🎨 Refactor ln.File (#163)

* 🎨 Refactor with storage

* 💚 Fix

docs/guide/1-data-validation.ipynb

@@ -106,7 +106,7 @@
    "outputs": [],
    "source": [
     "from lnschema_core._core import SQLModel\n",
-    "from lnschema_core.dev.type import usage as event_type\n",
+    "from lnschema_core.dev.type import Usage as UsageType\n",
     "from sqlmodel import Field"
    ]
   },
@@ -118,7 +118,7 @@
    "source": [
     "class Usage(SQLModel, table=True):  # type: ignore\n",
     "    id: str = Field(default=None, primary_key=True)\n",
-    "    type: event_type = Field(nullable=False, index=True)"
+    "    type: UsageType = Field(nullable=False, index=True)"
    ]
   },
   {

lnschema_core/_core.py

@@ -6,21 +6,19 @@
 import pandas as pd
 import sqlalchemy as sa
 from lamin_logger import logger
+from lndb.dev.upath import UPath
 from nbproject._is_run_from_ipython import is_run_from_ipython
 from pydantic.fields import PrivateAttr
 from sqlmodel import Field, ForeignKeyConstraint, Relationship
-from upath import UPath
 
 from . import _name as schema_name
 from ._link import FileFeatures, FolderFile, ProjectFolder, RunIn  # noqa
 from ._timestamps import CreatedAt, UpdatedAt
 from ._users import CreatedBy
 from .dev import id as idg
 from .dev.sqlmodel import schema_sqlmodel
-from .dev.type import TransformType
+from .types import DataLike, PathLike, TransformType
 
-PathLike = TypeVar("PathLike", str, Path, UPath)
-DataLike = TypeVar("DataLike", ad.AnnData, pd.DataFrame)
 SQLModel, prefix, schema_arg = schema_sqlmodel(schema_name)
 
 
@@ -480,7 +478,7 @@ def path(self) -> Union[Path, UPath]:
         return filepath_from_file_or_folder(self)
 
     # likely needs an arg `key`
-    def replace(self, data: Union[Path, str, pd.DataFrame, ad.AnnData], run: Optional[Run] = None, format: Optional[str] = None):
+    def replace(self, data: Union[PathLike, DataLike], run: Optional[Run] = None, format: Optional[str] = None) -> None:
         """Replace data object."""
         from lamindb._file import get_file_kwargs_from_data
 
@@ -528,29 +526,6 @@ def replace(self, data: Union[Path, str, pd.DataFrame, ad.AnnData], run: Optiona
         self._memory_rep = privates["memory_rep"]
         self._to_store = not privates["check_path_in_storage"]  # no need to upload if new file is already in storage
 
-    def stage(self, is_run_input: bool = False):
-        """Download from storage if newer than in the cache.
-
-        Returns a path to a locally cached on-disk object (say, a
-        `.jpg` file).
-        """
-        from lamindb._load import stage as lnstage
-
-        return lnstage(file=self, is_run_input=is_run_input)
-
-    def load(self, stream: bool = False, is_run_input: bool = False):
-        """Load from storage (stage on local disk or load to memory).
-
-        Returns in-memory representation if configured (say, an `AnnData` object
-        for an `h5ad` file).
-
-        Otherwise, returns a path to a locally cached on-disk object (say, a
-        `.jpg` file).
-        """
-        from lamindb._load import load as lnload
-
-        return lnload(file=self, stream=stream, is_run_input=is_run_input)
-
     @property
     def __name__(cls) -> str:
         return "File"

lnschema_core/dev/_type.py

@@ -1,7 +1,16 @@
 from enum import Enum
+from pathlib import Path
+from typing import TypeVar
 
+import anndata as ad
+import pandas as pd
+from lndb.dev.upath import UPath
 
-class usage(str, Enum):
+PathLike = TypeVar("PathLike", str, Path, UPath)
+DataLike = TypeVar("DataLike", ad.AnnData, pd.DataFrame)
+
+
+class Usage(str, Enum):
     """Data access types."""
 
     ingest = "ingest"

lnschema_core/dev/type.py

@@ -1,9 +1,2 @@
-"""Custom types.
-
-.. autosummary::
-   :toctree: .
-
-   usage
-   TransformType
-"""
-from ._type import TransformType, usage  # noqa
+# deprecated, use lnschema_core.types instead
+from ._type import TransformType, Usage  # noqa

lnschema_core/types.py

@@ -0,0 +1,10 @@
+"""Types.
+
+.. autosummary::
+   :toctree: .
+
+   PathLike
+   DataLike
+   TransformType
+"""
+from .dev._type import DataLike, PathLike, TransformType  # noqa