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Update to NCBI Dataset v2 API #477

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joverlee521 opened this issue Oct 2, 2024 · 2 comments · Fixed by #480
Closed

Update to NCBI Dataset v2 API #477

joverlee521 opened this issue Oct 2, 2024 · 2 comments · Fixed by #480
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@joverlee521
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NCBI Datasets announced v1 API has been deprecated and will no longer be available December 2024.

We are still using the v1 API in fetch-from-biosample. This should get updated to use the v2 API:

curl -o biosample.zip -X GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/virus/taxon/1335626/genome/download?aux_report=BIOSAMPLE_REPORT" -H "accept: application/zip"

Thanks to @olearyna for the heads up 🙏
@joverlee521 joverlee521 self-assigned this Oct 4, 2024
@joverlee521
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Oh oops, copied the wrong taxon id in the URL, should be

https://api.ncbi.nlm.nih.gov/datasets/v2alpha/virus/taxon/2697049/genome/download?aux_report=BIOSAMPLE_REPORT

Noting v1 included ncbi_dataset/data/biosample.jsonl in the ZIP archive, while v2 includes ncbi_dataset/data/biosample_report.jsonl in the ZIP archive.

@joverlee521
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Actually, since I'm updating the fetch-from-biosample, I might as well revisit #420.

joverlee521 added a commit that referenced this issue Oct 4, 2024
@joverlee521
Replace fetch-from-biosample with NCBI Dataset CLI
009169d 
Originally I was going to update `fetch-from-biosample` to use the v2
NCBI Dataset API as described in #477.
However, I remembered #420
and realized that we can remove the script entirely if we just download
the BioSample report as part of the NCBI Dataset CLI command.
@joverlee521 joverlee521 mentioned this issue Oct 7, 2024
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Replace fetch-from-biosample with NCBI Dataset CLI nextstrain/ncov-ingest
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