tests/testthat/test-read_validate_files.R

In glossa: User-Friendly 'shiny' App for Bayesian Species Distribution Models

# Read input data from user

test_that("Read presence/absence files", {
  # skip on CRAN
  skip_on_cran()

  # File paths
  file1 <- system.file("extdata", "sp1.txt", package="glossa")
  file2 <- system.file("extdata", "sp2.csv", package="glossa")

  expect_s3_class(glossa::read_presences_absences_csv(file_path = file1), "data.frame")

  expect_s3_class(glossa::read_presences_absences_csv(file_path = file2, file_name = "sp2" ), "data.frame")
})

test_that("Read fit_layers file", {
  # skip on CRAN
  skip_on_cran()

  # File path
  file1 <- system.file("extdata", "fit_layers.zip", package="glossa")

  suppressWarnings(
    expect_s4_class(glossa::read_layers_zip(file_path = file1)[[1]], "SpatRaster")
  )
})

test_that("Read projection layers", {
  # skip on CRAN
  skip_on_cran()

  # File path
  file1 <- system.file("extdata", "project_layers_1.zip", package="glossa")

  suppressWarnings(
    expect_type(glossa::read_layers_zip(file_path = file1), "list")
  )
})

test_that("Validate projection layers", {
  # skip on CRAN
  skip_on_cran()

  # File path
  file1 <- system.file("extdata", "fit_layers.zip", package="glossa")
  file2 <- system.file("extdata", "project_layers_1.zip", package="glossa")

  expect_type(suppressWarnings(glossa::validate_layers_zip(file_path = file1)), "logical")
  expect_equal(glossa::validate_fit_projection_layers(file1, file2), TRUE)
})

test_that("Read extent polygon", {
  # skip on CRAN
  skip_on_cran()

  # File path
  file1 <- system.file("extdata", "world.gpkg", package="glossa")

  suppressWarnings(
    expect_s3_class(glossa::read_extent_polygon(file_path = file1), "sfc")
  )
})

# Load toy data
pa_data <- system.file("extdata", "testthat_coords.csv", package="glossa")
fit_layers <- system.file("extdata", "testthat_layers.zip", package="glossa")
study_area <- system.file("extdata", "testthat_polygon.gpkg", package="glossa")

# Tests for read_presences_absences_csv
test_that("read_presences_absences_csv reads and validates CSV correctly", {
  data <- read_presences_absences_csv(pa_data, show_modal = FALSE)
  expect_s3_class(data, "data.frame")  # Expecting a data frame
  expect_equal(ncol(data), 4)  # Expecting 4 columns
  expect_true(all(c("decimalLongitude", "decimalLatitude", "timestamp", "pa") %in% colnames(data)))  # Check required columns
})

test_that("read_presences_absences_csv throws error for missing columns", {
  skip_on_cran()

  testhtat_file <- tempfile()
  write.table(data.frame(decimalLongitude = c(-123.1)), testhtat_file, row.names = FALSE, sep = "\t")
  expect_null(suppressWarnings(read_presences_absences_csv(testhtat_file)))
  unlink(testhtat_file)
})

# Tests for read_layers_zip
test_that("read_layers_zip loads layers correctly", {
  layers <- read_layers_zip(fit_layers, extend = TRUE, first_layer = TRUE)
  expect_true(is.list(layers))  # Expecting a list of raster layers
})

test_that("read_layers_zip loads layers correctly", {
  layers <- read_layers_zip(fit_layers, extend = FALSE, first_layer = FALSE)
  expect_true(is.list(layers))  # Expecting a list of raster layers
})

# Tests for read_extent_polygon
test_that("read_extent_polygon reads and validates polygon correctly", {
  extent_polygon <- read_extent_polygon(study_area)
  expect_s3_class(extent_polygon, "sfc")  # Expecting an sfc object
})

test_that("read_extent_polygon throws error for invalid geometry", {
  skip_on_cran()

  testhtat_file <- tempfile()
  writeLines("INVALID GEOMETRY", testhtat_file)
  expect_null(suppressWarnings(read_extent_polygon(testhtat_file)))
  unlink(testhtat_file)
})

# Tests for validate_layers_zip
test_that("validate_layers_zip validates layers correctly", {
  result <- suppressWarnings(validate_layers_zip(fit_layers))
  expect_true(result)  # Expecting TRUE for valid layers
})

# Tests for validate_fit_projection_layers
test_that("validate_fit_projection_layers checks covariates correctly", {
  result <- validate_fit_projection_layers(fit_layers, fit_layers)
  expect_true(result)  # Expecting TRUE for matching covariates
})

# Tests for validate_pa_fit_time
test_that("validate_pa_fit_time checks timestamps correctly", {
  result <- suppressWarnings(validate_pa_fit_time(read_presences_absences_csv(pa_data), fit_layers))
  expect_false(result)  # Expecting FALSE if the timestamps don't match
})