This ensures that the `subject` and `object` identifiers are CURIEs, and that `edge_label` is in the correct form.
Returns the CURIE identifiers used for the `subject` and `object` in the
networkx.MultiDiGraph, and the processed `edge_label`.
Parameters
----------
subject_iri: rdflib.URIRef
Subject IRI for the subject in a triple
object_iri: rdflib.URIRef
Object IRI for the object in a triple
predicate_iri: rdflib.URIRef
Predicate IRI for the predicate in a triple
Returns
-------
Tuple[str, str, str]
A 3-nary tuple (of the form subject, object, predicate) that represents the edge
"""
s = self.add_node(subject_iri)
o = self.add_node(object_iri)
relation = self.prefix_manager.contract(predicate_iri)
edge_label = process_iri(predicate_iri)
if ' ' in edge_label:
logging.debug("predicate IRI '{}' yields edge_label '{}' that not in snake_case form; replacing ' ' with '_'".format(predicate_iri, edge_label))
if edge_label.startswith(self.BIOLINK):
logging.debug("predicate IRI '{}' yields edge_label '{}' that starts with '{}'; removing IRI prefix".format(predicate_iri, edge_label, self.BIOLINK))
edge_label = edge_label.replace(self.BIOLINK, '')
if PrefixManager.is_curie(edge_label):
name = curie_lookup(edge_label)
if name:
logging.debug("predicate IRI '{}' yields edge_label '{}' that is actually a CURIE; Using its mapping instead: {}".format(predicate_iri, edge_label, name))
edge_label = name
else:
logging.debug("predicate IRI '{}' yields edge_label '{}' that is actually a CURIE; defaulting back to {}".format(predicate_iri, edge_label, self.DEFAULT_EDGE_LABEL))
edge_label = self.DEFAULT_EDGE_LABEL
kwargs = {
'subject': s,
'predicate': str(predicate_iri),
'object': o,
'relation': relation,
'edge_label': f"biolink:{edge_label}"
}
if 'provided_by' in self.graph_metadata:
kwargs['provided_by'] = self.graph_metadata['provided_by']
key = generate_edge_key(s, edge_label, o)
if not self.graph.has_edge(s, o, key=key):
self.graph.add_edge(s, o, key=key, **kwargs)
# TODO: support append
return s, o, edge_label
def add_edge_attribute(self, subject_iri: Union[URIRef, str],
object_iri: URIRef, predicate_iri: URIRef, key: str,
value: str) -> None:
"""
Adds an attribute to an edge, while taking into account whether the attribute
should be multi-valued.
Multi-valued properties will not contain duplicates.
The key may be a rdflib.URIRef or a URI string that maps onto a property name
as defined in `rdf_utils.property_mapping`.
If the nodes in the edge does not exist then they will be created
using subject_iri and object_iri.
If the edge itself does not exist then it will be created using
subject_iri, object_iri and predicate_iri.
Parameters
----------
subject_iri: [rdflib.URIRef, str]
The IRI of the subject node of an edge in rdflib.Graph
object_iri: rdflib.URIRef
The IRI of the object node of an edge in rdflib.Graph
predicate_iri: rdflib.URIRef
The IRI of the predicate representing an edge in rdflib.Graph
key: str
The name of the attribute. Can be a rdflib.URIRef or URI string
value: str
The value of the attribute
"""
if key.lower() in is_property_multivalued:
key = key.lower()
else:
if not isinstance(key, URIRef):
key = URIRef(key)
key = property_mapping.get(key)
if key is not None:
subject_curie = make_curie(subject_iri)
object_curie = make_curie(object_iri)
edge_label = process_iri(predicate_iri)
if is_curie(edge_label):
edge_label = curie_lookup(edge_label)
edge_key = generate_edge_key(subject_curie, edge_label,
object_curie)
attr_dict = self.graph.get_edge_data(subject_curie,
object_curie,
key=edge_key)
self._add_attribute(attr_dict, key, value)
def add_node_attribute(
self, iri: Union[URIRef, str], key: str, value: Union[str, List]
) -> None:
"""
Add an attribute to a node in cache, while taking into account whether the attribute
should be multi-valued.
The ``key`` may be a rdflib.URIRef or an URI string that maps onto a
property name as defined in ``rdf_utils.property_mapping``.
Parameters
----------
iri: Union[rdflib.URIRef, str]
The IRI of a node in the rdflib.Graph
key: str
The name of the attribute. Can be a rdflib.URIRef or URI string
value: Union[str, List]
The value of the attribute
Returns
-------
Dict
The node data
"""
if self.prefix_manager.is_iri(key):
key_curie = self.prefix_manager.contract(key)
else:
key_curie = key
c = curie_lookup(key_curie)
if c:
key_curie = c
if self.prefix_manager.is_curie(key_curie):
# property names will always be just the reference
mapped_key = self.prefix_manager.get_reference(key_curie)
else:
mapped_key = key_curie
if isinstance(value, rdflib.term.Identifier):
if isinstance(value, rdflib.term.URIRef):
value_curie = self.prefix_manager.contract(value)
# if self.prefix_manager.get_prefix(value_curie) not in {'biolink'} \
# and mapped_key not in {'type', 'category', 'predicate', 'relation', 'predicate'}:
# d = self.add_node(value)
# value = d['id']
# else:
# value = value_curie
value = value_curie
else:
value = value.toPython()
if mapped_key in is_property_multivalued and is_property_multivalued[mapped_key]:
value = [value]
if mapped_key in self.node_record:
if isinstance(self.node_record[mapped_key], str):
_ = self.node_record[mapped_key]
self.node_record[mapped_key] = [_]
self.node_record[mapped_key].append(value)
else:
self.node_record[mapped_key] = [value]
curie = self.prefix_manager.contract(iri)
if curie in self.node_cache:
if mapped_key in self.node_cache[curie]:
node = self.node_cache[curie]
updated_node = prepare_data_dict(node, {mapped_key: value})
self.node_cache[curie] = updated_node
else:
self.node_cache[curie][mapped_key] = value
else:
self.node_cache[curie] = {'id': curie, mapped_key: value}
def test_curie_lookup(query):
"""
Test look up of a CURIE.
"""
s = curie_lookup(query[0])
assert s == query[1]
def test_curie_lookup(query):
s = curie_lookup(query[0])
assert s == query[1]