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ReadTimeoutError while downloading files with the b.fetch() command using Quilt’s Python client #117

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EmiliyaStol opened this issue Jul 12, 2024 · 2 comments

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@EmiliyaStol
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I wrote Python code to download all Image.csv files from a single source folder (for example: "source_2") using Quilt’s Python client. I am using the b.fetch() command to dowload the files.
I am running into an issue where the run is timing out while downloading the files. I am receiving the message "TimeoutError: The read operation timed out" and "urllib3.exceptions.ReadTimeoutError: AWSHTTPSConnectionPool(host='cellpainting-gallery.s3.amazonaws.com', port=443): Read timed out." in the terminal.
How can I efficiently download a large amount of files from the Cell Painting Gallery?

@shntnu
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shntnu commented Jul 16, 2024

How can I efficiently download a large amount of files from the Cell Painting Gallery?

We recommend using https://github.com/broadinstitute/cpg/tree/main/cpgdata (cc @leoank: FYI)

@leoank
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leoank commented Jul 17, 2024

Hey @EmiliyaStol, Let me know if you face any issues using cpgdata. The readme exactly covers your user case.

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