tests/testthat/test-external.R

In rotl: Interface to the 'Open Tree of Life' API

context("Study external data")

if (identical(Sys.getenv("NOT_CRAN"), "true")) {
  all_sources <- c("doi", "pubmed_id", "external_data_url", "popset_ids", "nucleotide_ids")
  all_data <- study_external_IDs("pg_1940")
}

test_that("We can recover dois, pmids, NCBI IDs", {
  skip_on_cran()
  expect_that(all_data, is_a("study_external_data"))
  expect_named(all_data)
})

test_that("We can handle studies with missing external IDs", {
  skip_on_cran()
  expect_warning(
    missing_data <- study_external_IDs("ot_97"), "skipping NCBI"
  )
  expect_named(missing_data)
  expect_that(missing_data, is_a("study_external_data"))
  expect_equal(sum(is.na(match(all_sources, names(missing_data)))), 2) # we really skipped the NCBI
})

test_that("The print functions for external data objects work", {
  skip_on_cran()
  missing_data <- study_external_IDs("ot_91")
  expect_output(print(all_data), "External data identifiers for study")
  expect_output(print(missing_data), "External data identifiers for study")
})


context("Taxon external data")

test_that("We can recover external IDs for Open Tree taxa", {
  skip_on_cran()
  gibbon_IDs <- taxon_external_IDs(712902)
  expect_that(gibbon_IDs, is_a("data.frame"))
  expect_equal(names(gibbon_IDs), c("source", "id"))
})