When using TableModel.parse, region_key must be provided.

[yedeer12]

I want to use TableModel.parse to parse the whole anndata, I set region=None, region_key=None, instance_key=None. But there is an error says region_key must be provided. Could I combine the anndata and spatialdata without region and region_key?

[giovp]

hi @yedeer12 ,

no you can't, spatialdata assumes that when a table it's present, it annotates a region element (shapes, labels).

We are working toward building a converter for anndata to spatialdata for anndata that are already available. pinging @LLehner who is working on it.

[EliHei2]

Related to this, @giovp, if one plug in an anndata as the table using sd.TableModel.parse if the region_key column is not existing in the .obs the function does not return an error, while if one save the whole SpatialData object and try to reload it, they will receive the following error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/e915i/.conda/envs/py39/lib/python3.9/site-packages/spatialdata/_io/io_zarr.py", line 85, in read_zarr
    sdata = SpatialData(
  File "/home/e915i/.conda/envs/py39/lib/python3.9/site-packages/spatialdata/_core/spatialdata.py", line 161, in __init__
    Table_s.validate(table)
  File "/home/e915i/.conda/envs/py39/lib/python3.9/site-packages/spatialdata/models/models.py", line 644, in validate
    raise ValueError(f"`{attr[self.REGION_KEY_KEY]}` not found in `adata.obs`.")
ValueError: `None` not found in `adata.obs`.

I used the defaults (hence region_key=None)

I suggest either assert this in the TableModel.parse or write or drop the assert in read_zarr.

[LucaMarconato]

Thanks @EliHei2, I think we should assert it in TableModel.parse().

[LucaMarconato]

Now with #455, we support multiple tables and also tables that are not associated with any set of geometries (i.e. region_key not provided).