tests/testthat/test-as_OpenSpecy.R

In OpenSpecy: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra

data("raman_hdpe")
df <- read_extdata("raman_hdpe.csv") |> read.csv()

test_that("as_OpenSpecy() handles errors correctly", {
  as_OpenSpecy(df$wavenumber, as.data.frame(df$intensity)) |> expect_silent()
  as_OpenSpecy(df$wavenumber, df$intensity) |> expect_error()
  as_OpenSpecy(df$wavenumber) |> expect_error()
  as_OpenSpecy(df$wavenumber, as.data.frame(df$intensity[-1])) |> expect_error()
  as_OpenSpecy(df$wavenumber, data.table(intensity = df$intensity,
                                         intensity = df$intensity)) |>
    expect_error()

  as_OpenSpecy(data.frame(x = df$wavenumber, abs = df$intensity)) |>
    expect_message()
  as_OpenSpecy(data.frame(wav = df$wavenumber, y = df$intensity)) |>
    expect_message()

  amb <- df
  names(amb) <- c("a", "b")
  as_OpenSpecy(amb) |> expect_message() |> expect_message()

  as_OpenSpecy(df$wavenumber, as.data.frame(df$intensity), coords = "") |>
    expect_error()
  as_OpenSpecy(df$wavenumber, as.data.frame(df$intensity), coords = df) |>
    expect_error()
  as_OpenSpecy(df$wavenumber, as.data.frame(df$intensity), metadata = "") |>
    expect_error()
})

test_that("as_OpenSpecy() generates OpenSpecy objects", {
  as_OpenSpecy(df) |> expect_silent()
  as_OpenSpecy(raman_hdpe, session_id = T) |> expect_silent()

  osf <- as_OpenSpecy(df) |> expect_silent()
  ost <- data.table(df) |> as_OpenSpecy() |> expect_silent()
  osl <- list(df$wavenumber, df[2]) |> as_OpenSpecy() |> expect_silent()
  OpenSpecy(osf) |> expect_silent()

  expect_s3_class(osf, "OpenSpecy")
  expect_s3_class(ost, "OpenSpecy")
  expect_s3_class(osl, "OpenSpecy")

  expect_true(check_OpenSpecy(osf))
  expect_true(check_OpenSpecy(ost))
  expect_true(check_OpenSpecy(osl))

  expect_true(is_OpenSpecy(osf))
  expect_true(is_OpenSpecy(ost))
  expect_true(is_OpenSpecy(osl))
  expect_false(is_OpenSpecy(df))

  expect_equal(names(osf), c("wavenumber", "spectra", "metadata"))
  expect_equal(names(ost), c("wavenumber", "spectra", "metadata"))
  expect_equal(names(osl), c("wavenumber", "spectra", "metadata"))

  expect_equal(OpenSpecy(df), OpenSpecy(osf))
  expect_equal(ost$spectra, osf$spectra)
  expect_equal(ost$wavenumber, osf$wavenumber)
  expect_equal(ost$metadata, osf$metadata)
  expect_equal(osf$metadata$col_id, names(osf$spectra))
})

test_that("check_OpenSpecy() work as expected", {
  os <- as_OpenSpecy(df)
  check_OpenSpecy(os) |> expect_true()
  check_OpenSpecy(df) |> expect_error() |> expect_warning() |> expect_warning() |> expect_warning() |> expect_warning()

  osv <- osn <- oss <- ost <- osl <- os

  osv$wavenumber <- list(osv$wavenumber)
  check_OpenSpecy(osv) |> expect_false() |> expect_warning()

  names(osn) <- 1:3
  check_OpenSpecy(osn) |> expect_error() |> expect_warning() |> expect_warning()|> expect_warning() |> expect_warning()

  oss$wavenumber <- sample(oss$wavenumber)
  check_OpenSpecy(oss) |> expect_false() |> expect_warning()

  class(ost$metadata) <- class(ost$spectra) <- "data.frame"
  check_OpenSpecy(ost) |> expect_false() |> expect_warning() |> expect_warning()

  osl$metadata <- rbind(osl$metadata, osl$metadata)
  osl$spectra <- osl$spectra[-1]

  check_OpenSpecy(osl) |> expect_false() |> expect_warning() |> expect_warning()
})

test_that("'OpenSpecy' objects are read correctly", {
  os <- as_OpenSpecy(df)

  expect_true(check_OpenSpecy(os))

  expect_equal(range(os$wavenumber) |> round(2), c(301.04, 3198.12))
  expect_equal(range(os$spectra) |> round(2), c(26, 816))
  expect_length(os$wavenumber, 964)
  expect_equal(os$metadata$x, 1)
  expect_equal(os$metadata$y, 1)
  expect_equal(os$metadata$license, "CC BY-NC")
})

test_that("'OpenSpecy' objects are transcribed to and from 'hyperSpec' objects", {
  os <- as_OpenSpecy(df)
  hyper <- as_hyperSpec(os)
  expect_s4_class(hyper, "hyperSpec")

  openhyper <- as_OpenSpecy(hyper)

  expect_true(is_OpenSpecy(openhyper))
  expect_true(check_OpenSpecy(openhyper))

  expect_equal(openhyper$wavenumber, hyper@wavelength)
  expect_equal(unlist(openhyper$spectra$V1),unname(t(hyper$spc)[,1]))
})