resave.py only creates a zarr.json

[dominikl]

I tried resave.py on an image from idr0157 (converted to zarr with bioformats2raw). But the 'resaved' zarr only contains a zarr.json, nothing else:

(test_env) [dlindner@pilot-zarr3-dev 056332bf08fbc3c3a93cb893674f85]$ ls -lah asterella_gracilis_swe_stature.ome.zarr
total 12K
drwxr-xr-x. 4 dlindner dlindner   76 Jul 31 14:08 .
drwxr-xr-x. 4 dlindner dlindner 4.0K Jul 31 14:09 ..
-rw-r--r--. 1 dlindner dlindner   33 Jul 31 14:08 .zattrs
-rw-r--r--. 1 dlindner dlindner   23 Jul 31 14:08 .zgroup
drwxr-xr-x. 8 dlindner dlindner  126 Jul 31 14:08 0
drwxr-xr-x. 2 dlindner dlindner   76 Jul 31 14:08 OME

(test_env) [dlindner@pilot-zarr3-dev 056332bf08fbc3c3a93cb893674f85]$ resave.py  asterella_gracilis_swe_stature.ome.zarr v3/asterella_gracilis_swe_stature.ome.zarr

(test_env) [dlindner@pilot-zarr3-dev 056332bf08fbc3c3a93cb893674f85]$ ls -alh v3/asterella_gracilis_swe_stature.ome.zarr
total 4.0K
drwxr-xr-x. 2 dlindner dlindner 31 Jul 31 14:11 .
drwxr-xr-x. 3 dlindner dlindner 61 Jul 31 14:11 ..
-rw-r--r--. 1 dlindner dlindner 66 Jul 31 14:11 zarr.json

Unfortunately there isn't any other useful output.

[dominikl]

I added resave.py to my $PATH by linking it into my ~/bin directory:

(test_env) [dlindner@pilot-zarr3-dev 056332bf08fbc3c3a93cb893674f85]$ ls -lh ~/bin/
total 16K
lrwxrwxrwx. 1 dlindner dlindner  40 Jul 31 10:38 resave.py -> ../ome2024-ngff-challenge/dev2/resave.py

Maybe it doesn't like being called like that? But then I'd expect some kind of error output...

[joshmoore]

https://pypi.org/project/ome2024-ngff-challenge/ (v0.0.4) is now in place if you want to give it a try. I don't know that it's going to make much of a difference though.

[joshmoore]

#17 (>=0.0.5) should have taken care of this.