"""
TODO: add methods for ensuring that other biolink model specifications hold,
like that all required properties are present and that they have the correct
multiplicity, and that all identifiers are CURIE's.
"""
import networkx as nx
from kgx.utils.kgx_utils import get_toolkit
toolkit = get_toolkit()
[docs]def make_valid_types(G:nx.MultiDiGraph) -> None:
"""
Ensures that all the nodes have valid categories, and that all edges have
valid edge labels.
Nodes will be deleted if they have no name and have no valid categories. If
a node has no valid category but does have a name then its category will be
set to the default category "named thing".
Edges with invalid edge labels will have their edge label set to the default
value "related_to"
"""
nodes = []
for n, data in G.nodes(data=True):
data['category'] = [c for c in data.get('category', []) if toolkit.get_element(c) is not None]
if data['category'] == []:
if 'name' in data:
data['category'] = ['named thing']
else:
nodes.append(n)
G.remove_nodes_from(nodes)
for u, v, data in G.edges(data=True):
if toolkit.get_element(data.get('edge_label')) is None:
data['edge_label'] = 'related_to'
elif ' ' in data['edge_label']:
data['edge_label'] = data['edge_label'].replace(' ', '_')