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Add some Zarr-based datatypes #19040
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as suggested by @bernt-matthias
This will go into a sub-datatype when needed.
This should probably go in sub-classes that expect specific directory structures.
Compressed (Upload) -> Directory (Unpack) -> Compressed (Download)
- Rename generic to ZarrDirectory - Detect Zarr version in metadata - Add zarr.zip datatype
…older and metadata file
…file Instead of the default behavior of downloading an empty file.
Should help when opening the Zarr ZipStore if there is compression involved
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Requires #17614
Includes the following datatypes:
General Zarr datatypes
CompressedZarrZipArchive
(zarr.zip
): represents a Zarr ZipStore. It seems to have some limitations (i.e. doesn't behave exactly like a DirectoryStore) or I couldn't make it work 100% but it might be useful in some cases.ZarrDirectory
(zarr
): represents a Zarr DirectoryStore. Contains the zarr structure in theextra_files_path
of the dataset. I wonder if there is a way to make the "main" dataset to really point to the actual root folder in extra_files like a symlink or something like this, but I don't know if this really makes sense.ZarrRemoteUri
(zarr_uri
): represents a remote URI to a Zarr store. I'm not sure this is the best way to handle this, and it feels more like a "wonky workaround". It is just a text file with the URL (without the protocol, otherwise Galaxy will try to download it as a pasted URL) pointing to a remote S3 containing a zarr store (some examples can be obtained here https://www.openmicroscopy.org/2020/11/04/zarr-data.html). Obviously, this might not work if authentication is involved, etc. So there must be a better option to handle those.OME-Zarr datatypes
CompressedOMEZarrZipArchive
(ome_zarr.zip
): Similar to CompressedZarrZipArchive but expects to find anOME/METADATA.ome.xml
file in the store root so it can be easily converted/extracted to anOMEZarr
directory.OMEZarr
(ome_zarr
): Similar to ZarrDirectory but identify this datatype as an OME Zarr image.OMEZarrRemoteUri
(ome_zarr_uri
): A subclass of ZarrRemoteUri just to be specific about this uri being an OME-Zarr remote uri.How to test the changes?
Edit Attributes
then select theDatatypes
section and convert it tozarr
.uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr
. Notice there is no protocol (https://). You can find more examples here.zarr_uri
orome_zar_uri
or set it in the upload.License