name_lookup adding constituentKey #729

ropensci · May 1, 2024 · 3ae007a · 3ae007a
1 parent 9078e0e
commit 3ae007a
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Showing 4 changed files with 60 additions and 13 deletions.
diff --git a/R/name_lookup.r b/R/name_lookup.r
@@ -75,11 +75,28 @@
 #'   curlopts = list(verbose = TRUE))
 #' }
 
-name_lookup <- function(query=NULL, rank=NULL, higherTaxonKey=NULL, status=NULL,
-  isExtinct=NULL, habitat=NULL, nameType=NULL, datasetKey=NULL,
-  origin=NULL, nomenclaturalStatus=NULL, limit=100, start=0, facet=NULL,
-  facetMincount=NULL, facetMultiselect=NULL, type=NULL, hl=NULL, issue=NULL,
-  verbose=FALSE, return=NULL, curlopts = list()) {
+name_lookup <- function(query=NULL,
+                        rank=NULL,
+                        higherTaxonKey=NULL,
+                        status=NULL,
+                        isExtinct=NULL,
+                        habitat=NULL,
+                        nameType=NULL,
+                        datasetKey=NULL,
+                        origin=NULL,
+                        nomenclaturalStatus=NULL,
+                        limit=100,
+                        start=0,
+                        facet=NULL,
+                        facetMincount=NULL,
+                        facetMultiselect=NULL,
+                        type=NULL,
+                        hl=NULL,
+                        issue=NULL,
+                        constituentKey=NULL,
+                        verbose=FALSE,
+                        return=NULL,
+                        curlopts = list()) {
 
   pchk(return, "name_lookup")
   if (!is.null(facetMincount) && inherits(facetMincount, "numeric"))
@@ -99,15 +116,28 @@ name_lookup <- function(query=NULL, rank=NULL, higherTaxonKey=NULL, status=NULL,
   datasetKey <- as_many_args(datasetKey)
   origin <- as_many_args(origin)
   issue <- as_many_args(issue)
+  constituentKey <- as_many_args(constituentKey)
 
   url <- paste0(gbif_base(), '/species/search')
-  args <- rgbif_compact(list(q=query, isExtinct=as_log(isExtinct),
-            nomenclaturalStatus=nomenclaturalStatus, limit=limit, offset=start,
-            facetMincount=facetMincount,
-            facetMultiselect=as_log(facetMultiselect), hl=as_log(hl),
-            type=type))
-  args <- c(args, facetbyname, rank, higherTaxonKey, status,
-            habitat, nameType, datasetKey, origin, issue)
+  args <- rgbif_compact(list(q=query, 
+                             isExtinct=as_log(isExtinct),
+                             nomenclaturalStatus=nomenclaturalStatus, 
+                             limit=limit, offset=start,
+                             facetMincount=facetMincount,
+                             facetMultiselect=as_log(facetMultiselect), 
+                             hl=as_log(hl),
+                             type=type))
+  args <- c(args, 
+            facetbyname, 
+            rank, 
+            higherTaxonKey, 
+            status,
+            habitat, 
+            nameType, 
+            datasetKey, 
+            origin, 
+            issue,
+            constituentKey)
 
   # paging implementation
   if (limit > 1000) {

diff --git a/man-roxygen/namelkup.r b/man-roxygen/namelkup.r
@@ -86,10 +86,10 @@
 #' @param limit Number of records to return.
 #' Hard maximum limit set by GBIF API: 99999.
 #' @param start Record number to start at. Default: 0.
+#' @param constituentKey Filters by the dataset's constituent key (a uuid). 
 #' @param verbose (logical) If \code{TRUE}, all data is returned as a list for each
 #' element. If \code{FALSE} (default) a subset of the data that is thought to be most
 #' essential is organized into a data.frame.
-#'
 #' @param return Defunct. All components are returned; index to the
 #' one(s) you want
 #'

diff --git a/man/name_lookup.Rd b/man/name_lookup.Rd
diff --git a/tests/testthat/test-name_lookup.r b/tests/testthat/test-name_lookup.r
@@ -146,6 +146,20 @@ test_that("paging: name_usage returns all records from dataset: limit > n_record
   expect_gte(nrow(cc$data), 1051)
 })
 
+test_that("name_lookup constituentKey works as expected.", {
+
+  vcr::use_cassette("name_lookup_constituentKey", {
+    aa <- name_lookup(constituentKey = "7ddf754f-d193-4cc9-b351-99906754a03b")
+  }, preserve_exact_body_bytes = TRUE)
+
+  expect_is(aa, "gbif")
+  expect_is(aa$data, "data.frame")
+  expect_is(aa$data, "tbl_df")
+  expect_is(aa$data, "tbl")
+  expect_equal(unique(tolower(aa$data$constituentKey)), "7ddf754f-d193-4cc9-b351-99906754a03b")
+})
+
+
 test_that("name_lookup handles no results without failing", {
   skip_on_cran() # because fixture in .Rbuildignore