Nothing
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"))
})
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