tar_commands

Prepare tar commands for task-subfolder compression/extraction.

get_tar_compression_cmd(subfolder_path, filelist_path)

Prepare command to compress e.g. /path/dir into /path/dir.tar.gz.

Note that /path/dir.tar.gz may already exist. In this case, it will be overwritten.

PARAMETER	DESCRIPTION
subfolder_path	Absolute path to the folder to compress. TYPE: Path
filelist_path	If set, to be used in the --files-from option. TYPE: Path | None

RETURNS	DESCRIPTION
str	tar command

Source code in fractal_server/runner/executors/slurm_ssh/tar_commands.py

def get_tar_compression_cmd(
    subfolder_path: Path,
    filelist_path: Path | None,
) -> str:
    """
    Prepare command to compress e.g. `/path/dir` into `/path/dir.tar.gz`.

    Note that `/path/dir.tar.gz` may already exist. In this case, it will
    be overwritten.

    Args:
        subfolder_path: Absolute path to the folder to compress.
        filelist_path: If set, to be used in the `--files-from` option.

    Returns:
        tar command
    """
    tarfile_path = subfolder_path.with_suffix(".tar.gz")
    if filelist_path is None:
        cmd_tar = (
            f"tar -c -z "
            f"-f {tarfile_path} "
            f"--directory={subfolder_path.as_posix()} "
            "."
        )
    else:
        cmd_tar = (
            f"tar -c -z -f {tarfile_path} "
            f"--directory={subfolder_path.as_posix()} "
            f"--files-from={filelist_path.as_posix()} --ignore-failed-read"
        )

    return cmd_tar

get_tar_extraction_cmd(archive_path)

Prepare command to extract e.g. /path/dir.tar.gz into /path/dir.

PARAMETER	DESCRIPTION
archive_path	Absolute path to the tar.gz archive. TYPE: Path

RETURNS	DESCRIPTION
tuple[Path, str]	Target extraction folder and tar command

Source code in fractal_server/runner/executors/slurm_ssh/tar_commands.py

def get_tar_extraction_cmd(archive_path: Path) -> tuple[Path, str]:
    """
    Prepare command to extract e.g. `/path/dir.tar.gz` into `/path/dir`.

    Args:
        archive_path: Absolute path to the tar.gz archive.

    Returns:
        Target extraction folder and tar command
    """

    # Prepare subfolder path
    if archive_path.suffixes[-2:] != [".tar", ".gz"]:
        raise ValueError(
            "Archive path must end with `.tar.gz` "
            f"(given: {archive_path.as_posix()})"
        )
    subfolder_path = archive_path.with_suffix("").with_suffix("")

    cmd_tar = (
        f"tar -xzvf {archive_path} --directory={subfolder_path.as_posix()}"
    )
    return subfolder_path, cmd_tar