tests/testthat/test-sbe-run.R

In paleolimbot/sbe: Process and Convert Files Created by 'Seabird' Products

test_that("batchfile generator works", {
  batch_txt <- sbe_batch_generate(
     "datcnv",
     "thing.psa",
     c("input1.cnv", "input2.cnv"),
     "con.xmlcon",
     "some/path"
  )

  expect_match(batch_txt, "^Datcnv.*?\nDatcnv")

  expect_error(
    sbe_batch_generate(
      "not a tool",
      "thing.psa",
      c("input1.cnv", "input2.cnv"),
      "con.xmlcon",
      "some/path"
    ),
    "is not TRUE"
  )

  expect_error(
    sbe_batch_generate(
      "datcnv",
      "thing.wrongext",
      c("input1.cnv", "input2.cnv"),
      "con.xmlcon",
      "some/path"
    ),
    "ending with '.psa'"
  )

  expect_match(
    sbe_batch_generate(
      "datcnv",
      "thing.psa"
    ),
    "^Datcnv.*?\\.psa$"
  )
})

test_that("default PSA files are found", {
  tools <- c(
    "alignctd", "binavg", "celltm",
    "datcnv", "derive", "deriveteos_10",
    "filter", "loopedit", "wildedit"
  )

  expect_true(all(file.exists(sbe_psa_default(tools))))
})

test_that("sbe_temp_dir() works", {
  temp_dir <- sbe_temp_dir()
  expect_true(is_sbe_temp_dir(temp_dir))
  expect_true(dir.exists(temp_dir))
  unlink(temp_dir, recursive = TRUE)
})

test_that("sbe_run_tool() works on real data", {
  skip("Don't run batch processor automatically")
  faroe_dir <- system.file("extdata/faroe", package = "sbe")

  out_dir <- sbe_run_tool(
    "datcnv",
    psa = file.path(faroe_dir, "faroe.psa"),
    input = file.path(faroe_dir, "faroe.dat"),
    con = file.path(faroe_dir, "faroe.con")
  )

  out_sbe_cnv <- list.files(out_dir, full.names = TRUE)
  expect_identical(basename(out_sbe_cnv), "Faroe.cnv")
  unlink(out_dir, recursive = TRUE)
})