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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
XML-parsing abstraction layer.
"""
from xml.etree import ElementTree
from dendropy.utility.textprocessing import StringIO
class XmlNamespaces(object):
def __init__(self):
self.namespace_prefix_map = {}
self.prefix_namespace_map = {}
def add_namespace(self, prefix, namespace):
try:
self.namespace_prefix_map[namespace].append(prefix)
except KeyError:
self.namespace_prefix_map[namespace] = [prefix]
self.prefix_namespace_map[prefix] = namespace
class XmlObject(object):
def __init__(self):
pass
def recast_element(self, element, subelement_factory=None):
if element is None:
return None
if subelement_factory is not None:
return subelement_factory(element)
else:
return self.__class__(element)
def getiterator(self, tag, subelement_factory=None):
for element in self._element.getiterator(tag):
yield self.recast_element(element=element, subelement_factory=subelement_factory)
def findall(self, tag, subelement_factory=None):
for element in self._element.findall(tag):
yield self.recast_element(element, subelement_factory=subelement_factory)
def find(self, tag, subelement_factory=None):
return self.recast_element(self._element.find(tag), subelement_factory=subelement_factory)
def get(self, attrib_name, default=None):
return self._element.get(attrib_name, default)
def _get_attrib(self):
return self._element.attrib
attrib = property(_get_attrib)
def _get_text(self):
return self._element.text
text = property(_get_text)
class XmlElement(XmlObject):
"""
Abstraction layer around an item.
"""
def __init__(self, element, default_namespace=None):
XmlObject.__init__(self)
self._element = element
self.default_namespace = default_namespace
def subelement_factory(self, element):
return self.__class__(element, default_namespace=self.default_namespace)
def format_namespace(self, namespace=None):
if namespace:
return "{%s}" % namespace
if self.default_namespace:
return "{%s}" % self.default_namespace
return ""
def compose_tag(self, tag, namespace=None):
if namespace:
ns = "{%s}" % namespace
elif self.default_namespace:
ns = "{%s}" % self.default_namespace
else:
ns = ""
if isinstance(tag, list):
return "/".join( ("%s%s" % (ns, i)) for i in tag )
else:
return "%s%s" % (ns, tag)
def namespaced_getiterator(self, tag, namespace=None, subelement_factory=None):
if subelement_factory is None:
subelement_factory = self.subelement_factory
for element in self._element.getiterator(self.compose_tag(tag, namespace)):
yield self.recast_element(element=element, subelement_factory=subelement_factory)
def namespaced_findall(self, tag, namespace=None, subelement_factory=None):
if subelement_factory is None:
subelement_factory = self.subelement_factory
for element in self._element.findall(self.compose_tag(tag, namespace)):
yield self.recast_element(element=element, subelement_factory=subelement_factory)
def namespaced_find(self, tag, namespace=None, subelement_factory=None):
if subelement_factory is None:
subelement_factory = self.subelement_factory
e = self._element.find(self.compose_tag(tag, namespace))
return self.recast_element(e, subelement_factory=subelement_factory)
def namespaced_findtext(self, tag, namespace=None):
return self._element.findtext(self.compose_tag(tag, namespace))
class XmlDocument(XmlObject):
"""
Abstraction layer around an XML document.
"""
def __init__(self,
file_obj=None,
subelement_factory=None):
"""
__init__ initializes a reference to the ElementTree parser, passing it
the a file descripter object to be read and parsed or the
ElemenTree.Element object to be used as the root element.
"""
XmlObject.__init__(self)
if subelement_factory is None:
self.subelement_factory = XmlElement
else:
self.subelement_factory = subelement_factory
self.namespace_registry = XmlNamespaces()
self.root = None
if file_obj:
self.parse_file(file_obj)
def parse_string(self, source):
"Loads an XML document from an XML string, source."
s = StringIO(source)
return self.parse_file(source)
def parse_file(self, source):
"""
Loads an XML document from source, which can either be a
filepath string or a file object.
Custom parsing to make sure namespaces are saved.
"""
events = "start", "start-ns", "end-ns"
root = None
ns_map = []
for event, elem in ElementTree.iterparse(source, events):
if event == "start-ns":
ns_map.append(elem)
elif event == "start":
if root is None:
root = elem
# self.doctree = ElementTree.ElementTree(element=root)
self.root = self.subelement_factory(root)
for prefix, namespace in ns_map:
self.namespace_registry.add_namespace(prefix=prefix, namespace=namespace)
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