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gabrielaltay commited on
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upload hubscripts/pubhealth_hub.py to hub from bigbio repo

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  1. pubhealth.py +209 -0
pubhealth.py ADDED
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+ # coding=utf-8
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+ # Copyright 2020 The HuggingFace Datasets Authors and the current dataset script contributor.
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+ #
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+ # Licensed under the Apache License, Version 2.0 (the "License");
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+ # you may not use this file except in compliance with the License.
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+ # You may obtain a copy of the License at
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+ #
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+ # http://www.apache.org/licenses/LICENSE-2.0
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+ #
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+ # Unless required by applicable law or agreed to in writing, software
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+ # distributed under the License is distributed on an "AS IS" BASIS,
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+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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+ # See the License for the specific language governing permissions and
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+ # limitations under the License.
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+ """
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+ A dataset of 11,832 claims for fact- checking, which are related a range of health topics
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+ including biomedical subjects (e.g., infectious diseases, stem cell research), government healthcare policy
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+ (e.g., abortion, mental health, women’s health), and other public health-related stories
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+ """
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+
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+ import csv
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+ import os
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+ from pathlib import Path
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+
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+ import datasets
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+
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+ from .bigbiohub import pairs_features
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+ from .bigbiohub import BigBioConfig
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+ from .bigbiohub import Tasks
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+
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+ logger = datasets.utils.logging.get_logger(__name__)
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+
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+ _LANGUAGES = ['English']
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+ _PUBMED = False
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+ _LOCAL = False
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+ _CITATION = """\
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+ @article{kotonya2020explainable,
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+ title={Explainable automated fact-checking for public health claims},
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+ author={Kotonya, Neema and Toni, Francesca},
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+ journal={arXiv preprint arXiv:2010.09926},
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+ year={2020}
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+ }
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+ """
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+
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+ _DATASETNAME = "pubhealth"
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+ _DISPLAYNAME = "PUBHEALTH"
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+
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+ _DESCRIPTION = """\
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+ A dataset of 11,832 claims for fact- checking, which are related a range of health topics
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+ including biomedical subjects (e.g., infectious diseases, stem cell research), government healthcare policy
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+ (e.g., abortion, mental health, women’s health), and other public health-related stories
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+ """
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+
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+ _HOMEPAGE = "https://github.com/neemakot/Health-Fact-Checking/tree/master/data"
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+
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+ _LICENSE = 'MIT License'
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+
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+ _URLs = {
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+ _DATASETNAME: "https://drive.google.com/uc?export=download&id=1eTtRs5cUlBP5dXsx-FTAlmXuB6JQi2qj"
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+ }
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+
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+ _SUPPORTED_TASKS = [Tasks.TEXT_CLASSIFICATION]
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+ _SOURCE_VERSION = "1.0.0"
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+ _BIGBIO_VERSION = "1.0.0"
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+
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+ _CLASSES = ["true", "false", "unproven", "mixture"]
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+
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+
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+ class PUBHEALTHDataset(datasets.GeneratorBasedBuilder):
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+ """Pubhealth text classification dataset"""
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+
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+ SOURCE_VERSION = datasets.Version(_SOURCE_VERSION)
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+ BIGBIO_VERSION = datasets.Version(_BIGBIO_VERSION)
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+
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+ BUILDER_CONFIGS = [
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+ BigBioConfig(
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+ name="pubhealth_source",
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+ version=SOURCE_VERSION,
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+ description="PUBHEALTH source schema",
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+ schema="source",
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+ subset_id="pubhealth",
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+ ),
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+ BigBioConfig(
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+ name="pubhealth_bigbio_pairs",
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+ version=BIGBIO_VERSION,
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+ description="PUBHEALTH BigBio schema",
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+ schema="bigbio_pairs",
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+ subset_id="pubhealth",
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+ ),
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+ ]
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+
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+ DEFAULT_CONFIG_NAME = "pubhealth_source"
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+
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+ def _info(self):
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+
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+ if self.config.schema == "source":
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+ features = datasets.Features(
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+ {
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+ "claim_id": datasets.Value("string"),
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+ "claim": datasets.Value("string"),
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+ "date_published": datasets.Value("string"),
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+ "explanation": datasets.Value("string"),
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+ "fact_checkers": datasets.Value("string"),
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+ "main_text": datasets.Value("string"),
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+ "sources": datasets.Value("string"),
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+ "label": datasets.ClassLabel(names=_CLASSES),
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+ "subjects": datasets.Value("string"),
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+ }
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+ )
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+
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+ # Using in entailment schema
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+ elif self.config.schema == "bigbio_pairs":
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+ features = pairs_features
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+
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+ return datasets.DatasetInfo(
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+ description=_DESCRIPTION,
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+ features=features,
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+ homepage=_HOMEPAGE,
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+ license=str(_LICENSE),
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+ citation=_CITATION,
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+ )
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+
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+ def _split_generators(self, dl_manager):
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+ """Returns SplitGenerators."""
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+ urls = _URLs[_DATASETNAME]
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+ data_dir = Path(dl_manager.download_and_extract(urls))
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+
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+ return [
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+ datasets.SplitGenerator(
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+ name=datasets.Split.TRAIN,
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+ gen_kwargs={
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+ "filepath": os.path.join(data_dir, "PUBHEALTH/train.tsv"),
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+ "split": "train",
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+ },
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+ ),
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+ datasets.SplitGenerator(
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+ name=datasets.Split.TEST,
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+ gen_kwargs={
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+ "filepath": os.path.join(data_dir, "PUBHEALTH/test.tsv"),
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+ "split": "test",
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+ },
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+ ),
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+ datasets.SplitGenerator(
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+ name=datasets.Split.VALIDATION,
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+ gen_kwargs={
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+ "filepath": os.path.join(data_dir, "PUBHEALTH/dev.tsv"),
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+ "split": "validation",
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+ },
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+ ),
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+ ]
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+
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+ def _generate_examples(self, filepath, split):
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+ """Yields examples as (key, example) tuples."""
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+
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+ with open(filepath, encoding="utf-8") as csv_file:
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+ csv_reader = csv.reader(
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+ csv_file,
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+ quotechar='"',
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+ delimiter="\t",
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+ quoting=csv.QUOTE_NONE,
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+ skipinitialspace=True,
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+ )
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+ next(csv_reader, None) # remove column headers
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+ for id_, row in enumerate(csv_reader):
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+ # train.tsv/dev.tsv only has 9 columns
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+ # test.tsv has an additional column at the beginning
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+ # Some entries are malformed, will log skipped lines
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+ if len(row) < 9:
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+ logger.info("Line %s is malformed", id_)
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+ continue
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+ (
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+ claim_id,
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+ claim,
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+ date_published,
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+ explanation,
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+ fact_checkers,
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+ main_text,
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+ sources,
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+ label,
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+ subjects,
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+ ) = row[
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+ -9:
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+ ] # only take last 9 columns to fix test.tsv disparity
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+
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+ if label not in _CLASSES:
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+ logger.info("Line %s is missing label", id_)
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+ continue
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+
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+ if self.config.schema == "source":
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+ yield id_, {
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+ "claim_id": claim_id,
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+ "claim": claim,
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+ "date_published": date_published,
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+ "explanation": explanation,
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+ "fact_checkers": fact_checkers,
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+ "main_text": main_text,
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+ "sources": sources,
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+ "label": label,
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+ "subjects": subjects,
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+ }
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+
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+ elif self.config.schema == "bigbio_pairs":
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+ yield id_, {
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+ "id": id_, # uid is an unique identifier for every record that starts from 0
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+ "document_id": claim_id,
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+ "text_1": claim,
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+ "text_2": explanation,
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+ "label": label,
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+ }