test_cmsaf.cat.R
In cmsafops: Tools for CM SAF NetCDF Data

data_dir <- file.path("..", "testdata")
tempfile_nc <- function() {
  tempfile_helper("cmsaf.cat_")
}

########## output ncdf version 3 ##########
file_out <- tempfile_nc()
cmsaf.cat("SIS",
          c(file.path(data_dir, "ex_normal1.nc"),
            file.path(data_dir, "ex_normal2.nc")),
          file_out)
file <- nc_open(file_out)

test_that("data is correct", {
  actual <- ncvar_get(file)

  temp <- seq(250, 272)
  temp2 <- seq(230, 252)
  expected_data <- c(temp, temp, temp[1:3],
                     temp2, temp2, temp2[1:3])
  expected <- array(expected_data, dim = c(7, 7, 2))

  expect_equivalent(actual, expected)
})

test_that("attributes are correct", {
  actual <- ncatt_get(file, "lon", "units")$value
  expect_equal(actual, "degrees_east")

  actual <- ncatt_get(file, "lon", "long_name")$value
  expect_equal(actual, "longitude")

  actual <- ncatt_get(file, "lon", "standard_name")$value
  expect_equal(actual, "longitude")

  actual <- ncatt_get(file, "lon", "axis")$value
  expect_equal(actual, "X")

  actual <- ncatt_get(file, "lat", "units")$value
  expect_equal(actual, "degrees_north")

  actual <- ncatt_get(file, "lat", "long_name")$value
  expect_equal(actual, "latitude")

  actual <- ncatt_get(file, "lat", "standard_name")$value
  expect_equal(actual, "latitude")

  actual <- ncatt_get(file, "lat", "axis")$value
  expect_equal(actual, "Y")

  actual <- ncatt_get(file, "time", "units")$value
  expect_equal(actual, "hours since 1983-01-01 00:00:00")

  actual <- ncatt_get(file, "time", "long_name")$value
  expect_equal(actual, "time")

  actual <- ncatt_get(file, "time", "standard_name")$value
  expect_equal(actual, "time")

  actual <- ncatt_get(file, "time", "calendar")$value
  expect_equal(actual, "standard")

  actual <- ncatt_get(file, "SIS", "standard_name")$value
  expect_equal(actual, "SIS_standard")

  actual <- ncatt_get(file, "SIS", "long_name")$value
  expect_equal(actual, "Surface Incoming Shortwave Radiation")

  actual <- ncatt_get(file, "SIS", "units")$value
  expect_equal(actual, "W m-2")

  actual <- ncatt_get(file, "SIS", "_FillValue")$value
  expect_equal(actual, -999)

  actual <- ncatt_get(file, "SIS", "cmsaf_info")$value
  expect_equal(actual, "cmsafops::cmsaf.cat for variable SIS")

  global_attr <- ncatt_get(file, 0)
  expect_equal(length(global_attr), 1)

  actual <- names(global_attr[1])
  expect_equal(actual, "Info")

  actual <- global_attr[[1]]
  expect_equal(actual, "Created with the CM SAF R Toolbox.")
})

test_that("coordinates are correct", {
  actual <- ncvar_get(file, "lon")
  expect_identical(actual, array(seq(5, 8, 0.5)))

  actual <- ncvar_get(file, "lat")
  expect_identical(actual, array(seq(45, 48, 0.5)))

  actual <- ncvar_get(file, "time")
  expect_equal(actual, array(c(149016, 158544)))
})

nc_close(file)

########## output ncdf version 4 ##########
file_out <- tempfile_nc()
cmsaf.cat("SIS",
          c(file.path(data_dir, "ex_normal1.nc"),
            file.path(data_dir, "ex_normal2.nc")),
          file_out, nc34 = 4)
file <- nc_open(file_out)

test_that("data is correct in version 4", {
  actual <- ncvar_get(file)

  temp <- seq(250, 272)
  temp2 <- seq(230, 252)
  expected_data <- c(temp, temp, temp[1:3],
                     temp2, temp2, temp2[1:3])
  expected <- array(expected_data, dim = c(7, 7, 2))

  expect_equivalent(actual, expected)
})

test_that("attributes are correct in version 4", {
  actual <- ncatt_get(file, "lon", "units")$value
  expect_equal(actual, "degrees_east")

  actual <- ncatt_get(file, "lon", "long_name")$value
  expect_equal(actual, "longitude")

  actual <- ncatt_get(file, "lon", "standard_name")$value
  expect_equal(actual, "longitude")

  actual <- ncatt_get(file, "lon", "axis")$value
  expect_equal(actual, "X")

  actual <- ncatt_get(file, "lat", "units")$value
  expect_equal(actual, "degrees_north")

  actual <- ncatt_get(file, "lat", "long_name")$value
  expect_equal(actual, "latitude")

  actual <- ncatt_get(file, "lat", "standard_name")$value
  expect_equal(actual, "latitude")

  actual <- ncatt_get(file, "lat", "axis")$value
  expect_equal(actual, "Y")

  actual <- ncatt_get(file, "time", "units")$value
  expect_equal(actual, "hours since 1983-01-01 00:00:00")

  actual <- ncatt_get(file, "time", "long_name")$value
  expect_equal(actual, "time")

  actual <- ncatt_get(file, "time", "standard_name")$value
  expect_equal(actual, "time")

  actual <- ncatt_get(file, "time", "calendar")$value
  expect_equal(actual, "standard")

  global_attr <- ncatt_get(file, 0)
  expect_equal(length(global_attr), 1)

  actual <- names(global_attr[1])
  expect_equal(actual, "Info")

  actual <- global_attr[[1]]
  expect_equal(actual, "Created with the CM SAF R Toolbox.")
})

test_that("coordinates are correct in version 4", {
  actual <- ncvar_get(file, "lon")
  expect_identical(actual, array(seq(5, 8, 0.5)))

  actual <- ncvar_get(file, "lat")
  expect_identical(actual, array(seq(45, 48, 0.5)))

  actual <- ncvar_get(file, "time")
  expect_equal(actual, array(c(149016, 158544)))
})

nc_close(file)

########## output ncdf version 7 #########
file_out <- tempfile_nc()

test_that("error is thrown if ncdf version is wrong", {
  expect_error(
    cmsaf.cat("SIS",
              c(file.path(data_dir, "ex_normal1.nc"),
                file.path(data_dir, "ex_normal2.nc")),
              file_out, nc34 = 7),
    "nc version must be in c(3, 4), but was 7", fixed = TRUE
  )
})

########## output ncdf version is NULL #########
file_out <- tempfile_nc()

test_that("ncdf version NULL throws an error", {
  expect_error(
    cmsaf.cat("SIS",
              c(file.path(data_dir, "ex_normal1.nc"),
                file.path(data_dir, "ex_normal2.nc")),
              file_out, nc34 = NULL),
    "nc_version must not be NULL"
  )
})

########## variable does not exist #########
file_out <- tempfile_nc()
test_that("no error is thrown if var does not exist", {
  expect_warning(cmsaf.cat("lat",
                           c(file.path(data_dir, "ex_normal1.nc"),
                             file.path(data_dir, "ex_normal2.nc")),
                           file_out),
                 "Variable 'lat' not found. Variable 'SIS' will be used instead.")
})
file <- nc_open(file_out)

test_that("data is correct if non-existing variable is given", {
  actual <- ncvar_get(file)

  temp <- seq(250, 272)
  temp2 <- seq(230, 252)
  expected_data <- c(temp, temp, temp[1:3],
                     temp2, temp2, temp2[1:3])
  expected <- array(expected_data, dim = c(7, 7, 2))

  expect_equivalent(actual, expected)
})

test_that("attributes are correct if non-existing variable is given", {
  actual <- ncatt_get(file, "lon", "units")$value
  expect_equal(actual, "degrees_east")

  actual <- ncatt_get(file, "lon", "long_name")$value
  expect_equal(actual, "longitude")

  actual <- ncatt_get(file, "lon", "standard_name")$value
  expect_equal(actual, "longitude")

  actual <- ncatt_get(file, "lon", "axis")$value
  expect_equal(actual, "X")


  actual <- ncatt_get(file, "lat", "units")$value
  expect_equal(actual, "degrees_north")

  actual <- ncatt_get(file, "lat", "long_name")$value
  expect_equal(actual, "latitude")

  actual <- ncatt_get(file, "lat", "standard_name")$value
  expect_equal(actual, "latitude")

  actual <- ncatt_get(file, "lat", "axis")$value
  expect_equal(actual, "Y")

  actual <- ncatt_get(file, "time", "units")$value
  expect_equal(actual, "hours since 1983-01-01 00:00:00")

  actual <- ncatt_get(file, "time", "long_name")$value
  expect_equal(actual, "time")

  actual <- ncatt_get(file, "time", "standard_name")$value
  expect_equal(actual, "time")

  actual <- ncatt_get(file, "time", "calendar")$value
  expect_equal(actual, "standard")

  global_attr <- ncatt_get(file, 0)
  expect_equal(length(global_attr), 1)

  actual <- names(global_attr[1])
  expect_equal(actual, "Info")

  actual <- global_attr[[1]]
  expect_equal(actual, "Created with the CM SAF R Toolbox.")
})

test_that("coordinates are correct if non-existing variable is given", {
  actual <- ncvar_get(file, "lon")
  expect_identical(actual, array(seq(5, 8, 0.5)))

  actual <- ncvar_get(file, "lat")
  expect_identical(actual, array(seq(45, 48, 0.5)))

  actual <- ncvar_get(file, "time")
  expect_equal(actual, array(c(149016, 158544)))
})

nc_close(file)


########## variable is null #########
file_out <- tempfile_nc()

test_that("error is thrown if variable is NULL", {
  expect_error(
    cmsaf.cat(NULL,
              c(file.path(data_dir, "ex_normal1.nc"),
                file.path(data_dir, "ex_normal2.nc")),
              file_out),
    "variable must not be NULL"
  )
})

########## variable is empty #########
test_that("no error is thrown if var does not exist", {
  file_out <- tempfile_nc()
  expect_warning(cmsaf.cat("",
          c(file.path(data_dir, "ex_normal1.nc"),
            file.path(data_dir, "ex_normal2.nc")),
          file_out),
          "Variable '' not found. Variable 'SIS' will be used instead.")
})
########## input file does not exist #########
# TODO this should throw an error
file_out <- tempfile_nc()

test_that("error is thrown if input file does not exist", {
  expect_error(cmsaf.cat("SIS",
                         c(file.path(data_dir, "xemaple1.nc"),
                           file.path(data_dir, "ex_normal2.nc")),
                         file_out),
               "Input file ../testdata/xemaple1.nc does not exist")
})

########## input filename is empty #########
# TODO this should throw an error
file_out <- tempfile_nc()

test_that("error is thrown if input filename is empty", {
  expect_error(cmsaf.cat("SIS", c("",
                                  file.path(data_dir, "ex_normal2.nc")),
                         file_out),
               "Input file  does not exist")
})

########## input filename is NULL #########
file_out <- tempfile_nc()

test_that("no error is thrown if input filename is NULL", {
  expect_error(cmsaf.cat("SIS",
                         c(file.path(data_dir, "ex_normal1.nc"),
                           NULL),
                         file_out),
               NA)
})

########## output file already exists #########
file_out <- tempfile_nc()
cat("test\n", file = file_out)

test_that("no error is thrown if output file already exists", {
  expect_error(cmsaf.cat("SIS",
                         c(file.path(data_dir, "ex_normal1.nc"),
                           file.path(data_dir, "ex_normal2.nc")),
                         file_out),
               paste0("File '",
                      file_out,
                      "' already exists. Specify 'overwrite = TRUE' if you want to overwrite it."),
               fixed = TRUE)
})

########## time length is 2 and 2 ##########
file_out <- tempfile_nc()
cmsaf.cat("SIS",
          c(file.path(data_dir, "ex_time_dim1.nc"),
            file.path(data_dir, "ex_time_dim2.nc")),
          file_out)
file <- nc_open(file_out)

test_that("data is correct", {
  actual <- ncvar_get(file)

  temp <- seq(250, 272)
  temp2 <- seq(230, 252)
  expected_data <- c(rep(temp, 4), temp[1:6],
                     rep(temp2, 4), temp2[1:6])
  expected <- array(expected_data, dim = c(7, 7, 4))

  expect_equivalent(actual, expected)
})

test_that("attributes are correct", {
  actual <- ncatt_get(file, "lon", "units")$value
  expect_equal(actual, "degrees_east")

  actual <- ncatt_get(file, "lon", "long_name")$value
  expect_equal(actual, "longitude")

  actual <- ncatt_get(file, "lon", "standard_name")$value
  expect_equal(actual, "longitude")

  actual <- ncatt_get(file, "lon", "axis")$value
  expect_equal(actual, "X")


  actual <- ncatt_get(file, "lat", "units")$value
  expect_equal(actual, "degrees_north")

  actual <- ncatt_get(file, "lat", "long_name")$value
  expect_equal(actual, "latitude")

  actual <- ncatt_get(file, "lat", "standard_name")$value
  expect_equal(actual, "latitude")

  actual <- ncatt_get(file, "lat", "axis")$value
  expect_equal(actual, "Y")

  actual <- ncatt_get(file, "time", "units")$value
  expect_equal(actual, "hours since 1983-01-01 00:00:00")

  actual <- ncatt_get(file, "time", "long_name")$value
  expect_equal(actual, "time")

  actual <- ncatt_get(file, "time", "standard_name")$value
  expect_equal(actual, "time")

  actual <- ncatt_get(file, "time", "calendar")$value
  expect_equal(actual, "standard")

  global_attr <- ncatt_get(file, 0)
  expect_equal(length(global_attr), 1)

  actual <- names(global_attr[1])
  expect_equal(actual, "Info")

  actual <- global_attr[[1]]
  expect_equal(actual, "Created with the CM SAF R Toolbox.")
})

test_that("coordinates are correct", {
  actual <- ncvar_get(file, "lon")
  expect_identical(actual, array(seq(5, 8, 0.5)))

  actual <- ncvar_get(file, "lat")
  expect_identical(actual, array(seq(45, 48, 0.5)))

  actual <- ncvar_get(file, "time")
  expect_equal(actual, array(c(149016, 158544, 167976, 177480)))
})

nc_close(file)

########## time length is 1 and 2 ##########
file_out <- tempfile_nc()
cmsaf.cat("SIS",
          c(file.path(data_dir, "ex_normal1.nc"),
            file.path(data_dir, "ex_time_dim2.nc")),
          file_out)
file <- nc_open(file_out)

test_that("data is correct", {
  actual <- ncvar_get(file)

  temp <- seq(250, 272)
  temp2 <- seq(230, 252)
  expected_data <- c(temp, temp, temp[1:3],
                     rep(temp2, 5))
  expected <- array(expected_data, dim = c(7, 7, 3))

  expect_equivalent(actual, expected)
})

test_that("attributes are correct", {
  actual <- ncatt_get(file, "lon", "units")$value
  expect_equal(actual, "degrees_east")

  actual <- ncatt_get(file, "lon", "long_name")$value
  expect_equal(actual, "longitude")

  actual <- ncatt_get(file, "lon", "standard_name")$value
  expect_equal(actual, "longitude")

  actual <- ncatt_get(file, "lon", "axis")$value
  expect_equal(actual, "X")


  actual <- ncatt_get(file, "lat", "units")$value
  expect_equal(actual, "degrees_north")

  actual <- ncatt_get(file, "lat", "long_name")$value
  expect_equal(actual, "latitude")

  actual <- ncatt_get(file, "lat", "standard_name")$value
  expect_equal(actual, "latitude")

  actual <- ncatt_get(file, "lat", "axis")$value
  expect_equal(actual, "Y")

  actual <- ncatt_get(file, "time", "units")$value
  expect_equal(actual, "hours since 1983-01-01 00:00:00")

  actual <- ncatt_get(file, "time", "long_name")$value
  expect_equal(actual, "time")

  actual <- ncatt_get(file, "time", "standard_name")$value
  expect_equal(actual, "time")

  actual <- ncatt_get(file, "time", "calendar")$value
  expect_equal(actual, "standard")

  global_attr <- ncatt_get(file, 0)
  expect_equal(length(global_attr), 1)

  actual <- names(global_attr[1])
  expect_equal(actual, "Info")

  actual <- global_attr[[1]]
  expect_equal(actual, "Created with the CM SAF R Toolbox.")
})

test_that("coordinates are correct", {
  actual <- ncvar_get(file, "lon")
  expect_identical(actual, array(seq(5, 8, 0.5)))

  actual <- ncvar_get(file, "lat")
  expect_identical(actual, array(seq(45, 48, 0.5)))

  actual <- ncvar_get(file, "time")
  expect_equal(actual, array(c(149016, 167976, 177480)))
})

nc_close(file)

########## time length is 2 and 1 ##########
file_out <- tempfile_nc()
cmsaf.cat("SIS",
          c(file.path(data_dir, "ex_time_dim1.nc"),
            file.path(data_dir, "ex_normal2.nc")),
          file_out)
file <- nc_open(file_out)

test_that("data is correct", {
  actual <- ncvar_get(file)

  temp1 <- seq(250, 272)
  temp2 <- seq(230, 252)
  expected_data <- c(temp2, temp2, temp2[1:3],
                     rep(temp1, 7))
  expected <- array(expected_data, dim = c(7, 7, 3))

  expect_equivalent(actual, expected)
})

test_that("attributes are correct", {
  actual <- ncatt_get(file, "lon", "units")$value
  expect_equal(actual, "degrees_east")

  actual <- ncatt_get(file, "lon", "long_name")$value
  expect_equal(actual, "longitude")

  actual <- ncatt_get(file, "lon", "standard_name")$value
  expect_equal(actual, "longitude")

  actual <- ncatt_get(file, "lon", "axis")$value
  expect_equal(actual, "X")

  actual <- ncatt_get(file, "lat", "units")$value
  expect_equal(actual, "degrees_north")

  actual <- ncatt_get(file, "lat", "long_name")$value
  expect_equal(actual, "latitude")

  actual <- ncatt_get(file, "lat", "standard_name")$value
  expect_equal(actual, "latitude")

  actual <- ncatt_get(file, "lat", "axis")$value
  expect_equal(actual, "Y")

  actual <- ncatt_get(file, "time", "units")$value
  expect_equal(actual, "hours since 1983-01-01 00:00:00")

  actual <- ncatt_get(file, "time", "long_name")$value
  expect_equal(actual, "time")

  actual <- ncatt_get(file, "time", "standard_name")$value
  expect_equal(actual, "time")

  actual <- ncatt_get(file, "time", "calendar")$value
  expect_equal(actual, "standard")

  global_attr <- ncatt_get(file, 0)
  expect_equal(length(global_attr), 1)

  actual <- names(global_attr[1])
  expect_equal(actual, "Info")

  actual <- global_attr[[1]]
  expect_equal(actual, "Created with the CM SAF R Toolbox.")
})

test_that("coordinates are correct", {
  actual <- ncvar_get(file, "lon")
  expect_identical(actual, array(seq(5, 8, 0.5)))

  actual <- ncvar_get(file, "lat")
  expect_identical(actual, array(seq(45, 48, 0.5)))

  actual <- ncvar_get(file, "time")
  expect_equal(actual, array(c(158544, 149016, 158544)))
})

nc_close(file)

########## time length is 4 and 2 ##########
file_out <- tempfile_nc()
cmsaf.cat("SIS",
          c(file.path(data_dir, "ex_time_dim3.nc"),
            file.path(data_dir, "ex_time_dim2.nc")),
          file_out)
test_that("output file is created because dimensions match", {
  expect_true(file.exists(file_out))
})

########## additional attribute ##########
file_out <- tempfile_nc()
cmsaf.cat("SIS",
          c(file.path(data_dir, "ex_additional_attr.nc"),
            file.path(data_dir, "ex_normal2.nc")),
          file_out)
file <- nc_open(file_out)

test_that("data is correct", {
  actual <- ncvar_get(file)

  temp <- seq(250, 272)
  temp2 <- seq(230, 252)
  expected_data <- c(temp, temp, temp[1:3],
                     temp2, temp2, temp2[1:3])
  expected <- array(expected_data, dim = c(7, 7, 2))

  expect_equivalent(actual, expected)
})

test_that("attributes are correct", {
  actual <- ncatt_get(file, "lon", "units")$value
  expect_equal(actual, "degrees_east")

  actual <- ncatt_get(file, "lon", "long_name")$value
  expect_equal(actual, "longitude")

  actual <- ncatt_get(file, "lon", "standard_name")$value
  expect_equal(actual, "longitude")

  actual <- ncatt_get(file, "lon", "axis")$value
  expect_equal(actual, "X")

  actual <- ncatt_get(file, "lat", "units")$value
  expect_equal(actual, "degrees_north")

  actual <- ncatt_get(file, "lat", "long_name")$value
  expect_equal(actual, "latitude")

  actual <- ncatt_get(file, "lat", "standard_name")$value
  expect_equal(actual, "latitude")

  actual <- ncatt_get(file, "lat", "axis")$value
  expect_equal(actual, "Y")

  actual <- ncatt_get(file, "time", "units")$value
  expect_equal(actual, "hours since 1983-01-01 00:00:00")

  actual <- ncatt_get(file, "time", "long_name")$value
  expect_equal(actual, "time")

  actual <- ncatt_get(file, "time", "standard_name")$value
  expect_equal(actual, "time")

  actual <- ncatt_get(file, "time", "calendar")$value
  expect_equal(actual, "standard")

  global_attr <- ncatt_get(file, 0)
  expect_equal(length(global_attr), 2)

  actual <- names(global_attr[1])
  expect_equal(actual, "Info")

  actual <- global_attr[[1]]
  expect_equal(actual, "Created with the CM SAF R Toolbox.")

  actual <- names(global_attr[2])
  expect_equal(actual, "institution")

  actual <- global_attr[[2]]
  expect_equal(actual, "This is a test attribute.")
})

test_that("coordinates are correct", {
  actual <- ncvar_get(file, "lon")
  expect_identical(actual, array(seq(5, 8, 0.5)))

  actual <- ncvar_get(file, "lat")
  expect_identical(actual, array(seq(45, 48, 0.5)))

  actual <- ncvar_get(file, "time")
  expect_equal(actual, array(c(149016, 158544)))
})

nc_close(file)

########## input ncdf version 4 ##########
file_out <- tempfile_nc()
cmsaf.cat("SIS",
          c(file.path(data_dir, "ex_v4_1.nc"),
            file.path(data_dir, "ex_v4_2.nc")),
          file_out)
file <- nc_open(file_out)

test_that("data is correct", {
  actual <- ncvar_get(file)

  temp <- seq(250, 272)
  temp2 <- seq(230, 252)
  expected_data <- c(temp, temp, temp[1:3],
                     temp2, temp2, temp2[1:3])
  expected <- array(expected_data, dim = c(7, 7, 2))

  expect_equivalent(actual, expected)
})

test_that("attributes are correct", {
  actual <- ncatt_get(file, "lon", "units")$value
  expect_equal(actual, "degrees_east")

  actual <- ncatt_get(file, "lon", "long_name")$value
  expect_equal(actual, "longitude")

  actual <- ncatt_get(file, "lon", "standard_name")$value
  expect_equal(actual, "longitude")

  actual <- ncatt_get(file, "lon", "axis")$value
  expect_equal(actual, "X")

  actual <- ncatt_get(file, "lat", "units")$value
  expect_equal(actual, "degrees_north")

  actual <- ncatt_get(file, "lat", "long_name")$value
  expect_equal(actual, "latitude")

  actual <- ncatt_get(file, "lat", "standard_name")$value
  expect_equal(actual, "latitude")

  actual <- ncatt_get(file, "lat", "axis")$value
  expect_equal(actual, "Y")

  actual <- ncatt_get(file, "time", "units")$value
  expect_equal(actual, "hours since 1983-01-01 00:00:00")

  actual <- ncatt_get(file, "time", "long_name")$value
  expect_equal(actual, "time")

  actual <- ncatt_get(file, "time", "standard_name")$value
  expect_equal(actual, "time")

  actual <- ncatt_get(file, "time", "calendar")$value
  expect_equal(actual, "standard")

  global_attr <- ncatt_get(file, 0)
  expect_equal(length(global_attr), 1)

  actual <- names(global_attr[1])
  expect_equal(actual, "Info")

  actual <- global_attr[[1]]
  expect_equal(actual, "Created with the CM SAF R Toolbox.")
})

test_that("coordinates are correct", {
  actual <- ncvar_get(file, "lon")
  expect_identical(actual, array(seq(5, 8, 0.5)))

  actual <- ncvar_get(file, "lat")
  expect_identical(actual, array(seq(45, 48, 0.5)))

  actual <- ncvar_get(file, "time")
  expect_equal(actual, array(c(149016, 158544)))
})

nc_close(file)