def categorize(self):
memo = {}
with click.progressbar(self.graph.nodes(data=True)) as bar:
for n, data in bar:
if n == 'Orphanet:98818':
import pudb
pu.db
if 'category' not in data or data['category'] == [
'named thing'
]:
superclass = find_superclass(n, self.graph)
if superclass is not None:
data['category'] = [superclass]
with click.progressbar(self.graph.edges(data=True)) as bar:
for u, v, data in bar:
if 'edge_label' not in data or data[
'edge_label'] is None or data[
'edge_label'] == 'related_to':
relation = data.get('relation')
if relation not in memo:
memo[relation] = find_superclass(relation, self.graph)
if memo[relation] is not None:
data['edge_label'] = memo[relation]
def categorize(self) -> None:
"""
Checks for a node's category property and assigns a category from BioLink Model.
Checks for an edge's edge_label property and assigns a label from BioLink Model.
"""
memo = {}
with click.progressbar(
self.graph.nodes(data=True),
label='Finding superclass category for nodes') as bar:
for n, data in bar:
if 'category' not in data or data['category'] == [
'named thing'
]:
# if there is no category property for a node
# or category is simply 'named thing'
# then find a BioLink Model relevant category
superclass = find_superclass(n, self.graph)
if superclass is not None:
data['category'] = [superclass]
with click.progressbar(
self.graph.edges(data=True),
label='Finding superclass category for edges') as bar:
for u, v, data in bar:
if 'edge_label' not in data or data[
'edge_label'] is None or data[
'edge_label'] == 'related_to':
# if there is no edge_label property for an edge
# or if edge_label property is None
# or if edge_label is simply 'related_to'
# then find a BioLink Model relevant edge_label
relation = data.get('relation')
if relation not in memo:
superclass = find_superclass(relation, self.graph)
memo[relation] = fmt_edgelabel(superclass)
if memo[relation] is not None:
data['edge_label'] = memo[relation]
# Set all null categories to the default value, and format all others
with click.progressbar(self.graph.nodes(data='category'),
label='Ensuring valid categories') as bar:
for n, category in bar:
if not isinstance(category, list) or category == []:
self.graph.node[n]['category'] = ['named thing']
else:
category = [fmt_category(c) for c in category]
# Set all null edgelabels to the default value, and format all others
with click.progressbar(self.graph.edges(data=True),
label='Ensuring valid edge labels') as bar:
for u, v, data in bar:
if 'edge_label' not in data or data['edge_label'] is None:
data['edge_label'] = 'related_to'
else:
data['edge_label'] = fmt_edgelabel(data['edge_label'])