Merge pull request #3081 from PecanProject/history-bug

Bug fix for #3080 (write.config.xml.ED2() not using <revision> tag correctly)

CHANGELOG.md

@@ -66,6 +66,7 @@ convert data for a single PFT fixed (#1329, #2974, #2981)
   the cdo_setup argument in the template job file. In detail, people will need
   to specify cdosetup = "module load cdo/2.0.6" in the host section. More details
   are in the Create_Multi_settings.R script. (#3052)
+- write.config.xml.ED2() wasn't using the <revision> tag in settings correctly (#3080)
 - runModule.get.trait.data() now correctly respects the settings$database$bety$write setting (#2968)
 - Fixed a bug in `model2netcdf.ed2()` where .nc file connections were being closed multiple times, printing warnings (#3078)
 - Fixed a bug causing the model2netcdf.ED2() step in jobs.sh to be incorrectly written (#3075)

models/ed/NEWS.md

@@ -4,6 +4,7 @@
 * Fixed a bug in `model2netcdf.ed2()` where .nc file connections were being closed multiple times, printing warnings (#3078)
 * Fixed a bug affecting the generation of job.sh for runs with many PFTs (#3075)
 * Added optional `process_partial` argument to `model2netcdf.ED2()` to allow it to process existing output from failed runs.
+* write.config.xml.ED2() wasn't using the <revision> tag in settings correctly (#3080)
 
 # PEcAn.ED2 1.7.2.9000
 

models/ed/R/write.configs.ed.R

@@ -443,18 +443,28 @@ remove.config.ED2 <- function(main.outdir = settings$outdir, settings) {
 #' @author David LeBauer, Shawn Serbin, Carl Davidson, Alexey Shiklomanov
 write.config.xml.ED2 <- function(settings, trait.values, defaults = settings$constants) {
 
-  ## Find history file TODO this should come from the database
-  ed2_package_data <- data(package="PEcAn.ED2", envir = environment())
-  histfile <- paste0("history.r", settings$model$revision) # set history file name to look for in ed2_package_data
-  if (histfile %in% ed2_package_data$results[, "Item"]) {
-    PEcAn.logger::logger.debug(paste0("--- Using ED2 History File: ", histfile))
-    data(list=histfile, package = 'PEcAn.ED2', envir = environment())
-    edhistory <- get(histfile)
+  # TODO this should come from the database
+
+  # Internal data sets stored in sysdata.RDA are used to override defaults in
+  # config.xml.  This code looks for a history dataset that matches the
+  # "revision" number for ED2 set in settings (e.g. PEcAn.ED2:::history.r85) and
+  # if it doesn't find it, it uses a generic file (PEcAn.ED2:::history).  To add
+  # a new history file, add the .csv file to models/ed/data-raw and run the
+  # sysdata.R script in that folder
+
+  if(is.null(settings$model$revision)) {
+    PEcAn.logger::logger.debug("--- Using Generic ED2 History File")
+    edhistory <- history
   } else {
-    PEcAn.logger::logger.debug("--- Using Generic ED2 History File: history.csv")
-    histfile <- "history"
-    data(list=histfile, package = 'PEcAn.ED2', envir = environment())
-    edhistory <- get(histfile)
+    histfile <- paste0("history.r", settings$model$revision)
+    edhistory <- try(eval(str2lang(histfile)), silent = TRUE)
+  } 
+
+  if(inherits(edhistory, "try-error")) {
+    PEcAn.logger::logger.debug("--- Using Generic ED2 History File")
+    edhistory <- history
+  } else {
+    PEcAn.logger::logger.debug(paste0("--- Using ED2 History File: ", histfile))
   }
 
   edtraits <- names(edhistory)

models/ed/tests/testthat/test.write.configs.ed.R

@@ -6,6 +6,49 @@
 ## # which accompanies this distribution, and is available at
 ## # http://opensource.ncsa.illinois.edu/license.html
 ## #-------------------------------------------------------------------------------
+# dummy trait values
+trait.values <-
+  list(
+    SetariaWT = structure(
+      list(
+        mort2 = 19.9551305310619,
+        growth_resp_factor = 0.271418338660799,
+        leaf_turnover_rate = 4.08633744111248,
+        leaf_width = 4.16095405673501,
+        nonlocal_dispersal = 0.208572992916628,
+        fineroot2leaf = 2.25017242716454,
+        root_turnover_rate = 0.527523622000746,
+        seedling_mortality = 0.949939872416094,
+        stomatal_slope = 4.07086860946459,
+        quantum_efficiency = 0.0565042189665225,
+        Vcmax = 22.3047025944851,
+        r_fract = 0.313812660341759,
+        cuticular_cond = 12992.9906222683,
+        root_respiration_rate = 5.48040042748477,
+        Vm_low_temp = 10.0000004842057,
+        SLA = 40.1495401375622
+      ),
+      row.names = "50",
+      class = "data.frame"
+    ),
+    env = structure(
+      list(),
+      .Names = character(0),
+      row.names = "NA",
+      class = "data.frame"
+    )
+  )
+
+defaults <-
+  list(
+    pft = list(
+      name = "SetariaWT",
+      ed2_pft_number = "1",
+      outdir = "/home/ericrscott/model-vignettes/ED2/testoutput/two_pfts/outdir//pft/SetariaWT",
+      posteriorid = 9000001416
+    )
+  )
+
 test_that("convert.samples.ED works as expected",{
   testthat::local_edition(3)
   expect_equal(convert.samples.ED(c("Vcmax" = 1))[["Vcmax"]],
@@ -141,6 +184,36 @@ test_that("New ED2IN tags get added at bottom of file", {
 })
 
 
+test_that("write.config.xml.ED2() uses correct history file", {
+  #1. read in pecan.xml in data/pecan_checked.xml
+  settings <- PEcAn.settings::read.settings("data/pecan_checked.xml")
+  #for debugging:
+  # settings <- PEcAn.settings::read.settings("models/ed/tests/testthat/data/pecan_checked.xml")
+
+  #2. Set rundir to tempdir
+  rundir <- tempfile()
+  dir.create(rundir)
+  on.exit(unlink(rundir, recursive = TRUE))
+  settings$rundir <- rundir
+  run.id <- "ENS-00001-76"
+  dir.create(file.path(rundir, run.id))
+  #3. set revision to 81
+  settings$model$revision <- "81"
+
+  x <- capture.output(
+    write.config.xml.ED2(
+      settings = settings,
+      trait.values = trait.values,
+      defaults = defaults
+    ),
+    type = "message"
+  )
+
+  expect_true(any(stringr::str_detect(x, "history.r81")))
+
+})
+
+
 ## test_that("remove.configs.ED2 works with remote host",{
 ##   settings <- list(outdir = "/tmp/",
 ##                    run = list(host = list(name = "ebi-cluster.igb.illinois.edu",