[FIX] Address list read error when escape characters (e.g. comma) in …

…file paths

handler/ezBIDS_core/ezBIDS_core.py

@@ -3061,7 +3061,11 @@ def check_dwi_b0maps(dataset_list_unique_series):
 print("")
 
 # Load dataframe containing all uploaded files
-uploaded_img_list = natsorted(pd.read_csv("list", header=None, lineterminator='\n').to_numpy().flatten().tolist())
+try:
+    uploaded_img_list = natsorted(pd.read_csv("list", header=None, lineterminator='\n').to_numpy().flatten().tolist())
+except:
+    # Need for [rare] instances where a comma (or other escape character) is in the file path
+    uploaded_img_list = natsorted(pd.read_csv("list", sep=' ', header=None, lineterminator='\n').to_numpy().flatten().tolist())
 
 # Remove dots in file names (that aren't extensions). This screws up the bids-validator otherwise
 uploaded_img_list = fix_multiple_dots(uploaded_img_list)

handler/ezBIDS_core/update_ezBIDS_core.py

@@ -19,7 +19,12 @@
 DATA_DIR = sys.argv[1]
 os.chdir(DATA_DIR)
 
-img_list = natsorted(pd.read_csv("list", header=None, lineterminator="\n").to_numpy().flatten().tolist())
+try:
+    img_list = natsorted(pd.read_csv("list", header=None, lineterminator="\n").to_numpy().flatten().tolist())
+except:
+    # Need for [rare] instances where a comma (or other escape character) is in the file path
+    img_list = natsorted(pd.read_csv("list", sep=' ', header=None, lineterminator='\n').to_numpy().flatten().tolist())
+
 MEG_extensions = [".ds", ".fif", ".sqd", ".con", ".raw", ".ave", ".mrk", ".kdf", ".mhd", ".trg", ".chn", ".dat"]
 
 # place paths to image thumbnails in ezBIDS_core.json