Remove NCBI Virus #19
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Due to #18, the NCBI Virus API is more of a hassle to use. The data from NCBI Datasets CLI covers the standard fields that we use in pathogen ingests, so we can drop the use of the undocumented NCBI Virus API. If any pathogen needs additional custom fields that are not available through NCBI Datasets, the pipeline can use fetch-from-ncbi-entrez and parse the GenBank file.
Trim back CI jobs for reasons stated in nextstrain/cli@fab709a
The only tests we had were for fetch-from-ncbi-virus, which were removed in 6a76d0b
victorlin
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Sep 14, 2023
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Seems reasonable given these are now unused in downstream repos, as mentioned in #18 (comment).
🎉 Love a good net-negative change! |
joverlee521
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Dropping due to the changes of the NCBI Virus API described in nextstrain/ingest#18 and we are dropping the scripts for this in nextstrain/ingest#19.
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Copying two scripts that were in nextstrain/ingest before they were removed in <nextstrain/ingest#19> - ncbi-virus-url - fetch-from-ncbi-virus Done in preparation for editing the NCBI Virus URL to be used for ingest because the NCBI Datasets does not include strain, segment, and serotype fields.
joverlee521
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Copying two scripts that were in nextstrain/ingest before they were removed in <nextstrain/ingest#19> - ncbi-virus-url - fetch-from-ncbi-virus Done in preparation for editing the NCBI Virus URL to be used for ingest because the NCBI Datasets does not include strain, segment, and serotype fields.
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Copying two scripts that were in nextstrain/ingest before they were removed in <nextstrain/ingest#19> - ncbi-virus-url - fetch-from-ncbi-virus Done in preparation for editing the NCBI Virus URL to be used for ingest because the NCBI Datasets does not include strain, segment, and serotype fields.
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Resolves #18 by just completely removing the NCBI Virus scripts.
We can just stick to Entrez and NCBI Datasets for fetching public data.
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