[python] Update Scene create method in the Python API

apis/python/src/tiledbsoma/_scene.py

@@ -6,6 +6,7 @@
 Implementation of a SOMA Scene
 """
 
+import warnings
 from typing import Any, List, Optional, Sequence, Tuple, Type, TypeVar, Union
 
 import somacore
@@ -17,9 +18,13 @@
 from typing_extensions import Self
 
 from . import _funcs, _tdb_handles
+from . import pytiledbsoma as clib
 from ._collection import CollectionBase
-from ._constants import SOMA_COORDINATE_SPACE_METADATA_KEY
-from ._exception import SOMAError
+from ._constants import (
+    SOMA_COORDINATE_SPACE_METADATA_KEY,
+    SPATIAL_DISCLAIMER,
+)
+from ._exception import SOMAError, map_exception_for_create
 from ._geometry_dataframe import GeometryDataFrame
 from ._multiscale_image import MultiscaleImage
 from ._point_cloud_dataframe import PointCloudDataFrame
@@ -32,6 +37,7 @@
 )
 from ._types import OpenTimestamp
 from .options import SOMATileDBContext
+from .options._soma_tiledb_context import _validate_soma_tiledb_context
 
 _spatial_element = Union[GeometryDataFrame, MultiscaleImage, PointCloudDataFrame]
 
@@ -97,16 +103,29 @@
         Lifecycle:
             Experimental.
         """
-        if coordinate_space is not None:
-            raise NotImplementedError(
-                "Setting the coordinate space on create is not yet implemented."
+        warnings.warn(SPATIAL_DISCLAIMER)
+
+        context = _validate_soma_tiledb_context(context)
+        try:
+            timestamp_ms = context._open_timestamp_ms(tiledb_timestamp)
+            clib.SOMAScene.create(
+                ctx=context.native_context,
+                uri=uri,
+                timestamp=(0, timestamp_ms),
             )
-        return super().create(
-            uri=uri,
-            platform_config=platform_config,
-            context=context,
-            tiledb_timestamp=tiledb_timestamp,
-        )
+            handle = cls._wrapper_type.open(uri, "w", context, tiledb_timestamp)
+            if coordinate_space is not None:
+                if not isinstance(coordinate_space, CoordinateSpace):
+                    coordinate_space = CoordinateSpace.from_axis_names(coordinate_space)
+                handle.meta[SOMA_COORDINATE_SPACE_METADATA_KEY] = (
+                    coordinate_space_to_json(coordinate_space)
+                )
+            return cls(
+                handle,
+                _dont_call_this_use_create_or_open_instead="tiledbsoma-internal-code",
+            )
+        except SOMAError as e:
+            raise map_exception_for_create(e, uri) from None
 
     def __init__(
         self,

apis/python/src/tiledbsoma/soma_collection.cc

@@ -76,8 +76,22 @@ void load_soma_collection(py::module& m) {
     py::class_<SOMAMeasurement, SOMACollection, SOMAGroup, SOMAObject>(
         m, "SOMAMeasurement");
 
-    py::class_<SOMAScene, SOMACollection, SOMAGroup, SOMAObject>(
-        m, "SOMAScene");
+    py::class_<SOMAScene, SOMACollection, SOMAGroup, SOMAObject>(m, "SOMAScene")
+        .def_static(
+            "create",
+            [](std::shared_ptr<SOMAContext> ctx,
+               std::string_view uri,
+               std::optional<TimestampRange> timestamp) {
+                try {
+                    SOMAScene::create(uri, ctx, timestamp);
+                } catch (const std::exception& e) {
+                    TPY_ERROR_LOC(e.what());
+                }
+            },
+            py::kw_only(),
+            "ctx"_a,
+            "uri"_a,
+            "timestamp"_a = py::none());
 
     py::class_<SOMAMultiscaleImage, SOMACollection, SOMAGroup, SOMAObject>(
         m, "SOMAMultiscaleImage");

apis/python/tests/test_scene.py

@@ -111,7 +111,39 @@ def test_measurement_with_var_scene(tmp_path):
     assert soma.DataFrame.exists(obs_scene_uri)
 
 
-def test_scene_coord_space(tmp_path):
+def test_scene_coord_space_at_create(tmp_path):
+    uri = tmp_path.as_uri()
+
+    coord_space = soma.CoordinateSpace(
+        [
+            soma.Axis(name="x"),
+            soma.Axis(name="y"),
+        ]
+    )
+    coord_space_json = """
+    [
+        {"name": "x", "unit": null},
+        {"name": "y", "unit": null}
+    ]
+    """
+
+    with soma.Scene.create(uri, coordinate_space=("x", "y")) as scene:
+
+        # Reserved metadata key should not be settable?
+        # with pytest.raises(soma.SOMAError):
+        #     scene.metadata["soma_coordinate_space"] = coord_space_json
+
+        scene.coordinate_space = coord_space
+        assert scene.coordinate_space == coord_space
+        assert json.loads(scene.metadata["soma_coordinate_space"]) == json.loads(
+            coord_space_json
+        )
+
+    with soma.Scene.open(uri) as scene:
+        assert scene.coordinate_space == coord_space
+
+
+def test_scene_coord_space_after_create(tmp_path):
     uri = tmp_path.as_uri()
 
     coord_space = soma.CoordinateSpace(

libtiledbsoma/src/soma/soma_scene.cc

@@ -46,30 +46,9 @@ void SOMAScene::create(
     std::optional<TimestampRange> timestamp) {
     try {
         std::filesystem::path scene_uri(uri);
-
-        SOMAGroup::create(ctx, scene_uri.string(), "SOMAScene", timestamp);
-        SOMACollection::create((scene_uri / "img").string(), ctx, timestamp);
-        SOMACollection::create((scene_uri / "obsl").string(), ctx, timestamp);
-        SOMACollection::create((scene_uri / "varl").string(), ctx, timestamp);
-
-        auto name = std::string(std::filesystem::path(uri).filename());
-        auto group = SOMAGroup::open(
-            OpenMode::write, scene_uri.string(), ctx, name, timestamp);
-        group->set(
-            (scene_uri / "img").string(),
-            URIType::absolute,
-            "img",
-            "SOMACollection");
-        group->set(
-            (scene_uri / "obsl").string(),
-            URIType::absolute,
-            "obsl",
-            "SOMACollection");
-        group->set(
-            (scene_uri / "varl").string(),
-            URIType::absolute,
-            "varl",
-            "SOMAColelction");
+        auto group = SOMAGroup::create(
+            ctx, scene_uri.string(), "SOMAScene", timestamp);
+        // TODO: Set extra metadata.
         group->close();
     } catch (TileDBError& e) {
         throw TileDBSOMAError(e.what());

libtiledbsoma/src/soma/soma_scene.h

@@ -51,7 +51,7 @@ class SOMAScene : public SOMACollection {
      *
      * @param uri URI to create the SOMAScene
      * @param schema TileDB ArraySchema
-     * @param platform_config Optional config parameter dictionary
+     * @param timestamp Optional pair indicating timestamp start and end
      */
     static void create(
         std::string_view uri,