Merge pull request #3417 from qian587/fix-3416

[FIX] Escape metacharacters when parsing dcm2niix outputs

Author: effigies

.zenodo.json

@@ -860,6 +860,9 @@
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",
       "orcid": "0000-0002-5312-6729"
+    },
+    {
+      "name": "Hui Qian, Tan"
     }
   ],
   "keywords": [

nipype/interfaces/dcm2nii.py

@@ -4,6 +4,7 @@
 import re
 from copy import deepcopy
 import itertools as it
+import glob
 from glob import iglob
 
 from ..utils.filemanip import split_filename
@@ -494,4 +495,6 @@ def _list_outputs(self):
 
 # https://stackoverflow.com/a/4829130
 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
+    )

nipype/interfaces/tests/test_dcm2nii.py

@@ -0,0 +1,21 @@
+import pytest
+
+
+from nipype.interfaces import dcm2nii
+
+
+@pytest.mark.parametrize(
+    "fname, extension",
+    [
+        ("output_1", ".txt"),
+        ("output_w_[]_meta_1", ".json"),
+        ("output_w_**^$?_meta_2", ".txt"),
+    ],
+)
+def test_search_files(tmp_path, fname, extension):
+    tmp_fname = fname + extension
+    test_file = tmp_path / tmp_fname
+    test_file.touch()
+    actual_files_list = dcm2nii.search_files(str(tmp_path / fname), [extension])
+    for f in actual_files_list:
+        assert str(test_file) == f