How to use the ubiquerg.is_url function in ubiquerg

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github pepkit / peppy / peppy / project.py View on Github external
def _ensure_path_absolute(maybe_relpath, cfg_path):
    """ Ensure that a possibly relative path is absolute. """
    if not isinstance(maybe_relpath, str):
        raise TypeError(
            "Attempting to ensure non-text value is absolute path: {} ({})".
                format(maybe_relpath, type(maybe_relpath)))
    if os.path.isabs(maybe_relpath) or is_url(maybe_relpath):
        _LOGGER.debug("Already absolute")
        return maybe_relpath
    # Maybe we have env vars that make the path absolute?
    expanded = os.path.expanduser(os.path.expandvars(maybe_relpath))
    if os.path.isabs(expanded):
        _LOGGER.debug("Expanded: {}".format(expanded))
        return expanded
    # Set path to an absolute path, relative to project config.
    config_dirpath = os.path.dirname(cfg_path)
    _LOGGER.debug("config_dirpath: {}".format(config_dirpath))
    abs_path = os.path.join(config_dirpath, maybe_relpath)
    _LOGGER.debug("Expanded and/or made absolute: {}".format(abs_path))
    return abs_path
github pepkit / peppy / peppy / project2.py View on Github external
def _ensure_path_absolute(maybe_relpath, cfg_path):
    """ Ensure that a possibly relative path is absolute. """
    if not isinstance(maybe_relpath, str):
        raise TypeError(
            "Attempting to ensure non-text value is absolute path: {} ({})".
                format(maybe_relpath, type(maybe_relpath)))
    _LOGGER.debug("Ensuring absolute: '{}'".format(maybe_relpath))
    if os.path.isabs(maybe_relpath) or is_url(maybe_relpath):
        _LOGGER.debug("Already absolute")
        return maybe_relpath
    # Maybe we have env vars that make the path absolute?
    expanded = os.path.expanduser(os.path.expandvars(maybe_relpath))
    _LOGGER.debug("Expanded: '{}'".format(expanded))
    if os.path.isabs(expanded):
        _LOGGER.debug("Expanded is absolute")
        return expanded
    _LOGGER.debug("Making non-absolute path '{}' be absolute".
                  format(maybe_relpath))

    # Set path to an absolute path, relative to project config.
    config_dirpath = os.path.dirname(cfg_path)
    _LOGGER.debug("config_dirpath: {}".format(config_dirpath))
    abs_path = os.path.join(config_dirpath, maybe_relpath)
    return abs_path
github databio / refgenie / refgenie / refgenie.py View on Github external
def copy_or_download_file(input_string, outfolder):
    """
    Given an input file, which can be a local file or a URL, and output folder,
    this downloads or copies the file into the output folder.

    :param str input_string: Can be either a URL or a path to a local file
    :param str outfolder: Where to store the result.
    :return str, str: output/result file and command
    """
    result_file = os.path.join(outfolder, os.path.basename(input_string))
    parts = ["wget -O", result_file, input_string] \
        if is_url(input_string) else ["cp", input_string, result_file]
    return result_file, " ".join(parts)