diff --git a/tools/cellxgene_census_builder/pyproject.toml b/tools/cellxgene_census_builder/pyproject.toml index c7ab25b79..f48328f29 100644 --- a/tools/cellxgene_census_builder/pyproject.toml +++ b/tools/cellxgene_census_builder/pyproject.toml @@ -41,9 +41,9 @@ dependencies= [ # The compatibility matrix is defined here: # https://github.com/TileDB-Inc/TileDB/blob/dev/format_spec/FORMAT_SPEC.md # TODO (spatial): tiledbsoma pin to a PyPI release is temporarily commented out in favor git commit pin - # "tiledbsoma==1.9.3", + "tiledbsoma==1.15.3", # TODO (spatial): Pin tiledbsoma dependency to an actual released version after tiledbsoma spatial code has been released - "tiledbsoma @ git+https://github.com/single-cell-data/TileDB-SOMA.git@16467fa7405d59ab1763f103081318b839f87610#egg=tiledbsoma&subdirectory=apis/python/", + # "tiledbsoma @ git+https://github.com/single-cell-data/TileDB-SOMA.git@16467fa7405d59ab1763f103081318b839f87610#egg=tiledbsoma&subdirectory=apis/python/", # TODO (spatial): Deal with the following line before release "cellxgene-census @ {root:parent:parent:uri}/api/python/cellxgene_census", "cellxgene-ontology-guide>=1.2", diff --git a/tools/cellxgene_census_builder/src/cellxgene_census_builder/build_soma/consolidate.py b/tools/cellxgene_census_builder/src/cellxgene_census_builder/build_soma/consolidate.py index 2b3e5d68c..5137fe211 100644 --- a/tools/cellxgene_census_builder/src/cellxgene_census_builder/build_soma/consolidate.py +++ b/tools/cellxgene_census_builder/src/cellxgene_census_builder/build_soma/consolidate.py @@ -112,6 +112,9 @@ def list_uris_to_consolidate( else: n_columns = len(soma_obj.schema) n_fragments = len(tiledb.array_fragments(soma_obj.uri)) + # TODO: Consolidation for dense arrays is currently broken, tracked in https://github.com/single-cell-data/TileDB-SOMA/issues/3383 + if soma_obj.soma_type in ["SOMADenseNDArray", "SOMAPointCloudDataFrame"]: + continue uris.append( ConsolidationCandidate( uri=soma_obj.uri, soma_type=soma_obj.soma_type, n_columns=n_columns, n_fragments=n_fragments @@ -127,10 +130,6 @@ def _consolidate_array( consolidation_modes: list[str] | None = None, consolidation_config: dict[str, str] | None = None, ) -> None: - # TODO: Consolidation for dense arrays is currently broken, tracked in https://github.com/single-cell-data/TileDB-SOMA/issues/3383 - if obj.soma_type == "SOMADenseNDArray": - return - modes = consolidation_modes or ["fragment_meta", "array_meta", "commits", "fragments"] uri = obj.uri