diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/testthat/test_PELMO.R | 201 |
1 files changed, 0 insertions, 201 deletions
diff --git a/tests/testthat/test_PELMO.R b/tests/testthat/test_PELMO.R deleted file mode 100644 index ba6a04a..0000000 --- a/tests/testthat/test_PELMO.R +++ /dev/null @@ -1,201 +0,0 @@ -library(testthat) -library(pfm) -context("Create PELMO runs from psm files and execute them") -PELMO_base <- system.file("FOCUSPELMO.553", package = "PELMO.installeR") - -test_archive <- system.file("testdata/FOCUS_PELMO.tar.bz2", package = "pfm") -test_dir <- tempdir() -untar(test_archive, exdir = test_dir, compressed = "bzip2") - -runs <- list( - list( - psm = "Pesticide_D", - fbe = c("Por"), - vbe = c("Por")), - list( - psm = "Pesticide_D_1_day_pre_em_every_third_year", - pot = c("Cha", "Ham")), - list( - psm = "Pesticide_D_1_May_every_other_year_mets", - win = names(FOCUS_GW_scenarios_2012$names))) - -# Check if we have wine on the path -wine_installed <- system('wine --version', ignore.stdout = TRUE) == 0 -skip_if_no_wine <- function() { - if (!wine_installed) skip("wine is not available") -} - -test_that("PELMO paths are correctly created", { - skip_if_no_wine() - psm_paths = c( - PELMO_path(runs[[1]]$psm, "fbe", "Por"), - PELMO_path(runs[[2]]$psm, "pot", "Ham"), - PELMO_path(runs[[3]]$psm, "win", "Cha")) - - for (i in seq_along(psm_paths)) { - psm_file <- file.path(test_dir, psm_paths[i], paste0(runs[[i]]$psm, ".psm")) - expect_true(file.exists(psm_file)) - psm_new_location <- file.path(PELMO_base, basename(psm_file)) - file.copy(psm_file, psm_new_location, overwrite = TRUE) - } -}) - -test_that("PELMO runs are correctly set up", { - skip_if_no_wine() - - # Prepare runs in analogy to the test archive - skip_on_cran() - PELMO_runs(runs, psm_dir = PELMO_base, execute = FALSE, evaluate = FALSE, overwrite = TRUE) - - # Check that input files are correctly generated in the right location - for (run in runs) { - psm <- run$psm - crops <- setdiff(names(run), "psm") - for (crop in crops) { - for (scenario in run[[crop]]) { - pp <- PELMO_path(psm, crop, scenario) - - input_new <- readLines(file.path(PELMO_base, "FOCUS", pp, "pelmo.inp")) - input_test <- readLines(file.path(test_dir, pp, "pelmo.inp")) - - # Check if the input files are correctly reproduced - expect_identical(input_new, input_test) - } - } - } -}) - -test_that("PELMO runs can be run and give the expected result files", { - skip_if_no_wine() - skip_on_cran() - - run_PELMO(runs, cores = 7) - - plm_files <- c("CHEM.PLM", "ECHO.PLM", - "KONZCHEM.PLM", "KONZC_A1", "KONZC_B1", - "PLNTPEST.plm", "PLOT.PLM", "WASSER.PLM") - - # Check that if output is the same as in the test archive - for (run in runs) { - psm <- run$psm - crops <- setdiff(names(run), "psm") - for (crop in crops) { - for (scenario in run[[crop]]) { - pp <- PELMO_path(psm, crop, scenario) - - for (plm in plm_files) { - if (file.exists(file.path(test_dir, pp, plm))) { - new <- readLines(file.path(PELMO_base, "FOCUS", pp, plm)) - test <- readLines(file.path(test_dir, pp, plm)) - - # Don't check for differences in the PESTICIDE BALANCE ERROR - pest_balance_error <- suppressWarnings(grep("PESTICIDE BALANCE ERROR", new)) - # Suppress warnings about invalid strings in this locale caused by the files - - # Check if the ouput files are correctly reproduced - expect_identical(new[!pest_balance_error], test[!pest_balance_error]) - } - } - } - } - } -}) - -test_that("PELMO runs are correctly evaluated", { - skip_if_no_wine() - skip_on_cran() - - pfm_PECgw <- evaluate_PELMO(runs) - - # Check that if output is the same as in the test archive - for (run in runs) { - psm <- run$psm - crops <- setdiff(names(run), "psm") - for (crop in crops) { - for (scenario in run[[crop]]) { - pp <- PELMO_path(psm, crop, scenario) - - period_file <- readLines(file.path(test_dir, pp, "period.plm"), encoding = "latin1") - - result_lines <- grep("^\tResults for.*in the percolate at 1 m soil depth$", period_file) - acronyms <- gsub(".*\\((.*)\\).*", "\\1", period_file[result_lines]) - names(result_lines) <- acronyms - - results <- list() - for (acronym in acronyms) { - results[[acronym]] <- list() - conc_lines <- result_lines[acronym] + 5:24 - tmp <- read.table(text = period_file[conc_lines], sep = "\t") - results[[acronym]]$periods <- data.frame( - period = as.integer(tmp$V2), - flux = tmp$V3, - percolate = tmp$V4, - conc = tmp$V5) - tmp80 <- read.table(text = period_file[result_lines[acronym] + 27], sep = "\t") - results[[acronym]]$focus <- tmp80[[1, "V5"]] - } - - period_pfm_file <- file.path(PELMO_base, "FOCUS", pp, "period_pfm.rda") - load(period_pfm_file) - - #message(psm, " ", crop, " ", scenario) - - # Test for equality of all the components separately, - # as we need to adapt the tolerance - for (acronym in acronyms) { - p_pelmo <- results[[acronym]]$periods - p_test <- results_pfm[[acronym]]$periods - expect_equal(p_test$flux, p_pelmo$flux, tol = 1e-6) - expect_equal(p_test$percolate, p_pelmo$percolate) - # PELMO sets the concentration to 0 when the percolate is zero. - # We get NaN, which is more reasonable, but we need to - # take this into account for testing - p_test$conc <- ifelse(is.na(p_test$conc), 0, p_test$conc) - expect_equal(p_test$conc, p_pelmo$conc, tol = 1e-3, scale = 1) - - # FOCUS PEC - expect_equal(results_pfm[[acronym]]$focus, results[[acronym]]$focus, - tol = 1e-3, scale = 1) - } - } - } - } -}) - -test_that("PECgw from FOCUS summary files can be reproduced", { - skip_if_no_wine() - skip_on_cran() - - pfm_PECgw <- evaluate_PELMO(runs) - - focus_summary <- list() - - for (run in runs) { - psm <- run$psm - focus_summary[[psm]] <- list() - - crops <- setdiff(names(run), "psm") - for (crop in crops) { - scenarios <- run[[crop]] - - # Read contents of summary text file copied from the GUI output. We only - # have results for one crop per psm file, so the crop is not in the file - # name. - sumfile_path <- system.file(paste0("testdata/FOCUS_Summary_", psm, - ".txt"), package = "pfm") - sumfile <- readLines(sumfile_path, encoding = "latin1") - result_anchors <- grep("Results for", sumfile) - acronyms <- gsub(".*\\((.*)\\).*", "\\1", sumfile[result_anchors]) - names(result_anchors) <- acronyms - focus_summary[[psm]][[crop]] <- matrix(nrow = length(scenarios), ncol = length(acronyms), - dimnames = list(scenarios, acronyms)) - for (acronym in acronyms) { - tmp <- sumfile[result_anchors[acronym] + 4 + (1:length(scenarios))] - tmp_frame <- read.table(text = tmp, sep = "\t") - PECgw <- tmp_frame$V5 - focus_summary[[psm]][[crop]][, acronym] <- PECgw - } - } - } - expect_equal(pfm_PECgw, focus_summary) -}) |