Update syntax to search_taxa (#112)

* Also update test file name

NAMESPACE

@@ -2,8 +2,8 @@
 
 S3method(atlas_counts,data_request)
 S3method(atlas_counts,default)
-S3method(select_taxa,data_request)
-S3method(select_taxa,default)
+S3method(search_taxa,data_request)
+S3method(search_taxa,default)
 export(ala_citation)
 export(ala_config)
 export(ala_counts)
@@ -32,10 +32,10 @@ export(galah_geolocate)
 export(galah_group_by)
 export(galah_select)
 export(search_fields)
+export(search_taxa)
 export(select_columns)
 export(select_filters)
 export(select_locations)
-export(select_taxa)
 import(assertthat)
 import(httr)
 import(sf)

R/select_taxa.R → R/search_taxa.R

@@ -3,7 +3,7 @@
 #' In the ALA, all records are associated with an identifier that uniquely
 #' identifies the taxon to which that record belongs. However, taxonomic names
 #' are often ambiguous due to homonymy; i.e. re-use of names (common or
-#' scientific) in different clades. Hence, \code{select_taxa} provides a means
+#' scientific) in different clades. Hence, \code{search_taxa} provides a means
 #' to search for taxonomic names and check the results are 'correct' before
 #' proceeded to download data via \code{\link{ala_occurrences}()},
 #' \code{\link{ala_species}()} or \code{\link{ala_counts}()}. The resulting
@@ -27,42 +27,42 @@
 #' @examples
 #' \dontrun{
 #' # Search using a single term
-#' select_taxa("Reptilia")
+#' search_taxa("Reptilia")
 #' # or equivalently:
-#' select_taxa("reptilia") # not case sensitive
+#' search_taxa("reptilia") # not case sensitive
 #'
 #' # Search using an unique taxon identifier
-#' select_taxa(query = "https://id.biodiversity.org.au/node/apni/2914510")
+#' search_taxa(query = "https://id.biodiversity.org.au/node/apni/2914510")
 #'
 #' # Search multiple taxa
-#' select_taxa(c("reptilia", "mammalia")) # returns one row per taxon
+#' search_taxa(c("reptilia", "mammalia")) # returns one row per taxon
 #' }
 #' @export
-select_taxa <- function(...) {
-  UseMethod("select_taxa")
+search_taxa <- function(...) {
+  UseMethod("search_taxa")
 }
 
 #' @export
-#' @rdname select_taxa
-select_taxa.data_request <- function(request, ...) {
-  request$taxa <- do.call(select_taxa, merge_args(request, list(...)))
+#' @rdname search_taxa
+search_taxa.data_request <- function(request, ...) {
+  request$taxa <- do.call(search_taxa, merge_args(request, list(...)))
   return(request)
 }
 
 #' @export
-#' @rdname select_taxa
-select_taxa.default <- function(query, is_id = FALSE) {
+#' @rdname search_taxa
+search_taxa.default <- function(query, is_id = FALSE) {
   assert_that(is.logical(is_id))
   if(missing(is_id)){is_id <- FALSE}
   verbose <- getOption("galah_config")$verbose
 
   if (getOption("galah_config")$atlas != "Australia") {
-    stop("`select_taxa` only provides information on Australian taxonomy. To search taxonomy for ",
+    stop("`search_taxa` only provides information on Australian taxonomy. To search taxonomy for ",
          getOption("galah_config")$atlas, " use `taxize`. See vignette('international_atlases') for more information")
   }
 
   if (missing(query)) {
-    stop("`select_taxa` requires a query to search for")
+    stop("`search_taxa` requires a query to search for")
   }
 
   if (is_id) {

tests/testthat/test-search_taxa.R

@@ -0,0 +1,103 @@
+context("Taxa search")
+
+test_that("search_taxa checks inputs", {
+  expect_error(search_taxa())
+  expect_warning( #FIXME: There are no warnings, just an error. Did this change since adding ala_taxonomy()?
+    expect_error(search_taxa("Varanus varius", children = "false")))
+})
+
+test_that("search_taxa check atlas", {
+  galah_config(atlas = "Austria")
+  expect_error(search_taxa("Vulpes vulpes"))
+  galah_config(atlas = "Australia")
+})
+
+
+test_that("search_taxa works for simple queries", {
+  vcr::use_cassette("search_taxa_simple", {
+    taxa <- search_taxa("Microseris lanceolata")
+  })
+  expect_equal(nrow(taxa), 1)
+})
+
+
+test_that("search_taxa works for multiple queries", {
+  vcr::use_cassette("search_taxa_multiple", {
+    taxa <- search_taxa(c("Eucalyptus", "Banksia", "Acacia"))
+  })
+  expect_equal(nrow(taxa), 3)
+})
+
+
+test_that("search_taxa handles data.frame input", {
+  vcr::use_cassette("search_taxa_df", {
+    taxa <- search_taxa(
+      data.frame(genus = c("Banksia", "Microseris"), kingdom = "Plantae"))
+  })
+  expect_equal(nrow(taxa), 2)
+})
+
+vcr::use_cassette("search_taxa_valid_invalid", {
+  test_that("search_taxa handles a mix of valid and invalid queries", {
+    expect_message(taxa <- search_taxa(c("Eucalyptus", "Banksia", "Wattle")))
+    expect_equal(nrow(taxa), 3)
+  })
+})
+
+vcr::use_cassette("search_taxa_invalid", {
+  test_that("search_taxa gives a message for invalid ids", {
+    # unrecognised name
+    expect_message(search_taxa("bad_term"))
+    # unrecognised id
+    expect_message(search_taxa("1234", is_id = TRUE))
+  })
+})
+
+vcr::use_cassette("search_taxa_extended", { # FIXME: search_taxa() fails - search_taxa no longer accepts these arguments
+  test_that("search_taxa uses additional arguments", {
+    expect_warning(
+      taxa <- search_taxa("Anas", all_ranks = TRUE, children = TRUE,
+                          counts = TRUE)
+      )
+    expect_true("subfamily" %in% names(taxa))
+    expect_gt(nrow(taxa), 1)
+    expect_true("count" %in% names(taxa))
+  })
+})
+
+
+test_that("child_concepts behaves correctly", {
+  vcr::use_cassette("child_concepts", {
+    id <- "urn:lsid:biodiversity.org.au:afd.taxon:e4c87583-08ed-4183-8653-c8f487a93735"
+    children <- child_concepts(id)
+  }, preserve_exact_body_bytes = TRUE)
+
+  expect_s3_class(children, "data.frame")
+  expect_equal(nrow(children), 1)
+})
+
+
+test_that("search_taxa searches using multiple ranks", {
+  vcr::use_cassette("search_taxa_rank_search", {
+    taxa <- search_taxa(list(genus = "Acacia", kingdom = "Plantae"))
+  })
+    expect_s3_class(taxa, "data.frame")
+    expect_equal(taxa$rank, "genus")
+    expect_equal(nrow(taxa), 1)
+})
+
+
+test_that("search_taxa searches using identifier", {
+  vcr::use_cassette("search_taxa_id_search", {
+    # check different types of id
+    query <- c("urn:lsid:biodiversity.org.au:afd.taxon:08b9a1f0-62ae-45ca-9208-e773b00021ed",
+               "NZOR-6-1742", "https://id.biodiversity.org.au/node/apni/2910467")
+    taxa <- search_taxa(query)
+  })
+    expect_s3_class(taxa, "data.frame")
+    expect_equal(nrow(taxa), 3)
+})
+
+test_that("search_taxa handles name issues", {
+  expect_warning(search_taxa("Microseris"))
+})