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Source code for tool_shed.util.xml_util

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

from galaxy.util import listify

log = logging.getLogger(__name__)
using_python_27 = sys.version_info[:2] >= (2, 7)

[docs]class Py27CommentedTreeBuilder(XmlET.TreeBuilder): # Python 2.7 uses ElementTree 1.3.x.
[docs] def comment(self, data): self.start(XmlET.Comment, {}) self.data(data) self.end(XmlET.Comment)
[docs]def create_and_write_tmp_file(elems, use_indent=False): tmp_str = '' for elem in listify(elems): tmp_str += xml_to_string(elem, use_indent=use_indent) fh = tempfile.NamedTemporaryFile('wb', prefix="tmp-toolshed-cawrf") tmp_filename = fh.name fh.close() fh = open(tmp_filename, 'wb') fh.write('<?xml version="1.0"?>\n') fh.write(tmp_str) fh.close() 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 indent(elem, level=0): """ Prints an XML tree with each node indented according to its depth. This method is used to print the shed tool config (e.g., shed_tool_conf.xml from the in-memory list of config_elems because each config_elem in the list may be a hierarchical structure that was not created using the parse_xml() method below, and so will not be properly written with xml.etree.ElementTree.tostring() without manually indenting the tree first. """ i = "\n" + level * " " if len(elem): if not elem.text or not elem.text.strip(): elem.text = i + " " if not elem.tail or not elem.tail.strip(): elem.tail = i for child in elem: indent(child, level + 1) if not child.tail or not child.tail.strip(): child.tail = i if not elem.tail or not elem.tail.strip(): elem.tail = i else: if level and (not elem.tail or not elem.tail.strip()): elem.tail = i
[docs]def parse_xml(file_name): """Returns a parsed xml tree with comments intact.""" error_message = '' if not os.path.exists(file_name): return None, "File does not exist %s" % str(file_name) fobj = open(file_name, 'r') if using_python_27: try: tree = XmlET.parse(fobj, parser=XmlET.XMLParser(target=Py27CommentedTreeBuilder())) except Exception as e: fobj.close() error_message = "Exception attempting to parse %s: %s" % (str(file_name), str(e)) log.exception(error_message) return None, error_message else: try: tree = XmlET.parse(fobj) except Exception as e: fobj.close() error_message = "Exception attempting to parse %s: %s" % (str(file_name), str(e)) log.exception(error_message) return None, error_message fobj.close() return tree, error_message
[docs]def xml_to_string(elem, encoding='utf-8', use_indent=False, level=0): if elem is not None: if use_indent: # We were called from ToolPanelManager.config_elems_to_xml_file(), so # set the level to 1 since level 0 is the <toolbox> tag set. indent(elem, level=level) if using_python_27: xml_str = '%s\n' % xml.etree.ElementTree.tostring(elem, encoding=encoding, method="xml") else: xml_str = '%s\n' % xml.etree.ElementTree.tostring(elem, encoding=encoding) else: xml_str = '' return xml_str