annotate data_manager/gtdbtk_database_installer.py @ 9:3248e43703e7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1696bfc7f5bade0686ad6731da06a436c43b59e5

#!/usr/bin/env python

import argparse
import gzip
import json
import os
import shutil
import sys
import tarfile
from datetime import date
from urllib.parse import urlparse
from urllib.request import HTTPError, Request, urlopen

# rather provide the urls based on the release, less error potential for the admins !
urls = {
    "202": {
        "full": "https://data.gtdb.ecogenomic.org/releases/release202/202.0/auxillary_files/gtdbtk_r202_data.tar.gz",
        "meta_ar": "https://data.gtdb.ecogenomic.org/releases/release202/202.0/ar122_metadata_r202.tar.gz",
        "meta_bac": "https://data.gtdb.ecogenomic.org/releases/release202/202.0/bac120_metadata_r202.tar.gz",
    },
    "207": {
        "full": "https://data.gtdb.ecogenomic.org/releases/release207/207.0/auxillary_files/gtdbtk_r207_data.tar.gz",
        "meta_ar": "https://data.gtdb.ecogenomic.org/releases/release207/207.0/ar53_metadata_r207.tar.gz",
        "meta_bac": "https://data.gtdb.ecogenomic.org/releases/release207/207.0/bac120_metadata_r207.tar.gz",
    },
    "214": {
        "full": "https://data.gtdb.ecogenomic.org/releases/release214/214.0/auxillary_files/gtdbtk_r214_data.tar.gz",
        "meta_ar": "https://data.gtdb.ecogenomic.org/releases/release214/214.1/ar53_metadata_r214.tsv.gz",
        "meta_bac": "https://data.gtdb.ecogenomic.org/releases/release214/214.1/bac120_metadata_r214.tsv.gz",
    },
    "220": {
        "full": "https://data.gtdb.ecogenomic.org/releases/release220/220.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r220_data.tar.gz",
        "meta_ar": "https://data.gtdb.ecogenomic.org/releases/release220/220.0/ar53_metadata_r220.tsv.gz",
        "meta_bac": "https://data.gtdb.ecogenomic.org/releases/release220/220.0/bac120_metadata_r220.tsv.gz",
    },
    "226": {
        "full": "https://data.ace.uq.edu.au/public/gtdb/data/releases/release226/226.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r226_data.tar.gz",
        "meta_ar": "https://data.ace.uq.edu.au/public/gtdb/data/releases/release226/226.0/ar53_metadata_r226.tsv.gz",
        "meta_bac": "https://data.ace.uq.edu.au/public/gtdb/data/releases/release226/226.0/bac120_metadata_r226.tsv.gz",
    },
}


def is_urlfile(url):
    # Check if online file exists
    try:
        r = urlopen(url)  # response
        return r.getcode() < 400
    except HTTPError:
        return False


def extract_tar_iteratively(tarball, target_directory):
    """
    Extracts a .tar, .tar.gz, or .tar.bz2 archive iteratively in a memory-efficient manner.

    This function processes the contents of the archive member-by-member, ensuring only
    one file or directory is loaded into memory at any given time. It handles the creation
    of directories and symbolic links, and streams large files to disk in chunks to avoid
    memory overload.

    Args:
        tarball (str): Path to the tar archive (e.g., .tar, .tar.gz, .tar.bz2) to be extracted.
        target_directory (str): The destination directory where the archive content
                                will be extracted.

    Raises:
        OSError: If there is an issue with file or directory creation, or writing to disk.
        tarfile.TarError: If there is an issue opening or reading the tar archive.

    Example Usage:
        extract_tar_iteratively("archive.tar.gz", "/path/to/extract")

    Notes:
        - The function supports symbolic and hard links present in the tar archive.
        - It ensures that directories are created before files are extracted.
        - Large files are streamed to disk in 1 MB chunks to minimize memory usage.
        - This function does not return anything but will populate the target directory with
          the extracted content.
    """

    with tarfile.open(tarball, "r:*") as fh:
        for member in fh:
            # Full path to where the member should be extracted
            member_path = os.path.join(target_directory, member.name)

            if member.isdir():
                # If it's a directory, ensure it exists
                os.makedirs(member_path, exist_ok=True)
            elif member.isfile():
                # If it's a file, extract it in chunks to avoid memory spikes
                with fh.extractfile(member) as source, open(
                    member_path, "wb"
                ) as target:
                    shutil.copyfileobj(
                        source, target, length=1024 * 1024
                    )  # 1 MB chunks
            elif member.issym() or member.islnk():
                # Handle symlinks or hard links if necessary
                target_link = os.path.join(target_directory, member.name)
                if member.issym():
                    os.symlink(member.linkname, target_link)
                elif member.islnk():
                    os.link(member.linkname, target_link)


def url_download(url, target_directory, meta):

    # download the url
    url_parts = urlparse(url)
    tarball = os.path.abspath(
        os.path.join(target_directory, os.path.basename(url_parts.path))
    )
    src = None
    dst = None
    try:
        req = Request(url)
        src = urlopen(req)
        with open(tarball, "wb") as dst:
            while True:
                chunk = src.read(2**16)  # Read in 64 KB chunks instead of 1 KB
                if chunk:
                    dst.write(chunk)
                else:
                    break
    except Exception as e:
        sys.exit(str(e))
    finally:
        if src is not None:
            src.close()

    # extract the metadata
    if meta:
        # extract the content of *.tar.gz into the target dir
        if tarfile.is_tarfile(tarball):
            extract_tar_iteratively(tarball, target_directory)
            os.remove(tarball)
            return target_directory  # return path to output folder
        # extract the content of *.gz into the target dir
        elif ".gz" in tarball:
            with gzip.open(tarball, "rb") as f_in:
                unzipped_file = tarball.strip(".gz")
                with open(unzipped_file, "wb") as f_out:
                    shutil.copyfileobj(f_in, f_out)
                    os.remove(tarball)
                    folder_of_unzipped_file = os.path.dirname(unzipped_file)
            return folder_of_unzipped_file
        else:
            sys.exit(
                "No correct input format for metadata file, must be .tar.gz or .gz"
            )
    else:
        # handle the DB
        # extract the content of the folder in the tar.gz into the target dir
        if tarfile.is_tarfile(tarball):
            extract_tar_iteratively(tarball, target_directory)
            os.remove(tarball)
        else:
            # handle the test case for the DB
            return tarball

        # The tarball extraction will create a directory named
        # something like release202 in the target_directory, so
        # we need to move the items in that directory to the
        # target directory.
        subdir = next(os.walk(target_directory))[1][0]
        subdir_path = os.path.join(target_directory, subdir)
        items = os.listdir(subdir_path)
        for item in items:
            item_path = os.path.join(subdir_path, item)
            shutil.move(item_path, target_directory)
        os.rmdir(subdir_path)
        return target_directory


def create_data_manager_entry(database_name, release, file_path):
    time = date.today().strftime("%Y-%m-%d")
    data_manager_entry = {}
    data_manager_entry["value"] = (
        f"{database_name.replace(' ', '_').lower()}_release_{release}_downloaded_{time}"
    )
    data_manager_entry["name"] = f"{database_name} - release {release} ({time})"
    data_manager_entry["path"] = file_path
    data_manager_entry["version"] = release
    return data_manager_entry


def download(release, meta, test, out_file):

    with open(out_file) as fh:
        params = json.load(fh)

    target_directory = params["output_data"][0]["extra_files_path"]
    os.makedirs(target_directory)

    if test:
        # switch the DB to use the test case
        urls[release][
            "full"
        ] = "https://zenodo.org/records/13734217/files/release220-test.tar.gz"

        # make use of the test to check if all urls exists
        for _version, items in urls.items():
            for url in items.values():
                assert is_urlfile(url)

    data_manager_json = {"data_tables": {}}

    # download taxonomy metadata tables
    if meta:
        url = urls[release]["meta_ar"]
        url_download(url, target_directory, meta)
        url = urls[release]["meta_bac"]
        file_path = url_download(url, target_directory, meta)

        data_manager_json["data_tables"]["gtdbtk_database_metadata_versioned"] = [
            create_data_manager_entry("Metadata Tables", release, file_path)
        ]
    # download the full DB
    else:
        url = urls[release]["full"]
        file_path = url_download(url, target_directory, meta)
        data_manager_json["data_tables"]["gtdbtk_database_versioned"] = [
            create_data_manager_entry("Full Database", release, file_path)
        ]

    # store in dedicated metadata table
    with open(out_file, "w") as fh:
        json.dump(data_manager_json, fh, sort_keys=True)


if __name__ == "__main__":
    parser = argparse.ArgumentParser()

    parser.add_argument("--version", dest="version", help="DB version")
    parser.add_argument(
        "--release", dest="release", help="Release of the GTDB-Tk database version"
    )
    parser.add_argument("--out_file", dest="out_file", help="JSON output file")
    parser.add_argument(
        "--meta",
        dest="meta",
        action="store_true",
        help="Store meta data flag",
    )
    parser.add_argument(
        "--test",
        dest="test",
        action="store_true",
        help="Run test",
    )
    args = parser.parse_args()

    download(
        args.release,
        args.meta,
        args.test,
        args.out_file,
    )