Skip to content
This repository was archived by the owner on Oct 24, 2024. It is now read-only.
This repository was archived by the owner on Oct 24, 2024. It is now read-only.

Opening a datatree from S3 bucket #322

Closed
@vlevasseur073

Description

@vlevasseur073

Dears,

it seems that the current version of datatree can't handle stores from cloud storage (tests made with S3 only).
For instance, trying to open a datatree following the same syntax as xarray.open_dataset (using fsspec chain URLs):

store="zip::s3://bucket/path/product.zarr.zip"
dt = datatree.open_datatree(store,engine="zarr",backend_kwargs={"storage_options": {"s3":secrets["s3input"]}})

where secrets["s3input"] is a dict containing the AWS secret keys and endpoint URLs.

fails with

ClientError                               Traceback (most recent call last)
File [/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/s3fs/core.py:113](https://file+.vscode-resource.vscode-cdn.net/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/s3fs/core.py:113), in _error_wrapper(func, args, kwargs, retries)
    [112](https://file+.vscode-resource.vscode-cdn.net/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/s3fs/core.py:112) try:
--> [113](https://file+.vscode-resource.vscode-cdn.net/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/s3fs/core.py:113)     return await func(*args, **kwargs)
    [114](https://file+.vscode-resource.vscode-cdn.net/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/s3fs/core.py:114) except S3_RETRYABLE_ERRORS as e:

File [/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/aiobotocore/client.py:408](https://file+.vscode-resource.vscode-cdn.net/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/aiobotocore/client.py:408), in AioBaseClient._make_api_call(self, operation_name, api_params)
    [407](https://file+.vscode-resource.vscode-cdn.net/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/aiobotocore/client.py:407)     error_class = self.exceptions.from_code(error_code)
--> [408](https://file+.vscode-resource.vscode-cdn.net/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/aiobotocore/client.py:408)     raise error_class(parsed_response, operation_name)
    [409](https://file+.vscode-resource.vscode-cdn.net/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/aiobotocore/client.py:409) else:

ClientError: An error occurred (403) when calling the HeadObject operation: Forbidden

Indeed in _open_datatree_zarr from datatree/io.py, the kwargs are not given to the zarr.open_group function, so that specifically in this case the storage_options are ignored.
As a workaround in my specific case, replacing in datatree/io.py l.87 (v0.0.14)

zds = zarr.open_group(store, mode="r")

by

storage_options = kwargs["backend_kwargs"]
zds = zarr.open_group(store, mode="r",**storage_options)

works just fine.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions