bwm_usage_notebook.ipynb fails on colab

[asmacdo]

cell 18 fails for a known reason

# Workaround: brainglobe-atlasapi 2.3.1 fetches its atlas-version manifest
# from a Colab-unfriendly S3 endpoint that returns 403 for some Colab IPs.
# Pre-seed the cache so BrainGlobeAtlas() below can find a version manifest
# even when the live fetch fails. See https://github.com/brainglobe/brainglobe-atlasapi/issues/738

However it seems that the fallback doesnt work either.

Full output

Could not fetch the latest atlas versions: 403
Using the last cached version from /root/.brainglobe/last_versions.conf
Could not fetch the latest atlas versions: 403
Using the last cached version from /root/.brainglobe/last_versions.conf
Could not fetch the latest atlas versions: 403
Using the last cached version from /root/.brainglobe/last_versions.conf
Could not fetch the latest atlas versions: 403
Using the last cached version from /root/.brainglobe/last_versions.conf

Downloading... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0.0% • 0/93 bytes • speed: ? • ETA: -:--:--

---------------------------------------------------------------------------

ReadError                                 Traceback (most recent call last)

[/usr/local/lib/python3.12/dist-packages/brainglobe_atlasapi/bg_atlas.py](https://localhost:8080/#) in download_extract_file(self)
    203         try:
--> 204             tar = tarfile.open(destination_path)
    205             tar.extractall(path=self.brainglobe_dir)

3 frames

ReadError: file could not be opened successfully:
- method gz: ReadError('not a gzip file')
- method bz2: ReadError('not a bzip2 file')
- method xz: ReadError('not an lzma file')
- method tar: ReadError('truncated header')


The above exception was the direct cause of the following exception:

ReadError                                 Traceback (most recent call last)

[/usr/local/lib/python3.12/dist-packages/brainglobe_atlasapi/bg_atlas.py](https://localhost:8080/#) in download_extract_file(self)
    208             # Delete corrupted file so we can try again later
    209             destination_path.unlink(missing_ok=True)
--> 210             raise tarfile.ReadError(
    211                 f"Atlas download was interrupted or corrupted. "
    212                 f"Please try again. Details: {e}"

ReadError: Atlas download was interrupted or corrupted. Please try again. Details: file could not be opened successfully:
- method gz: ReadError('not a gzip file')
- method bz2: ReadError('not a bzip2 file')
- method xz: ReadError('not an lzma file')
- method tar: ReadError('truncated header')

I tried clearing the cache, and retrying the download but this error seems to persist.

[bendichter]

Thanks for this issue, @asmacdo. I suspect brainglobe changed the way they are serving their atlas data in a way that has broken earlier versions of the brainglobe API. I'm investigating now.

[bendichter]

See brainglobe/brainglobe-atlasapi#847