CODEWITHSUNDEEP
pythonsortinglxmlelementtree
nh_
nh_

Reputation: 299

python lxml write to file in predefined order

I want to write following lxml etree subelements:

<ElementProtocolat0x3803048>,
<ElementStudyEventDefat0x3803108>,
<ElementFormDefat0x3803248>,
<ElementItemGroupDefat0x38032c8>,
<ElementClinicalDataat0x3803408>,
<ElementItemGroupDataat0x38035c8>,
<ElementFormDefat0x38036c8>,

to my odm xml file in a predefined order. i.e.

<ElementProtocolat0x3803048>,
<ElementStudyEventDefat0x3803108>,
<ElementFormDefat0x3803248>,
<ElementFormDefat0x38036c8>,
<ElementItemGroupDefat0x38032c8>,
<ElementItemGroupDataat0x38035c8>,
<ElementClinicalDataat0x3803408>,
....

is there any way to sort the elements i.e. with a predefined list?

predefined_order = ['Protocol', 'StudyEventDef','FormDef','ItemGroupDef','ItemDef','CodeList']

Upvotes: 1

Views: 2112

Answers (2)

Robᵩ
Robᵩ

Reputation: 168876

This sample demonstrates:

  • How to read in an XMl file,
  • That an Element is a list, and can be manipulated as such
  • How to sort a list based on the predefined order of a matchable substring
  • How to write out an XML file
from lxml import etree
import re

# Parse the XML and find the root
with open('input.xml') as input_file:
    tree = etree.parse(input_file)
root = tree.getroot()

# Find the list to sort and sort it
some_arbitrary_expression_to_find_the_list = '.'
element_list = tree.xpath(some_arbitrary_expression_to_find_the_list)[0]

predefined_order = [
    'Protocol',
    'StudyEventDef',
    'FormDef',
    'ItemGroupDef',
    'ItemGroupData',
    'ItemDef',
    'CodeList',
    'ClinicalData']
filter = re.compile(r'Element(.*)at0x.*')

element_list[:] = sorted(
    element_list[:],
    key = lambda x: predefined_order.index(filter.match(x.tag).group(1)))

# Write the XML to the output file
with open('output.xml', 'w') as output_file:
    output_file.write(etree.tostring(tree, pretty_print = True))

Sample input: 

<stuff>
<ElementProtocolat0x3803048 />
<ElementStudyEventDefat0x3803108 />
<ElementFormDefat0x3803248 />
<ElementItemGroupDefat0x38032c8>Random Text</ElementItemGroupDefat0x38032c8>
<ElementClinicalDataat0x3803408 />
<ElementItemGroupDataat0x38035c8><tag1><tag2 attr="random tags"/></tag1></ElementItemGroupDataat0x38035c8>
<ElementFormDefat0x38036c8 />
</stuff>

OUtput: 

<stuff>
<ElementProtocolat0x3803048/>
<ElementStudyEventDefat0x3803108/>
<ElementFormDefat0x3803248/>
<ElementFormDefat0x38036c8/>
<ElementItemGroupDefat0x38032c8>Random Text</ElementItemGroupDefat0x38032c8>
<ElementItemGroupDataat0x38035c8><tag1><tag2 attr="random tags"/></tag1></ElementItemGroupDataat0x38035c8>
<ElementClinicalDataat0x3803408/>
</stuff>

Upvotes: 5

Tanmaya Meher
Tanmaya Meher

Reputation: 1476

Sorry for my lack of knowledge on xml but I tried to format your data in sorted order using my basic knowledge of Python only.

import re
data = """<ElementProtocolat0x3803048>,
<ElementStudyEventDefat0x3803108>,
<ElementFormDefat0x3803248>,
<ElementItemGroupDefat0x38032c8>,
<ElementClinicalDataat0x3803408>,
<ElementItemGroupDataat0x38035c8>,
<ElementFormDefat0x38036c8>,"""

predefined_order = ['Protocol','StudyEventDef','FormDef','ItemGroupDef','ItemGroupData','CodeList', 'ClinicalData']

fh1 = open("something.xml","w")
for i in predefined_order:
    for j in data.split(','):
        if re.search(i,j):
            fh1.write(j + ',')

Output:

<ElementProtocolat0x3803048>,
<ElementStudyEventDefat0x3803108>,
<ElementFormDefat0x3803248>,
<ElementFormDefat0x38036c8>,
<ElementItemGroupDefat0x38032c8>,
<ElementItemGroupDataat0x38035c8>,
<ElementClinicalDataat0x3803408>,

Upvotes: 0

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