tests/testthat/test-galah_select.R

In galah: Biodiversity Data from the GBIF Node Network

test_that("`galah_select()` doesn't return error when columns don't exist", {
  expect_no_error(galah_select(basisOfRecors))
  expect_no_error(galah_select(year, basisOfRecord, eventdate))
})

test_that("`galah_select()` triggers error during `compute()` when columns don't exist", {
  skip_if_offline()
  expect_error(
    galah_call() |>
      identify("perameles") |>
      filter(year == 2003) |>
      galah_select(basisOfRecors) |>
      compute(),
    "Can't subset columns that don't exist."
  )
  expect_error(
    galah_call() |>
      identify("perameles") |>
      filter(year == 2003) |>
      select(year, basisOfRecord, eventdate) |>
      compute(),
    "Can't subset columns that don't exist."
  )
})

test_that("`galah_select()` returns requested columns", {
  skip_if_offline()
  galah_config(email = "ala4r@ala.org.au", run_checks = FALSE)
  selected_columns <- galah_select(year, basisOfRecord)
  query <- atlas_occurrences(
    identify = galah_identify("oxyopes dingo"),
    select = selected_columns)
  expect_s3_class(query, c("tbl_df", "tbl", "data.frame" ))
  expect_equal(names(query), c("year", "basisOfRecord"))
  expect_gte(nrow(query), 10)
})

test_that("`galah_select()` returns requested columns when piped", {
  skip_if_offline()
  galah_config(email = "ala4r@ala.org.au", run_checks = FALSE)
  query <- galah_call() |>
    identify("oxyopes dingo") |>
    select(year, basisOfRecord) |>
    collect()
  expect_s3_class(query, c("tbl_df", "tbl", "data.frame" ))
  expect_equal(names(query), c("year", "basisOfRecord"))
  expect_gte(nrow(query), 10)
})

test_that("`galah_select()` builds expected columns when group = basic", {
  skip_if_offline()
  x <- galah_call() |>
    identify("oxyopes dingo") |>
    select(group = "basic") |>
    collapse() |>
    # from here is internal functions from `compute()`
    build_checks() |>
    compute_checks()
  # this approach runs all the internal code within compute(),
  # except the stage where it sends the query to ALA
  # i.e. this is internal code for checking and debugging
  y <- url_parse(x$url)$query
  expect_equal(strsplit(y$fields, ",")[[1]], preset_groups("basic"))
  expect_equal(y$qa, "none")
})

test_that("`galah_select()` builds expected columns when group = event", {
  skip_if_offline()
  x <- galah_call() |>
    identify("oxyopes dingo") |>
    select(group = "event") |>
    collapse() |>
    build_checks() |>
    compute_checks()
  y <- url_parse(x$url)$query
  expect_equal(strsplit(y$fields, ",")[[1]], 
               c("recordID", preset_groups("event")))
  expect_equal(y$qa, "none")
})

# test multiple groups work
test_that("`galah_select()` accepts multiple groups", {
  skip_if_offline()
  x <- galah_call() |>
    identify("oxyopes dingo") |>
    select(group = c("basic", "assertions")) |>
    collapse() |>
    build_checks() |>
    compute_checks()
  y <- url_parse(x$url)$query
  expect_equal(strsplit(y$fields, ",")[[1]], 
               preset_groups("basic"))
  expect_equal(y$qa, "includeall")
})

test_that("galah_select defaults to group = 'basic' when there are no args", {
  skip_if_offline()
  galah_config(run_checks = FALSE)
  x <- galah_call() |>
    identify("oxyopes dingo") |>
    collapse() |>
    build_checks() |>
    compute_checks()
  y <- url_parse(x$url)$query
  expect_equal(strsplit(y$fields, ",")[[1]], preset_groups("basic"))
  expect_equal(y$qa, "none")
  galah_config(run_checks = TRUE)
})

test_that("galah_select returns assertions + recordID when group = assertions", {
  skip_if_offline()
  x <- galah_call() |>
    identify("oxyopes dingo") |>
    select(group = "assertions") |>
    collapse() |>
    build_checks() |>
    compute_checks()
  y <- url_parse(x$url)$query
  expect_equal(y$fields, "recordID")
  expect_equal(y$qa, "includeall")
})

test_that("galah_select combines requested columns and group columns", {
  skip_if_offline()
  x <- galah_call() |>
    identify("oxyopes dingo") |>
    select(year, basisOfRecord, group = "basic") |>
    collapse() |>
    build_checks() |>
    compute_checks()
  y <- url_parse(x$url)$query
  expect_equal(strsplit(y$fields, ",")[[1]], 
               c(preset_groups("basic"), "year", "basisOfRecord"))
})

test_that("galah_select can use tidyselect::contains", {
  skip_if_offline()
  x <- galah_call() |>
    identify("oxyopes dingo") |>
    select(tidyselect::contains("el")) |>
    collapse() |>
    build_checks() |>
    compute_checks()
  y <- url_parse(x$url)$query
  fields <- strsplit(tolower(y$fields), ",")[[1]]
  assertions <- strsplit(tolower(y$qa), ",")[[1]]
  expect_true(all(grepl("el", fields)))
  expect_true(all(grepl("el", assertions)))
})

test_that("galah_select can use tidyselect::starts_with", {
  skip_if_offline()
  x <- galah_call() |>
    identify("oxyopes dingo") |>
    select(tidyselect::starts_with("el")) |>
    collapse() |>
    build_checks() |>
    compute_checks()
  y <- url_parse(x$url)$query
  fields <- strsplit(tolower(y$fields), ",")[[1]]
  assertions <- strsplit(tolower(y$qa), ",")[[1]]
  expect_true(all(grepl("^el", fields)))
  expect_true(all(grepl("^el", assertions)))
})

test_that("galah_select can use tidyselect::last_col", {
  skip_if_offline()
  x <- galah_call() |>
    identify("oxyopes dingo") |>
    select(tidyselect::last_col()) |>
    collapse() |>
    build_checks() |>
    compute_checks()
  y <- url_parse(x$url)$query
  expect_equal(y$fields, "recordID")
  expect_equal(y$qa, "ZERO_COORDINATE")
})

test_that("galah_select can use tidyselect::last_col & user-defined queries", {
  skip_if_offline()
  x <- galah_call() |>
    identify("oxyopes dingo") |>
    select(year, basisOfRecord, tidyselect::last_col()) |>
    collapse() |>
    build_checks() |>
    compute_checks()
  y <- url_parse(x$url)$query
  expect_equal(y$fields, "year,basisOfRecord")
  expect_equal(y$qa, "ZERO_COORDINATE")
})

test_that("galah_select can use tidyselect::last_col & group", {
  skip_if_offline()
  x <- galah_call() |>
    identify("oxyopes dingo") |>
    select(tidyselect::last_col(), group = "basic") |>
    collapse() |>
    build_checks() |>
    compute_checks()
  y <- url_parse(x$url)$query
  expect_equal(strsplit(y$fields, ",")[[1]], 
               preset_groups("basic"))
  expect_equal(y$qa, "ZERO_COORDINATE")
})