lamindb 0.63.5__py3-none-any.whl → 0.64.1__py3-none-any.whl

lamindb/dev/storage/file.py

@@ -13,7 +13,7 @@ from lamindb_setup.dev.upath import (
     create_path,
     infer_filesystem,
 )
-from lnschema_core.models import File, Storage
+from lnschema_core.models import Artifact, Storage
 
 try:
     from ._zarr import read_adata_zarr
@@ -27,31 +27,42 @@ AUTO_KEY_PREFIX = ".lamindb/"
 
 
 # add type annotations back asap when re-organizing the module
-def auto_storage_key_from_file(file: File):
-    if file.key is None or file.key_is_virtual:
-        return auto_storage_key_from_id_suffix(file.uid, file.suffix)
+def auto_storage_key_from_artifact(artifact: Artifact):
+    if artifact.key is None or artifact.key_is_virtual:
+        is_dir = artifact.n_objects is not None
+        return auto_storage_key_from_artifact_uid(artifact.uid, artifact.suffix, is_dir)
     else:
-        return file.key
+        return artifact.key
 
 
-def auto_storage_key_from_id_suffix(uid: str, suffix: str) -> str:
-    assert isinstance(uid, str)
+def auto_storage_key_from_artifact_uid(uid: str, suffix: str, is_dir: bool) -> str:
     assert isinstance(suffix, str)
-    storage_key = f"{AUTO_KEY_PREFIX}{uid}{suffix}"
+    if is_dir:
+        uid_storage = uid[:16]  # 16 chars, leave 4 chars for versioning
+    else:
+        uid_storage = uid
+    storage_key = f"{AUTO_KEY_PREFIX}{uid_storage}{suffix}"
     return storage_key
 
 
-def attempt_accessing_path(file: File, storage_key: str):
+def attempt_accessing_path(artifact: Artifact, storage_key: str):
     # check whether the file is in the default db and whether storage
     # matches default storage
-    if file._state.db in ("default", None) and file.storage_id == settings.storage.id:
+    if (
+        artifact._state.db in ("default", None)
+        and artifact.storage_id == settings.storage.id
+    ):
         path = settings.storage.key_to_filepath(storage_key)
     else:
-        logger.debug("file.path is slightly slower for files outside default storage")
-        if file._state.db not in ("default", None):
-            storage = Storage.using(file._state.db).filter(id=file.storage_id).one()
+        logger.debug(
+            "artifact.path is slightly slower for files outside default storage"
+        )
+        if artifact._state.db not in ("default", None):
+            storage = (
+                Storage.using(artifact._state.db).filter(id=artifact.storage_id).one()
+            )
         else:
-            storage = Storage.filter(id=file.storage_id).one()
+            storage = Storage.filter(id=artifact.storage_id).one()
         # find a better way than passing None to instance_settings in the future!
         storage_settings = StorageSettings(storage.root)
         path = storage_settings.key_to_filepath(storage_key)
@@ -59,11 +70,11 @@ def attempt_accessing_path(file: File, storage_key: str):
 
 
 # add type annotations back asap when re-organizing the module
-def filepath_from_file(file: File):
-    if hasattr(file, "_local_filepath") and file._local_filepath is not None:
-        return file._local_filepath.resolve()
-    storage_key = auto_storage_key_from_file(file)
-    path = attempt_accessing_path(file, storage_key)
+def filepath_from_artifact(artifact: Artifact):
+    if hasattr(artifact, "_local_filepath") and artifact._local_filepath is not None:
+        return artifact._local_filepath.resolve()
+    storage_key = auto_storage_key_from_artifact(artifact)
+    path = attempt_accessing_path(artifact, storage_key)
     return path
 
 
@@ -75,20 +86,15 @@ def read_adata_h5ad(filepath, **kwargs) -> ad.AnnData:
         return adata
 
 
-def store_object(localpath: Union[str, Path, UPath], storagekey: str) -> float:
-    """Store arbitrary file to configured storage location.
+def store_artifact(localpath: Union[str, Path, UPath], storagekey: str) -> None:
+    """Store directory or file to configured storage location.
 
     Returns size in bytes.
     """
     storagepath: UPath = settings.instance.storage.key_to_filepath(storagekey)
     localpath = Path(localpath)
-
-    if localpath.is_file():
-        size = localpath.stat().st_size
-    else:
-        size = sum(f.stat().st_size for f in localpath.rglob("*") if f.is_file())
-
     if not isinstance(storagepath, LocalPathClasses):
+        # this uploads files and directories
         storagepath.upload_from(localpath, recursive=True, print_progress=True)
     else:  # storage path is local
         storagepath.parent.mkdir(parents=True, exist_ok=True)
@@ -101,16 +107,15 @@ def store_object(localpath: Union[str, Path, UPath], storagekey: str) -> float:
             if storagepath.exists():
                 shutil.rmtree(storagepath)
             shutil.copytree(localpath, storagepath)
-    return float(size)  # because this is how we store in the db
 
 
-def delete_storage_using_key(file: File, storage_key: str):
-    filepath = attempt_accessing_path(file, storage_key)
+def delete_storage_using_key(artifact: Artifact, storage_key: str):
+    filepath = attempt_accessing_path(artifact, storage_key)
     delete_storage(filepath)
 
 
 def delete_storage(storagepath: Union[Path, UPath]):
-    """Delete arbitrary file."""
+    """Delete arbitrary artifact."""
     if storagepath.is_file():
         storagepath.unlink()
     elif storagepath.is_dir():

lamindb/dev/versioning.py

@@ -1,7 +1,7 @@
 from typing import Optional, Tuple, Union
 
 from lnschema_core import ids
-from lnschema_core.models import File, Transform
+from lnschema_core.models import Artifact, Transform
 
 
 def set_version(version: Optional[str] = None, previous_version: Optional[str] = None):
@@ -46,7 +46,7 @@ def init_uid(
     return gen_full_id()
 
 
-def get_initial_version_id(is_new_version_of: Union[File, Transform]):
+def get_initial_version_id(is_new_version_of: Union[Artifact, Transform]):
     if is_new_version_of.initial_version_id is None:
         initial_version_id = is_new_version_of.id
     else:
@@ -55,7 +55,7 @@ def get_initial_version_id(is_new_version_of: Union[File, Transform]):
 
 
 def get_ids_from_old_version(
-    is_new_version_of: Union[File, Transform],
+    is_new_version_of: Union[Artifact, Transform],
     version: Optional[str],
     n_full_id: int = 20,
 ) -> Tuple[str, int, str]:

{lamindb-0.63.5.dist-info → lamindb-0.64.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.63.5
+Version: 0.64.1
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -8,10 +8,10 @@ Description-Content-Type: text/markdown
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
-Requires-Dist: lnschema_core==0.57.6
-Requires-Dist: lamindb_setup==0.61.2
+Requires-Dist: lnschema_core==0.58.1
+Requires-Dist: lamindb_setup==0.61.4
 Requires-Dist: lamin_utils==0.12.0
-Requires-Dist: lamin_cli==0.2.5
+Requires-Dist: lamin_cli==0.3.0
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -27,7 +27,7 @@ Requires-Dist: boto3==1.28.17 ; extra == "aws"
 Requires-Dist: aiobotocore==2.5.4 ; extra == "aws"
 Requires-Dist: fsspec[s3]==2023.9.0 ; extra == "aws"
 Requires-Dist: s3fs>=2023.9.0 ; extra == "aws"
-Requires-Dist: lnschema_bionty==0.35.3 ; extra == "bionty"
+Requires-Dist: lnschema_bionty==0.36.1 ; extra == "bionty"
 Requires-Dist: pandas<2 ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"

lamindb-0.64.1.dist-info/RECORD

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lamindb-0.63.5.dist-info/RECORD

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