def main(args=None):
parser = ArgumentParser()
parser.add_argument('input_file')
parser.add_argument('output_file')
conf = parser.parse_args(args)
with open(conf.input_file, 'r') as io:
conllu_document = io.read()
for document in read_into_documents(conllu_document):
PickleSerializer.event_to_file(
document.event,
conf.output_file + '/' + document.event.event_id + '.pickle')
def test_concepts_performance(events_service, concepts_service, test_results):
input_dir = Path(os.environ['BIOMEDICUS_TEST_DATA']) / 'concepts'
recall = Accuracy(name='recall', mode='any', fields=['cui'])
precision = Accuracy(name='precision', mode='any', fields=['cui'])
with EventsClient(address=events_service) as client, \
Pipeline(
RemoteProcessor(processor_id='biomedicus-concepts', address=concepts_service),
LocalProcessor(Metrics(recall, tested='umls_concepts', target='gold_concepts'),
component_id='metrics'),
LocalProcessor(Metrics(precision, tested='gold_concepts', target='umls_concepts'),
component_id='metrics_reverse'),
events_client=client
) as pipeline:
for test_file in input_dir.glob('**/*.pickle'):
with PickleSerializer.file_to_event(test_file, client=client) as event:
document = event.documents['plaintext']
pipeline.run(document)
print('Precision:', precision.value)
print('Recall:', recall.value)
timing_info = pipeline.processor_timer_stats('biomedicus-concepts').timing_info
test_results['Concepts'] = {
'Precision': precision.value,
'Recall': recall.value,
'Remote Call Duration': str(timing_info['remote_call'].mean),
'Process Method Duration': str(timing_info['process_method'].mean)
}
assert recall.value > 0.6
def test_tnt_performance(events_service, pos_tags_service, test_results):
input_dir = Path(os.environ['BIOMEDICUS_TEST_DATA']) / 'pos_tags'
accuracy = Accuracy()
with EventsClient(address=events_service) as client, Pipeline(
RemoteProcessor(processor_id='biomedicus-tnt-tagger',
address=pos_tags_service,
params={'token_index': 'gold_tags'}),
LocalProcessor(Metrics(accuracy,
tested='pos_tags',
target='gold_tags'),
component_id='metrics'),
events_client=client) as pipeline:
for test_file in input_dir.glob('**/*.pickle'):
event = PickleSerializer.file_to_event(test_file, client=client)
with event:
document = event.documents['gold']
results = pipeline.run(document)
print(
'Accuracy for event - ', event.event_id, ':',
results.component_result(
'metrics').result_dict['accuracy'])
print('Accuracy:', accuracy.value)
pipeline.print_times()
timing_info = pipeline.processor_timer_stats(
'biomedicus-tnt-tagger').timing_info
test_results['TnT Pos Tagger'] = {
'Accuracy': accuracy.value,
'Remote Call Duration': str(timing_info['remote_call'].mean),
'Process Method Duration': str(timing_info['process_method'].mean)
}
assert accuracy.value > 0.9
def test_dependencies(events_service, dependencies_service, test_results):
test_dir = Path(os.environ['BIOMEDICUS_TEST_DATA']) / 'dependencies'
uas = Accuracy('UAS', equivalence_test=uas_equal)
las = Accuracy('LAS', equivalence_test=las_equal)
with EventsClient(address=events_service) as client, \
Pipeline(
RemoteProcessor(processor_id='biomedicus-dependencies',
address=dependencies_service),
LocalProcessor(Metrics(uas, las, tested='dependencies', target='gold_dependencies'),
component_id='accuracy', client=client)
) as pipeline:
for test_file in test_dir.glob('**/*.pickle'):
with PickleSerializer.file_to_event(test_file,
client=client) as event:
document = event.documents['plaintext']
results = pipeline.run(document)
accuracy_dict = results.component_result(
'accuracy').result_dict
print('Results for document: UAS: {}. LAS: {}.'.format(
accuracy_dict['UAS'], accuracy_dict['LAS']))
print('UAS:', uas.value)
print('LAS:', las.value)
timing_info = pipeline.processor_timer_stats(
'biomedicus-dependencies').timing_info
test_results['biomedicus-dependencies'] = {
'UAS': uas.value,
'LAS': las.value,
'Corpus': "MiPACQ converted to UD from PTB test set",
'Remote Call Duration': str(timing_info['remote_call'].mean),
'Process Method Duration': str(timing_info['process_method'].mean)
}
def test_modification_detector_performance(events_service, modification_detector_service,
test_results):
input_dir = Path(os.environ['BIOMEDICUS_TEST_DATA']) / 'negation' / 'i2b2_2010'
confusion = metrics.FirstTokenConfusion()
metrics_processor = metrics.Metrics(confusion, tested='negated', target='i2b2concepts',
target_filter=is_negated)
with EventsClient(address=events_service) as client, Pipeline(
RemoteProcessor('biomedicus-negation', address=modification_detector_service,
params={'terms_index': 'i2b2concepts'}),
LocalProcessor(metrics_processor, component_id='metrics', client=client)
) as pipeline:
for test_file in input_dir.glob('**/*.pickle'):
with PickleSerializer.file_to_event(test_file, client=client) as event:
document = event.documents['plaintext']
results = pipeline.run(document)
print('F1 for event - "{}": {:0.3f} - elapsed: {}'.format(
event.event_id,
results.component_result('metrics').result_dict['first_token_confusion']['f1'],
results.component_result('biomedicus-negation').timing_info['process_method']
))
print('Overall Precision:', confusion.precision)
print('Overall Recall:', confusion.recall)
print('Overall F1:', confusion.f1)
pipeline.print_times()
timing_info = pipeline.processor_timer_stats('biomedicus-negation').timing_info
test_results['biomedicus-modification'] = {
'Gold Standard': "2010 i2b2-VA",
'Precision': confusion.precision,
'Recall': confusion.recall,
'F1': confusion.f1,
'Per-Document Mean Remote Call Duration': str(timing_info['remote_call'].mean),
'Per-Document Mean Process Method Duration': str(timing_info['process_method'].mean)
}
def test_yml_deserialization():
f = Path(__file__).parent / 'event.pickle'
event = PickleSerializer.file_to_event(f)
assert event.event_id == '12345'
assert event.metadata['foo'] == 'bar'
d = event.documents['plaintext']
assert d.text == "The quick brown fox jumps over the lazy dog."
assert len(d.get_label_indices_info()) == 3
assert d.get_label_index("one") == [
label(start_index=0, end_index=10, a="b"),
label(start_index=12, end_index=25, a="c"),
label(start_index=26, end_index=52, a="d"),
label(start_index=53, end_index=85, a="e"),
]
assert d.get_label_index("two") == [
label(start_index=0, end_index=10, x=1),
label(start_index=3, end_index=9, x=3),
label(start_index=4, end_index=25, x=2),
label(start_index=5, end_index=25, x=4),
]
assert d.get_label_index("three") == [
label(start_index=0, end_index=10, x=True),
label(start_index=3, end_index=9, x=True),
label(start_index=4, end_index=25, x=False),
label(start_index=5, end_index=25, x=False),
]
def test_pickle_serializer():
event = Event(event_id='1')
event.metadata['foo'] = "bar"
document = Document('plaintext', text='Some text.')
event.add_document(document)
one = label(start_index=0, end_index=5, x=10)
two = label(start_index=6, end_index=10, x=15)
document.add_labels('one', [one, two])
document.add_labels('two', [
label(start_index=0, end_index=25, a='b', b=one),
label(start_index=26, end_index=42, a='c', b=two)
])
document.add_labels('three', [
label(start_index=0, end_index=10, foo=True),
label(start_index=11, end_index=15, foo=False)
],
distinct=True)
with TemporaryFile('wb+') as tf:
PickleSerializer.event_to_file(event, tf)
tf.flush()
tf.seek(0)
e = PickleSerializer.file_to_event(tf)
assert e.event_id == event.event_id
assert e.metadata['foo'] == 'bar'
d = e.documents['plaintext']
assert d.text == document.text
index_one = d.labels['one']
assert index_one == [one, two]
index_two = d.labels['two']
assert index_two == [
label(start_index=0, end_index=25, a='b', b=one),
label(start_index=26, end_index=42, a='c', b=two)
]
index_three = d.labels['three']
assert index_three == [
label(start_index=0, end_index=10, foo=True),
label(start_index=11, end_index=15, foo=False)
]
def test_normalization(events_service, normalization_processor):
with EventsClient(address=events_service) as client, \
Pipeline(RemoteProcessor(processor_id='biomedicus_normalizer',
address=normalization_processor)) as pipeline, \
PickleSerializer.file_to_event(Path(__file__).parent / '97_95.pickle',
client=client) as event:
document = event.documents['plaintext']
pipeline.run(document)
for norm_form in document.get_label_index('norm_forms'):
if norm_form.text == "according":
assert norm_form.norm == "accord"
if norm_form.text == "expressing":
assert norm_form.norm == "express"
if norm_form.text == "receiving":
assert norm_form.norm == "receive"
if norm_form.text == "days":
assert norm_form.norm == "day"
def test_pickle_serializer():
event = Event(event_id='1')
event.metadata['foo'] = "bar"
document = Document('plaintext', text='Some text.')
event.add_document(document)
document.add_labels('one', [
label(start_index=0, end_index=5, x=10),
label(start_index=6, end_index=10, x=15)
])
document.add_labels('two', [
label(start_index=0, end_index=25, a='b'),
label(start_index=26, end_index=42, a='c')
])
document.add_labels('three', [
label(start_index=0, end_index=10, foo=True),
label(start_index=11, end_index=15, foo=False)
],
distinct=True)
with NamedTemporaryFile('rb') as tf:
PickleSerializer.event_to_file(event, tf.name)
tf.flush()
tf.seek(0)
o = pickle.load(tf)
assert o['event_id'] == '1'
assert o['metadata']['foo'] == 'bar'
d = o['documents']['plaintext']
assert d['text'] == 'Some text.'
assert len(d['label_indices']) == 3
assert d['label_indices']['one'] == {
'json_labels': [{
'start_index': 0,
'end_index': 5,
'x': 10
}, {
'start_index': 6,
'end_index': 10,
'x': 15
}],
'distinct':
False
}
assert d['label_indices']['two'] == {
'json_labels': [{
'start_index': 0,
'end_index': 25,
'a': 'b'
}, {
'start_index': 26,
'end_index': 42,
'a': 'c'
}],
'distinct':
False
}
assert d['label_indices']['three'] == {
'json_labels': [{
'start_index': 0,
'end_index': 10,
'foo': True
}, {
'start_index': 11,
'end_index': 15,
'foo': False
}],
'distinct':
True
}