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NASA_OSDR

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NASA_OSDR / NASA_OSDR.py

anz2

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	# 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.
	"""NASA_OSDR dataset"""

	import json
	import os

	import datasets
	import pandas as pd

	_CITATION = """
	@inproceedings{singh2019towards,
	title={},
	author={},
	booktitle={},
	pages={},
	year={}
	}
	"""

	_DESCRIPTION = """
	TODO: write description
	"""

	_HOMEPAGE = "https://"

	_LICENSE = ""

	_SPLITS = ["train"]

	_FIFTYONE_DATASET_URL = ""


	class NasaOsdr(datasets.GeneratorBasedBuilder):
	"""NASA OSDR dataset."""

	BUILDER_CONFIGS = [
	datasets.BuilderConfig(
	name="NASA_OSDR",
	version=datasets.Version("1.0.0"),
	description=_DESCRIPTION,
	)
	]

	DEFAULT_CONFIG_NAME = "NASA_OSDR"

	def _info(self):
	ASSAY_COLUMNS = ['Sample Name', 'Protocol REF', 'Parameter Value: DNA Fragmentation',
	'Parameter Value: DNA Fragment Size', 'Extract Name', 'Protocol REF.1',
	'Parameter Value: Library Strategy',
	'Parameter Value: Library Selection', 'Parameter Value: Library Layout',
	'Protocol REF.2', 'Parameter Value: Sequencing Instrument',
	'Assay Name', 'Parameter Value: Read Length', 'Raw Data File',
	'Protocol REF.3', 'Parameter Value: Read Depth',
	'Parameter Value: MultiQC File Names']

	# SAMPLE_COLUMNS = ['Source Name', 'Sample Name', 'Characteristics: Organism',
	# 'Characteristics: Strain', 'Characteristics: Genotype',
	# 'Characteristics: Material Type', 'Factor Value: Ionizing Radiation',
	# 'Factor Value: Generation', 'Protocol REF', 'Protocol REF.1',
	# 'Parameter Value: ionizing radiation energy',
	# 'Parameter Value: exposure duration',
	# 'Parameter Value: absorbed radiation dose',
	# 'Parameter Value: absorbed radiation dose rate',
	# 'Parameter Value: ionizing radiation categorized by source',
	# 'Protocol REF.2', 'Parameter Value: Sample Preservation Method',
	# 'Parameter Value: Sample Storage Temperature',
	# 'Parameter Value: Age at time of sample collection',
	# 'Comment: Animal Source', 'Comment: Parental Treatment']

	features = datasets.Features(
	{
	column_name: datasets.Value("string")
	for column_name in ASSAY_COLUMNS
	# for column_name in sorted(list(set(ASSAY_COLUMNS + SAMPLE_COLUMNS)))
	}
	)

	return datasets.DatasetInfo(
	description=_DESCRIPTION,
	features=features,
	supervised_keys=None,
	homepage=_HOMEPAGE,
	license=_LICENSE,
	citation=_CITATION,
	)

	_URL = "https://raw.githubusercontent.com/AnzorGozalishvili/NASA_ODSR_DATA/main"
	_ASSAYS_FILE = "assays.csv"
	_SAMPLES_FILE = "samples.csv"

	def _split_generators(self, dl_manager):
	downloaded_files = dl_manager.download_and_extract(
	{
	"train": {
	"assays": os.path.join(self._URL, self._ASSAYS_FILE),
	"samples": os.path.join(self._URL, self._ASSAYS_FILE)
	},
	}
	)

	return [
	datasets.SplitGenerator(
	name=datasets.Split.TRAIN,
	gen_kwargs={
	"assays_file": downloaded_files['train']['assays'],
	"samples_file": downloaded_files['train']['samples'],
	},
	),
	]

	def _generate_examples(self, assays_file: str, samples_file):
	# assays = os.path.join(dataset_root, "assays.csv")
	# samples = os.path.join(dataset_root, "samples.csv")
	# there can be other metadata tables merged

	assays_df = pd.read_csv(assays_file)
	samples_df = pd.read_csv(samples_file)

	for (idx, assay_row), (_, sample_row) in zip(assays_df.iterrows(), samples_df.iterrows()):
	_item = {**assay_row.to_dict()}
	# _item = {assay_row.to_dict(), sample_row.to_dict()}

	yield idx, _item