def check_validity_of_conll_bioes(bioes_filepath):
dataset_type = utils.get_basename_without_extension(bioes_filepath).split(
'_')[0]
print("Checking validity of CONLL BIOES format... ".format(dataset_type),
end='')
input_conll_file = codecs.open(bioes_filepath, 'r', 'UTF-8')
labels_bioes = []
labels_bio = []
for line in input_conll_file:
split_line = line.strip().split(' ')
# New sentence
if len(split_line) == 0 or len(
split_line[0]) == 0 or '-DOCSTART-' in split_line[0]:
if check_bio_bioes_compatibility(labels_bio, labels_bioes):
continue
return False
label_bioes = split_line[-1]
label_bio = split_line[-2]
labels_bioes.append(label_bioes)
labels_bio.append(label_bio)
input_conll_file.close()
if check_bio_bioes_compatibility(labels_bio, labels_bioes):
print("Done.")
return True
return False
def convert_conll_from_bio_to_bioes(input_conll_filepath,
output_conll_filepath):
if os.path.exists(output_conll_filepath):
if check_validity_of_conll_bioes(output_conll_filepath):
return
dataset_type = utils.get_basename_without_extension(
input_conll_filepath).split('_')[0]
print("Converting CONLL from BIO to BIOES format... ".format(dataset_type),
end='')
input_conll_file = codecs.open(input_conll_filepath, 'r', 'UTF-8')
output_conll_file = codecs.open(output_conll_filepath, 'w', 'UTF-8')
labels = []
split_lines = []
for line in input_conll_file:
split_line = line.strip().split(' ')
# New sentence
if len(split_line) == 0 or len(
split_line[0]) == 0 or '-DOCSTART-' in split_line[0]:
output_conll_lines_with_bioes(split_lines, labels,
output_conll_file)
output_conll_file.write(line)
continue
label = split_line[-1]
labels.append(label)
split_lines.append(split_line)
output_conll_lines_with_bioes(split_lines, labels, output_conll_file)
input_conll_file.close()
output_conll_file.close()
print("Done.")
def generate_reference_text_file_for_conll(conll_input_filepath,
conll_output_filepath, text_folder):
'''
generates reference text files and adds the corresponding filename and token offsets to conll file.
conll_input_filepath: path to a conll-formatted file without filename and token offsets
text_folder: folder to write the reference text file to
'''
dataset_type = utils.get_basename_without_extension(conll_input_filepath)
conll_file = codecs.open(conll_input_filepath, 'r', 'UTF-8')
utils.create_folder_if_not_exists(text_folder)
text = ''
new_conll_string = ''
character_index = 0
document_count = 0
text_base_filename = '{0}_text_{1}'.format(dataset_type,
str(document_count).zfill(5))
for line in conll_file:
split_line = line.strip().split(' ')
# New document
if '-DOCSTART-' in split_line[0]:
new_conll_string += line
if len(text) != 0:
with codecs.open(
os.path.join(text_folder,
'{0}.txt'.format(text_base_filename)),
'w', 'UTF-8') as f:
f.write(text)
text = ''
character_index = 0
document_count += 1
text_base_filename = '{0}_text_{1}'.format(
dataset_type,
str(document_count).zfill(5))
continue
# New sentence
elif len(split_line) == 0 or len(split_line[0]) == 0:
new_conll_string += '\n'
if text != '':
text += '\n'
character_index += 1
continue
token = split_line[0]
start = character_index
end = start + len(token)
text += token + ' '
character_index += len(token) + 1
new_conll_string += ' '.join(
[token, text_base_filename,
str(start), str(end)] + split_line[1:]) + '\n'
if len(text) != 0:
with codecs.open(
os.path.join(text_folder,
'{0}.txt'.format(text_base_filename)), 'w',
'UTF-8') as f:
f.write(text)
conll_file.close()
with codecs.open(conll_output_filepath, 'w', 'UTF-8') as f:
f.write(new_conll_string)
def xml_to_brat(input_folder, output_folder, overwrite=True):
print('input_folder: {0}'.format(input_folder))
start_time = time.time()
if overwrite:
shutil.rmtree(output_folder, ignore_errors=True)
utils.create_folder_if_not_exists(output_folder)
for input_filepath in sorted(glob.glob(os.path.join(input_folder, '*.xml'))):
filename = utils.get_basename_without_extension(input_filepath)
output_text_filepath = os.path.join(output_folder, '{0}.txt'.format(filename))
xmldoc = xml.etree.ElementTree.parse(input_filepath).getroot()
# Get text
text = xmldoc.findtext('TEXT')
with codecs.open(output_text_filepath, 'w', 'UTF-8') as f:
f.write(text)
# Get PHI tags
tags = xmldoc.findall('TAGS')[0] # [0] because there is only one <TAGS>...</TAGS>
entities = []
for tag in tags:
entity = {}
entity['label'] = tag.get('TYPE')
entity['text'] = tag.get('text')
entity['start'] = int(tag.get('start'))
entity['end'] = int(tag.get('end'))
entities.append(entity)
output_entities(output_folder, filename, entities, output_text_filepath, text, overwrite=overwrite)
time_spent = time.time() - start_time
print("Time spent formatting: {0:.2f} seconds".format(time_spent))
def _create_stats_graph_folder(self, parameters):
# Initialize stats_graph_folder
experiment_timestamp = utils.get_current_time_in_miliseconds()
dataset_name = utils.get_basename_without_extension(
parameters['dataset_text_folder'])
model_name = '{0}_{1}'.format(dataset_name, experiment_timestamp)
utils.create_folder_if_not_exists(parameters['output_folder'])
stats_graph_folder = os.path.join(
parameters['output_folder'],
model_name) # Folder where to save graphs
utils.create_folder_if_not_exists(stats_graph_folder)
return stats_graph_folder, experiment_timestamp
def check_compatibility_between_conll_and_brat_text(conll_filepath,
brat_folder):
'''
check if token offsets match between conll and brat .txt files.
conll_filepath: path to conll file
brat_folder: folder that contains the .txt (and .ann) files that are formatted according to brat.
'''
verbose = False
dataset_type = utils.get_basename_without_extension(conll_filepath)
print("Checking compatibility between CONLL and BRAT for {0} set ... ".
format(dataset_type),
end='')
conll_file = codecs.open(conll_filepath, 'r', 'UTF-8')
previous_filename = ''
for line in conll_file:
line = line.strip().split(' ')
# New sentence
if len(line) == 0 or len(line[0]) == 0 or '-DOCSTART-' in line[0]:
continue
filename = str(line[1])
# New file
if filename != previous_filename:
text_filepath = os.path.join(brat_folder,
'{0}.txt'.format(filename))
with codecs.open(text_filepath, 'r', 'UTF-8') as f:
text = f.read()
previous_filename = filename
label = str(line[-1]).replace('_', '-') # For LOCATION-OTHER
token = {}
token['text'] = str(line[0])
token['start'] = int(line[2])
token['end'] = int(line[3])
# check that the token text matches the original
if token['text'] != text[token['start']:token['end']]:
print(str(line[1]))
print("Warning: conll and brat text do not match.")
print("\tCONLL: {0}".format(token['text']))
print("\tBRAT : {0}".format(text[token['start']:token['end']]))
if token['text'] != text[token['start']:token['end']].replace(
' ', '-'):
raise AssertionError("CONLL and BRAT files are incompatible.")
print("Done.")
def predict(self, text):
"""
Predict
Args:
text (str): Description.
"""
self.prediction_count += 1
if self.prediction_count == 1:
self.parameters['dataset_text_folder'] = os.path.join(
'.', 'data', 'temp')
self.stats_graph_folder, _ = self._create_stats_graph_folder(
self.parameters)
# Update the deploy folder, file, and modeldata
dataset_type = 'deploy'
# Delete all deployment data
for filepath in glob.glob(
os.path.join(self.parameters['dataset_text_folder'],
'{0}*'.format(dataset_type))):
if os.path.isdir(filepath):
shutil.rmtree(filepath)
else:
os.remove(filepath)
# Create brat folder and file
dataset_brat_deploy_folder = os.path.join(
self.parameters['dataset_text_folder'], dataset_type)
utils.create_folder_if_not_exists(dataset_brat_deploy_folder)
dataset_brat_deploy_filepath = os.path.join(
dataset_brat_deploy_folder,
'temp_{0}.txt'.format(str(self.prediction_count).zfill(5)))
#self._get_dataset_brat_deploy_filepath(dataset_brat_deploy_folder)
with codecs.open(dataset_brat_deploy_filepath, 'w', 'UTF-8') as f:
f.write(text)
# Update deploy filepaths
dataset_filepaths, dataset_brat_folders = self._get_valid_dataset_filepaths(
self.parameters, dataset_types=[dataset_type])
self.dataset_filepaths.update(dataset_filepaths)
self.dataset_brat_folders.update(dataset_brat_folders)
# Update the dataset for the new deploy set
self.modeldata.update_dataset(self.dataset_filepaths, [dataset_type])
# Predict labels and output brat
output_filepaths = {}
prediction_output = train.prediction_step(
self.sess, self.modeldata, dataset_type, self.model,
self.transition_params_trained, self.stats_graph_folder,
self.prediction_count, self.parameters, self.dataset_filepaths)
_, _, output_filepaths[dataset_type] = prediction_output
conll_to_brat.output_brat(output_filepaths,
self.dataset_brat_folders,
self.stats_graph_folder,
overwrite=True)
# Print and output result
text_filepath = os.path.join(
self.stats_graph_folder, 'brat', 'deploy',
os.path.basename(dataset_brat_deploy_filepath))
annotation_filepath = os.path.join(
self.stats_graph_folder, 'brat', 'deploy', '{0}.ann'.format(
utils.get_basename_without_extension(
dataset_brat_deploy_filepath)))
text2, entities = brat_to_conll.get_entities_from_brat(
text_filepath, annotation_filepath, verbose=True)
assert (text == text2)
return entities
def _get_valid_dataset_filepaths(self,
parameters,
dataset_types=[
'train', 'valid', 'test', 'deploy'
]):
"""
Get paths for the datasets.
Args:
parameters (type): description.
dataset_types (type): description.
"""
dataset_filepaths = {}
dataset_brat_folders = {}
for dataset_type in dataset_types:
dataset_filepaths[dataset_type] = os.path.join(
parameters['dataset_text_folder'],
'{0}.txt'.format(dataset_type))
dataset_brat_folders[dataset_type] = os.path.join(
parameters['dataset_text_folder'], dataset_type)
dataset_compatible_with_brat_filepath = os.path.join(
parameters['dataset_text_folder'],
'{0}_compatible_with_brat.txt'.format(dataset_type))
# Conll file exists
if os.path.isfile(dataset_filepaths[dataset_type]) \
and os.path.getsize(dataset_filepaths[dataset_type]) > 0:
# Brat text files exist
if os.path.exists(dataset_brat_folders[dataset_type]) and \
len(glob.glob(os.path.join(dataset_brat_folders[dataset_type], '*.txt'))) > 0:
# Check compatibility between conll and brat files
brat_to_conll.check_brat_annotation_and_text_compatibility(
dataset_brat_folders[dataset_type])
if os.path.exists(dataset_compatible_with_brat_filepath):
dataset_filepaths[
dataset_type] = dataset_compatible_with_brat_filepath
conll_to_brat.check_compatibility_between_conll_and_brat_text(
dataset_filepaths[dataset_type],
dataset_brat_folders[dataset_type])
# Brat text files do not exist
else:
# Populate brat text and annotation files based on conll file
conll_to_brat.conll_to_brat(
dataset_filepaths[dataset_type],
dataset_compatible_with_brat_filepath,
dataset_brat_folders[dataset_type],
dataset_brat_folders[dataset_type])
dataset_filepaths[
dataset_type] = dataset_compatible_with_brat_filepath
# Conll file does not exist
else:
# Brat text files exist
if os.path.exists(dataset_brat_folders[dataset_type]) \
and len(glob.glob(os.path.join(dataset_brat_folders[dataset_type], '*.txt'))) > 0:
dataset_filepath_for_tokenizer = os.path.join(
parameters['dataset_text_folder'],
'{0}_{1}.txt'.format(dataset_type,
parameters['tokenizer']))
if os.path.exists(dataset_filepath_for_tokenizer):
conll_to_brat.check_compatibility_between_conll_and_brat_text(
dataset_filepath_for_tokenizer,
dataset_brat_folders[dataset_type])
else:
# Populate conll file based on brat files
brat_to_conll.brat_to_conll(
dataset_brat_folders[dataset_type],
dataset_filepath_for_tokenizer,
parameters['tokenizer'],
parameters['spacylanguage'])
dataset_filepaths[
dataset_type] = dataset_filepath_for_tokenizer
# Brat text files do not exist
else:
del dataset_filepaths[dataset_type]
del dataset_brat_folders[dataset_type]
continue
if parameters['tagging_format'] == 'bioes':
# Generate conll file with BIOES format
bioes_filepath = os.path.join(
parameters['dataset_text_folder'], '{0}_bioes.txt'.format(
utils.get_basename_without_extension(
dataset_filepaths[dataset_type])))
utils_nlp.convert_conll_from_bio_to_bioes(
dataset_filepaths[dataset_type], bioes_filepath)
dataset_filepaths[dataset_type] = bioes_filepath
return dataset_filepaths, dataset_brat_folders
def conll_to_brat(conll_input_filepath,
conll_output_filepath,
brat_original_folder,
brat_output_folder,
overwrite=False):
'''
convert conll file in conll-filepath to brat annotations and output to brat_output_folder,
with reference to the existing text files in brat_original_folder
if brat_original_folder does not exist or contain any text file, then the text files are generated from conll files,
and conll file is updated with filenames and token offsets accordingly.
conll_input_filepath: path to conll file to convert to brat annotations
conll_output_filepath: path to output conll file with filename and offsets that are compatible with brat annotations
brat_original_folder: folder that contains the original .txt (and .ann) files that are formatted according to brat.
.txt files are used to check if the token offsets match and generate the annotation from conll.
brat_output_folder: folder to output the text and brat annotations
.txt files are copied from brat_original_folder to brat_output_folder
'''
verbose = False
dataset_type = utils.get_basename_without_extension(conll_input_filepath)
print("Formatting {0} set from CONLL to BRAT... ".format(dataset_type),
end='')
# if brat_original_folder does not exist or have any text file
if not os.path.exists(brat_original_folder) or len(
glob.glob(os.path.join(brat_original_folder, '*.txt'))) == 0:
assert (conll_input_filepath != conll_output_filepath)
generate_reference_text_file_for_conll(conll_input_filepath,
conll_output_filepath,
brat_original_folder)
utils.create_folder_if_not_exists(brat_output_folder)
conll_file = codecs.open(conll_output_filepath, 'r', 'UTF-8')
previous_token_label = 'O'
previous_filename = ''
text_filepath = ''
text = ''
entity_id = 1
entities = []
entity = {}
for line in conll_file:
line = line.strip().split(' ')
# New sentence
if len(line) == 0 or len(line[0]) == 0 or '-DOCSTART-' in line[0]:
# Add the last entity
if entity != {}:
if verbose: print("entity: {0}".format(entity))
entities.append(entity)
entity_id += 1
entity = {}
previous_token_label = 'O'
continue
filename = str(line[1])
# New file
if filename != previous_filename:
output_entities(brat_output_folder,
previous_filename,
entities,
text_filepath,
text,
overwrite=overwrite)
text_filepath = os.path.join(brat_original_folder,
'{0}.txt'.format(filename))
with codecs.open(text_filepath, 'r', 'UTF-8') as f:
text = f.read()
previous_token_label = 'O'
previous_filename = filename
entity_id = 1
entities = []
entity = {}
label = str(line[-1]).replace('_', '-') # For LOCATION-OTHER
if label == 'O':
# Previous entity ended
if previous_token_label != 'O':
if verbose: print("entity: {0}".format(entity))
entities.append(entity)
entity_id += 1
entity = {}
previous_token_label = 'O'
continue
token = {}
token['text'] = str(line[0])
token['start'] = int(line[2])
token['end'] = int(line[3])
# check that the token text matches the original
if token['text'] != text[token['start']:token['end']].replace(
' ', '-'):
print("Warning: conll and brat text do not match.")
print("\tCONLL: {0}".format(token['text']))
print("\tBRAT : {0}".format(text[token['start']:token['end']]))
token['label'] = label[2:]
if label[:2] == 'B-':
if previous_token_label != 'O':
# End the previous entity
if verbose: print("entity: {0}".format(entity))
entities.append(entity)
entity_id += 1
# Start a new entity
entity = token
elif label[:2] == 'I-':
# Entity continued
if previous_token_label == token['label']:
# if there is no newline between the entity and the token
if '\n' not in text[entity['end']:token['start']]:
# Update entity
entity['text'] = entity['text'] + ' ' + token['text']
entity['end'] = token['end']
else: # newline between the entity and the token
# End the previous entity
if verbose: print("entity: {0}".format(entity))
entities.append(entity)
entity_id += 1
# Start a new entity
entity = token
elif previous_token_label != 'O':
# TODO: count BI or II incompatibility
# End the previous entity
if verbose: print("entity: {0}".format(entity))
entities.append(entity)
entity_id += 1
# Start new entity
entity = token
else: # previous_token_label == 'O'
# TODO: count OI incompatibility
# Start new entity
entity = token
previous_token_label = token['label']
output_entities(brat_output_folder,
previous_filename,
entities,
text_filepath,
text,
overwrite=overwrite)
conll_file.close()
print('Done.')
