Unsupported SOMA object encoding version 1.1.0

[inestm28]

Hi,

Until around 17th January the 'latest' version of the API was working for me, but now it's not...

When I run

with cellxgene_census.open_soma(census_version='latest') as census:
    adata = cellxgene_census.get_anndata(
        census = census,
        organism = "Homo sapiens",
        var_value_filter = f"feature_name in ['NLRP3', 'TACR2', 'GLP1R', 'GIPR']",
        obs_value_filter = f"dataset_version_id == '982952fb-dee0-4498-a072-3dc498b06aae' and disease in ['normal', 'Alzheimer disease']",)

it gives me this error:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
File Untitled-1:5
      2 import cellxgene_census
      3 import pandas as pd
----> 5 with cellxgene_census.open_soma(census_version='latest') as census:
      6     adata = cellxgene_census.get_anndata(
      7         census = census,
      8         organism = "Homo sapiens",
      9         var_value_filter = f"feature_name in ['NLRP3', 'TACR2', 'GLP1R', 'GIPR']",
     10         obs_value_filter = f"dataset_version_id == '982952fb-dee0-4498-a072-3dc498b06aae' and disease in ['normal', 'Alzheimer disease']",)

File ~/miniconda3/envs/census_env/lib/python3.10/site-packages/cellxgene_census/_open.py:260, in open_soma(census_version, mirror, uri, tiledb_config, context)
    252     api_logger.info(
    253         f"The \"{census_version}\" release is currently {description['release_build']}. Specify "
    254         f"'census_version=\"{description['release_build']}\"' in future calls to open_soma() to ensure data "
    255         "consistency."
    256     )
    258 locator = _resolve_census_locator(description["soma"], selected_mirror)
--> 260 return _open_soma(locator, context)

File ~/miniconda3/envs/census_env/lib/python3.10/site-packages/cellxgene_census/_open.py:85, in _open_soma(locator, context)
     82 if locator["provider"] == "S3":
     83     context = context.replace(tiledb_config={"vfs.s3.region": locator.get("region")})
---> 85 return soma.open(locator["uri"], mode="r", soma_type=soma.Collection, context=context)
...
    203 if encoding_version != SOMA_ENCODING_VERSION:
--> 204     raise ValueError(f"Unsupported SOMA object encoding version {encoding_version}")
    206 return obj_type

ValueError: Unsupported SOMA object encoding version 1.1.0

I have done this and it still does not work:
pip install --upgrade cellxgene-census

but the versions seem to be upgraded in my census:

version_directory = cellxgene_census.get_census_version_directory()
data = [(key, value['release_build']) for key, value in version_directory.items()]
df = pd.DataFrame(data, columns=["Version", "Release Build"])
df

	Version	Release Build
0	stable	2024-07-01
1	latest	2025-01-21
2	2025-01-21	2025-01-21
3	2025-01-15	2025-01-15
4	2025-01-06	2025-01-06
5	2024-12-23	2024-12-23
6	2024-12-16	2024-12-16
7	2024-12-10	2024-12-10
8	2024-07-01	2024-07-01
9	2024-05-20	2024-05-20
10	2023-12-15	2023-12-15
11	2023-07-25	2023-07-25
12	2023-05-15	2023-05-15

could you help me, please?
Kind regards,
Inês

[johnkerl]

cc @ivirshup @jp-dark

[jp-dark]

Does upgrading the TileDB-SOMA version help?

pip install --upgrade tiledbsoma

[inestm28]

Upgrading the TileDB-SOMA worked! Thank you very much!!