tests/testthat/test_names.R

In phylotastic/rphylotastic: An R Interface to 'Phylotastic' Web Services

test_that("Loading names from a standard web page works correctly", {
  results <- url_get_scientific_names("http://en.wikipedia.org/wiki/Ant")
  expect_gte(length(results), 50)
  expect_true( any(grepl("Formicidae", results)))
})

test_that("Loading names from an online PDF works correctly", {
  results <- url_get_scientific_names("https://www.fws.gov/westvirginiafieldoffice/PDF/beechridgehcp/Appendix_D_Table_D-1.pdf")
  expect_gte(length(results), 50)
  expect_true( any(grepl("Micropterus", results)))
})


test_that("Loading names from a text string works correctly", {
  results <- text_get_scientific_names("Formica polyctena is a species of European red wood ant in the genus Formica. The pavement ant, Tetramorium caespitum is an ant native to Europe. Pseudomyrmex is a genus of stinging, wasp-like ants. Adetomyrma venatrix is an endangered species of ants endemic to Madagascar. Carebara diversa is a species of ants in the subfamily Formicinae. It is found in many Asian countries.")
  expect_gte(length(results), 2)
  expect_true( any(grepl("Formica", results)))
})

test_that("Resolving names with OToL works", {
  taxa <- c("Setophaga striata", "Setophaga megnolia", "Setophaga angilae", "Setophaga plumbea", "Setophaga virens")
  taxa.new <- taxa_resolve_names_with_otol(taxa)
  expect_gte(length(taxa.new), length(taxa))  # because it has fuzzy matching now
  expect_message(taxa.new <- taxa_resolve_names_with_otol(letters[1:3]))
  expect_true(is.null(taxa.new))
})

test_that("Getting names from txt and pdf files works correctly", {
  original.dir <- getwd()
  setwd(testthat::test_path())
  names_txt <- file_get_scientific_names(file_name = "subset2.txt")
  names_pdf <- file_get_scientific_names(file_name = "Appendix_D_Table_D-1.pdf")
  setwd(original.dir)
})