BadZipFile Error

[Acaro12]

Hi,

I used this pipeline a year ago and got it working nicely in the end. However, when trying to analyze new data now using the IMC preprocessing script, I encounter the following error:

---

BadZipFile Traceback (most recent call last)
Cell In[20], line 10
8 temp_dirs.append(temp_dir)
9 for zip_file in sorted(zip_files):
---> 10 imcsegpipe.extract_zip_file(zip_file, temp_dir.name)
11 acquisition_metadatas = []
12 for raw_dir in raw_dirs + [Path(temp_dir.name) for temp_dir in temp_dirs]:

File ~/ImcSegmentationPipeline/src/imcsegpipe/_imcsegpipe.py:23, in extract_zip_file(zip_file, dest_dir)
20 def extract_zip_file(
21 zip_file: Union[str, PathLike], dest_dir: Union[str, PathLike]
22 ) -> None:
---> 23 with ZipFile(zip_file, allowZip64=True) as f:
24 f.extractall(dest_dir)

File ~/miniconda3/envs/imcsegpipe/lib/python3.9/zipfile.py:1266, in ZipFile.init(self, file, mode, compression, allowZip64, compresslevel, strict_timestamps)
1264 try:
1265 if mode == 'r':
-> 1266 self._RealGetContents()
1267 elif mode in ('w', 'x'):
1268 # set the modified flag so central directory gets written
1269 # even if no files are added to the archive
1270 self._didModify = True

File ~/miniconda3/envs/imcsegpipe/lib/python3.9/zipfile.py:1333, in ZipFile._RealGetContents(self)
1331 raise BadZipFile("File is not a zip file")
1332 if not endrec:
-> 1333 raise BadZipFile("File is not a zip file")
1334 if self.debug > 1:
1335 print(endrec)

BadZipFile: File is not a zip file

I ran the analysis using MacOS Sonoma as well as Linux/Ubuntu.
I compressed mcd+txt files using both above-mentioned systems with default compression but also using a third party tool on mac.
I updated conda, deleted the IMCsegmentationPipeline repository and cloned it again.
When I used the script to preprocess data from one year ago or your example data, everything worked nicely. However when I extracted your example data and zipped it again, the same error as above occurred.
None of the above worked - the same error persisted.

From the above I suspect that the error might be due to an old version of the imcsegpipe. When I tried to update the imcsegpipe python package using

pip install imcsegpipe --upgrade

, the following error was reported:

ERROR: Could not find a version that satisfies the requirement imcsegpipe (from versions: none)
ERROR: No matching distribution found for imcsegpipe

What could be the problem here?
Thank you in advance!

[Acaro12]

Apparently, the fact that the .zip files were located on a ExFAT-formatted external SSD drive caused the problem...
Relocating them to the internal HD drive of the M3 Mac book solved the issue.