parse xml file with python3

Question

I am not familiar with xml files at all but trying to parse this:

<?xml version="1.0" encoding="ISO-8859-1"?>
<modeling>
 <generator>
  <i name="subversion" type="string">(build Dec 07 2018 23:19:03) complex            parallel </i>
  <i name="platform" type="string">LinuxIFC </i>
  <i name="date" type="string">2019 07 11 </i>
  <i name="time" type="string">11:56:12 </i>
 </generator>
 <incar>
  <i type="int" name="ISTART">     0</i>
  <i type="string" name="PREC">accurate</i>
  <i type="int" name="ISPIN">     2</i>
  <i type="int" name="NELMDL">    -8</i>
  <i type="int" name="IBRION">     2</i>
  <i name="EDIFF">      0.00001000</i>
  <i name="EDIFFG">     -0.01000000</i>
  <i type="int" name="NSW">   200</i>
  <i type="int" name="ISIF">     2</i>
  <i type="int" name="ISYM">     2</i>
  <i name="ENCUT">    750.00000000</i>
  <i name="POTIM">      0.30000000</i>
</incar>

till now,I have managed to write code to get Elements as:

#!/usr/bin/env python
import xml.etree.ElementTree as ET

tree = ET.parse("vasprun.xml")
root = tree.getroot()
for child in root:
  print({x for x in root.findall(child.tag)})

which is giving output as:

{<Element 'generator' at 0x7f342220ca90>}
{<Element 'incar' at 0x7f342220cd10>}

I am trying to get the file from incar as:

IStart=0
Prec=accurate

Can someone help me getting this?

[{n.get("name"): n.text.strip() for n in node} for node in root] — Olvin Roght
– Olvin Roght, Commented Dec 8, 2021 at 19:21

S_i_l_e_n_t C_o_d_e_r · Accepted Answer · 2021-12-07 03:42:30Z

2

The below works (XPath)

import xml.etree.ElementTree as ET


xml = '''<?xml version="1.0" encoding="UTF-8"?>
<modeling>
   <generator>
      <i name="subversion" type="string">(build Dec 07 2018 23:19:03) complex            parallel</i>
      <i name="platform" type="string">LinuxIFC</i>
      <i name="date" type="string">2019 07 11</i>
      <i name="time" type="string">11:56:12</i>
   </generator>
   <incar>
      <i type="int" name="ISTART">0</i>
      <i type="string" name="PREC">accurate</i>
      <i type="int" name="ISPIN">2</i>
      <i type="int" name="NELMDL">-8</i>
      <i type="int" name="IBRION">2</i>
      <i name="EDIFF">0.00001000</i>
      <i name="EDIFFG">-0.01000000</i>
      <i type="int" name="NSW">200</i>
      <i type="int" name="ISIF">2</i>
      <i type="int" name="ISYM">2</i>
      <i name="ENCUT">750.00000000</i>
      <i name="POTIM">0.30000000</i>
   </incar>
</modeling>'''

root = ET.fromstring(xml)
names = ['ISTART','PREC']
for name in names:
  i = root.find(f'.//i[@name="{name}"]')
  print(i.text)

output

0
accurate

edited Dec 7, 2021 at 3:42

S_i_l_e_n_t C_o_d_e_r

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answered Dec 6, 2021 at 18:17

balderman

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1 Comment

BaRud Over a year ago

Thanks, but I didn't mean that. I am trying to get all the name=value inside incar. Upvoted though.

jackal · Accepted Answer · 2021-12-06 18:39:11Z

0

Added your sample XML to a file after appending the missing final tag </modeling>

Then:

import xml.etree.ElementTree as ET

with open('vasprun.xml') as xml:
    root = ET.fromstring(xml.read())
    for name in ['ISTART', 'PREC']:
        if (t := root.find(f'.//i[@name="{name}"]')) is not None:
            print(f'{name}:{t.text.strip()}')

answered Dec 6, 2021 at 18:39

jackal

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Comments

S_i_l_e_n_t C_o_d_e_r · Accepted Answer · 2021-12-07 03:43:10Z

If the close modeling tag is present, you can use XPath for the job.

xpath to get ISTART value is : //incar/*[@name='ISTART']

xpath to get PREC value is : //incar/*[@name='PREC']

then :


from lxml import etree

xml_doc = """
        <?xml version="1.0" encoding="ISO-8859-1"?>
            <modeling>
                <generator>
                      <i name="subversion" type="string">(build Dec 07 2018 23:19:03) complex            parallel </i>
                      <i name="platform" type="string">LinuxIFC </i>
                      <i name="date" type="string">2019 07 11 </i>
                      <i name="time" type="string">11:56:12 </i>
                </generator>
                     <incar>
                        <i type="int" name="ISTART">     0</i>
                        <i type="string" name="PREC">accurate</i>
                        <i type="int" name="ISPIN">     2</i>
                        <i type="int" name="NELMDL">    -8</i>
                        <i type="int" name="IBRION">     2</i>
                        <i name="EDIFF">      0.00001000</i>
                        <i name="EDIFFG">     -0.01000000</i>
                        <i type="int" name="NSW">   200</i>
                        <i type="int" name="ISIF">     2</i>
                        <i type="int" name="ISYM">     2</i>
                        <i name="ENCUT">    750.00000000</i>
                        <i name="POTIM">      0.30000000</i>
                     </incar>
            </modeling>
            """
parser = etree.XMLParser(resolve_entities=False, strip_cdata=False, recover=True, ns_clean=True)
xml_tree = etree.fromstring(xml_doc.encode(), parser=parser)
istart = xml_tree.xpath('//incar/*[@name="ISTART"]')
prec = xml_tree.xpath('//incar/*[@name="PREC"]')
print(f'ISTART={int(istart[0].text)}')
print(f'Prec={prec[0].text}')

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