def test_process_predicate(query):
"""
Test behavior of process_predicate method.
"""
pm = PrefixManager()
x = process_predicate(pm, query[0])
assert x[0] == query[1]
assert x[1] == query[2]
assert x[2] == query[3]
assert x[3] == query[4]
def set_property_types(self, m: Dict) -> None:
"""
Set export type for properties that are not in
Biolink Model.
Parameters
----------
m: Dict
A dictionary where the keys are property names and values
are their corresponding types.
"""
for k, v in m.items():
(element_uri, canonical_uri, predicate,
property_name) = process_predicate(self.prefix_manager, k)
if element_uri:
key = element_uri
elif predicate:
key = predicate
else:
key = property_name
self.property_types[key] = v
def load_edge(self, edge: Dict) -> Generator:
"""
Load an edge into an instance of BaseGraph
Parameters
----------
edge : Dict
An edge
Returns
-------
Generator
A generator for node and edge records
"""
(element_uri, canonical_uri, predicate, property_name) = process_predicate(
self.prefix_manager, edge["predicate_id"], self.predicate_mapping
)
if element_uri:
edge_predicate = element_uri
elif predicate:
edge_predicate = predicate
else:
edge_predicate = property_name
if canonical_uri:
edge_predicate = element_uri
data = {
"subject": edge["subject_id"],
"predicate": edge_predicate,
"object": edge["object_id"],
}
del edge["predicate_id"]
data = self.validate_edge(data)
if not data:
return # ?
subject_node = {}
object_node = {}
for k, v in edge.items():
if k in SSSOM_NODE_PROPERTY_MAPPING:
if k.startswith("subject"):
mapped_k = SSSOM_NODE_PROPERTY_MAPPING[k]
if mapped_k == "category" and not PrefixManager.is_curie(v):
v = f"biolink:OntologyClass"
subject_node[mapped_k] = v
elif k.startswith("object"):
mapped_k = SSSOM_NODE_PROPERTY_MAPPING[k]
if mapped_k == "category" and not PrefixManager.is_curie(v):
v = f"biolink:OntologyClass"
object_node[mapped_k] = v
else:
log.info(f"Ignoring {k} {v}")
else:
data[k] = v
subject_node = self.load_node(subject_node)
object_node = self.load_node(object_node)
if not (subject_node and object_node):
return # ?
objs = [subject_node, object_node]
for k, v in self.graph_metadata.items():
if k not in {"curie_map"}:
data[k] = v
edge_data = sanitize_import(data.copy())
if "subject" in edge_data and "object" in edge_data:
if "id" not in edge_data:
edge_data["id"] = generate_uuid()
s = edge_data["subject"]
o = edge_data["object"]
self.set_edge_provenance(edge_data)
key = generate_edge_key(s, edge_data["predicate"], o)
self.edge_properties.update(list(edge_data.keys()))
objs.append((s, o, key, edge_data))
else:
self.owner.log_error(
entity=str(edge_data),
error_type=ErrorType.MISSING_NODE,
message="Ignoring edge with either a missing 'subject' or 'object'",
message_level=MessageLevel.WARNING
)
for o in objs:
yield o
def load_edge(self, edge: Dict) -> Generator:
"""
Load an edge into an instance of BaseGraph
Parameters
----------
edge : Dict
An edge
Returns
-------
Generator
A generator for node and edge records
"""
(element_uri, canonical_uri, predicate,
property_name) = process_predicate(self.prefix_manager,
edge['predicate_id'],
self.predicate_mapping)
if element_uri:
edge_predicate = element_uri
elif predicate:
edge_predicate = predicate
else:
edge_predicate = property_name
if canonical_uri:
edge_predicate = element_uri
data = {
'subject': edge['subject_id'],
'predicate': edge_predicate,
'object': edge['object_id'],
}
del edge['predicate_id']
data = validate_edge(data)
subject_node = {}
object_node = {}
for k, v in edge.items():
if k in SSSOM_NODE_PROPERTY_MAPPING:
if k.startswith('subject'):
mapped_k = SSSOM_NODE_PROPERTY_MAPPING[k]
if mapped_k == 'category' and not PrefixManager.is_curie(
v):
v = f"biolink:OntologyClass"
subject_node[mapped_k] = v
elif k.startswith('object'):
mapped_k = SSSOM_NODE_PROPERTY_MAPPING[k]
if mapped_k == 'category' and not PrefixManager.is_curie(
v):
v = f"biolink:OntologyClass"
object_node[mapped_k] = v
else:
log.info(f"Ignoring {k} {v}")
else:
data[k] = v
objs = [self.load_node(subject_node), self.load_node(object_node)]
for k, v in self.graph_metadata.items():
if k not in {'curie_map'}:
data[k] = v
edge_data = sanitize_import(data.copy())
if 'subject' in edge_data and 'object' in edge_data:
if 'id' not in edge_data:
edge_data['id'] = generate_uuid()
s = edge_data['subject']
o = edge_data['object']
if 'provided_by' in self.graph_metadata and 'provided_by' not in edge_data.keys(
):
edge_data['provided_by'] = self.graph_metadata['provided_by']
key = generate_edge_key(s, edge_data['predicate'], o)
self.edge_properties.update(list(edge_data.keys()))
objs.append((s, o, key, edge_data))
else:
log.info(
"Ignoring edge with either a missing 'subject' or 'object': {}"
.format(edge_data))
for o in objs:
yield o