from collections import defaultdict
from os.path import basename, join, splitext
from loguru import logger
from deidentify.base import Annotation
def load_brat_annotations(ann_file):
"""Load a brat standoff annotations (.ann) files.
This method does not support brat fragment annotations. These annotations are inserted when
annotating text spanning multiple lines.
Example of fragment annotation that is not supported:
`T30 Address 3232 3245;3246 3263 Calslaan 11 1234AB Wildervank`
```
Parameters
----------
ann_file : str
Full path to .ann file.
Returns
-------
list of deidentify.base.Annotation
The annotations
"""
annotations = []
doc_id = splitext(basename(ann_file))[0]
with open(ann_file) as file:
lines = file.readlines()
for line in lines:
if not line.startswith('T'):
continue
splitted = line.split(None, 4)
ann_id, tag, start, end, text = splitted
text = text.rstrip('\n')
try:
annotation = Annotation(text=text, start=int(start), end=int(end), tag=tag,
doc_id=doc_id, ann_id=ann_id)
annotations.append(annotation)
except ValueError:
logger.warning(
'Brat fragment annotations are not supported, skipping line\n{}'.format(line))
return annotations
def load_brat_text(txt_file):
# disable universal newline translation.
# Otherwise there is a character mismatch between .ann/.txt files
#
# See https://github.com/nlplab/brat/issues/853
with open(txt_file, newline='') as file:
content = file.read()
return content
def load_brat_document(path, doc_name):
ann_file = join(path, '{}.ann'.format(doc_name))
txt_file = join(path, '{}.txt'.format(doc_name))
return load_brat_annotations(ann_file), load_brat_text(txt_file)
def write_brat_text(txt, output_file):
# Disable universal newline translation.
# Otherwise there is a character mismatch between .ann/.txt files
#
# See https://github.com/nlplab/brat/issues/853
with open(output_file, 'w', newline='') as file:
file.write(txt)
def write_brat_annotations(annotations, output_file):
with open(output_file, 'w') as file:
for annotation in annotations:
annotation_txt = '{}\t{} {} {}\t{}\n'.format(annotation.ann_id,
annotation.tag,
annotation.start,
annotation.end,
annotation.text)
file.write(annotation_txt)
def write_brat_document(path, doc_name, text, annotations):
ann_file = join(path, '{}.ann'.format(doc_name))
txt_file = join(path, '{}.txt'.format(doc_name))
write_brat_annotations(annotations, ann_file)
write_brat_text(text, txt_file)
def load_brat_config(config_file):
with open(config_file) as f:
sections = defaultdict(list)
section = ''
for line in f.readlines():
line = line.strip()
if not line or line.startswith('#') or line.startswith('!'):
continue
elif line.startswith('['):
section = line[1:len(line) - 1]
else:
sections[section].append(line)
return sections
