ADNI_to_BIDS utils : load_clinical_csv, hidden csv file matching, issue #1163
#1195
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I would prefer changing the rglob regex to not consider hidden files at all (either check on beginning of string or different rglob match but I would need to check how to). WDYT @NicolasGensollen ? |
| @@ -1644,7 +1644,7 @@ def load_clinical_csv(clinical_dir: str, filename: str) -> pd.DataFrame: | |||
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| pattern = filename + r"(_\d{1,2}[A-Za-z]{3}\d{4})?.csv" | |||
| files_matching_pattern = [ | |||
| f for f in Path(clinical_dir).rglob("*.csv") if re.search(pattern, (f.name)) | |||
| f for f in Path(clinical_dir).rglob("*.csv") if re.match(pattern, (f.name)) | |||
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I agree with @AliceJoubert. Not listing hidden files and folders will be more explicit than changing search for match.
I believe changing the rglob pattern for .rglob("[!.]*.csv") should do the trick.
Would be nice to add some unit tests to make sure this is working as expected, especially if there are csv files in subfolders where both the subfolders and the files could be hidden.
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Fix issue #1163
Change
re.searchbyre.match.It will avoid hidden file matching by constraining to an exact match with the pattern
if we have two files:
ADNIMERGE_25Apr2024.csv.ADNIMERGE_25Apr2024.csvthe pattern is
"ADNIMERGE"+ r"(_\d{1,2}[A-Za-z]{3}\d{4})?.csv", only the correct file will be returned.