tests/testthat/test-read-annotations.R

In SomaDataIO: Input/Output 'SomaScan' Data

file <- test_path("testdata", "test-anno.xlsx")

test_that("`ver_dict` is updated and correct", {
  expect_length(ver_dict, 6L)
  expect_named(ver_dict,
               c("SL-99999999-rev99-1999-01",
                 "SL-12345678-rev0-2021-01",
                 "SL-00000571-rev2-2021-06",
                 "SL-00000246-rev5-2021-06",
                 "SL-00000571-rev7-2024-02",
                 "SL-00000906-rev4-2024-03"))
})

test_that("`getAnnoVer()` parses the version correctly", {
  expect_equal(getAnnoVer(file), "SL-12345678-rev0-2021-01")
})

test_that("`read_annotations()` parses the annotations file correctly", {
  tbl <- read_annotations(file)
  expect_s3_class(tbl, "tbl_df")
  expect_equal(dim(tbl), c(1L, 43L))
  ver <- attr(tbl, "version")
  expect_equal(ver, "SL-12345678-rev0-2021-01")
  expect_true(ver_dict[[ver]]$col_serum == names(tbl)[ver_dict[[ver]]$which_serum])
  expect_true(ver_dict[[ver]]$col_plasma == names(tbl)[ver_dict[[ver]]$which_plasma])
})

test_that("error conditions trigger stops when appropriate", {

  expect_error(
    read_annotations("foo.txt"),
    "Annotations file must be either"
  )

  expect_error(
    with_pkg_object(SomaDataIO:::ver_dict[-2L], read_annotations(file)),
    "Unknown version of the annotations file:"
  )

  # temp modify md5sha
  tmp <- SomaDataIO:::ver_dict
  tmp$`SL-12345678-rev0-2021-01`$sha <- "x0x0x0x0x"
  expect_warning(
    with_pkg_object(tmp, read_annotations(file)),
    "Checksum mismatch. 'test-anno.xlsx' may have been modified"
  )
})