Fix from_visium to use Scene class and _factory to read Scene

single-cell-data · Apr 25, 2024 · dda6862 · dda6862
1 parent 36d9c1e
commit dda6862
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/apis/python/src/tiledbsoma/_factory.py b/apis/python/src/tiledbsoma/_factory.py
@@ -28,6 +28,7 @@
     _dense_nd_array,
     _experiment,
     _measurement,
+    _scene,
     _sparse_nd_array,
     _tdb_handles,
     _tiledb_object,
@@ -219,12 +220,13 @@ def _type_name_to_cls(type_name: str) -> Type[AnyTileDBObject]:
             _experiment.Experiment,
             _measurement.Measurement,
             _sparse_nd_array.SparseNDArray,
+            _scene.Scene,
         )
     }
     try:
         return type_map[type_name.lower()]
     except KeyError as ke:
-        options = sorted(type_map)
+        _options = sorted(type_map)
         raise SOMAError(
-            f"{type_name!r} is not a recognized SOMA type; expected one of {options}"
+            f"{type_name!r} is not a recognized SOMA type; expected one of {_options}"
         ) from ke
diff --git a/apis/python/src/tiledbsoma/experimental/ingest.py b/apis/python/src/tiledbsoma/experimental/ingest.py
@@ -153,9 +153,7 @@ def from_visium(
                 experiment, "spatial", spatial, use_relative_uri=use_relative_uri
             )
             scene_uri = f"{spatial_uri}/{scene_name}"
-            with _create_or_open_collection(
-                Collection[Collection[AnyTileDBObject]], scene_uri, **ingest_ctx
-            ) as scene:
+            with _create_or_open_collection(Scene, scene_uri, **ingest_ctx) as scene:
                 _maybe_set(
                     spatial, scene_name, scene, use_relative_uri=use_relative_uri
                 )