Convert zarr helpers to utilities, update numpy chunk encoding in zarr router #260
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| """Returns a consolidated zmetadata dictionary, using the cache when possible.""" | ||
| cache_key = dataset.attrs.get(DATASET_ID_ATTR_KEY, '') + '/' + ZARR_METADATA_KEY | ||
| zmeta = cache.get(cache_key) |
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This may be an issue for nested datasets, have to verify
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DATASET_ID_ATTR_KEY = '_xpublish_id'
Ok I think it just needs to be documented that if you build a dataset provider you should provide _xpublish_id as an attribute on the dataset or else the zarr attrs will be cached for the remote zarr dataset. Alternative is to change the dataset provider hook to assign an ID if it does not exist.
Currently there is no DATASET_ID set for datasets that are provided bytthe dataset provider so the .zmetadata etc is cached across datasets
Any thoughts @abkfenris ?
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That makes sense, as I definitely think I've got dataset provider implementations that would have problems with this.
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| @@ -348,7 +348,7 @@ def test_cache(airtemp_ds): | |||
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| response1 = client.get('/zarr/air/0.0.0') | |||
| assert response1.status_code == 200 | |||
| assert '/air/0.0.0' in rest.cache | |||
| assert 'airtemp/air/0.0.0' in rest.cache | |||
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All datasets now have an _xpublish_id attr so the cache string changed in this test
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Okay think this is good to go now |
docs/source/user-guide/plugins.md
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| ```{note} | ||
| Some routers may want to cache data computed from datasets that they serve to avoid unnecessary recomputation. In this case, routers may rely on the | ||
| `_xpublish_id` attribute (`DATASET_ID_ATTR_KEY` from `xpublish.api`) on each dataset. If this attribute is set, it should be a unique identifier for the dataset, otherwise the `dataset_id` used to load the dataset will be set as the `_xpublish_id` automatically. | ||
| ``` | ||
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It's probably worth being more explicit, and making it more important than alert. Also could you tweak the example above to explicit set the attr as an example?
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Do you mean move that up and change it to a warning? Ill update the example code too
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Ya, warning is probably the right level. I was thinking tweaking the tone as well, 'you need to set a uniqueDATASET_ID_ATTR_KEY from xpublish.api on each dataset for routers to manage caching appropriately' to go with the warning.
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Nice. I like that, K updated it!
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Co-authored-by: Alex Kerney <abk@mac.com>
Co-authored-by: Alex Kerney <abk@mac.com>
Great catches!! Thank you! |
We have been working on building a subset router (https://github.com/asascience-open/xreds/blob/fa3aa81e398c280cef34fd6e0846880df0bb2aef/xreds/plugins/subset_plugin.py#L138) which introduces a nested dataset router. The core zarr plugin did not work with this because of zmetadata and zvariable dependencies using the xpublish global get_dataset dependency. Instead this simply moves those functions to utils and removes the Depends functionality. If there is a better way to handle this i am all ears, I was not sure of why they were dependencies in the first place so this may be incorrect.
This also includes a patch for numpy arrays when using the zarr router (#207). In some cases (especially kerchunk concatenated datasets) there may be a combination of numpy and dask arrays, and the numpy arrays may include encoding information even if the encoding is reset beforehand. This PR changes this functionality to force the encoding to match the array shape when the underlying array is not a dask array.