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Source code for galaxy.util.tool_shed.xml_util
import io
import logging
import os
import tempfile
from galaxy.util import (
etree,
parse_xml as galaxy_parse_xml,
unicodify,
xml_to_string,
)
log = logging.getLogger(__name__)
[docs]def create_and_write_tmp_file(elem):
tmp_str = xml_to_string(elem, pretty=True)
with tempfile.NamedTemporaryFile(prefix="tmp-toolshed-cawrf", delete=False) as fh:
tmp_filename = fh.name
with io.open(tmp_filename, mode='w', encoding='utf-8') as fh:
fh.write(tmp_str)
return tmp_filename
[docs]def create_element(tag, attributes=None, sub_elements=None):
"""
Create a new element whose tag is the value of the received tag, and whose attributes are all
key / value pairs in the received attributes and sub_elements.
"""
if tag:
elem = etree.Element(tag)
if attributes:
# The received attributes is an odict to preserve ordering.
for k, v in attributes.items():
elem.set(k, v)
if sub_elements:
# The received attributes is an odict. These handle information that tends to be
# long text including paragraphs (e.g., description and long_description.
for k, v in sub_elements.items():
# Don't include fields that are blank.
if v:
if k == 'packages':
# The received sub_elements is an odict whose key is 'packages' and whose
# value is a list of ( name, version ) tuples.
for v_tuple in v:
sub_elem = etree.SubElement(elem, 'package')
sub_elem_name, sub_elem_version = v_tuple
sub_elem.set('name', sub_elem_name)
sub_elem.set('version', sub_elem_version)
elif isinstance(v, list):
sub_elem = etree.SubElement(elem, k)
# If v is a list, then it must be a list of tuples where the first
# item is the tag and the second item is the text value.
for v_tuple in v:
if len(v_tuple) == 2:
v_tag = v_tuple[0]
v_text = v_tuple[1]
# Don't include fields that are blank.
if v_text:
v_elem = etree.SubElement(sub_elem, v_tag)
v_elem.text = v_text
else:
sub_elem = etree.SubElement(elem, k)
sub_elem.text = v
return elem
return None
[docs]def parse_xml(file_name, check_exists=True):
"""Returns a parsed xml tree with comments intact."""
error_message = ''
if check_exists and not os.path.exists(file_name):
return None, "File does not exist %s" % str(file_name)
try:
tree = galaxy_parse_xml(file_name, remove_comments=False, strip_whitespace=False)
except (IOError, OSError):
raise
except Exception as e:
error_message = "Exception attempting to parse %s: %s" % (str(file_name), unicodify(e))
log.exception(error_message)
return None, error_message
return tree, error_message