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feat: Support whitelist of cuis for UMLS dictionary install #21

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feat: Support whitelist of cuis for UMLS dictionary install #21

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23 changes: 20 additions & 3 deletions quickumls/install.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,15 +39,16 @@ def get_mrconso_iterator(path, headers, lang='ENG'):
for i, ln in enumerate(f):
content = dict(zip(headers, ln.strip().split('|')))

if content['lat'] != lang:
if content.get('lat', None) != lang:
continue

yield content


def extract_from_mrconso(
mrconso_path, mrsty_path, opts,
mrconso_header=HEADERS_MRCONSO, mrsty_header=HEADERS_MRSTY):
mrconso_header=HEADERS_MRCONSO, mrsty_header=HEADERS_MRSTY,
cui_whitelist=None):

start = time.time()
print('loading semantic types...', end=' ')
Expand Down Expand Up @@ -81,6 +82,9 @@ def extract_from_mrconso(
cui = content['cui']
preferred = 1 if content['ispref'] == 'Y' else 0

if cui_whitelist is not None and cui not in cui_whitelist:
continue

if opts.lowercase:
concept_text = concept_text.lower()

Expand Down Expand Up @@ -161,6 +165,10 @@ def parse_args():
'-E', '--language', default='ENG', choices=LANGUAGES,
help='Extract concepts of the specified language'
)
ap.add_argument(
'-C', '--include-cuis',
help='Whitelist of cuis to include in installation'
)
opts = ap.parse_args()
return opts

Expand Down Expand Up @@ -220,7 +228,16 @@ def main():
mrconso_path = os.path.join(opts.umls_installation_path, 'MRCONSO.RRF')
mrsty_path = os.path.join(opts.umls_installation_path, 'MRSTY.RRF')

mrconso_iterator = extract_from_mrconso(mrconso_path, mrsty_path, opts)
if opts.include_cuis is not None:
with open(opts.include_cuis) as f:
cui_whitelist = f.read().splitlines()
else:
cui_whitelist = None

mrconso_iterator = extract_from_mrconso(
mrconso_path, mrsty_path,
opts, cui_whitelist=cui_whitelist,
)

simstring_dir = os.path.join(opts.destination_path, 'umls-simstring.db')
cuisty_dir = os.path.join(opts.destination_path, 'cui-semtypes.db')
Expand Down