tests/testthat/test-tax_name.R

In ropensci/taxize: Taxonomic Information from Around the Web

context("tax_name")

test_that("tax_name: ncbi", {
  skip_on_cran() # uses secrets
  vcr::use_cassette("tax_name_ncbi", {
    tmp_ncbi  <- tax_name("Baetis", get = c("family", "order"),
                          db = "ncbi", messages=FALSE)
    tmp_ncbi2 <- tax_name(c("Helianthus annuus", 'Baetis rhodani'),
                          get = c("genus", "kingdom"), db = "ncbi", messages=FALSE)
  })

	expect_is(tmp_ncbi, "data.frame")
  expect_equal(ncol(tmp_ncbi), 4)
	expect_equal(tmp_ncbi$family, "Baetidae")
	expect_equal(tmp_ncbi$order, "Ephemeroptera")
  expect_that(nrow(tmp_ncbi2), equals(2))
})

test_that("tax_name: NA's", {
  skip_on_cran() # uses secrets
  vcr::use_cassette("tax_name_na", {
    tmp_na2 <- tax_name(c("Helianthus annuus", 'xxxx'),
                        get=c("family", "order"), db="ncbi", messages=FALSE)
    tmp_na3 <- sw(tax_name(c("Helianthus annuus", 'xxxx'), rows = 1,
                        get = c("family", "order"), db="itis", messages = FALSE))
  })

  expect_is(tmp_na2, "data.frame")
  expect_is(tmp_na3, "data.frame")
  expect_equal(ncol(tmp_na2), 4)
  expect_equal(ncol(tmp_na3), 4)
  expect_true(any(is.na(tmp_na2[2, ])))
  expect_true(any(is.na(tmp_na3[2, ])))
})

test_that("tax_name: itis", {
  skip_on_cran()
  vcr::use_cassette("tax_name_itis", {
    tmp_itis <- sw(tax_name("Helianthus annuus", rows = 1,
                        get = c("family", "order"), db="itis", messages = FALSE))
  })

  expect_is(tmp_itis, "data.frame")
  expect_equal(ncol(tmp_itis), 4)
  expect_equal(tmp_itis$family, "Asteraceae")
  expect_equal(tmp_itis$order, "Asterales")
})

test_that("tax_name: rows arg", {
  skip_on_cran() # uses secrets
  vcr::use_cassette("tax_name_rows_Arg", {
    aa <- tax_name('Bacillus', c("family", "order"), db="ncbi", rows=1)
  })
  
  expect_is(aa, "data.frame")
  expect_equal(NCOL(aa), 4)
  expect_equal(NROW(aa), 1)
  expect_named(aa, c("db", "query", "family", "order"))
})

test_that("tax_name accepts ask-argument", {
  skip_on_cran() # uses secrets
  vcr::use_cassette("tax_name_arg_arg", {
    x <- sw(tax_name("Dugesia", get = "family", db = "ncbi",
                             ask = FALSE, messages = FALSE))$family
  })

  expect_true(is.na(x))
})

test_that("taxon with no data returned from classification() works", {
  skip_on_cran() # uses secrets
  vcr::use_cassette("tax_name_no_data", {
    aa <- sw(tax_name("foo bar", get = "species",
      rows = 1, messages = FALSE))
    bb <- sw(tax_name("Asterias helianthus", get = "genus", 
      messages = FALSE))
    cc <- sw(tax_name("Stellonia helianthus", get = "genus", 
      messages = FALSE))
  })
  
  expect_is(aa, "data.frame")
  expect_true(is.na(aa$species))

  expect_is(bb, "data.frame")
  expect_true(is.na(bb$genus))
  # expect_warning(tax_name("Asterias helianthus", get = "genus", messages = FALSE),
  #                "rank requested")

  expect_is(cc, "data.frame")
  expect_true(is.na(cc$genus))

  vcr::use_cassette("tax_name_throws_warning", {
    expect_warning(tax_name("Stellonia helianthus", get = "genus", messages = FALSE),
                 "rank requested")
  })
})