PAIR.py

# 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.


import json

import datasets
from datasets import BuilderConfig

# TODO: Add BibTeX citation
# Find for instance the citation on arxiv or on the dataset repo/website
_CITATION = """\
@article{duan2024boosting,
  title={Boosting the Predictive Power of Protein Representations with a Corpus of Text Annotations},
  author={Duan, Haonan and Skreta, Marta and Cotta, Leonardo and Rajaonson, Ella Miray and Dhawan, Nikita and Aspuru-Guzik, Alán and Maddison, Chris J},
  journal={bioRxiv},
  pages={2024--07},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}
"""

_DESCRIPTION = """\
This new dataset is designed to solve this great NLP task and is crafted with a lot of care.
"""

# TODO: Add a link to an official homepage for the dataset here
_HOMEPAGE = ""

# TODO: Add the licence for the dataset here if you can find it
_LICENSE = ""

# TODO: Add link to the official dataset URLs here
# The HuggingFace Datasets library doesn't host the datasets but only points to the original files.
# This can be an arbitrary nested dict/list of URLs (see below in `_split_generators` method)
_URLS = {
    "first_domain": "https://huggingface.co/datasets/mskrt/PAIR/raw/main/test.json",
}


# TODO: Name of the dataset usually matches the script name with CamelCase instead of snake_case
annotation2type = {
    "names": datasets.Value("string"),
    "function": datasets.Value("string"),
    "EC": datasets.Sequence(datasets.Value("string")),
}


class CustomConfig(datasets.BuilderConfig):
    """CustomConfig."""

    def __init__(self, **kwargs):
        """__init__.

        Parameters
        ----------
        kwargs :
            kwargs
        """
        self.annotation_type = kwargs.pop("annotation_type", "function")
        super(CustomConfig, self).__init__(**kwargs)


class PAIRDataset(datasets.GeneratorBasedBuilder):
    """PAIRDataset."""

    BUILDER_CONFIGS = [
        CustomConfig(
            name="custom_config",
            version="1.0.0",
            description="your description",
        ),
    ]  # Configs initialization
    BUILDER_CONFIG_CLASS = CustomConfig  # Must specify this to use custom config

    def _info(self):
        """_info."""
        self.annotation_type = self.config_kwargs["annotation_type"]
        # Confirm annotation_type is set before continuing
        return datasets.DatasetInfo(
            description="My custom dataset.",
            features=datasets.Features(
                {
                    self.annotation_type: annotation2type[self.annotation_type],
                    "sequence": datasets.Value("string"),
                    "pid": datasets.Value("string"),
                }
            ),
            supervised_keys=None,
        )
        # "annotation_type": datasets.Value("string"),
        # "annotation": datasets.Value("string"),

    def _split_generators(self, dl_manager):
        """_split_generators.

        Parameters
        ----------
        dl_manager :
            dl_manager
        """
        # Implement logic to download and extract data files
        # For simplicity, assume data_files is a dict with paths to your data
        print("in generator self.annotation", self.annotation_type)
        data_files = {
            "train": "train.json",
            "test": "test.json",
        }
        return [
            # datasets.SplitGenerator(
            #    name=datasets.Split.TRAIN,
            #    gen_kwargs={'filepath': data_files['train']},
            # ),
            datasets.SplitGenerator(
                name=datasets.Split.TEST,
                gen_kwargs={"filepath": data_files["test"]},
            ),
        ]

    def _generate_examples(self, filepath):
        """_generate_examples.

        Parameters
        ----------
        filepath :
            filepath
        """
        # Implement your data reading logic here
        print("in generator 2 self.annotation", self.annotation_type)
        with open(filepath, encoding="utf-8") as f:
            data = json.load(f)
            counter = 0
            for idx, annotation_type in enumerate(data.keys()):
                print(annotation_type, self.annotation_type)
                if annotation_type != self.annotation_type:
                    continue
                # Parse your line into the appropriate fields
                samples = data[annotation_type]
                for idx_2, elem in enumerate(samples):
                    # example = parse_line_to_example(line)
                    if elem["content"] != [None]:
                        content = elem["content"][0]
                        # print(literal_eval(content), "done")
                        yield counter, {
                            "sequence": elem["seq"],
                            "pid": elem["pid"],
                            annotation_type: content,
                        }
                        counter += 1

                        # "annotation_type": annotation_type,