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from dataclasses import dataclass
from typing import Any, Dict, Optional, Union
import datasets
from pie_modules.annotations import BinaryRelation, LabeledSpan
from pie_modules.documents import (
AnnotationLayer,
TextBasedDocument,
TextDocumentWithLabeledSpansAndBinaryRelations,
TextDocumentWithLabeledSpansBinaryRelationsAndLabeledPartitions,
annotation_field,
)
from pie_datasets import GeneratorBasedBuilder
@dataclass
class DrugprotDocument(TextBasedDocument):
title: Optional[str] = None
abstract: Optional[str] = None
entities: AnnotationLayer[LabeledSpan] = annotation_field(target="text")
relations: AnnotationLayer[BinaryRelation] = annotation_field(target="entities")
@dataclass
class DrugprotBigbioDocument(TextBasedDocument):
passages: AnnotationLayer[LabeledSpan] = annotation_field(target="text")
entities: AnnotationLayer[LabeledSpan] = annotation_field(target="text")
relations: AnnotationLayer[BinaryRelation] = annotation_field(target="entities")
def example2drugprot(example: Dict[str, Any]) -> DrugprotDocument:
metadata = {"entity_ids": []}
id2labeled_span: Dict[str, LabeledSpan] = {}
document = DrugprotDocument(
text=example["text"],
title=example["title"],
abstract=example["abstract"],
id=example["document_id"],
metadata=metadata,
)
for span in example["entities"]:
labeled_span = LabeledSpan(
start=span["offset"][0],
end=span["offset"][1],
label=span["type"],
)
document.entities.append(labeled_span)
document.metadata["entity_ids"].append(span["id"])
id2labeled_span[span["id"]] = labeled_span
for relation in example["relations"]:
document.relations.append(
BinaryRelation(
head=id2labeled_span[relation["arg1_id"]],
tail=id2labeled_span[relation["arg2_id"]],
label=relation["type"],
)
)
return document
def example2drugprot_bigbio(example: Dict[str, Any]) -> DrugprotBigbioDocument:
text = " ".join([" ".join(passage["text"]) for passage in example["passages"]])
doc_id = example["document_id"]
metadata = {"entity_ids": []}
id2labeled_span: Dict[str, LabeledSpan] = {}
document = DrugprotBigbioDocument(
text=text,
id=doc_id,
metadata=metadata,
)
for passage in example["passages"]:
document.passages.append(
LabeledSpan(
start=passage["offsets"][0][0],
end=passage["offsets"][0][1],
label=passage["type"],
)
)
# We sort labels and relation to always have an deterministic order for testing purposes.
for span in example["entities"]:
labeled_span = LabeledSpan(
start=span["offsets"][0][0],
end=span["offsets"][0][1],
label=span["type"],
)
document.entities.append(labeled_span)
document.metadata["entity_ids"].append(span["id"])
id2labeled_span[span["id"]] = labeled_span
for relation in example["relations"]:
document.relations.append(
BinaryRelation(
head=id2labeled_span[relation["arg1_id"]],
tail=id2labeled_span[relation["arg2_id"]],
label=relation["type"],
)
)
return document
class Drugprot(GeneratorBasedBuilder):
DOCUMENT_TYPES = {
"drugprot_source": DrugprotDocument,
"drugprot_bigbio_kb": DrugprotBigbioDocument,
}
BASE_DATASET_PATH = "bigbio/drugprot"
BASE_DATASET_REVISION = "38ff03d68347aaf694e598c50cb164191f50f61c"
BUILDER_CONFIGS = [
datasets.BuilderConfig(
name="drugprot_source",
version=datasets.Version("1.0.2"),
description="DrugProt source version",
),
datasets.BuilderConfig(
name="drugprot_bigbio_kb",
version=datasets.Version("1.0.0"),
description="DrugProt BigBio version",
),
]
@property
def document_converters(self):
if self.config.name == "drugprot_source":
return {
TextDocumentWithLabeledSpansAndBinaryRelations: {
"entities": "labeled_spans",
"relations": "binary_relations",
}
}
elif self.config.name == "drugprot_bigbio_kb":
return {
TextDocumentWithLabeledSpansBinaryRelationsAndLabeledPartitions: {
"passages": "labeled_partitions",
"entities": "labeled_spans",
"relations": "binary_relations",
}
}
else:
raise ValueError(f"Unknown dataset name: {self.config.name}")
def _generate_document(
self,
example: Dict[str, Any],
) -> Union[DrugprotDocument, DrugprotBigbioDocument]:
if self.config.name == "drugprot_source":
return example2drugprot(example)
elif self.config.name == "drugprot_bigbio_kb":
return example2drugprot_bigbio(example)
else:
raise ValueError(f"Unknown dataset config name: {self.config.name}")
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