aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2017-01-27 08:17:08 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2017-01-27 08:48:29 +0100
commit3c82d26206e2f2e74600acd71a49c70eaed555c4 (patch)
tree22c524a90d6d27f77e2abbc759281359eda69c45
parent536c49fefc6c46b2263c806b383339662174fc49 (diff)
Also test run with metabolites
-rw-r--r--ChangeLog11
-rw-r--r--R/PELMO_runs.R5
-rw-r--r--tests/testthat/test_PELMO.R63
3 files changed, 45 insertions, 34 deletions
diff --git a/ChangeLog b/ChangeLog
index 19fe18d..762acf3 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,10 +1,17 @@
-commit 8f943c9dd2322482f64e1c6348c1ad7cfd253ee8
+commit 8fd050e57b7babfbdb1ccfabb468a0398396d466
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date: 2017-01-27 07:54:53 +0100
+
+ Include a run with metabolites in PELMO test data
+
+commit b38055278d4a801598ece9d2c93716a9bf67134a
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-27 01:00:07 +0100
Set up FOCUS PELMO runs and run them in parallel
- - This works on Linux using wine.
+ - 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
diff --git a/R/PELMO_runs.R b/R/PELMO_runs.R
index 7430b40..f599110 100644
--- a/R/PELMO_runs.R
+++ b/R/PELMO_runs.R
@@ -158,7 +158,7 @@ PELMO_runs <- function(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "aut
#' @inheritParams PELMO_runs
#' @importFrom parallel mclapply
#' @export
-run_PELMO <- function(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "auto",
+run_PELMO <- function(runs, version = "5.5.3", PELMO_base = "auto",
cores = getOption("mc.cores", 2L))
{
@@ -204,7 +204,8 @@ run_PELMO <- function(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "auto
# We need to go the directory to simplify calling pelmo with wine
setwd(run_dir_exe)
- psm_file <- file.path(psm_dir, paste0(psm, ".psm"))
+ psm_file <- paste0(psm, ".psm")
+ message("Starting ", pelmo_exe, " with ", psm_file)
system(paste("wine", pelmo_exe, psm_file), ignore.stdout = TRUE)
# Copy the results to the original run directory
diff --git a/tests/testthat/test_PELMO.R b/tests/testthat/test_PELMO.R
index 4bd36ef..7b7e2b6 100644
--- a/tests/testthat/test_PELMO.R
+++ b/tests/testthat/test_PELMO.R
@@ -1,10 +1,4 @@
-# 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(testthat)
library(pfm)
context("Create PELMO runs from psm files and execute them")
PELMO_base <- system.file("FOCUSPELMO.553", package = "PELMO.installeR")
@@ -22,22 +16,26 @@ runs <- list(
psm = "Pesticide_D_1_day_pre_em_every_third_year",
pot = c("Cha", "Ham")),
list(
- psm = "Pesticide_D_1_May_every_other_year",
+ psm = "Pesticide_D_1_May_every_other_year_mets",
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 paths are correctly created", {
+ psm_paths = c(
+ PELMO_path(runs[[1]]$psm, "fbe", "Por"),
+ PELMO_path(runs[[2]]$psm, "pot", "Ham"),
+ PELMO_path(runs[[3]]$psm, "mai", "Cha"))
+
+ # Check for psm files and put them into PELMO_base
+ psm_new_locations <- character(0)
+ for (i in seq_along(psm_paths)) {
+ psm_file <- file.path(test_dir, psm_paths[i], paste0(runs[[i]]$psm, ".psm"))
+ expect_true(file.exists(psm_file))
+ psm_new_location <- file.path(PELMO_base, basename(psm_file))
+ psm_new_locations[i] <- psm_new_location
+ file.copy(psm_file, psm_new_location)
+ }
+})
test_that("PELMO runs are correctly set up", {
@@ -47,12 +45,12 @@ test_that("PELMO runs are correctly set up", {
# Check that input files are correctly generated in the right location
for (run in runs) {
psm <- run$psm
- message(psm)
+ # message(psm)
crops <- setdiff(names(run), "psm")
for (crop in crops) {
- message(crop)
+ # message(crop)
for (scenario in run[[crop]]) {
- message(scenario)
+ # message(scenario)
pp <- PELMO_path(psm, crop, scenario)
input_new <- readLines(file.path(PELMO_base, "FOCUS", pp, "pelmo.inp"))
@@ -66,10 +64,11 @@ test_that("PELMO runs are correctly set up", {
})
test_that("PELMO runs can be run and give the expected result files", {
- run_PELMO(runs, psm_dir = PELMO_base, cores = 5)
+ run_PELMO(runs, cores = 5)
- plm_files <- c("CHEM.PLM", "ECHO.PLM", "KONZCHEM.PLM", "PLNTPEST.plm",
- "PLOT.PLM", "WASSER.PLM")
+ 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) {
@@ -82,11 +81,13 @@ test_that("PELMO runs can be run and give the expected result files", {
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))
+ 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))
- # Check if the ouput files are correctly reproduced
- expect_identical(new, test)
+ # Check if the ouput files are correctly reproduced
+ expect_identical(new, test)
+ }
}
}
}
@@ -94,6 +95,8 @@ test_that("PELMO runs can be run and give the expected result files", {
})
test_that("PELMO runs are correctly evaluated", {
+ evaluate_PELMO(runs, psm_dir = PELMO_base)
+
})

Contact - Imprint