Updating chunks fails with ValueError #105
Description
Describe the bug
I have a time-optimised xarray dataset (meaning that the time dimension is rather large and the spatial dimension are small). I want to add new time steps to this cube, which causes that existing chunks have to be updated.
The chunking eventually fails during adding the first time step with this error message: ValueError: Value of 'action' argument must be one of 'delete_dir', 'delete_file', 'replace_file', but was 'create_file'
I was able to update other time-optimised cubes, so I don't know why the error occurs here.
I inspected the stack trace though and found that something does not look right in the last two lines. zappend itself creates a rollback callback for a "create_file" action which is not allowed and causes the ValueError. See full stacktrace below.
To Reproduce
Not sure, as I could not figure out which aspect of my dataset provoked this behaviour.
Expected behavior
I expect that the time steps would be added, one after the other, and that existing chunks would be updated appropriately.
If this is not possible due to an error, I would like to have an error reported to me.
Python Environment
- operating system: Linux Mint 22
- zappend version, output of
zappend --version: 0.8.0 - optional: packages and their versions, output of
pip listorconda list:
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
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affine 2.4.0 pyhd8ed1ab_1 conda-forge
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aiohttp 3.11.11 py312h178313f_0 conda-forge
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terminado 0.18.1 pyh0d859eb_0 conda-forge
threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge
tifffile 2025.1.10 pyhd8ed1ab_0 conda-forge
tinycss2 1.4.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.2.1 pyhd8ed1ab_1 conda-forge
toolz 1.0.0 pyhd8ed1ab_1 conda-forge
tornado 6.4.2 py312h66e93f0_0 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
trove-classifiers 2025.1.15.22 pyhd8ed1ab_0 conda-forge
types-python-dateutil 2.9.0.20241206 pyhd8ed1ab_0 conda-forge
typing-extensions 4.12.2 hd8ed1ab_1 conda-forge
typing_extensions 4.12.2 pyha770c72_1 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_1 conda-forge
tzdata 2025a h78e105d_0 conda-forge
ujson 5.10.0 py312h2ec8cdc_1 conda-forge
unicodedata2 16.0.0 py312h66e93f0_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_1 conda-forge
uriparser 0.9.8 hac33072_0 conda-forge
urllib3 2.3.0 pyhd8ed1ab_0 conda-forge
waitress 3.0.2 pyhd8ed1ab_1 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_1 conda-forge
webcolors 24.11.1 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_3 conda-forge
webob 1.8.9 pyhd8ed1ab_1 conda-forge
websocket-client 1.8.0 pyhd8ed1ab_1 conda-forge
werkzeug 3.1.3 pyhd8ed1ab_1 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
wrapt 1.17.2 py312h66e93f0_0 conda-forge
x265 3.5 h924138e_3 conda-forge
xarray 2025.1.1 pyhd8ed1ab_0 conda-forge
xcube 1.8.3 pyhd8ed1ab_0 conda-forge
xcube-cmems 0.1.6.dev0 pypi_0 pypi
xcube_geodb 1.0.9 pyhd8ed1ab_0 conda-forge
xerces-c 3.2.5 h988505b_2 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xyzservices 2025.1.0 pyhd8ed1ab_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.18.3 py312h178313f_1 conda-forge
zappend 0.8.0 pyhd8ed1ab_1 conda-forge
zarr 2.18.4 pyhd8ed1ab_0 conda-forge
zeromq 4.3.5 h3b0a872_7 conda-forge
zfp 1.0.1 h5888daf_2 conda-forge
zict 3.0.0 pyhd8ed1ab_1 conda-forge
zipp 3.21.0 pyhd8ed1ab_1 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zlib-ng 2.2.3 h7955e40_0 conda-forge
zstandard 0.23.0 py312hef9b889_1 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
Traceback
Error in transaction
Traceback (most recent call last):
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/zappend/processor.py", line 123, in process_slice
update_target_from_slice(ctx, slice_dataset, rollback_callback)
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/zappend/processor.py", line 180, in update_target_from_slice
slice_ds.to_zarr(
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/xarray/core/dataset.py", line 2622, in to_zarr
return to_zarr( # type: ignore[call-overload,misc]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/xarray/backends/api.py", line 2217, in to_zarr
writes = writer.sync(
^^^^^^^^^^^^
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/xarray/backends/common.py", line 358, in sync
delayed_store = chunkmanager.store(
^^^^^^^^^^^^^^^^^^^
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/xarray/namedarray/daskmanager.py", line 247, in store
return store(
^^^^^^
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/dask/array/core.py", line 1253, in store
compute_as_if_collection(Array, store_dsk, map_keys, **kwargs)
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/dask/base.py", line 399, in compute_as_if_collection
return schedule(dsk2, keys, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/dask/threaded.py", line 91, in get
results = get_async(
^^^^^^^^^^
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/dask/local.py", line 516, in get_async
raise_exception(exc, tb)
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/dask/local.py", line 324, in reraise
raise exc
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/dask/local.py", line 229, in execute_task
result = task(data)
^^^^^^^^^^
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/dask/_task_spec.py", line 741, in call
return self.func(*new_argspec)
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/dask/_task_spec.py", line 203, in _execute_subgraph
res = execute_graph(final, keys=[outkey])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/dask/_task_spec.py", line 987, in execute_graph
cache[key] = node(cache)
^^^^^^^^^^^
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/dask/_task_spec.py", line 741, in call
return self.func(*new_argspec)
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/dask/array/core.py", line 4582, in store_chunk
return load_store_chunk(x, out, index, lock, return_stored, False)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/dask/array/core.py", line 4564, in load_store_chunk
out[index] = x
~~~^^^^^^^
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/zarr/core.py", line 1448, in setitem
self.set_orthogonal_selection(pure_selection, value, fields=fields)
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/zarr/core.py", line 1637, in set_orthogonal_selection
self._set_selection(indexer, value, fields=fields)
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/zarr/core.py", line 1989, in _set_selection
self._chunk_setitem(chunk_coords, chunk_selection, chunk_value, fields=fields)
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/zarr/core.py", line 2262, in _chunk_setitem
self._chunk_setitem_nosync(chunk_coords, chunk_selection, value, fields=fields)
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/zarr/core.py", line 2270, in _chunk_setitem_nosync
self._chunk_delitem(ckey)
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/zarr/core.py", line 2235, in _chunk_delitem
del self.chunk_store[ckey]
~~~~~~~~~~~~~~~~^^^^^^
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/zappend/rollbackstore.py", line 65, in delitem
self._rollback_cb("create_file", key, old_value)
File "/home/tonio/miniconda3/envs/doors/lib/python3.12/site-packages/zappend/fsutil/transaction.py", line 197, in _add_rollback_action
raise ValueError(
ValueError: Value of 'action' argument must be one of 'delete_dir', 'delete_file', 'replace_file', but was 'create_file'