<filename>uta_tools/data/data_downloads.py
"""Module for downloading data files."""
from ftplib import FTP
from os import remove
import gzip
import shutil
import datetime

from dateutil import parser

from uta_tools import APP_ROOT


class DataDownload:
    """Class for downloading data files."""

    def __init__(self) -> None:
        """Initialize DataDownload."""
        self._make_data_dir()
        self._download_data()

    def _make_data_dir(self) -> None:
        """Make data directory"""
        self._data_dir = APP_ROOT / "data"
        self._data_dir.mkdir(exist_ok=True, parents=True)

    def _download_data(self) -> None:
        """Download data files needed for uta_tools."""
        with FTP("ftp.ncbi.nlm.nih.gov") as ftp:
            ftp.login()
            self._download_mane_summary(ftp)
            self._download_lrg_refseq_gene_data(ftp)

    def _download_mane_summary(self, ftp: FTP) -> None:
        """Download latest MANE summary data and set path

        :param FTP ftp: FTP connection
        """
        ftp.cwd("/refseq/MANE/MANE_human/current")
        files = ftp.nlst()
        mane_summary_file = \
            [f for f in files if f.endswith(".summary.txt.gz")]
        if not mane_summary_file:
            raise Exception("Unable to download MANE summary data")
        mane_summary_file = mane_summary_file[0]
        self._mane_summary_path = \
            self._data_dir / mane_summary_file[:-3]
        mane_data_path = self._data_dir / mane_summary_file
        if not self._mane_summary_path.exists():
            with open(mane_data_path, "wb") as fp:
                ftp.retrbinary(f"RETR {mane_summary_file}", fp.write)
            with gzip.open(mane_data_path, "rb") as f_in:
                with open(self._mane_summary_path, "wb") as f_out:
                    shutil.copyfileobj(f_in, f_out)
            remove(mane_data_path)

    def _download_lrg_refseq_gene_data(self, ftp: FTP) -> None:
        """Download latest LRG_RefSeqGene and set path

        :param FTP ftp: FTP connection
        """
        lrg_refseqgene_file = "LRG_RefSeqGene"
        ftp_dir_path = "/refseq/H_sapiens/RefSeqGene/"
        ftp_file_path = f"{ftp_dir_path}{lrg_refseqgene_file}"
        timestamp = ftp.voidcmd(f"MDTM {ftp_file_path}")[4:].strip()
        date = str(parser.parse(timestamp)).split()[0]
        version = datetime.datetime.strptime(date,
                                             "%Y-%m-%d").strftime("%Y%m%d")

        fn_versioned = f"{lrg_refseqgene_file}_{version}"
        lrg_refseqgene_path = self._data_dir / lrg_refseqgene_file
        self._lrg_refseqgene_path = self._data_dir / fn_versioned
        if not self._lrg_refseqgene_path.exists():
            ftp.cwd(ftp_dir_path)
            with open(lrg_refseqgene_path, "wb") as fp:
                ftp.retrbinary(f"RETR {lrg_refseqgene_file}", fp.write)
            with open(lrg_refseqgene_path, "rb") as f_in:
                with open(self._lrg_refseqgene_path, "wb") as f_out:
                    shutil.copyfileobj(f_in, f_out)
            remove(lrg_refseqgene_path)

<filename>uta_tools/data/data_downloads.py
"""Module for downloading data files."""
from ftplib import FTP
from os import remove
import gzip
import shutil
import datetime

from dateutil import parser

from uta_tools import APP_ROOT


class DataDownload:
    """Class for downloading data files."""

    def __init__(self) -> None:
        """Initialize DataDownload."""
        self._make_data_dir()
        self._download_data()

    def _make_data_dir(self) -> None:
        """Make data directory"""
        self._data_dir = APP_ROOT / "data"
        self._data_dir.mkdir(exist_ok=True, parents=True)

    def _download_data(self) -> None:
        """Download data files needed for uta_tools."""
        with FTP("ftp.ncbi.nlm.nih.gov") as ftp:
            ftp.login()
            self._download_mane_summary(ftp)
            self._download_lrg_refseq_gene_data(ftp)

    def _download_mane_summary(self, ftp: FTP) -> None:
        """Download latest MANE summary data and set path

        :param FTP ftp: FTP connection
        """
        ftp.cwd("/refseq/MANE/MANE_human/current")
        files = ftp.nlst()
        mane_summary_file = \
            [f for f in files if f.endswith(".summary.txt.gz")]
        if not mane_summary_file:
            raise Exception("Unable to download MANE summary data")
        mane_summary_file = mane_summary_file[0]
        self._mane_summary_path = \
            self._data_dir / mane_summary_file[:-3]
        mane_data_path = self._data_dir / mane_summary_file
        if not self._mane_summary_path.exists():
            with open(mane_data_path, "wb") as fp:
                ftp.retrbinary(f"RETR {mane_summary_file}", fp.write)
            with gzip.open(mane_data_path, "rb") as f_in:
                with open(self._mane_summary_path, "wb") as f_out:
                    shutil.copyfileobj(f_in, f_out)
            remove(mane_data_path)

    def _download_lrg_refseq_gene_data(self, ftp: FTP) -> None:
        """Download latest LRG_RefSeqGene and set path

        :param FTP ftp: FTP connection
        """
        lrg_refseqgene_file = "LRG_RefSeqGene"
        ftp_dir_path = "/refseq/H_sapiens/RefSeqGene/"
        ftp_file_path = f"{ftp_dir_path}{lrg_refseqgene_file}"
        timestamp = ftp.voidcmd(f"MDTM {ftp_file_path}")[4:].strip()
        date = str(parser.parse(timestamp)).split()[0]
        version = datetime.datetime.strptime(date,
                                             "%Y-%m-%d").strftime("%Y%m%d")

        fn_versioned = f"{lrg_refseqgene_file}_{version}"
        lrg_refseqgene_path = self._data_dir / lrg_refseqgene_file
        self._lrg_refseqgene_path = self._data_dir / fn_versioned
        if not self._lrg_refseqgene_path.exists():
            ftp.cwd(ftp_dir_path)
            with open(lrg_refseqgene_path, "wb") as fp:
                ftp.retrbinary(f"RETR {lrg_refseqgene_file}", fp.write)
            with open(lrg_refseqgene_path, "rb") as f_in:
                with open(self._lrg_refseqgene_path, "wb") as f_out:
                    shutil.copyfileobj(f_in, f_out)
            remove(lrg_refseqgene_path)

Module for downloading data files. Class for downloading data files. Initialize DataDownload. Make data directory Download data files needed for uta_tools. Download latest MANE summary data and set path          :param FTP ftp: FTP connection Download latest LRG_RefSeqGene and set path          :param FTP ftp: FTP connection