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add environment api to enable cdse tests
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‎DESCRIPTION

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'api_data.R'
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'api_debug.R'
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'api_download.R'
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'api_environment.R'
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'api_factory.R'
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'api_file_info.R'
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'api_file.R'

‎NAMESPACE

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S3method(.source_collection_access_test,stac_cube)
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S3method(.source_collection_access_test,usgs_cube)
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S3method(.source_cube,stac_cube)
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S3method(.source_filter_tiles,"cdse_cube_sentinel-1-rtc")
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S3method(.source_filter_tiles,"mpc_cube_sentinel-1-grd")
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S3method(.source_filter_tiles,stac_cube)
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S3method(.source_item_get_bands,stac_cube)

‎R/api_environment.R

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# ---- Environment operations ----
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#' @title Function to patch environment variables (Developer only).
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#' @keywords internal
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#' @noRd
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#'
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#' @description
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#' This function patches environment variables, swapping them from a `source`
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#' to a `target` variable. You can rollback the swap operation using the
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#' `.environment_rollback.`
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#'
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#' @note
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#' This function is suitable only for internal `sits` tests and should not be
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#' used for any other purpose.
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#' @param env_config List with the configuration of the environment.
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#' @return Called for side effects.
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.environment_patch <- function(env_config) {
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env_prefix <- env_config[["name"]]
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env_variables <- env_config[["variables"]]
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purrr::map(1:length(env_variables), function(var_idx) {
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var_source <- names(env_variables)[[var_idx]]
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var_target <- unname(env_variables)[[var_idx]]
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# Get current value of the target variable
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var_target_value <- Sys.getenv(var_target)
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# Save current value of the target variable in the "swap area"
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var_target_swap <- paste(env_prefix, var_target, sep = "_SWAP_")
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var_target_swap_value <- list(tmp = var_target_value)
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var_target_swap_value <- stats::setNames(
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var_target_swap_value,
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var_target_swap
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)
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# Save variable
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do.call(Sys.setenv, var_target_swap_value)
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# Get the new value of the target variable
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var_source_value <- Sys.getenv(var_source)
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# Save new value in the target variable
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var_target_new_value <- list(tmp = var_source_value)
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var_target_new_value <- stats::setNames(
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var_target_new_value,
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var_target
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)
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# Save variable
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do.call(Sys.setenv, var_target_new_value)
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})
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return(invisible(NULL))
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}
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#' @title Function to rollback patch in environment variables (Developer only).
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#' @keywords internal
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#' @noRd
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#'
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#' @description
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#' This function rollback patches in environment variables created with the
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#' function `.environment_patch`.
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#' @note
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#' This function is suitable only for internal `sits` tests and should not be
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#' used for any other purpose.
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#' @param env_config List with the configuration of the environment.
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#' @return Called for side effects.
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.environment_rollback <- function(env_config) {
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env_prefix <- env_config[["name"]]
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env_variables <- env_config[["variables"]]
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purrr::map(1:length(env_variables), function(var_idx) {
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var_source <- names(env_variables)[[var_idx]]
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var_target <- unname(env_variables)[[var_idx]]
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# Get current value of the target variable
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var_target_value <- Sys.getenv(var_target)
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# Save current value in the source variable
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var_source_new_value <- list(tmp = var_target_value)
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var_source_new_value <- stats::setNames(
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var_source_new_value,
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var_source
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)
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do.call(Sys.setenv, var_source_new_value)
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# Get current value of the target variable in the "swap area"
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var_target_swap <- paste(env_prefix, var_target, sep = "_SWAP_")
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var_target_swap_value <- Sys.getenv(var_target_swap)
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# Prepare current target
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var_target_swap_value <- list(tmp = var_target_swap_value)
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var_target_swap_value <- stats::setNames(
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var_target_swap_value,
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var_target
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)
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do.call(Sys.setenv, var_target_swap_value)
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})
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return(invisible(NULL))
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}
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# ---- Environment configurations ----
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#' @title Function to create patch configuration for the CDSE source.
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#' @keywords internal
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#' @noRd
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#'
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#' @description
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#' This function creates a configuration for the `patch` and `rollback`
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#' specialized for the CDSE requirements.
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#' @note
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#' This function is suitable only for internal `sits` tests and should not be
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#' used for any other purpose.
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#' @return List with the configuration of the CDSE environment.
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.environment_cdse <- function() {
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# Define environment name. This name is used as a prefix for the
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# "swap area" which is used to keep values saved
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env_name <- "CDSE"
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# Create the environment variables
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env_variables <- list(
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"CDSE_ACCESS_KEY_ID" = "AWS_ACCESS_KEY_ID",
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"CDSE_SECRET_ACCESS_KEY" = "AWS_SECRET_ACCESS_KEY",
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"CDSE_S3_ENDPOINT" = "AWS_S3_ENDPOINT",
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"CDSE_VIRTUAL_HOSTING" = "AWS_VIRTUAL_HOSTING"
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)
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# Create a base environment definition
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env_definition <-
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list(name = env_name, variables = env_variables)
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# Define a class, based on the name
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class(env_definition) <- c(env_name, "list")
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# Done!
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env_definition
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}

‎tests/testthat/test-cube-cdse.R

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test_that("Creating S2 cubes from CDSE with ROI", {
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# Configure environment
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cdse_env_config <- .environment_cdse()
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# Patch environment variables
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.environment_patch(cdse_env_config)
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# Test
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roi <- c(
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lon_min = -48.28579, lat_min = -16.05026,
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lon_max = -47.30839, lat_max = -15.50026
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)
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s2_cube_cdse <- .try(
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{
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sits_cube(
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source = "CDSE",
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collection = "SENTINEL-2-L2A",
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roi = roi,
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bands = c("B05", "CLOUD"),
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start_date = as.Date("2018-07-18"),
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end_date = as.Date("2018-08-23"),
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progress = FALSE,
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multicores = 1L
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)
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},
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.default = NULL
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)
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testthat::skip_if(purrr::is_null(s2_cube_cdse), "CDSE is not accessible")
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expect_true(all(sits_bands(s2_cube_cdse) %in% c("B05", "CLOUD")))
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expect_equal(nrow(s2_cube_cdse), 3)
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bbox_cube <- sits_bbox(s2_cube_cdse, as_crs = "EPSG:4326")
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bbox_cube_1 <- sits_bbox(.tile(s2_cube_cdse), as_crs = "EPSG:4326")
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expect_true(bbox_cube["xmax"] >= bbox_cube_1["xmax"])
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expect_true(bbox_cube["ymax"] >= bbox_cube_1["ymax"])
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r_obj <- .raster_open_rast(s2_cube_cdse$file_info[[1]]$path[1])
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cube_nrows <- .tile_nrows(s2_cube_cdse)
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expect_true(.raster_nrows(r_obj) == cube_nrows)
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# Rollback environment changes
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.environment_rollback(cdse_env_config)
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})
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test_that("Creating S2 cubes from CDSE with tiles", {
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# Configure environment
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cdse_env_config <- .environment_cdse()
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# Patch environment variables
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.environment_patch(cdse_env_config)
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# Test
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s2_cube <- .try(
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{
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sits_cube(
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source = "CDSE",
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collection = "SENTINEL-2-L2A",
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tiles = "20LKP",
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bands = c("B05", "CLOUD"),
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start_date = as.Date("2018-07-18"),
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end_date = as.Date("2018-08-23"),
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progress = FALSE,
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multicores = 1L
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)
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},
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.default = NULL
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)
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expect_true(all(sits_bands(s2_cube) %in% c("B05", "CLOUD")))
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r <- .raster_open_rast(.tile_path(s2_cube))
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expect_equal(s2_cube$xmax[[1]], .raster_xmax(r), tolerance = 1)
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expect_equal(s2_cube$xmin[[1]], .raster_xmin(r), tolerance = 1)
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r_obj <- .raster_open_rast(s2_cube$file_info[[1]]$path[1])
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cube_nrows <- .tile_nrows(s2_cube)
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expect_true(.raster_nrows(r_obj) == cube_nrows)
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# Rollback environment changes
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.environment_rollback(cdse_env_config)
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})
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test_that("Creating Sentinel-1 RTC cubes from CDSE", {
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# Configure environment
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cdse_env_config <- .environment_cdse()
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# Patch environment variables
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.environment_patch(cdse_env_config)
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# Test
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cube_s1_rtc <- sits_cube(
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source = "CDSE",
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collection = "SENTINEL-1-RTC",
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bands = c("VV"),
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orbit = "descending",
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tiles = c("36NWH"),
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start_date = "2021-07-01",
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end_date = "2021-09-30",
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multicores = 1L
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)
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bbox <- sits_bbox(cube_s1_rtc[1,])
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expect_true(grepl("4326", bbox[["crs"]]))
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expect_equal(32, bbox[["xmin"]])
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expect_equal(34, bbox[["xmax"]])
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expect_equal(nrow(cube_s1_rtc$file_info[[1]]), 68)
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output_dir <- paste0(tempdir(), "/s1rtcreg")
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if (!dir.exists(output_dir)) {
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dir.create(output_dir)
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}
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cube_s1_rtc_reg <- sits_regularize(
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cube = cube_s1_rtc,
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period = "P1M",
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res = 240,
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tiles = c("36NXG", "36NVG"),
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multicores = 1,
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output_dir = output_dir,
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progress = TRUE
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)
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expect_equal(length(sits_timeline(cube_s1_rtc_reg)), 3)
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expect_true(all(c("36NXG", "36NVG") %in%
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cube_s1_rtc_reg$tile))
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expect_true("EPSG:32636" %in% cube_s1_rtc_reg$crs)
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bbox <- sits_bbox(cube_s1_rtc_reg, as_crs = "EPSG:4326")
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roi_cube_s1 <- sits_mgrs_to_roi(c("36NXG", "36NVG"))
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expect_equal(bbox[["xmin"]], roi_cube_s1[["lon_min"]], tolerance = 0.01)
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expect_equal(bbox[["xmax"]], roi_cube_s1[["lon_max"]], tolerance = 0.03)
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expect_equal(bbox[["ymin"]], roi_cube_s1[["lat_min"]], tolerance = 0.25)
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expect_equal(bbox[["ymax"]], roi_cube_s1[["lat_max"]], tolerance = 0.01)
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expect_true(all(c("VV") %in% sits_bands(cube_s1_rtc_reg)))
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# Rollback environment changes
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.environment_rollback(cdse_env_config)
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})

‎tests/testthat/test-environment.R

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test_that("Test environment variables swap", {
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# Setup - Environment configuration
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env_config <- list(
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name = "SITS_TEST",
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variables = list(
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"A" = "B",
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"C" = "D"
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)
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)
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# Setup - Env variables
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Sys.setenv("A" = 123)
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Sys.setenv("B" = 321)
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Sys.setenv("C" = "ABC")
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Sys.setenv("D" = "CBA")
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# Test - Swapped variables
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.environment_patch(env_config)
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expect_equal(Sys.getenv("B"), "123")
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expect_equal(Sys.getenv("D"), "ABC")
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expect_equal(Sys.getenv("SITS_TEST_SWAP_B"), "321")
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expect_equal(Sys.getenv("SITS_TEST_SWAP_D"), "CBA")
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# Test - Rollback variables
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.environment_rollback(env_config)
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expect_equal(Sys.getenv("B"), "321")
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expect_equal(Sys.getenv("D"), "CBA")
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})

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