From 29af330234fb9b88d978a2b8a3afa6a9221165e8 Mon Sep 17 00:00:00 2001
From: MarsMellow <mpzwiers@gmail.com>
Date: Thu, 6 Jul 2023 11:14:18 +0200
Subject: [PATCH] Replace the `tarfile` and `zipfile` dependency with
 `shutil.unpack_archive`

---
 bidscoin/bcoin.py | 13 +++++++------
 bidscoin/bids.py  | 14 +++++---------
 2 files changed, 12 insertions(+), 15 deletions(-)

diff --git a/bidscoin/bcoin.py b/bidscoin/bcoin.py
index 961409b6..1be47fd4 100755
--- a/bidscoin/bcoin.py
+++ b/bidscoin/bcoin.py
@@ -21,7 +21,6 @@
 import shutil
 import subprocess
 import sys
-import tarfile
 import textwrap
 import urllib.request
 from functools import lru_cache
@@ -635,12 +634,14 @@ def pulltutorialdata(tutorialfolder: str) -> None:
         urllib.request.urlretrieve(tutorialurl, tutorialtargz, reporthook=t.update_to)  # NB: Much faster than requests.get(url, stream=True). In case of ssl certificate issues use: with urllib.request.urlopen(tutorialurl, context=ssl.SSLContext()) as data, open(tutorialtargz, 'wb') as targz_fid: shutil.copyfileobj(data, targz_fid)
 
     # Unzip the data in the target folder
-    LOGGER.info(f"Unzipping the downloaded data in: {tutorialfolder}")
-    with tarfile.open(tutorialtargz, 'r') as targz_fid:
-        for member in tqdm(iterable=targz_fid.getmembers(), total=len(targz_fid.getmembers()), leave=False):
-            targz_fid.extract(member, tutorialfolder)
+    LOGGER.info(f"Unpacking the downloaded data in: {tutorialfolder}")
+    try:
+        shutil.unpack_archive(tutorialtargz, tutorialfolder)
+        LOGGER.success(f"Done")
+    except Exception as unpackerror:
+        LOGGER.error(f"Could not unpack: {tutorialtargz}\n{unpackerror}")
+
     tutorialtargz.unlink()
-    LOGGER.success(f"Done")
 
 
 def main():
diff --git a/bidscoin/bids.py b/bidscoin/bids.py
index c785a9dc..72dee62f 100644
--- a/bidscoin/bids.py
+++ b/bidscoin/bids.py
@@ -13,10 +13,8 @@
 import logging
 import re
 import shutil
-import tarfile
 import tempfile
 import warnings
-import zipfile
 import fnmatch
 from functools import lru_cache
 from pathlib import Path
@@ -355,13 +353,11 @@ def unpack(sourcefolder: Path, wildcard: str='', workfolder: Path='') -> Tuple[L
         recursive = False
         for tarzipfile in [worksubses/tarzipfile.name for tarzipfile in tarzipfiles]:
             LOGGER.info(f"Unpacking: {tarzipfile.name} -> {worksubses}")
-            ext = tarzipfile.suffixes
-            if ext and ext[-1] == '.zip':
-                with zipfile.ZipFile(tarzipfile, 'r') as zip_fid:
-                    zip_fid.extractall(worksubses)
-            elif '.tar' in ext:
-                with tarfile.open(tarzipfile, 'r') as tar_fid:
-                    tar_fid.extractall(worksubses)
+            try:
+                shutil.unpack_archive(tarzipfile, worksubses)
+            except Exception as unpackerror:
+                LOGGER.warning(f"Could not unpack: {tarzipfile}\n{unpackerror}")
+                continue
 
             # Sort the DICOM files in the worksubses rootfolder immediately (to avoid name collisions)
             if not (worksubses/'DICOMDIR').is_file():