merging xml files using python's ElementTree

Question

I need to merge two xml files on the third block of the xml. So, files A.xml and B.xml look like this:

A.xml

<sample id="1">
<workflow value="x" version="1"/>
  <results>
   <result type="T">
      <result_data type="value" value="19"/>
      <result_data type="value" value="15"/>
      <result_data type="value" value="14"/>
      <result_data type="value" value="13"/>
      <result_data type="value" value="12"/>
    </result>
  </results>
</sample>

B.xml

<sample id="1">
<workflow value="x" version="1"/>
  <results>
   <result type="Q">
      <result_data type="value" value="11"/>
      <result_data type="value" value="21"/>
      <result_data type="value" value="13"/>
      <result_data type="value" value="12"/>
      <result_data type="value" value="15"/>
    </result>
  </results>
</sample>

I need to merge on 'results'

<sample id="1">
<workflow value="x" version="1"/>
  <results>
   <result type="T">
      <result_data type="value" value="19"/>
      <result_data type="value" value="15"/>
      <result_data type="value" value="14"/>
      <result_data type="value" value="13"/>
      <result_data type="value" value="12"/>
   </result>
   <result type="Q">
      <result_data type="value" value="11"/>
      <result_data type="value" value="21"/>
      <result_data type="value" value="13"/>
      <result_data type="value" value="12"/>
      <result_data type="value" value="15"/>
   </result>
  </results>
</sample>

What I have done so far is this:

import os, os.path, sys
import glob
from xml.etree import ElementTree

def run(files):
    xml_files = glob.glob(files +"/*.xml")
    xml_element_tree = None
    for xml_file in xml_files:
        # get root
        data = ElementTree.parse(xml_file).getroot()
        # print ElementTree.tostring(data)
        for result in data.iter('result'):
            if xml_element_tree is None:
                xml_element_tree = data 
            else:
                xml_element_tree.extend(result) 
    if xml_element_tree is not None:
        print ElementTree.tostring(xml_element_tree)

As you can see, I assign the initial xml_element_tree to data which has the heading etc, and then extend with 'result'. However, this gives me this:

<sample id="1">
<workflow value="x" version="1"/>
  <results>
   <result type="T">
      <result_data type="value" value="19"/>
      <result_data type="value" value="15"/>
      <result_data type="value" value="14"/>
      <result_data type="value" value="13"/>
      <result_data type="value" value="12"/>
   </result>
  </results>
   <result_data type="value" value="11"/>
      <result_data type="value" value="21"/>
      <result_data type="value" value="13"/>
      <result_data type="value" value="12"/>
      <result_data type="value" value="15"/>
   </result>
</sample>

where the results need to be at the bottom. Any help will be appreciated.

Possible duplicate of my question: http://stackoverflow.com/questions/14878706/merge-xml-files-with-nested-elements-without-external-libraries — Inbar Rose, Apr 10 '13 at 09:27
Your sample XML files are malformed, and yeah its a duplicate — joojaa, Apr 10 '13 at 09:27
is not valid xml. Anyway this is a duplicate question so read the answer in that. — joojaa, Apr 10 '13 at 09:35

score 14 · Accepted Answer · edited May 23 '17 at 12:34

Although this is mostly a duplicate and the answer can be found here, I already did this so i can share this python code:

import os, os.path, sys
import glob
from xml.etree import ElementTree

def run(files):
    xml_files = glob.glob(files +"/*.xml")
    xml_element_tree = None
    for xml_file in xml_files:
        data = ElementTree.parse(xml_file).getroot()
        # print ElementTree.tostring(data)
        for result in data.iter('results'):
            if xml_element_tree is None:
                xml_element_tree = data 
                insertion_point = xml_element_tree.findall("./results")[0]
            else:
                insertion_point.extend(result) 
    if xml_element_tree is not None:
        print ElementTree.tostring(xml_element_tree)

However this question contains another problem not present in the other post. The sample XML files are not valid XML so its not possible to have a XML tag with:

<sample="1">
    ...
</sample>

is not possible change to something like:

<sample id="1">
    ...
</sample>

score 0 · Answer 2 · answered Apr 24 '19 at 10:16

You could try this solution:

import glob
from xml.etree import ElementTree

def newRunRun(folder):
    xml_files = glob.glob(folder+"/*.xml")
    node = None
    for xmlFile in xml_files:      
        tree = ElementTree.parse(xmlFile)
        root = tree.getroot()
        if node is None:
            node = root
        else:
            elements = root.find("./results")           
            for element in elements._children:
                node[1].append(element)                
    print ElementTree.tostring(node)

folder = "resources"
newRunRun(folder)

As you can see, I´m using the first doc as a container, inserting inside it the elements of others docs... This is the ouput generated:

<sample id="1">
<workflow value="x" version="1" />
  <results>
   <result type="Q">
      <result_data type="value" value="11" />
      <result_data type="value" value="21" />
      <result_data type="value" value="13" />
      <result_data type="value" value="12" />
      <result_data type="value" value="15" />
    </result>
  <result type="T">
      <result_data type="value" value="19" />
      <result_data type="value" value="15" />
      <result_data type="value" value="14" />
      <result_data type="value" value="13" />
      <result_data type="value" value="12" />
    </result>
  </results>
</sample>

Using the version: Python 2.7.15

merging xml files using python's ElementTree

2 Answers2

Linked