more

apis/python/src/tiledbsc/raw_group.py

@@ -35,10 +35,14 @@ def __init__(
         super().__init__(uri=uri, name=name, parent=parent)
         self.parent_obs = obs
 
-        X_uri = self._get_child_uri("X")  # See comments in that function
-        var_uri = self._get_child_uri("var")
-        varm_uri = self._get_child_uri("varm")
-        varp_uri = self._get_child_uri("varp")
+        # TODO: COMMENT
+        member_names = ["X", "var", "varm", "varp"]
+        child_uris = self._get_child_uris(member_names)  # See comments in that function
+
+        X_uri = child_uris["X"]  # See comments in that function
+        var_uri = child_uris["var"]
+        varm_uri = child_uris["varm"]
+        varp_uri = child_uris["varp"]
 
         self.var = AnnotationDataFrame(uri=var_uri, name="var", parent=self)
         self.X = AssayMatrixGroup(

apis/python/src/tiledbsc/soma_collection.py

@@ -162,6 +162,9 @@ def __getitem__(self, name: str) -> Optional[SOMA]:
         Returns a `SOMA` element at the given name within the group, or `None` if no such
         member exists.  Overloads the `[...]` operator.
         """
+        if name in self._somas:
+            return self._somas[name]
+
         with self._open("r") as G:
             try:
                 obj = G[name]  # This returns a tiledb.object.Object.

apis/python/src/tiledbsc/tiledb_group.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import Dict, Optional, Sequence, List
+from typing import Dict, Optional, Sequence
 import time
 
 import tiledb
@@ -90,7 +90,7 @@ def _open(self, mode: str = "r") -> tiledb.Group:
         return tiledb.Group(self.uri, mode=mode, ctx=self._ctx)
 
     # XXX COMMENT
-    def _get_child_uris(self, member_names: List[str]) -> Dict[str, str]:
+    def _get_child_uris(self, member_names: Sequence[str]) -> Dict[str, str]:
         """
         Computes the URI for a child of the given object. For local disk, S3, and
         tiledb://.../s3://...  pre-creation URIs, this is simply the parent's URI, a slash, and the

apis/python/src/tiledbsc/uns_group.py

@@ -143,8 +143,10 @@ def from_anndata_uns(self, uns: Mapping[str, Any]) -> None:
         # Must be done first, to create the parent directory
         self.create_unless_exists()
 
+        child_uris = self._get_child_uris(list(uns.keys()))  # See comments in that function
+
         for key in uns.keys():
-            component_uri = self._get_child_uri(key)  # See comments in that function
+            component_uri = child_uris[key]  # See comments in that function
             value = uns[key]
 
             if key == "rank_genes_groups":