fix consolidation for point cloud and dense arrays

chanzuckerberg · Jan 11, 2025 · 3fe22e8 · 3fe22e8
1 parent 196f11a
commit 3fe22e8
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Showing 2 changed files with 5 additions and 6 deletions.
diff --git 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
@@ -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