tests/testthat/test-data-code.R

In rfair: Assess the FAIRness of Research Data Objects and Software

# rtransparent harmony: batch assessment of shared data/code identifiers.

test_that("split_identifiers splits, trims, and drops empties", {
  expect_equal(
    split_identifiers("https://doi.org/10.5061/dryad.x ; geo:GSE12345 ; NA ;  "),
    c("https://doi.org/10.5061/dryad.x", "geo:GSE12345")
  )
  expect_equal(split_identifiers(""), character())
  expect_equal(split_identifiers(NA_character_), character())
  expect_equal(split_identifiers(c("a ; b", "c")), c("a", "b", "c"))
})

test_that("assess_data_code ingests an rtransparent-shaped data frame", {
  rt <- data.frame(
    pmid = c("111", "222"),
    open_data_links = c("https://doi.org/10.5281/zenodo.8347772 ; geo:GSE12345", ""),
    open_code_links = c("https://github.com/owner/repo", ""),
    stringsAsFactors = FALSE
  )
  out <- assess_data_code(rt, id_col = "pmid", resolve = FALSE,
                          use_datacite = FALSE, quiet = TRUE)
  expect_s3_class(out, "data.frame")
  expect_true(all(c("source", "kind", "identifier", "scheme", "is_persistent",
                    "fair_percent", "F", "A", "I", "R", "maturity", "error") %in% names(out)))
  expect_equal(nrow(out), 3L)                       # 2 data + 1 code for pmid 111
  expect_setequal(out$source, "111")
  expect_setequal(out$kind, c("data", "code"))
  expect_equal(out$scheme[out$identifier == "geo:GSE12345"], "geo")
  expect_true(out$is_persistent[out$identifier == "geo:GSE12345"])
})

test_that("assess_data_code accepts a named list and dedups identifiers", {
  out <- assess_data_code(
    list(open_data_links = "geo:GSE1 ; geo:GSE1", open_code_links = ""),
    resolve = FALSE, use_datacite = FALSE, quiet = TRUE
  )
  # both work rows resolve to the one unique identifier (assessed once)
  expect_equal(nrow(out), 2L)
  expect_equal(unique(out$identifier), "geo:GSE1")
})

test_that("assess_data_code returns a typed 0-row frame for no links", {
  e <- assess_data_code(data.frame(open_data_links = "", open_code_links = ""))
  expect_s3_class(e, "data.frame")
  expect_equal(nrow(e), 0L)
  expect_true(all(c("source", "kind", "identifier", "fair_percent") %in% names(e)))
})

test_that("assess_fair_batch captures failures in the error column", {
  out <- assess_fair_batch("geo:GSE99", resolve = FALSE, use_datacite = FALSE, quiet = TRUE)
  expect_equal(nrow(out), 1L)
  expect_equal(out$scheme, "geo")
})