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🎨 Self-contained definition of CellxGene
schema
#2412
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laminlabs/cellxene
via using_key
to CellxGene
Curator
laminlabs/cellxene
via using_key
to CellxGene
Curator
laminlabs/cellxgene
via using_key
to CellxGene
Curator
falexwolf
commented
Feb 1, 2025
lamindb/curators/__init__.py
Outdated
) | ||
len(nonval_keys) | ||
# throwing an error here is problematic because my dataset might have missing columns | ||
# and I still want to define sources mappings on the Curator level |
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I don't know who wrote this, so FYI @Zethson @sunnyosun -- I don't think this makes sense for the reason defined in the comment
We definitely want to be able to pass datasets with missing columns to the Curator constructor without raising an error
laminlabs/cellxgene
via using_key
to CellxGene
Curator
CellxGene
schema / validation constraints
This was referenced Feb 1, 2025
CellxGene
schema / validation constraintsCellxGene
schema
This was referenced Feb 2, 2025
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Is part of a sequence of PRs that refactors the curators:
CatCurator
#2413PertCurator
fromwetlab
here and addCellxGene
Curator
test #2408CellxGene
Curator
fromcellxgene-lamin
here #2403DataFrameCurator
#2388This PR simplifies the definition of constraints to validate against the CxG schema:
using_key
parameter toAnnDataCurator
.CellxGeneAnnDataCurator
class.It also brings down the run time of the CxG test further down from 50s to 20s:
Collateral:
_check_valid_keys()
utils function because throwing an error upon Curator init upon missing columns/features is problematic: we do want to be able to validate datasets with missing columns and then receive this as a SchemaError during.validate()
. This is a common type of error.Feature
,ULabel
&Schema
to now includetype
andis_type
.