def process_document(self, document: mtap.Document, params: Dict[str,
Any]):
referenced = [
mtap.GenericLabel(0, 1),
mtap.GenericLabel(1, 2),
mtap.GenericLabel(2, 3),
mtap.GenericLabel(3, 4)
]
# references can be a map of strings to labels
with document.get_labeler('map_references') as label_map_references:
label_map_references(0,
4,
ref={
'a': referenced[0],
'b': referenced[1],
'c': referenced[2],
'd': referenced[3]
})
# references can be a list of labels
with document.get_labeler('list_references') as label_list_references:
label_list_references(0, 2, ref=[referenced[0], referenced[1]])
label_list_references(2, 3, ref=[referenced[2], referenced[3]])
# references can be direct
with document.get_labeler('references') as label_references:
label_references(0, 2, a=referenced[0], b=referenced[1])
label_references(2, 3, a=referenced[2], b=referenced[3])
# referenced labels don't need to be added via "addLabels" or "Labeler.close" before label
# indices that reference them.
# The Document will delay uploading any label indices to the server until they are.
document.add_labels('referenced', referenced)
def test_labeler_distinct_and_type_id_raises(mocker):
with pytest.raises(ValueError):
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)
document.get_labeler('index',
distinct=True,
label_adapter=DistinctGenericLabelAdapter)
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 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: mtap.Document,
params: Dict[str, Any]) -> Optional[Dict[str, Any]]:
if params['do_work']:
with self.started_stopwatch('fetch_time'):
text = document.text
a_count = text.count('a')
b_count = text.count('b')
with document.get_labeler('mtap.examples.letter_counts') as label_letter_count:
label_letter_count(start_index=0, end_index=len(document.text), letter='a',
count=a_count)
label_letter_count(start_index=0, end_index=len(document.text), letter='b',
count=b_count)
return {'answer': 42}
def test_copy_document():
e = Event()
doc = Document(document_name='first',
text='The quick brown fox jumped over the lazy dog.')
e.add_document(doc)
with doc.get_labeler('some_index') as label:
label(0, 3, word='The')
label(4, 9, word='quick')
label(10, 15, word='brown')
processor = CopyDocument('first', 'second')
processor.process(e, {})
second = e.documents['second']
assert second is not None
assert second.labels['some_index'] == [
GenericLabel(0, 3, word='The'),
GenericLabel(4, 9, word='quick'),
GenericLabel(10, 15, word='brown')
]
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_labeler_distinct(mocker):
client = mocker.Mock(EventsClient)
client.get_local_instance.return_value = client
client.get_label_index_info.return_value = []
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 = DISTINCT_GENERIC_ADAPTER
client.add_labels.assert_called_with(event_id='1',
document_name='plaintext',
index_name='index',
labels=labels,
adapter=label_adapter)
assert document.labels['index'] == labels
def process_document(self, document: Document, params: Dict[str, Any]):
with document.get_labeler('sentences', distinct=True) as add_sentence:
for start, end in predict_text(self.model, self.input_mapper,
document.text, self.device):
add_sentence(start, end)
def process_document(self, document: Document, params: Dict[str, Any]):
with document.get_labeler('sentences') as sentence_labeler:
for start, end in get_sentences(document.text):
sentence_labeler(start, end)
def process_document(self, document: Document, params: Dict[str, Any]):
text = document.text
result = self.pool.apply(predict_sentences_async, args=(text, ))
with document.get_labeler('sentences', distinct=True) as add_sentence:
for start, end in result:
add_sentence(start, end)
