#! /bin/bash

usage () {
cat<<EOF
usage: `basename $0` [options] ConfigFile

Options:
-h, --help                          This help message
-d, --debug                         Enable debug output
-n, --jobs <N_JOBS>                 Number of jobs to submit
-f, --first <JOBS>                  First task-id for job to submit
-s, --stamp <STAMP>                 Batch stamp to use [ default: current time]

-e, --exists <recreate|append|fail> Specify what action should be taken if the
                                    output directory already exists.

-o, --output <DIRECTORY>            Ouptut directory [ default:
                                    \$ICEDUST_LOCAL_STORAGE/<STAMP> ]

-Q, --qsub-options <OPTIONS>        Specify additional options for qsub, eg.
                                    "-q hepmedium.q"

-I, --icedust-options <OPTIONS>     Specify additional options for the
                                    RunIcedustControl command, eg "-t ~/myTmp"

-i, --inputfiles <List of files>    A (unexpanded) wild-carding to provide
                                    input files. Make sure to escape any
                                    wild-carding and white-space in the
                                    filenames.
EOF
  exit $1
}

CommandLine="$@"
VERBOSE=1
VERBOSE_STREAM=/dev/stderr
DEBUG_STREAM=/dev/null
NoPrimaries=100
FirstJob=1
NoJobs=10
RunStamp=`date +%y%m%d-%H%M`
OutputDir=$ICEDUST_LOCAL_STORAGE
QsubOptions=""
IcedOptions=""
InputFiles=""
IfExists="fail"
Debug=false
while [ "$#" != 0 ]; do
  case "$1" in
    -h | --help )
      usage 0;;
    -d | --debug )
      shift;Debug=true; set -x; DEBUG_STREAM=/dev/stderr ;;
    -f | --first )
      shift; FirstJob="$1" ; shift;;
    -n | --jobs )
      shift; NoJobs="$1" ; shift;;
    -s | --stamp )
      shift; RunStamp="$1" ; shift;;
    -o | --out-dir )
      shift; OutputDir="$1" ; shift;;
    -i | --inputfiles )
      shift; InputFiles="$1" ; shift;;
    -e | --exists )
      shift; IfExists="`tr 'A-Z' 'a-z' <<<"$1"`" ; shift;;
    -Q | --qsub-options )
      shift; QsubOptions="$QsubOptions $1" ; shift;;
    -I | --icedust-options )
      shift; IcedOptions="$IcedOptions $1" ; shift;;
    -*)
      echo Unknown option $1 ; usage 1 ;;
    *)
      ConfigFile=$1; shift || true;;
  esac
done
OutputDir="$OutputDir/$RunStamp"

if [ -z "$ICEDUST_HOME" ];then
        echo Error: Missing ICEDUST_HOME variable
        echo "      Please setup ICEDUST by sourcing the appropriate setup.sh file"
	echo 
	usage 1
elif [ -z "$ConfigFile" ];then
	echo Error: I need the name of a config to run with
	echo 
	usage 1
elif [ ! -r "$ConfigFile" ];then
    echo Error: Cannot find input config file: "'$ConfigFile'"
	exit 1
elif   [ ! "$IfExists" == fail ] \
    && [ ! "$IfExists" == append ] \
    && [ ! "$IfExists" == recreate ] ;then
    echo "Error: Bad option given to `-e, --exists` option: '$IfExists'"
    echo "       Should be one of: FAIL, APPEND, RECREATE"
	exit 1
fi

# Handle existing output directories
AppendVal=""
if [[ "$OutputDir/*" != `echo "$OutputDir/"*` ]];then
    if [ "$IfExists" == fail ]; then
        echo "Error: Output directory: '$OutputDir' already exists!"
        exit 1
    elif [ "$IfExists" == recreate ]; then
        rm -rf "$OutputDir"
    elif [ "$IfExists" == append ]; then
        AppendVal=2
        while [ -e "$OutputDir/BatchConfig-$AppendVal" ];do
            AppendVal=$((AppendVal+1))
        done
        AppendVal=-"$AppendVal"
    fi
fi

# Setup all the filename variables
BatchConfig="$OutputDir/BatchConfig$AppendVal"
RunBatch="$OutputDir/RunBatch$AppendVal.sh"
ActualConfig="`basename "$ConfigFile"|cut -f1 -d. `$AppendVal".cfg
InputFileList="$OutputDir/InputFiles"

# Prepare the output directory
mkdir -p "$OutputDir/"{batch_output,output,{timers,configs}/$AppendVal}
cp "$ConfigFile" "$OutputDir/$ActualConfig"

# Sort out the input file list
touch "$InputFileList"
if [ -n "${InputFiles}" ];then
    [ "${InputFiles:0:1}" != '/' ]  && InputFiles="`pwd`/$InputFiles"
    ls $InputFiles > "$InputFileList"
fi


cat <<EOF |tee "$BatchConfig" 
Command Line for submitting = $CommandLine
PWD when submitting: `pwd`
Time when submitting: `date`
FirstJob: $FirstJob
NoJobs: $NoJobs
RunStamp: $RunStamp
OutputDir: $OutputDir
ICEDUST_HOME: $ICEDUST_HOME
ICEDUST_PROJECT: $ICEDUST_PROJECT
`git --work-tree="$ICEDUST_HOME/$ICEDUST_PROJECT/packages/EXTERNALS" icedust-describe || true`
Qsub options: $QsubOptions
Input files: ` cat "$InputFileList"`
Batch run script: $RunBatch
EOF

SetupFile="$ICEDUST_HOME/$ICEDUST_PROJECT/setup.sh"

cat > "$RunBatch" <<EOF
set -e
set `$Debug && echo - || echo +`x
pwd

SetupFile="$SetupFile"

OutputDir="$OutputDir"
ConfigFile="$ActualConfig"
AppendVal="$AppendVal"
InputFileList="$InputFileList"
NumInputFiles=`cat "${InputFileList}" |wc -l`
EOF

cat  >> $RunBatch<<"EOF"
cat "$SetupFile"
. "$SetupFile"

echo "Disk Usage Before running:"
df -lh

[ -z "$SGE_TASK_ID" ] && export SGE_TASK_ID=1
TaskId=${SGE_TASK_ID}
PaddedId=`printf "%03d" ${TaskId}`
export INPUT_FILE=""
export OUTPUT_DIR="${OutputDir}/output"

date +"%y%m%d-%H:%M:%S:%N" > "$OutputDir/timers/$AppendVal/${PaddedId}.start"
if [ "$TaskId" -gt ${NumInputFiles} ] ;then
    if [ ${NumInputFiles} -gt 0 ] ;then
        echo "FATAL ERROR: No more input files ( File index: $TaskId )"
        echo "             Input files: "
        cat "$InputFileList"
        exit 1
    fi
else
    INPUT_FILE="`head -${TaskId} "${InputFileList}" |tail -1`"
    INPUT_FILE="`readlink -f "${INPUT_FILE}"`"
fi
export INPUT_FILE_LIST="${InputFileList}"
printenv

time RunIcedustControl -c "$OutputDir/$ConfigFile" 
date +"%y%m%d-%H:%M:%S:%N" > "$OutputDir/timers/$AppendVal/${PaddedId}.stop"
echo "Disk Usage After running:"
df -lh
ls -ltrh $TMPDIR
EOF

Jobname="`cut -f1 -d. <<<"$ActualConfig"`"

CMD='qsub '"$QsubOptions"' -N "$Jobname" -t "$FirstJob"-"$NoJobs" -e "$OutputDir/batch_output" -o "$OutputDir/batch_output" "$RunBatch"'
echo ${CMD}

echo -n "qsub response: " >>"$BatchConfig"
eval $CMD |tee -a "$BatchConfig"