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Source code for tool_shed.util.xml_util

import logging
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 Py26CommentedTreeBuilder( XmlET.XMLTreeBuilder ): # Python 2.6 uses ElementTree 1.2.x.
[docs] def __init__( self, html=0, target=None ): XmlET.XMLTreeBuilder.__init__( self, html, target ) self._parser.CommentHandler = self.handle_comment
[docs] def handle_comment( self, data ): self._target.start( XmlET.Comment, {} ) self._target.data( data ) self._target.end( XmlET.Comment )
[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 = '' 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, parser=Py26CommentedTreeBuilder() ) 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