#!/usr/bin/env python
# coding=utf-8
# Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
# SPDX-License-Identifier: MIT-0
"""Paired sequences from the Observed Antibody Space database"""
import csv
import datasets
import os

_CITATION = """\
@article{Olsen_Boyles_Deane_2022, 
title={Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences}, 
volume={31}, rights={© 2021 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.}, 
ISSN={1469-896X}, DOI={10.1002/pro.4205}, 
number={1}, journal={Protein Science}, author={Olsen, Tobias H. and Boyles, Fergus and Deane, Charlotte M.}, 
year={2022}, pages={141–146}, language={en} }

"""
_DESCRIPTION = """\
Paired heavy and light chain antibody sequences for multiple species.
"""

_HOMEPAGE = "https://opig.stats.ox.ac.uk/webapps/oas/"

_LICENSE = "cc-by-4.0"

_BASE_URL = "https://aws-hcls-ml.s3.amazonaws.com/oas-paired-sequence-data/"
_URLS = {
    "human": _BASE_URL + "human.zip",
    "rat_SD": _BASE_URL + "rat_SD.zip",
    "mouse_BALB_c": _BASE_URL + "mouse_BALB_c.zip",
    "mouse_C57BL_6": _BASE_URL + "mouse_C57BL_6.zip",
}

_FEATURES = datasets.Features(
    {
        "pair_id": datasets.Value("string"),
        "sequence_alignment_aa_heavy": datasets.Value("string"),
        "cdr1_aa_heavy": datasets.Value("string"),
        "cdr2_aa_heavy": datasets.Value("string"),
        "cdr3_aa_heavy": datasets.Value("string"),
        "sequence_alignment_aa_light": datasets.Value("string"),
        "cdr1_aa_light": datasets.Value("string"),
        "cdr2_aa_light": datasets.Value("string"),
        "cdr3_aa_light": datasets.Value("string"),
        "cdr1_aa_heavy_start": datasets.Value("int16"),
        "cdr1_aa_heavy_end": datasets.Value("int16"),
        "cdr1_aa_light_start": datasets.Value("int16"),
        "cdr1_aa_light_end": datasets.Value("int16"),
        "cdr2_aa_heavy_start": datasets.Value("int16"),
        "cdr2_aa_heavy_end": datasets.Value("int16"),
        "cdr2_aa_light_start": datasets.Value("int16"),
        "cdr2_aa_light_end": datasets.Value("int16"),
        "cdr3_aa_heavy_start": datasets.Value("int16"),
        "cdr3_aa_heavy_end": datasets.Value("int16"),
        "cdr3_aa_light_start": datasets.Value("int16"),
        "cdr3_aa_light_end": datasets.Value("int16"),
    }
)


class OasPairedSequenceData(datasets.GeneratorBasedBuilder):
    """OAS paired sequence data."""

    VERSION = datasets.Version("1.2.0")
    BUILDER_CONFIGS = [
        datasets.BuilderConfig(name="human", version=VERSION, description="Human"),
        datasets.BuilderConfig(name="rat_SD", version=VERSION, description="rat_SD"),
        datasets.BuilderConfig(
            name="mouse_BALB_c", version=VERSION, description="mouse_BALB_c"
        ),
        datasets.BuilderConfig(
            name="mouse_C57BL_6", version=VERSION, description="mouse_C57BL_6"
        ),
    ]

    def _info(self):
        return datasets.DatasetInfo(
            description=_DESCRIPTION,
            features=_FEATURES,
            homepage=_HOMEPAGE,
            license=_LICENSE,
            citation=_CITATION,
        )

    def _split_generators(self, dl_manager):
        urls = _URLS[self.config.name]
        data_dir = dl_manager.download_and_extract(urls)
        return [
            datasets.SplitGenerator(
                name=datasets.Split.TRAIN,
                gen_kwargs={
                    "filepath": os.path.join(data_dir, "train.csv"),
                    "split": "train",
                },
            ),
        ]

    def _generate_examples(self, filepath, split):
        with open(filepath, newline="") as f:
            reader = csv.reader(f, delimiter=",")
            for key, row in enumerate(reader):
                if key == 0:
                    continue
                yield key, {
                    "pair_id": row[0],
                    "sequence_alignment_aa_heavy": row[1],
                    "cdr1_aa_heavy": row[2],
                    "cdr2_aa_heavy": row[3],
                    "cdr3_aa_heavy": row[4],
                    "sequence_alignment_aa_light": row[5],
                    "cdr1_aa_light": row[6],
                    "cdr2_aa_light": row[7],
                    "cdr3_aa_light": row[8],
                    "cdr1_aa_heavy_start": row[9],
                    "cdr1_aa_heavy_end": row[10],
                    "cdr1_aa_light_start": row[11],
                    "cdr1_aa_light_end": row[12],
                    "cdr2_aa_heavy_start": row[13],
                    "cdr2_aa_heavy_end": row[14],
                    "cdr2_aa_light_start": row[15],
                    "cdr2_aa_light_end": row[16],
                    "cdr3_aa_heavy_start": row[17],
                    "cdr3_aa_heavy_end": row[18],
                    "cdr3_aa_light_start": row[19],
                    "cdr3_aa_light_end": row[20],
                }