Convert Deeply Nested XML to CSV in Python [duplicate] - python

This question already has answers here:
How to parse XML and get instances of a particular node attribute?
(19 answers)
Closed 6 years ago.
I'm new to Python and have heard that it is one of the best ways to parse fairly large XML files (150MB). I can't get my head around how to iterate through the tags and extract only the <hw> and <defunit> tags as it's fairly deeply nested.
I have some XML formatted as below, and I need to extract the "hw" and "defunit" tags from it using Python and convert them into a .csv format.
<?xml version="1.0" encoding="UTF-8"?>
<dps-data xmlns="urn:DPS2-metadata" project="SCRABBLELARGE" guid="7d6b7164fde1e064:34368a61:14306b637ab:-8000--4a25ae5c-c104-4c7a-bba5-b434dd4d9314">
<superentry xmlns="urn:COLL" xmlns:d="urn:COLL" xmlns:e="urn:IDMEE" e:id="u583c10bfdbd326ba.31865a51.12110e76de1.-336">
<entry publevel="1" id="a000001" e:id="u583c10bfdbd326ba.31865a51.12110e76de1.-335">
<hwblk>
<hwgrp>
<hwunit>
<hw>aa</hw>
<ulsrc>edsh</ulsrc>
</hwunit>
</hwgrp>
</hwblk>
<datablk>
<gramcat publevel="1" id="a000001.001">
<pospgrp>
<pospunit>
<posp value="noun" />
</pospunit>
</pospgrp>
<sensecat id="a000001.001.01" publevel="1">
<defgrp>
<defunit>
<def>volcanic rock</def>
</defunit>
</defgrp>
</sensecat>
</gramcat>
</datablk>
</entry>
</superentry>
</dps-data>
The .csv format I'd like to see it in is simply:
hw, defunit
aa, volcanic rock

How about this:
from xml.dom import minidom
xmldoc = minidom.parse('your.xml')
hw_lst = xmldoc.getElementsByTagName('hw')
defu_lst = xmldoc.getElementsByTagName('def')
with open('your.csv', 'a') as out_file:
for i in range(len(hw_lst)):
out_file.write('{0}, {1}\n'.format(hw_lst[i].firstChild.data, defu_lst[i].firstChild.data))

Consider XSLT, the XML transformation language that can manipulate source .xml files to various end use structures including text files like .csv, specifying method="text" in <xsl:output>.
Python's lxml module can run XSLT 1.0 scripts. Below assumes the <entry> tag and its children repeat with different data. And two undeclared namespaces had to be handled in the xsl. Also, XSLT tends to be very efficient on smaller sized XML but varies depending on computer environments.
XSLT Script (save as .xsl to be referenced below)
<xsl:transform xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0"
xmlns:ns1="urn:DPS2-metadata" xmlns="urn:COLL">
<xsl:output version="1.0" encoding="UTF-8" indent="yes" method="text"/>
<xsl:strip-space elements="*"/>
<xsl:template match="/ns1:dps-data/ns1:superentry">
<xsl:text>hw,defunit</xsl:text><xsl:text>
</xsl:text>
<xsl:apply-templates select="ns1:entry"/>
</xsl:template>
<xsl:template match="ns1:entry" namespace="urn:COLL">
<xsl:value-of select="descendant::ns1:hw" namespace="urn:COLL"/><xsl:text>,</xsl:text>
<xsl:value-of select="descendant::ns1:defunit" namespace="urn:COLL"/>
<xsl:text>
</xsl:text>
</xsl:template>
Pyton Script
import lxml.etree as ET
// LOAD XML AND XSL SOURCES
xml = ET.parse('Input.xml')
xsl = ET.parse('XSLTScript.xsl')
// TRANSFORM SOURCE
transform = ET.XSLT(xsl)
newdom = transform(xml)
// SAVE AS .CSV
with open('Output.csv'), 'wb') as f:
f.write(newdom)
# hw,defunit
# aa,volcanic rock

The lxml library is capable of very powerful XML parsing, and can be used to iterate over an XML tree to search for specific elements.
from lxml import etree
with open(r'path/to/xml', 'r') as xml:
text = xml.read()
tree = lxml.etree.fromstring(text)
row = ['', '']
for item in tree.iter('hw', 'def'):
if item.tag == 'hw':
row[0] = item.text
elif item.tag == 'def':
row[1] = item.text
line = ','.join(row)
with open(r'path/to/csv', 'a') as csv:
csv.write(line + '\n')
How you build the CSV file is largely based upon preference, but I have provided a trivial example above. If there are multiple <dps-data> tags, you could extract those elements first (which can be done with the same tree.iter method shown above), and then apply the above logic to each of them.
EDIT: I should point out that this particular implementation reads the entire XML file into memory. If you are working with a single 150mb file at a time, this should not be a problem, but it's just something to be aware of.

Related

Read XML block in Python

I have an XML file like below which contain multiple xml. I want to fetch <Sacd> content.
<?xml version="1.0" encoding="utf-8"?>
<Sacd>
<Acdpktg> <Acdpktg/>
</Sacd>
<?xml version="1.0" encoding="utf-8"?>
<Sacd>
<Acdpktg/>
</Sacd>
<?xml version="1.0" encoding="utf-8"?>
<Sacd>
<AcdpktG>
<Result Value="0"/>
<Packet Value="Dnd"/>
<Invoke Value="abc"/>
</AcdpktG>
</Sacd>
How do I extract the value inside Sacd tag?
Well, your xml is problematic in several respects. First, it contains multiple xml files within in - not a good idea; they have to be split into separate xml files. Second, the first <Acdpktg> <Acdpktg/> tag pair is invalid; it should be <Acdpktg> </Acdpktg>.
But once it's all fixed, you can get your expected output. So:
from lxml import etree
big = """[your xml above,fixed]"""
smalls = big.replace('<?xml','xxx<?xml').split('xxx')[1:] #split it into small xml files
for small in smalls:
xml = bytes(bytearray(small, encoding='utf-8')) #either this, or remove the xml declarations from each small file
doc = etree.XML(xml)
for value in doc.xpath('.//AcdpktG//*/#Value'):
print(value)
Output:
0
Dnd
abc
Or, a bit fancier output can be obtained by changing the inner for loop a bit:
for value in doc.xpath('.//AcdpktG//*'):
print(value.tag, value.xpath('./#Value')[0])
Output:
Result 0
Packet Dnd
Invoke abc

Splitting large xml file into multiple files by using beautifulsoup

I am trying to split large xml file into smaller ones, first I started off beautifulsoup:
from bs4 import BeautifulSoup
import os
# Core settings
rootdir = r'C:\Users\XX\Documents\Grant Data\2010_xml'
extension = ".xml"
to_save = r'C:\Users\XX\Documents\all_patents_as_xml'
index = 0
for root, dirs, files in os.walk(rootdir):
for file in files:
if file.endswith(extension):
print(file)
file_name = os.path.join(root,file)
with open(file_name) as f:
data = f.read()
texts = data.split('?xml version="1.0" encoding="UTF-8"?')
for text in texts:
index += 1
filename = to_save + "\\"+ str(index) + ".txt"
with open(filename, 'w') as f:
f.write(text)
However, I got a memory error. Then I switched to xml etree:
from xml.etree import ElementTree as ET
import re
file_name = r'C:\Users\XX\Documents\Grant Data\2010_xml\2010cat_xml.xml'
with open(file_name) as f:
xml = f.read()
tree = ET.fromstring(re.sub(r"(<\?xml[^>]+\?>)", r"\1<root>", xml) + "</root>")
parser = ET.iterparse(tree)
to_save = r'C:\Users\Yilmaz\Documents\all_patents_as_xml'
index = 0
for event, element in parser:
# element is a whole element
if element.tag == '?xml version="1.0" encoding="UTF-8"?':
index += 1
filename = to_save + "\\"+ str(index) + ".txt"
with open(filename, 'w') as f:
f.write(ET.tostring(element))
# do something with this element
# then clean up
element.clear()
and I get the following error:
OverflowError: size does not fit in an int
I am using windows operating system, I know in Linux you can split the xmls from consule but in my case I don't know what to do.
If your XML can not be loaded because of memory limits, you should consider using SAX.
With SAX you will read "small bites" of the document, do what ever you want to do with them (Example: Save every N elements to a new file).
Python SAX example 1.
Python SAX example 2.
There are major issues with your question and your attempts at solving it:
You mention using Beautiful Soup. However, while you import Beautiful Soup in your code, you don't actually do anything with it.
The code you show that uses xml.etree is grossly incorrect. At the line parser = ET.iterparse(tree), tree is an XML tree already parsed with ET.fromstring, but the argument to iterparse must either be a file name or a file object. An XML tree is neither of those. So that attempt is dead on arrival.
But more importantly, it looks like what you are trying to process is a file which contains a bunch of concatenated XML files. In your xml.etree attempt you have this test:
element.tag == '?xml version="1.0" encoding="UTF-8"?'
The only intent I can imagine for this test is that you think that xml.etree will somehow interpret <?xml version="1.0" encoding="UTF-8"?> as an XML element which has a name of '?xml version="1.0" encoding="UTF-8"?'. However, the structure <?xml version="1.0" encoding="UTF-8"?> is not an XML element, it is an XML declaration.
And since your code seems to be attempting to split every time an XML declaration is encountered, it seems that your input is a file that contains multiple XML declarations. This file is not valid XML. The XML specification allows the XML declaration to appear once, and only once at the beginning of an XML file. (Don't confuse the XML declaration with a processing instruction. They look similar because they are both delimited by <? and ?>, but the XML declaration is not a processing instruction.) If you use an XML parser on your input file, and this parser conforms to the XML specification, then it has to reject your file as being not XML because XML does not allow XML declarations to appear at random positions in documents.
Where does that leave you? If all XML declarations present in your source document are the same, there's a relatively easy way to make your document parsable by an XML parser. (The attempts you made suggest that they are all the same since you do not use a regular expressions to match different forms of the XML declaration (e.g. one that would specify the standalone parameter).) You can just remove all XML declarations from your source document, wrap it in a new root element, and parse that with xml.etree. (This assumes that the individual XML documents that were concatenated to make up your source document were all individually well-formed. If they weren't then this won't work.)
Note, however, that the string <?xml version="1.0" encoding="UTF-8"?> can appear in an XML document in contexts where this string is not actually an XML declaration. Here is a well-formed XML document that would throw off an algorithm that just looks for a string that looks like an XML declaration:
<?xml version = "1.0" encoding = "UTF-8"?>
<a>
<![CDATA[
<?xml version = "1.0" encoding = "UTF-8"?>
]]>
<?q <?xml version = "1.0" encoding = "UTF-8"?> ?>
<!-- <?xml version = "1.0" encoding = "UTF-8"?> -->
</a>
If you know how your source file was created, you may already be able to know for sure that you don't have any of the cases above. Otherwise, you may want to examine your source to make sure none of the above happens.
Once you take care of this, then using a strategy based on ET.iterparse, or SAX should work.

Python Element Tree: Namespace location is changed when writing the XML file back [duplicate]

I use the xml library in Python3.5 for reading and writing an xml-file. I don't modify the file. Just open and write. But the library modifes the file.
Why is it modified?
How can I prevent this? e.g. I just want to replace specific tag or it's value in a quite complex xml-file without loosing any other informations.
This is the example file
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<movie>
<title>Der Eisbär</title>
<ids>
<entry>
<key>tmdb</key>
<value xsi:type="xs:int" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">9321</value>
</entry>
<entry>
<key>imdb</key>
<value xsi:type="xs:string" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">tt0167132</value>
</entry>
</ids>
</movie>
This is the code
import xml.etree.ElementTree as ET
tree = ET.parse('x.nfo')
tree.write('y.nfo', encoding='utf-8')
And the xml-file becomes this
<movie xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<title>Der Eisbär</title>
<ids>
<entry>
<key>tmdb</key>
<value xsi:type="xs:int">9321</value>
</entry>
<entry>
<key>imdb</key>
<value xsi:type="xs:string">tt0167132</value>
</entry>
</ids>
</movie>
Line 1 is gone.
The <movie>-tag in line 2 has attributes now.
The <value>-tag in line 7 and 11 now has less attributes.
Note that "xml package" and "the xml library" are ambiguous. There are several XML-related modules in the standard library: https://docs.python.org/3/library/xml.html.
Why is it modified?
ElementTree moves namespace declarations to the root element, and namespaces that aren't actually used in the document are removed.
Why does ElementTree do this? I don't know, but perhaps it is a way to make the implementation simpler.
How can I prevent this? e.g. I just want to replace specific tag or it's value in a quite complex xml-file without loosing any other informations.
I don't think there is a way to prevent this. The issue has been brought up before. Here are two very similar questions with no answers:
How do I parse and write XML using Python's ElementTree without moving namespaces around?
Keep Existing Namespaces when overwriting XML file with ElementTree and Python
My suggestion is to use lxml instead of ElementTree. With lxml, the namespace declarations will remain where they occur in the original file.
Line 1 is gone.
That line is the XML declaration. It is recommended but not mandatory to have one.
If you always want an XML declaration, use xml_declaration=True in the write() method call.

Write Open Office XML (e.g. docx) with XML that matches the OOXML namespace

I have a python program that edits the XML in a .docx file. I'd like to edit the XML with ETree.
When I read the XML from the .docx file, it begins like this:
b'<?xml version="1.0" encoding="UTF-8" standalone="yes"?>\r\n<w:document xmlns:wpc="http://schemas.micro'...
This is in a variable called data. I create the element tree with:
import xml.etree.ElementTree as ElementTree
tree = ElementTree.XML(data)
I convert it back with:
data = ElementTree.tostring(tree)
However, there have been subtle changes to the XML. It now looks like this:
b'<ns0:document xmlns:ns0="http://schemas.openxmlformats.org/wordprocessingml/2006/main" xmlns:ns1="ht...
Word won't read this, even though it is standard XML.
EDIT: I tried adding the string to my XML, just to get it to round-trip:
XML_HEADER=b'<?xml version="1.0" encoding="UTF-8" standalone="yes"?>\r\n'
tree = ElementTree.XML(data)
data = XML_HEADER + ElementTree.tostring(tree)
But I still get the error:
We're sorry. We can't open <filename>.docx because we found a problem with its contents.
Details:
The XML data is invalid according to the schema.
Location: Part: /word/document.xml, Line: 0, Column:0
I can't fix word. I've got to generate XML that looks exactly like the XML that I started with. How do I get ETree to generate that?

Python:JS: How to parse multiple kml node in one xml file?

<xml>
<mapshape title="Bar" extras="">
<kml></kml>
</mapshape>
<mapshape title="Foo" extras="">
<kml></kml>
</mapshape>
</xml>
I've got a xml doc like that, multiple mapshape nodes in one xml, and each contains one valid kml file. I need to plot them all on google maps.
I have tried libraries like geoxml(3), they can parse one kml file, but my document has many kmls, how can I deal with this?
You can use lxml to extract the kml sections and then pass them on to the other library:
doc = """<xml>
<mapshape title="Bar" extras="">
<kml></kml>
</mapshape>
<mapshape title="Foo" extras="">
<kml></kml>
</mapshape>
</xml>"""
import lxml.etree as etree
xml = etree.fromstring(doc)
for mapshape in xml:
kml = etree.tostring(mapshape.getchildren()[0])
parseKML(kml)

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