failure in `get_anndata` when querying for tissue and cell type metadata
bug
## Describe the bug
the schema doesn't seem to match what is documented using `cellxgene-census==1.17.0`
## To Reproduce
this fails
```python
obs_filter=None
var_filter="tissue_general in ['brain', 'heart', 'lung'] and cell_type in ['neurons', 'glia'] and is_primary_data == True"
with cellxgene_census.open_soma(census_version="2025-01-30") as census:
adata = cellxgene_census.get_anndata(
census=census,
organism="Homo sapiens",
obs_value_filter=obs_filter,
var_value_filter=var_filter,
obs_column_names=["tissue", "tissue_general", "cell_type", "donor_id", "sex", "disease"],
)
print(data)
```
with error
```bash
tiledbsoma._exception.SOMAError: SOMAError: 'Column tissue_general does not exist in schema'
```
incidentally the [example from the doc](https://chanzuckerberg.github.io/cellxgene-census/cellxgene_census_docsite_quick_start.html#obtaining-a-slice-as-anndata) works (with the deprecation warning about `column_names`:
```python
with cellxgene_census.open_soma() as census:
adata = cellxgene_census.get_anndata(
census = census,
organism = "Homo sapiens",
var_value_filter = "feature_id in ['ENSG00000161798', 'ENSG00000188229']",
obs_value_filter = "sex == 'female' and cell_type in ['microglial cell', 'neuron']",
column_names = {"obs": ["assay", "cell_type", "tissue", "tissue_general", "suspension_type", "disease"]},
)
```
output of `print(adata)`:
```python
AnnData object with n_obs × n_vars = 796426 × 2
obs: 'assay', 'cell_type', 'tissue', 'tissue_general', 'suspension_type', 'disease', 'sex'
var: 'soma_joinid', 'feature_id', 'feature_name', 'feature_type', 'feature_length', 'nnz', 'n_measured_obs'
```
## Expected behavior
with `cellxgene-census==1.17.0` I expected the query to yield an AnnData object with obs metadata columns
```python
["tissue", "tissue_general", "cell_type", "donor_id", "sex", "disease"]
```
## Environment
- Machine: Apple Macbook Pro 16" Nov 2024
- OS: macOS Sequoia 15.5
- Software versions:
```bash
anndata 0.12.2
cellxgene-census 1.17.0
numba 0.61.2
numpy 2.2.6
pandas 2.3.1
pyarrow 18.1.0
scanpy 1.11.4
scipy 1.16.1
tiledbsoma 1.17.1
```
## Additional context
Add any other context about the problem here.
关闭于 2025-08-25 3 条评论