[FIX] ADNI utils load_clinical_csv should avoid hidden files (#1343)

aramis-lab · Oct 22, 2024 · 48c12ab · 48c12ab
1 parent cd447d5
commit 48c12ab
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Showing 2 changed files with 3 additions and 4 deletions.
diff --git a/clinica/iotools/converters/adni_to_bids/adni_utils.py b/clinica/iotools/converters/adni_to_bids/adni_utils.py
@@ -1109,7 +1109,7 @@ def load_clinical_csv(clinical_dir: Path, filename: str) -> pd.DataFrame:
 
     pattern = filename + r"(_\d{1,2}[A-Za-z]{3}\d{4})?.csv"
     files_matching_pattern = [
-        f for f in clinical_dir.rglob("*.csv") if re.search(pattern, f.name)
+        f for f in clinical_dir.rglob("[!.]*.csv") if re.search(pattern, f.name)
     ]
     if len(files_matching_pattern) != 1:
         raise IOError(

diff --git a/test/unittests/iotools/converters/adni_to_bids/test_adni_utils.py b/test/unittests/iotools/converters/adni_to_bids/test_adni_utils.py
@@ -236,7 +236,7 @@ def test_compute_session_id(csv_filename, visit_code_column_name):
 
 
 @pytest.fixture
-def input_df():
+def input_df() -> pd.DataFrame:
     return pd.DataFrame(
         {
             "foo": ["foo1", "foo2", "foo3"],
@@ -255,6 +255,7 @@ def test_load_clinical_csv(tmp_path, input_df, csv_name, csv_to_look_for):
     from clinica.iotools.converters.adni_to_bids.adni_utils import load_clinical_csv
 
     input_df.to_csv(tmp_path / csv_name, index=False)
+    pd.DataFrame().to_csv(tmp_path / f".{csv_name}")
     assert_frame_equal(load_clinical_csv(tmp_path, csv_to_look_for), input_df)
 
 
@@ -278,8 +279,6 @@ def test_load_clinical_csv_error(
 
 
 def test_load_clinical_csv_value_error(tmp_path):
-    import re
-
     from clinica.iotools.converters.adni_to_bids.adni_utils import load_clinical_csv
 
     with open(tmp_path / "adnimerge.csv", "w") as fp: