Python - Elementtree - Search through tree using a variable

Question

I have this xml file that has a lot of chemical groups and their properties. Here is a slice of the file:

 <groups>
  <group name='CH3'>
   <mw>15.03502</mw>
   <heatCapacity>
    <a>19.5</a>
   </heatCapacity>
  </group>
  <group name='CH2'>
   <mw>14.02708</mw>
   <heatCapacity>
    <a>-0.909</a>
   </heatCapacity>
  </group>
  <group name='COOH'>
   <mw>45.02</mw>
   <heatCapacity>
    <a>-24.1</a>
   </heatCapacity>
   </heatCapacity>
  </group>
  <group name='OH'>
   <mw>17.0073</mw>
   <heatCapacity>
    <a>25.7</a>
   </heatCapacity>
  </group>
<\groups>

In my python code that parses this file using ElementTree I have a list blocks=['CH3','CH2'] and I want to use this to find the two groups. I tried the following:

import elementtree.ElementTree as ET
document = ET.parse( 'groups.xml' )
blocks=['CH3','CH2']
for item in blocks:
   group1 = document.find(item)
   print group1

And all I get is 'None'. Can you please help me?

Many thanks

in lxml you can just do doc.xpath("//group[starts-with(@name,'CH')]"), but I don't think elementtree has proper xpath support to handle that expression. — roippi
– roippi, Commented Jul 29, 2014 at 16:28
Is that your actual code? Because I'm used to seeing import xml.etree.ElementTree as ET as the import statement. — Robᵩ
– Robᵩ, Commented Jul 29, 2014 at 16:43

Robᵩ · Accepted Answer · 2014-07-30 13:28:49Z

3

You can find an element's attributes via its .get() method. Here is one way to look there:

import xml.etree.ElementTree as ET
document = ET.parse( 'groups.xml' )
blocks=['CH3','CH2']
for group in document.getroot():
   if group.get('name') in blocks:
     print group

If you need access to the data through arbitrary selection criteria, you can create your own dictionary:

import xml.etree.ElementTree as ET

# Parse
document = ET.parse( 'groups.xml' )

# Add a dictionary so that <group>s
# are easy to find by name
groups = {}
for group in document.getroot():
   groups[group.get('name')] = group

# Look up our compounds in the dictionary
blocks=['CH3', 'CH2']
for item in blocks:
    group = groups[item]
    mw = group.find('mw').text
    print item, mw

edited Jul 30, 2014 at 13:28

answered Jul 29, 2014 at 16:48

Robᵩ

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2 Comments

Onizuka Over a year ago

Hi Rob, thanks for your reply. It is essential for me to iterate on my list because I want to get groups in the correct order.

Robᵩ Over a year ago

Use a dictionary to store the group data in a convenient fashion. See my recent edit.

Paulo Scardine · Accepted Answer · 2014-07-29 16:36:45Z

2

Try this:

for block in blocks:
    group = document.find('./group[@name="{}"]'.format(block))
    if group:
        xml.etree.ElementTree.dump(group)
    else:
        print "Group {} not found.".format(group)

edited Jul 29, 2014 at 16:36

answered Jul 29, 2014 at 16:28

Paulo Scardine

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3 Comments

Onizuka Over a year ago

Hi Paulo thanks for your reply. I am using Python 2.4 which does not support this. How can I achieve this in 2.4?

Paulo Scardine Over a year ago

replace './group[@name="{}"]'.format(block) by './group[@name="%s"]' % block

Paulo Scardine Over a year ago

Sorry, I don't have 2.4 around in order to reproduce the problem. Update the question with the error message you got and I will be glad to help.

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