tests/testthat/test_00_correctTaxo.R

In ArthurPERE/biomass: Estimating Aboveground Biomass and Its Uncertainty in Tropical Forests

require(data.table)

data("KarnatakaForest")
genus <- KarnatakaForest$genus[1:10]
species <- KarnatakaForest$species[1:10]

skip_if_not_function <- function(name) {
  if (!exists(name)) {
    skip(paste("The function", name, "is internal"))
  }
}

context("CorrectTaxo")
test_that("CorrectTaxo", {
  skip_if_not_installed("httr")

  expect_is(correctTaxo(genus, species), "data.frame")

  taxo <- correctTaxo(genus, species)
  taxoFalse <- taxo[taxo$nameModified == FALSE, ]
  taxoBegin <- data.frame(as.character(genus), as.character(species), stringsAsFactors = F)

  expect_equivalent(taxoFalse[, 1:2], taxoBegin[taxo$nameModified == FALSE, ])
  expect_error(correctTaxo(genus, species[1:9]), "You should provide two vectors of genera and species of the same length")

  expect_equal(correctTaxo(paste(genus, species)), taxo)
  expect_error(correctTaxo(genus = rep(NA, 20), species = rep(NA, 20)), "Please supply at least one name")
  expect_error(correctTaxo(genus = rep(NA, 20)), "Please supply at least one name")
  expect_equal(correctTaxo(genus = c(NA, "Astrocarium", "Astrocarium"), species = c("lalal", NA, "standleanum")), 
               data.frame(
                 genusCorrected = c(NA, "Astrocaryum", "Astrocaryum"),
                 speciesCorrected = c(NA, NA, "standleyanum"),
                 nameModified = c(NA, "TRUE", "TRUE"), stringsAsFactors = F
               ))

  expect_equal(
    correctTaxo(genus = c("Magnophyton", "?"), species = c("fulvum", "?")),
    data.frame(
      genusCorrected = c("Manniophyton", "?"),
      speciesCorrected = c("fulvum", "?"),
      nameModified = c("TRUE", "TaxaNotFound"), stringsAsFactors = F
    )
  )

  skip_if_not_function("cacheManager")

  path <- cacheManager("correctTaxo")
  expect_true(dir.exists(rappdirs::user_data_dir("BIOMASS")))
  expect_true(file.exists(path))

  a <- setDF(fread(path, header = T, sep = ","))
  expect_equal(names(a), c("submittedName", "acceptedName", "sourceId", "score", "matchedName", "annotations", "uri"))
  expect_gt(nrow(a), 0)

  expect_equal(
    correctTaxo(genus = c("Magnophyton", "?"), species = c("fulvum", "?"), score = 0.97),
    data.frame(
      genusCorrected = c("Magnophyton", "?"),
      speciesCorrected = c("fulvum", "?"),
      nameModified = c("NoMatch(low_score)", "TaxaNotFound"), stringsAsFactors = F
    )
  )


  file.rename(path, paste0(path, 0))
  # test multiple things here :
  #   1) if the useCache is NULL but there is no Cache to remove
  #   2) if the genus is nonsense, there is no error message that appear if there is no cache
  #   3) The connectivity
  expect_equal(
    correctTaxo(genus = "bvgaeuigareuiguei", useCache = NULL),
    data.frame(
      genusCorrected = "bvgaeuigareuiguei",
      speciesCorrected = NA_character_,
      nameModified = "TaxaNotFound", stringsAsFactors = F
    )
  )
  # If there is no cache and the genus is nonsense a second that come on sense
  expect_equal(
    correctTaxo(genus = c("bvgaeuigareuiguei", "Astrocarium standleanum"), useCache = NULL),
    data.frame(
      genusCorrected = c("bvgaeuigareuiguei", "Astrocaryum"),
      speciesCorrected = c(NA_character_, "standleyanum"),
      nameModified = c("TaxaNotFound", TRUE), stringsAsFactors = F
    )
  )
  file.remove(path)
  file.rename(paste0(path, 0), path)
})