best way to compare xml files in python

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, i.e. what has been deleted compared to the file b.xml. Anyone recommend any other way of comparing xml files in python?

edited Nov 22 at 13:51

asked Nov 22 at 12:23

Mark

1611516

add a comment |

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, i.e. what has been deleted compared to the file b.xml. Anyone recommend any other way of comparing xml files in python?

edited Nov 22 at 13:51

asked Nov 22 at 12:23

Mark

1611516

add a comment |

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, i.e. what has been deleted compared to the file b.xml. Anyone recommend any other way of comparing xml files in python?

edited Nov 22 at 13:51

asked Nov 22 at 12:23

Mark

1611516

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, i.e. what has been deleted compared to the file b.xml. Anyone recommend any other way of comparing xml files in python?

python xml compare xmldiff

edited Nov 22 at 13:51

asked Nov 22 at 12:23

Mark

1611516

edited Nov 22 at 13:51

asked Nov 22 at 12:23

Mark

1611516

edited Nov 22 at 13:51

asked Nov 22 at 12:23

Mark

1611516

asked Nov 22 at 12:23

Mark

1611516

asked Nov 22 at 12:23

Mark

1611516

add a comment |

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