def process_document(self, document: Document, params: Dict[str, Any]):
terms_index_name = params.get('terms_index', 'umls_terms')
label_negated = document.get_labeler('negated')
terms = document.get_label_index(terms_index_name)
triggers = document.labels['negation_triggers']
deps = document.get_label_index('dependencies')
upos_tags = document.get_label_index('upos_tags')
with label_negated:
for sentence in document.get_label_index('sentences'):
sentence_terms = terms.inside(sentence)
sentence_triggers = triggers.inside(sentence)
if len(sentence_triggers) > 0:
negations, _ = self.negex.check_sentence(
sentence_terms, sentence_triggers, deps, upos_tags)
for start_index, end_index in negations:
label_negated(start_index, end_index)
def process_document(self, document: Document, params: Dict[str, Any]):
label_trigger = document.get_labeler('negation_triggers')
with label_trigger:
for sentence in document.get_label_index('sentences'):
triggers = self.negex.detect_negex_triggers(sentence.text)
for start_index, end_index, tags in triggers:
label_trigger(sentence.start_index + start_index,
sentence.start_index + end_index,
tags=tags)
def process_document(self, document: Document, params: Dict[str, Any]):
terms_index_name = params.get('terms_index', 'umls_terms')
label_negated = document.get_labeler('negated')
label_trigger = document.get_labeler('negation_trigger')
terms = document.get_label_index(terms_index_name)
with label_negated, label_trigger:
for sentence in document.get_label_index('sentences'):
sentence_terms = [(t.start_index - sentence.start_index,
t.end_index - sentence.start_index)
for t in terms.inside(sentence)]
negations, triggers = self.negex.check_sentence(
sentence.text, sentence_terms)
for start_index, end_index in negations:
label_negated(sentence.start_index + start_index,
sentence.start_index + end_index)
for start_index, end_index in triggers:
label_trigger(sentence.start_index + start_index,
sentence.start_index + end_index)
def test_labeler_distinct(mocker):
client = mocker.Mock(EventsClient)
event = Event(event_id='1', client=client)
document = Document(document_name='plaintext',
text='The quick brown fox jumped over the lazy dog.',
event=event)
with document.get_labeler('index', distinct=True) as add_generic_label:
add_generic_label(0, 10, x=1)
add_generic_label(11, 15, x=2)
add_generic_label(16, 20, x=3)
labels = [
GenericLabel(0, 10, document=document, x=1),
GenericLabel(11, 15, document=document, x=2),
GenericLabel(16, 20, document=document, x=3)
]
label_adapter = DistinctGenericLabelAdapter
client.add_labels.assert_called_with(event_id='1',
document_name='plaintext',
index_name='index',
labels=labels,
adapter=label_adapter)
assert document.get_label_index('index') == labels
def test_sentences_unknown_character(bi_lstm_model):
document = Document('plaintext',
text='• Sentence which contains unknown character.')
bi_lstm_model.process_document(document, {})
assert document.get_label_index('sentences') == [GenericLabel(2, 44)]
# Copyright 2019 Regents of the University of Minnesota.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Hello world tutorial pipeline."""
import sys
if __name__ == '__main__':
from mtap import Document, Event, EventsClient, Pipeline, RemoteProcessor
with EventsClient(address=sys.argv[1]) as client, \
Pipeline(
RemoteProcessor(processor_id='hello', address=sys.argv[2])
) as pipeline:
with Event(event_id='1', client=client) as event:
document = Document(document_name='name', text='YOUR NAME')
event.add_document(document)
pipeline.run(document)
index = document.get_label_index('hello')
for label in index:
print(label.response)