tests/testthat/test-olink_lod.R

In OlinkAnalyze: Facilitate Analysis of Proteomic Data from Olink

lod_file <- data.frame(OlinkID = "OID12345",
                       AssayType = "assay",
                       UniProt = "Q12345",
                       Assay = "TestAssay",
                       Panel = "TestPanel",
                       Block = 1,
                       DataAnalysisRefID = "D10010",
                       LODNPX = 1,
                       LODCount = 1000,
                       LODMethod = "lod_npx")

df <- npx_data1 |>
  dplyr::mutate(OlinkID = ifelse(OlinkID == npx_data1$OlinkID[1],
                                 "OID12345",
                                 OlinkID)) |>
  dplyr::mutate(DataAnalysisRefID = "D10010") |>
  dplyr::mutate(PanelDataArchiveVersion = "1.5")


test_that("No message", {
  expect_no_message(check_lod_darid(lod_file |>
                                      mutate(Version = "9.0.0"),
                                    df))

  expect_no_message(check_lod_darid(lod_file,
                                    df |>
                                      mutate(PanelDataArchiveVersion = "1.0")))

})

test_that("LOD DARID message is triggered", {
  messages <- capture_messages(
    check_lod_darid(lod_file, df)
  )

  expect_true(any(grepl("Outdated version .* detected", messages)))
  expect_true(any(grepl(".* newest version from Olink.com", messages)))

})