I have a program that reads an XML document from a socket. I have the XML document stored in a string which I would like to convert directly to a Python dictionary, the same way it is done in Django's simplejson library.
Take as an example:
str ="<?xml version="1.0" ?><person><name>john</name><age>20</age></person"
dic_xml = convert_to_dic(str)
Then dic_xml would look like {'person' : { 'name' : 'john', 'age' : 20 } }
xmltodict (full disclosure: I wrote it) does exactly that:
xmltodict.parse("""
<?xml version="1.0" ?>
<person>
<name>john</name>
<age>20</age>
</person>""")
# {u'person': {u'age': u'20', u'name': u'john'}}
This is a great module that someone created. I've used it several times.
http://code.activestate.com/recipes/410469-xml-as-dictionary/
Here is the code from the website just in case the link goes bad.
from xml.etree import cElementTree as ElementTree
class XmlListConfig(list):
def __init__(self, aList):
for element in aList:
if element:
# treat like dict
if len(element) == 1 or element[0].tag != element[1].tag:
self.append(XmlDictConfig(element))
# treat like list
elif element[0].tag == element[1].tag:
self.append(XmlListConfig(element))
elif element.text:
text = element.text.strip()
if text:
self.append(text)
class XmlDictConfig(dict):
'''
Example usage:
>>> tree = ElementTree.parse('your_file.xml')
>>> root = tree.getroot()
>>> xmldict = XmlDictConfig(root)
Or, if you want to use an XML string:
>>> root = ElementTree.XML(xml_string)
>>> xmldict = XmlDictConfig(root)
And then use xmldict for what it is... a dict.
'''
def __init__(self, parent_element):
if parent_element.items():
self.update(dict(parent_element.items()))
for element in parent_element:
if element:
# treat like dict - we assume that if the first two tags
# in a series are different, then they are all different.
if len(element) == 1 or element[0].tag != element[1].tag:
aDict = XmlDictConfig(element)
# treat like list - we assume that if the first two tags
# in a series are the same, then the rest are the same.
else:
# here, we put the list in dictionary; the key is the
# tag name the list elements all share in common, and
# the value is the list itself
aDict = {element[0].tag: XmlListConfig(element)}
# if the tag has attributes, add those to the dict
if element.items():
aDict.update(dict(element.items()))
self.update({element.tag: aDict})
# this assumes that if you've got an attribute in a tag,
# you won't be having any text. This may or may not be a
# good idea -- time will tell. It works for the way we are
# currently doing XML configuration files...
elif element.items():
self.update({element.tag: dict(element.items())})
# finally, if there are no child tags and no attributes, extract
# the text
else:
self.update({element.tag: element.text})
Example usage:
tree = ElementTree.parse('your_file.xml')
root = tree.getroot()
xmldict = XmlDictConfig(root)
//Or, if you want to use an XML string:
root = ElementTree.XML(xml_string)
xmldict = XmlDictConfig(root)
The following XML-to-Python-dict snippet parses entities as well as attributes following this XML-to-JSON "specification". It is the most general solution handling all cases of XML.
from collections import defaultdict
def etree_to_dict(t):
d = {t.tag: {} if t.attrib else None}
children = list(t)
if children:
dd = defaultdict(list)
for dc in map(etree_to_dict, children):
for k, v in dc.items():
dd[k].append(v)
d = {t.tag: {k:v[0] if len(v) == 1 else v for k, v in dd.items()}}
if t.attrib:
d[t.tag].update(('#' + k, v) for k, v in t.attrib.items())
if t.text:
text = t.text.strip()
if children or t.attrib:
if text:
d[t.tag]['#text'] = text
else:
d[t.tag] = text
return d
It is used:
from xml.etree import cElementTree as ET
e = ET.XML('''
<root>
<e />
<e>text</e>
<e name="value" />
<e name="value">text</e>
<e> <a>text</a> <b>text</b> </e>
<e> <a>text</a> <a>text</a> </e>
<e> text <a>text</a> </e>
</root>
''')
from pprint import pprint
pprint(etree_to_dict(e))
The output of this example (as per above-linked "specification") should be:
{'root': {'e': [None,
'text',
{'#name': 'value'},
{'#text': 'text', '#name': 'value'},
{'a': 'text', 'b': 'text'},
{'a': ['text', 'text']},
{'#text': 'text', 'a': 'text'}]}}
Not necessarily pretty, but it is unambiguous, and simpler XML inputs result in simpler JSON. :)
Update
If you want to do the reverse, emit an XML string from a JSON/dict, you can use:
try:
basestring
except NameError: # python3
basestring = str
def dict_to_etree(d):
def _to_etree(d, root):
if not d:
pass
elif isinstance(d, basestring):
root.text = d
elif isinstance(d, dict):
for k,v in d.items():
assert isinstance(k, basestring)
if k.startswith('#'):
assert k == '#text' and isinstance(v, basestring)
root.text = v
elif k.startswith('#'):
assert isinstance(v, basestring)
root.set(k[1:], v)
elif isinstance(v, list):
for e in v:
_to_etree(e, ET.SubElement(root, k))
else:
_to_etree(v, ET.SubElement(root, k))
else:
raise TypeError('invalid type: ' + str(type(d)))
assert isinstance(d, dict) and len(d) == 1
tag, body = next(iter(d.items()))
node = ET.Element(tag)
_to_etree(body, node)
return ET.tostring(node)
pprint(dict_to_etree(d))
This lightweight version, while not configurable, is pretty easy to tailor as needed, and works in old pythons. Also it is rigid - meaning the results are the same regardless of the existence of attributes.
import xml.etree.ElementTree as ET
from copy import copy
def dictify(r,root=True):
if root:
return {r.tag : dictify(r, False)}
d=copy(r.attrib)
if r.text:
d["_text"]=r.text
for x in r.findall("./*"):
if x.tag not in d:
d[x.tag]=[]
d[x.tag].append(dictify(x,False))
return d
So:
root = ET.fromstring("<erik><a x='1'>v</a><a y='2'>w</a></erik>")
dictify(root)
Results in:
{'erik': {'a': [{'x': '1', '_text': 'v'}, {'y': '2', '_text': 'w'}]}}
Disclaimer:
This modified XML parser was inspired by Adam Clark
The original XML parser works for most of simple cases. However, it didn't work for some complicated XML files. I debugged the code line by line and finally fixed some issues. If you find some bugs, please let me know. I am glad to fix it.
class XmlDictConfig(dict):
'''
Note: need to add a root into if no exising
Example usage:
>>> tree = ElementTree.parse('your_file.xml')
>>> root = tree.getroot()
>>> xmldict = XmlDictConfig(root)
Or, if you want to use an XML string:
>>> root = ElementTree.XML(xml_string)
>>> xmldict = XmlDictConfig(root)
And then use xmldict for what it is... a dict.
'''
def __init__(self, parent_element):
if parent_element.items():
self.updateShim( dict(parent_element.items()) )
for element in parent_element:
if len(element):
aDict = XmlDictConfig(element)
# if element.items():
# aDict.updateShim(dict(element.items()))
self.updateShim({element.tag: aDict})
elif element.items(): # items() is specialy for attribtes
elementattrib= element.items()
if element.text:
elementattrib.append((element.tag,element.text )) # add tag:text if there exist
self.updateShim({element.tag: dict(elementattrib)})
else:
self.updateShim({element.tag: element.text})
def updateShim (self, aDict ):
for key in aDict.keys(): # keys() includes tag and attributes
if key in self:
value = self.pop(key)
if type(value) is not list:
listOfDicts = []
listOfDicts.append(value)
listOfDicts.append(aDict[key])
self.update({key: listOfDicts})
else:
value.append(aDict[key])
self.update({key: value})
else:
self.update({key:aDict[key]}) # it was self.update(aDict)
The most recent versions of the PicklingTools libraries (1.3.0 and 1.3.1) support tools for converting from XML to a Python dict.
The download is available here: PicklingTools 1.3.1
There is quite a bit of documentation for the converters here: the documentation describes in detail all of the decisions and issues that will arise when converting between XML and Python dictionaries (there are a number of edge cases: attributes, lists, anonymous lists, anonymous dicts, eval, etc. that most converters don't handle). In general, though,
the converters are easy to use. If an 'example.xml' contains:
<top>
<a>1</a>
<b>2.2</b>
<c>three</c>
</top>
Then to convert it to a dictionary:
>>> from xmlloader import *
>>> example = file('example.xml', 'r') # A document containing XML
>>> xl = StreamXMLLoader(example, 0) # 0 = all defaults on operation
>>> result = xl.expect XML()
>>> print result
{'top': {'a': '1', 'c': 'three', 'b': '2.2'}}
There are tools for converting in both C++ and Python: the C++ and Python do indentical conversion, but the C++ is about 60x faster
You can do this quite easily with lxml. First install it:
[sudo] pip install lxml
Here is a recursive function I wrote that does the heavy lifting for you:
from lxml import objectify as xml_objectify
def xml_to_dict(xml_str):
""" Convert xml to dict, using lxml v3.4.2 xml processing library """
def xml_to_dict_recursion(xml_object):
dict_object = xml_object.__dict__
if not dict_object:
return xml_object
for key, value in dict_object.items():
dict_object[key] = xml_to_dict_recursion(value)
return dict_object
return xml_to_dict_recursion(xml_objectify.fromstring(xml_str))
xml_string = """<?xml version="1.0" encoding="UTF-8"?><Response><NewOrderResp>
<IndustryType>Test</IndustryType><SomeData><SomeNestedData1>1234</SomeNestedData1>
<SomeNestedData2>3455</SomeNestedData2></SomeData></NewOrderResp></Response>"""
print xml_to_dict(xml_string)
The below variant preserves the parent key / element:
def xml_to_dict(xml_str):
""" Convert xml to dict, using lxml v3.4.2 xml processing library, see http://lxml.de/ """
def xml_to_dict_recursion(xml_object):
dict_object = xml_object.__dict__
if not dict_object: # if empty dict returned
return xml_object
for key, value in dict_object.items():
dict_object[key] = xml_to_dict_recursion(value)
return dict_object
xml_obj = objectify.fromstring(xml_str)
return {xml_obj.tag: xml_to_dict_recursion(xml_obj)}
If you want to only return a subtree and convert it to dict, you can use Element.find() to get the subtree and then convert it:
xml_obj.find('.//') # lxml.objectify.ObjectifiedElement instance
See the lxml docs here. I hope this helps!
I wrote a simple recursive function to do the job:
from xml.etree import ElementTree
root = ElementTree.XML(xml_to_convert)
def xml_to_dict_recursive(root):
if len(root.getchildren()) == 0:
return {root.tag:root.text}
else:
return {root.tag:list(map(xml_to_dict_recursive, root.getchildren()))}
def xml_to_dict(node):
u'''
#param node:lxml_node
#return: dict
'''
return {'tag': node.tag, 'text': node.text, 'attrib': node.attrib, 'children': {child.tag: xml_to_dict(child) for child in node}}
The code from http://code.activestate.com/recipes/410469-xml-as-dictionary/ works well, but if there are multiple elements that are the same at a given place in the hierarchy it just overrides them.
I added a shim between that looks to see if the element already exists before self.update(). If so, pops the existing entry and creates a lists out of the existing and the new. Any subsequent duplicates are added to the list.
Not sure if this can be handled more gracefully, but it works:
import xml.etree.ElementTree as ElementTree
class XmlDictConfig(dict):
def __init__(self, parent_element):
if parent_element.items():
self.updateShim(dict(parent_element.items()))
for element in parent_element:
if len(element):
aDict = XmlDictConfig(element)
if element.items():
aDict.updateShim(dict(element.items()))
self.updateShim({element.tag: aDict})
elif element.items():
self.updateShim({element.tag: dict(element.items())})
else:
self.updateShim({element.tag: element.text.strip()})
def updateShim (self, aDict ):
for key in aDict.keys():
if key in self:
value = self.pop(key)
if type(value) is not list:
listOfDicts = []
listOfDicts.append(value)
listOfDicts.append(aDict[key])
self.update({key: listOfDicts})
else:
value.append(aDict[key])
self.update({key: value})
else:
self.update(aDict)
#dibrovsd: Solution will not work if the xml have more than one tag with same name
On your line of thought, I have modified the code a bit and written it for general node instead of root:
from collections import defaultdict
def xml2dict(node):
d, count = defaultdict(list), 1
for i in node:
d[i.tag + "_" + str(count)]['text'] = i.findtext('.')[0]
d[i.tag + "_" + str(count)]['attrib'] = i.attrib # attrib gives the list
d[i.tag + "_" + str(count)]['children'] = xml2dict(i) # it gives dict
return d
From #K3---rnc response (the best for me) I've added a small modifications to get an OrderedDict from an XML text (some times order matters):
def etree_to_ordereddict(t):
d = OrderedDict()
d[t.tag] = OrderedDict() if t.attrib else None
children = list(t)
if children:
dd = OrderedDict()
for dc in map(etree_to_ordereddict, children):
for k, v in dc.iteritems():
if k not in dd:
dd[k] = list()
dd[k].append(v)
d = OrderedDict()
d[t.tag] = OrderedDict()
for k, v in dd.iteritems():
if len(v) == 1:
d[t.tag][k] = v[0]
else:
d[t.tag][k] = v
if t.attrib:
d[t.tag].update(('#' + k, v) for k, v in t.attrib.iteritems())
if t.text:
text = t.text.strip()
if children or t.attrib:
if text:
d[t.tag]['#text'] = text
else:
d[t.tag] = text
return d
Following #K3---rnc example, you can use it:
from xml.etree import cElementTree as ET
e = ET.XML('''
<root>
<e />
<e>text</e>
<e name="value" />
<e name="value">text</e>
<e> <a>text</a> <b>text</b> </e>
<e> <a>text</a> <a>text</a> </e>
<e> text <a>text</a> </e>
</root>
''')
from pprint import pprint
pprint(etree_to_ordereddict(e))
Hope it helps ;)
An alternative (builds a lists for the same tags in hierarchy):
from xml.etree import cElementTree as ElementTree
def xml_to_dict(xml, result):
for child in xml:
if len(child) == 0:
result[child.tag] = child.text
else:
if child.tag in result:
if not isinstance(result[child.tag], list):
result[child.tag] = [result[child.tag]]
result[child.tag].append(xml_to_dict(child, {}))
else:
result[child.tag] = xml_to_dict(child, {})
return result
xmlTree = ElementTree.parse('my_file.xml')
xmlRoot = xmlTree.getroot()
dictRoot = xml_to_dict(xmlRoot, {})
result = {xmlRoot.tag: dictRoot}
Here's a link to an ActiveState solution - and the code in case it disappears again.
==================================================
xmlreader.py:
==================================================
from xml.dom.minidom import parse
class NotTextNodeError:
pass
def getTextFromNode(node):
"""
scans through all children of node and gathers the
text. if node has non-text child-nodes, then
NotTextNodeError is raised.
"""
t = ""
for n in node.childNodes:
if n.nodeType == n.TEXT_NODE:
t += n.nodeValue
else:
raise NotTextNodeError
return t
def nodeToDic(node):
"""
nodeToDic() scans through the children of node and makes a
dictionary from the content.
three cases are differentiated:
- if the node contains no other nodes, it is a text-node
and {nodeName:text} is merged into the dictionary.
- if the node has the attribute "method" set to "true",
then it's children will be appended to a list and this
list is merged to the dictionary in the form: {nodeName:list}.
- else, nodeToDic() will call itself recursively on
the nodes children (merging {nodeName:nodeToDic()} to
the dictionary).
"""
dic = {}
for n in node.childNodes:
if n.nodeType != n.ELEMENT_NODE:
continue
if n.getAttribute("multiple") == "true":
# node with multiple children:
# put them in a list
l = []
for c in n.childNodes:
if c.nodeType != n.ELEMENT_NODE:
continue
l.append(nodeToDic(c))
dic.update({n.nodeName:l})
continue
try:
text = getTextFromNode(n)
except NotTextNodeError:
# 'normal' node
dic.update({n.nodeName:nodeToDic(n)})
continue
# text node
dic.update({n.nodeName:text})
continue
return dic
def readConfig(filename):
dom = parse(filename)
return nodeToDic(dom)
def test():
dic = readConfig("sample.xml")
print dic["Config"]["Name"]
print
for item in dic["Config"]["Items"]:
print "Item's Name:", item["Name"]
print "Item's Value:", item["Value"]
test()
==================================================
sample.xml:
==================================================
<?xml version="1.0" encoding="UTF-8"?>
<Config>
<Name>My Config File</Name>
<Items multiple="true">
<Item>
<Name>First Item</Name>
<Value>Value 1</Value>
</Item>
<Item>
<Name>Second Item</Name>
<Value>Value 2</Value>
</Item>
</Items>
</Config>
==================================================
output:
==================================================
My Config File
Item's Name: First Item
Item's Value: Value 1
Item's Name: Second Item
Item's Value: Value 2
At one point I had to parse and write XML that only consisted of elements without attributes so a 1:1 mapping from XML to dict was possible easily. This is what I came up with in case someone else also doesnt need attributes:
def xmltodict(element):
if not isinstance(element, ElementTree.Element):
raise ValueError("must pass xml.etree.ElementTree.Element object")
def xmltodict_handler(parent_element):
result = dict()
for element in parent_element:
if len(element):
obj = xmltodict_handler(element)
else:
obj = element.text
if result.get(element.tag):
if hasattr(result[element.tag], "append"):
result[element.tag].append(obj)
else:
result[element.tag] = [result[element.tag], obj]
else:
result[element.tag] = obj
return result
return {element.tag: xmltodict_handler(element)}
def dicttoxml(element):
if not isinstance(element, dict):
raise ValueError("must pass dict type")
if len(element) != 1:
raise ValueError("dict must have exactly one root key")
def dicttoxml_handler(result, key, value):
if isinstance(value, list):
for e in value:
dicttoxml_handler(result, key, e)
elif isinstance(value, basestring):
elem = ElementTree.Element(key)
elem.text = value
result.append(elem)
elif isinstance(value, int) or isinstance(value, float):
elem = ElementTree.Element(key)
elem.text = str(value)
result.append(elem)
elif value is None:
result.append(ElementTree.Element(key))
else:
res = ElementTree.Element(key)
for k, v in value.items():
dicttoxml_handler(res, k, v)
result.append(res)
result = ElementTree.Element(element.keys()[0])
for key, value in element[element.keys()[0]].items():
dicttoxml_handler(result, key, value)
return result
def xmlfiletodict(filename):
return xmltodict(ElementTree.parse(filename).getroot())
def dicttoxmlfile(element, filename):
ElementTree.ElementTree(dicttoxml(element)).write(filename)
def xmlstringtodict(xmlstring):
return xmltodict(ElementTree.fromstring(xmlstring).getroot())
def dicttoxmlstring(element):
return ElementTree.tostring(dicttoxml(element))
I have modified one of the answers to my taste and to work with multiple values with the same tag for example consider the following xml code saved in XML.xml file
<A>
<B>
<BB>inAB</BB>
<C>
<D>
<E>
inABCDE
</E>
<E>value2</E>
<E>value3</E>
</D>
<inCout-ofD>123</inCout-ofD>
</C>
</B>
<B>abc</B>
<F>F</F>
</A>
and in python
import xml.etree.ElementTree as ET
class XMLToDictionary(dict):
def __init__(self, parentElement):
self.parentElement = parentElement
for child in list(parentElement):
child.text = child.text if (child.text != None) else ' '
if len(child) == 0:
self.update(self._addToDict(key= child.tag, value = child.text.strip(), dict = self))
else:
innerChild = XMLToDictionary(parentElement=child)
self.update(self._addToDict(key=innerChild.parentElement.tag, value=innerChild, dict=self))
def getDict(self):
return {self.parentElement.tag: self}
class _addToDict(dict):
def __init__(self, key, value, dict):
if not key in dict:
self.update({key: value})
else:
identical = dict[key] if type(dict[key]) == list else [dict[key]]
self.update({key: identical + [value]})
tree = ET.parse('./XML.xml')
root = tree.getroot()
parseredDict = XMLToDictionary(root).getDict()
print(parseredDict)
the output is
{'A': {'B': [{'BB': 'inAB', 'C': {'D': {'E': ['inABCDE', 'value2', 'value3']}, 'inCout-ofD': '123'}}, 'abc'], 'F': 'F'}}
Updated method posted by firelion.cis (since getchildren is deprecated):
from xml.etree import ElementTree
root = ElementTree.XML(xml_to_convert)
def xml_to_dict_recursive(root):
if len(list(root)) == 0:
return {root.tag:root.text}
else:
return {root.tag:list(map(xml_to_dict_recursive, list(root)))}
import xml.etree.ElementTree as ET
root = ET.parse(xml_filepath).getroot()
def parse_xml(node):
ans = {}
for child in node:
if len(child) == 0:
ans[child.tag] = child.text
elif child.tag not in ans:
ans[child.tag] = parse_xml(child)
elif not isinstance(ans[child.tag], list):
ans[child.tag] = [ans[child.tag]]
ans[child.tag].append(parse_xml(child))
else:
ans[child.tag].append(parse_xml(child))
return ans
it merges same field into list and squeezes fields containing one child.
Super simple code
#Follow this, its easy and nothing required, convert the XML into a string and use the find command to find the word that you are looking for as following
#hope this is easy and simple
def xml_key(key, text1):
tx1 = "<" + key + ">"
tx2 = "</" + key + ">"
tx = text1.find(tx1)
ty = text1.find(tx2)
tx = tx + len(tx1)
tw = text1[tx:ty]
return(tw)
text1 = "<person><name>john</name><age>20</age></person>"
dict1 = {"name": xml_key("name",text1),"age":xml_key("age",text1)}
print(dict1)
output :
{'name': 'john'}
I have a recursive method to get a dictionary from a lxml element
def recursive_dict(element):
return (element.tag.split('}')[1],
dict(map(recursive_dict, element.getchildren()),
**element.attrib))
I use python with lxml to process the xml. After I query/filter to get to a nodes I want but I have some problem. How to get its attribute's value by xpath ? Here is my input example.
>print(etree.tostring(node, pretty_print=True ))
<rdf:li xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:resource="urn:miriam:obo.chebi:CHEBI%3A37671"/>
The value I want is in resource=... . Currently I just use the lxml to get the value. I wonder if it is possible to do in pure xpath ? thanks
EDIT: Forgot to said, this is not a root nodes so I can't use // here. I have like 2000-3000 others in xml file. My first attempt was playing around with ".#attrib" and "self::*#" but those does not seems to work.
EDIT2: I will try my best to explain (well, this is my first time to deal with xml problem using xpath. and english is not one of my favorite field....). Here is my input snippet http://pastebin.com/kZmVdbQQ (full one from here http://www.comp-sys-bio.org/yeastnet/ using version 4).
In my code, I try to get speciesTypes node with resource link chebi (<rdf:li rdf:resource="urn:miriam:obo.chebi:...."/>). and then I tried to get value from rdf:resource attribute in rdf:li. The thing is, I am pretty sure it would be easy to get attribute in child node if I start from parent node like speciesTypes, but I wonder how to do if I start from rdf:li. From my understanding, the "//" in xpath will looking for node from everywhere not just only in the current node.
below is my code
import lxml.etree as etree
tree = etree.parse("yeast_4.02.xml")
root = tree.getroot()
ns = {"sbml": "http://www.sbml.org/sbml/level2/version4",
"rdf":"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"body":"http://www.w3.org/1999/xhtml",
"re": "http://exslt.org/regular-expressions"
}
#good enough for now
maybemeta = root.xpath("//sbml:speciesType[descendant::rdf:li[starts-with(#rdf:resource, 'urn:miriam:obo.chebi') and not(starts-with(#rdf:resource, 'urn:miriam:uniprot'))]]", namespaces = ns)
def extract_name_and_chebi(node):
name = node.attrib['name']
chebies = node.xpath("./sbml:annotation//rdf:li[starts-with(#rdf:resource, 'urn:miriam:obo.chebi') and not(starts-with(#rdf:resource, 'urn:miriam:uniprot'))]", namespaces=ns) #get all rdf:li node with chebi resource
assert len(chebies) == 1
#my current solution to get rdf:resource value from rdf:li node
rdfNS = "{" + ns.get('rdf') + "}"
chebi = chebies[0].attrib[rdfNS + 'resource']
#do protein later
return (name, chebi)
metaWithChebi = map(extract_name_and_chebi, maybemeta)
fo = open("metabolites.txt", "w")
for name, chebi in metaWithChebi:
fo.write("{0}\t{1}\n".format(name, chebi))
Prefix the attribute name with # in the XPath query:
>>> from lxml import etree
>>> xml = """\
... <?xml version="1.0" encoding="utf8"?>
... <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
... <rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A37671"/>
... </rdf:RDF>
... """
>>> tree = etree.fromstring(xml)
>>> ns = {'rdf': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'}
>>> tree.xpath('//rdf:li/#rdf:resource', namespaces=ns)
['urn:miriam:obo.chebi:CHEBI%3A37671']
EDIT
Here's a revised version of the script in the question:
import lxml.etree as etree
ns = {
'sbml': 'http://www.sbml.org/sbml/level2/version4',
'rdf':'http://www.w3.org/1999/02/22-rdf-syntax-ns#',
'body':'http://www.w3.org/1999/xhtml',
're': 'http://exslt.org/regular-expressions',
}
def extract_name_and_chebi(node):
chebies = node.xpath("""
.//rdf:li[
starts-with(#rdf:resource, 'urn:miriam:obo.chebi')
]/#rdf:resource
""", namespaces=ns)
return node.attrib['name'], chebies[0]
with open('yeast_4.02.xml') as xml:
tree = etree.parse(xml)
maybemeta = tree.xpath("""
//sbml:speciesType[descendant::rdf:li[
starts-with(#rdf:resource, 'urn:miriam:obo.chebi')]]
""", namespaces = ns)
with open('metabolites.txt', 'w') as output:
for node in maybemeta:
output.write('%s\t%s\n' % extract_name_and_chebi(node))
To select off the current node its attribute named rdf:resource, use this XPath expression:
#rdf:resource
In order for this to "work correctly" you must register the association of the prefix "rdf:" to the corresponding namespace.
If you don't know how to register the rdf namespace, it is still possible to select the attribute -- with this XPath expression:
#*[name()='rdf:resource']
Well, I got it. The xpath expression I need here is "./#rdf:resource" not ".#rdf:resource". But why ? I thought "./" indicate the child of current node.