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Fixes for better performance #11

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merged 2 commits into from
Oct 14, 2022
Merged

Fixes for better performance #11

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bd6b3ff
Fixes for better performance
caufieldjh Oct 14, 2022
89cd0a0
Typing fix / bugfix
caufieldjh Oct 14, 2022
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19 changes: 8 additions & 11 deletions universalizer/norm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ def clean_and_normalize_graph(filepath,
remap_these_nodes = make_id_maps(nodepath,
os.path.dirname(nodepath))

remove_these_edges: List[list] = []
remove_these_edges: List[str] = []

if update_categories:
remap_these_categories, \
Expand All @@ -95,6 +95,7 @@ def clean_and_normalize_graph(filepath,
os.path.dirname(nodepath),
use_oak)

print("Updating graph files...")
# Continue with mapping if everything's OK so far
# Sometimes prefixes get capitalized, so we check for that too
try:
Expand All @@ -115,30 +116,27 @@ def clean_and_normalize_graph(filepath,
new_node_id = remap_these_nodes[line_split[0]]
line_split[0] = new_node_id
changed_this_line = True
line = "\t".join(line_split) + "\n"
if update_categories:
if line_split[0] in remap_these_categories:
new_node_cat = \
remap_these_categories[line_split[0]]
line_split[1] = new_node_cat
changed_this_line = True
line = "\t".join(line_split) + "\n"
if using_sssom:
if line_split[0] in recats:
line_split[1] = recats[line_split[0]]
changed_this_line = True
if line_split[0] in remaps:
line_split[0] = remaps[line_split[0]]
changed_this_line = True
line = "\t".join(line_split) + "\n"
if changed_this_line:
mapcount = mapcount + 1
line = "\t".join(line_split) + "\n"
outnodefile.write(line)
for line in inedgefile:
rem_edge_count = 0
line_split = (line.rstrip()).split("\t")
if [line_split[1], line_split[2], line_split[3]] \
in remove_these_edges:
if line_split[0] in remove_these_edges:
rem_edge_count = rem_edge_count + 1
continue
if mapping:
Expand All @@ -148,13 +146,12 @@ def clean_and_normalize_graph(filepath,
new_node_id = \
remap_these_nodes[line_split[col]]
line_split[col] = new_node_id
line = "\t".join(line_split) + "\n"
if using_sssom:
if line_split[col] in remaps:
new_node_id = \
remaps[line_split[col]]
line_split[col] = new_node_id
line = "\t".join(line_split) + "\n"
line = "\t".join(line_split) + "\n"
outedgefile.write(line)

os.replace(outnodepath, nodepath)
Expand Down Expand Up @@ -293,7 +290,7 @@ def make_cat_maps(input_nodes: str,
id_and_cat_map: Dict[str, str] = {}
mal_cat_list = []
update_cats: Dict[str, str] = {}
remove_edges: List[list] = []
remove_edges: List[str] = []

print(f"Retrieving categories in {input_nodes}...")

Expand Down Expand Up @@ -328,14 +325,14 @@ def make_cat_maps(input_nodes: str,
edgefile.readline()
for line in edgefile:
splitline = line.rstrip().split("\t")
edge_id = splitline[0]
subj_node_id = splitline[1]
pred = splitline[2]
obj_node_id = splitline[3]
if pred.lower() == "biolink:category":
remove_edges.append([subj_node_id, pred, obj_node_id])
if obj_node_id not in \
["biolink:NamedThing", "biolink:OntologyClass"]:
remove_edges.append([subj_node_id, pred, obj_node_id])
remove_edges.append(edge_id)
update_cats[subj_node_id] = obj_node_id

# For each id, check its category in the nodelist first
Expand Down