# function that retrieves the data of the relevant pre-computed synthetic # dataset of wide Olink data get_wide_synthetic_data <- function(olink_platform, data_type, n_panels, n_assays, n_samples, show_dev_int_ctrl, show_int_ctrl, version) { # check inputs check_olink_platform(x = olink_platform) check_olink_data_type(x = data_type) check_is_scalar_integer(x = n_panels, error = TRUE) check_is_scalar_integer(x = n_assays, error = TRUE) check_is_scalar_integer(x = n_samples, error = TRUE) check_is_scalar_boolean(x = show_dev_int_ctrl, error = TRUE) check_is_scalar_boolean(x = show_int_ctrl, error = TRUE) check_is_scalar_integer(x = version, error = TRUE) # get internal variables olink_p <- accepted_olink_platforms |> dplyr::filter( .data[["name"]] == .env[["olink_platform"]] ) |> dplyr::pull( .data[["short_name"]] ) data_t <- ifelse(data_type == "Quantified", "quant", tolower(data_type)) int_ctrl <- show_int_ctrl |> as.character() |> stringr::str_sub(start = 1L, end = 1L) dev_int_ctrl <- show_dev_int_ctrl |> as.character() |> stringr::str_sub(start = 1L, end = 1L) # file name df_rand_file <- paste0("p=", n_panels, "_", "a=", n_assays, "_", "s=", n_samples, "_", "ic=", int_ctrl, "_", "dic=", dev_int_ctrl, "_", "v=", version, ".rds") # get full path df_rand_path <- test_path("data", "synthetic_dt_wide", olink_p, data_t, df_rand_file) if (file.exists(df_rand_path)) { # return full file path return(readRDS(file = df_rand_path)) } else { # if not, skip the test testthat::skip() return(NULL) } } # load example datasets for Olink Explore products get_example_data <- function(filename) { # get file path under tests/testthat/data ref_norm_res_file <- test_path("data", filename) # check that file exists if (file.exists(ref_norm_res_file)) { # return full file path return(readRDS(file = ref_norm_res_file)) } else { # if not, skip the test testthat::skip() return(NULL) } } # load example files living under inst/extdata get_inst_extdata_file <- function(filename) { # get file path under inst/extdata sample_data_file <- system.file("extdata", filename, package = "OlinkAnalyze") # check that file exists if (file.exists(sample_data_file)) { # return full file path return(sample_data_file) } else { # if not, skip the test testthat::skip() return(NULL) } } # check if snapshot exists. if not skip the test. check_snap_exist <- function(test_dir_name, snap_name) { # check that "_snaps" exist, otherwise skip base_test_dir <- test_path("_snaps") skip_if_not(dir.exists(base_test_dir)) # check that test-specific snaps directory exist. if not skip. test_dir <- test_path("_snaps", test_dir_name) skip_if_not(dir.exists(test_dir)) # check that snapshot exist. if not skip stopifnot(rlang::is_scalar_character(snap_name)) snap_name_clean <- gsub("[^a-z0-9]", "-", tolower(snap_name)) snap_name_clean <- gsub(paste0("-", "-", "+"), "-", snap_name_clean) snap_name_clean <- gsub(paste0("^", "-", "|", "-", "$"), "", snap_name_clean) snap_name_clean <- paste0(snap_name_clean, ".svg") snap_path <- test_path("_snaps", test_dir_name, snap_name_clean) skip_if_not(file.exists(snap_path)) return(invisible(NULL)) }