With lots of help from stack overflow, I managed to get some python code working to process xml files (using lxml). I've been able to adapt it for lots of different purposes, but there is one thing I can't work out.
Example XML:
<?xml version="1.0" encoding="UTF-8" ?>
<TVAMain xml:lang="PL" publisher="Someone" publicationTime="2014-01-03T06:24:24+00:00" version="217" xmlns="urn:tva:metadata:2010" xmlns:mpeg7="urn:tva:mpeg7:2008" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="urn:tva:metadata:2010 http://Something.xsd">
<ProgramDescription>
<ProgramInformationTable>
<ProgramInformation programId="crid://bds.tv/88032"><BasicDescription>
<Title xml:lang="PL" type="episodeTitle">Some Title</Title>
<Synopsis xml:lang="PL" length="short">Some Synopsis</Synopsis>
<Genre href="urn:tva:metadata:cs:EventGenreCS:2009:96">
<Name xml:lang="EN">Some Genre</Name>
</Genre>
<Language>PL</Language>
<RelatedMaterial>
<HowRelated href="urn:eventis:metadata:cs:HowRelatedCS:2010:boxCover">
<Name>Box cover</Name>
</HowRelated>
<MediaLocator>
<mpeg7:MediaUri>file://Images/98528834.p.jpg</mpeg7:MediaUri>
</MediaLocator>
</RelatedMaterial>
The python code will return the Title, Genre and Synopsis, but it will not return the image reference (3rd line from the bottom). I presume this is because of the name format 'mpeg7:MediaUri' (which I cannot change). The code will return the 'No Image' string instead.
This is the relavent python code
file_name = input('Enter the file name, including .xml extension: ')
print('Parsing ' + file_name)
from lxml import etree
parser = etree.XMLParser()
tree = etree.parse(file_name, parser)
root = tree.getroot()
nsmap = {'xmlns': 'urn:tva:metadata:2010'}
with open(file_name+'.log', 'w', encoding='utf-8') as f:
for info in root.xpath('//xmlns:ProgramInformation', namespaces=nsmap):
crid = (info.get('programId'))
titlex = (info.find('.//xmlns:Title', namespaces=nsmap))
title = (titlex.text if titlex != None else 'No title')
genrex = (info.find('.//xmlns:Genre/xmlns:Name', namespaces=nsmap))
genre = (genrex.text if genrex != None else 'No Genre')
imagex = (info.find('.//xmlns:RelatedMaterial/xmlns:MediaLocator/xmlns:"mpeg7:MediaUri"', namespaces=nsmap))
image = (image.text if imagex != None else 'No Image')
f.write('{}|{}|{}|{}\n'.format(crid, title, genre, image))
Can someone explain how I can adapt the 'imagex' line, so that it returns 'file://Images/98528834.p.jpg' from the example? I had a look at using square brackets, but it caused an error.
That node you are interested in, has mpeg7 namespace instead of default namespace. You can try with this syntax *[local-name() = "elementName"] to match element by it's local name (ignoring the namespace) :
imagex = info.xpath(
'.//xmlns:RelatedMaterial/xmlns:MediaLocator/*[local-name() = "MediaUri"]',
namespaces=nsmap)[0]
Or add the mpeg7 in namespaces declaration :
nsmap = {'xmlns': 'urn:tva:metadata:2010', 'mpeg7':'urn:tva:mpeg7:2008'}
then you can use mpeg7 prefix in xpath query :
imagex = (info.find('.//xmlns:RelatedMaterial/xmlns:MediaLocator/mpeg7:MediaUri', namespaces=nsmap))
Related
I'm coding a script to extract information from several XML files with the same structure but with missing sections when there is no information related to a tag. The easiest way to achieve this was using try/except so instead of getting a "AtributeError: 'NoneType' object has no atrribute 'find'" I assign an empty string('') to the object in the exeption. Something like this:
try:
string1=root.find('value1').find('value2').find('value3').text
except:
string1=''
The issue is that I want to shrink my code by using a function:
def extract(string):
tempstr=''
try:
tempstr=string.replace("\n", "")
except:
if tempstr is None:
tempstr=""
return string
And then I try to called it like this:
string1=extract(root.find('value1').find('value2').find('value3').text)
and value2 or value3 does not exist for the xml that is being processed, I get and AttributeError even if I don't use the variable in the function making the function useless.
Is there a way to make a function work, maybe there is a way to make it run without checking if the value entered is invalid?
Solution:
I'm using a mix of both answers:
def extract(root, xpath):
tempstr=''
try:
tempstr=root.findall(xpath)[0].text.replace("\n", "")
except:
tempstr=''#To avoid getting a Nonetype object
return tempstr
You can try something like that:
def extract(root, children_keys: list):
target_object = root
result_text = ''
try:
for child_key in children_keys:
target_object = target_object.find(child_key)
result_text = target_object.text
except:
pass
return result_text
You will go deeper at XML structure with for loop (children_keys - is predefined by you list of nested keys of XML - xml-path to your object).
And if error will throw inside that code - you will get '' as result.
Example XML (source):
<?xml version="1.0" encoding="UTF-8"?>
<note>
<to>Tove</to>
<from>Jani</from>
<heading>Reminder</heading>
<body>
<y>Don't forget me this weekend!</y>
</body>
</note>
Example:
import xml.etree.ElementTree as ET
tree = ET.parse('note.xml')
root = tree.getroot()
children_keys = ['body', 'y']
result_string = extract(root, children_keys)
print(result_string)
Output:
"Don't forget me this weekend!"
Use XPATH expression
import xml.etree.ElementTree as ET
xml1 = '''<r><v1><v2><v3>a string</v3></v2></v1></r>'''
root = ET.fromstring(xml1)
v3 = root.findall('./v1/v2/v3')
if v3:
print(v3[0].text)
else:
print('v3 not found')
xml2 = '''<r><v1><v3>a string</v3></v1></r>'''
root = ET.fromstring(xml2)
v3 = root.findall('./v1/v2/v3')
if v3:
print(v3[0].text)
else:
print('v3 not found')
output
a string
v3 not found
Hi I am very new to python programming. I have an xml file of structure:
<?xml version="1.0" encoding="UTF-8"?>
-<LidcReadMessage xsi:schemaLocation="http://www.nih.gov http://troll.rad.med.umich.edu/lidc/LidcReadMessage.xsd"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns="http://www.nih.gov" uid="1.3.6.1.4.1.14519.5.2.1.6279.6001.1307390687803.0">
-<ResponseHeader>
<Version>1.8.1</Version>
<MessageId>-421198203</MessageId>
<DateRequest>2007-11-01</DateRequest>
<TimeRequest>12:30:44</TimeRequest>
<RequestingSite>removed</RequestingSite>
<ServicingSite>removed</ServicingSite>
<TaskDescription>Second unblinded read</TaskDescription>
<CtImageFile>removed</CtImageFile>
<SeriesInstanceUid>1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192</SeriesInstanceUid>
<DateService>2008-08-18</DateService>
<TimeService>02:05:51</TimeService>
<ResponseDescription>1 - Reading complete</ResponseDescription>
<StudyInstanceUID>1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178</StudyInstanceUID>
</ResponseHeader>
-<readingSession>
<annotationVersion>3.12</annotationVersion>
<servicingRadiologistID>540461523</servicingRadiologistID>
-<unblindedReadNodule>
<noduleID>Nodule 001</noduleID>
-<characteristics>
<subtlety>5</subtlety>
<internalStructure>1</internalStructure>
<calcification>6</calcification>
<sphericity>3</sphericity>
<margin>3</margin>
<lobulation>3</lobulation>
<spiculation>4</spiculation>
<texture>5</texture>
<malignancy>5</malignancy>
</characteristics>
-<roi>
<imageZposition>-125.000000 </imageZposition>
<imageSOP_UID>1.3.6.1.4.1.14519.5.2.1.6279.6001.110383487652933113465768208719</imageSOP_UID>
......
There are four which contains multiple . Each contains an . I need to extract the information in from all of these headers.
Right now I am doing this:
import xml.etree.ElementTree as ET
tree = ET.parse('069.xml')
root = tree.getroot()
#lst = []
for readingsession in root.iter('readingSession'):
for roi in readingsession.findall('roi'):
id = roi.findtext('imageSOP_UID')
print(id)
but it ouputs like this:
Process finished with exit code 0.
If anyone can help.
The real problem as been wit the namespace. I tried with and without it, but it didn't work with this code.
ds = pydicom.dcmread("000071.dcm")
uid = ds.SOPInstanceUID
tree = ET.parse("069.xml")
root = tree.getroot()
for child in root:
print(child.tag)
if child.tag == '{http://www.nih.gov}readingSession':
read = child.find('{http://www.nih.gov}unblindedReadNodule')
if read != None:
nodule_id = read.find('{http://www.nih.gov}noduleID').text
xml_uid = read.find('{http://www.nih.gov}roi').find('{http://www.nih.gov}imageSOP_UID').text
if xml_uid == uid:
print(xml_uid, "=", uid)
roi= read.find('{http://www.nih.gov}roi')
print(roi)
This work completely fine to get a uid from dicom image of LIDC/IDRI dataset and then extract the same uid from xml file for it region of interest.
I 'am trying to parse a XML file using the Python library minidom (even tried xml.etree.ElementTree API).
My XML (resource.xml)
<?xml version='1.0'?>
<quota_result xmlns="https://some_url">
</quota_rule>
<quota_rule name='max_mem_per_user/5'>
<users>user1</users>
<limit resource='mem' limit='1550' value='921'/>
</quota_rule>
<quota_rule name='max_mem_per_user/6'>
<users>user2 /users>
<limit resource='mem' limit='2150' value='3'/>
</quota_rule>
</quota_result>
I would like to parse this file and store inside a dictionnary the information in the following form and be able to access it:
dict={user1=[resource,limit,value],user2=[resource,limit,value]}
So far I have only been able to do things like:
docXML = minidom.parse("resource.xml")
for node in docXML.getElementsByTagName('limit'):
print node.getAttribute('value')
You can use getElementsByTagName and getAttribute to trace the result:
dict_users = dict()
docXML = parse('mydata.xml')
users= docXML.getElementsByTagName("quota_rule")
for node in users:
user = 'None'
tag_user = node.getElementsByTagName("users") #check the length of the tag_user to see if tag <users> is exist or not
if len(tag_user) ==0:
print "tag <users> is not exist"
else:
user = tag_user[0]
resource = node.getElementsByTagName("limit")[0].getAttribute("resource")
limit = node.getElementsByTagName("limit")[0].getAttribute("limit")
value = node.getElementsByTagName("limit")[0].getAttribute("value")
dict_users[user.firstChild.data]=[resource, limit, value]
if user == 'None':
dict_users['None']=[resource, limit, value]
else:
dict_users[user.firstChild.data]=[resource, limit, value]
print(dict_users) # remove the <users>user1</users> in xml
Output:
tag <users> is not exist
{'None': [u'mem', u'1550', u'921'], u'user2': [u'mem', u'2150', u'3']}
I'm trying to get the attribute of a child element in Python, using lxml.
This is the structure of the xml:
<GroupInformation groupId="crid://thing.com/654321" ordered="true">
<GroupType value="show" xsi:type="ProgramGroupTypeType"/>
<BasicDescription>
<Title type="main" xml:lang="EN">A programme</Title>
<RelatedMaterial>
<HowRelated href="urn:eventis:metadata:cs:HowRelatedCS:2010:boxCover">
<Name>Box cover</Name>
</HowRelated>
<MediaLocator>
<mpeg7:MediaUri>file://ftp.something.com/Images/123456.jpg</mpeg7:MediaUri>
</MediaLocator>
</RelatedMaterial>
</BasicDescription>
The code I've got is below. The bit I want to return is the 'value' attribute ("Show" in the example) under 'grouptype' (third line from the bottom):
file_name = input('Enter the file name, including .xml extension: ')
print('Parsing ' + file_name)
from lxml import etree
parser = etree.XMLParser()
tree = etree.parse(file_name, parser)
root = tree.getroot()
nsmap = {'xmlns': 'urn:tva:metadata:2010','mpeg7':'urn:tva:mpeg7:2008'}
with open(file_name+'.log', 'w', encoding='utf-8') as f:
for info in root.xpath('//xmlns:GroupInformation', namespaces=nsmap):
crid = info.get('groupId'))
grouptype = info.find('.//xmlns:GroupType', namespaces=nsmap)
gtype = grouptype.get('value')
titlex = info.find('.//xmlns:BasicDescription/xmlns:Title', namespaces=nsmap)
title = titlex.text if titlex != None else 'Missing'
Can anyone explain to me how to implement it? I had a quick look at the xsi namespace, but was unable to get it to work (and didn't know if it was the right thing to do).
Is this what you are looking for?
grouptype.attrib['value']
PS: why the parenthesis around assignment values? Those look unnecessary.
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.