def main():
args = parse_args(__doc__, version='negbio version 2', options_first=True)
logging.debug('CWD: %s', os.getcwd())
argv = [args['<command>']] + args['<args>']
if args['<command>'] == 'text2bioc':
exit(call(['python', '-m', 'negbio.negbio_text2bioc'] + argv))
elif args['<command>'] == 'normalize':
exit(call(['python', '-m', 'negbio.negbio_normalize'] + argv))
elif args['<command>'] == 'section_split':
exit(call(['python', '-m', 'negbio.negbio_section_split'] + argv))
elif args['<command>'] == 'ssplit':
exit(call(['python', '-m', 'negbio.negbio_ssplit'] + argv))
elif args['<command>'] == 'parse':
exit(call(['python', '-m', 'negbio.negbio_parse'] + argv))
elif args['<command>'] == 'ptb2ud':
exit(call(['python', '-m', 'negbio.negbio_ptb2ud'] + argv))
elif args['<command>'] == 'dner_mm':
exit(call(['python', '-m', 'negbio.negbio_dner_matamap'] + argv))
elif args['<command>'] == 'dner_chexpert':
exit(call(['python', '-m', 'negbio.negbio_dner_chexpert'] + argv))
elif args['<command>'] == 'neg':
exit(call(['python', '-m', 'negbio.negbio_neg'] + argv))
elif args['<command>'] == 'neg_chexpert':
exit(call(['python', '-m', 'negbio.negbio_neg_chexpert'] + argv))
elif args['<command>'] == 'cleanup':
exit(call(['python', '-m', 'negbio.negbio_clean'] + argv))
elif args['<command>'] in ['help', None]:
exit(call(['python', '-m', 'negbio.negbio_pipeline', '--help']))
else:
exit("%r is not a negbio command. See 'negbio help'." %
args['<command>'])
def main():
argv = parse_args(__doc__, version='version 2')
print(argv)
lemmatizer = Lemmatizer()
ptb2dep = NegBioPtb2DepConverter(lemmatizer, universal=True)
splitter = NegBioSSplitter(newline=argv['--newline_is_sentence_break'])
parser = NegBioParser(model_dir=argv['--bllip-model'])
argv = get_absolute_path(argv, '--neg-patterns',
'negbio/patterns/neg_patterns.txt')
argv = get_absolute_path(argv, '--uncertainty-patterns',
'negbio/patterns/uncertainty_patterns.txt')
mm = pymetamap.MetaMap.get_instance(argv['--metamap'])
neg_detector = negdetect.Detector(argv['--neg-patterns'],
argv['--uncertainty-patterns'])
if argv['--cuis'] == 'None':
cuis = None
else:
cuis = read_cuis(argv['--cuis'])
if argv['text']:
collection = text2bioc.text2collection(argv['SOURCES'])
elif argv['bioc']:
with open(argv['SOURCE']) as fp:
collection = bioc.load(fp)
else:
raise KeyError
pipeline(collection, mm, splitter, parser, ptb2dep, neg_detector, cuis)
with open(os.path.expanduser(argv['--output']), 'w') as fp:
bioc.dump(collection, fp)
def main():
argv = parse_args(__doc__, version='version 2')
print(argv)
lemmatizer = Lemmatizer()
ptb2dep = NegBioPtb2DepConverter(lemmatizer, universal=True)
ssplitter = NegBioSSplitter(newline=argv['--newline_is_sentence_break'])
parser = NegBioParser(model_dir=argv['--bllip-model'])
argv = get_absolute_path(argv, '--mention_phrases_dir',
'negbio/chexpert/phrases/mention')
argv = get_absolute_path(argv, '--unmention_phrases_dir',
'negbio/chexpert/phrases/unmention')
argv = get_absolute_path(
argv, '--pre-negation-uncertainty-patterns',
'negbio/chexpert/patterns/pre_negation_uncertainty.txt')
argv = get_absolute_path(
argv, '--post-negation-uncertainty-patterns',
'negbio/chexpert/patterns/post_negation_uncertainty.txt')
argv = get_absolute_path(argv, '--neg-patterns',
'negbio/chexpert/patterns/negation.txt')
# chexpert
loader = NegBioLoader()
extractor = NegBioExtractor(Path(argv['--mention_phrases_dir']),
Path(argv['--unmention_phrases_dir']),
verbose=argv['--verbose'])
neg_detector = ModifiedDetector(
argv['--pre-negation-uncertainty-patterns'], argv['--neg-patterns'],
argv['--post-negation-uncertainty-patterns'])
aggregator = NegBioAggregator(CATEGORIES, verbose=argv['--verbose'])
if argv['text']:
collection = text2bioc.text2collection(argv['SOURCES'])
elif argv['bioc']:
with open(argv['SOURCE']) as fp:
collection = bioc.load(fp)
else:
raise KeyError
pipeline(collection,
loader,
ssplitter,
extractor,
parser,
ptb2dep,
neg_detector,
aggregator,
verbose=argv['--verbose'])
with open(os.path.expanduser(argv['--output']), 'w') as fp:
bioc.dump(collection, fp)
from negbio.pipeline2.dner_mm import MetaMapExtractor
from negbio.pipeline2.pipeline import NegBioPipeline
from pymetamap import MetaMap
def read_cuis(pathname):
cuis = set()
with open(pathname) as fp:
for line in fp:
line = line.strip()
if line:
cuis.add(line)
return cuis
if __name__ == '__main__':
argv = parse_args(__doc__)
mm = MetaMap.get_instance(argv['--metamap'])
if argv['--cuis'] is None:
cuis = None
else:
cuis = read_cuis(argv['--cuis'])
extractor = MetaMapExtractor(mm, cuis)
pipeline = NegBioPipeline(pipeline=[('MetaMapExtractor', extractor)])
pipeline.scan(source=argv['<file>'],
directory=argv['--output'],
suffix=argv['--suffix'],
overwrite=argv['--overwrite'])
