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Source code for galaxy.util.tool_shed.xml_util

import logging
import os
import tempfile
from typing import (

from galaxy.util import (
    parse_xml as galaxy_parse_xml,
from galaxy.util.path import StrPath

log = logging.getLogger(__name__)

[docs]def create_and_write_tmp_file(elem: etree.Element) -> str: tmp_str = xml_to_string(elem, pretty=True) with tempfile.NamedTemporaryFile(prefix="tmp-toolshed-cawrf", delete=False) as fh: tmp_filename = fh.name with open(tmp_filename, mode="w", encoding="utf-8") as fh: fh.write(tmp_str) return tmp_filename
[docs]def parse_xml(file_name: StrPath, check_exists=True) -> Tuple[Optional[etree.ElementTree], str]: """Returns a parsed xml tree with comments intact.""" error_message = "" if check_exists and not os.path.exists(file_name): return None, f"File does not exist {str(file_name)}" try: tree = galaxy_parse_xml(file_name, remove_comments=False, strip_whitespace=False) except OSError: raise except Exception as e: error_message = f"Exception attempting to parse {str(file_name)}: {unicodify(e)}" log.exception(error_message) return None, error_message return tree, error_message
__all__ = ( "create_and_write_tmp_file", "parse_xml", )