def create_store(self, normalize_keys=False, key_separator=".", **kwargs):
# Since the user is passing key_separator, that will take priority.
skip_if_nested_chunks(**kwargs)
path = tempfile.mkdtemp()
atexit.register(atexit_rmtree, path)
return FSStoreV3(path,
normalize_keys=normalize_keys,
key_separator=key_separator)
def create_store(self,
normalize_keys=False,
dimension_separator=".",
path=None,
**kwargs):
if path is None:
path = tempfile.mkdtemp()
atexit.register(atexit_rmtree, path)
store = FSStoreV3(path,
normalize_keys=normalize_keys,
dimension_separator=dimension_separator,
**kwargs)
return store
def dest(self, request, tmpdir):
if request.param == 'hdf5':
h5py = pytest.importorskip('h5py')
fn = tmpdir.join('dest.h5')
with h5py.File(str(fn), mode='w') as h5f:
yield h5f
elif request.param == 'zarr':
yield group(path='group2', zarr_version=3)
elif request.param == 'zarr_kvstore':
store = KVStoreV3(dict())
yield group(store, path='group2', zarr_version=3)
elif request.param == 'zarr_fsstore':
fn = tmpdir.join('dest.zr3')
store = FSStoreV3(str(fn), auto_mkdir=True)
yield group(store, path='group2', zarr_version=3)
elif request.param == 'zarr_directorystore':
fn = tmpdir.join('dest.zr3')
store = DirectoryStoreV3(str(fn))
yield group(store, path='group2', zarr_version=3)
elif request.param == 'zarr_sqlitestore':
fn = tmpdir.join('dest.db')
store = SQLiteStoreV3(str(fn))
yield group(store, path='group2', zarr_version=3)
def test_consolidate_metadata(with_chunk_store,
zarr_version,
listable,
monkeypatch,
stores_from_path):
# setup initial data
if stores_from_path:
store = tempfile.mkdtemp()
atexit.register(atexit_rmtree, store)
if with_chunk_store:
chunk_store = tempfile.mkdtemp()
atexit.register(atexit_rmtree, chunk_store)
else:
chunk_store = None
version_kwarg = {'zarr_version': zarr_version}
else:
if zarr_version == 2:
store = MemoryStore()
chunk_store = MemoryStore() if with_chunk_store else None
elif zarr_version == 3:
store = MemoryStoreV3()
chunk_store = MemoryStoreV3() if with_chunk_store else None
version_kwarg = {}
path = 'dataset' if zarr_version == 3 else None
z = group(store, chunk_store=chunk_store, path=path, **version_kwarg)
# Reload the actual store implementation in case str
store_to_copy = z.store
z.create_group('g1')
g2 = z.create_group('g2')
g2.attrs['hello'] = 'world'
arr = g2.create_dataset('arr', shape=(20, 20), chunks=(5, 5), dtype='f8')
assert 16 == arr.nchunks
assert 0 == arr.nchunks_initialized
arr.attrs['data'] = 1
arr[:] = 1.0
assert 16 == arr.nchunks_initialized
if stores_from_path:
# get the actual store class for use with consolidate_metadata
store_class = z._store
else:
store_class = store
if zarr_version == 3:
# error on v3 if path not provided
with pytest.raises(ValueError):
consolidate_metadata(store_class, path=None)
with pytest.raises(ValueError):
consolidate_metadata(store_class, path='')
# perform consolidation
out = consolidate_metadata(store_class, path=path)
assert isinstance(out, Group)
assert ['g1', 'g2'] == list(out)
if not stores_from_path:
if zarr_version == 2:
assert isinstance(out._store, ConsolidatedMetadataStore)
assert '.zmetadata' in store
meta_keys = ['.zgroup',
'g1/.zgroup',
'g2/.zgroup',
'g2/.zattrs',
'g2/arr/.zarray',
'g2/arr/.zattrs']
else:
assert isinstance(out._store, ConsolidatedMetadataStoreV3)
assert 'meta/root/consolidated/.zmetadata' in store
meta_keys = ['zarr.json',
meta_root + 'dataset.group.json',
meta_root + 'dataset/g1.group.json',
meta_root + 'dataset/g2.group.json',
meta_root + 'dataset/g2/arr.array.json',
'meta/root/consolidated.group.json']
for key in meta_keys:
del store[key]
# https://github.com/zarr-developers/zarr-python/issues/993
# Make sure we can still open consolidated on an unlistable store:
if not listable:
fs_memory = pytest.importorskip("fsspec.implementations.memory")
monkeypatch.setattr(fs_memory.MemoryFileSystem, "isdir", lambda x, y: False)
monkeypatch.delattr(fs_memory.MemoryFileSystem, "ls")
fs = fs_memory.MemoryFileSystem()
if zarr_version == 2:
store_to_open = FSStore("", fs=fs)
else:
store_to_open = FSStoreV3("", fs=fs)
# copy original store to new unlistable store
store_to_open.update(store_to_copy)
else:
store_to_open = store
# open consolidated
z2 = open_consolidated(store_to_open, chunk_store=chunk_store, path=path, **version_kwarg)
assert ['g1', 'g2'] == list(z2)
assert 'world' == z2.g2.attrs['hello']
assert 1 == z2.g2.arr.attrs['data']
assert (z2.g2.arr[:] == 1.0).all()
assert 16 == z2.g2.arr.nchunks
if listable:
assert 16 == z2.g2.arr.nchunks_initialized
else:
with pytest.raises(NotImplementedError):
_ = z2.g2.arr.nchunks_initialized
if stores_from_path:
# path string is note a BaseStore subclass so cannot be used to
# initialize a ConsolidatedMetadataStore.
if zarr_version == 2:
with pytest.raises(ValueError):
cmd = ConsolidatedMetadataStore(store)
elif zarr_version == 3:
with pytest.raises(ValueError):
cmd = ConsolidatedMetadataStoreV3(store)
else:
# tests del/write on the store
if zarr_version == 2:
cmd = ConsolidatedMetadataStore(store)
with pytest.raises(PermissionError):
del cmd['.zgroup']
with pytest.raises(PermissionError):
cmd['.zgroup'] = None
else:
cmd = ConsolidatedMetadataStoreV3(store)
with pytest.raises(PermissionError):
del cmd[meta_root + 'dataset.group.json']
with pytest.raises(PermissionError):
cmd[meta_root + 'dataset.group.json'] = None
# test getsize on the store
assert isinstance(getsize(cmd), Integral)
# test new metadata are not writeable
with pytest.raises(PermissionError):
z2.create_group('g3')
with pytest.raises(PermissionError):
z2.create_dataset('spam', shape=42, chunks=7, dtype='i4')
with pytest.raises(PermissionError):
del z2['g2']
# test consolidated metadata are not writeable
with pytest.raises(PermissionError):
z2.g2.attrs['hello'] = 'universe'
with pytest.raises(PermissionError):
z2.g2.arr.attrs['foo'] = 'bar'
# test the data are writeable
z2.g2.arr[:] = 2
assert (z2.g2.arr[:] == 2).all()
# test invalid modes
with pytest.raises(ValueError):
open_consolidated(store, chunk_store=chunk_store, mode='a', path=path)
with pytest.raises(ValueError):
open_consolidated(store, chunk_store=chunk_store, mode='w', path=path)
with pytest.raises(ValueError):
open_consolidated(store, chunk_store=chunk_store, mode='w-', path=path)
# make sure keyword arguments are passed through without error
open_consolidated(
store, chunk_store=chunk_store, path=path, cache_attrs=True, synchronizer=None,
**version_kwarg,
)