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 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 = ''
    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, 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