#!/bin/sh 
version="Queue v0.1 Copyright (C) 1994 Karl J. Runge";
# Queue: Script to take batchqueue command with flags to be run, create a
# script file, submit job, watch for finished file flag, clean up, then exit.
#
# Usage:
# Queue [-debug] [-s delay] [-mail [user --]] [-help] [-norc] [-eof]  \
#	[-show] [-cmd queue_cmd] [-f queue_flag ] [-i insert] [-del patt] \
#       [-rc file]  [-v version] command
# examples:
# Queue -cmd qsub -f "-q small" a.out \< infile \> outfile

# Queue -s 5 -mail -cmd "at.pl -s 10" "ls -l | wc -l > gat ; ls -l >> gat"

# Options:
# -debug:	print out info that would be used but do not submit job.
# -show:	print out info and prompt whether to submit it or not.
# -s delay:	set time to sleep between checks for signal file (space reqd).
# -mail -m:	mail the user after job has finished.
#		use  "-m user@host --" to specify to mail to other than $USER 
# -cmd q_cmd:	the job submission command (e.g. "at" or "qsub" or "llsubmit").
# -f q_flag:	flag(s) for command q_cmd (can be included in -cmd if you like)
# -norc:	do not add lines from Queuerc file to Script.
# -rc file:	use "file" instead of standard Queuerc file(s).
# -del patt:	delete lines matching pattern from Queuerc file 
# -i insert:	insert the line(s) to the command script.
# -eof:		append EOF to end of script. Also done if Queuerc contains EOF
# -help:	print out this information.
#
# command:	desired command, with protected >, <, |, and ;
# NOTE: -rc -del -i flags are interpreted in the order they appear.
#
# Lines from the file $HOME/.Queuerc ./Queuerc or ./.Queuerc will be added to
# Script automatically (the first one found in the above order).
# if Queuerc file contains cd "`pwd`" it is subbed before placing into Script
#    ""     ""  `SCRIPT` or `FLAG` it is $SCRIPT or $FLAG value is substituted 
# Queuerc file can contain lines '#Q QUEUE qsub' or '#Q SLEEP 30' to set those
# variables. (they are overidden by command line flags -cmd or -s)

QUEUE="llsubmit ";	# batch submit command | CHANGE TO LOCAL CASE  
SLEEP="10";		# sleep interval       | or overide in Queuerc
helpline="41";
QUEUE_ON="";
SLEEP_ON="";
DEBUG="";
NORC="";
EOF="";
SHOW="";
MAILIT="";
MAILTO="";
QueueOpts="";
QueueRC="$HOME/.Queuerc";

SCRIPT="QueueTmp$$";	# tmp file for script
FLAG="QueueFlag$$";	# tmp file for signal file
QueueRC1="Queue1RC$$";	# tmp file for .Queuerc work
QueueRC2="Queue2RC$$";	# tmp file for .Queuerc work

if [ -f "$HOME/.Queuerc" ]; then
	QueueRC="$HOME/.Queuerc";
	cat $QueueRC > $QueueRC1;
elif [ -f "./Queuerc" ]; then
	QueueRC="./Queuerc";
	cat $QueueRC > $QueueRC1;
elif [ -f "./.Queuerc" ]; then
	QueueRC="./.Queuerc";
	cat $QueueRC > $QueueRC1;
fi

cleanRC () {
	rm -f $QueueRC1 $QueueRC2;
}

BREAK="";
while [ 1 ]
do
case $1 in
	"-debug")	DEBUG="True";
			;;
	"-eof")		EOF="True";
			;;
	"-show")	SHOW="True";
			;;
	"-s")		shift; SLEEP="$1"; SLEEP_ON='True';
			;;
	"-s"*)		echo; cleanRC; head -$helpline $0 | more; exit 1;# bail on -s5
			;;
	"-m"|"-mail")	MAILIT="True";
			case $3 in
				"--")	MAILTO="$2"; shift; shift;
					;;
			esac
			;;
	"-norc")	NORC="True";
			;;
	"-rc")		shift; 
			if [ -f "$1" ]; then
				QueueRC="$1"; cat $QueueRC > $QueueRC1;
			elif [ -f "$HOME/$1" ]; then
				QueueRC="$HOME/$1"; cat $QueueRC > $QueueRC1;
			else
				echo "$0: no such file $1";
			fi
			;;
	"-i")		shift; echo "$1" >> $QueueRC1;
			;;
	"-del")		shift; grep -v -e "$1" $QueueRC1 > $QueueRC2;
			cp $QueueRC2 $QueueRC1;
			;;
	"-v"*)		echo; cleanRC; echo "$version"; echo; exit 0;
			;;
	"-h"*)		echo; cleanRC; head -$helpline $0 | more; exit 0;
			;;
	"-cmd")		shift; QUEUE="$1"; QUEUE_ON='True';
			;;
	"-f")		shift; QueueOpts="$1";
			;;
	"-"*)		case $1 in
				"-i")	BREAK="True"; ;;
				*)	echo; head -$helpline $0;
					echo; echo "$1 not an option, Bye!";
					cleanRC;
					exit 1;
					;;
			esac
			;;
	*)		BREAK="True";
			;;
esac
if [ "$BREAK" = "True" ]; then
	break;
fi
shift;
done

echo '#!/bin/sh' > $SCRIPT;	# start making batch script

if [ -f "$QueueRC1" ] && [ "$NORC" != "True" ]; then	# add lines from ~/.Queuerc
	if [ "$QUEUE_ON" = "" ]; then	# check Queuerc for "#Q QUEUE switch
		Test="`grep -i '#Q *QUEUE' $QueueRC1 | awk '{print $3}'`";
		if [ "$Test" != "" ]; then
			QUEUE="$Test";
		fi
	fi
	if [ "$SLEEP_ON" = "" ]; then	# check Queuerc for "#Q SLEEP switch
		Test="`grep -i '#Q *SLEEP' $QueueRC1 | awk '{print $3}'`";
		if [ "$Test" != "" ]; then
			SLEEP="$Test";
		fi
	fi
	if [ "$EOF" = "" ]; then
		if [ "`grep EOF $QueueRC1`" != "" ]; then
			EOF="True";
		fi
	fi
	Pwd="`pwd`";

	PwdX="`type Pwd 2>&1 | grep 'not found'`";
#	echo "PwdX= $PwdX"			# yes, messy isn't it
						# I wanted to avoid eval
	if [ "$PwdX" ]; then
#		echo "NoHave Pwd"; exit;
		cat $QueueRC1 | sed -e s:cd\ \"\`pwd\`\":cd\ \"$Pwd\": | sed -e s:\`SCRIPT\`:$SCRIPT: | sed -e s:\`FLAG\`:$FLAG: >> $SCRIPT;
	else
#		echo "Have Pwd"; exit;
		PwdY="`Pwd`";
		cat $QueueRC1 | sed -e s:cd\ \"\`pwd\`\":cd\ \"$Pwd\": | sed -e s:\`Pwd\`:"$PwdY": | sed -e s:\`SCRIPT\`:$SCRIPT: | sed -e s:\`FLAG\`:$FLAG: >> $SCRIPT;
	fi
fi

cleanRC;

echo "$*" >> $SCRIPT;			# put in actual command
echo "touch $FLAG" >> $SCRIPT;		# signal for finished job
if [ "$EOF" ]; then
	echo "EOF" >> $SCRIPT;		# Script wrapped with <<EOF
fi
chmod 755 $SCRIPT;

SUBJECT="Finished: $*";			# make mail command
if [ "$MAILTO" = "" ]; then
	MAIL="mail -s \"$SUBJECT\" $USER";
else
	MAIL="mail -s \"$SUBJECT\" $MAILTO";
fi

if [ "$SLEEP" -lt 1 ]; then		# just in case...
	SLEEP="1";
fi

if [ $DEBUG ] || [ $SHOW ]; then		# dump info to screen and exit
	echo;
	echo "Batch submission command is:";
	echo;
	echo "$QUEUE $QueueOpts $SCRIPT";
	echo
	echo "Script $SCRIPT contains:";
	echo;
	cat $SCRIPT;
	if [ "$MAILIT" = "True" ]; then
		echo;
		echo "Mail command is:";
		echo;
		echo $MAIL;
	fi
	echo; echo "Watching sleep period set to $SLEEP (seconds)";
	echo;

	if [ $SHOW ]; then
		echo; echo -n "Should we continue? ([y]/n) ";
		read R;
		if [ "$R" = "n" ] || [ "$R" = "N" ] || [ "$R" = "no" ]; then
			rm $SCRIPT;
			exit 0;
		fi
	fi
	if [ $DEBUG ]; then
		rm $SCRIPT;
		exit 0;
	fi
fi

rm -f $FLAG;				# make sure flag file absent

$QUEUE $QueueOpts $SCRIPT;		# submitted for your approval...

while [ 1 ]				# watch for flag file
do
	if [  ! -f "$FLAG" ]; then
		sleep $SLEEP;
	else
		break;
	fi
done

if [ "$MAILIT" = "True" ]; then		# mail user if desired

DATE="`date`";
MESSAGE="`cat $SCRIPT`";
eval $MAIL <<_EOM 

On $DATE (evidently) finished run:

$MESSAGE

_EOM

fi

sleep 1;
	
rm -f $SCRIPT;				# clean up a bit
rm -f $FLAG;