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from os import PathLike
from pathlib import Path
from typing import Optional, Union, Iterator
import h5py
from . import anndata
from .sparse_dataset import SparseDataset
from ..compat import Literal
class AnnDataFileManager:
"""Backing file manager for AnnData."""
def __init__(
self,
adata: "anndata.AnnData",
filename: Optional[PathLike] = None,
filemode: Optional[Literal["r", "r+"]] = None,
):
self._adata = adata
self.filename = filename
self._filemode = filemode
self._file = None
if filename:
self.open()
def __repr__(self) -> str:
if self.filename is None:
return "Backing file manager: no file is set."
else:
return f"Backing file manager of file {self.filename}."
def __contains__(self, x) -> bool:
return x in self._file
def __iter__(self) -> Iterator[str]:
return iter(self._file)
def __getitem__(self, key: str) -> Union[h5py.Group, h5py.Dataset, SparseDataset]:
return self._file[key]
def __setitem__(
self, key: str, value: Union[h5py.Group, h5py.Dataset, SparseDataset]
):
self._file[key] = value
def __delitem__(self, key: str):
del self._file[key]
@property
def filename(self) -> Path:
return self._filename
@filename.setter
def filename(self, filename: Optional[PathLike]):
self._filename = None if filename is None else Path(filename)
def open(
self,
filename: Optional[PathLike] = None,
filemode: Optional[Literal["r", "r+"]] = None,
):
if filename is not None:
self.filename = filename
if filemode is not None:
self._filemode = filemode
if self.filename is None:
raise ValueError("Cannot open backing file if backing not initialized.")
self._file = h5py.File(self.filename, self._filemode)
def close(self):
"""Close the backing file, remember filename, do *not* change to memory mode."""
if self._file is not None:
self._file.close()
def _to_memory_mode(self):
"""Close the backing file, forget filename, *do* change to memory mode."""
self._adata.__X = self._adata.X[()]
self._file.close()
self._file = None
self._filename = None
@property
def is_open(self) -> bool:
"""State of backing file."""
if self._file is None:
return False
# try accessing the id attribute to see if the file is open
return bool(self._file.id)
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