RyanCheley.com

The Problem

Data exchange in healthcare is … harder than it needs to be. Not all partners in the healthcare arena understand and use technology to its fullest benefit.

Take for example several health plans which want data reported to them for CMS (Centers for Medicare and Medicaid Services) regulations. They will ask their ‘delegated’ groups to fill out an excel file. As in, they expect you will actually fill out an excel file, either by manually entering the data OR by potentially copying and pasting your data into their excel file.

They will also, quite frequently, change their mind on what they want AND the order in which they want the data to appear in their excel file. But there’s no change log to tell you what (if anything has changed). All that you will get is an email which states, “Here’s the new template to be used for report XYZ” … even if this ‘new’ report is the same as the last one that was sent.

Some solutions might be to use versioning software (like Git) but all they will do is tell you that there is a difference, not what the difference is. For example, when looking at a simple excel file added to git and using git diff you see:

diff --git a/Book3.xlsx b/Book3.xlsx
index 05a8b41..e96cdb5 100644
Binary files a/Book3.xlsx and b/Book3.xlsx differ

This has been a giant pain in the butt for a while, but with the recent shelter-in-place directives, I have a bit more time on the weekends to solve these kinds of problems.

The Solution

Why Python of Course!

Only two libraries are needed to make the comparison: (1) os, (2) pandas

The basic idea is to:

1. Load the files
2. use pandas to compare the files
3. write out the differences, if they exist
   

Load the Files

The code below loads the necessary libraries, and then loads the excel files into 2 pandas dataframes. One thing that my team has to watch out for are tab names that have leading spaces that aren’t easy to see inside of excel. This can cause all sorts of nightmares from a troubleshooting perspective.

import os
import pandas as pd

file_original = os.path.join(\\path\\to\\original\\file, original_file.xlsx)
file_new = os.path.join(\\path\\to\\new\\file, new_file.xlsx)

sheet_name_original = name_of_sheet_in_original_file
sheet_name_new = name_of_sheet_in_new_file

df1 = pd.read_excel(file_original, sheet_name_original)
df2 = pd.read_excel(file_new, sheet_name_new)

Use Pandas to compare

This is just a one liner, but is super powerful. Pandas DataFrames have a method to see if two frames are the same. So easy!

data_frame_same = df1.equals(df2)

Write out the differences if they exist:

First we specify where we’re going to write out the differences to. We use w+ because we’ll be writing out to a file AND potentially appending, depending on differences that are found. The f.truncate(0) will clear out the file so that we get just the differences on this run. If we don’t do this then we’ll just append to the file over and over again … and that can get confusing.

f.open(\\path\\to\\file\\to\\write\\differences.txt, 'w+')
f.truncate(0)

Next, we check to see if there are any differences and if they are, we write a simple message to our text file from above:

if data_frame_same:
	f.write('No differences detected')

If differences are found, then we loop through the lines of the file, finding the differences and and writing them to our file:

else:
	f.write('*** WARNING *** Differences Found\n\n')
	for c in range(max(len(df1.columns), len(df2.columns))):
		try:
			header1 = df1.columns[c].strip().lower().replace('\n', '')
			header2 = df2.columns[c].strip().lower().replace('\n', '')
			if header1 == header2:
				f.write(f'Headers are the same: {header1}\n')
			else:
				f.write(f'Difference Found: {header1} -> {header2}\n')
		except:
			pass

f.close()

The code above finds the largest column header list (the file may have had a new column added) and uses a try/except to let us get the max of that to loop over.

Next, we check for differences between header1 and header2. If they are the same, we just write that out, if they aren’t, we indicate that header1 was transformed to header2

A sample of the output when the column headers have changed is below:

*** WARNING *** Differences Found

Headers are the same: beneficiary first name
...
Difference Found: person who made the request -> who made the request?
...

Future Enhancements

In just using it a couple of times I’ve already spotted a couple of spots for enhancements:

1. Use input to allow the user to enter the names/locations of the files
2. Read the tab names and allow user to select from command line
   

Conclusion

I’m looking forward to implementing the enhancements mentioned above to make this even more user friendly. In the mean time, it’ll get the job done and allow someone on my team to work on something more interesting then comparing excel files to try (and hopefully find) differences.