#!/bin/bash

submission_gen_params () {
cat <<END
###############################################################
#             PBS SUBMISSION OPTIONS                          #
###############################################################

# Use local PBS submission
PBS_LOCAL="yes"

# Remote PBS cluster SSH access parameters
#PBS_SUBMIT_USER="user01"
#PBS_SUBMIT_HOST="cluster.imbg.org.ua"
#PBS_SUBMIT_PORT=22

# Extra headers for PBS file
PBS_EXTRA_HEADER="#TASK TYPE MD.
#TASK OBJECT Tyrosyl tRNA Synthetase
#TASK CONDITIONS 150 mM KCl, 37oC (310 K), 100ns
#TASK SOFTWARE Gromacs-5.1.4
#TASK COMMENTS MD"

# Extra commands to run (e.g. environmental modules load)
#PBS_EXTRA_COMMANDS="module load gromacs/5.1.4"

END
}

create_pre_exec () {
    local f1_base="INPUT_FILES_NAME_"
    local f2_base="INPUT_FILES_LOCATION_"
    f_url=""
    f_idx=0
    f_var="${f1_base}${f_idx}"
    echo "cat > proxy.pem <<__END__"
    cat $X509_USER_PROXY
    echo "__END__"
    echo -e "\nexport X509_USER_PROXY=proxy.pem"
    echo -e "chmod 600 proxy.pem\n"
    echo "wget $PORTABLE_CLIENT_URL"
    echo "tar -xf ${PORTABLE_CLIENT_URL##*/}"
    echo -e "cd arc-client && . setup.sh && cd .. \n"
    while [ -n "${!f_var}" ]; do
        f_location_var="${f2_base}${f_idx}"
        eval URL$((f_idx+1))_NAME="${!f_var}"
        eval URL$((f_idx+1))="${!f_location_var}"
        echo "arccp ${!f_location_var} ${!f_var}"
        f_idx=$((f_idx+1))
        f_var="${f1_base}${f_idx}"
    done

    chmod +x $EXECUTABLE
    echo -e "#Pre-exec section ended\n"
}

create_post_exec () {
local f1_base="OUTPUT_FILES_NAME_"
    local f2_base="OUTPUT_FILES_LOCATION_"
    f_url=""
    f_idx=0
    f_var="${f1_base}${f_idx}"
    while [ -n "${!f_var}" ]; do
        f_location_var="${f2_base}${f_idx}"
        echo "arccp ${!f_var} ${!f_location_var}"
        f_idx=$((f_idx+1))
        f_var="${f1_base}${f_idx}"
    done

}

grid_job_submit () {
    local jdfile=$1
    local jobid_file=$2
    local exec_file=$3

    if [ -z "$PBS_LOCAL" ]; then
      if [ -z "$PBS_SUBMIT_HOST" -o -z "$PBS_SUBMIT_USER" ]; then
        echo_r "FATAL: PBS submission host and credentials are not configured!"
        exit 1
      fi

      PBS_SUBMIT_PORT=${PBS_SUBMIT_PORT:-22}

      echo_g "Sending executable to the PBS cluster."
      scp -P $PBS_SUBMIT_PORT $jdfile $CONDOR_SUBMIT_USER@$CONDOR_SUBMIT_HOST:~

      echo_g "Submitting PBS job."
      ssh $PBS_SUBMIT_USER@$PBS_SUBMIT_HOST -p $PBS_SUBMIT_PORT "qsub $jdfile"
    else
      echo_g "Submitting PBS job."
      qsub $jdfile
    fi

    # no MDS portal connection with pilots submission
    export DISABLEPORTAL=1 
}

grid_job_kill () {
    local jobid_file=$1
    echo "INFO: Job removal is not yet supported by PBS interface"
}