pubhealth.py

# coding=utf-8
# Copyright 2020 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.
"""
A dataset of 11,832 claims for fact- checking, which are related a range of health topics
including biomedical subjects (e.g., infectious diseases, stem cell research), government healthcare policy
(e.g., abortion, mental health, women’s health), and other public health-related stories
"""

import csv
import os
from pathlib import Path

import datasets

from .bigbiohub import pairs_features
from .bigbiohub import BigBioConfig
from .bigbiohub import Tasks

logger = datasets.utils.logging.get_logger(__name__)

_LANGUAGES = ['English']
_PUBMED = False
_LOCAL = False
_CITATION = """\
@article{kotonya2020explainable,
  title={Explainable automated fact-checking for public health claims},
  author={Kotonya, Neema and Toni, Francesca},
  journal={arXiv preprint arXiv:2010.09926},
  year={2020}
}
"""

_DATASETNAME = "pubhealth"
_DISPLAYNAME = "PUBHEALTH"

_DESCRIPTION = """\
A dataset of 11,832 claims for fact- checking, which are related a range of health topics
including biomedical subjects (e.g., infectious diseases, stem cell research), government healthcare policy
(e.g., abortion, mental health, women’s health), and other public health-related stories
"""

_HOMEPAGE = "https://github.com/neemakot/Health-Fact-Checking/tree/master/data"

_LICENSE = 'MIT License'

_URLs = {
    _DATASETNAME: "https://drive.google.com/uc?export=download&id=1eTtRs5cUlBP5dXsx-FTAlmXuB6JQi2qj"
}

_SUPPORTED_TASKS = [Tasks.TEXT_CLASSIFICATION]
_SOURCE_VERSION = "1.0.0"
_BIGBIO_VERSION = "1.0.0"

_CLASSES = ["true", "false", "unproven", "mixture"]


class PUBHEALTHDataset(datasets.GeneratorBasedBuilder):
    """Pubhealth text classification dataset"""

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

    BUILDER_CONFIGS = [
        BigBioConfig(
            name="pubhealth_source",
            version=SOURCE_VERSION,
            description="PUBHEALTH source schema",
            schema="source",
            subset_id="pubhealth",
        ),
        BigBioConfig(
            name="pubhealth_bigbio_pairs",
            version=BIGBIO_VERSION,
            description="PUBHEALTH BigBio schema",
            schema="bigbio_pairs",
            subset_id="pubhealth",
        ),
    ]

    DEFAULT_CONFIG_NAME = "pubhealth_source"

    def _info(self):

        if self.config.schema == "source":
            features = datasets.Features(
                {
                    "claim_id": datasets.Value("string"),
                    "claim": datasets.Value("string"),
                    "date_published": datasets.Value("string"),
                    "explanation": datasets.Value("string"),
                    "fact_checkers": datasets.Value("string"),
                    "main_text": datasets.Value("string"),
                    "sources": datasets.Value("string"),
                    "label": datasets.ClassLabel(names=_CLASSES),
                    "subjects": datasets.Value("string"),
                }
            )

        # Using in entailment schema
        elif self.config.schema == "bigbio_pairs":
            features = pairs_features

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

    def _split_generators(self, dl_manager):
        """Returns SplitGenerators."""
        urls = _URLs[_DATASETNAME]
        data_dir = Path(dl_manager.download_and_extract(urls))

        return [
            datasets.SplitGenerator(
                name=datasets.Split.TRAIN,
                gen_kwargs={
                    "filepath": os.path.join(data_dir, "PUBHEALTH/train.tsv"),
                    "split": "train",
                },
            ),
            datasets.SplitGenerator(
                name=datasets.Split.TEST,
                gen_kwargs={
                    "filepath": os.path.join(data_dir, "PUBHEALTH/test.tsv"),
                    "split": "test",
                },
            ),
            datasets.SplitGenerator(
                name=datasets.Split.VALIDATION,
                gen_kwargs={
                    "filepath": os.path.join(data_dir, "PUBHEALTH/dev.tsv"),
                    "split": "validation",
                },
            ),
        ]

    def _generate_examples(self, filepath, split):
        """Yields examples as (key, example) tuples."""

        with open(filepath, encoding="utf-8") as csv_file:
            csv_reader = csv.reader(
                csv_file,
                quotechar='"',
                delimiter="\t",
                quoting=csv.QUOTE_NONE,
                skipinitialspace=True,
            )
            next(csv_reader, None)  # remove column headers
            for id_, row in enumerate(csv_reader):
                # train.tsv/dev.tsv only has 9 columns
                # test.tsv has an additional column at the beginning
                #  Some entries are malformed, will log skipped lines
                if len(row) < 9:
                    logger.info("Line %s is malformed", id_)
                    continue
                (
                    claim_id,
                    claim,
                    date_published,
                    explanation,
                    fact_checkers,
                    main_text,
                    sources,
                    label,
                    subjects,
                ) = row[
                    -9:
                ]  # only take last 9 columns to fix test.tsv disparity

                if label not in _CLASSES:
                    logger.info("Line %s is missing label", id_)
                    continue

                if self.config.schema == "source":
                    yield id_, {
                        "claim_id": claim_id,
                        "claim": claim,
                        "date_published": date_published,
                        "explanation": explanation,
                        "fact_checkers": fact_checkers,
                        "main_text": main_text,
                        "sources": sources,
                        "label": label,
                        "subjects": subjects,
                    }

                elif self.config.schema == "bigbio_pairs":
                    yield id_, {
                        "id": id_,  # uid is an unique identifier for every record that starts from 0
                        "document_id": claim_id,
                        "text_1": claim,
                        "text_2": explanation,
                        "label": label,
                    }