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Source code for galaxy.util.tool_shed.xml_util

import io
import logging
import os
import tempfile
from xml.etree import ElementTree as XmlET

from galaxy.util import (

log = logging.getLogger(__name__)

[docs]class CommentedTreeBuilder(XmlET.TreeBuilder): non_comment_seen = False
[docs] def doctype(*args): # handle deprecation warning for XMLParsing a file with DOCTYPE pass
[docs] def start(self, tag, attrib): if tag is not XmlET.Comment: self.non_comment_seen = True super(CommentedTreeBuilder, self).start(tag, attrib)
[docs] def comment(self, data): if self.non_comment_seen: # Cannot start XML file with comment self.start(XmlET.Comment, {}) self.data(data) self.end(XmlET.Comment)
[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 = XmlET.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 = XmlET.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 = XmlET.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 = XmlET.SubElement(sub_elem, v_tag) v_elem.text = v_text else: sub_elem = XmlET.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) with open(file_name, 'r') as fobj: try: tree = XmlET.parse(fobj, parser=XmlET.XMLParser(target=CommentedTreeBuilder())) except Exception as e: error_message = "Exception attempting to parse %s: %s" % (str(file_name), str(e)) log.exception(error_message) return None, error_message return tree, error_message