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fix: add acceptedUsageKey and acceptedScientificName to name_backbone… #826

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Merged
jhnwllr merged 1 commit into from
Dec 12, 2025
Merged

fix: add acceptedUsageKey and acceptedScientificName to name_backbone… #826

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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ Description: A programmatic interface to the Web Service methods
retrieving information on data providers, getting species occurrence
records, getting counts of occurrence records, and using the GBIF
tile map service to make rasters summarizing huge amounts of data.
Version: 3.8.4.1
Version: 3.8.4.2
License: MIT + file LICENSE
Authors@R: c(
person("Scott", "Chamberlain", role = "aut", comment = c("0000-0003-1444-9135")),
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11 changes: 10 additions & 1 deletion R/name_backbone.r
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Original file line number Diff line number Diff line change
Expand Up @@ -262,6 +262,14 @@ process_name_backbone_output <- function(tt, args) {
} else {
NULL
}
acceptedUsage <- if (!is.null(tt$acceptedUsage)) {
a <- tibble::as_tibble(tt$acceptedUsage)[c("key","name")]
colnames(a)[colnames(a) == "key"] <- "acceptedUsageKey"
colnames(a)[colnames(a) == "name"] <- "acceptedScientificName"
Comment on lines +266 to +268
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Copilot AI Dec 12, 2025

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The acceptedUsage processing subsets only the "key" and "name" fields, which is inconsistent with how the usage object is processed (lines 231-235). The usage processing converts the entire object to a tibble and then renames specific columns. Consider following the same pattern here: convert the entire acceptedUsage object to a tibble first, then rename the columns, to maintain consistency and allow any additional fields from the API to be included.

Suggested change
a <- tibble::as_tibble(tt$acceptedUsage)[c("key","name")]
colnames(a)[colnames(a) == "key"] <- "acceptedUsageKey"
colnames(a)[colnames(a) == "name"] <- "acceptedScientificName"
a <- tibble::as_tibble(tt$acceptedUsage)
if ("key" %in% colnames(a)) colnames(a)[colnames(a) == "key"] <- "acceptedUsageKey"
if ("name" %in% colnames(a)) colnames(a)[colnames(a) == "name"] <- "acceptedScientificName"

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a
} else {
NULL
}
verbatim <- if (!is.null(args)) {
input_args_clean <- args[!names(args) %in%
c("strict","verbose","start","limit","curlopts")]
Expand All @@ -273,7 +281,8 @@ process_name_backbone_output <- function(tt, args) {
} else {
NULL
}
out <- do.call("cbind", rgbif_compact(list(usage,
out <- do.call("cbind", rgbif_compact(list(usage,
acceptedUsage,
diagnostics,
classification,
synonym,
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20 changes: 20 additions & 0 deletions tests/fixtures/name_backbone_acceptedUsageKey.yml
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11 changes: 11 additions & 0 deletions tests/testthat/test-name_backbone.r
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Expand Up @@ -127,3 +127,14 @@ test_that("name_backbone verbose=TRUE", {
expect_true(all(vv$verbatim_name == "Calopteryx"))
expect_true(nrow(vv) > nrow(tt))
})

test_that("name_backbone returns acceptedUsageKey", {
vcr::use_cassette("name_backbone_acceptedUsageKey", {
aa <- name_backbone(name = 'Anastrophyllum minutum')
})
expect_is(aa, "tbl")
expect_is(aa, "tbl_df")
expect_is(aa, "data.frame")
expect_true("acceptedUsageKey" %in% colnames(aa))
expect_true("acceptedScientificName" %in% colnames(aa))
Comment on lines +138 to +139
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Copilot AI Dec 12, 2025

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The test verifies that the columns exist but doesn't check their actual values. Based on the fixture data, the test should verify that acceptedUsageKey is "2689422" and acceptedScientificName is "Sphenolobus minutus (Schreb. ex Cranz) Berggr." to ensure the function correctly extracts these values from the API response.

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})
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