#!/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

  ## Environment variables to be set
  envs <- resources[["envs"]]
  if (length(envs) > 0) {
    stopifnot(is.character(envs), !is.null(names(envs)))
  }
  resources[["envs"]] <- NULL

  ## Custom "Rscript" command and Rscript arguments
  rscript <- resources[["rscript"]]
  if (is.null(rscript)) {
    rscript <- "Rscript"
  } else if (length(rscript) == 0 || !nzchar(rscript)[1]) {
    stop("Argument 'resources' specifies an empty 'rscript' field")
  }
  resources[["rscript"]] <- NULL
  rscript_args <- resources[["rscript_args"]]
  resources[["rscript_args"]] <- NULL
  rscript_call <- paste(c(rscript, rscript_args), collapse = " ")
    
  ## As-is resource specifications
  job_declarations <- resources[["asis"]]
  resources[["asis"]] <- NULL

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

<% if (length(envs) > 0) {
  writeLines(c(
    sprintf("echo 'Setting environment variables: [n=%d]'", length(envs)),
    sprintf("echo ' - %s=%s'", names(envs), shQuote(envs)),
    sprintf("export %s=%s", names(envs), shQuote(envs))
  ))
} %>

echo "Session information:"
echo "- timestamp: $(date +"%Y-%m-%d %H:%M:%S%z")"
echo "- hostname: $(hostname)"
echo "- Rscript call: <%= rscript_call %>"
if ! command -v <%= rscript[1] %> &> /dev/null; then
    >&2 echo "ERROR: Argument 'resources' specifies a non-existing 'Rscript' launch command: <%= rscript[1] %>. Maybe you need to specify which environment modules to load in the 'resources' argument, e.g. 'plan(future.batchtools::batchtools_slurm, resources = list(modules = c(\"r\")))'. The search PATH for '%<= rscript[1] %>' was ${PATH}"
    exit 1
fi
echo "- Rscript version: $(<%= paste(rscript, collapse = " ") %> --version)"
echo "- R_LIBS_USER=${R_LIBS_USER:-<not set>}"
echo "- R_LIBS_SITE=${R_LIBS_SITE:-<not set>}"
echo "- R_LIBS=${R_LIBS:-<not set>}"
echo "- Rscript library paths: $(<%= rscript_call %> -e "cat(shQuote(.libPaths()), sep = ' ')")"
echo


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