import dataclasses import logging from typing import Any import datasets from pytorch_ie import AnnotationLayer, annotation_field from pytorch_ie.annotations import BinaryRelation, LabeledSpan, Span from pytorch_ie.documents import ( TextBasedDocument, TextDocumentWithLabeledSpansAndBinaryRelations, ) from pie_datasets import ArrowBasedBuilder, GeneratorBasedBuilder logger = logging.getLogger(__name__) warning_counter = 0 @dataclasses.dataclass(frozen=True) class SpanWithIdAndName(Span): id: str name: str def resolve(self) -> Any: return self.id, self.name, super().resolve() @dataclasses.dataclass class BioRelDocument(TextBasedDocument): entities: AnnotationLayer[SpanWithIdAndName] = annotation_field(target="text") relations: AnnotationLayer[BinaryRelation] = annotation_field(target="entities") def example_to_document(example) -> BioRelDocument: document = BioRelDocument(text=example["text"]) head = SpanWithIdAndName( id=example["h"]["id"], name=example["h"]["name"], start=example["h"]["pos"][0], end=example["h"]["pos"][1], ) tail = SpanWithIdAndName( id=example["t"]["id"], name=example["t"]["name"], start=example["t"]["pos"][0], end=example["t"]["pos"][1], ) document.entities.extend([head, tail]) relation = BinaryRelation(head=head, tail=tail, label=example["relation"]) document.relations.append(relation) return document def document_to_example(document): head = document.entities[0] tail = document.entities[1] return { "text": document.text, "relation": document.relations[0].label, "h": {"id": head.id, "name": head.name, "pos": [head.start, head.end]}, "t": {"id": tail.id, "name": tail.name, "pos": [tail.start, tail.end]}, } def convert_to_text_document_with_labeled_spans_and_binary_relations( document: BioRelDocument, ) -> TextDocumentWithLabeledSpansAndBinaryRelations: text_document = TextDocumentWithLabeledSpansAndBinaryRelations(text=document.text) old2new_spans = {} ids = [] names = [] for entity in document.entities: # in our case two entities (head and tail) # create LabeledSpan and append labeled_span = LabeledSpan(start=entity.start, end=entity.end, label="ENTITY") text_document.labeled_spans.append(labeled_span) # Map the original entity to the new labeled span old2new_spans[entity] = labeled_span ids.append(entity.id) names.append(entity.name) if len(document.relations) != 1: # one relation between two entities raise ValueError(f"Expected exactly one relation, got {len(document.relations)}") old_rel = document.relations[0] # create BinaryRelation and append rel = BinaryRelation( head=old2new_spans[old_rel.head], tail=old2new_spans[old_rel.tail], label=old_rel.label, ) text_document.binary_relations.append(rel) text_document.metadata["entity_ids"] = ids text_document.metadata["entity_names"] = names return text_document class BioRel(ArrowBasedBuilder): DOCUMENT_TYPE = BioRelDocument BASE_DATASET_PATH = "DFKI-SLT/BioRel" BASE_DATASET_REVISION = "e4869c484c582cfbc7ead10d4d421bd4b275fa4e" BUILDER_CONFIGS = [ datasets.BuilderConfig( version=datasets.Version("1.0.0"), description="BioRel dataset", ) ] DOCUMENT_CONVERTERS = { TextDocumentWithLabeledSpansAndBinaryRelations: convert_to_text_document_with_labeled_spans_and_binary_relations } def _generate_document(self, example, **kwargs): return example_to_document(example) def _generate_example(self, document: BioRelDocument, **kwargs): return document_to_example(document)