| 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 ${scriptName} at `date`"
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| 28 |
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| 29 | #$ECHO "SHOULD BE RETUNED FOR THE inPath cmd line of analyse.cc (Sorry...): 21/7/11 by JEC"
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| 30 | #exit 1
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| 31 |
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| 32 | #Process cmd line args: the -src option is mandatory (source name as Abell85)
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| 33 | sourceRadio=
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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 | -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 [-sim]"
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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 ${scriptName} running in SIMUL mode"
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| 52 | fi
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| 53 |
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| 54 |
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| 55 | if [ "<${sourceRadio}>" = "<>" ]; then
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| 56 | $ECHO "FATAL: You have forgotten to select the source option (-src)"
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| 57 | exit 1
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| 58 | fi
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| 59 |
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| 60 | case ${sourceRadio} in
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| 61 | Abell85) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
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| 62 | Abell2440) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
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| 63 | Abell1205) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
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| 64 | *) ECHO "FATAL (${scriptName}): process ${sourceRadio} not yet foreseen"
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| 65 | exit 1;;
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| 66 | esac
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| 67 |
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| 68 |
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| 69 | srclower=`${ECHO} ${sourceRadio} | ${TR} "[:upper:]" "[:lower:]" `
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| 70 |
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| 71 | #Path to public backupable path
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| 72 | publicpath="/afs/in2p3.fr/home/c/campagne/public"
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| 73 |
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| 74 |
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| 75 | #temporary files to synchronize scripts
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| 76 | tmppublicpath=${TMPPUBLICPATH}
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| 77 | $LS -l ${tmppublicpath} > /dev/null
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| 78 |
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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 | $ECHO "Usage in INTERACTIVE may be destructive... To be used with great care !!!!"
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| 85 | exit 0;
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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 ./${localpath}
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| 97 |
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| 98 | #save the top directory
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| 99 | topDir=`pwd`
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| 100 |
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| 101 | #Path of the utility scripts
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| 102 | scriptpath="/afs/in2p3.fr/home/c/campagne/private/work/AmasNancay"
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| 103 |
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| 104 |
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| 105 | #JEC 1/10/11 Use generic baodaqstatus name
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| 106 | #get the daq current irod status
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| 107 | #tag=`${DATE} +%F`
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| 108 | #OUT1=${publicpath}/baodaqstatus-${tag}.txt
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| 109 | OUT1=${publicpath}/baodaqstatus-current.txt
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| 110 |
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| 111 | if [ ! -e ${OUT1} -o ! -r ${OUT1} ]; then
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| 112 | $ECHO "FATAL (${scriptName}): ${OUT1} has a problem"
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| 113 | exit 1
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| 114 | # $RM -f ${tmppublicpath}/statusdaq.finished
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| 115 | # ${scriptpath}/statusdaq.sh > ${OUT1}
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| 116 | # while [ ! -f "${tmppublicpath}/statusdaq.finished" ]; do
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| 117 | # sleep 30
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| 118 | # done
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| 119 | # $RM ${tmppublicpath}/statusdaq.finished
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| 120 | #protect against remove/rewriting
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| 121 | # $CHMOD -v 444 ${OUT1}
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| 122 | #
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| 123 | fi
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| 124 |
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| 125 | #
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| 126 | #We forbib to perform the gain for all the sources in one shot!
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| 127 | #
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| 128 | #if [ ! "<${sourceRadio}>" = "All" ]; then
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| 129 | $ECHO "You have selected sourceRadio = $sourceRadio"
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| 130 | tableau=( `$GREP -i ${sourceRadio} ${OUT1} | $AWK '( NF==4 ) { print $2 }' ` )
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| 131 | #else
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| 132 | # tableau=( `$CAT ${OUT1} | $AWK '( NF==4 ) { print $2 }'` )
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| 133 | #fi
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| 134 | IFS='
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| 135 | '
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| 136 | tableau=( $( $PRINTF "%s\n" "${tableau[@]}" | $AWK 'x[$0]++ == 0' ) )
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| 137 | IFS=$DefaultIFS
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| 138 |
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| 139 |
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| 140 | for i in ${tableau[@]}
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| 141 | do
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| 142 | $ECHO "DEBUG (${scriptName}): irods root dir $i"
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| 143 | dateDAQ=`$ECHO ${i} | $AWK '{split($0,a,"/"); print a[6];}' | $AWK "{sub(/${srclower}/,\"\"); print}"`
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| 144 | #JEC 1/10/11 Use generic baodaqstatus name
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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 fits file of the gains already exists
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| 163 | alreadyDone=`ils ${i} 2>&1 | $GREP -i "gain_.*\.fits" | $WC -l`
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| 164 | if [ ${alreadyDone} -gt 0 ]; then
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| 165 | $ECHO "INFO (${scriptName}): Fits file for gains already exists"
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| 166 | continue
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| 167 | fi
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| 168 | # Something should be done...
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| 169 | #look if the files for the input to gain computations have been done
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| 170 | somethingTodo=1
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| 171 | input4gainOk1=`ils ${i}/Off 2>&1 | $GREP -i "^ERROR" | $WC -l`
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| 172 | input4gainOk2=`ils ${i}/Off 2>&1 | $GREP -i "gaincycle"`
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| 173 | if [ $input4gainOk1 -eq 0 -a "<${input4gainOk2}>" != "<>" ]; then
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| 174 | gaincycle=`$ECHO ${input4gainOk2} | $AWK '($1 == "C-"){print $2}'| $XARGS -i basename {}`
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| 175 | input4gainOk3=`ils ${i}/Off/${gaincycle} 2>&1 | $GREP -i "medfiltmtx" | $WC -l`
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| 176 | if [ $input4gainOk3 -gt 0 ]; then
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| 177 | somethingTodo=0
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| 178 | fi
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| 179 | fi
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| 180 | if [ $somethingTodo -eq 1 ]; then
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| 181 | #
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| 182 | $ECHO ">>>>>>>>>>>>>>>> Do proc_script $sourceRadio $dateDAQ GAIN"
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| 183 | $RM -f ${tmppublicpath}/proc_script.finished
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| 184 | if [ ${simulationMode} = "On" ]; then
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| 185 | $ECHO "SIMUL: ${scriptpath}/proc_script.sh $sourceRadio $dateDAQ GAIN"
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| 186 | else
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| 187 | ${scriptpath}/proc_script.sh $sourceRadio $dateDAQ GAIN
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| 188 | while [ ! -e "${tmppublicpath}/proc_script.finished" ]; do
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| 189 | $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/proc_script.finished"
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| 190 | date +%T
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| 191 | sleep 60
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| 192 | done
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| 193 | fi
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| 194 | $ECHO "INFO (${scriptName}): proc_script has finished"
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| 195 | $RM ${tmppublicpath}/proc_script.finished
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| 196 | #Todo see if there is errors in the log file before copy
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| 197 | $ECHO ">>>>>>>>>>>>>>>> Done proc_script $sourceRadio $dateDAQ GAIN"
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| 198 | ######
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| 199 | fi
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| 200 | ######
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| 201 | $ECHO ">>>>>>>>>>>>> ANALYSIS Part of ${sourceRadio} ${dateDAQ}"
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| 202 | #go to the .../source/date-sourcelowercase directory
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| 203 | $MKDIR -p ${topDir}/${dateDAQ}${srclower}
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| 204 | cd ${topDir}/${dateDAQ}${srclower}
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| 205 | aboveOnOffDir=`pwd`
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| 206 | $ECHO "DEBUG (${scriptName}): we are in directory: <`pwd`>"
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| 207 | # So the input files are there, so the fits file can be determined
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| 208 | mode="Off"
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| 209 | spectraGenDirName=`$ECHO ${gaincycle} | $AWK '{match($0,"[a-zA-Z]+",arr); print arr[0]}'`
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| 210 | cycleNumber=`$ECHO ${gaincycle} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
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| 211 | #care: the gaincycle variable contains the cycle number
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| 212 | $ECHO "DEBUG (${scriptName}): START download the fits files"
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| 213 | inFileDirectory="./${mode}"
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| 214 | $MKDIR -p ${inFileDirectory}
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| 215 | irodsDownDir="${i}/${mode}/${gaincycle}"
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| 216 | OUT=./getInFits.$$
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| 217 | iget -r -f -K ${irodsDownDir} ${inFileDirectory} > ${OUT} 2>&1
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| 218 | $LS ${inFileDirectory}/${gaincycle}
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| 219 | igetStatus=`$GREP "^ERROR" ${OUT}`
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| 220 | if [ "<$igetStatus>" != "<>" ]; then
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| 221 | $ECHO "FATAL (${scriptName}): error while iget fits files:"
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| 222 | $ECHO $igetStatus
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| 223 | continue
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| 224 | fi
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| 225 | $RM -f ${OUT}
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| 226 | $ECHO "DEBUG (${scriptName}): END download the fits files"
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| 227 | #Get sca files
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| 228 | $ECHO "DEBUG (${scriptName}): START call getscafiles.sh ${sourceRadio} ${dateDAQ}"
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| 229 | OUT1=./getScaStatus.$$
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| 230 | $RM -f ${tmppublicpath}/getscafiles.finished
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| 231 | ${scriptpath}/getscafiles.sh ${sourceRadio} ${dateDAQ} > ${OUT1} 2>&1
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| 232 | while [ ! -f "${tmppublicpath}/getscafiles.finished" ]; do
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| 233 | $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/getscafiles.finished"
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| 234 | date +%T
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| 235 | sleep 30
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| 236 | done
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| 237 | $RM ${tmppublicpath}/getscafiles.finished
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| 238 | $ECHO "DEBUG (${scriptName}): END"
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| 239 | #
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| 240 | getScaStatus=`$GREP "^\(FATAL\|ERROR\)" ${OUT1}`
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| 241 | #
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| 242 | if [ "<${getScaStatus}>" != "<>" ]; then
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| 243 | $ECHO "FATAL (${scriptName}): error to get sca file for $sourceRadio $dateDAQ"
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| 244 | $ECHO "DEBUG (${scriptName}): START with cat ${OUT1}"
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| 245 | $CAT ${OUT1}
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| 246 | $ECHO "DEBUG (${scriptName}): END"
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| 247 | continue
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| 248 | fi
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| 249 | $RM -f ${OUT1}
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| 250 | $ECHO "DEBUG (${scriptName}): where am i `pwd`"
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| 251 | $LS -lrt
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| 252 |
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| 253 | scaFile=`$FIND . -name "sca*.sum.trans" | $XARGS -i basename {}`
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| 254 | #
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| 255 | #the default spectra name is medfiltmtx, otherwise use -specname <a_string>
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| 256 | logFile="analyse_GAIN_${sourceRadio}_${dateDAQ}.log"
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| 257 | $ECHO "DEBUG (${scriptName}): execute the analysis... should not take long. `date`"
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| 258 | if [ ${simulationMode} = "On" ]; then
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| 259 | $ECHO "SIMUL: ${scriptpath}/Objs/analyse -act gain -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir ${spectraGenDirName} -mode ${mode} -numcycle ${cycleNumber},${cycleNumber} -debug 1 >& ${logFile}"
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| 260 | cat > ${logFile} <<EOF
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| 261 | Ok gain finished
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| 262 | EOF
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| 263 |
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| 264 | else
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| 265 | ${scriptpath}/Objs/analyse -act gain -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir ${spectraGenDirName} -mode ${mode} -numcycle ${cycleNumber},${cycleNumber} -debuglev 1 >& ${logFile}
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| 266 | fi
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| 267 | #
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| 268 | $ECHO "DEBUG (${scriptName}): analysis finished `date`. Look for errors before saving to Irods"
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| 269 | rcstatus=`$GREP -i "OK gain finished" ${logFile} | $WC -l`
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| 270 | if [ ${rcstatus} -eq 0 ]; then
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| 271 | $ECHO "INFO (${scriptName}): analysis problem for ${sourceRadio} ${dateDAQ}"
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| 272 | $ECHO " START logfile"
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| 273 | $CAT ${logFile}
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| 274 | $ECHO " END logFile"
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| 275 | #clean and leave
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| 276 | cd ${aboveOnOffDir}
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| 277 | $RM -rf ./*
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| 278 | continue
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| 279 | fi
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| 280 | #Save into Irods
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| 281 | $ECHO "DEBUG (${scriptName}): START save output files"
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| 282 | $LS ${aboveOnOffDir}
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| 283 | #use -f option of iput ONLY to force override
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| 284 | if [ ${simulationMode} = "On" ]; then
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| 285 | $ECHO "SIMUL: here we look for gain file and put them in Irods"
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| 286 | else
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| 287 | $FIND . -name "gain_*" -print | $XARGS -i iput -v -K {} ${i}
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| 288 | fi
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| 289 | #save analysis logfile
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| 290 | $LS -l ${tmppublicpath} > /dev/null
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| 291 | $CP ${logFile} ${tmppublicpath}
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| 292 | $ECHO "DEBUG (${scriptName}): END save output files"
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| 293 | #clean
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| 294 | cd ${aboveOnOffDir}
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| 295 | $RM -rf ./*
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| 296 | done
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| 297 |
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| 298 | exit 0 |
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