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Add test cases for LINDI #47

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oruebel opened this issue Apr 24, 2024 · 3 comments
Open

Add test cases for LINDI #47

oruebel opened this issue Apr 24, 2024 · 3 comments
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@oruebel
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oruebel commented Apr 24, 2024

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@oruebel
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oruebel commented Apr 24, 2024

Similar to #43 we should also add lindi to the test suite

@oruebel oruebel changed the title Addd test cases for LINDI Add test cases for LINDI Apr 24, 2024
@rly
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rly commented May 16, 2024

We currently have a benchmark to create a LINDI file from a remote NWB file. In my experience, for some large files with many chunks (such as the ophys file which has ~1 million chunks), that is slower than downloading the entire NWB file and creating a LINDI file with the downloaded local NWB file using references to the remote asset. It probably has to do with the many requests to the remote NWB file, one per chunk(?). So I think we should add such a benchmark where we download the file locally and create the LINDI file from that downloaded file.

class NWBLindiFileCreateLocalReferenceFileSystemBenchmark(BaseBenchmark):
"""
Time the creation of a local Lindi JSON reference filesystem for a remote NWB file
as well as reading the NWB file with PyNWB when the local reference filesystem does not
yet exist.
"""

@rly
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rly commented May 16, 2024

Separately, I think it would be good to have a benchmark that is simply download the entire file, as a point of comparison for some of these streaming methods. For some of the c elegans files with thousands of groups, it is actually faster to download and read than stream with fsspec/ros3, but it also depends on the read pattern.

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