geodiff-example-data.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.
"""A tiny dataset containing 5 molecule configurations for fast inference example."""


import csv
import json
import os
import torch
import datasets
# import pickle

# You can copy an official description
_DESCRIPTION = """\
This data is a trimmed version of the GEOM Drugs Dataset. """

_HOMEPAGE = "https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/JNGTDF"

_LICENSE = "Creative Commons 1.0 Universal: https://creativecommons.org/publicdomain/zero/1.0/"
_CITATION = """\
@data{DVN/JNGTDF_2021,
author = {Axelrod, Simon and Gomez-Bombarelli, Rafael},
publisher = {Harvard Dataverse},
title = {{GEOM}},
year = {2021},
version = {V4},
doi = {10.7910/DVN/JNGTDF},
url = {https://doi.org/10.7910/DVN/JNGTDF}
}
"""

# 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 = {
    "drugs": "https://huggingface.co/datasets/fusing/geodiff-example-data/blob/main/data/molecules.pkl",
}


class GeoDiffExampleData(datasets.GeneratorBasedBuilder):
    VERSION = datasets.Version("1.1.0")

    # This is an example of a dataset with multiple configurations.
    # If you don't want/need to define several sub-sets in your dataset,
    # just remove the BUILDER_CONFIG_CLASS and the BUILDER_CONFIGS attributes.

    # If you need to make complex sub-parts in the datasets with configurable options
    # You can create your own builder configuration class to store attribute, inheriting from datasets.BuilderConfig
    # BUILDER_CONFIG_CLASS = MyBuilderConfig

    # You will be able to load one or the other configurations in the following list with
    # data = datasets.load_dataset('my_dataset', 'first_domain')
    # data = datasets.load_dataset('my_dataset', 'second_domain')
    BUILDER_CONFIGS = [
        datasets.BuilderConfig(name="drugs", version=VERSION, description="This part of my dataset covers a first domain"),
    ]

    DEFAULT_CONFIG_NAME = "drugs"  # It's not mandatory to have a default configuration. Just use one if it make sense.

    def _info(self):
        if self.config.name == "drugs":  # This is the name of the configuration selected in BUILDER_CONFIGS above
            features = datasets.Features(
                {
                    "num_molecules": 5, #datasets.Value("string"),
                   # These are the features of your dataset like images, labels ...
                }
            )
        else:  
            raise NotImplementedError("Other Domains Not Added")
        return datasets.DatasetInfo(
            # This is the description that will appear on the datasets page.
            description=_DESCRIPTION,
            # This defines the different columns of the dataset and their types
            features=features,  # Here we define them above because they are different between the two configurations
            # If there's a common (input, target) tuple from the features, uncomment supervised_keys line below and
            # specify them. They'll be used if as_supervised=True in builder.as_dataset.
            # supervised_keys=("sentence", "label"),
            # Homepage of the dataset for documentation
            homepage=_HOMEPAGE,
            # License for the dataset if available
            license=_LICENSE,
            # Citation for the dataset
            citation=_CITATION,
        )

    def _split_generators(self, dl_manager):
        # TODO: This method is tasked with downloading/extracting the data and defining the splits depending on the configuration
        # If several configurations are possible (listed in BUILDER_CONFIGS), the configuration selected by the user is in self.config.name

        # dl_manager is a datasets.download.DownloadManager that can be used to download and extract URLS
        # It can accept any type or nested list/dict and will give back the same structure with the url replaced with path to local files.
        # By default the archives will be extracted and a path to a cached folder where they are extracted is returned instead of the archive
        urls = _URLS[self.config.name]
        data_dir = dl_manager.download_and_extract(urls)
        return [
            datasets.SplitGenerator(
                name=datasets.Split.TRAIN,
                # These kwargs will be passed to _generate_examples
                gen_kwargs={
                    "filepath": data_dir,
                    "split": "train",
                },
            )
        ]

    # method parameters are unpacked from `gen_kwargs` as given in `_split_generators`
    def _generate_examples(self, filepath, split):
        # The `key` is for legacy reasons (tfds) and is not important in itself, but must be unique for each example.
        with open(filepath, "rb") as f:
            data = torch.load(f)
            # data = pickle.load(f)
            yield data