tests/testthat/test-downstream.R

In taxizedb: Tools for Working with 'Taxonomic' Databases

context("downstream")

skip_on_cran()

test_that("taxizedb::downstream matches taxize::downstream - NCBI", {
  skip_on_ci()
  arab_id <- name2taxid('Arabidopsis')
  tax <- taxize::downstream('Arabidopsis', db='ncbi', downto='species',
    messages = FALSE)[[1]]
  taxdb <- taxizedb::downstream(arab_id, db='ncbi', downto='species')[[1]]
  expect_gt(NROW(tax), NROW(taxdb))
})

test_that("taxizedb::downstream matches taxize::downstream - ITIS", {
  skip("Test is skipped until function is updated in taxize")
  skip_on_ci()
  arab_id_itis <- name2taxid('Arabidopsis', db="itis")
  expect_equal(
    NROW(taxize::downstream('Arabidopsis', db='itis', downto='species',
      messages = FALSE)[[1]]),
    NROW(taxizedb::downstream(arab_id_itis, db='itis', downto='species')[[1]])
  )
})

test_that("downstream dies on ambiguities", {
  expect_error(taxizedb::downstream("Bacteria"))
})

test_that("downstream works with GBIF", {
  id <- name2taxid('Pinaceae', db = "gbif")
  x <- downstream(id, db = "gbif", downto = "genus")
  expect_is(x, "downstream")
  expect_is(unclass(x), "list")
  expect_named(unclass(x), id)
  expect_is(unclass(x)[[1]], "tbl")
  expect_named(x[[1]], c("id", "name", "rank"))
})

test_that('downstream fails well', {
  # tpl not supported
  expect_error(
    downstream("Poa", db = "tpl"),
    "TPL database is not supported"
  )
  # abc does not exist
  expect_error(
    downstream("Poa annua", db = "abc"),
    "Database 'abc' is not supported"
  )
  # param types
  expect_error(downstream("Poa annua", db=5), "class character")
  expect_error(downstream("Poa annua", verbose = 5), "class logical")
})