| 1 | #!/bin/sh -xvf
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| 2 | #do calibration
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| 3 | DATE=/bin/date
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| 4 | GREP=/bin/grep
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| 5 | AWK=/bin/awk
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| 6 | ECHO=/bin/echo
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| 7 | WC=/usr/bin/wc
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| 8 | CAT=/bin/cat
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| 9 | PRINTF=/usr/bin/printf
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| 10 | FIND=/usr/bin/find
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| 11 | MKDIR=/bin/mkdir
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| 12 | XARGS=/usr/bin/xargs
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| 13 | SORT=/bin/sort
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| 14 | RM=/bin/rm
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| 15 | TR=/usr/bin/tr
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| 16 | CP=/bin/cp
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| 17 | LS=/bin/ls
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| 18 | CHMOD=/bin/chmod
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| 19 |
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| 20 | DefaultIFS=$' \t\n'
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| 21 | IFS=$DefaultIFS
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| 22 |
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| 23 | #set Irods environment
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| 24 | . /usr/local/shared/bin/irods_env.sh -noverbose
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| 25 |
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| 26 | scriptName="`basename $0`"
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| 27 | $ECHO "Processing script ${scriptName} at `date`"
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| 28 | #which source to analyse
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| 29 |
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| 30 | #Process cmd line args: the -src option is mandatory (source name as Abell85)
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| 31 | sourceRadio=
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| 32 | dateSelected=
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| 33 | freqBAOCalib=1346
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| 34 | bwBAOCalib=6.25
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| 35 | #use -sim option to simulate processing (debug the script as if...)
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| 36 | simulationMode=Off
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| 37 | while [ $# -gt 0 ]
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| 38 | do
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| 39 | case "$1" in
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| 40 | -src) sourceRadio=$2; shift;;
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| 41 | -date) dateSelected=$2; shift;;
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| 42 | -freq) freqBAOCalib=$2; shift;;
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| 43 | -bwd) bwBAOCalib=$2; shift;;
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| 44 | -sim) simulationMode=On;;
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| 45 | -h)
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| 46 | echo >&2 \
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| 47 | "usage: $0 -src souce -date YYYYMMDD [-freq freq in MHz (default ${freqBAOCalib})] [-bwd bandwidth in MHz (default ${bwBAOCalib})]"
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| 48 | exit 1;;
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| 49 | *) break;; # terminate while loop
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| 50 | esac
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| 51 | shift
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| 52 | done
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| 53 |
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| 54 | if [ ${simulationMode} = "On" ]; then
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| 55 | $ECHO "INFO ${scriptName} running in SIMUL mode"
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| 56 | fi
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| 57 |
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| 58 | if [ "<${sourceRadio}>" = "<>" ]; then
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| 59 | $ECHO "FATAL: You have forgotten to select the source option (-src)"
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| 60 | exit 1
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| 61 | fi
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| 62 |
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| 63 | case ${sourceRadio} in
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| 64 | Abell85) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
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| 65 | Abell2440) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
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| 66 | Abell1205) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
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| 67 | NGC4383) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
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| 68 | *) ECHO "FATAL (${scriptName}): process ${sourceRadio} not yet foreseen"
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| 69 | exit 1;;
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| 70 | esac
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| 71 |
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| 72 | srclower=`${ECHO} ${sourceRadio} | ${TR} "[:upper:]" "[:lower:]" `
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| 73 |
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| 74 | #Path to public backupable path
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| 75 | publicpath="/afs/in2p3.fr/home/c/campagne/public"
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| 76 |
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| 77 |
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| 78 | #temporary files to synchronize scripts
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| 79 | tmppublicpath=${TMPPUBLICPATH}
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| 80 | #wakeup the NFS disk
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| 81 | $LS -l ${tmppublicpath} > /dev/null
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| 82 | #clean previous spurious files
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| 83 | $RM -f ${tmppublicpath}/*.finished
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| 84 |
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| 85 | #Path where the job will do temporary IO
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| 86 | . ${SCRIPTPATH}/isInteractive.sh
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| 87 | isInteractive=$(isInteractive)
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| 88 | if [ ${isInteractive} == "1" ]; then
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| 89 | $ECHO "Usage in INTERACTIVE may be destructive... To be used with great care !!!!"
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| 90 | exit 0;
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| 91 | fi
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| 92 |
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| 93 | . ${SCRIPTPATH}/set_iojobpath.sh
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| 94 | iojobpath=$(set_iojobpath)
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| 95 | cd ${iojobpath}
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| 96 |
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| 97 | localpath="${sourceRadio}"
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| 98 | $MKDIR -p ./${localpath}
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| 99 | cd ./${localpath}
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| 100 |
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| 101 | #save the top directory
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| 102 | topDir=`pwd`
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| 103 |
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| 104 | #Path of the utility scripts
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| 105 | scriptpath=${SCRIPTPATH}
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| 106 |
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| 107 | #JEC 1/10/11 Use generic baodaqstatus name
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| 108 | OUT1=${publicpath}/baodaqstatus-current.txt
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| 109 | #
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| 110 | #get the daq current irod status
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| 111 | #tag=`${DATE} +%F`
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| 112 | #OUT1=${publicpath}/baodaqstatus-${tag}.txt
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| 113 | #
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| 114 | if [ ! -e ${OUT1} -o ! -r ${OUT1} ]; then
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| 115 | $ECHO "FATAL (${scriptName}): ${OUT1} has a problem"
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| 116 | exit 1
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| 117 | fi
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| 118 |
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| 119 |
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| 120 | #Nb: if we want to implement a loop on sources we have to take care of srclower...
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| 121 |
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| 122 | $ECHO "You have selected sourceRadio = $sourceRadio[date = ${dateSelected}]"
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| 123 | #JEC 14/12/11 One should take care of DR extension for Drift Scan
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| 124 | #tableau=( `$GREP -i "${dateSelected}${srclower}" ${OUT1} | $AWK '( NF==4 ) { print $2 }' ` )
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| 125 | tableau=( `$GREP -i "${sourceRadio}/${dateSelected}${srclower}" ${OUT1} | $AWK '( NF==4 ) { print $2 }' ` )
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| 126 | IFS='
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| 127 | '
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| 128 | tableau=( $( $PRINTF "%s\n" "${tableau[@]}" | $AWK 'x[$0]++ == 0' ) )
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| 129 | IFS=$DefaultIFS
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| 130 |
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| 131 |
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| 132 | for i in ${tableau[@]}
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| 133 | do
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| 134 | #
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| 135 | # start a "fresh" session
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| 136 | cd ${topDir}
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| 137 | $LS | $XARGS -i $RM -rf {}
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| 138 |
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| 139 |
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| 140 | $ECHO "DEBUG: (${scriptName}) irods root dir $i"
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| 141 | dateDAQ=`$ECHO ${i} | $AWK '{split($0,a,"/"); print a[6];}' | $AWK "{sub(/${srclower}/,\"\"); print}"`
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| 142 |
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| 143 | $ECHO "DEBUG: (${scriptName}): we are in directory `pwd` the topDir=${topDir}"
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| 144 | $LS -lrt
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| 145 |
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| 146 |
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| 147 | # alreadyDone=`ils ${i} 2>&1 | $GREP -i "calib_.*\.txt" | $WC -l`
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| 148 | # if [ ${alreadyDone} -gt 0 ]; then
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| 149 | # $ECHO "INFO (${scriptName}): calibration coef files already exist"
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| 150 | # continue
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| 151 | # fi
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| 152 |
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| 153 | gainDone=`ils ${i} 2>&1 | $GREP -i "gain_.*\.fits" | $WC -l`
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| 154 | if [ ! ${gainDone} -gt 0 ]; then
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| 155 | $ECHO "FATAL (${scriptName}): gain file DOES NOT exist skip `basename $i` "
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| 156 | continue
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| 157 | fi
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| 158 |
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| 159 | ######
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| 160 | $ECHO ">>>>>>>>>>>>> ANALYSIS Part of ${sourceRadio} ${dateDAQ}"
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| 161 | #go to the .../source/date-sourcelowercase directory
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| 162 | #download Off/calibcycle<> and On/calibcycle<> directories
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| 163 | $MKDIR -p ${topDir}/${dateDAQ}${srclower}
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| 164 | cd ${topDir}/${dateDAQ}${srclower}
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| 165 | aboveOnOffDir=`pwd`
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| 166 | $ECHO "DEBUG (${scriptName}): we are in directory: <`pwd`>"
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| 167 | #
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| 168 | mode="Off"
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| 169 | $ECHO "DEBUG (${scriptName}): START download the ${mode} calib fits files"
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| 170 | inFileDirectory="./${mode}"
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| 171 | $MKDIR -p ${inFileDirectory}
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| 172 | listOfCalibCycle=( `ils ${i}/${mode} 2>&1 | $GREP -i "calibcycle"|$AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.11n` )
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| 173 | IFS='
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| 174 | '
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| 175 | listOfCalibCycle=( $( $PRINTF "%s\n" "${listOfCalibCycle[@]}" | $AWK 'x[$0]++ == 0' ) )
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| 176 | IFS=$DefaultIFS
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| 177 |
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| 178 | firstCycleOff=`$ECHO ${listOfCalibCycle[0]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
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| 179 | nCyclesOff=`expr ${#listOfCalibCycle[*]} - 1`
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| 180 |
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| 181 | lastCycleOff=`$ECHO ${listOfCalibCycle[${nCyclesOff}]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
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| 182 |
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| 183 | listOfCalibCycle=( "${listOfCalibCycle[@]/#/${i}/${mode}/}" )
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| 184 |
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| 185 |
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| 186 | for j in ${listOfCalibCycle[@]}
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| 187 | do
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| 188 | irodsDownDir="${j}"
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| 189 | OUT=./getInFits.$$
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| 190 | iget -r -f -K ${irodsDownDir} ${inFileDirectory} > ${OUT} 2>&1
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| 191 | igetStatus=`$GREP "^ERROR" ${OUT}`
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| 192 | if [ "<$igetStatus>" != "<>" ]; then
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| 193 | $ECHO "FATAL (${scriptName}): error while iget fits files:"
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| 194 | $ECHO $igetStatus
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| 195 | $ECHO " ==> skip this run $sourceRadio $dateDAQ"
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| 196 | continue
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| 197 | fi
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| 198 | $RM -f ${OUT}
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| 199 | done
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| 200 | $ECHO "DEBUG (${scriptName}): END download the ${mode} calib fits files"
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| 201 | #
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| 202 | mode="On"
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| 203 | $ECHO "DEBUG (${scriptName}): START download the ${mode} calib fits files"
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| 204 | inFileDirectory="./${mode}"
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| 205 | $MKDIR -p ${inFileDirectory}
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| 206 |
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| 207 | listOfCalibCycle=( `ils ${i}/${mode} 2>&1 | $GREP -i "calibcycle" |$AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.11n` )
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| 208 | IFS='
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| 209 | '
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| 210 | listOfCalibCycle=( $( $PRINTF "%s\n" "${listOfCalibCycle[@]}" | $AWK 'x[$0]++ == 0' ) )
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| 211 | IFS=$DefaultIFS
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| 212 |
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| 213 | firstCycleOn=`$ECHO ${listOfCalibCycle[0]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
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| 214 | nCyclesOn=`expr ${#listOfCalibCycle[*]} - 1`
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| 215 |
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| 216 | lastCycleOn=`$ECHO ${listOfCalibCycle[${nCyclesOn}]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
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| 217 |
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| 218 | listOfCalibCycle=( "${listOfCalibCycle[@]/#/${i}/${mode}/}" )
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| 219 |
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| 220 |
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| 221 | #
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| 222 | #Check if there is the same number of cycles in Off and On mode
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| 223 | #
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| 224 | #first cycle = max(firstCycleOn, firstCycleOff)
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| 225 | #last cycle = min(lastCycleOn,lastCycleOff)
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| 226 |
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| 227 | if [ ${firstCycleOn} -eq ${firstCycleOff} -a ${lastCycleOn} -eq ${lastCycleOff} ]; then
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| 228 | firstCycle=${firstCycleOff}
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| 229 | lastCycle=${lastCycleOff}
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| 230 | else
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| 231 | $ECHO "INFO (${scriptName}): missmatch between Off and On mode"
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| 232 | $ECHO "${firstCycleOn} != ${firstCycleOff} OR ${lastCycleOn} != ${lastCycleOff}"
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| 233 | firstCycle=${firstCycleOff}
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| 234 | if [ ${firstCycleOn} -gt ${firstCycle} ]; then
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| 235 | firstCycle=${firstCycleOn}
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| 236 | fi
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| 237 | lastCycle=${lastCycleOff}
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| 238 | if [ ${lastCycleOn} -lt ${lastCycle} ]; then
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| 239 | lastCycle=${lastCycleOn}
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| 240 | fi
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| 241 | fi
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| 242 | $ECHO "INFO (${scriptName}): use cycles [${firstCycle}, ${lastCycle}]"
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| 243 |
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| 244 |
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| 245 | for j in ${listOfCalibCycle[@]}
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| 246 | do
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| 247 | irodsDownDir="${j}"
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| 248 | OUT=./getInFits.$$
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| 249 | iget -r -f -K ${irodsDownDir} ${inFileDirectory} > ${OUT} 2>&1
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| 250 | igetStatus=`$GREP "^ERROR" ${OUT}`
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| 251 | if [ "<$igetStatus>" != "<>" ]; then
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| 252 | $ECHO "FATAL (${scriptName}): error while iget fits files:"
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| 253 | $ECHO $igetStatus
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| 254 | $ECHO " ==> skip this run $sourceRadio $dateDAQ"
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| 255 | continue
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| 256 | fi
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| 257 | $RM -f ${OUT}
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| 258 | done
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| 259 | $ECHO "DEBUG (${scriptName}): END download the ${mode} calib fits files"
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| 260 | #Get sca file
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| 261 | $ECHO "DEBUG (${scriptName}): START call getscafiles.sh ${sourceRadio} ${dateDAQ}"
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| 262 | OUT1=./getScaStatus.$$
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| 263 | $RM -f ${tmppublicpath}/getscafiles.finished
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| 264 | ${scriptpath}/getscafiles.sh ${sourceRadio} ${dateDAQ} > ${OUT1} 2>&1
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| 265 | # while [ ! -f "${tmppublicpath}/getscafiles.finished" ]; do
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| 266 | # $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/getscafiles.finished"
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| 267 | # date +%T
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| 268 | # sleep 30
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| 269 | # done
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| 270 | $RM ${tmppublicpath}/getscafiles.finished
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| 271 | $ECHO "DEBUG (${scriptName}): END"
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| 272 | #
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| 273 | getScaStatus=`$GREP "^\(FATAL\|ERROR\)" ${OUT1}`
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| 274 | #
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| 275 | if [ "<${getScaStatus}>" != "<>" ]; then
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| 276 | $ECHO "FATAL (${scriptName}): error to get sca file for $sourceRadio $dateDAQ"
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| 277 | $ECHO "DEBUG (${scriptName}): START with cat ${OUT1}"
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| 278 | $CAT ${OUT1}
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| 279 | $ECHO "DEBUG (${scriptName}): END"
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| 280 | continue
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| 281 | fi
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| 282 | $RM -f ${OUT1}
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| 283 |
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| 284 | scaFile=`$FIND . -name "sca*.sum.trans" | $XARGS -i basename {}`
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| 285 |
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| 286 | #prepare job submission
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| 287 | cd ${aboveOnOffDir}
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| 288 | #the default spectra name is medfiltmtx, otherwise use -specname <a_string>
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| 289 |
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| 290 | logFile="analyse_CALIB_${sourceRadio}_${dateDAQ}.log"
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| 291 | $ECHO "DEBUG (${scriptName}): execute the analysis... should not take long. `date`"
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| 292 | if [ ${simulationMode} = "On" ]; then
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| 293 | $ECHO "SIMUL: ${scriptpath}/Objs/analyse -act calib -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir calibcycle -numcycle ${firstCycle},${lastCycle} -calibopt mean -debug 1 -freqBAOCalib ${freqBAOCalib} -bwBAOCalib ${bwBAOCalib} >& ${logFile}"
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| 294 | cat > ${logFile} <<EOF
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| 295 | Ok calibration finished
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| 296 | EOF
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| 297 | #WARNING: the EOF must start at 1st column overwise the rest of the script is part of the file cat...
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| 298 | else
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| 299 | ${scriptpath}/Objs/analyse -act calib -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir calibcycle -numcycle ${firstCycle},${lastCycle} -calibopt mean -debug 1 -freqBAOCalib ${freqBAOCalib} -bwBAOCalib ${bwBAOCalib} >& ${logFile}
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| 300 | fi
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| 301 | #
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| 302 | $ECHO "DEBUG (${scriptName}): analysis finished `date`. Look for errors before saving to Irods"
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| 303 | rcstatus=`$GREP -i "Ok calibration finished" ${logFile} | $WC -l`
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| 304 | if [ ${rcstatus} -eq 0 ]; then
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| 305 | $ECHO "INFO (${scriptName}): analysis problem for ${sourceRadio} ${dateDAQ}"
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| 306 | $ECHO " START logfile"
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| 307 | $CAT ${logFile}
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| 308 | $ECHO " END logFile"
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| 309 | #clean and leave
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| 310 | cd ${aboveOnOffDir}
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| 311 | $LS | $XARGS -i $RM -rf {}
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| 312 | continue
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| 313 | fi
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| 314 | #Save into Irods
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| 315 | $ECHO "DEBUG (${scriptName}): START save output files"
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| 316 | $LS ${aboveOnOffDir}
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| 317 | #use -f option for iput ONLY to force override
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| 318 | if [ ${simulationMode} = "On" ]; then
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| 319 | $ECHO "SIMUL: here we look for calib file and put them in Irods"
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| 320 | else
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| 321 | $LS -lrth
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| 322 | $FIND . -name "calib_*" -print | $XARGS -i iput -f -v -K {} ${i}
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| 323 | fi
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| 324 | #save analysis logfile
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| 325 | $LS -l ${tmppublicpath} > /dev/null
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| 326 | $CP ${logFile} ${tmppublicpath}
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| 327 | $ECHO "DEBUG (${scriptName}): END save output files"
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| 328 | #clean up to avoid scratch SIZE EXCEED LIMIT
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| 329 | cd ${aboveOnOffDir}
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| 330 | $LS | $XARGS -i $RM -rf {}
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| 331 |
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| 332 | done
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| 333 |
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| 334 | exit 0
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