cli

gen3(verbose, destination_dir, manifest_path, drs_column_name, api_key_path, endpoint, duplicate)

Copy files from gen3 server.

Source code in drs_downloader/cli.py

@cli.command()
@click.option(
    "--verbose",
    "-v",
    is_flag=True,
    show_default=True,
    default=False,
    help="Display every logger",
)
@click.option(
    "--destination-dir",
    "-d",
    show_default=True,
    default=os.getcwd(),
    help="Destination directory.",
    required=True
)
@click.option(
    "--manifest-path",
    "-m",
    show_default=True,
    help="Path to manifest tsv.",
    required=True
)
@click.option(
    "--drs-column-name",
    default="ga4gh_drs_uri",
    show_default=True,
    help="The column header in the TSV file associated with the DRS URIs."
         "Example: pfb:ga4gh_drs_uri",
)
@click.option(
    "--api-key-path",
    show_default=True,
    help="Gen3 credentials file"
)
@click.option("--endpoint", show_default=True, required=True, help="Gen3 endpoint")
@click.option(
    "--duplicate",
    default=False,
    is_flag=True,
    show_default=True,
    help="This flag is used to specify wether"
         "or not to download the file again if it already exists in the directory"
         "Example: True",
)
def gen3(
    verbose: bool,
    destination_dir: str,
    manifest_path: str,
    drs_column_name: str,
    api_key_path: str,
    endpoint: str,
    duplicate: bool,
):
    """Copy files from gen3 server."""
    # read from manifest
    assert api_key_path is not None, "If using gen3 mode an api key path must be provided with --api-key-path"
    ids_from_manifest = _extract_tsv_info(Path(manifest_path), drs_column_name)

    _perform_downloads(
        destination_dir,
        Gen3DrsClient(api_key_path=api_key_path, endpoint=endpoint),
        ids_from_manifest,
        verbose=verbose,
        duplicate=duplicate,
        user_project=None
    )

mock(verbose, destination_dir, manifest_path, drs_column_name, duplicate)

Generate test files locally, without the need for server.

Source code in drs_downloader/cli.py

@cli.command()
@click.option(
    "--verbose",
    "-v",
    is_flag=True,
    show_default=True,
    default=False,
    help="Display every logger",
)
@click.option(
    "--destination-dir",
    "-d",
    show_default=True,
    default=os.getcwd(),
    help="Destination directory.",
    required=True
)
@click.option("--manifest-path", "-m", show_default=True, help="Path to manifest tsv.")
@click.option(
    "--drs-column-name",
    default="ga4gh_drs_uri",
    show_default=True,
    help="The column header in the TSV file associated with the DRS URIs."
    "Example: pfb:ga4gh_drs_uri",
    required=True
)
@click.option(
    "--duplicate",
    default=False,
    is_flag=True,
    show_default=True,
    help="This flag is used to specify wether"
    "or not to download the file again if it already exists in the directory"
    "Example: True",
)
def mock(
    verbose: bool,
    destination_dir: str,
    manifest_path: str,
    drs_column_name: str,
    duplicate: bool,
):
    """Generate test files locally, without the need for server."""

    #
    # get ids from manifest
    ids_from_manifest = _extract_tsv_info(Path(manifest_path), drs_column_name)

    # perform downloads with a mock drs client
    _perform_downloads(
        destination_dir, MockDrsClient(), ids_from_manifest, user_project=None, verbose=verbose, duplicate=duplicate,
    )

pretty_size(bytes)

Integer -> human readable Data Size Pretty Printer

Source code in drs_downloader/cli.py

def pretty_size(bytes):
    """Integer -> human readable Data Size Pretty Printer"""
    assert (bytes and bytes > 0), f"ERROR, The total download size {bytes} is Zero or None"
    units = [
        (1 << 50, " PB"),
        (1 << 40, " TB"),
        (1 << 30, " GB"),
        (1 << 20, " MB"),
        (1 << 10, " KB"),
        (1, (" bytes")),
    ]
    if (bytes / 1000000000 < 1):
        price = 0.1
    else:
        price = '%.2f' % ((bytes / 1000000000) * 0.1)

    for factor, suffix in units:
        if bytes >= factor:
            break
    amount = int(bytes / factor)
    return str(amount) + suffix, price

terra(verbose, destination_dir, manifest_path, drs_column_name, user_project, duplicate, string_mode)

Copy files from terra.bio

Source code in drs_downloader/cli.py

@cli.command()
@click.option(
    "--verbose",
    "-v",
    is_flag=True,
    show_default=True,
    default=False,
    help="Display every logger",
)
@click.option(
    "--destination-dir",
    "-d",
    show_default=True,
    default=os.getcwd(),
    help="Destination directory.",
    required=True
)
@click.option(
    "--manifest-path",
    "-m",
    show_default=True,
    help="Path to manifest tsv.",
    required=True
)
@click.option(
    "--drs-column-name",
    default=None,
    help="The column header in the TSV file associated with the DRS URIs."
    "Example: pfb:ga4gh_drs_uri",
)
@click.option(
    "--user-project", "-u",
    default=None,
    show_default=True,
    help="This option is used to specify the Terra Workspace"
         "Google project id if the requester is paying for the download",
)
@click.option(
    "--duplicate",
    default=False,
    is_flag=True,
    show_default=True,
    help="This flag is used to specify wether"
    "or not to download the file again if it already exists in the directory"
    "Example: True",
)
@click.option(
    "--string-mode",
    default=None,
    show_default=True,
    help="This option is used when you want to run the downloader with URIS"
         "that you provide in string form with uris seperated by commas the command line. ex: 'uri1, uri2, uri3'",
)
def terra(
    verbose: bool,
    destination_dir: str,
    manifest_path: str,
    drs_column_name: str,
    user_project: str,
    duplicate: bool,
    string_mode: str,
):
    """Copy files from terra.bio"""

    # get ids from manifest
    if string_mode is not None:
        ids_from_manifest = string_mode.split(",")
        ids_from_manifest = [s.replace(" ", "") for s in ids_from_manifest]
    else:
        ids_from_manifest = _extract_tsv_info(Path(manifest_path), drs_column_name)

    Contains_AnVIL_Uris = check_for_AnVIL_URIS(ids_from_manifest)
    if Contains_AnVIL_Uris and not user_project:
        file_logger.error(
            ("ERROR: AnVIL Drs URIS starting with  'drs://drs.anv0:' or 'drs://dg.anv0: were"
             "provided in the manifest but no Terra workspace Google project id was given. Specify one with"
             "the --user-project option")
        )
        logger.error(
            ("ERROR: AnVIL Drs URIS starting with  'drs://drs.anv0:' or 'drs://dg.anv0: were"
             "provided in the manifest but no Terra workspace Google project id was given. Specify one with"
             "the --user-project option")
        )
        exit(1)

    # perform downloads with a terra drs client
    _perform_downloads(
        destination_dir,
        TerraDrsClient(),
        ids_from_manifest=ids_from_manifest,
        user_project=user_project,
        verbose=verbose,
        duplicate=duplicate,

    )