Fixes to tests to avoid deprecated functions

- remove `without_internet()` which calls `with_mock`, which is deprecated - remove `httptest2` from Suggests - remove unused `with_mock_dir()` calls
AtlasOfLivingAustralia · Nov 16, 2023 · d426cbe · d426cbe
1 parent b1fb9c3
commit d426cbe
Show file tree

Hide file tree

Showing 9 changed files with 28 additions and 123 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -48,7 +48,6 @@ Imports:
 Suggests: 
     covr,
     gt,
-    httptest2,
     kableExtra,
     knitr,
     magrittr,

diff --git a/R/build.R b/R/build.R
@@ -145,10 +145,11 @@ build_taxa_query <- function(ids) {
     list(taxonKey = ids)
   }else{
     wrapped_ids <- paste0("\"", ids, "\"")
+    id_tag <- "lsid"
     glue(
-      "(lsid:",
+      "({id_tag}:",
       glue_collapse(wrapped_ids,
-                    sep = glue(" OR lsid:")),
+                    sep = glue(" OR {id_tag}:")),
       ")")
   }
 }

diff --git a/R/collect_taxa.R b/R/collect_taxa.R
@@ -64,16 +64,10 @@ collect_taxa_la <- function(.query){
       clean_la_taxa(search_terms = search_terms) |>
       bind_rows()
     if(ncol(result) > 1){
-      atlas <- pour("atlas", "region")
-      if(atlas == "France") {
-        name <- c("referenceID")
-      } else {
-        if (atlas == "Portugal") {
-          name <- c("usageKey")
-        } else {
-          name <- c("guid")
-        }
-      }
+      name <- switch(pour("atlas", "region"),
+                     "France" = "referenceID",
+                     "Portugal" = "usageKey",
+                     "guid")
       result <- result |>
         filter(!duplicated({{name}})) |>
         mutate("search_term" = search_terms, .before = 1)
@@ -104,7 +98,7 @@ clean_la_taxa <- function(result, search_terms){
         list_of_results <- list(a)
       }
     }
-    
+
     # find best string match to search term
     if (length(list_of_results) > 1) { # i.e. more than one match
       if ("name" %in% list_of_results[[1]]) {

diff --git a/tests/testthat.R b/tests/testthat.R
@@ -1,7 +1,5 @@
 library(testthat)
 library(galah)
-library(httptest2)
-
 galah_config(directory = tempdir(), 
              email = "ala4r@ala.org.au",
              caching = FALSE, 

diff --git a/tests/testthat/_snaps/galah_identify.md b/tests/testthat/_snaps/galah_identify.md
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
diff --git a/tests/testthat/test-atlas_counts.R b/tests/testthat/test-atlas_counts.R
@@ -111,9 +111,6 @@ test_that("atlas_counts filters correctly with galah_geolocate/galah_polygon", {
   skip_if_offline()
   wkt <- "POLYGON ((146.5425 -42.63203, 146.8312 -43.13203, 147.4085 -43.13203, 147.6972 -42.63203, 147.4085 -42.13203, 146.8312 -42.13203, 146.5425 -42.63203))" |>
     sf::st_as_sfc()
-  with_mock_dir("galah_identify", {
-    identify <- galah_identify("Perameles")
-  })  
   base_query <- galah_call() |>
     identify("Perameles") |>
     filter(year >= 2020) |>
@@ -132,9 +129,6 @@ test_that("atlas_counts filters correctly with galah_geolocate/galah_bbox", {
   skip_if_offline()
   wkt <- "POLYGON ((146.5425 -42.63203, 146.8312 -43.13203, 147.4085 -43.13203, 147.6972 -42.63203, 147.4085 -42.13203, 146.8312 -42.13203, 146.5425 -42.63203))" |>
     sf::st_as_sfc()
-  with_mock_dir("galah_identify", {
-    identify <- galah_identify("Perameles")
-  })
   base_query <- galah_call() |>
     identify("Perameles") |>
     filter(year >= 2020) |>

diff --git a/tests/testthat/test-atlas_occurrences.R b/tests/testthat/test-atlas_occurrences.R
@@ -1,13 +1,11 @@
-without_internet({
-  test_that("atlas_occurrences fails nicely if no email is provided", {
-    galah_config(email = "", run_checks = FALSE)
-    expect_error({
-      galah_call() |>
-        filter(year == 1900) |>
-        compute()
-    })
-    galah_config(email = "ala4r@ala.org.au", run_checks = TRUE)
+test_that("atlas_occurrences fails nicely if no email is provided", {
+  galah_config(email = "", run_checks = FALSE)
+  expect_error({
+    galah_call() |>
+      filter(year == 1900) |>
+      compute()
   })
+  galah_config(email = "ala4r@ala.org.au", run_checks = TRUE)
 })
 
 test_that("atlas_occurrences doesn't allow large downloads", {
@@ -25,20 +23,18 @@ test_that("atlas_occurrences gives a nice error for invalid emails", {
   galah_config(email = "ala4r@ala.org.au")
 })
 
-without_internet({
-  test_that("collapse(type = 'occurrences') creates an object, but doesn't ping an API", {
-    result <- galah_call() |> 
-      identify("Perameles") |>
-      collapse()
-    expect_equal(length(result), 4)
-    expect_true(inherits(result, "query_set"))
-    types <- unlist(lapply(result, function(a){a$type}))
-    expect_equal(types,
-                 c("metadata/fields",
-                   "metadata/reasons",
-                   "metadata/taxa-single",
-                   "data/occurrences"))
-  })
+test_that("collapse(type = 'occurrences') creates an object, but doesn't ping an API", {
+  result <- galah_call() |> 
+    identify("Perameles") |>
+    collapse()
+  expect_equal(length(result), 4)
+  expect_true(inherits(result, "query_set"))
+  types <- unlist(lapply(result, function(a){a$type}))
+  expect_equal(types,
+               c("metadata/fields",
+                 "metadata/reasons",
+                 "metadata/taxa-single",
+                 "data/occurrences"))
 })
 
 test_that("`compute(type = 'occurrences')` works", {

diff --git a/tests/testthat/test-international-Brazil.R b/tests/testthat/test-international-Brazil.R
@@ -67,7 +67,7 @@ test_that("search_all(taxa) works for Brazil", {
   skip_if_offline()
   x <- search_all(taxa, "Mammalia")
   # Just a side note: 
-  # Searching on the brazilian atlas is pretty unpredictable. 
+  # Searching on the Brazilian atlas is pretty unpredictable. 
   # e.g. "Animalia" & "Mammalia" do not return results in search
   #      "Fungi" returns a Candelaria species, rather than the kingdom
   expect_gte(nrow(x), 1)