Closed will-moore closed 3 months ago
To test:
pip install git+https://github.com/IDR/omero-mkngff.git@refs/pull/17/head
As omero-server, delete the manually created bfoptions for idr0025
bash-4.2$ rm /data/OMERO/ManagedRepository/demo_2/2017-03/13/15-19-51.590_mkngff/52304cdf-4eba-4f0a-84b1-690e0d66add9.zarr.bfoptions
bash-4.2$
bash-4.2$ rm /data/OMERO/ManagedRepository/demo_2/2017-03/17/15-15-54.747_mkngff/72cc291b-a4e0-4807-bd23-22e9ad75c0dd.zarr.bfoptions
bash-4.2$ cat /data/OMERO/ManagedRepository/demo_2/2017-03/13/15-26-46.818_mkngff/3c534b4f-12be-4881-a84a-af6b65e142ea.zarr.bfoptions
omezarr.list_pixels=false
omezarr.quick_read=true
omezarr.alt_store=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD846/3c534b4f-12be-4881-a84a-af6b65e142ea/3c534b4f-12be-4881-a84a-af6b65e142ea.zarr
bash-4.2$
bash-4.2$ rm !$
rm /data/OMERO/ManagedRepository/demo_2/2017-03/13/15-26-46.818_mkngff/3c534b4f-12be-4881-a84a-af6b65e142ea.zarr.bfoptions
Then create again with omero-mkngff...
git clone https://github.com/IDR/mkngff_upgrade_scripts.git
cd ngff_filesets
export IDRID=idr0025
for r in $(cat $IDRID.csv); do
biapath=$(echo $r | cut -d',' -f2)
uuid=$(echo $biapath | cut -d'/' -f2)
fsid=$(echo $r | cut -d',' -f3 | tr -d '[:space:]')
omero mkngff symlink /data/OMERO/ManagedRepository $fsid "/bia-integrator-data/$biapath/$uuid.zarr" --bfoptions --clientpath="https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/$biapath/$uuid.zarr"
done
...
Checking for prefix_dir /data/OMERO/ManagedRepository/demo_2/2017-03/17/15-15-54.747
write bfoptions to: /data/OMERO/ManagedRepository/demo_2/2017-03/17/15-15-54.747_mkngff/72cc291b-a4e0-4807-bd23-22e9ad75c0dd.zarr.bfoptions
Check bfoptions...
(venv3) bash-4.2$ cat /data/OMERO/ManagedRepository/demo_2/2017-03/17/15-15-54.747_mkngff/72cc291b-a4e0-4807-bd23-22e9ad75c0dd.zarr.bfoptions
omezarr.list_pixels=false
omezarr.quick_read=true
omezarr.alt_store=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD846/72cc291b-a4e0-4807-bd23-22e9ad75c0dd/72cc291b-a4e0-4807-bd23-22e9ad75c0dd.zarr
Looks good.
@joshmoore - This is working at https://github.com/IDR/idr-metadata/issues/675#issuecomment-2050137532 and ready to be reviewed, thx.
This is now conflicting
Changes generally look good. If we ever decide to move this outside of IDR, we probably want a round of refactoring, but once the conflict is fixed, :+1:
@joshmoore - Good to merge now? Thanks (I can't merge)
@joshmoore - Good to merge now? Thanks (I can't merge)
Should work now. Merging.
Fixes #15.
Add support for adding the
clientpath
as theomezarr.alt_store
to the bfoptions file created beside the symlink.See https://github.com/ome/ZarrReader/pull/82