Datasets:
Tasks:
Token Classification
Sub-tasks:
parsing
File size: 12,257 Bytes
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import glob
import logging
from dataclasses import dataclass
from os import listdir, path
from typing import Dict, List, Optional
import datasets
from datasets import BuilderConfig, DatasetInfo, Features, Sequence, SplitGenerator, Value
logger = logging.getLogger(__name__)
@dataclass
class BratConfig(BuilderConfig):
"""BuilderConfig for BRAT."""
url: str = None # type: ignore
description: Optional[str] = None
citation: Optional[str] = None
homepage: Optional[str] = None
subdirectory_mapping: Optional[Dict[str, str]] = None
file_name_blacklist: Optional[List[str]] = None
ann_file_extension: str = "ann"
txt_file_extension: str = "txt"
class Brat(datasets.GeneratorBasedBuilder):
BUILDER_CONFIG_CLASS = BratConfig
def _info(self):
return DatasetInfo(
description=self.config.description,
citation=self.config.citation,
homepage=self.config.homepage,
features=Features(
{
"context": Value("string"),
"file_name": Value("string"),
"spans": Sequence(
{
"id": Value("string"),
"type": Value("string"),
"locations": Sequence(
{
"start": Value("int32"),
"end": Value("int32"),
}
),
"text": Value("string"),
}
),
"relations": Sequence(
{
"id": Value("string"),
"type": Value("string"),
"arguments": Sequence(
{"type": Value("string"), "target": Value("string")}
),
}
),
"equivalence_relations": Sequence(
{
"type": Value("string"),
"targets": Sequence(Value("string")),
}
),
"events": Sequence(
{
"id": Value("string"),
"type": Value("string"),
"trigger": Value("string"),
"arguments": Sequence(
{"type": Value("string"), "target": Value("string")}
),
}
),
"attributions": Sequence(
{
"id": Value("string"),
"type": Value("string"),
"target": Value("string"),
"value": Value("string"),
}
),
"normalizations": Sequence(
{
"id": Value("string"),
"type": Value("string"),
"target": Value("string"),
"resource_id": Value("string"),
"entity_id": Value("string"),
}
),
"notes": Sequence(
{
"id": Value("string"),
"type": Value("string"),
"target": Value("string"),
"note": Value("string"),
}
),
}
),
)
@staticmethod
def _get_location(location_string):
parts = location_string.split(" ")
assert (
len(parts) == 2
), f"Wrong number of entries in location string. Expected 2, but found: {parts}"
return {"start": int(parts[0]), "end": int(parts[1])}
@staticmethod
def _get_span_annotation(annotation_line):
"""
example input:
T1 Organization 0 4 Sony
"""
_id, remaining, text = annotation_line.split("\t", maxsplit=2)
_type, locations = remaining.split(" ", maxsplit=1)
return {
"id": _id,
"text": text,
"type": _type,
"locations": [Brat._get_location(loc) for loc in locations.split(";")],
}
@staticmethod
def _get_event_annotation(annotation_line):
"""
example input:
E1 MERGE-ORG:T2 Org1:T1 Org2:T3
"""
_id, remaining = annotation_line.strip().split("\t")
args = [dict(zip(["type", "target"], a.split(":"))) for a in remaining.split(" ")]
return {
"id": _id,
"type": args[0]["type"],
"trigger": args[0]["target"],
"arguments": args[1:],
}
@staticmethod
def _get_relation_annotation(annotation_line):
"""
example input:
R1 Origin Arg1:T3 Arg2:T4
"""
_id, remaining = annotation_line.strip().split("\t")
_type, remaining = remaining.split(" ", maxsplit=1)
args = [dict(zip(["type", "target"], a.split(":"))) for a in remaining.split(" ")]
return {"id": _id, "type": _type, "arguments": args}
@staticmethod
def _get_equivalence_relation_annotation(annotation_line):
"""
example input:
* Equiv T1 T2 T3
"""
_, remaining = annotation_line.strip().split("\t")
parts = remaining.split(" ")
return {"type": parts[0], "targets": parts[1:]}
@staticmethod
def _get_attribute_annotation(annotation_line):
"""
example input (binary: implicit value is True, if present, False otherwise):
A1 Negation E1
example input (multi-value: explicit value)
A2 Confidence E2 L1
"""
_id, remaining = annotation_line.strip().split("\t")
parts = remaining.split(" ")
# if no value is present, it is implicitly "true"
if len(parts) == 2:
parts.append("true")
return {
"id": _id,
"type": parts[0],
"target": parts[1],
"value": parts[2],
}
@staticmethod
def _get_normalization_annotation(annotation_line):
"""
example input:
N1 Reference T1 Wikipedia:534366 Barack Obama
"""
_id, remaining, text = annotation_line.split("\t", maxsplit=2)
_type, target, ref = remaining.split(" ")
res_id, ent_id = ref.split(":")
return {
"id": _id,
"type": _type,
"target": target,
"resource_id": res_id,
"entity_id": ent_id,
}
@staticmethod
def _get_note_annotation(annotation_line):
"""
example input:
#1 AnnotatorNotes T1 this annotation is suspect
"""
_id, remaining, note = annotation_line.split("\t", maxsplit=2)
_type, target = remaining.split(" ")
return {
"id": _id,
"type": _type,
"target": target,
"note": note,
}
@staticmethod
def _read_annotation_file(filename):
"""
reads a BRAT v1.3 annotations file (see https://brat.nlplab.org/standoff.html)
"""
res = {
"spans": [],
"events": [],
"relations": [],
"equivalence_relations": [],
"attributions": [],
"normalizations": [],
"notes": [],
}
with open(filename) as file:
for i, line in enumerate(file):
if len(line.strip()) == 0:
continue
ann_type = line[0]
# strip away the new line character
if line.endswith("\n"):
line = line[:-1]
if ann_type == "T":
res["spans"].append(Brat._get_span_annotation(line))
elif ann_type == "E":
res["events"].append(Brat._get_event_annotation(line))
elif ann_type == "R":
res["relations"].append(Brat._get_relation_annotation(line))
elif ann_type == "*":
res["equivalence_relations"].append(
Brat._get_equivalence_relation_annotation(line)
)
elif ann_type in ["A", "M"]:
res["attributions"].append(Brat._get_attribute_annotation(line))
elif ann_type == "N":
res["normalizations"].append(Brat._get_normalization_annotation(line))
elif ann_type == "#":
res["notes"].append(Brat._get_note_annotation(line))
else:
raise ValueError(
f'unknown BRAT annotation id type: "{line}" (from file {filename} @line {i}). '
f"Annotation ids have to start with T (spans), E (events), R (relations), "
f"A (attributions), or N (normalizations). See "
f"https://brat.nlplab.org/standoff.html for the BRAT annotation file "
f"specification."
)
return res
def _generate_examples(self, files=None, directory=None):
"""Read context (.txt) and annotation (.ann) files."""
if files is None:
assert (
directory is not None
), "If files is None, directory has to be provided, but it is also None."
_files = glob.glob(f"{directory}/*.{self.config.ann_file_extension}")
files = sorted(path.splitext(fn)[0] for fn in _files)
for filename in files:
basename = path.basename(filename)
if (
self.config.file_name_blacklist is not None
and basename in self.config.file_name_blacklist
):
logger.info(f"skip annotation file: {basename} (blacklisted)")
continue
ann_fn = f"{filename}.{self.config.ann_file_extension}"
brat_annotations = Brat._read_annotation_file(ann_fn)
txt_fn = f"{filename}.{self.config.txt_file_extension}"
txt_content = open(txt_fn).read()
brat_annotations["context"] = txt_content
brat_annotations["file_name"] = basename
yield basename, brat_annotations
def _split_generators(self, dl_manager):
"""Returns SplitGenerators."""
subdirectory_mapping = self.config.subdirectory_mapping
# since subclasses of BuilderConfig are not allowed to define
# attributes without defaults, check here
assert self.config.url is not None, "data url not specified"
# if url points to a local directory, just point to that
if path.exists(self.config.url) and path.isdir(self.config.url):
data_dir = self.config.url
# otherwise, download and extract
else:
data_dir = dl_manager.download_and_extract(self.config.url)
logging.info(f"load from data dir: {data_dir}")
# if no subdirectory mapping is provided, ...
if subdirectory_mapping is None:
# ... use available subdirectories as split names ...
subdirs = [f for f in listdir(data_dir) if path.isdir(path.join(data_dir, f))]
if len(subdirs) > 0:
subdirectory_mapping = {subdir: subdir for subdir in subdirs}
else:
# ... otherwise, default to a single train split with the base directory
subdirectory_mapping = {"": "train"}
return [
SplitGenerator(
name=split,
# These kwargs will be passed to _generate_examples
gen_kwargs={
"directory": path.join(data_dir, subdir),
},
)
for subdir, split in subdirectory_mapping.items()
] |