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When retrieving data from S3, account for chunking #1085

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merged 5 commits into from
May 15, 2023

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horsto
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@horsto horsto commented May 12, 2023

There seems to be an issue with retrieval of larger ("external") files from S3 compatible buckets. I documented the error here: #1083. I brought it up as issue in the minio-api repository as well: minio/minio-py#1280.

The problem is that files can be returned as chunks via the minio API, such that .data cannot be called directly. Instead, .stream and subsequent concatenation of bytes seems to work for all cases. This behavior is already correctly implemented in fget() (

for d in data.stream(1 << 16):
)

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horsto commented May 12, 2023

This PR changes the .data method to .stream in the get() method for S3 (external) objects, which accommodates chunking of larger files (opposed to assuming that every / the whole file is loaded at once).

@dimitri-yatsenko
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@horsto Would you merge this PR horsto#1 ?

pull from upstream and update changelog
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horsto commented May 15, 2023

Done!

@dimitri-yatsenko dimitri-yatsenko merged commit 97e34a6 into datajoint:master May 15, 2023
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3 participants