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NCBI changed 'country' qualifier to 'geo_loc_name' in ncbi_byid() #135

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boopsboops opened this issue Jul 16, 2024 · 1 comment
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@boopsboops
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As per link below, NCBI have changed the 'country' qualifier to 'geo_loc_name', which mean the ncbi_byid() function no longer parses the XML and produces a 'country' field.

https://ncbiinsights.ncbi.nlm.nih.gov/2023/12/14/update-genbank-qualifier/

It's simple fix and I've issued a pull request.

Code to test:

# load
library("renv")
library("dplyr")

# test traits at current commit
renv::install("ropensci/traits@ee58d04")
traits::ncbi_byid(ids="MT523282.1") |> dplyr::distinct(country) |> print()
# result is 'NA'

# text fix on fork
# restart R
renv::install("boopsboops/traits@ccd098a")
traits::ncbi_byid(ids="MT523282.1") |> dplyr::distinct(country) |> print()
# result is 'Uganda: Kyambura river, mouth, Kazinga Channel' (expected result)
@boopsboops boopsboops changed the title NCBI changed 'country' qualifier to 'geo_loc_name' NCBI changed 'country' qualifier to 'geo_loc_name' in ncbi_byid() Jul 16, 2024
dlebauer added a commit that referenced this issue Oct 1, 2024
Changed 'country' to 'geo_loc_name' in `ncbi_byid()` #135
@dlebauer
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dlebauer commented Oct 1, 2024

@boopsboops thank you for reporting this and submitting a PR! I've merged your PR and will push to CRAN.

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