Add tables to metadata

[tcompa]

As per ome/ngff#64, there should be a tables key in .../tables/.zattrs.

# The tables group is a container which holds one or multiple tables that are compatible with AnnData.
        |
        │                     # The tables group MAY be in the root of the zarr file.
        ├── .zgroup           # The tables group MAY be in root or in another group.
        |
        ├── .zattrs           # .zattrs MUST contain "tables", which lists the keys of the subgroups that are tables. In this case, the only table is "my_table".
                              # hence .zattrs should be equal to { "tables": [ "my_table" ] }.
        |
        └── my_table
            │                     # The table group MAY be in the root of the zarr file.
            ├── .zgroup           # The table group MAY be in root or in another group.
            |
            ├── .zattrs           # .zattrs MUST contain "type", which is set to "ngff:region_table"
            |                     # .zattrs MUST contain "region", which is the path to the data the table is annotating.
            |                     # "region" MUST be a single path (single region) or an array of paths (multiple regions).
            |                     # "region" paths MUST be objects with a key "path" and the path value MUST be a string.
            |                     # .zattrs MUST contain "region_key" if "region" is an array. "region_key" is the key in obs denoting which region a given row corresponds to.
            |                     # .zattrs MAY contain "instance_key", which is the key in obs that denotes which instance in "region" the row corresponds to. If "instance_key" is not provided, the values from the obs .zattrs "_index" key is used.
            │
            ├── X                 # You MAY add an zarr array X.
            │   │                 # X MUST not be a complex type (i.e., MUST be a single type)
            │   │                 # X MAY be chunked as the user desires.
            │   ├── .zarray
            │   ├── 0.0
            │   │   ...
            │   └── n.m

[jluethi]

Let's also check whether with the current writer we use we get the relevant metadata in the obs & var folders etc :)

[tcompa]

Let's also check whether with the current writer we use we get the relevant metadata in the obs & var folders etc :)

We currently write anndata tables to disk via the anndata.experimental.write_elem function, which does not handle anything but the table - as far as I understand.
At the moment, I'm adding the OME-NGFF metadata by hand, acting on the zarr attrs objects. This can look like

        # (1) DEFINE ZARR GROUP
        group_tables = zarr.group(f"{in_path}/{component}/tables/")

        # (2) WRITE ANNDATA TABLE
        write_elem(group_tables, bounding_box_ROI_table_name, bbox_table)

        # (3) WRITE OME-NGFF METADATA
        if "tables" in group_tables.attrs.keys():   # FIXME: simplify this if/else
            current_tables = group_tables.attrs["tables"]
        else:
            current_tables = []
        if bounding_box_ROI_table_name in current_tables:  # FIXME: move this check to an earlier stage of the task
            raise ValueError(
                f"{in_path}/{component}/tables/ already includes "
                f"{bounding_box_ROI_table_name=} in {current_tables=}"
            )
        new_tables = current_tables + [bounding_box_ROI_table_name]
        group_tables.attrs["tables"] = new_tables

If we need to add zarr attrs for other hierarchy levels (e.g. inside obs or var), the simplest way would be to proceed in the same way, that is, by opening the right zarr group and acting on its attrs.

It seems to me that the anndata write_elem function does not mention anything related to writing zarr attrs.

[jluethi]

Ok. Let's see if ome-zarr-py comes up with useful wrappers for table writing and otherwise, once the spec is fully defined, manually write those .zattrs :)