for length, tags in hits:
first_token_idx = i + 1 - length
triggers.append(
(tokens[first_token_idx][0], tokens[i][1], tags))
return triggers
@processor(
name='biomedicus-negex-triggers',
human_name='Negex Triggers Tagger',
description='Labels phrases which are negation triggers.',
entry_point=__name__,
parameters=[
parameter(
name='terms_index',
data_type='str',
description=
'The label index containing terms that should be checked for negation'
)
],
inputs=[
label_index(name='sentences',
reference='biomedicus-sentences/sentences'),
label_index(name='umls_terms',
reference='biomedicus-concepts/umls_terms',
name_from_parameter='terms_index')
],
outputs=[
label_index("negation_trigger",
description="Spans of phrases that trigger negation.",
properties=[
label_property(
from typing import Dict, Any, Optional
import mtap
from mtap.events import Document
from mtap.processing import DocumentProcessor, run_processor
from mtap.processing.descriptions import label_index, label_property, parameter
@mtap.processor(
'mtap-example-processor-python',
human_name="Python Example Processor",
description=
"counts the number of times the letters a and b occur in a document",
parameters=[
parameter('do_work',
required=True,
data_type='bool',
description="Whether the processor should do anything.")
],
outputs=[
label_index('mtap.examples.letter_counts',
properties=[
label_property('letter', data_type='str'),
label_property('count', data_type='int')
])
])
class ExampleProcessor(DocumentProcessor):
"""Does some labeling of the counts of the letter 'a' and 'b' in a document.
"""
def process_document(self, document: Document,
params: Dict[str, Any]) -> Optional[Dict[str, Any]]:
if params['do_work']:
import grpc
import grpc_testing
import pytest
from mtap import processor, Document
from mtap.api.v1 import processing_pb2
from mtap.processing import DocumentProcessor, _runners
from mtap.processing.descriptions import parameter, labels, label_property
from mtap.processing._service import _ProcessorServicer
@processor('mtap-test-processor',
description='Processor desc.',
parameters=[
parameter('a_param',
required=True,
data_type='bool',
description="desc.")
],
inputs=[
labels('input_index',
properties=[label_property('bar', data_type='bool')])
],
outputs=[
labels('output_index',
description='desc.',
properties=[
label_property('foo',
data_type='str',
nullable=True,
description='A label property.')
])
f (~typing.Union[~pathlib.Path, str, ~io.IOBase]): The file to load from.
client (~typing.Optional[EventsClient]): The events service to load the event into.
Returns:
Event: The loaded event object.
"""
...
@processor(
'mtap-serializer',
description='Serializes events to a specific directory',
parameters=[
parameter(
'filename',
data_type='str',
description='Optional override for the filename to write the '
'document to.')
])
class SerializationProcessor(EventProcessor):
"""An MTAP :obj:`EventProcessor` that serializes events to a specific directory.
Args:
ser (Serializer): The serializer to use.
output_dir (str): The output_directory.
"""
def __init__(self,
ser: Serializer,
output_dir: str,
include_label_text: bool = False):
self.serializer = ser