| 1 | #!/bin/sh -xvf
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| 2 | #download SCA file, proceed to introspection, and upload results
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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 | freqBAOCalib=1346
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| 33 | bwBAOCalib=6.25
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| 34 | #use -sim option to simulate processing (debug the script as if...)
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| 35 | simulationMode=Off
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| 36 | while [ $# -gt 0 ]
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| 37 | do
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| 38 | case "$1" in
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| 39 | -src) sourceRadio=$2; shift;;
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| 40 | -freq) freqBAOCalib=$2; shift;;
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| 41 | -bwd) bwBAOCalib=$2; shift;;
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| 42 | -sim) simulationMode=On; shift;;
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| 43 | -h)
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| 44 | echo >&2 \
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| 45 | "usage: $0 -src souce [-freq freq in MHz (default ${freqBAOCalib})] [-bwd bandwidth in MHz (default ${bwBAOCalib})]"
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| 46 | exit 1;;
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| 47 | *) break;; # terminate while loop
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| 48 | esac
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| 49 | shift
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| 50 | done
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| 51 |
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| 52 | if [ ${simulationMode} = "On" ]; then
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| 53 | $ECHO "INFO ${scriptName} running in SIMUL mode"
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| 54 | fi
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| 55 |
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| 56 | if [ "<${sourceRadio}>" = "<>" ]; then
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| 57 | $ECHO "FATAL: You have forgotten to select the source option (-src)"
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| 58 | exit 1
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| 59 | fi
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| 60 |
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| 61 | case ${sourceRadio} in
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| 62 | Abell85) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
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| 63 | Abell2440) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
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| 64 | Abell1205) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
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| 65 | *) ECHO "FATAL (${scriptName}): process ${sourceRadio} not yet foreseen"
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| 66 | exit 1;;
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| 67 | esac
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| 68 |
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| 69 | srclower=`${ECHO} ${sourceRadio} | ${TR} "[:upper:]" "[:lower:]" `
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| 70 |
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| 71 | #Path to public backupable path
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| 72 | publicpath="/afs/in2p3.fr/home/c/campagne/public"
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| 73 |
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| 74 |
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| 75 | #temporary files to synchronize scripts
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| 76 | tmppublicpath="/sps/baoradio/AmasNancay"
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| 77 | #wakeup the NFS disk
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| 78 | $LS -l ${tmppublicpath} > /dev/null
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| 79 | #clean previous spurious files
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| 80 | $RM -f ${tmppublicpath}/*.finished
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| 81 |
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| 82 | #Path where the job will do temporary IO
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| 83 | if [ ${ENVIRONMENT} = "INTERACTIVE" ]; then
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| 84 | iojobpath="/sps/baoradio/AmasNancay/JEC"
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| 85 | $MKDIR -p $iojobpath
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| 86 | elif [ ${ENVIRONMENT} = "BATCH" ] ; then
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| 87 | iojobpath=${TMPBATCH}
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| 88 | else
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| 89 | $ECHO "FATAL (${scriptName}): environment is ${ENVIRONMENT} not allowed"
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| 90 | exit 1
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| 91 | fi
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| 92 | cd ${iojobpath}
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| 93 |
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| 94 | localpath="${sourceRadio}"
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| 95 | $MKDIR -p ./${localpath}
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| 96 | cd ./${localpath}
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| 97 |
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| 98 | #save the top directory
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| 99 | topDir=`pwd`
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| 100 |
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| 101 | #Path of the utility scripts
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| 102 | scriptpath="/afs/in2p3.fr/home/c/campagne/private/work/AmasNancay"
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| 103 |
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| 104 | #get the daq current irod status
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| 105 | tag=`${DATE} +%F`
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| 106 | OUT1=${publicpath}/baodaqstatus-${tag}.txt
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| 107 |
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| 108 | if [ ! -e ${OUT1} -o ! -r ${OUT1} ]; then
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| 109 | $ECHO "We should bring the DAQ status more up to date, this take 1 or 2sec..."
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| 110 | $RM -f ${tmppublicpath}/statusdaq.finished
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| 111 | ${scriptpath}/statusdaq.sh > ${OUT1}
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| 112 | while [ ! -f "${tmppublicpath}/statusdaq.finished" ]; do
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| 113 | sleep 30
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| 114 | done
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| 115 | $RM ${tmppublicpath}/statusdaq.finished
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| 116 | #protect against remove/rewriting
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| 117 | $CHMOD -v 444 ${OUT1}
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| 118 | fi
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| 119 |
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| 120 |
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| 121 | #Nb: if we want to implement a loop on sources we have to take care of srclower...
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| 122 |
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| 123 | $ECHO "You have selected sourceRadio = $sourceRadio"
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| 124 | tableau=( `$GREP -i ${sourceRadio} ${OUT1} | $AWK '( NF==4 ) { print $2 }' ` )
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| 125 | IFS='
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| 126 | '
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| 127 | tableau=( $( $PRINTF "%s\n" "${tableau[@]}" | $AWK 'x[$0]++ == 0' ) )
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| 128 | IFS=$DefaultIFS
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| 129 |
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| 130 |
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| 131 | for i in ${tableau[@]}
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| 132 | do
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| 133 | #
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| 134 | # start a "fresh" session
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| 135 | cd ${topDir}
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| 136 | $LS | $XARGS -i $RM -rf {}
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| 137 |
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| 138 | $ECHO "DEBUG: (${scriptName}) irods root dir $i"
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| 139 | dateDAQ=`$ECHO ${i} | $AWK '{split($0,a,"/"); print a[6];}' | $AWK "{sub(/${srclower}/,\"\"); print}"`
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| 140 |
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| 141 | $ECHO "DEBUG: (${scriptName}): we are in directory `pwd` the topDir=${topDir}"
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| 142 | $LS -lrt
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| 143 |
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| 144 |
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| 145 | #Look if the date has changed since beginning of the job!
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| 146 | curtag=`${DATE} +%F`
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| 147 | if [ "<${curtag}>" != "<${tag}>" ]; then
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| 148 | tag=${curtag}
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| 149 | #it is necessary to update the daq status as the day has changed during the processing... (batch can take a long time...)
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| 150 | OUT1=${publicpath}/baodaqstatus-${curtag}.txt
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| 151 | $ECHO "We should bring the DAQ status more up to date, this take 1 or 2sec..."
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| 152 | $RM -f ${tmppublicpath}/statusdaq.finished
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| 153 | ${scriptpath}/statusdaq.sh > ${OUT1}
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| 154 | while [ ! -f "${tmppublicpath}/statusdaq.finished" ]; do
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| 155 | sleep 30
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| 156 | done
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| 157 | $RM ${tmppublicpath}/statusdaq.finished
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| 158 | #protect against remove/rewriting
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| 159 | $CHMOD -v 444 ${OUT1}
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| 160 | fi
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| 161 | #
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| 162 | # look if the calibration files already exist
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| 163 | #
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| 164 | alreadyDone=`ils ${i} 2>&1 | $GREP -i "calib_.*\.txt" | $WC -l`
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| 165 | if [ ${alreadyDone} -gt 0 ]; then
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| 166 | $ECHO "INFO (${scriptName}): calibration coef files already exist"
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| 167 | continue
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| 168 | fi
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| 169 | #
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| 170 | somethingTodo=1
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| 171 | input4calibOff=`ils ${i}/Off 2>&1 | $GREP -i "calibcycle" | $AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.11n`
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| 172 | input4calibOn=`ils ${i}/On 2>&1 | $GREP -i "calibcycle" | $AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.11n`
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| 173 | #
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| 174 | if [ "<${input4calibOff}>" != "<>" -a "<${input4calibOn}>" != "<>" ]; then
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| 175 | #look at the content of the calibcycle directory as may be the previous batch job has crashed
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| 176 | tableauOff=( `$ECHO ${input4calibOff}` )
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| 177 | IFS='
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| 178 | '
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| 179 | tableauOff=( $( $PRINTF "%s\n" "${tableauOff[@]}" | $AWK 'x[$0]++ == 0' ) )
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| 180 | IFS=$DefaultIFS
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| 181 | #
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| 182 | nTotFilesOff=0
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| 183 | for j in ${tableauOff[@]}
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| 184 | do
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| 185 | nFiles=`ils ${i}/Off/${j} | $GREP -i "medfiltmtx" | $WC -l`
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| 186 | nTotFilesOff=`expr ${nTotFilesOff} + ${nFiles}`
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| 187 | done
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| 188 | #
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| 189 | tableauOn=( `$ECHO ${input4calibOn}` )
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| 190 | IFS='
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| 191 | '
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| 192 | tableauOn=( $( $PRINTF "%s\n" "${tableauOn[@]}" | $AWK 'x[$0]++ == 0' ) )
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| 193 | IFS=$DefaultIFS
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| 194 | #
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| 195 | nTotFilesOn=0
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| 196 | for j in ${tableauOn[@]}
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| 197 | do
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| 198 | nFiles=`ils ${i}/On/${j} | $GREP -i "medfiltmtx" | $WC -l`
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| 199 | nTotFilesOn=`expr ${nTotFilesOn} + ${nFiles}`
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| 200 | done
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| 201 | diffOnOff=`expr ${nTotFilesOff} - ${nTotFilesOn}`
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| 202 | if [ ${diffOnOff} -lt 0 ]; then
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| 203 | zero=0
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| 204 | diffOnOff=`expr ${zero} - ${diffOnOff}`
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| 205 | fi
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| 206 | #allow up to 5 files differences
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| 207 | if [ ${nTotFilesOff} -gt 0 -a ${nTotFilesOn} -gt 0 ]; then
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| 208 | somethingTodo=0
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| 209 | $ECHO "DEBUG (${scriptName}): $sourceRadio $dateDAQ has <${nTotFilesOff}> Off-files and <${nTotFilesOn}> On-files but OK"
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| 210 | else
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| 211 | $ECHO "INFO (${scriptName}): $sourceRadio $dateDAQ has <${nTotFilesOff}> Off-files and <${nTotFilesOn}> On-files => one should rebuild has something is wrong"
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| 212 | fi
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| 213 | #
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| 214 | fi
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| 215 | if [ ${somethingTodo} -eq 1 ]; then
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| 216 | #
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| 217 | $ECHO ">>>>>>>>>>>>>>>> Do $sourceRadio $dateDAQ CALIBOFF"
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| 218 | $RM -f ${tmppublicpath}/proc_script.finished
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| 219 | if [ ${simulationMode} = "On" ]; then
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| 220 | $ECHO "SIMUL: ${scriptpath}/proc_script.sh $sourceRadio $dateDAQ CALIBOFF"
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| 221 | else
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| 222 | ${scriptpath}/proc_script.sh $sourceRadio $dateDAQ CALIBOFF
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| 223 | while [ ! -e "${tmppublicpath}/proc_script.finished" ]; do
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| 224 | $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/proc_script.finished"
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| 225 | date +%T
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| 226 | sleep 60
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| 227 | done
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| 228 | fi
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| 229 | $ECHO "INFO (${scriptName}): proc_script has finished"
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| 230 | $ECHO ">>>>>>>>>>>> Done $sourceRadio $dateDAQ CALIBOFF"
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| 231 | $ECHO ">>>>>>>>>>>>>>>> Do $sourceRadio $dateDAQ CALIBON"
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| 232 | $RM ${tmppublicpath}/proc_script.finished
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| 233 |
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| 234 | if [ ${simulationMode} = "On" ]; then
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| 235 | $ECHO "SIMUL: ${scriptpath}/proc_script.sh $sourceRadio $dateDAQ CALIBON"
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| 236 | else
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| 237 | ${scriptpath}/proc_script.sh $sourceRadio $dateDAQ CALIBON
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| 238 | while [ ! -e "${tmppublicpath}/proc_script.finished" ]; do
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| 239 | $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/proc_script.finished"
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| 240 | date +%T
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| 241 | sleep 60
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| 242 | done
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| 243 | fi
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| 244 | $ECHO "INFO (${scriptName}): proc_script has finished"
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| 245 | $RM ${tmppublicpath}/proc_script.finished
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| 246 | #Todo see if there is errors in the log file before copy
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| 247 | $ECHO ">>>>>>>>>>>> Done $sourceRadio $dateDAQ CALIBON"
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| 248 | ######
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| 249 | else
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| 250 | ######
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| 251 | $ECHO ">>>>>>>>>>>>> ANALYSIS Part of ${sourceRadio} ${dateDAQ}"
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| 252 | #go to the .../source/date-sourcelowercase directory
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| 253 | #download Off/calibcycle<> and On/calibcycle<> directories
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| 254 | $MKDIR -p ${topDir}/${dateDAQ}${srclower}
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| 255 | cd ${topDir}/${dateDAQ}${srclower}
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| 256 | aboveOnOffDir=`pwd`
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| 257 | $ECHO "DEBUG (${scriptName}): we are in directory: <`pwd`>"
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| 258 | #
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| 259 | mode="Off"
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| 260 | $ECHO "DEBUG (${scriptName}): START download the ${mode} calib fits files"
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| 261 | inFileDirectory="./${mode}"
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| 262 | $MKDIR -p ${inFileDirectory}
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| 263 | 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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| 264 | IFS='
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| 265 | '
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| 266 | listOfCalibCycle=( $( $PRINTF "%s\n" "${listOfCalibCycle[@]}" | $AWK 'x[$0]++ == 0' ) )
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| 267 | IFS=$DefaultIFS
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| 268 |
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| 269 | firstCycleOff=`$ECHO ${listOfCalibCycle[0]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
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| 270 | nCyclesOff=`expr ${#listOfCalibCycle[*]} - 1`
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| 271 |
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| 272 | lastCycleOff=`$ECHO ${listOfCalibCycle[${nCyclesOff}]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
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| 273 |
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| 274 | listOfCalibCycle=( "${listOfCalibCycle[@]/#/${i}/${mode}/}" )
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| 275 |
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| 276 |
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| 277 | for j in ${listOfCalibCycle[@]}
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| 278 | do
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| 279 | irodsDownDir="${j}"
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| 280 | OUT=./getInFits.$$
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| 281 | iget -r -f -K ${irodsDownDir} ${inFileDirectory} > ${OUT} 2>&1
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| 282 | igetStatus=`$GREP "^ERROR" ${OUT}`
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| 283 | if [ "<$igetStatus>" != "<>" ]; then
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| 284 | $ECHO "FATAL (${scriptName}): error while iget fits files:"
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| 285 | $ECHO $igetStatus
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| 286 | $ECHO " ==> skip this run $sourceRadio $dateDAQ"
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| 287 | continue
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| 288 | fi
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| 289 | $RM -f ${OUT}
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| 290 | done
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| 291 | $ECHO "DEBUG (${scriptName}): END download the ${mode} calib fits files"
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| 292 | #
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| 293 | mode="On"
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| 294 | $ECHO "DEBUG (${scriptName}): START download the ${mode} calib fits files"
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| 295 | inFileDirectory="./${mode}"
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| 296 | $MKDIR -p ${inFileDirectory}
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| 297 |
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| 298 | 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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| 299 | IFS='
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| 300 | '
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| 301 | listOfCalibCycle=( $( $PRINTF "%s\n" "${listOfCalibCycle[@]}" | $AWK 'x[$0]++ == 0' ) )
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| 302 | IFS=$DefaultIFS
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| 303 |
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| 304 | firstCycleOn=`$ECHO ${listOfCalibCycle[0]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
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| 305 | nCyclesOn=`expr ${#listOfCalibCycle[*]} - 1`
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| 306 |
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| 307 | lastCycleOn=`$ECHO ${listOfCalibCycle[${nCyclesOn}]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
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| 308 |
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| 309 | listOfCalibCycle=( "${listOfCalibCycle[@]/#/${i}/${mode}/}" )
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| 310 |
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| 311 |
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| 312 | #
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| 313 | #Check if there is the same number of cycles in Off and On mode
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| 314 | #
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| 315 | #first cycle = max(firstCycleOn, firstCycleOff)
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| 316 | #last cycle = min(lastCycleOn,lastCycleOff)
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| 317 |
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| 318 | if [ ${firstCycleOn} -eq ${firstCycleOff} -a ${lastCycleOn} -eq ${lastCycleOff} ]; then
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| 319 | firstCycle=${firstCycleOff}
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| 320 | lastCycle=${lastCycleOff}
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| 321 | else
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| 322 | $ECHO "INFO (${scriptName}): missmatch between Off and On mode"
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| 323 | $ECHO "${firstCycleOn} != ${firstCycleOff} OR ${lastCycleOn} != ${lastCycleOff}"
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| 324 | firstCycle=${firstCycleOff}
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| 325 | if [ ${firstCycleOn} -gt ${firstCycle} ]; then
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| 326 | firstCycle=${firstCycleOn}
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| 327 | fi
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| 328 | lastCycle=${lastCycleOff}
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| 329 | if [ ${lastCycleOn} -lt ${lastCycle} ]; then
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| 330 | lastCycle=${lastCycleOn}
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| 331 | fi
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| 332 | fi
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| 333 | $ECHO "INFO (${scriptName}): use cycles [${firstCycle}, ${lastCycle}]"
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| 334 |
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| 335 |
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| 336 | for j in ${listOfCalibCycle[@]}
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| 337 | do
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| 338 | irodsDownDir="${j}"
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| 339 | OUT=./getInFits.$$
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| 340 | iget -r -f -K ${irodsDownDir} ${inFileDirectory} > ${OUT} 2>&1
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| 341 | igetStatus=`$GREP "^ERROR" ${OUT}`
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| 342 | if [ "<$igetStatus>" != "<>" ]; then
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| 343 | $ECHO "FATAL (${scriptName}): error while iget fits files:"
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| 344 | $ECHO $igetStatus
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| 345 | $ECHO " ==> skip this run $sourceRadio $dateDAQ"
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| 346 | continue
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| 347 | fi
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| 348 | $RM -f ${OUT}
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| 349 | done
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| 350 | $ECHO "DEBUG (${scriptName}): END download the ${mode} calib fits files"
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| 351 | #Get sca file
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| 352 | $ECHO "DEBUG (${scriptName}): START call getscafiles.sh ${sourceRadio} ${dateDAQ}"
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| 353 | OUT1=./getScaStatus.$$
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| 354 | $RM -f ${tmppublicpath}/getscafiles.finished
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| 355 | ${scriptpath}/getscafiles.sh ${sourceRadio} ${dateDAQ} > ${OUT1} 2>&1
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| 356 | while [ ! -f "${tmppublicpath}/getscafiles.finished" ]; do
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| 357 | $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/getscafiles.finished"
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| 358 | date +%T
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| 359 | sleep 30
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| 360 | done
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| 361 | $RM ${tmppublicpath}/getscafiles.finished
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| 362 | $ECHO "DEBUG (${scriptName}): END"
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| 363 | #
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| 364 | getScaStatus=`$GREP "^\(FATAL\|ERROR\)" ${OUT1}`
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| 365 | #
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| 366 | if [ "<${getScaStatus}>" != "<>" ]; then
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| 367 | $ECHO "FATAL (${scriptName}): error to get sca file for $sourceRadio $dateDAQ"
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| 368 | $ECHO "DEBUG (${scriptName}): START with cat ${OUT1}"
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| 369 | $CAT ${OUT1}
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| 370 | $ECHO "DEBUG (${scriptName}): END"
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| 371 | continue
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| 372 | fi
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| 373 | $RM -f ${OUT1}
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| 374 |
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| 375 | scaFile=`$FIND . -name "sca*.sum.trans" | $XARGS -i basename {}`
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| 376 |
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| 377 | #prepare job submission
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| 378 | cd ${aboveOnOffDir}
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| 379 | #the default spectra name is medfiltmtx, otherwise use -specname <a_string>
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| 380 |
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| 381 | logFile="analyse_CALIB_${sourceRadio}_${dateDAQ}.log"
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| 382 | $ECHO "DEBUG (${scriptName}): execute the analysis... should not take long. `date`"
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| 383 | if [ ${simulationMode} = "On" ]; then
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| 384 | $ECHO "SIMUL: ${scriptpath}/Objs/analyse -act calib -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir calibcycle -numcycle ${firstCycle},${lastCycle} -calibopt mean -debuglev 1 -freqBAOCalib ${freqBAOCalib} -bwBAOCalib ${bwBAOCalib} >& ${logFile}"
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| 385 | cat > ${logFile} <<EOF
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| 386 | Ok calibration finished
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| 387 | EOF
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| 388 | else
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| 389 | ${scriptpath}/Objs/analyse -act calib -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir calibcycle -numcycle ${firstCycle},${lastCycle} -calibopt mean -debuglev 1 -freqBAOCalib ${freqBAOCalib} -bwBAOCalib ${bwBAOCalib} >& ${logFile}
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| 390 | fi
|
|---|
| 391 | $ECHO "DEBUG (${scriptName}): analysis finished `date`. Look for errors before saving to Irods"
|
|---|
| 392 | rcstatus=`$GREP -i "Ok calibration finished" ${logFile} | $WC -l`
|
|---|
| 393 | if [ ${rcstatus} -eq 0 ]; then
|
|---|
| 394 | $ECHO "INFO (${scriptName}): analysis problem for ${sourceRadio} ${dateDAQ}"
|
|---|
| 395 | $ECHO " START logfile"
|
|---|
| 396 | $CAT ${logFile}
|
|---|
| 397 | $ECHO " END logFile"
|
|---|
| 398 | #clean and leave
|
|---|
| 399 | cd ${aboveOnOffDir}
|
|---|
| 400 | $LS | $XARGS -i $RM -rf {}
|
|---|
| 401 | continue
|
|---|
| 402 | fi
|
|---|
| 403 | #Save into Irods
|
|---|
| 404 | $ECHO "DEBUG (${scriptName}): START save output files"
|
|---|
| 405 | $LS ${aboveOnOffDir}
|
|---|
| 406 | #use -f option for iput ONLY to force override
|
|---|
| 407 | if [ ${simulationMode} = "On" ]; then
|
|---|
| 408 | $ECHO "SIMUL: here we look for calib file and put them in Irods"
|
|---|
| 409 | else
|
|---|
| 410 | $FIND . -name "calib_*" -print | $XARGS -i iput -v -K {} ${i}
|
|---|
| 411 | fi
|
|---|
| 412 | #save analysis logfile
|
|---|
| 413 | $LS -l ${tmppublicpath} > /dev/null
|
|---|
| 414 | $CP ${logFile} ${tmppublicpath}
|
|---|
| 415 | $ECHO "DEBUG (${scriptName}): END save output files"
|
|---|
| 416 | #clean up to avoid scratch SIZE EXCEED LIMIT
|
|---|
| 417 | cd ${aboveOnOffDir}
|
|---|
| 418 | $LS | $XARGS -i $RM -rf {}
|
|---|
| 419 | fi
|
|---|
| 420 | done
|
|---|
| 421 |
|
|---|
| 422 | exit 0
|
|---|
