compare xml files using python
0
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 at 13:58
Mark
1611516
add a comment |
0
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 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 secondtypetag underngs_sample/...prelim_st/was deleted). Did you mean you wanted to see the values being deleted?
– Idlehands
Nov 22 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 at 15:45
What exactly are you expecting from the output that's missing then? It's already telling you that secondtypetag has been deleted. As it stands it's not clear, would be helpful if you stated your expected output instead.
– Idlehands
Nov 22 at 15:52
Helpful to say <type st="9999" /> is deleted.
– Mark
Nov 22 at 16:25
add a comment |
0
0
0
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 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
python xml xmldiff
asked Nov 22 at 13:58
Mark
1611516
asked Nov 22 at 13:58
Mark
1611516
asked Nov 22 at 13:58
Mark
1611516
asked Nov 22 at 13:58
Mark
1611516
asked Nov 22 at 13:58
Mark
1611516
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 secondtypetag underngs_sample/...prelim_st/was deleted). Did you mean you wanted to see the values being deleted?
– Idlehands
Nov 22 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 at 15:45
What exactly are you expecting from the output that's missing then? It's already telling you that secondtypetag has been deleted. As it stands it's not clear, would be helpful if you stated your expected output instead.
– Idlehands
Nov 22 at 15:52
Helpful to say <type st="9999" /> is deleted.
– Mark
Nov 22 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 secondtypetag underngs_sample/...prelim_st/was deleted). Did you mean you wanted to see the values being deleted?
– Idlehands
Nov 22 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 at 15:45
What exactly are you expecting from the output that's missing then? It's already telling you that secondtypetag has been deleted. As it stands it's not clear, would be helpful if you stated your expected output instead.
– Idlehands
Nov 22 at 15:52
Helpful to say <type st="9999" /> is deleted.
– Mark
Nov 22 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 at 14:33
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 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 at 15:45
Yes I want to see what has been deleted, i.e. what is the difference between the two xmls.
– Mark
Nov 22 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 at 15:52
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 at 15:52
Helpful to say <type st="9999" /> is deleted.
– Mark
Nov 22 at 16:25
Helpful to say <type st="9999" /> is deleted.
– Mark
Nov 22 at 16:25
add a comment |
2 Answers
2
active
oldest
votes
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=""/>
answered Nov 22 at 18:01
Idlehands
3,9721417
add a comment |
0
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 at 14:09
Victor 'Chris' Cabral
1,4341221
Not sure if you read the question but this doesnt answer my query
– Mark
Nov 22 at 14:10
add a comment |
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2 Answers
2
active
oldest
votes
2 Answers
2
active
oldest
votes
active
oldest
votes
active
oldest
votes
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=""/>
answered Nov 22 at 18:01
Idlehands
3,9721417
add a comment |
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=""/>
answered Nov 22 at 18:01
Idlehands
3,9721417
add a comment |
1
1
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=""/>
answered Nov 22 at 18:01
Idlehands
3,9721417
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 at 18:01
Idlehands
3,9721417
answered Nov 22 at 18:01
Idlehands
3,9721417
answered Nov 22 at 18:01
Idlehands
3,9721417
answered Nov 22 at 18:01
Idlehands
3,9721417
3,9721417
add a comment |
add a comment |
0
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 at 14:09
Victor 'Chris' Cabral
1,4341221
Not sure if you read the question but this doesnt answer my query
– Mark
Nov 22 at 14:10
add a comment |
0
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 at 14:09
Victor 'Chris' Cabral
1,4341221
Not sure if you read the question but this doesnt answer my query
– Mark
Nov 22 at 14:10
add a comment |
0
0
0
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 at 14:09
Victor 'Chris' Cabral
1,4341221
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 at 14:09
Victor 'Chris' Cabral
1,4341221
answered Nov 22 at 14:09
Victor 'Chris' Cabral
1,4341221
answered Nov 22 at 14:09
Victor 'Chris' Cabral
1,4341221
answered Nov 22 at 14:09
Victor 'Chris' Cabral
1,4341221
1,4341221
Not sure if you read the question but this doesnt answer my query
– Mark
Nov 22 at 14:10
add a comment |
Not sure if you read the question but this doesnt answer my query
– Mark
Nov 22 at 14:10
Not sure if you read the question but this doesnt answer my query
– Mark
Nov 22 at 14:10
Not sure if you read the question but this doesnt answer my query
– Mark
Nov 22 at 14:10
add a comment |
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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
typetag underngs_sample/...prelim_st/was deleted). Did you mean you wanted to see the values being deleted?– Idlehands
Nov 22 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 at 15:45
What exactly are you expecting from the output that's missing then? It's already telling you that second
typetag has been deleted. As it stands it's not clear, would be helpful if you stated your expected output instead.– Idlehands
Nov 22 at 15:52
Helpful to say <type st="9999" /> is deleted.
– Mark
Nov 22 at 16:25