monero.py

# coding=utf-8
# Copyright 2022 The HuggingFace Datasets Authors and the current dataset script contributor.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

import os
from pathlib import Path
from typing import Any, Dict, List, Tuple

import datasets

from .bigbiohub import BigBioConfig, Tasks, kb_features

_LANGUAGES = ["Romanian"]
_PUBMED = False
_LOCAL = False

_CITATION = """\
@inproceedings{,
    title = {{M}o{NER}o: a Biomedical Gold Standard Corpus for the {R}omanian Language},
    author = {Mitrofan, Maria  and Barbu Mititelu, Verginica  and Mitrofan, Grigorina},
    booktitle = "Proceedings of the 18th BioNLP Workshop and Shared Task",
    month = aug,
    year = "2019",
    address = "Florence, Italy",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/W19-5008",
    doi = "10.18653/v1/W19-5008",
    pages = "71--79",
    biburl    = {https://aclanthology.org/W19-5008.bib},
    bibsource = {https://aclanthology.org/W19-5008/}
}
"""

_DATASETNAME = "monero"
_DISPLAYNAME = "MoNERo"

_DESCRIPTION = """\
MoNERo: a Biomedical Gold Standard Corpus for the Romanian Language for part of speech tagging and named \
entity recognition.
"""

_HOMEPAGE = "https://www.racai.ro/en/tools/text/"
_LICENSE = "CC_BY_SA_4p0"

_URLS = {
    # The original dataset is in 7z format hence I have downloaded and reuploded it as tar.gz format.
    # Converted via the following command:
    # curl -JLO https://www.racai.ro/media/MoNERo_2019.7z
    # mkdir -p ./MoNERo
    # pushd ./MoNERo && 7z x ../MoNERo_2019.7z && popd
    # tar -czf MoNERo.tar.gz ./MoNERo
    _DATASETNAME: "https://github.com/bigscience-workshop/biomedical/files/8550757/MoNERo.tar.gz",
}

_SUPPORTED_TASKS = [Tasks.NAMED_ENTITY_RECOGNITION]

_SOURCE_VERSION = "1.0.0"
_BIGBIO_VERSION = "1.0.0"


class MoneroDataset(datasets.GeneratorBasedBuilder):
    """MoNERo: a Biomedical Gold Standard Corpus for the Romanian Language for part of speech tagging
    and named entity recognition."""

    SOURCE_VERSION = datasets.Version(_SOURCE_VERSION)
    BIGBIO_VERSION = datasets.Version(_BIGBIO_VERSION)

    BUILDER_CONFIGS = [
        BigBioConfig(
            name=f"{_DATASETNAME}_source",
            version=SOURCE_VERSION,
            description=f"{_DATASETNAME} source schema",
            schema="source",
            subset_id=f"{_DATASETNAME}",
        ),
        BigBioConfig(
            name=f"{_DATASETNAME}_bigbio_kb",
            version=BIGBIO_VERSION,
            description=f"{_DATASETNAME} BigBio schema",
            schema="bigbio_kb",
            subset_id=f"{_DATASETNAME}",
        ),
    ]

    DEFAULT_CONFIG_NAME = f"{_DATASETNAME}_source"

    def _info(self) -> datasets.DatasetInfo:
        if self.config.schema == "source":
            features = datasets.Features(
                {
                    "doc_id": datasets.Value("string"),
                    "tokens": [datasets.Value("string")],
                    "lemmas": [datasets.Value("string")],
                    "ner_tags": [datasets.Value("string")],
                    "pos_tags": [datasets.Value("string")],
                }
            )

        elif self.config.schema == "bigbio_kb":
            features = kb_features
        else:
            raise NotImplementedError(f"Schema {self.config.schema} not supported")

        return datasets.DatasetInfo(
            description=_DESCRIPTION,
            features=features,
            homepage=_HOMEPAGE,
            license=_LICENSE,
            citation=_CITATION,
        )

    def _split_generators(self, dl_manager) -> List[datasets.SplitGenerator]:
        """Returns SplitGenerators."""
        urls = _URLS[_DATASETNAME]
        data_dir = dl_manager.download_and_extract(urls)

        return [
            datasets.SplitGenerator(
                name=datasets.Split.TRAIN,
                gen_kwargs={
                    "filepath": Path(os.path.join(data_dir, "MoNERo", "MoNERo.txt")),
                    "split": "train",
                },
            ),
        ] + [
            datasets.SplitGenerator(
                name=split,
                gen_kwargs={
                    "filepath": Path(os.path.join(data_dir, "MoNERo", f"MoNERo_{split}.txt")),
                    "split": split,
                },
            )
            for split in ["cardiology", "endocrinology", "diabetes"]
        ]

    def _generate_examples(self, filepath: Path, split: str) -> Tuple[int, Dict]:
        """Yields examples as (key, example) tuples."""
        if self.config.schema == "source":
            for key, example in self._read_example_from_file(filepath):
                yield key, example

        elif self.config.schema == "bigbio_kb":
            for key, example in self._read_example_from_file_in_kb_schema(filepath):
                yield key, example

    def _read_example_from_file(self, filepath: Path) -> Tuple[str, Dict]:
        """Read examples from the given file in source schema"""
        with filepath.open("r", encoding="utf8") as fp:
            sequences = fp.read().split("\n\n")

        for i, seq in enumerate(sequences):
            key = f"docid-{i}"
            seq = [line.rstrip().split("\t") for line in seq.rstrip().splitlines()]

            # There are few lines which only have two columns. Skipping those.
            seq = [line for line in seq if len(line) == 4]
            tokens, lemmas, ner_tags, pos_tags = zip(*seq)
            example = {
                "doc_id": key,
                "tokens": tokens,
                "lemmas": lemmas,
                "ner_tags": ner_tags,
                "pos_tags": pos_tags,
            }
            yield key, example

    @staticmethod
    def _assign_offsets(tokens: List[str]) -> List[Tuple[int, int]]:
        """Compute token offsets from list of tokens"""

        offsets = []
        start = 0
        for t in tokens:
            s = start
            e = s + len(t)
            offsets.append((s, e))
            start = e + 1  # Add one to include space.

        return offsets

    @staticmethod
    def _extract_entities(ner_tags: List[str]) -> List[Dict]:
        """Extract the entity token offsets / indices given the NER tags.

        Note: The dataset contains discontinuous entities, unfortunately, in some cases it's not transparent to
        which entity a part (i.e., an I-Tag without having a B-Tag before) should be linked. In this implementation
        we append the entity part to previous entity of that type. If there is no previous entity we construct
        a new entity from the part.
        """
        ner_tags = tuple(ner_tags) + ("O",)
        entities = []
        stack = []
        is_discontinuation = False

        for index, ner_tag in enumerate(ner_tags):
            if stack and (ner_tag == "O" or ner_tag.startswith("B-")):
                entity_type, start_index = stack[0]
                entity_type, end_index = stack[-1]

                if not is_discontinuation:
                    # Standard case - create a new entity
                    entities.append({"type": entity_type, "offsets": [(start_index, end_index)]})
                else:
                    # Try to append the offsets to the previous entity of the same type
                    prev_entity = None
                    for i in range(len(entities) - 1, 0, -1):
                        if entities[i]["type"] == entity_type:
                            prev_entity = entities[i]
                            break

                    if prev_entity:
                        prev_entity["offsets"].append((start_index, end_index))
                    else:
                        # If can't find a previous entity - create a new one
                        entities.append({"type": entity_type, "offsets": [(start_index, end_index)]})

                stack = []
                is_discontinuation = False

            if ner_tag.startswith("I-") and len(stack) == 0 and len(entities) > 0:
                # The corpus contains some discontinuous entities
                is_discontinuation = True

            if ner_tag.startswith(("B-", "I-")):
                _, entity_type = ner_tag.split("-", 1)
                stack.append((entity_type, index))

        return entities

    def _parse_example_to_kb_schema(self, example: Dict) -> Dict[str, Any]:
        """Maps a source example to BigBio kb schema"""

        text = " ".join(example["tokens"])
        doc_id = example["doc_id"]
        passages = [
            {
                "id": f"{doc_id}-P0",
                "type": "abstract",
                "text": [text],
                "offsets": [[0, len(text)]],
            }
        ]

        offsets = self._assign_offsets(example["tokens"])
        entities_with_token_indices = self._extract_entities(example["ner_tags"])

        entities = []
        for i, entity_type_and_token_indices in enumerate(entities_with_token_indices):
            entity_texts = []
            entity_offsets = []

            for start_token, end_token in entity_type_and_token_indices["offsets"]:
                start_offset, end_offset = offsets[start_token][0], offsets[end_token][1]
                entity_offsets.append((start_offset, end_offset))
                entity_texts.append(text[start_offset:end_offset])

            entity = {
                "id": f"{doc_id}-E{i}",
                "text": entity_texts,
                "offsets": entity_offsets,
                "type": entity_type_and_token_indices["type"],
                "normalized": [],
            }
            entities.append(entity)

        data = {
            "id": doc_id,
            "document_id": doc_id,
            "passages": passages,
            "entities": entities,
            "relations": [],
            "events": [],
            "coreferences": [],
        }
        return data

    def _read_example_from_file_in_kb_schema(self, filepath: Path) -> Tuple[str, Dict]:
        for key, example in self._read_example_from_file(filepath):
            example = self._parse_example_to_kb_schema(example)
            yield key, example