source: trunk/Mars/hawc/processing/DiskToDB/run-callisto2.sh

#!/bin/bash
#
# Runs callisto macro on all files in directory DIR for a given telescope TEL
# and night NIGHT and writes output to DIR/../callisto
#
# Example:
#       bash run-callisto2.sh cred-file 1 /data/HE01/raw 20201111

set -o errexit
set -o errtrace
set -o nounset
set -o pipefail

function ErrExit()
{
        echo "ERROR: Line `caller`: ${BASH_COMMAND}" >&2
        exit 1
}

function StrgCExit()
{
        echo " "
        echo "$0 was forcefully terminated" >&2
        exit 1
}

trap ErrExit ERR
trap StrgCExit INT

readonly CALLISTO=callisto
# The .success file in /data/star will be resetted
readonly STAR=star
# Directory to Mars environment (usually Mars/build)
readonly MARS="/home/hawc/Desktop/Mars/"
# Absolut path to macros
readonly MACROS="/home/hawc/Desktop/Mars-src/hawc"
readonly PROGRAM=$0
REPLACE=false

usage()
{
        echo "usage: $PROGRAM [-hr] [Credentials Telescope Dir Night]" 
        echo "  -h              display help"
        echo "  -r              replace data"
        exit 1;
}

# Check for flags
while getopts 'hr' flag
do
        case "${flag}" in
                h) usage ;;
                r) REPLACE=true ;;
                *) usage ;;
        esac
done
shift $(($OPTIND-1))

# Check if Mars exists
if [ ! -d "${MARS}" ]
then
        echo "Mars does not exists at ${MARS}. Please change in \\
                script ${PROGRAM}."
        exit 1
fi

# Check if MACROS exists
if [ ! -d "${MACROS}" ]
then
        echo "Macros directorey does not exists at ${MACROS}. Please change in \\
                script ${PROGRAM}."
        exit 1
fi

# Check if at least two arguments are provided
if [ -z "${1}" ] || [ -z "${2}" ] || [ -z "${3}" ] || [ -z "${4}" ]
then
        echo "Not enough arguments. Check -h for help!"
        exit 1
fi

# File containing the access credentials for the database
CRED="${1}"
# Specify the telescope for which to run the script.
TEL="${2}"
# The data is expected to be found in /data/raw and data/callisto
DATA="${3}"
NIGHT="${4}"

function UpdateStatus()
{
        local tel="${1}"
        local night="${2}"
        local runid="${3}"
        local stat="${4}"

        mysql --defaults-file=${CRED} \
                --compress \
                -e "UPDATE DataOnDisk \
                SET DataOnDisk.callisto = ${stat} \
                WHERE DataOnDisk.Telescope = ${tel} \
                AND DataOnDisk.NIGHT = ${night} \
                AND DataOnDisk.RUNID = ${runid};"
}

# Get all runs that can (and should) be calibrated
# Pipe the output to mysql and read the
# mysql output line-by-libe
echo \
"\
SELECT 
        Calibration.NIGHT,
        Calibration.RUNID,
        Calibration.DrsNight,
        Calibration.DrsRunID
FROM 
        Calibration
INNER JOIN
        DataOnDisk
ON
        DataOnDisk.Telescope = Calibration.Telescope
AND
        DataOnDisk.NIGHT = Calibration.NIGHT
AND
        DataOnDisk.RUNID = Calibration.RUNID
WHERE
        Calibration.Telescope = ${TEL}
AND     
        Calibration.NIGHT = ${NIGHT}
AND
        DataOnDisk.calibration = 0
ORDER BY
        Calibration.NIGHT, Calibration.RUNID\
"\
|  mysql \
       --defaults-file=${CRED} \
       --skip-column-names \
       --batch --raw \
       --compress \
       | \
        while read -r -a LINE
        do
                # Extract night/runid for data file and calibration file
                DATNIGHT=${LINE[0]}
                DATRUNID=${LINE[1]}
                DRSNIGHT=${LINE[2]}
                DRSRUNID=${LINE[3]}

                # Formatting of the file paths and names
                DATPATH=${DATNIGHT:0:4}/${DATNIGHT:4:2}/${DATNIGHT:6:2}
                DRSPATH=${DRSNIGHT:0:4}/${DRSNIGHT:4:2}/${DRSNIGHT:6:2}

                PREFIX=`printf ${DATNIGHT}_%03d ${DATRUNID}`

                DATNAME=`printf ${DATNIGHT}_%03d.fits.fz ${DATRUNID}`
                DRSNAME=`printf ${DRSNIGHT}_%03d.drs.fits ${DRSRUNID}`

                OUT="${DATA}"/../${CALLISTO}/${DATPATH}

                echo DAT=${DATNAME} [${DATPATH}]
                echo DRS=${DRSNAME} [${DRSPATH}]


                if [ ${REPLACE} = true ]
                then
                        echo "deleting ${OUT}/.${PREFIX}.succsess !!!"
                        rm -f "${OUT}"/.${PREFIX}.success
                fi

                # Check if not yet successfully processed
                # Removing this file can be used to trigger a re-processing
                # the next time this script is executed
                if [ ! -f "${OUT}/.${PREFIX}.success" ]
                then

                        cd ${MARS}

                        mkdir -p "${OUT}"

                        # Trigger reprocessing of the process-fils in the star directory
                        rm -f "${DATA}/${STAR}/${DATPATH}/.${PREFIX}.*"

                        # Flag that a process is running
                        rm -f "${OUT}"/.${PREFIX}.done
                        rm -f "${OUT}"/.${PREFIX}.success

                        touch "${OUT}"/.${PREFIX}.running

                        echo ${DATA}

                        RC=0
                        # Execute the calibration and write output to log-file
                        root -b -q -l ${MACROS}/callisto.C'("'"${DATA}"/${DATPATH}/${DATNAME}'","'"${DATA}"/${DRSPATH}/${DRSNAME}'", 0 ,"'"${OUT}"'")' \
                               2>&1 | tee "${OUT}"/${PREFIX}.log || RC=1

                        # Remember exit status of callisto
                        echo RC=${RC} | tee -a "${OUT}"/${PREFIX}.log
                        echo ${RC} > "${OUT}"/.${PREFIX}.done
                        # Processing is finished
                        rm -f "${OUT}"/.${PREFIX}.running

                        # If processing was successfull write corresponding flag
                        if [ "${RC}" == "0" ]
                        then
                                touch "${OUT}"/.${PREFIX}.success
                        fi

                        cd -

                        echo "-----End of first iteration-----"
                else
                        echo Skipped.
                fi

        done