#!/bin/bash
######################################################################
# A batchtools launch script template for SGE
#
# Author: Henrik Bengtsson 
######################################################################
## Shell
#$ -S /bin/bash

## Job name
#$ -N <%= job.name %>

## Direct streams to logfile
#$ -o <%= log.file %>

## Merge standard error and output
#$ -j y

## Tell the queue system to use the current directory
## as the working directory
#$ -cwd

## Resources needed:
<%
  ## Should scheduler "details" be seen?
  details <- isTRUE(resources[["details"]])
  resources[["details"]] <- NULL

  ## Shell "startup" code to evaluate
  startup <- resources[["startup"]]
  resources[["startup"]] <- NULL
     
  ## Shell "shutdown" code to evaluate
  shutdown <- resources[["shutdown"]]
  resources[["shutdown"]] <- NULL
     
  ## Environment modules specifications
  modules <- resources[["modules"]]
  resources[["modules"]] <- NULL
     
  ## As-is resource specifications
  job_declarations <- resources[["asis"]]
  resources[["asis"]] <- NULL
    
  ## SPECIAL: For R CMD check package testing on HPC environments, which
  ## typically uses a temporary working directory that is local, we force
  ## it to use HPC-wide working directory
  path <- tools::R_user_dir("future.batchtools", "cache")
  path <- file.path(path, "R_CMD_check")
  if (!utils::file_test("-d", path)) dir.create(path, recursive = TRUE)
  job_declarations <- c(job_declarations, sprintf("-wd %s", path))
  
  ## SPECIAL: Since we change working directory, the 'startup.Rs' file used
  ## by R CMD check is no longer found
  env <- Sys.getenv("R_TESTS", NA_character_)
  if (!is.na(env)) startup <- c(startup, sprintf("export R_TESTS=%s", normalizePath(env)))
  
  ## SPECIAL: Use the 'Rscript' on PATH when processing this template; not
  ## the dummy one injected by 'R CMD check'
  startup <- c(startup, sprintf('export PATH="%s:${PATH}"', R.home("bin")))

  ## SPECIAL: Use the 'R_LIBS_USER' at compile time, because of 'R CMD check'
  libs <- dirname(unique(vapply(c("future.batchtools", "batchtools"), FUN = find.package, FUN.VALUE = "")))
  startup <- c(startup, sprintf("export R_LIBS_USER=%s", paste(libs, collapse = .Platform[["path.sep"]])))

  ## Remaining resources are assumed to be of type '-l <key>=<value>'
  opts <- unlist(resources, use.names = TRUE)
  opts <- sprintf("-l %s=%s", names(opts), opts)
  job_declarations <- sprintf("#$ %s", c(job_declarations, opts))
  writeLines(job_declarations)
%>

## Bash settings
set -e          # exit on error
set -u          # error on unset variables
set -o pipefail # fail a pipeline if any command fails
trap 'echo "ERROR: future.batchtools job script failed on line $LINENO" >&2; exit 1' ERR

<% if (length(job_declarations) > 0) {
  writeLines(c(
    "echo 'Job submission declarations:'",
    sprintf("echo '%s'", job_declarations),
    "echo"
  ))
} %>

<% if (details) { %>
if command -v qstat > /dev/null; then
  echo "Job information:"
  qstat -j "${JOB_ID}"
  echo
fi
<% } %>

<% if (length(startup) > 0) {
  writeLines(startup)
} %>

<% if (length(modules) > 0) {
  writeLines(c(
    "echo 'Load environment modules:'",
    sprintf("echo '- modules: %s'", paste(modules, collapse = ", ")),
    sprintf("module load %s", paste(modules, collapse = " ")),
    "module list"
  ))
} %>

echo "Session information:"
echo "- timestamp: $(date +"%Y-%m-%d %H:%M:%S%z")"
echo "- hostname: $(hostname)"
echo "- Rscript path: $(which Rscript)"
echo "- Rscript version: $(Rscript --version)"
echo "- Rscript library paths: $(Rscript -e "cat(shQuote(.libPaths()), sep = ' ')")"
echo


## Launch R and evaluate the batchtools R job
echo "Rscript -e 'batchtools::doJobCollection()' ..."
echo "- job name: '<%= job.name %>'"
echo "- job log file: '<%= log.file %>'"
echo "- job uri: '<%= uri %>'"
Rscript -e 'batchtools::doJobCollection("<%= uri %>")'
res=$?
echo " - exit code: ${res}"
echo "Rscript -e 'batchtools::doJobCollection()' ... done"
echo

<% if (details) { %>
if command -v qstat > /dev/null; then
  echo "Job summary:"
  qstat -j "${JOB_ID}"
fi  
<% } %>

<% if (length(shutdown) > 0) {
  writeLines(shutdown)
} %>

echo "End time: $(date +"%Y-%m-%d %H:%M:%S%z")"

## Relay the exit code from Rscript
exit "${res}"
