VCR tests for ebirdtaxonomy

DESCRIPTION

@@ -33,7 +33,8 @@ Suggests:
     rmarkdown,
     testthat,
     covr,
-    vcr (>= 0.6.0)
+    vcr (>= 0.6.0),
+    withr
 RoxygenNote: 7.3.1
 X-schema.org-applicationCategory: Data Access
 X-schema.org-keywords: birds, birding, ebird, database, data, biology, observations, sightings, ornithology

R/ebirdtaxonomy.R

@@ -17,6 +17,8 @@
 #'    See \url{https://docs.oracle.com/javase/6/docs/api/java/util/Locale.html} and 
 #'    \url{https://support.ebird.org/en/support/solutions/articles/48000804865-bird-names-in-ebird} 
 #'    (defaults to en_US).
+#' @param species Character vector of eBird taxonomy species code(s). Limits query
+#'    results to only these taxa. Default is NULL, which does not limit taxa.
 #' @param key eBird API key. You can obtain one from https://ebird.org/api/keygen.
 #'    We strongly recommend storing it in your \code{.Renviron} file as an 
 #'    environment variable called \code{EBIRD_KEY} to avoid having to constantly 
@@ -46,14 +48,18 @@
 #'    Sebastian Pardo \email{sebpardo@@gmail.com}
 #' @references \url{http://ebird.org/}
 
-ebirdtaxonomy <- function(cat=NULL, locale=NULL, key = NULL, ...){
+ebirdtaxonomy <- function(cat=NULL, locale=NULL, species = NULL, key = NULL, ...){
   cats <- c("domestic", "form", "hybrid", "intergrade", "issf", "slash", "species", "spuh")
 
   if (!all(vapply(cat, function(x) x %in% cats, FUN.VALUE = logical(1)))) {
     stop("You have supplied an invalid species category")
   }
   cat <- if(!is.null(cat)) cat <- paste0(cat, collapse = ",")
-  args <- list(fmt='json', cat=cat, locale=locale)
+  if (!is.null(species) && (length(species) == 0 || any(is.na(species)))){
+    stop('Invalid species code(s)')
+  }
+  species <- if(!is.null(species)) species <- paste0(species, collapse = ",")
+  args <- list(fmt='json', cat=cat, locale=locale, species=species)
 
   # Allow not using a key for just this function, it's the only endpoint 
   # that allows it

tests/fixtures/ebirdtaxonomy.yml

@@ -0,0 +1,120 @@
+http_interactions:
+- request:
+    method: get
+    uri: https://ebird.org/ws2.0/ref/taxonomy/ebird?fmt=json&cat=domestic&species=btbwar%2Cmallar2%2Cgragoo1
+    body:
+      encoding: ''
+      string: ''
+    headers:
+      Accept: application/json, text/xml, application/xml, */*
+      X-eBirdApiToken: <<<redacted>>>
+  response:
+    status:
+      status_code: 200
+      category: Success
+      reason: OK
+      message: 'Success: (200) OK'
+    headers:
+      cache-control: no-cache, no-store, max-age=0, must-revalidate
+      content-encoding: gzip
+      content-length: '297'
+      content-type: application/json;charset=utf-8
+      date: Sat, 09 Mar 2024 04:35:17 GMT
+      expires: '0'
+      pragma: no-cache
+      server: Apache
+      strict-transport-security: max-age=31536000 ; includeSubDomains
+      vary:
+      - Accept-Encoding
+      - Accept-Encoding,Origin,Access-Control-Request-Method,Access-Control-Request-Headers
+      x-content-type-options: nosniff
+      x-frame-options: DENY
+      x-xss-protection: 1; mode=block
+    body:
+      encoding: ''
+      file: no
+      string: '[{"sciName":"Anser anser (Domestic type)","comName":"Graylag Goose
+        (Domestic type)","speciesCode":"gragoo1","category":"domestic","taxonOrder":266.0,"bandingCodes":[],"comNameCodes":["GRGO"],"sciNameCodes":["ANAN"],"order":"Anseriformes","familyCode":"anatid1","familyComName":"Ducks,
+        Geese, and Waterfowl","familySciName":"Anatidae","reportAs":"gragoo"},{"sciName":"Anas
+        platyrhynchos (Domestic type)","comName":"Mallard (Domestic type)","speciesCode":"mallar2","category":"domestic","taxonOrder":518.0,"bandingCodes":[],"comNameCodes":["MALL"],"sciNameCodes":["ANPL"],"order":"Anseriformes","familyCode":"anatid1","familyComName":"Ducks,
+        Geese, and Waterfowl","familySciName":"Anatidae","reportAs":"mallar3"}]'
+  recorded_at: 2024-03-09 04:38:56 GMT
+  recorded_with: vcr/1.2.2, webmockr/0.9.0
+- request:
+    method: get
+    uri: https://ebird.org/ws2.0/ref/taxonomy/ebird?fmt=json&cat=spuh%2Cslash&species=passer1%2Cbird1%2Camewoo%2Cy00335
+    body:
+      encoding: ''
+      string: ''
+    headers:
+      Accept: application/json, text/xml, application/xml, */*
+      X-eBirdApiToken: <<<redacted>>>
+  response:
+    status:
+      status_code: 200
+      category: Success
+      reason: OK
+      message: 'Success: (200) OK'
+    headers:
+      cache-control: no-cache, no-store, max-age=0, must-revalidate
+      content-encoding: gzip
+      content-length: '312'
+      content-type: application/json;charset=utf-8
+      date: Sat, 09 Mar 2024 04:35:17 GMT
+      expires: '0'
+      pragma: no-cache
+      server: Apache
+      strict-transport-security: max-age=31536000 ; includeSubDomains
+      vary:
+      - Accept-Encoding
+      - Accept-Encoding,Origin,Access-Control-Request-Method,Access-Control-Request-Headers
+      x-content-type-options: nosniff
+      x-frame-options: DENY
+      x-xss-protection: 1; mode=block
+    body:
+      encoding: ''
+      file: no
+      string: '[{"sciName":"Passerina amoena/cyanea","comName":"Lazuli/Indigo Bunting","speciesCode":"y00335","category":"slash","taxonOrder":34063.0,"bandingCodes":[],"comNameCodes":["LAZB","INBU","LABU"],"sciNameCodes":["PAAM","PACY"],"order":"Passeriformes","familyCode":"cardin1","familyComName":"Cardinals
+        and Allies","familySciName":"Cardinalidae"},{"sciName":"Passeriformes sp.","comName":"passerine
+        sp.","speciesCode":"passer1","category":"spuh","taxonOrder":35292.0,"bandingCodes":[],"comNameCodes":[],"sciNameCodes":[],"order":"Passeriformes"},{"sciName":"Aves
+        sp.","comName":"bird sp.","speciesCode":"bird1","category":"spuh","taxonOrder":35293.0,"bandingCodes":["UNBI"],"comNameCodes":[],"sciNameCodes":[]}]'
+  recorded_at: 2024-03-09 04:38:56 GMT
+  recorded_with: vcr/1.2.2, webmockr/0.9.0
+- request:
+    method: get
+    uri: https://ebird.org/ws2.0/ref/taxonomy/ebird?fmt=json&species=rewbla
+    body:
+      encoding: ''
+      string: ''
+    headers:
+      Accept: application/json, text/xml, application/xml, */*
+      X-eBirdApiToken: ''
+  response:
+    status:
+      status_code: 200
+      category: Success
+      reason: OK
+      message: 'Success: (200) OK'
+    headers:
+      cache-control: no-cache, no-store, max-age=0, must-revalidate
+      content-encoding: gzip
+      content-length: '218'
+      content-type: application/json;charset=utf-8
+      date: Sat, 09 Mar 2024 04:35:18 GMT
+      expires: '0'
+      pragma: no-cache
+      server: Apache
+      strict-transport-security: max-age=31536000 ; includeSubDomains
+      vary:
+      - Accept-Encoding
+      - Accept-Encoding,Origin,Access-Control-Request-Method,Access-Control-Request-Headers
+      x-content-type-options: nosniff
+      x-frame-options: DENY
+      x-xss-protection: 1; mode=block
+    body:
+      encoding: ''
+      file: no
+      string: '[{"sciName":"Agelaius phoeniceus","comName":"Red-winged Blackbird","speciesCode":"rewbla","category":"species","taxonOrder":33251.0,"bandingCodes":["RWBL"],"comNameCodes":[],"sciNameCodes":["AGPH"],"order":"Passeriformes","familyCode":"icteri1","familyComName":"Troupials
+        and Allies","familySciName":"Icteridae"}]'
+  recorded_at: 2024-03-09 04:38:56 GMT
+  recorded_with: vcr/1.2.2, webmockr/0.9.0

tests/testthat/test-ebirdtaxonomy.R

@@ -1,38 +1,38 @@
-context("ebirdtaxonomy")
+vcr::use_cassette("ebirdtaxonomy", {
+  test_that("ebirdtaxonomy works correctly", {
+    out <- ebirdtaxonomy("domestic", species = c('btbwar', 'mallar2', 'gragoo1'))
+    expect_true(inherits(out, "data.frame"))
+    expect_true(inherits(out, "tbl_df"))
+    expect_equal(nrow(out), 2)
 
-test_that("ebirdtaxonomy works correctly", {
-  skip_on_cran()
-  skip_on_ci()
-
-  out <- ebirdtaxonomy("domestic")
-  out2 <- ebirdtaxonomy(cat=c("spuh", "slash"))
-
-  expect_is(out, "data.frame")
-  expect_is(out, "tbl_df")
-  expect_is(out2, "data.frame")
-  expect_is(out2, "tbl_df")
-
-  expect_is(out$comName, "character")
-  expect_is(out$taxonOrder, "numeric")
-})
-
-test_that("ebirdtaxonomy fails correctly", {
-  skip_on_cran()
-  skip_on_ci()
-
-  mssg <- "You have supplied an invalid species category"
-  expect_error(ebirdtaxonomy("asf"), mssg)
-  expect_error(ebirdtaxonomy(2), mssg)
-
-  expect_error(ebirdtaxonomy("spuh", config=timeout(0.02)))
-})
+    out2 <- ebirdtaxonomy(cat=c("spuh", "slash"),
+                          species = c('passer1', 'bird1', 'amewoo', 'y00335'))
+    expect_equal(nrow(out2), 3)
+    expect_true(inherits(out2, "data.frame"))
+    expect_true(inherits(out2, "tbl_df"))
+    expect_true(inherits(out2$comName, "character"))
+    expect_true(inherits(out2$taxonOrder, "numeric"))
+  })
 
-test_that_without_key("ebirdtaxonomy works without an API key", {
-  skip_on_cran()
-  skip_on_ci()
+  test_that("ebirdtaxonomy fails correctly", {
+    mssg <- "You have supplied an invalid species category"
+    expect_error(ebirdtaxonomy("asf"), mssg)
+    expect_error(ebirdtaxonomy(2), mssg)
+    isc <- 'Invalid species code'
+    expect_error(ebirdtaxonomy(species = character(0)), isc)
+    expect_error(ebirdtaxonomy(species = NA_character_), isc)
+  })
 
-  tax <- ebirdtaxonomy()
-  expect_is(tax, "data.frame")
-  expect_gte(ncol(tax), 12L)
+  test_that("ebirdtaxonomy works without an API key", {
+    withr::with_envvar(
+      c('EBIRD_KEY' = NA),
+      {
+        expect_equal(Sys.getenv('EBIRD_KEY'), "")
+        rwbl <- ebirdtaxonomy(species = 'rewbla')
+        expect_true(inherits(rwbl, "data.frame"))
+        expect_gte(ncol(rwbl), 12L)
+        expect_true(nrow(rwbl) == 1)
+      }
+    )
+  })
 })
-