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remove unused code and fix invalid total terms percentage (#324)
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Anita Caron authored May 24, 2024
1 parent 8be835f commit 251326f
Showing 1 changed file with 4 additions and 26 deletions.
30 changes: 4 additions & 26 deletions src/ccf_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,6 @@ def no_parent(log_dict, cell_type, row_number):
ct_invalid_terms = set()
ct_temp_terms = set()
ct_out_ct = set()
unique_terms = set()
as_valid_terms = set()
ct_valid_terms = set()
rt = []
Expand All @@ -73,10 +72,6 @@ def no_parent(log_dict, cell_type, row_number):
for current, next in zip(anatomical_structures, anatomical_structures[1:]):
log_dict, terms_set = is_valid_id(log_dict, current, row["rowNumber"], terms_set)
log_dict, terms_set = is_valid_id(log_dict, next, row["rowNumber"], terms_set)
if current['id'] != '':
unique_terms.add(current['id'])
if next['id'] != '':
unique_terms.add(next['id'])
if check_id(current['id']) and check_id(next['id']):
d = {}
d['s'] = next['id']
Expand All @@ -96,29 +91,25 @@ def no_parent(log_dict, cell_type, row_number):
else:
as_temp_terms.add(current['rdfs_label'])
as_invalid_terms.add(current['rdfs_label'])
unique_terms.add(current['rdfs_label'])
elif not check_id(current['id']) and current['name'] != '':
if current['id'] != '':
as_out_ub.add(current['id'])
else:
as_temp_terms.add(current['name'])
as_invalid_terms.add(current['name'])
unique_terms.add(current['name'])

if not check_id(next['id']) and next['rdfs_label'] != '':
if next['id'] != '':
as_out_ub.add(next['id'])
else:
as_temp_terms.add(next['rdfs_label'])
as_invalid_terms.add(next['rdfs_label'])
unique_terms.add(next['rdfs_label'])
elif not check_id(next['id']) and next['name'] != '':
if next['id'] != '':
as_out_ub.add(next['id'])
else:
as_temp_terms.add(next['name'])
as_invalid_terms.add(next['name'])
unique_terms.add(next['name'])

# CT-CT RELATIONSHIP
cell_types = row['cell_types']
Expand All @@ -127,10 +118,6 @@ def no_parent(log_dict, cell_type, row_number):
for current, next in zip(cell_types, cell_types[1:]):
log_dict, terms_set = is_valid_id(log_dict, current, row["rowNumber"], terms_set)
log_dict, terms_set = is_valid_id(log_dict, next, row["rowNumber"], terms_set)
if current['id'] != '':
unique_terms.add(current['id'])
if next['id'] != '':
unique_terms.add(next['id'])
if check_id(current['id']) and check_id(next['id']):
d = {}
d['row_number'] = row['rowNumber']
Expand All @@ -150,29 +137,25 @@ def no_parent(log_dict, cell_type, row_number):
else:
ct_temp_terms.add(current['rdfs_label'])
ct_invalid_terms.add(current['rdfs_label'])
unique_terms.add(current['rdfs_label'])
elif not check_id(current['id']) and current['name'] != '':
if current['id'] != '':
ct_out_ct.add(current['id'])
else:
ct_temp_terms.add(current['name'])
ct_invalid_terms.add(current['name'])
unique_terms.add(current['name'])

if not check_id(next['id']) and next['rdfs_label'] != '':
if next['id'] != '':
ct_out_ct.add(next['id'])
else:
ct_temp_terms.add(next['rdfs_label'])
ct_invalid_terms.add(next['rdfs_label'])
unique_terms.add(next['rdfs_label'])
elif not check_id(next['id']) and next['name'] != '':
if next['id'] != '':
ct_out_ct.add(next['id'])
else:
ct_temp_terms.add(next['name'])
ct_invalid_terms.add(next['name'])
unique_terms.add(next['name'])

if not check_id(current['id']) and (check_id(next['id']) or not check_id(next['id'])):
log_dict = no_parent(log_dict, next, row['rowNumber'])
Expand All @@ -199,8 +182,6 @@ def no_parent(log_dict, cell_type, row_number):
dl.append(d)
as_valid_terms.add(last_as['id'])
ct_valid_terms.add(last_ct['id'])
unique_terms.add(last_as['id'])
unique_terms.add(last_ct['id'])
else:
if check_id(last_as['id']):
as_valid_terms.add(last_as['id'])
Expand All @@ -212,29 +193,25 @@ def no_parent(log_dict, cell_type, row_number):
else:
as_temp_terms.add(last_as['rdfs_label'])
as_invalid_terms.add(last_as['rdfs_label'])
unique_terms.add(last_as['rdfs_label'])
elif not check_id(last_as['id']) and last_as['name'] != '':
if last_as['id'] != '':
as_out_ub.add(last_as['id'])
else:
as_temp_terms.add(last_as['name'])
as_invalid_terms.add(last_as['name'])
unique_terms.add(last_as['name'])

if not check_id(last_ct['id']) and last_ct['rdfs_label'] != '':
if last_ct['id'] != '':
ct_out_ct.add(last_ct['id'])
else:
ct_temp_terms.add(last_ct['rdfs_label'])
ct_invalid_terms.add(last_ct['rdfs_label'])
unique_terms.add(last_ct['rdfs_label'])
elif not check_id(last_ct['id']) and last_ct['name'] != '':
if last_ct['id'] != '':
ct_out_ct.add(last_ct['id'])
else:
ct_temp_terms.add(last_ct['name'])
ct_invalid_terms.add(last_ct['name'])
unique_terms.add(last_ct['name'])

# NEW CL TERMS REPORT
for cl in cell_types:
Expand Down Expand Up @@ -267,16 +244,17 @@ def no_parent(log_dict, cell_type, row_number):
rut.append(r)



total_terms = len(as_valid_terms) + len(as_invalid_terms) + len(ct_valid_terms) + len(ct_invalid_terms)
as_invalid_term_percent = 0
ct_invalid_terms_percent = 0
invalid_terms_percent = 0
if len(as_valid_terms) + len(ct_invalid_terms) > 0:
as_invalid_term_percent = round((len(as_invalid_terms)*100)/(len(as_valid_terms)+len(as_invalid_terms)), 2)
if len(ct_valid_terms) + len(ct_invalid_terms) > 0:
ct_invalid_terms_percent = round((len(ct_invalid_terms)*100)/(len(ct_valid_terms)+len(ct_invalid_terms)), 2)
if len(unique_terms) > 0:
invalid_terms_percent = round((len(as_invalid_terms)+len(ct_invalid_terms))*100/len(unique_terms), 2)
if total_terms > 0:
print(total_terms)
invalid_terms_percent = round(((len(as_invalid_terms)+len(ct_invalid_terms))/total_terms)*100, 2)

report_terms = {
'Table': '',
Expand Down

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