Nothing
# set verbose to off
galah_config(verbose = FALSE, run_checks = FALSE)
test_that("swapping to atlas = Spain works", {
expect_message(galah_config(atlas = "Spain"))
})
test_that("show_all(fields) works for Spain", {
skip_if_offline()
x <- show_all(fields)
expect_gt(nrow(x), 1)
expect_true(inherits(x, c("tbl_df", "tbl", "data.frame")))
# also that fields match those returned by default_columns()
y <- default_columns() # internal function called by `galah_select()`
expect_true(all(y %in% x$id))
})
test_that("show_all(licences) works for Spain", {
skip_if_offline()
x <- show_all(licences)
expect_gt(nrow(x), 1)
expect_true(inherits(x, c("tbl_df", "tbl", "data.frame")))
})
test_that("show_all(collections) works for Spain", {
skip_if_offline()
x <- show_all(collections, limit = 10)
expect_lte(nrow(x), 10)
expect_true(inherits(x, c("tbl_df", "tbl", "data.frame")))
})
test_that("show_all(datasets) works for Spain", {
skip_if_offline()
x <- show_all(datasets, limit = 10)
expect_lte(nrow(x), 10)
expect_true(inherits(x, c("tbl_df", "tbl", "data.frame")))
})
test_that("show_all(providers) works for Spain", {
skip_if_offline()
x <- show_all(providers, limit = 10)
expect_lte(nrow(x), 10)
expect_true(inherits(x, c("tbl_df", "tbl", "data.frame")))
})
test_that("show_all(reasons) works for Spain", {
skip_if_offline()
x <- show_all(reasons)
expect_gt(nrow(x), 1)
expect_true(inherits(x, c("tbl_df", "tbl", "data.frame")))
})
test_that("show_all(assertions) works for Spain", {
skip_if_offline()
x <- show_all(assertions)
expect_gt(nrow(x), 1)
expect_true(inherits(x, c("tbl_df", "tbl", "data.frame")))
})
test_that("show_all(profiles) works for Spain", {
skip_if_offline()
x <- show_all(profiles)
expect_gt(nrow(x), 1)
expect_true(inherits(x, c("tbl_df", "tbl", "data.frame")))
})
test_that("show_all(lists) works for Spain", {
skip_if_offline()
x <- show_all(lists, limit = 10)
expect_lte(nrow(x), 10)
expect_true(inherits(x, c("tbl_df", "tbl", "data.frame")))
})
test_that("search_all(fields) works for Spain", {
skip_if_offline()
x <- search_all(fields, "year")
expect_gte(nrow(x), 1)
expect_true(inherits(x, c("tbl_df", "tbl", "data.frame")))
})
test_that("search_all(taxa) works for Spain", {
skip_if_offline()
x <- search_all(taxa, "Mammalia")
expect_gte(nrow(x), 1)
expect_true(inherits(x, c("tbl_df", "tbl", "data.frame")))
})
test_that("search_all(taxa) works using data.frames for Spain", {
skip_if_offline()
x <- search_all(taxa,
data.frame(kingdom = "Animalia",
phylum = "Chordata"))
expect_gte(nrow(x), 1)
expect_true(inherits(x, c("tbl_df", "tbl", "data.frame")))
})
test_that("search_all(identifiers) works for Spain", {
skip_if_offline()
x <- search_all(identifiers, "359")
expect_gte(nrow(x), 1)
expect_true(inherits(x, c("tbl_df", "tbl", "data.frame")))
})
test_that("show_values works for fields for Spain", {
skip_if_offline()
x <- search_all(fields, "basisOfRecord") |>
show_values()
expect_gte(nrow(x), 1)
expect_true(inherits(x, c("tbl_df", "tbl", "data.frame")))
})
test_that("show_values works for profiles for Spain", {
skip_if_offline()
x <- search_all(profiles, "LA") |>
show_values()
expect_gte(nrow(x), 1)
expect_true(inherits(x, c("tbl_df", "tbl", "data.frame")))
})
test_that("atlas_counts works for Spain", {
skip_if_offline()
expect_gt(atlas_counts()$count, 0)
expect_gt(atlas_counts(type = "species")$count, 0)
})
test_that("atlas_counts works with galah_identify for Spain", {
skip_if_offline()
result <- galah_call() |>
identify("Mammalia") |>
count() |>
collect()
expect_gt(result$count, 1)
result2 <- galah_call() |>
filter(class == "Mammalia") |>
count() |>
collect()
expect_lt(
sqrt((result2$count - result$count)^2) / result$count,
0.1) # i.e. <1% margin of error
})
test_that("atlas_counts works with group_by for Spain", {
skip_if_offline()
result <- galah_call() |>
filter(year >= 2000) |>
group_by(basis_of_record) |>
count() |>
collect()
expect_gt(nrow(result), 1)
expect_equal(names(result), c("basis_of_record", "count"))
})
## profiles system is available for Spain, but not implemented in biocache
# test_that("galah_apply_profile filters counts for Spain", {
# vcr::use_cassette("IA_Spain_apply_profile_counts", {
# without_profile <- galah_call() |>
# atlas_counts()
# with_profile <- galah_call() |>
# galah_apply_profile(LA) |>
# atlas_counts()
# })
#
# expect_gt(with_profile[[1]], 0)
# expect_equal(class(without_profile), class(with_profile))
# expect_lt(with_profile[[1]], without_profile[[1]])
# })
test_that("galah_select works for Spain", {
skip_if_offline()
x <- galah_select()
y <- galah_select(basisOfRecord)
expect_equal(length(x), 2)
expect_equal(x$summary, "group = basic")
expect_equal(x$group, "basic")
expect_true(inherits(x, c("list")))
expect_equal(length(y), 3)
expect_equal(y$summary, "basisOfRecord")
expect_equal(y$group, character(0))
expect_true(inherits(y, c("list")))
expect_true(inherits(y[[1]], c("quosure", "formula")))
})
# Occurrences working as of 2023/10/31
test_that("atlas_occurrences works for Spain", {
skip_on_cran()
skip_if_offline()
galah_config(
atlas = "Spain",
email = "test@ala.org.au",
send_email = FALSE)
occ <- galah_call() |>
galah_identify("Mammalia") |>
galah_filter(year <= 1800) |>
galah_select(species, year) |>
atlas_occurrences()
expect_gt(nrow(occ), 0)
expect_equal(ncol(occ), 2)
expect_true(inherits(occ, c("tbl_df", "tbl", "data.frame")))
})
galah_config(atlas = "Australia")
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