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  • Error when writing string coordinate variables to zarr · 4 ✖

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  • CONTRIBUTOR · 4 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
1485362670 https://github.com/pydata/xarray/issues/3476#issuecomment-1485362670 https://api.github.com/repos/pydata/xarray/issues/3476 IC_kwDOAMm_X85YiNXu saschahofmann 24508496 2023-03-27T15:40:06Z 2023-03-27T15:40:06Z CONTRIBUTOR

My impression is that keeping the zarr encoding leads to a bunch of issues (see my issue above) or the current one. There also seems to be an issue with chunking being preserved because the array encodings arent overwritten, but I cant find that issue right now. Since all of these issues are resolved by popping the zarr encoding I am wondering what are the downsides of this and whether it'd be easier to not keep that encoding at all?

 
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   Error when writing string coordinate variables to zarr 516306758
1115045538 https://github.com/pydata/xarray/issues/3476#issuecomment-1115045538 https://api.github.com/repos/pydata/xarray/issues/3476 IC_kwDOAMm_X85Cdj6i delgadom 3698640 2022-05-02T15:38:11Z 2022-08-08T15:32:52Z CONTRIBUTOR

This has been happening a lot to me lately when writing to zarr. Thanks to @bolliger32 for the tip - this usually works like a charm:

```python for v in list(ds.coords.keys()): if ds.coords[v].dtype == object: ds.coords[v] = ds.coords[v].astype("unicode")

for v in list(ds.variables.keys()): if ds[v].dtype == object: ds[v] = ds[v].astype("unicode") `` For whatever reason, clearing the encoding and/or using.astype(str)` doesn't seem to work as reliably. I don't have a good MRE for this but hope it helps others with the same issue.

note the flag raised by @FlorisCalkoen below - don't just throw this at all your writes! there are other object types (e.g. CFTime) which you probably don't want to convert to string. This is just a patch to get around this issue for dataarrays with string coords/variables.

 
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   Error when writing string coordinate variables to zarr 516306758
1208280450 https://github.com/pydata/xarray/issues/3476#issuecomment-1208280450 https://api.github.com/repos/pydata/xarray/issues/3476 IC_kwDOAMm_X85IBOWC delgadom 3698640 2022-08-08T15:30:52Z 2022-08-08T15:31:13Z CONTRIBUTOR

ha - yeah that's a good flag. I definitely didn't intend for that to be a universally applied patch! so probably should have included a buyer beware. but we did find that clearing the encoding doesn't always do the trick for string arrays. So a comprehensive patch will probably need to be more nuanced.

 
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   Error when writing string coordinate variables to zarr 516306758
1012775723 https://github.com/pydata/xarray/issues/3476#issuecomment-1012775723 https://api.github.com/repos/pydata/xarray/issues/3476 IC_kwDOAMm_X848Xbsr RichardScottOZ 72196131 2022-01-14T04:55:03Z 2022-01-14T04:55:03Z CONTRIBUTOR

Think it worked with one variable - @Hoeze workaround was necessary for more than one.

 
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   Error when writing string coordinate variables to zarr 516306758

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