compare xml files using 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?

asked Nov 22 '18 at 13:58

Mark

1611516

For comparing differences in general I use WinMerge, so if you don't need to do it in python, it's a pretty handy tool. But if you must, it seems the output already tells you the difference exactly? (That the second type tag under ngs_sample/...prelim_st/ was deleted). Did you mean you wanted to see the values being deleted?

– Idlehands
Nov 22 '18 at 14:33

Yes I want to see what has been deleted, i.e. what is the difference between the two xmls.

– Mark
Nov 22 '18 at 15:45

What exactly are you expecting from the output that's missing then? It's already telling you that second type tag has been deleted. As it stands it's not clear, would be helpful if you stated your expected output instead.

– Idlehands
Nov 22 '18 at 15:52

Helpful to say <type st="9999" /> is deleted.

– Mark
Nov 22 '18 at 16:25

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?

asked Nov 22 '18 at 13:58

Mark

1611516

For comparing differences in general I use WinMerge, so if you don't need to do it in python, it's a pretty handy tool. But if you must, it seems the output already tells you the difference exactly? (That the second type tag under ngs_sample/...prelim_st/ was deleted). Did you mean you wanted to see the values being deleted?

– Idlehands
Nov 22 '18 at 14:33

Yes I want to see what has been deleted, i.e. what is the difference between the two xmls.

– Mark
Nov 22 '18 at 15:45

What exactly are you expecting from the output that's missing then? It's already telling you that second type tag has been deleted. As it stands it's not clear, would be helpful if you stated your expected output instead.

– Idlehands
Nov 22 '18 at 15:52

Helpful to say <type st="9999" /> is deleted.

– Mark
Nov 22 '18 at 16:25

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?

asked Nov 22 '18 at 13:58

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 xmldiff

asked Nov 22 '18 at 13:58

Mark

1611516

asked Nov 22 '18 at 13:58

Mark

1611516

asked Nov 22 '18 at 13:58

Mark

1611516

asked Nov 22 '18 at 13:58

Mark

1611516

asked Nov 22 '18 at 13:58

Mark

1611516

For comparing differences in general I use WinMerge, so if you don't need to do it in python, it's a pretty handy tool. But if you must, it seems the output already tells you the difference exactly? (That the second type tag under ngs_sample/...prelim_st/ was deleted). Did you mean you wanted to see the values being deleted?

– Idlehands
Nov 22 '18 at 14:33

Yes I want to see what has been deleted, i.e. what is the difference between the two xmls.

– Mark
Nov 22 '18 at 15:45

What exactly are you expecting from the output that's missing then? It's already telling you that second type tag has been deleted. As it stands it's not clear, would be helpful if you stated your expected output instead.

– Idlehands
Nov 22 '18 at 15:52

Helpful to say <type st="9999" /> is deleted.

– Mark
Nov 22 '18 at 16:25

add a comment |

For comparing differences in general I use WinMerge, so if you don't need to do it in python, it's a pretty handy tool. But if you must, it seems the output already tells you the difference exactly? (That the second type tag under ngs_sample/...prelim_st/ was deleted). Did you mean you wanted to see the values being deleted?

– Idlehands
Nov 22 '18 at 14:33

Yes I want to see what has been deleted, i.e. what is the difference between the two xmls.

– Mark
Nov 22 '18 at 15:45

What exactly are you expecting from the output that's missing then? It's already telling you that second type tag has been deleted. As it stands it's not clear, would be helpful if you stated your expected output instead.

– Idlehands
Nov 22 '18 at 15:52

Helpful to say <type st="9999" /> is deleted.

– Mark
Nov 22 '18 at 16:25

For comparing differences in general I use WinMerge, so if you don't need to do it in python, it's a pretty handy tool. But if you must, it seems the output already tells you the difference exactly? (That the second type tag under ngs_sample/...prelim_st/ was deleted). Did you mean you wanted to see the values being deleted?

– Idlehands
Nov 22 '18 at 14:33

Yes I want to see what has been deleted, i.e. what is the difference between the two xmls.

– Mark
Nov 22 '18 at 15:45

What exactly are you expecting from the output that's missing then? It's already telling you that second type tag has been deleted. As it stands it's not clear, would be helpful if you stated your expected output instead.

– Idlehands
Nov 22 '18 at 15:52

Helpful to say <type st="9999" /> is deleted.

– Mark
Nov 22 '18 at 16:25

add a comment |

3 Answers
3

active

oldest

votes

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=""/>

answered Nov 22 '18 at 18:01

Idlehands

5,6651620

add a comment |

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]')]

answered Nov 22 '18 at 14:09

Victor 'Chris' Cabral

1,5201222

Not sure if you read the question but this doesnt answer my query

– Mark
Nov 22 '18 at 14:10

add a comment |

-1

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

edited Jan 6 at 21:54

Kingsley

3,03021326

answered Jan 6 at 21:05

mmoosstt

add a comment |

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3 Answers
3

active

oldest

votes

3 Answers
3

active

oldest

votes

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=""/>

answered Nov 22 '18 at 18:01

Idlehands

5,6651620

add a comment |

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=""/>

answered Nov 22 '18 at 18:01

Idlehands

5,6651620

add a comment |

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=""/>

answered Nov 22 '18 at 18:01

Idlehands

5,6651620

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=""/>

answered Nov 22 '18 at 18:01

Idlehands

5,6651620

answered Nov 22 '18 at 18:01

Idlehands

5,6651620

answered Nov 22 '18 at 18:01

Idlehands

5,6651620

answered Nov 22 '18 at 18:01

Idlehands

5,6651620

add a comment |

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]')]

answered Nov 22 '18 at 14:09

Victor 'Chris' Cabral

1,5201222

Not sure if you read the question but this doesnt answer my query

– Mark
Nov 22 '18 at 14:10

add a comment |

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]')]

answered Nov 22 '18 at 14:09

Victor 'Chris' Cabral

1,5201222

Not sure if you read the question but this doesnt answer my query

– Mark
Nov 22 '18 at 14:10

add a comment |

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]')]

answered Nov 22 '18 at 14:09

Victor 'Chris' Cabral

1,5201222

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]')]

answered Nov 22 '18 at 14:09

Victor 'Chris' Cabral

1,5201222

answered Nov 22 '18 at 14:09

Victor 'Chris' Cabral

1,5201222

answered Nov 22 '18 at 14:09

Victor 'Chris' Cabral

1,5201222

answered Nov 22 '18 at 14:09

Victor 'Chris' Cabral

1,5201222

Not sure if you read the question but this doesnt answer my query

– Mark
Nov 22 '18 at 14:10

add a comment |

Not sure if you read the question but this doesnt answer my query

– Mark
Nov 22 '18 at 14:10

Not sure if you read the question but this doesnt answer my query

– Mark
Nov 22 '18 at 14:10

add a comment |

-1

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

edited Jan 6 at 21:54

Kingsley

3,03021326

answered Jan 6 at 21:05

mmoosstt

add a comment |

-1

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

edited Jan 6 at 21:54

Kingsley

3,03021326

answered Jan 6 at 21:05

mmoosstt

add a comment |

-1

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

edited Jan 6 at 21:54

Kingsley

3,03021326

answered Jan 6 at 21:05

mmoosstt

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

edited Jan 6 at 21:54

Kingsley

3,03021326

answered Jan 6 at 21:05

mmoosstt

edited Jan 6 at 21:54

Kingsley

3,03021326

edited Jan 6 at 21:54

Kingsley

3,03021326

edited Jan 6 at 21:54

Kingsley

3,03021326

answered Jan 6 at 21:05

mmoosstt

answered Jan 6 at 21:05

mmoosstt

answered Jan 6 at 21:05

mmoosstt

add a comment |

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