lint

apis/python/src/tiledbsc/soma_collection.py

@@ -132,7 +132,6 @@ def __iter__(self) -> Iterator[SOMA]:
                 self._somas[name] = SOMA(uri=uri, name=name, parent=self, ctx=self._ctx)
             yield self._somas[name]
 
-
     # ----------------------------------------------------------------
     def __contains__(self, name: str) -> bool:
         """

apis/python/src/tiledbsc/tiledb_group.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 from typing import Dict, Optional, Sequence
-import time
 
 import tiledb
 
@@ -16,6 +15,7 @@ class TileDBGroup(TileDBObject):
     Wraps groups from TileDB-Py by retaining a URI, options, etc.
     """
 
+    _cached_exists: bool
     _cached_member_names_to_uris: Dict[str, str]
 
     def __init__(
@@ -33,6 +33,7 @@ def __init__(
         See the TileDBObject constructor.
         """
         super().__init__(uri, name, parent=parent, soma_options=soma_options, ctx=ctx)
+        self._cached_exists = None
         self._cached_member_names_to_uris = None
 
     def exists(self) -> bool:
@@ -41,7 +42,12 @@ def exists(self) -> bool:
         object has not yet been populated, e.g. before calling `from_anndata` -- or, if the
         SOMA has been populated but doesn't have this member (e.g. not all SOMAs have a `varp`).
         """
-        return bool(tiledb.object_type(self.uri, ctx=self._ctx) == "group")
+        # TODO: NOTE WHAT IF VFS.DELETE AFTER INSTANTIATION
+        if self._cached_exists is None:
+            self._cached_exists = bool(
+                tiledb.object_type(self.uri, ctx=self._ctx) == "group"
+            )
+        return self._cached_exists
 
     def create_unless_exists(self) -> None:
         """
@@ -83,6 +89,7 @@ def _open(self, mode: str = "r") -> tiledb.Group:
         This is just a convenience wrapper around tiledb group-open.
         It works asa `with self._open() as G:` as well as `G = self._open(); ...; G.close()`.
         """
+        print("OPEN", self.uri)
         assert mode in ("r", "w")
         if mode == "r" and not self.exists():
             raise Exception(f"Does not exist: {self.uri}")
@@ -181,8 +188,7 @@ def _add_object(self, obj: TileDBObject, relative: Optional[bool] = None) -> Non
             child_uri = obj.name
         self._cached_member_names_to_uris = None  # invalidate
         with self._open("w") as G:
-            retval = G.add(uri=child_uri, relative=relative, name=obj.name)
-            #####print("RETVAL ", retval)
+            G.add(uri=child_uri, relative=relative, name=obj.name)
         # See _get_child_uri. Key point is that, on TileDB Cloud, URIs change from pre-creation to
         # post-creation. Example:
         # * Upload to pre-creation URI tiledb://namespace/s3://bucket/something/something/somaname
@@ -191,7 +197,6 @@ def _add_object(self, obj: TileDBObject, relative: Optional[bool] = None) -> Non
         # * Member pre-creation URI tiledb://namespace/s3://bucket/something/something/somaname/obs
         # * Member post-creation URI tiledb://somaname/e4de581a-1353-4150-b1f4-6ed12548e497
         obj.uri = self._get_child_uri(obj.name)
-        ####print("REMAP", child_uri, "TO", obj.uri)
 
     def _remove_object(self, obj: TileDBObject) -> None:
         self._remove_object_by_name(obj.name)
@@ -231,6 +236,7 @@ def _get_member_names_to_uris(self) -> Dict[str, str]:
         if self._cached_member_names_to_uris is None:
             with self._open("r") as G:
                 self._cached_member_names_to_uris = {obj.name: obj.uri for obj in G}
+                print("GMN2U", self.uri)
         return self._cached_member_names_to_uris
 
     def show_metadata(self, recursively: bool = True, indent: str = "") -> None:

apis/python/src/tiledbsc/uns_group.py

@@ -143,7 +143,9 @@ 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
+        child_uris = self._get_child_uris(
+            list(uns.keys())
+        )  # See comments in that function
 
         for key in uns.keys():
             component_uri = child_uris[key]  # See comments in that function

apis/python/tools/ingestor

@@ -231,6 +231,8 @@ def ingest_one(
                     f"Already exists; replacing: {output_path}"
                 )
                 shutil.rmtree(output_path)  # Overwrite
+                # TODO: COMMENT
+                soma = tiledbsc.SOMA(uri=output_path, soma_options=soma_options)
             else:
                 raise Exception(
                     "Internal coding error in --ifexists handling.", ifexists, "<"