When using TableModel.parse, region_key must be provided. #306

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1. giovp commented on Jun 22, 2023

   

   giovp

   on Jun 22, 2023

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   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.
2. EliHei2 commented on Jun 27, 2023

   

   EliHei2

   on Jun 27, 2023

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   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.
3. LucaMarconato commented on Jun 28, 2023

   

   LucaMarconato

   on Jun 28, 2023

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

   added

   element: table 📑

   on Jan 25, 2024
5. LucaMarconato commented on Feb 22, 2024

   

   LucaMarconato

   on Feb 22, 2024

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   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).
6. LucaMarconato

   linked a pull request that will close this issuemulti table support #455on Feb 22, 2024
7. melonora

   closed this as completedin #455on Mar 14, 2024