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  • Zarr error when trying to overwrite part of existing store · 3 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
1379504132 https://github.com/pydata/xarray/issues/7403#issuecomment-1379504132 https://api.github.com/repos/pydata/xarray/issues/7403 IC_kwDOAMm_X85SOZAE slevang 39069044 2023-01-11T21:26:10Z 2023-01-11T21:26:10Z CONTRIBUTOR

Personally, I'll make the argument that we should switch (carefully) from -w to w for the default case.

This makes sense in principal for consistency with other i/o methods, but I think could go very wrong in practice, especially for inexperienced users.

For example, a misplaced command of ds.to_zarr("gs://bucket_name") with default mode="w" overwrites a user's entire bucket, and same thing for local storage. to_netcdf doesn't have the capability to rm -r a directory, so I would argue to_zarr(mode="w") is much more dangerous.

 
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   Zarr error when trying to overwrite part of existing store 1512290017
1371540921 https://github.com/pydata/xarray/issues/7403#issuecomment-1371540921 https://api.github.com/repos/pydata/xarray/issues/7403 IC_kwDOAMm_X85RwA25 jhamman 2443309 2023-01-04T23:24:46Z 2023-01-04T23:24:46Z MEMBER

I think the above example can be reduced to just:

python ds = xr.Dataset() ds.to_zarr('test.zarr') ds.to_zarr('test.zarr')

An interesting data point here is that to_netcdf defaults to w mode. And this works fine:

python ds = xr.Dataset() ds.to_netcdf('test.nc') ds.to_netcdf('test.nc')

Personally, I'll make the argument that we should switch (carefully) from -w to w for the default case.

 
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   Zarr error when trying to overwrite part of existing store 1512290017
1366882900 https://github.com/pydata/xarray/issues/7403#issuecomment-1366882900 https://api.github.com/repos/pydata/xarray/issues/7403 IC_kwDOAMm_X85RePpU slevang 39069044 2022-12-28T19:53:05Z 2022-12-28T19:53:05Z CONTRIBUTOR

Your MCVE has mode="a", is that intentional? As far as defaults, what the docstring says is:

The default mode is “a” if append_dim is set. Otherwise, it is “r+” if region is set and w- otherwise.

So without specifying mode, you get mode="w-" which will not overwrite anything. With mode="a", your MCVE runs fine for me.

From using these a bit, my understanding is:

  • mode="w-" is the safe default that won't overwrite anything
  • mode="w" is only if you want to rewrite the entire zarr store, not for rewriting a subset of existing data
  • mode="r+" is for modifying values on some subset of the existing store specified by the index with region, but doesn't allow changing any dimension sizes
  • mode="a" is for completely overwriting existing variables*, appending new variables, or appending data along an existing dimension, paired with append_dim

* I actually didn't realize this behavior until testing it out just now, but it is described in the docstring

 
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   Zarr error when trying to overwrite part of existing store 1512290017

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