使用python比较xml文件

Question

I want to compare these two xml files:

File1.xml:

<ngs_sample id="40332">
  <workflow value="salmonella" version="101_provisional" />
  <results>
  <gastro_prelim_st reason="not novel" success="false">
      <type st="1364" />
      <type st="9999" />
  </gastro_prelim_st>
 </results>
</ngs_sample>

File2.xml:

<ngs_sample id="40332">
  <workflow value="salmonella" version="101_provisional" />
  <results>
  <gastro_prelim_st reason="not novel" success="false">
      <type st="1364" />
   </gastro_prelim_st>
 </results>
</ngs_sample>

I've used xmldiff to compare a.xml with b.xml:

def compare_xmls(observed,expected):

    from xmldiff import main, formatting
    formatter = formatting.DiffFormatter()
    diff = main.diff_files(observed,expected,formatter=formatter)
    return diff

out = compare_xmls(a.xml, b.xml)
print(out)

OUTPUT:

[delete, /ngs_sample/results/gastro_prelim_st/type[2]]

Anyone know how to identify what is the difference between the two xml files, ie what has been deleted compared to the file b.xml. Anyone recommend any other way of comparing xml files in python?

Answer 1

You can switch to the XMLFormatter and manually filter out the results:

...
# Change formatter:
formatter = formatting.XMLFormatter(normalize=formatting.WS_BOTH)

...

# after `out` has been retrieved:
import re
for i in out.splitlines():
  if re.search(r'\bdiff:\w+', i):
    print(i)

# Result:
#       <type st="9999" diff:delete=""/>

Answer 2

Use the xmldiff to perform this exact task.

main.py

from xmldiff import main
diff = main.diff_files("file1.xml", "file2.xml")
print(diff)

output

[DeleteNode(node='/ngs_sample/results/gastro_prelim_st/type[2]')]

Answer 3

Another option is use xml2 https://github.com/clone/xml2 (and something like bash process substitution)

$ diff --color <(xml2 < File1.xml) <(xml2 < File2.xml)

7,8d6
< /ngs_sample/results/gastro_prelim_st/type
< /ngs_sample/results/gastro_prelim_st/type/@st=9999

Answer 4

Try XmlXdiff , currently only svg output available. But it should be quite simple to provied a text output or an interface class.

Some example code from the XmlXDiff website:

from XmlXdiff.XReport import DrawXmlDiff

_xml1 = """<root><deleted>with content</deleted><unchanged/><changed name="test1" /></root>"""
_xml2 = """<root><unchanged/><changed name="test2" /><added/></root>"""

with open("test1.xml", "w") as f:
    f.write(_xml1)

with open("test2.xml", "w") as f:
    f.write(_xml2)

x = DrawXmlDiff("test1.xml", "test2.xml")
x.saveSvg('xdiff.svg')

Example Output