| 1 | #!/bin/sh -xvf
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| 2 | #Perform the ON-OFF analysis
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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 | #use -sim option to simulate processing (debug the script as if...)
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| 34 | simulationMode=Off
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| 35 | while [ $# -gt 0 ]
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| 36 | do
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| 37 | case "$1" in
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| 38 | -src) sourceRadio=$2; shift;;
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| 39 | -date) dateSelected=$2; shift;;
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| 40 | -sim) simulationMode=On;;
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| 41 | -h)
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| 42 | echo >&2 \
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| 43 | "usage: $0 -src souce -date YYYYMMDD [-freq freq in MHz (default ${freqBAOCalib})] [-sim to trig simulation mode]"
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| 44 | exit 1;;
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| 45 | *) break;; # terminate while loop
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| 46 | esac
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| 47 | shift
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| 48 | done
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| 49 |
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| 50 | if [ ${simulationMode} = "On" ]; then
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| 51 | $ECHO "INFO ${scriptName} running in SIMUL mode"
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| 52 | fi
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| 53 |
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| 54 | if [ "<${sourceRadio}>" = "<>" ]; then
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| 55 | $ECHO "FATAL: You have forgotten to select the source option (-src)"
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| 56 | exit 1
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| 57 | fi
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| 58 |
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| 59 | case ${sourceRadio} in
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| 60 | Abell85) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
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| 61 | Abell2440) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
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| 62 | Abell1205) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
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| 63 | *) ECHO "FATAL (${scriptName}): process ${sourceRadio} not yet foreseen"
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| 64 | exit 1;;
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| 65 | esac
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| 66 |
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| 67 | srclower=`${ECHO} ${sourceRadio} | ${TR} "[:upper:]" "[:lower:]" `
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| 68 |
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| 69 | #Path to public backupable path
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| 70 | publicpath="/afs/in2p3.fr/home/c/campagne/public"
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| 71 |
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| 72 |
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| 73 | #temporary files to synchronize scripts
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| 74 | tmppublicpath=${TMPPUBLICPATH}
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| 75 | #wakeup the NFS disk
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| 76 | $LS -l ${tmppublicpath} > /dev/null
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| 77 | #clean previous spurious files
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| 78 | $RM -f ${tmppublicpath}/*.finished
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| 79 |
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| 80 | #Path where the job will do temporary IO
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| 81 | if [ ${ENVIRONMENT} = "INTERACTIVE" ]; then
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| 82 | iojobpath="/sps/baoradio/AmasNancay/JEC"
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| 83 | $MKDIR -p $iojobpath
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| 84 | elif [ ${ENVIRONMENT} = "BATCH" ] ; then
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| 85 | iojobpath=${TMPBATCH}
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| 86 | else
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| 87 | $ECHO "FATAL (${scriptName}): environment is ${ENVIRONMENT} not allowed"
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| 88 | exit 1
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| 89 | fi
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| 90 | cd ${iojobpath}
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| 91 |
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| 92 | localpath="${sourceRadio}"
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| 93 | $MKDIR -p ./${localpath}
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| 94 | cd ./${localpath}
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| 95 |
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| 96 | #save the top directory
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| 97 | topDir=`pwd`
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| 98 |
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| 99 | #Path of the utility scripts
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| 100 | scriptpath="/afs/in2p3.fr/home/c/campagne/private/work/AmasNancay"
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| 101 |
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| 102 | #JEC 1/10/11 Use generic baodaqstatus name
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| 103 | #get the daq current irod status
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| 104 | #tag=`${DATE} +%F`
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| 105 | #OUT1=${publicpath}/baodaqstatus-${tag}.txt
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| 106 | OUT1=${publicpath}/baodaqstatus-current.txt
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| 107 |
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| 108 | if [ ! -e ${OUT1} -o ! -r ${OUT1} ]; then
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| 109 | $ECHO "FATAL (${scriptName}): ${OUT1} has a problem"
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| 110 | exit 1
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| 111 | # $ECHO "We should bring the DAQ status more up to date, this take 1 or 2sec..."
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| 112 | # $RM -f ${tmppublicpath}/statusdaq.finished
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| 113 | # ${scriptpath}/statusdaq.sh > ${OUT1}
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| 114 | # while [ ! -f "${tmppublicpath}/statusdaq.finished" ]; do
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| 115 | # sleep 30
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| 116 | # done
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| 117 | # $RM ${tmppublicpath}/statusdaq.finished
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| 118 | #protect against remove/rewriting
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| 119 | # $CHMOD -v 444 ${OUT1}
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| 120 | fi
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| 121 |
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| 122 |
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| 123 |
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| 124 | $ECHO "You have selected sourceRadio = ${sourceRadio} [date = ${dateSelected}]"
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| 125 | tableau=( `$GREP -i "${dateSelected}${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 | $ECHO "DEBUG: (${scriptName}) irods root dir $i"
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| 140 | dateDAQ=`$ECHO ${i} | $AWK '{split($0,a,"/"); print a[6];}' | $AWK "{sub(/${srclower}/,\"\"); print}"`
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| 141 |
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| 142 | $ECHO "DEBUG: (${scriptName}): we are in directory `pwd` the topDir=${topDir}"
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| 143 | $LS -lrt
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| 144 |
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| 145 |
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| 146 | #JEC 1/10/11 Use generic baodaqstatus name
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| 147 | #Look if the date has changed since beginning of the job!
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| 148 | # curtag=`${DATE} +%F`
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| 149 | # if [ "<${curtag}>" != "<${tag}>" ]; then
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| 150 | # tag=${curtag}
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| 151 | #it is necessary to update the daq status as the day has changed during the processing... (batch can take a long time...)
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| 152 | # OUT1=${publicpath}/baodaqstatus-${curtag}.txt
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| 153 | # $ECHO "We should bring the DAQ status more up to date, this take 1 or 2sec..."
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| 154 | # $RM -f ${tmppublicpath}/statusdaq.finished
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| 155 | # ${scriptpath}/statusdaq.sh > ${OUT1}
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| 156 | # while [ ! -f "${tmppublicpath}/statusdaq.finished" ]; do
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| 157 | # sleep 30
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| 158 | # done
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| 159 | # $RM ${tmppublicpath}/statusdaq.finished
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| 160 | #protect against remove/rewriting
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| 161 | # $CHMOD -v 444 ${OUT1}
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| 162 | # fi
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| 163 | #
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| 164 | # look if the gain & calibration files exist
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| 165 | #
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| 166 | gainDone=`ils ${i} 2>&1 | $GREP -i "gain_.*\.fits" | $WC -l`
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| 167 | if [ ! ${gainDone} -gt 0 ]; then
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| 168 | $ECHO "FATAL (${scriptName}): gain file DOES NOT exist skip `basename $i` "
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| 169 | continue
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| 170 | fi
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| 171 |
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| 172 | ######
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| 173 | $ECHO ">>>>>>>>>>>>> ANALYSIS Part of ${sourceRadio} ${dateDAQ}"
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| 174 | #go to the .../source/date-sourcelowercase directory
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| 175 | #download Off/datacycle<> and On/datacycle<> directories
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| 176 | $MKDIR -p ${topDir}/${dateDAQ}${srclower}
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| 177 | cd ${topDir}/${dateDAQ}${srclower}
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| 178 | aboveOnOffDir=`pwd`
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| 179 | $ECHO "DEBUG (${scriptName}): we are in directory: <`pwd`>"
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| 180 | #
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| 181 | mode="Off"
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| 182 | $ECHO "DEBUG (${scriptName}): START download the ${mode} data fits files"
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| 183 | inFileDirectory="./${mode}"
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| 184 | $MKDIR -p ${inFileDirectory}
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| 185 | listOfDataCycle=( `ils ${i}/${mode} 2>&1 | $GREP -i "datacycle"|$AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.10n` )
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| 186 | IFS='
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| 187 | '
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| 188 | listOfDataCycle=( $( $PRINTF "%s\n" "${listOfDataCycle[@]}" | $AWK 'x[$0]++ == 0' ) )
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| 189 | IFS=$DefaultIFS
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| 190 |
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| 191 | firstCycleOff=`$ECHO ${listOfDataCycle[0]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
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| 192 | nCyclesOff=`expr ${#listOfDataCycle[*]} - 1`
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| 193 |
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| 194 | if [ ${nCyclesOff} -eq -1 ]; then
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| 195 | continue
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| 196 | fi
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| 197 |
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| 198 | lastCycleOff=`$ECHO ${listOfDataCycle[${nCyclesOff}]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
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| 199 |
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| 200 | listOfDataCycle=( "${listOfDataCycle[@]/#/${i}/${mode}/}" )
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| 201 |
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| 202 |
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| 203 | for j in ${listOfDataCycle[@]}
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| 204 | do
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| 205 | irodsDownDir="${j}"
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| 206 | OUT=./getInFits.$$
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| 207 | iget -r -f -K ${irodsDownDir} ${inFileDirectory} > ${OUT} 2>&1
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| 208 | igetStatus=`$GREP "^ERROR" ${OUT}`
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| 209 | if [ "<$igetStatus>" != "<>" ]; then
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| 210 | $ECHO "FATAL (${scriptName}): error while iget fits files:"
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| 211 | $ECHO $igetStatus
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| 212 | $ECHO " ==> skip this run $sourceRadio $dateDAQ"
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| 213 | continue
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| 214 | fi
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| 215 | $RM -f ${OUT}
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| 216 | done
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| 217 | $ECHO "DEBUG (${scriptName}): END download the ${mode} data fits files"
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| 218 | #
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| 219 | mode="On"
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| 220 | $ECHO "DEBUG (${scriptName}): START download the ${mode} data fits files"
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| 221 | inFileDirectory="./${mode}"
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| 222 | $MKDIR -p ${inFileDirectory}
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| 223 |
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| 224 | listOfDataCycle=( `ils ${i}/${mode} 2>&1 | $GREP -i "datacycle" |$AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.10n` )
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| 225 | IFS='
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| 226 | '
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| 227 | listOfDataCycle=( $( $PRINTF "%s\n" "${listOfDataCycle[@]}" | $AWK 'x[$0]++ == 0' ) )
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| 228 | IFS=$DefaultIFS
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| 229 |
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| 230 | firstCycleOn=`$ECHO ${listOfDataCycle[0]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
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| 231 | nCyclesOn=`expr ${#listOfDataCycle[*]} - 1`
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| 232 |
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| 233 | if [ ${nCyclesOn} -eq -1 ]; then
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| 234 | continue
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| 235 | fi
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| 236 |
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| 237 | lastCycleOn=`$ECHO ${listOfDataCycle[${nCyclesOn}]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
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| 238 |
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| 239 | listOfDataCycle=( "${listOfDataCycle[@]/#/${i}/${mode}/}" )
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| 240 |
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| 241 | #
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| 242 | #Check if there is the same number of cycles in Off and On mode
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| 243 | #
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| 244 | #first cycle = max(firstCycleOn, firstCycleOff)
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| 245 | #last cycle = min(lastCycleOn,lastCycleOff)
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| 246 |
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| 247 | if [ ${firstCycleOn} -eq ${firstCycleOff} -a ${lastCycleOn} -eq ${lastCycleOff} ]; then
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| 248 | firstCycle=${firstCycleOff}
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| 249 | lastCycle=${lastCycleOff}
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| 250 | else
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| 251 | $ECHO "INFO (${scriptName}): missmatch between Off and On mode"
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| 252 | $ECHO "${firstCycleOn} != ${firstCycleOff} OR ${lastCycleOn} != ${lastCycleOff}"
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| 253 | firstCycle=${firstCycleOff}
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| 254 | if [ ${firstCycleOn} -gt ${firstCycle} ]; then
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| 255 | firstCycle=${firstCycleOn}
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| 256 | fi
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| 257 | lastCycle=${lastCycleOff}
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| 258 | if [ ${lastCycleOn} -lt ${lastCycle} ]; then
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| 259 | lastCycle=${lastCycleOn}
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| 260 | fi
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| 261 | fi
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| 262 | $ECHO "INFO (${scriptName}): use cycles [${firstCycle}, ${lastCycle}]"
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| 263 |
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| 264 |
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| 265 | for j in ${listOfDataCycle[@]}
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| 266 | do
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| 267 | irodsDownDir="${j}"
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| 268 | OUT=./getInFits.$$
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| 269 | iget -r -f -K ${irodsDownDir} ${inFileDirectory} > ${OUT} 2>&1
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| 270 | igetStatus=`$GREP "^ERROR" ${OUT}`
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| 271 | if [ "<$igetStatus>" != "<>" ]; then
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| 272 | $ECHO "FATAL (${scriptName}): error while iget fits files:"
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| 273 | $ECHO $igetStatus
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| 274 | $ECHO " ==> skip this run $sourceRadio $dateDAQ"
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| 275 | continue
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| 276 | fi
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| 277 | $RM -f ${OUT}
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| 278 | done
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| 279 | $ECHO "DEBUG (${scriptName}): END download the ${mode} data fits files"
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| 280 | #Get sca file
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| 281 | $ECHO "DEBUG (${scriptName}): START call getscafiles.sh ${sourceRadio} ${dateDAQ}"
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| 282 | OUT1=./getScaStatus.$$
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| 283 | $RM -f ${tmppublicpath}/getscafiles.finished
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| 284 | ${scriptpath}/getscafiles.sh ${sourceRadio} ${dateDAQ} > ${OUT1} 2>&1
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| 285 | while [ ! -f "${tmppublicpath}/getscafiles.finished" ]; do
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| 286 | $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/getscafiles.finished"
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| 287 | date +%T
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| 288 | sleep 30
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| 289 | done
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| 290 | $RM ${tmppublicpath}/getscafiles.finished
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| 291 | $ECHO "DEBUG (${scriptName}): END"
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| 292 | #
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| 293 | getScaStatus=`$GREP "^\(FATAL\|ERROR\)" ${OUT1}`
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| 294 | #
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| 295 | if [ "<${getScaStatus}>" != "<>" ]; then
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| 296 | $ECHO "FATAL (${scriptName}): error to get sca file for $sourceRadio $dateDAQ"
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| 297 | $ECHO "DEBUG (${scriptName}): START with cat ${OUT1}"
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| 298 | $CAT ${OUT1}
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| 299 | $ECHO "DEBUG (${scriptName}): END"
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| 300 | continue
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| 301 | fi
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| 302 | $RM -f ${OUT1}
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| 303 |
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| 304 | scaFile=`$FIND . -name "sca*.sum.trans" | $XARGS -i basename {}`
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| 305 |
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| 306 |
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| 307 | #prepare job submission
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| 308 | cd ${aboveOnOffDir}
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| 309 | #the default spectra name is medfiltmtx, otherwise use -specname <a_string>
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| 310 |
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| 311 | logFile="analyse_RAWDATA_${sourceRadio}_${dateDAQ}.log"
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| 312 | $ECHO "DEBUG (${scriptName}): execute the analysis... should not take long. `date`"
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| 313 | if [ ${simulationMode} = "On" ]; then
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| 314 | $ECHO "SIMUL: ${scriptpath}/Objs/analyse -act rawOnOff -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir datacycle -numcycle ${firstCycle},${lastCycle} -debug 1 >& ${logFile}"
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| 315 | cat > ${logFile} <<EOF
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| 316 | Ok rawOnOff finished
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| 317 | EOF
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| 318 | else
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| 319 | ${scriptpath}/Objs/analyse -act rawOnOff -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir datacycle -numcycle ${firstCycle},${lastCycle} -debug 1 >& ${logFile}
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| 320 | fi
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| 321 | $ECHO "DEBUG (${scriptName}): analysis finished `date`. Look for errors before saving to Irods"
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| 322 | rcstatus=`$GREP -i "Ok rawOnOff finished" ${logFile} | $WC -l`
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| 323 | if [ ${rcstatus} -eq 0 ]; then
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| 324 | $ECHO "INFO (${scriptName}): analysis problem for ${sourceRadio} ${dateDAQ}"
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| 325 | $ECHO " START logfile"
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| 326 | $CAT ${logFile}
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| 327 | $ECHO " END logFile"
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| 328 | #clean and leave
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| 329 | cd ${aboveOnOffDir}
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| 330 | $LS | $XARGS -i $RM -rf {}
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| 331 | continue
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| 332 | fi
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| 333 | #Save into Irods
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| 334 | $ECHO "DEBUG (${scriptName}): START save output files"
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| 335 | $LS ${aboveOnOffDir}
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| 336 | #use -f option for iput ONLY to force override
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| 337 | if [ ${simulationMode} = "On" ]; then
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| 338 | $ECHO "SIMUL: here we look for output files and put them in Irods"
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| 339 | else
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| 340 | $LS -lrth
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| 341 | $FIND . -name "dataRaw_*" -print | $XARGS -i iput -f -v -K {} ${i}
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| 342 | $FIND . -name "diffOnOffRaw_*" -print | $XARGS -i iput -f -v -K {} ${i}
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| 343 | fi
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| 344 | #save analysis logfile
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| 345 | $LS -l ${tmppublicpath} > /dev/null
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| 346 | $CP ${logFile} ${tmppublicpath}
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| 347 | $ECHO "DEBUG (${scriptName}): END save output files"
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| 348 | #clean up to avoid scratch SIZE EXCEED LIMIT
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| 349 | cd ${aboveOnOffDir}
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| 350 | $LS | $XARGS -i $RM -rf {}
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| 351 |
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| 352 | done
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| 353 |
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| 354 | exit 0
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