[FIX] Escape metacharacters when parsing dcm2niix outputs

[qian587]

Summary

This PR should fix the issue with dcm2niix interface not able to parse the output files when the file name contains meta characters.

Fixes #3416 .

List of changes proposed in this PR (pull-request)

Acknowledgment

• (Mandatory) I acknowledge that this contribution will be available under the Apache 2 license.

[effigies]

This looks reasonable, though I'd suggest escaping just before the glob, rather than passing around an escaped filename:

 def search_files(prefix, outtypes):
-    return it.chain.from_iterable(iglob(prefix + outtype) for outtype in outtypes)
+    return it.chain.from_iterable(iglob(glob.escape(prefix + outtype))
+                                  for outtype in outtypes)

[effigies]

Would you mind writing a small test for search_files() that validates this behavior, by the way?

[qian587]

Yea for sure, unsure where exactly I should be putting the escape in the first place. Will modify the code and add a testing too. Thanks 🙏

[qian587]

@effigies May I know where should I put the test for search_files() ?

[effigies]

We put tests for nipype/subdir/x.py in nipype/subdir/tests/test_x.py, so in this case it would be nipype/interfaces/tests/test_dcm2nii.py.

[codecov]

Codecov Report

Merging #3417 (09ff390) into master (f756b71) will increase coverage by 0.02%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master    #3417      +/-   ##
==========================================
+ Coverage   65.21%   65.23%   +0.02%     
==========================================
  Files         307      307              
  Lines       40474    40538      +64     
  Branches     5351     5370      +19     
==========================================
+ Hits        26395    26446      +51     
- Misses      13004    13016      +12     
- Partials     1075     1076       +1     

Flag	Coverage Δ
unittests	64.95% <100.00%> (+0.01%)	⬆️

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Impacted Files	Coverage Δ
nipype/interfaces/dcm2nii.py	65.27% <100.00%> (+0.16%)	⬆️
nipype/interfaces/dipy/base.py	76.70% <0.00%> (+1.48%)	⬆️

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[qian587]

@effigies I have added the test for search_files() let me know what you think. Thank you

[effigies]

LGTM. Let's make sure the tests pass...