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from __future__ import annotations
from importlib.util import find_spec
from typing import TYPE_CHECKING
import pytest
from anndata.compat import DaskArray
from anndata.experimental import read_lazy
from anndata.tests.helpers import AccessTrackingStore, assert_equal, gen_adata
from .conftest import ANNDATA_ELEMS
if TYPE_CHECKING:
from collections.abc import Callable
from pathlib import Path
from anndata import AnnData
from anndata._types import AnnDataElem
pytestmark = pytest.mark.skipif(not find_spec("xarray"), reason="xarray not installed")
@pytest.mark.parametrize(
("elem_key", "sub_key"),
[
("raw", "X"),
("obs", "cat"),
("obs", "int64"),
*((elem_name, None) for elem_name in ANNDATA_ELEMS),
],
)
def test_access_count_elem_access(
remote_store_tall_skinny: AccessTrackingStore,
adata_remote_tall_skinny: AnnData,
elem_key: AnnDataElem,
sub_key: str,
simple_subset_func: Callable[[AnnData], AnnData],
):
full_path = f"{elem_key}/{sub_key}" if sub_key is not None else elem_key
remote_store_tall_skinny.initialize_key_trackers({full_path, "X"})
# a series of methods that should __not__ read in any data
elem = getattr(simple_subset_func(adata_remote_tall_skinny), elem_key)
if sub_key is not None:
getattr(elem, sub_key)
remote_store_tall_skinny.assert_access_count(full_path, 0)
remote_store_tall_skinny.assert_access_count("X", 0)
def test_access_count_subset(
remote_store_tall_skinny: AccessTrackingStore,
adata_remote_tall_skinny: AnnData,
):
non_obs_elem_names = filter(lambda e: e != "obs", ANNDATA_ELEMS)
remote_store_tall_skinny.initialize_key_trackers(
["obs/cat/codes", *non_obs_elem_names]
)
adata_remote_tall_skinny[adata_remote_tall_skinny.obs["cat"] == "a", :]
# all codes read in for subset (from 1 chunk)
remote_store_tall_skinny.assert_access_count("obs/cat/codes", 1)
for elem_name in non_obs_elem_names:
remote_store_tall_skinny.assert_access_count(elem_name, 0)
def test_access_count_subset_column_compute(
remote_store_tall_skinny: AccessTrackingStore,
adata_remote_tall_skinny: AnnData,
):
remote_store_tall_skinny.initialize_key_trackers(["obs/int64"])
adata_remote_tall_skinny[adata_remote_tall_skinny.shape[0] // 2, :].obs[
"int64"
].compute()
# two chunks needed for 0:10 subset
remote_store_tall_skinny.assert_access_count("obs/int64", 1)
def test_access_count_index(
remote_store_tall_skinny: AccessTrackingStore,
):
remote_store_tall_skinny.initialize_key_trackers(["obs/_index"])
read_lazy(remote_store_tall_skinny, load_annotation_index=False)
remote_store_tall_skinny.assert_access_count("obs/_index", 0)
read_lazy(remote_store_tall_skinny)
# 4 is number of chunks
remote_store_tall_skinny.assert_access_count("obs/_index", 4)
def test_access_count_dtype(
remote_store_tall_skinny: AccessTrackingStore,
adata_remote_tall_skinny: AnnData,
):
remote_store_tall_skinny.initialize_key_trackers(["obs/cat/categories"])
remote_store_tall_skinny.assert_access_count("obs/cat/categories", 0)
# This should only cause categories to be read in once
adata_remote_tall_skinny.obs["cat"].dtype
adata_remote_tall_skinny.obs["cat"].dtype
adata_remote_tall_skinny.obs["cat"].dtype
remote_store_tall_skinny.assert_access_count("obs/cat/categories", 1)
def test_uns_uses_dask(adata_remote: AnnData):
assert isinstance(adata_remote.uns["nested"]["nested_further"]["array"], DaskArray)
def test_to_memory(adata_remote: AnnData, adata_orig: AnnData):
remote_to_memory = adata_remote.to_memory()
assert_equal(remote_to_memory, adata_orig)
def test_view_to_memory(adata_remote: AnnData, adata_orig: AnnData):
obs_cats = adata_orig.obs["obs_cat"].cat.categories
subset_obs = adata_orig.obs["obs_cat"] == obs_cats[0]
assert_equal(adata_orig[subset_obs, :], adata_remote[subset_obs, :].to_memory())
var_cats = adata_orig.var["var_cat"].cat.categories
subset_var = adata_orig.var["var_cat"] == var_cats[0]
assert_equal(adata_orig[:, subset_var], adata_remote[:, subset_var].to_memory())
def test_view_of_view_to_memory(adata_remote: AnnData, adata_orig: AnnData):
cats_obs = adata_orig.obs["obs_cat"].cat.categories
subset_obs = (adata_orig.obs["obs_cat"] == cats_obs[0]) | (
adata_orig.obs["obs_cat"] == cats_obs[1]
)
subsetted_adata = adata_orig[subset_obs, :]
subset_subset_obs = subsetted_adata.obs["obs_cat"] == cats_obs[1]
subsetted_subsetted_adata = subsetted_adata[subset_subset_obs, :]
assert_equal(
subsetted_subsetted_adata,
adata_remote[subset_obs, :][subset_subset_obs, :].to_memory(),
)
cats_var = adata_orig.var["var_cat"].cat.categories
subset_var = (adata_orig.var["var_cat"] == cats_var[0]) | (
adata_orig.var["var_cat"] == cats_var[1]
)
subsetted_adata = adata_orig[:, subset_var]
subset_subset_var = subsetted_adata.var["var_cat"] == cats_var[1]
subsetted_subsetted_adata = subsetted_adata[:, subset_subset_var]
assert_equal(
subsetted_subsetted_adata,
adata_remote[:, subset_var][:, subset_subset_var].to_memory(),
)
def test_unconsolidated(tmp_path: Path, mtx_format):
adata = gen_adata((1000, 1000), mtx_format)
orig_pth = tmp_path / "orig.zarr"
adata.write_zarr(orig_pth)
(orig_pth / ".zmetadata").unlink()
store = AccessTrackingStore(orig_pth)
store.initialize_key_trackers(["obs/.zgroup", ".zgroup"])
with pytest.warns(UserWarning, match=r"Did not read zarr as consolidated"):
remote = read_lazy(store)
remote_to_memory = remote.to_memory()
assert_equal(remote_to_memory, adata)
store.assert_access_count("obs/.zgroup", 1)
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