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)
negbio_pipeline neg [options] --output=<directory> <file> ...
Options:
--neg-patterns=<file> Specify negation rules [default: negbio/patterns/neg_patterns.txt]
--uncertainty-patterns=<file> Specify uncertainty rules [default: negbio/patterns/uncertainty_patterns.txt]
--suffix=<suffix> Append an additional SUFFIX to file names. [default: .neg.xml]
--verbose Print more information about progress.
--output=<directory> Specify the output directory.
"""
import os
from negbio.cli_utils import parse_args, get_absolute_path
from negbio.neg.neg_detector import Detector
from negbio.pipeline.negdetect import detect
from negbio.pipeline.scan import scan_document
if __name__ == '__main__':
argv = parse_args(__doc__)
argv = get_absolute_path(argv,
'--neg-patterns',
'negbio/patterns/neg_patterns.txt')
argv = get_absolute_path(argv,
'--uncertainty-patterns',
'negbio/patterns/uncertainty_patterns.txt')
neg_detector = Detector(os.path.realpath(argv['--neg-patterns']),
os.path.realpath(argv['--uncertainty-patterns']))
scan_document(source=argv['<file>'], directory=argv['--output'], suffix=argv['--suffix'],
fn=detect, non_sequences=[neg_detector])
from negbio.chexpert.stages.extract import NegBioExtractor
from negbio.cli_utils import parse_args, get_absolute_path
from negbio.pipeline.scan import scan_collection
def run_extractor(collection, extractor):
"""
Args:
collection (BioCCollection):
extractor (NegBioExtractor):
"""
extractor.extract_all(collection)
if __name__ == '__main__':
argv = parse_args(__doc__)
argv = get_absolute_path(argv, '--mention_phrases_dir',
'negbio/chexpert/phrases/mention')
argv = get_absolute_path(argv, '--unmention_phrases_dir',
'negbio/chexpert/phrases/unmention')
extractor = NegBioExtractor(Path(argv['--mention_phrases_dir']),
Path(argv['--unmention_phrases_dir']),
verbose=argv['--verbose'])
scan_collection(source=argv['<file>'],
directory=argv['--output'],
suffix=argv['--suffix'],
fn=run_extractor,
non_sequences=[extractor])
--suffix=<suffix> Append an additional SUFFIX to file names. [default: .neg.xml]
--verbose Print more information about progress.
--output=<directory> Specify the output directory.
"""
import os
from negbio.chexpert.stages.classify import ModifiedDetector
from negbio.cli_utils import parse_args, get_absolute_path
from negbio.pipeline.negdetect import detect
from negbio.pipeline.scan import scan_document
if __name__ == '__main__':
argv = parse_args(__doc__)
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')
neg_detector = ModifiedDetector(
argv['--pre-negation-uncertainty-patterns'], argv['--neg-patterns'],
argv['--post-negation-uncertainty-patterns'])
scan_document(source=argv['<file>'],
directory=argv['--output'],
suffix=argv['--suffix'],
fn=detect,
non_sequences=[neg_detector])