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Download NCBI Taxdmp file in CI #41

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merged 9 commits into from
Mar 14, 2024

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stijndcl
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We discussed adding this file to the automatic releases because it is sometimes arbitrarily slow to download

@stijndcl stijndcl added the enhancement New feature or request label Feb 26, 2024
@stijndcl stijndcl self-assigned this Feb 26, 2024
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This looks good. Can you update the build_database-script accordingly such that it uses our mirrored version of the taxon dump? Ideally the script should check if our "mirrored version" is available, and automatically fallback to the old URL if not.

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stijndcl commented Mar 6, 2024

Will do. I didn't do it yet in this PR because the very first time the file will not exist, but using the default as a fallback is a good idea and fixes that problem as well.

@stijndcl stijndcl requested a review from pverscha March 8, 2024 11:13
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stijndcl commented Mar 8, 2024

Very ironically showing that this is already a good change, NCBI just changed their endpoint and the original download URL no longer works. I've updated the script.

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Thanks! This code looks great as well :) I'll start the run to create a new version of the static database (and upload our new taxon file) right now.

@pverscha pverscha merged commit 7aa805e into unipept:master Mar 14, 2024
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