tests/testthat/test-02_clean_metadata.R

In dhope/ARUtools: Tools for management of Acoustic Recording Unit (ARU) data

test_that("clean_metadata()", {

  expect_message(m <- clean_metadata(project_files = example_files),
                 "Extracting ARU info..") |>
    expect_message("Extracting Dates and Times...")

  expect_s3_class(m, "data.frame")
  expect_named(m, c("file_name", "type", "path", "aru_type", "aru_id", "site_id",
                    "date_time", "date"))
  expect_equal(nrow(m), length(example_files))
  expect_equal(unique(m$aru_id), sort(unique(example_clean$aru_id)))
  expect_equal(unique(m$type), "wav")
  expect_equal(unique(m$aru_type), c("BarLT", "SongMeter"))
  expect_equal(sort(unique(m$site_id)), sort(unique(example_clean$site_id)))
  expect_true(all(!is.na(m$date_time)))
  expect_true(all(!is.na(m$date)))

})



test_that("clean_metadata() with multiple patterns in create_pattern_XXX", {

  f <- c("P01_1/2020-01-01T09:00:00.wav",
         "P02_01/01012020 10:00.wav")

  # Problem date/time, problem site_id
  expect_message(m <- clean_metadata(project_files = f)) |> suppressMessages()
  expect_equal(m$date_time, lubridate::as_datetime(c(NA, "2020-01-01 09:00:00")))
  expect_equal(m$site_id, c("P02_0", "P01_1"))

  # Fix pattern matching of date
  expect_message(
    m <- clean_metadata(
      project_files = f,
      pattern_date = create_pattern_date(c("mdy", "ymd"), sep = c("", "-")),
      pattern_time = create_pattern_time(seconds = "maybe"),
      pattern_dt_sep = create_pattern_dt_sep(sep = c("T", " ")))) |>
    suppressMessages()
  expect_equal(m$date_time,
               lubridate::as_datetime(c("2020-01-01 09:00:00",
                                        "2001-01-20 20:10:00")))

  # Fix parsing of date
  expect_message(
    m <- clean_metadata(
      project_files = f,
      pattern_date = create_pattern_date(c("mdy", "ymd"), sep = c("", "-")),
      pattern_time = create_pattern_time(seconds = "maybe"),
      pattern_dt_sep = create_pattern_dt_sep(sep = c("T", " ")),
      order_date = c("mdy", "ymd"))) |>
    suppressMessages()
  expect_equal(m$date_time,
               lubridate::as_datetime(c("2020-01-01 09:00:00",
                                        "2020-01-01 10:00:00")))

  # Fix pattern matching of site_id
  expect_message(
    m <- clean_metadata(
      project_files = f,
      pattern_date = create_pattern_date(c("mdy", "ymd"), sep = c("", "-")),
      pattern_time = create_pattern_time(sep = ":", seconds = "maybe"),
      pattern_dt_sep = create_pattern_dt_sep(sep = c("T", " ")),
      order_date = c("mdy", "ymd"),
      pattern_site_id = create_pattern_site_id(s_digits = c(1, 2)))) |>
    suppressMessages()
  expect_equal(m$site_id, c("P01_1", "P02_01"))

})

test_that("clean_metadata() with multiple patterns in args", {

  f <- c("P01_1/2020-01-01T09:00:00.wav",
         "P02_01/01012020 10:00.wav")

  # Fix pattern matching of date
  expect_message(
    m <- clean_metadata(
      project_files = f,
      pattern_date = c(create_pattern_date("ymd", sep = "-"),
                       create_pattern_date("mdy", sep = "")),
      pattern_time = c(create_pattern_time(seconds = "yes"),
                       create_pattern_time(seconds = "no")),
      pattern_dt_sep = c("T", " "))) |>
    suppressMessages()
  expect_equal(m$date_time,
               lubridate::as_datetime(c("2020-01-01 09:00:00",
                                        "2001-01-20 20:10:00")))

  # Fix parsing of date
  expect_message(
    m <- clean_metadata(
      project_files = f,
      pattern_date = c(create_pattern_date("ymd", sep = "-"),
                       create_pattern_date("mdy", sep = "")),
      pattern_time = c(create_pattern_time(seconds = "yes"),
                       create_pattern_time(seconds = "no")),
      pattern_dt_sep = c("T", " "),
      order_date = c("mdy", "ymd"))) |>
    suppressMessages()
  expect_equal(m$date_time,
               lubridate::as_datetime(c("2020-01-01 09:00:00",
                                        "2020-01-01 10:00:00")))

  # Fix pattern matching of site_id
  expect_message(
    m <- clean_metadata(
      project_files = f,
      pattern_date = c(create_pattern_date("ymd", sep = "-"),
                       create_pattern_date("mdy", sep = "")),
      pattern_time = c(create_pattern_time(seconds = "yes"),
                       create_pattern_time(seconds = "no")),
      pattern_dt_sep = c("T", " "),
      order_date = c("mdy", "ymd"),
      pattern_site_id = c(create_pattern_site_id(),
                          create_pattern_site_id(s_digits = 2)))) |>
    suppressMessages()
  expect_equal(m$site_id, c("P01_1", "P02_01"))

})

test_that("clean_metadata() with numeric aru_id", {
  bad <- example_files |>
    stringr::str_remove("BARLT|S4A") |>
    clean_metadata(project_files = _) |>
    suppressMessages()
  expect_true(all(is.na(bad$aru_id)))

  good <- example_files |>
    stringr::str_remove("BARLT|S4A") |>
    clean_metadata(
      project_files = _,
      pattern_aru_id = create_pattern_aru_id(
        arus = "", n_digits = 5, prefix = "(?<=_)", suffix = "(?=_)")) |>
    suppressMessages()
  expect_true(all(!is.na(good$aru_id)))
})