Set up FOCUS PELMO runs and run them in parallel

- This works on Linux using wine
- PELMO runs (including pelmo.inp files) are correctly generated
- The PLM files for FOCUS Pesticide_D in the test data archive are
  correctly reproduced
- The data files (including FOCUS groundwater scenario data) are now
  created and documented in R files

2 files changed, 101 insertions, 0 deletions

diff --git a/tests/testthat/test_PELMO.R b/tests/testthat/test_PELMO.R
new file mode 100644
index 0000000..4bd36ef
--- /dev/null
+++ b/tests/testthat/test_PELMO.R
@@ -0,0 +1,101 @@
+# Remove when the test is ready to be run by testthat
+#library(testthat)
+#test_dir <- "/tmp/Rtmp8DFCT5"
+#psm_name <- "D_rel_1"
+#source("~/git/pfm/inst/extdata/FOCUS_PELMO_data.R")
+#source("~/git/pfm/R/PELMO_runs.R")
+
+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",
+    mai = c("Cha")))
+
+psm_paths = c(
+   D_rel_1 = PELMO_path(runs[1]$psm, "fbe", "Por"),
+   D_rel_3 = PELMO_path(runs[2]$psm, "pot", "Ham"),
+   D_abs_2 = PELMO_path(runs[3]$psm, "mai", "Cha"))
+
+# Get psm files and put them into PELMO_base
+psm_new_locations <- character(0)
+for (psm_name in names(psm_paths)) {
+  psm_file <- file.path(test_dir, psm_paths[psm_name], paste0(runs[1]$psm, ".psm"))
+  psm_new_location <- file.path(PELMO_base, basename(psm_file))
+  psm_new_locations[psm_name] <- psm_new_location
+  file.copy(psm_file, psm_new_location)
+}
+
+test_that("PELMO runs are correctly set up", {
+
+  # Prepare runs in analogy to the test archive
+  PELMO_runs(runs, psm_dir = PELMO_base, execute = FALSE, overwrite = TRUE)
+
+  # Check that input files are correctly generated in the right location
+  for (run in runs) {
+    psm <- run$psm
+    message(psm)
+    crops <- setdiff(names(run), "psm")
+    for (crop in crops) {
+       message(crop)
+      for (scenario in run[[crop]]) {
+         message(scenario)
+        pp <- PELMO_path(psm, crop, scenario)
+
+        input_new <- readLines(file.path(PELMO_base, "FOCUS", pp, "pelmo.inp"))
+        input_test <- readLines(file.path(test_dir, pp, "pelmo.inp"))
+
+        # Check if the input files are correctly reproduced
+        expect_identical(input_new, input_test)
+      }
+    }
+  }
+})
+
+test_that("PELMO runs can be run and give the expected result files", {
+  run_PELMO(runs, psm_dir = PELMO_base, cores = 5)
+
+  plm_files <- c("CHEM.PLM", "ECHO.PLM", "KONZCHEM.PLM", "PLNTPEST.plm",
+                 "PLOT.PLM", "WASSER.PLM")
+
+  # Check that if output is the same as in the test archive
+  for (run in runs) {
+    psm <- run$psm
+    crops <- setdiff(names(run), "psm")
+    for (crop in crops) {
+      # message(crop)
+      for (scenario in run[[crop]]) {
+        # message(scenario)
+        pp <- PELMO_path(psm, crop, scenario)
+
+        for (plm in plm_files) {
+          new <- readLines(file.path(PELMO_base, "FOCUS", pp, plm))
+          test <- readLines(file.path(test_dir, pp, plm))
+
+          # Check if the ouput files are correctly reproduced
+          expect_identical(new, test)
+        }
+      }
+    }
+  }
+})
+
+test_that("PELMO runs are correctly evaluated", {
+
+})
+
+# Clean up
+unlink(psm_new_locations)
diff --git a/tests/testthat/test_TOXSWA_cwa.R b/tests/testthat/test_TOXSWA.R
index 7c9a73c..7c9a73c 100644
--- a/tests/testthat/test_TOXSWA_cwa.R
+++ b/tests/testthat/test_TOXSWA.R