From c221799fccc8ccf4674530b34a67522111620a75 Mon Sep 17 00:00:00 2001 From: Emanuele Bezzi Date: Wed, 28 Feb 2024 13:27:31 -0800 Subject: [PATCH] Feedback --- .../src/cellxgene_census/_get_anndata.py | 10 ++++++++-- tools/census_contrib/src/census_contrib/metadata.py | 6 +++--- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/api/python/cellxgene_census/src/cellxgene_census/_get_anndata.py b/api/python/cellxgene_census/src/cellxgene_census/_get_anndata.py index 03c155063..6ce220807 100644 --- a/api/python/cellxgene_census/src/cellxgene_census/_get_anndata.py +++ b/api/python/cellxgene_census/src/cellxgene_census/_get_anndata.py @@ -28,6 +28,8 @@ def get_anndata( var_value_filter: Optional[str] = None, var_coords: Optional[SparseDFCoord] = None, column_names: Optional[soma.AxisColumnNames] = None, + add_obs_embeddings: Optional[Sequence[str]] = (), + add_var_embeddings: Optional[Sequence[str]] = (), ) -> anndata.AnnData: """Convenience wrapper around :class:`tiledbsoma.Experiment` query, to build and execute a query, and return it as an :class:`anndata.AnnData` object. @@ -59,10 +61,14 @@ def get_anndata( Columns to fetch for ``obs`` and ``var`` dataframes. obsm_layers: Additional obsm layers to read and return in the ``obsm`` slot. - Use :func:`get_all_available_embeddings` to retrieve available embeddings - for this Census version and organism. varm_layers: Additional varm layers to read and return in the ``varm`` slot. + add_obs_embeddings: + Embeddings to be returned as part of the ``obsm`` slot. + Use :func:`get_all_available_embeddings` to retrieve available embeddings + for this Census version and organism. + add_var_embeddings: + Embeddings to be returned as part of the ``varm`` slot. Use :func:`get_all_available_embeddings` to retrieve available embeddings for this Census version and organism. diff --git a/tools/census_contrib/src/census_contrib/metadata.py b/tools/census_contrib/src/census_contrib/metadata.py index 280d5ca2f..faae70363 100644 --- a/tools/census_contrib/src/census_contrib/metadata.py +++ b/tools/census_contrib/src/census_contrib/metadata.py @@ -119,7 +119,7 @@ def validate_metadata(args: Arguments, metadata: EmbeddingMetadata) -> Embedding 4. All supplied URLs must resolve 5. Title must have length < 128 characters 6. Description must have length < 2048 characters - 7. Name must have length < 24 characters + 7. Name must have length < 128 characters """ if not metadata.id: raise ValueError("metadata is missing 'id' (accession)") @@ -142,8 +142,8 @@ def validate_metadata(args: Arguments, metadata: EmbeddingMetadata) -> Embedding "Metadata: description must be string between 1 and {MAX_DESCRIPTION_LENGTH} characters in length", ) - # 7. Name must have length < 24 characters - MAX_NAME_LENGTH = 24 + # 7. Name must have length < 128 characters + MAX_NAME_LENGTH = 128 if not metadata.name or len(metadata.name) > MAX_NAME_LENGTH: raise ValueError( f"Metadata: name must be string between 1 and {MAX_NAME_LENGTH} characters in length",