tests/testthat/test-external.R

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

if (FALSE) {
  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()
    skip("NCBI seems to be down")
    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()
    skip("NCBI seems to be down")
    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()
    skip("NCBI seems to be down")
    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()
    skip("NCBI seems to be down")
    gibbon_IDs <- taxon_external_IDs(712902)
    expect_that(gibbon_IDs, is_a("data.frame"))
    expect_equal(names(gibbon_IDs), c("source", "id"))
  })
}