lamindb 0.74.1__py3-none-any.whl → 0.74.2__py3-none-any.whl

lamindb/core/storage/_backed_access.py

@@ -28,6 +28,8 @@ if TYPE_CHECKING:
     from pathlib import Path
 
     from fsspec.core import OpenFile
+    from tiledbsoma import Collection as SOMACollection
+    from tiledbsoma import Experiment as SOMAExperiment
 
 anndata_version_parse = version.parse(anndata_version)
 
@@ -100,7 +102,7 @@ def _records_to_df(obj):
         return obj
 
 
-class AccessRegistry:
+class AccessRecord:
     def __init__(self):
         self._registry = {}
         self._openers = {}
@@ -141,7 +143,7 @@ class AccessRegistry:
 
 
 # storage specific functions should be registered and called through the registry
-registry = AccessRegistry()
+registry = AccessRecord()
 
 
 @registry.register_open("h5py")
@@ -207,8 +209,10 @@ def safer_read_partial(elem, indices):
             try:
                 ds = CSRDataset(elem)
                 result = _subset_sparse(ds, indices)
-            except Exception:
-                pass
+            except Exception as e:
+                logger.debug(
+                    f"Encountered an exception while attempting to subset a sparse dataset by indices.\n{e}"
+                )
         if result is None:
             raise ValueError(
                 "Can not get a subset of the element of type"
@@ -305,8 +309,10 @@ if ZARR_INSTALLED:
                 try:
                     ds = CSRDataset(elem)
                     return _subset_sparse(ds, indices)
-                except Exception:
-                    pass
+                except Exception as e:
+                    logger.debug(
+                        f"Encountered an exception while attempting to subset a sparse dataset by indices.\n{e}"
+                    )
             raise ValueError(
                 "Can not get a subset of the element of type"
                 f" {type(elem).__name__} with an empty spec."
@@ -734,24 +740,62 @@ class BackedAccessor:
 
 def backed_access(
     artifact_or_filepath: Artifact | Path, using_key: str | None = None
-) -> AnnDataAccessor | BackedAccessor:
+) -> AnnDataAccessor | BackedAccessor | SOMACollection | SOMAExperiment:
     if isinstance(artifact_or_filepath, Artifact):
         filepath = filepath_from_artifact(artifact_or_filepath, using_key=using_key)
     else:
         filepath = artifact_or_filepath
     name = filepath.name
+    suffix = filepath.suffix
+
+    if name == "soma" or suffix == ".tiledbsoma":
+        try:
+            import tiledbsoma as soma
+        except ImportError as e:
+            raise ImportError(
+                "Please install tiledbsoma: pip install tiledbsoma"
+            ) from e
+        filepath_str = filepath.as_posix()
+        if filepath.protocol == "s3":
+            from lamindb_setup.core._settings_storage import get_storage_region
+
+            region = get_storage_region(filepath_str)
+            tiledb_config = {"vfs.s3.region": region}
+            storage_options = filepath.storage_options
+            if "key" in storage_options:
+                tiledb_config["vfs.s3.aws_access_key_id"] = storage_options["key"]
+            if "secret" in storage_options:
+                tiledb_config["vfs.s3.aws_secret_access_key"] = storage_options[
+                    "secret"
+                ]
+            if "token" in storage_options:
+                tiledb_config["vfs.s3.aws_session_token"] = storage_options["token"]
+            ctx = soma.SOMATileDBContext(tiledb_config=tiledb_config)
+            # this is a strange bug
+            # for some reason iterdir futher gives incorrect results
+            # if cache is not invalidated
+            # instead of obs and ms it gives ms and ms in the list of names
+            filepath.fs.invalidate_cache()
+        else:
+            ctx = None
 
-    if filepath.suffix in (".h5", ".hdf5", ".h5ad"):
+        soma_objects = [obj.name for obj in filepath.iterdir()]
+        if "obs" in soma_objects and "ms" in soma_objects:
+            SOMAType = soma.Experiment
+        else:
+            SOMAType = soma.Collection
+        return SOMAType.open(filepath_str, context=ctx)
+    elif suffix in {".h5", ".hdf5", ".h5ad"}:
         conn, storage = registry.open("h5py", filepath)
-    elif filepath.suffix == ".zarr":
+    elif suffix == ".zarr":
         conn, storage = registry.open("zarr", filepath)
     else:
         raise ValueError(
-            "object should have .h5, .hdf5, .h5ad, .zarr suffix, not"
-            f" {filepath.suffix}."
+            "object should have .h5, .hdf5, .h5ad, .zarr, .tiledbsoma suffix, not"
+            f" {suffix}."
         )
 
-    if filepath.suffix == ".h5ad":
+    if suffix == ".h5ad":
         return AnnDataAccessor(conn, storage, name)
     else:
         if get_spec(storage).encoding_type == "anndata":

lamindb/core/storage/paths.py

@@ -47,7 +47,7 @@ def auto_storage_key_from_artifact(artifact: Artifact):
 
 
 def auto_storage_key_from_artifact_uid(uid: str, suffix: str, is_dir: bool) -> str:
-    assert isinstance(suffix, str)
+    assert isinstance(suffix, str)  # noqa: S101 Suffix cannot be None.
     if is_dir:
         uid_storage = uid[:16]  # 16 chars, leave 4 chars for versioning
     else:

lamindb/core/versioning.py

@@ -97,7 +97,7 @@ def get_uid_from_old_version(
     version: str | None = None,
     using_key: str | None = None,
 ) -> tuple[str, str]:
-    """{}."""
+    """{}"""  # noqa: D415
     msg = ""
     if is_new_version_of.version is None:
         previous_version = "1"

lamindb/integrations/_vitessce.py

@@ -39,9 +39,10 @@ def save_vitessce_config(vitessce_config: VitessceConfig, description: str) -> A
             if "url" not in file:
                 raise ValueError("Each file must have a 'url' key.")
             filename = file["url"].split("/")[-1]
-            assert filename.endswith(
-                (".anndata.zarr", ".spatialdata.zarr", ".ome.zarr")
-            )
+            if not filename.endswith((".anndata.zarr", ".zarr", ".ome.zarr")):
+                logger.warning(
+                    "filename should end with '.anndata.zarr', '.zarr', or '.ome.zarr'."
+                )
             filestem = (
                 filename.replace(".anndata.zarr", "")
                 .replace(".spatialdata.zarr", "")

{lamindb-0.74.1.dist-info → lamindb-0.74.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.74.1
+Version: 0.74.2
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,10 +9,10 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Dist: lnschema_core==0.70.0
-Requires-Dist: lamindb_setup==0.73.2
+Requires-Dist: lnschema_core==0.70.5
+Requires-Dist: lamindb_setup==0.74.1
 Requires-Dist: lamin_utils==0.13.2
-Requires-Dist: lamin_cli==0.14.0
+Requires-Dist: lamin_cli==0.15.0
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -23,10 +23,8 @@ Requires-Dist: fsspec
 Requires-Dist: pandas
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
-Requires-Dist: psutil
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.44.0 ; extra == "bionty"
-Requires-Dist: pandas<2 ; extra == "dev"
+Requires-Dist: bionty==0.44.2 ; extra == "bionty"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
 Requires-Dist: laminci>=0.3 ; extra == "dev"

lamindb-0.74.2.dist-info/RECORD

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lamindb-0.74.1.dist-info/RECORD

@@ -1,57 +0,0 @@
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