additional tests (#132)

Add tests for parts of functions not being tested

R/join_.R

@@ -280,7 +280,7 @@ join_contributors <- function(database,
 
     compacted_contributors_column <-
       contributors_tmp %>% 
-      tidyr::nest(-dplyr::all_of("dataset_id")) %>%
+      tidyr::nest(data = -dplyr::all_of(c("dataset_id"))) %>%
       dplyr::mutate(data_contributors = purrr::map_chr(data, jsonlite::toJSON)) %>%
       dplyr::select(-dplyr::any_of("data")) %>%
       dplyr::ungroup()

tests/testthat/test-as_wide_table.R

@@ -10,3 +10,19 @@ test_that("Function is working", {
   })
 
 expect_error(as_wide_table())
+
+
+test_that("old versions will complain", {
+    expect_error(as_wide_table(austraits_3.0.2_lite))
+    expect_error(as_wide_table(austraits_4.2.0_lite))
+    expect_error(join_contexts_old(austraits_3.0.2_lite))
+    expect_error(join_contexts_old(austraits_4.2.0_lite))
+  })
+
+
+test_that("function `collapse_cols` works", {
+    data <- (austraits_5.0.0_lite %>% extract_dataset("Bloomfield_2018"))$locations
+    data_collapsed <- (data %>% collapse_cols())[[1]]
+    expect_equal(stringr::str_count(data_collapsed, "="), 5)
+    expect_equal(stringr::str_count(data_collapsed, "; "), 4)
+})

tests/testthat/test-extract_.R

@@ -17,6 +17,8 @@ test_extract_error <- function(austraits){
     expect_error(austraits %>% extract_taxa())
     expect_error(austraits %>% extract_dataset())
     expect_error(austraits %>% extract_trait())
+    expect_error(austraits_3.0.2_lite %>% extract_data())
+    expect_error(austraits_4.2.0_lite %>% extract_data())
   })
 }
 
@@ -188,6 +190,12 @@ test_that("Extraction of dataset was successful", {
   expect_equal(1, dplyr::n_distinct(trait_subset$traits$trait_name))
 })
 
+test_that("Expect error if taxon_name column missing", {
+  traits_without_taxon_name <- extract_dataset(austraits_5.0.0_lite, dataset_id = dataset_id)
+  traits_without_taxon_name$traits <- traits_without_taxon_name$traits %>% dplyr::select(-taxon_name)
+  expect_error((traits_without_taxon_name %>% extract_trait("leaf_area"))$traits)
+})
+
 test_that("Extraction of dataset was successful using `extract_data`", {
   subset <- extract_data(database = austraits_5.0.0_lite, table = "traits", col = "dataset_id", col_value = dataset_id)
   trait_subset <- extract_data(database = austraits_5.0.0_lite, table = "traits", col = "trait_name", col_value = trait_name)

tests/testthat/test-flatten_database.R

@@ -8,7 +8,6 @@ combined_table <- flatten_database(database)
 # Crous_2013 has many context properties, from 4 of 5 possible categories
 dataset_id_2 <- "Crous_2013"
 database_2 <- extract_dataset(austraits_5.0.0_lite, dataset_id_2)
-combined_table_2 <- flatten_database(database_2)
 
 #expected_output <- readr::read_csv("tests/testthat/Falster_2003_combined_format.csv", show_col_types = FALSE)
 expected_output <- readr::read_csv("Falster_2003_combined_format.csv", show_col_types = FALSE)
@@ -21,6 +20,27 @@ test_that("`flatten_database` is working with format = single_column_pretty", {
     expect_true(stringr::str_detect(combined_table$data_contributors[1], "<"))
 })
 
+database_3 <- extract_dataset(austraits_5.0.0_lite, "Bloomfield_2018")
+combined_table_3a <- flatten_database(database_3, format = "single_column_pretty")
+combined_table_3b <- flatten_database(database_3, format = "many_columns")
+
+test_that("`flatten_database` defaults to `single_column_pretty` for contributors", {
+  expect_equal(combined_table_3a$data_contributors, combined_table_3b$data_contributors)
+})
+
+# test that join_location_coordinates works as intended
+
+database_no_coord <- austraits_5.0.0_lite %>% extract_dataset("Kooyman_2011")
+
+test_that("`join_location_coordinate` works as intended", {
+
+expect_contains(names(combined_table), c("latitude (deg)", "longitude (deg)")) # proper columns present in full combined table
+expect_contains(names(join_location_coordinates(database)$traits), c("latitude (deg)", "longitude (deg)"))  # proper columns present when just `join_location_coordinate` used
+expect_contains(names(join_location_coordinates(database_no_coord)$traits), c("latitude (deg)", "longitude (deg)"))  # proper columns present if dataset without location coordinates is used
+
+})
+
+
 # test different packing formats for locations
 
 location_vars <- (database$locations %>% dplyr::distinct(location_property))$location_property
@@ -51,12 +71,14 @@ test_that("`join_locations` is working with different formats, vars", {
 contributors_no_ORCID <- (database %>% join_contributors(vars = c("affiliation", "additional_role")))$traits
 contributors_with_ORCID <- (database %>% join_contributors(vars = "all"))$traits
 contributors_default <- (database %>% join_contributors())$traits
+contributors_json <- (database %>% join_contributors(format = "single_column_json"))$traits
 
 test_that("`join_contributors` is working with vars options", {
   expect_equal(length(contributors_no_ORCID), length(contributors_default))
   expect_equal(contributors_with_ORCID, contributors_default)
   expect_true(stringr::str_detect(contributors_with_ORCID$data_contributors[3], "ORCID"))
   expect_false(stringr::str_detect(contributors_no_ORCID$data_contributors[3], "ORCID"))
+  expect_equal(stringr::str_extract(contributors_json$data_contributors[[1]], "^[:punct:]+"), "[{\"")
 })
 
 # test different packing formats & `include_description` for contexts