Use SOMAContext in SparseNDArray

single-cell-data · Feb 23, 2024 · e60bb37 · e60bb37
1 parent 0ec160a
commit e60bb37
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Showing 4 changed files with 10 additions and 5 deletions.
diff --git a/apis/python/src/tiledbsoma/_sparse_nd_array.py b/apis/python/src/tiledbsoma/_sparse_nd_array.py
@@ -161,8 +161,11 @@ def read(
         self._check_open_read()
         _util.check_unpartitioned(partitions)
 
-        config = handle.config().copy()
-        config.update(platform_config or {})
+        context = handle.context()
+        if platform_config is not None:
+            config = context.tiledb_config.copy()
+            config.update(platform_config or {})
+            context = clib.SOMAContext(config)
 
         ts = None
         if handle.timestamp is not None:
@@ -171,7 +174,7 @@ def read(
         sr = clib.SOMASparseNDArray.open(
             uri=handle.uri,
             mode=clib.OpenMode.read,
-            platform_config=config,
+            context=context,
             column_names=[],
             result_order=_util.to_clib_result_order(result_order),
             timestamp=ts,

diff --git a/apis/python/src/tiledbsoma/_tdb_handles.py b/apis/python/src/tiledbsoma/_tdb_handles.py
@@ -74,6 +74,8 @@ def open(
         return DataFrameWrapper._from_soma_object(soma_object, context)
     elif open_mode == clib.OpenMode.read and obj_type == "SOMADenseNDArray":
         return DenseNDArrayWrapper._from_soma_object(soma_object, context)
+    elif open_mode == clib.OpenMode.read and obj_type == "SOMASparseNDArray":
+        return SparseNDArrayWrapper._from_soma_object(soma_object, context)
 
     if obj_type in (
         "SOMADataFrame",

diff --git a/apis/python/src/tiledbsoma/_tiledb_object.py b/apis/python/src/tiledbsoma/_tiledb_object.py
@@ -42,7 +42,7 @@ class TileDBObject(somacore.SOMAObject, Generic[_WrapperType_co]):
     """Class variable of the Wrapper class used to open this object type."""
     _wrapper_type: Type[_WrapperType_co]
     _reader_wrapper_type: Union[
-        Type[_WrapperType_co], Type[_tdb_handles.DataFrameWrapper]
+        Type[_WrapperType_co], Type[_tdb_handles.SOMAArrayWrapper]
     ]
 
     __slots__ = ("_close_stack", "_handle")

diff --git a/apis/python/src/tiledbsoma/soma_sparse_ndarray.cc b/apis/python/src/tiledbsoma/soma_sparse_ndarray.cc
@@ -60,7 +60,7 @@ void load_soma_sparse_ndarray(py::module &m) {
             std::optional<std::pair<uint64_t, uint64_t>>>(&SOMASparseNDArray::open),
         "uri"_a,
         "mode"_a,
-        "ctx"_a,
+        "context"_a,
         py::kw_only(),
         "column_names"_a = py::none(),
         "result_order"_a = ResultOrder::automatic,