Fix to job.sh model2netcdf line

CHANGELOG.md

@@ -64,6 +64,7 @@ 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)
+- Fixed a bug causing the model2netcdf.ED2() step in jobs.sh to be incorrectly written (#3075)
 
 
 ### Changed

models/ed/DESCRIPTION

@@ -23,7 +23,7 @@ Authors@R: c(person("Mike", "Dietze", role = c("aut", "cre"),
                      comment = c(ORCID = "0000-0002-7430-7879")),
              person("University of Illinois, NCSA", role = c("cph")))
 Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang, Carl
-    Davidson, Rob Kooper, Shawn Serbin, Alexey Shiklomanov
+    Davidson, Rob Kooper, Shawn Serbin, Alexey Shiklomanov, Eric R. Scott
 Maintainer: Mike Dietze <[email protected]>
 Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     workflow management tool that is designed to simplify the management of

models/ed/NEWS.md

@@ -1,5 +1,6 @@
 # PEcAn.ED2 (development version)
 
+* Fixed a bug effecting 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.
 
 # PEcAn.ED2 1.7.2

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

@@ -647,7 +647,7 @@ write.config.jobsh.ED2 <- function(settings, run.id) {
   jobsh <- gsub("@BINARY@", settings$model$binary, jobsh)
 
   pft_names <- extract_pfts(settings$pfts)
-  pft_names <- deparse(dput(pft_names))
+  pft_names <- deparse1(dput(pft_names))
   jobsh <- gsub("@PFT_NAMES@", pft_names, jobsh)
 
   return(jobsh)

models/ed/inst/template.job

@@ -1,5 +1,7 @@
 #!/bin/bash -l
 
+# Parsed by PEcAn.ED2::write.config.jobsh.ED2() to generate job.sh files
+
 # create output folder
 mkdir -p "@OUTDIR@"
 @SCRATCH_MKDIR@

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

@@ -21,6 +21,7 @@ testdir <- tempfile()
 dir.create(testdir)
 withr::defer(unlink(testdir, recursive = TRUE))
 unzip("data/outdir.zip", exdir = testdir)
+# unzip("models/ed/tests/testthat/data/outdir.zip", exdir = testdir)
 outdir <- file.path(testdir, "outdir")
 
 test_that("write.config.jobsh.ED2() writes correct model2netcdf.ED2() args", {
@@ -32,6 +33,22 @@ test_that("write.config.jobsh.ED2() writes correct model2netcdf.ED2() args", {
   expect_true(any(stringr::str_detect(job.sh, stringr::fixed(expect))))
 })
 
+test_that("write.config.jobsh.ED2() works with long list of PFTs", {
+  settings <- 
+    PEcAn.settings::read.settings(file.path(outdir, "pecan_checked.xml"))
+  more_pfts <- list(
+    pft = list(name = "tempconif", ed2_pft_number = 7),
+    pft = list(name = "temperate.Evergreen_Hardwood", ed2_pft_number = 8),
+    pft = list(name = "temperate.Early_Hardwood", ed2_pft_number = 9),
+    pft = list(name = "temperate.North_Mid_Hardwood", ed2_pft_number = 10),
+    pft = list(name = "temperate.Late_Hardwood", ed2_pft_number = 11)
+    )
+  settings$pfts <- append(settings$pfts, more_pfts)
+  job.sh <- write.config.jobsh.ED2(settings, run.id = "test_run")
+  expect <- deparse1(dput(extract_pfts(settings$pfts)))
+  expect_true(any(stringr::str_detect(job.sh, stringr::fixed(expect))))
+})
+
 test_that("New ED2IN tags get added at bottom of file", {
   #1. read in pecan.xml in data/pecan_checked.xml
   settings <- PEcAn.settings::read.settings("data/pecan_checked.xml")
@@ -89,6 +106,7 @@ test_that("New ED2IN tags get added at bottom of file", {
         posteriorid = 9000001416
       )
     )
+  old_level <- PEcAn.logger::logger.setLevel("DEBUG")
   x <- capture.output(
     write.config.ED2(
       trait.values = trait.values,
@@ -99,12 +117,15 @@ test_that("New ED2IN tags get added at bottom of file", {
     ),
     type = "message"
   )
+  PEcAn.logger::logger.setLevel(old_level)
+
 
   #5. check if new tag exists
   ed2in_out <- read_ed2in(file.path(rundir, run.id, "ED2IN"))
   expect_equal(ed2in_out$NEW_TAG, 0)
 
   #check that info is printed
+
   expect_true(any(stringr::str_detect(x, "NEW_TAG")))
 
   #check that last non-comment line of ED2IN is "$END"