tests/testthat/test-bold_identify_taxonomy.R

In bold: Interface to Bold Systems API

context("bold_identify_taxonomy")

# bold_identify_list <- bold_identify(sequences = sequences$seq2)
# save(bold_identify_list, file = "tests/testthat/bold_identify_list.rda")
# load("tests/testthat/bold_identify_list.rda")
load("bold_identify_list.rda")

test_that("bold_identify_taxonomy works as expected", {
  vcr::use_cassette("bold_identify_taxonomy", {
    test <- bold_identify_taxonomy(bold_identify_list)
  })
  expect_is(test, "list")
  expect_equal(length(test), 1)
  expect_is(test[[1]], "data.frame")
  expect_equal(NROW(test[[1]]), 100)
  expect_is(test[[1]]$ID, "character")
  expect_is(test[[1]]$sequencedescription, "character")
  expect_equal(length(unique(test[[1]]$ID)), length(test[[1]]$ID))
})

test_that("bold_identify_taxonomy works as expected (taxOnly TRUE)", {
  vcr::use_cassette("bold_identify_taxonomy", {
    test <<- bold_identify_taxonomy(bold_identify_list)
  })
  expect_is(test, "list")
  expect_equal(length(test), 1)
  expect_is(test[[1]], "data.frame")
  expect_equal(NROW(test[[1]]), 100)
  expect_equal(NCOL(test[[1]]), 24)
  expect_is(test[[1]]$ID, "character")
  expect_is(test[[1]]$sequencedescription, "character")
  expect_equal(length(unique(test[[1]]$ID)), length(test[[1]]$ID))
})
test_that("bold_identify_taxonomy works as expected (taxOnly FALSE)", {
  vcr::use_cassette("bold_identify_taxonomy", {
    test <- bold_identify_taxonomy(bold_identify_list, taxOnly = FALSE)
  })
  expect_is(test, "list")
  expect_equal(length(test), 1)
  expect_is(test[[1]], "data.frame")
  expect_equal(NROW(test[[1]]), 100)
  expect_gt(NCOL(test[[1]]), 24)
  expect_is(test[[1]]$ID, "character")
  expect_is(test[[1]]$sequencedescription, "character")
  expect_equal(length(unique(test[[1]]$ID)), length(test[[1]]$ID))
})

test_that("bold_identify_taxonomy fails well", {
  # x required
  expect_error(bold_identify_taxonomy(), "argument 'x' is missing")
  expect_error(bold_identify_taxonomy(list()), "'x' can't be empty")
  expect_error(bold_identify_taxonomy(data.frame()), "'x' can't be empty")
  expect_error(bold_identify_taxonomy(matrix(logical(0L))), "'x' can't be empty")
  # only supported types
  expect_error(bold_identify_taxonomy(numeric()), "unable to find an inherited method for function")
  expect_error(bold_identify_taxonomy(x = bold_identify_list, taxOnly = 5), "'taxOnly' should be one of TRUE or FALSE")
  # required column ID
  expect_error(bold_identify_taxonomy(list(mtcars, mtcars)),
               "no column 'ID' found in x")
  expect_warning(bold_identify_taxonomy(mtcars),
               "No column 'ID' found, skipped")
  expect_warning(bold_identify_taxonomy(as.matrix(mtcars)),
               "No column 'ID' found, skipped")
})