refactor: add write_job_sh helper to PEcAn.utils to reduce duplicated job.sh logic

base/utils/R/write_job_sh.R

@@ -0,0 +1,21 @@
+#' Write a job.sh script for a PEcAn model run
+#'
+#' This helper function writes the job.sh shell script used to execute
+#' a model run. It centralizes duplicated logic previously found in
+#' individual write.config.* functions across model packages.
+#'
+#' @param rundir character. Path to the run directory
+#' @param run.id character. The run ID
+#' @param jobsh character vector. Lines of the job.sh script content
+#' @param chmod logical. Whether to make job.sh executable. Default TRUE
+#'
+#' @return invisible path to the written job.sh file
+#' @export
+write_job_sh <- function(rundir, run.id, jobsh, chmod = TRUE) {
+  job_path <- file.path(rundir, run.id, "job.sh")
+  writeLines(jobsh, con = job_path)
+  if (chmod) {
+    Sys.chmod(job_path)
+  }
+  invisible(job_path)
+}

base/utils/tests/testthat/test.write_job_sh.R

@@ -0,0 +1,45 @@
+test_that("write_job_sh creates job.sh file", {
+  # Create a temporary directory for testing
+  tmpdir <- tempfile()
+  dir.create(tmpdir)
+  run.id <- "test_run_001"
+  dir.create(file.path(tmpdir, run.id))
+
+  # Define simple job script content
+  jobsh <- c(
+    "#!/bin/bash",
+    "echo 'running model'"
+  )
+
+  # Call the helper function
+  result <- write_job_sh(tmpdir, run.id, jobsh)
+
+  # Test 1 - file exists
+  expect_true(file.exists(file.path(tmpdir, run.id, "job.sh")))
+
+  # Test 2 - file content is correct
+  written <- readLines(file.path(tmpdir, run.id, "job.sh"))
+  expect_equal(written, jobsh)
+
+  # Test 3 - function returns the path invisibly
+  expect_equal(result, file.path(tmpdir, run.id, "job.sh"))
+
+  # Cleanup
+  unlink(tmpdir, recursive = TRUE)
+})
+
+test_that("write_job_sh chmod parameter works", {
+  tmpdir <- tempfile()
+  dir.create(tmpdir)
+  run.id <- "test_run_002"
+  dir.create(file.path(tmpdir, run.id))
+
+  jobsh <- c("#!/bin/bash", "./model")
+
+  # Test with chmod = FALSE
+  write_job_sh(tmpdir, run.id, jobsh, chmod = FALSE)
+  expect_true(file.exists(file.path(tmpdir, run.id, "job.sh")))
+
+  # Cleanup
+  unlink(tmpdir, recursive = TRUE)
+})

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

@@ -122,8 +122,7 @@ write.config.ED2 <- function(trait.values, settings, run.id, defaults = settings
 
   jobsh <- write.config.jobsh.ED2(settings = settings, run.id = run.id)
 
-  writeLines(jobsh, con = file.path(settings$rundir, run.id, "job.sh"))
-  Sys.chmod(file.path(settings$rundir, run.id, "job.sh"))
+  PEcAn.utils::write_job_sh(settings$rundir, run.id, jobsh)
 
   ## Write ED2 config.xml file
   xml <- write.config.xml.ED2(defaults = defaults, settings = settings, trait.values = trait.values)

models/ed/R/write_restart.ED2.R

@@ -268,7 +268,7 @@ write_restart.ED2 <- function(outdir, runid, start.time, stop.time,
   mod2cf_string      <- gsub(begin_from, begin_to, mod2cf_string) # e.g. change from (...'1961/01/01', '1963/01/01'...) to (...'1962/01/01', '1963/01/01'...)
   jobsh[mod2cf_line] <- mod2cf_string
 
-  writeLines(jobsh, file.path(rundir, runid, "job.sh"))
+  PEcAn.utils::write_job_sh(rundir, runid, jobsh)
 
   PEcAn.logger::logger.info("Finished --", runid)
 

models/fates/R/write.configs.FATES.R

@@ -189,8 +189,7 @@ write.config.FATES <- function(defaults, trait.values, settings, run.id){
 #   jobsh <- gsub('@SITE_MET@', settings$run$inputs$met$path, jobsh)
    ## FOR FIRST STEP, CAN USE DEFAULT
 
-   writeLines(jobsh, con=file.path(settings$rundir, run.id, "job.sh"))
-   Sys.chmod(file.path(settings$rundir, run.id, "job.sh"))
+   PEcAn.utils::write_job_sh(settings$rundir, run.id, jobsh)
 #   
 #   ## Write PARAMETER file
 

models/gday/R/write.config.GDAY.R

@@ -95,6 +95,5 @@ write.config.GDAY <- function(defaults, trait.values, settings, run.id) {
 
     jobsh <- gsub("@BINARY@", settings$model$binary, jobsh)
 
-    writeLines(jobsh, con = file.path(settings$rundir, run.id, "job.sh"))
-    Sys.chmod(file.path(settings$rundir, run.id, "job.sh"))
+    PEcAn.utils::write_job_sh(settings$rundir, run.id, jobsh)
 } # write.config.GDAY

models/jules/R/write.config.JULES.R

@@ -64,8 +64,7 @@ write.config.JULES <- function(defaults, trait.values, settings, run.id) {
   jobsh <- gsub("@RUNDIR@", rundir, jobsh)
   jobsh <- gsub("@RUNID@", run.id, jobsh)
   jobsh <- gsub("@BINARY@", settings$model$binary, jobsh)
-  writeLines(jobsh, con = file.path(local.rundir, "job.sh"))
-  Sys.chmod(file.path(local.rundir, "job.sh"))
+  PEcAn.utils::write_job_sh(local.rundir, run.id, jobsh)
 
   #-----------------------------------------------------------------------
   ### Copy templated NAMELIST files to local rundir

models/ldndc/R/write.config.LDNDC.R

@@ -133,8 +133,7 @@ write.config.LDNDC <- function(defaults, trait.values, settings, run.id) {
   jobsh <- gsub("@DELETE.RAW@", settings$model$delete.raw, jobsh)
 
   # Write job.sh file to rundir
-  writeLines(jobsh, con = file.path(settings$rundir, run.id, "job.sh"))
-  Sys.chmod(file.path(rundir, "job.sh")) # Permissions
+  PEcAn.utils::write_job_sh(settings$rundir, run.id, jobsh)
 
 
 

models/linkages/R/write.config.LINKAGES.R

@@ -295,6 +295,5 @@ write.config.LINKAGES <- function(defaults = NULL, trait.values, settings, run.i
   pft_names <- unlist(sapply(settings$pfts, `[[`, "name"))
   pft_names <- paste0("pft_names = c('", paste(pft_names, collapse = "','"), "')")
   jobsh <- gsub("@PFT_NAMES@", pft_names, jobsh)
-  writeLines(jobsh, con = file.path(settings$rundir, run.id, "job.sh"))
-  Sys.chmod(file.path(settings$rundir, run.id, "job.sh"))
+  PEcAn.utils::write_job_sh(settings$rundir, run.id, jobsh)
 } # write.config.LINKAGES

models/lpjguess/R/write.config.LPJGUESS.R

@@ -71,8 +71,7 @@ write.config.LPJGUESS <- function(defaults, trait.values, settings, run.id, rest
   jobsh <- gsub("@BINARY@", settings$model$binary, jobsh)
   jobsh <- gsub("@INSFILE@", settings$model$insfile, jobsh)
 
-  writeLines(jobsh, con = file.path(settings$rundir, run.id, "job.sh"))
-  Sys.chmod(file.path(settings$rundir, run.id, "job.sh"))
+  PEcAn.utils::write_job_sh(settings$rundir, run.id, jobsh)
 } # write.config.LPJGUESS
 
 # ==================================================================================================#

models/maat/R/write.config.MAAT.R

@@ -243,8 +243,7 @@ write.config.MAAT <- function(defaults = NULL, trait.values, settings, run.id) {
   }  #End if/else
 
   # Write the job.sh script
-  writeLines(jobsh, con = file.path(settings$rundir, run.id, "job.sh"))
-  Sys.chmod(file.path(settings$rundir, run.id, "job.sh"))
+  PEcAn.utils::write_job_sh(settings$rundir, run.id, jobsh)
 
 } # write.config.MAAT
 ##-------------------------------------------------------------------------------------------------#

models/maespa/R/write.config.MAESPA.R

@@ -144,6 +144,5 @@ write.config.MAESPA <- function(defaults, trait.values, settings, run.id) {
 
   jobsh <- gsub("@BINARY@", settings$model$binary, jobsh)
 
-  writeLines(jobsh, con = file.path(settings$rundir, run.id, "job.sh"))
-  Sys.chmod(file.path(settings$rundir, run.id, "job.sh"))
+  PEcAn.utils::write_job_sh(settings$rundir, run.id, jobsh)
 } # write.config.MAESPA

models/peprmt/R/write.configs.peprmt.R

@@ -105,6 +105,5 @@ write.config.PEPRMT <- function(defaults, trait.values, settings, run.id) {
     dplyr::filter(.data$site == settings$run$site$id)
 
   utils::write.csv(run_data, file.path(rundir, "run_data.csv"), row.names = FALSE)
-  writeLines(jobsh, con = file.path(rundir, "job.sh"))
-  Sys.chmod(file.path(rundir, "job.sh"))
+  PEcAn.utils::write_job_sh(rundir, run.id, jobsh)
 } # write.config.PEPRMT

models/preles/R/write.config.PRELES.R

@@ -34,6 +34,5 @@ write.config.PRELES <- function(defaults, trait.values, settings, run.id) {
                   "'",settings$run$end.date,"') ",
                   '" | R --vanilla'
   )
-  writeLines(jobsh, con = file.path(settings$rundir, run.id, "job.sh"))
-  Sys.chmod(file.path(settings$rundir, run.id, "job.sh"))
+  PEcAn.utils::write_job_sh(settings$rundir, run.id, jobsh)
 } # write.config.PRELES

models/rothc/R/write.config.RothC.R

@@ -75,8 +75,7 @@ write.config.RothC <- function(defaults, trait.values, settings, run.id) {
 
   jobsh <- gsub("@BINARY@", settings$model$binary, jobsh)
 
-  writeLines(jobsh, con = file.path(settings$rundir, run.id, "job.sh"))
-  Sys.chmod(file.path(settings$rundir, run.id, "job.sh"))
+  PEcAn.utils::write_job_sh(settings$rundir, run.id, jobsh)
 
   #-----------------------------------------------------------------------
   ### Edit a templated config file for runs

models/sibcasa/R/write.config.SIBCASA.R

@@ -1,4 +1,5 @@
 
+
 #-------------------------------------------------------------------------------------------------#
 #' Writes a SIBCASA config file.
 #'
@@ -60,8 +61,7 @@ write.config.SIBCASA <- function(defaults, trait.values, settings, run.id) {
 
   jobsh <- gsub("@BINARY@", settings$model$binary, jobsh)
 
-  writeLines(jobsh, con = file.path(settings$rundir, run.id, "job.sh"))
-  Sys.chmod(file.path(settings$rundir, run.id, "job.sh"))
+  PEcAn.utils::write_job_sh(settings$rundir, run.id, jobsh)
 
   #-----------------------------------------------------------------------
   ### Edit a templated config file for runs

models/sipnet/R/write.configs.SIPNET.R

@@ -224,8 +224,7 @@ write.config.SIPNET <- function(defaults, trait.values, settings, run.id, inputs
   }
   jobsh <- gsub("@DELETE.RAW@", settings$model$delete.raw, jobsh)
 
-  writeLines(jobsh, con = file.path(settings$rundir, run.id, "job.sh"))
-  Sys.chmod(file.path(settings$rundir, run.id, "job.sh"))
+  PEcAn.utils::write_job_sh(settings$rundir, run.id, jobsh)
 
 
   ### Copy event file

models/stics/R/write.config.STICS.R

@@ -919,8 +919,7 @@ write.config.STICS <- function(defaults, trait.values, settings, run.id) {
   jobsh <- gsub("@MODFILE@", paste0("mod_s", basename(usmdirs[1]), ".sti"), jobsh)
   jobsh <- gsub("@STICSEXE@", stics_exe, jobsh)
 
-  writeLines(jobsh, con = file.path(settings$rundir, run.id, "job.sh"))
-  Sys.chmod(file.path(settings$rundir, run.id, "job.sh"))
+  PEcAn.utils::write_job_sh(settings$rundir, run.id, jobsh)
 
 
 } # write.config.STICS

models/template/R/write.config.MODEL.R

@@ -69,8 +69,7 @@ write.config.MODEL <- function(defaults, trait.values, settings, run.id) {
 
   jobsh <- gsub("@BINARY@", settings$model$binary, jobsh)
 
-  writeLines(jobsh, con = file.path(settings$rundir, run.id, "job.sh"))
-  Sys.chmod(file.path(settings$rundir, run.id, "job.sh"))
+  PEcAn.utils::write_job_sh(settings$rundir, run.id, jobsh)
 
   #-----------------------------------------------------------------------
   ### Edit a templated config file for runs