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ropensci / taxizedb

Tools for Working with Taxonomic SQL Databases
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update ncbi endpoint #73

Closed KaiAragaki closed 5 months ago

KaiAragaki commented 5 months ago

The NBCI taxonomy endpoint must have changed at one point, causing calls to db_download_ncbi to fail. This fixes this.

Related Issue

May be an alternate solution to #72 (since the impetus was timeout on download)

Examples

Might be wise to add some kind of test like

"ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip" |> curl_fetch_memory()

And test for no error. Might also be wise to somehow link the test URL and the package function URL so that a change in the function would invalidate the test. Seemed kinda out of scope though and also I'm not terribly sure how to do this well, so we're flying testless.

stitam commented 5 months ago

Thanks @KaiAragaki for opening this PR and apologies for the delay in my response.

I have checked both URLs in my browser and their contents seem to be identical (which is strange):

https://ftp.ncbi.nih.gov/pub/taxonomy/ https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/

The URL which is currently in the package seems to be working on my end. I wonder if this was just a temporary issue at NCBI rather than a permanent change in the URL? Can you please check if the original URL works on your end now?

KaiAragaki commented 5 months ago

@stitam Thanks so much for your reply!

It looks like it works now - maybe there was a broken redirect that got fixed? Maybe I'm just dumb. Either way, I'll close this PR. Thank you!