test_change_att.R
In cmsafops: Tools for CM SAF NetCDF Data

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

########## default parameters ##########
file_out <- tempfile_nc()
file.copy(file.path(data_dir, "ex_normal1.nc"), file_out, overwrite = TRUE)
change_att("SIS", file_out)
file <- nc_open(file_out)

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

  expected_data <- rep(seq(250, 272), 3)
  expected <- array(expected_data, dim = c(7, 7))

  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, "lon")

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

  actual <- ncatt_get(file, "lon", "axis")$value
  expect_equal(actual, 0)

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

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

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

  actual <- ncatt_get(file, "lat", "axis")$value
  expect_equal(actual, 0)

  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, 0)

  actual <- ncatt_get(file, "time", "calendar")$value
  expect_equal(actual, 0)

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

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

  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(149016))
})

nc_close(file)

########## variable does not exist #########
# TODO this should throw a clearer error
file_out <- tempfile_nc()
file.copy(file.path(data_dir, "ex_normal1.nc"), file_out, overwrite = TRUE)
test_that("error is thrown if variable does not exist", {
  expect_error(change_att("lat", file_out))
})

file <- nc_open(file_out)

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

  expected_data <- rep(seq(250, 272), 3)
  expected <- array(expected_data, dim = c(7, 7))

  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, "lon")

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

  actual <- ncatt_get(file, "lon", "axis")$value
  expect_equal(actual, 0)

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

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

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

  actual <- ncatt_get(file, "lat", "axis")$value
  expect_equal(actual, 0)

  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, 0)

  actual <- ncatt_get(file, "time", "calendar")$value
  expect_equal(actual, 0)

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

  # TODO global_attr isn't written in this case
  actual <- names(global_attr[1])
  expect_equal(actual, NULL)
})

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(149016))
})

nc_close(file)

########## variable is null #########
file_out <- tempfile_nc()
file.copy(file.path(data_dir, "ex_normal1.nc"), file_out, overwrite = TRUE)

test_that("error is thrown if variable is NULL", {
  expect_error(
    change_att(NULL, file_out),
    "variable must not be NULL"
  )
})

########## variable is empty #########
# TODO this should throw a clearer error?
file_out <- tempfile_nc()
file.copy(file.path(data_dir, "ex_normal1.nc"), file_out, overwrite = TRUE)

test_that("error is thrown if variable is empty", {
  expect_error(change_att("", file_out))
})

########## input file does not exist #########
# TODO this should throw a clearer error
file_out <- tempfile_nc()

test_that("no error is thrown if input file does not exist", {
  expect_error(change_att("SIS", file_out),
               "Input file does not exist")
})

########## input filename is empty #########
test_that("no error is thrown if input filename is empty", {
  expect_error(change_att("SIS", ""),
               "Input file does not exist")
})

########## input filename is NULL #########
test_that("error is thrown if input filename is NULL", {
  expect_error(change_att("SIS", NULL),
               "Input filepath must be of length one and not NULL")
})

########## time length is 2 ##########
file_out <- tempfile_nc()
file.copy(file.path(data_dir, "ex_time_dim1.nc"), file_out, overwrite = TRUE)

test_that("no error is thrown if output file already exists", {
  expect_error(change_att("SIS", file_out),
               NA)
})

file <- nc_open(file_out)

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

  expected_data <- rep(seq(250, 272), 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, "lon")

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

  actual <- ncatt_get(file, "lon", "axis")$value
  expect_equal(actual, 0)


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

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

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

  actual <- ncatt_get(file, "lat", "axis")$value
  expect_equal(actual, 0)

  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, 0)

  actual <- ncatt_get(file, "time", "calendar")$value
  expect_equal(actual, 0)

  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)

########## time length is 4 ##########
file_out <- tempfile_nc()
file.copy(file.path(data_dir, "ex_time_dim3.nc"), file_out, overwrite = TRUE)
change_att("SIS", file_out)
file <- nc_open(file_out)

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

  expected_data <- rep(seq(250, 272), 3)
  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, "lon")

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

  actual <- ncatt_get(file, "lon", "axis")$value
  expect_equal(actual, 0)

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

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

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

  actual <- ncatt_get(file, "lat", "axis")$value
  expect_equal(actual, 0)

  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, 0)

  actual <- ncatt_get(file, "time", "calendar")$value
  expect_equal(actual, 0)

  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(192864, 202368, 211800, 221328)))
})

nc_close(file)

########## different lon length ##########
file_out <- tempfile_nc()
file.copy(file.path(data_dir, "ex_different_lon_length.nc"),
          file_out, overwrite = TRUE)
change_att("SIS", file_out)

file <- nc_open(file_out)

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

  expected_data <- rep(seq(250, 272), 3)
  expected <- array(expected_data, dim = c(5, 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, "lon")

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

  actual <- ncatt_get(file, "lon", "axis")$value
  expect_equal(actual, 0)

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

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

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

  actual <- ncatt_get(file, "lat", "axis")$value
  expect_equal(actual, 0)

  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, 0)

  actual <- ncatt_get(file, "time", "calendar")$value
  expect_equal(actual, 0)

  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, 7, 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)

########## additional attribute ##########
file_out <- tempfile_nc()
file.copy(file.path(data_dir, "ex_additional_attr.nc"), file_out, overwrite = TRUE)
change_att("SIS", file_out)
file <- nc_open(file_out)

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

  expected_data <- rep(seq(250, 272), 3)
  expected <- array(expected_data, dim = c(7, 7))

  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, "lon")

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

  actual <- ncatt_get(file, "lon", "axis")$value
  expect_equal(actual, 0)

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

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

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

  actual <- ncatt_get(file, "lat", "axis")$value
  expect_equal(actual, 0)

  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, 0)

  actual <- ncatt_get(file, "time", "calendar")$value
  expect_equal(actual, 0)

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

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

  actual <- global_attr[[1]]
  expect_equal(actual, "This is a test attribute.")

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

  actual <- global_attr[[2]]
  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(149016))
})

nc_close(file)

########## input ncdf version 4 ##########
file_out <- tempfile_nc()
file.copy(file.path(data_dir, "ex_v4_1.nc"), file_out, overwrite = TRUE)
change_att("SIS", file_out)
file <- nc_open(file_out)

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

  expected_data <- rep(seq(250, 272), 3)
  expected <- array(expected_data, dim = c(7, 7))

  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, "lon")

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

  actual <- ncatt_get(file, "lon", "axis")$value
  expect_equal(actual, 0)

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

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

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

  actual <- ncatt_get(file, "lat", "axis")$value
  expect_equal(actual, 0)

  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, 0)

  actual <- ncatt_get(file, "time", "calendar")$value
  expect_equal(actual, 0)

  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(149016))
})

nc_close(file)

########## change variable ##########
file_out <- tempfile_nc()
file.copy(file.path(data_dir, "ex_normal1.nc"), file_out, overwrite = TRUE)
change_att("SIS", file_out,
           v_name = "new", s_name = "newnew",
           l_name = "this is a new name for the variable", u_name = "m",
           F_val = -9, m_val = -99)
file <- nc_open(file_out)

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

  expected_data <- rep(seq(250, 272), 3)
  expected <- array(expected_data, dim = c(7, 7))

  expect_equivalent(actual, expected)
})

varnames <- file$var
test_that("old variable does not exist any more", {
  expect_false("SIS" %in% varnames)
})

test_that("new variable attributes are correct", {
  actual <- ncatt_get(file, "new", "units")$value
  expect_equal(actual, "m")

  actual <- ncatt_get(file, "new", "_FillValue")$value
  expect_equal(actual, -9)

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

  actual <- ncatt_get(file, "new", "long_name")$value
  expect_equal(actual, "this is a new name for the variable")

  actual <- ncatt_get(file, "new", "missing_value")$value
  expect_equal(actual, -99)
})

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, "lon")

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

  actual <- ncatt_get(file, "lon", "axis")$value
  expect_equal(actual, 0)

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

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

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

  actual <- ncatt_get(file, "lat", "axis")$value
  expect_equal(actual, 0)

  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, 0)

  actual <- ncatt_get(file, "time", "calendar")$value
  expect_equal(actual, 0)

  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(149016))
})

nc_close(file)