| 1 | #!/bin/bash
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| 2 |
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| 3 | # missing
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| 4 | # entry in status table
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| 5 |
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| 6 | # options:
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| 7 | skipmd5sum="no" # fill md5 sums in any case
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| 8 | skipmd5sum="iffilled" # fill md5 sum only if they are not yet in db
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| 9 | #skipmd5sum="yes" # do not fill md5 sums in any case
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| 10 |
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| 11 | doupdate="yes" # update all entries
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| 12 | doupdate="no" # fill only entries which are not yet existing
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| 13 |
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| 14 | source `dirname $0`/Sourcefile.sh
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| 15 | printprocesslog "INFO starting $0 with options doupdate="$doupdate" and skipmd5sum="$skipmd5sum
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| 16 |
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| 17 | # setup to use ftools
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| 18 | source $HEADAS/headas-init.sh
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| 19 |
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| 20 | pwfile=`dirname $0`/.pw
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| 21 | password=`cat $pwfile 2>/dev/null`
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| 22 | if [ "$password" == "" ]
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| 23 | then
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| 24 | echo "please insert password in $pwfile"
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| 25 | printprocesslog "ERROR password for DB access in $pwfile missing"
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| 26 | finish
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| 27 | fi
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| 28 |
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| 29 | # check if software is available
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| 30 | if ! ls $factpath/fitsdump >/dev/null 2>&1
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| 31 | then
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| 32 | printprocesslog "ERROR "$factpath"/fitsdump is not available."
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| 33 | finish
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| 34 | fi
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| 35 |
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| 36 | # get last 3 nights
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| 37 | dates=( `date +%Y/%m/%d --date="-12hour"` `date +%Y/%m/%d --date="-36hour"` )
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| 38 | #dates=( `find /loc_data/zipraw/ -mindepth 3 -type d | sort | sed -e 's/\/loc_data\/zipraw\///g'` ) #all available dates in /loc_data/zipraw
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| 39 |
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| 40 | # do check for rawfiles of these dates
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| 41 | for date in ${dates[@]}
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| 42 | do
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| 43 | ziprawdir=/loc_data/zipraw/$date
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| 44 | # check if data are available from that night
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| 45 | if ! [ -d $ziprawdir ]
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| 46 | then
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| 47 | printprocesslog "INFO "$ziprawdir" does not exist."
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| 48 | continue
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| 49 | else
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| 50 | printprocesslog "INFO processing "$ziprawdir"..."
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| 51 | fi
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| 52 |
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| 53 | # find all fits.gz files starting with the oldest file
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| 54 | printprocesslog "INFO finding files to be checked in $ziprawdir..."
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| 55 | fitsgzfiles=`find $ziprawdir -type f -name '*.fits.gz'| sort `
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| 56 |
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| 57 | # get runnumber from date
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| 58 | runnumber=`echo $date | sed -e 's/\///g'`
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| 59 |
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| 60 | # loop to check files
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| 61 | for file in $fitsgzfiles
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| 62 | do
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| 63 | printprocesslog "INFO checking file "$file
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| 64 |
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| 65 | # raw and original file
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| 66 | rawfile=`echo $file | sed -e 's/zipraw/raw/' -e 's/fits[.]gz/fits/'`
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| 67 | origfile=`echo $rawfile | sed -e 's/loc_data/daq/'`
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| 68 |
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| 69 | # check if raw file was changed in the last 30 minutes
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| 70 | isnew=`find $file -cmin -30`
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| 71 | if [ "$isnew" != "" ]
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| 72 | then
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| 73 | printprocesslog "INFO "$file" is not older than 30 min. -> continue"
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| 74 | continue
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| 75 | fi
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| 76 |
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| 77 | # check if it is drs file
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| 78 | isnew=`ls $file | grep drs`
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| 79 | if [ "$isnew" != "" ]
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| 80 | then
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| 81 | printprocesslog "INFO "$file" is a drs file. -> continue"
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| 82 | continue
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| 83 | fi
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| 84 |
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| 85 | # check if file is already finished
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| 86 | # original file on daq (if data was taken on daq
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| 87 | if [ -e $origfile ]
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| 88 | then
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| 89 | # get time of last modification as seconds since Epoch for both files
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| 90 | timeorig=`stat -c %Y $origfile`
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| 91 | timecopy=`stat -c %Y $rawfile`
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| 92 | # compare times
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| 93 | if ! [ $timeorig -eq $timecopy ]
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| 94 | then
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| 95 | # if times are not the same, the file is still open => no check
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| 96 | printprocesslog "INFO file "$rawfile" not yet closed. -> continue"
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| 97 | continue
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| 98 | fi
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| 99 | else
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| 100 | # if the origfile doesn't exist, the data was probably written not on daq but on data
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| 101 | printprocesslog "INFO file "$rawfile" was probably taken on data and not daq."
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| 102 | fi
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| 103 |
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| 104 | # get run and file number form filename
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| 105 | runnumbererror="no"
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| 106 | numbererror="no"
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| 107 | numberfromname=`echo $file | grep -E -o '20[1-9][0-9][01][0-9][0-3][0-9]_[0-9]{3}'`
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| 108 | runnumberfromname=`echo $numberfromname | cut -d_ -f1`
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| 109 | filenumberfromname=`echo $numberfromname | cut -d_ -f2 | sed -e 's/^0//g' -e 's/^0//g'`
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| 110 | if [ "$runnumber" != "$runnumberfromname" ]
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| 111 | then
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| 112 | runnumbererror="yes"
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| 113 | printprocesslog "ERROR for file "$file": runnumber from date ("$runnumber") and filename ("$runnumberfromname") don't agree."
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| 114 | fi
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| 115 |
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| 116 | # check if entry already exists
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| 117 | query3="SELECT fRunNumber FROM RunInfo WHERE Concat(fRunNumber, '_', LPAD(fFileNumber, 3, 0))='"$numberfromname"'"
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| 118 | printprocesslog "DEBUG check if entry already exists in DB. QUERY: "$query3
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| 119 | result3=`/usr/bin/mysql -u operator --host=fact01.fact.local --password=$password FactData -e "$query3"`
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| 120 |
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| 121 | # only proceed with file
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| 122 | # if information is not yet in database
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| 123 | # and no update is wished ($doupdate)
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| 124 | if [ "$result3" != "" ] && [ "$doupdate" == "no" ]
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| 125 | then
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| 126 | printprocesslog "INFO "$file" has been inserted already. -> continue "
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| 127 | continue
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| 128 | fi
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| 129 |
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| 130 | runtype=
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| 131 | # check if fits file is corrupted
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| 132 | numfitserrors=0
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| 133 | checkfitsfile=`fverify $rawfile | grep '0 error(s)'`
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| 134 | if [ "$checkfitsfile" == "" ]
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| 135 | then
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| 136 | numfitserrors=1
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| 137 | fi
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| 138 |
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| 139 | if [ $numfitserrors -eq 0 ]
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| 140 | then
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| 141 | # get run and file number from file
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| 142 | runnumberfromfile=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep NIGHT | grep -E -o '20[1-9][0-9][01][0-9][0-3][0-9]'`
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| 143 | filenumberfromfileorig=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep RUNID | grep -E -o '[0-9]{1,3}'`
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| 144 | if [ "$runnumberfromfile" = "" ] || [ "$filenumberfromfileorig" = "" ]
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| 145 | then
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| 146 | printprocesslog "ERROR couldn't get run or file number from file name ("$file")."
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| 147 | fi
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| 148 | numberfromfile=$runnumberfromfile"_"`printf %03d $filenumberfromfileorig`
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| 149 | # compare numbers
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| 150 | if [ "$numberfromfile" != "$numberfromname" ]
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| 151 | then
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| 152 | numbererror="yes"
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| 153 | printprocesslog "ERROR for file "$file": number from filename ("$numberfromname") and file ("$numberfromfile") don't agree."
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| 154 | fi
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| 155 |
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| 156 | # check if this run has drs file
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| 157 | # in case file is available, get STEP from header
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| 158 | # in the very beginning only drs-files were existing
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| 159 | # in the beginning the keywords DRSCALIB and STEP were not existing
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| 160 | step=
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| 161 | drsfile=`echo $file | sed -e 's/fits/drs.fits/'`
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| 162 | numdrsfiles=`ls $drsfile 2>/dev/null | wc -l`
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| 163 | drscalib=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep DRSCALIB | grep -E -o "['][TF][']" | sed -e "s/'//g"`
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| 164 | if [ "$drscalib" == "T" ]
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| 165 | then
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| 166 | step=`$factpath/fitsdump -h -t Events $drsfile 2>/dev/null | grep STEP | grep -E -o "['][012][']" | sed -e "s/'//g"`
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| 167 | if ! [ $numdrsfiles -eq 1 ]
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| 168 | then
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| 169 | printprocesslog "ERROR for file "$file" number of drsfiles ("$numdrsfiles") and information from header ("$drscalib") don't agree."
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| 170 | fi
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| 171 | fi
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| 172 |
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| 173 | # get other variables from header
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| 174 | runtype=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep RUNTYPE | grep -E -o "['][a-z0-9._-]+[']" | sed -e "s/'//g" -e "s/_/-/g" -e "s/[.]//g"`
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| 175 | #echo "runtype for file "$file": "$runtype
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| 176 | roi=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep NROI | grep -v NROITM | grep -E -o '[0-9]{1,4}'`
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| 177 | roitm=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep NROITM | grep -E -o '[0-9]{1,4}'`
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| 178 | numevents=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep Events | grep -E -o '[0-9]+'`
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| 179 | numphys=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRG ' | grep -E -o '[0-9]+'`
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| 180 | numext1=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGEXT1' | grep -E -o '[ ][0-9]+[ ]' | sed -e 's/\ //g'`
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| 181 | numext2=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGEXT2' | grep -E -o '[ ][0-9]+[ ]' | sed -e 's/\ //g'`
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| 182 | numelp=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGLPE' | grep -E -o '[0-9]+'`
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| 183 | numilp=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGLPI' | grep -E -o '[0-9]+'`
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| 184 | numoth=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGMISC' | grep -E -o '[0-9]+'`
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| 185 | numped=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGPED' | grep -E -o '[0-9]+'`
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| 186 | numtime=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGTIM' | grep -E -o '[0-9]+'`
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| 187 | # in newest data start time is in DATE-OBS
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| 188 | # in older data start time is in TSTART
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| 189 | # in the beginning TSTART was empty
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| 190 | runstart=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep DATE-OBS | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 191 | runstart2=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep TSTART | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 192 | if [ "$runstart" == "" ]
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| 193 | then
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| 194 | if [ "$runstart2" == "" ]
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| 195 | then
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| 196 | runstart=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep DATE | grep -v 'DATE-' | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 197 | else
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| 198 | runstart=$runstart2
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| 199 | fi
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| 200 | fi
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| 201 | # in newest data start time is in DATE-END
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| 202 | # in older data start time is in TSTOP
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| 203 | # in the beginning TSTOP was empty
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| 204 | runstop=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep DATE-END | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 205 | runstop2=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep TSTOP | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 206 | if [ "$runstop" == "" ]
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| 207 | then
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| 208 | if [ "$runstop2" == "" ]
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| 209 | then
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| 210 | runstop=`stat $file 2>/dev/null | grep Modify | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9][ ][0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{9}'`
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| 211 | else
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| 212 | runstop=$runstop2
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| 213 | fi
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| 214 | fi
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| 215 | fi
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| 216 |
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| 217 | # set runtype to 'unknown', if no runtype could be retrieved from file
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| 218 | if [ "$runtype" == "" ]
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| 219 | then
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| 220 | runtype="n/a"
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| 221 | fi
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| 222 | # on 15.11.2011 the runtypes had different names
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| 223 | if [ "$date" == "2011/11/15" ]
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| 224 | then
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| 225 | if [ "$runtype" == "drs-calib" ]
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| 226 | then
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| 227 | runtype="drs-gain"
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| 228 | fi
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| 229 | if [ "$runtype" == "drs-time-calib" ]
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| 230 | then
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| 231 | runtype="drs-time"
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| 232 | fi
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| 233 | if [ "$runtype" == "pedestal" ]
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| 234 | then
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| 235 | runtype="drs-pedestal"
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| 236 | fi
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| 237 | if [ "$runtype" == "light-pulser" ]
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| 238 | then
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| 239 | runtype="light-pulser-ext"
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| 240 | fi
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| 241 | if [ "$runtype" == "pedestal-on" ]
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| 242 | then
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| 243 | runtype="pedestal"
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| 244 | fi
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| 245 | fi
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| 246 | # get runtype
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| 247 | query2="SELECT fRunTypeKEY FROM RunType WHERE fRunTypeName='"$runtype"'"
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| 248 | printprocesslog "DEBUG get run type from DB. QUERY:"$query2
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| 249 | result2=( `/usr/bin/mysql -u operator --host=fact01.fact.local --password=$password FactData -e "$query2"` )
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| 250 | if [ ${#result2} -eq 0 ]
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| 251 | then
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| 252 | printprocesslog "ERROR "$numberfromname": Could not query fRunTypeKey for runtype "$runtype" ."
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| 253 | continue
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| 254 | fi
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| 255 |
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| 256 | # check if entry has already checksums
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| 257 | query5="SELECT fRunNumber FROM RunInfo WHERE Concat(fRunNumber, '_', LPAD(fFileNumber, 3, 0))='"$numberfromname"'"
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| 258 | query5=$query5" AND NOT ISNULL(fMd5sumRaw) AND NOT ISNULL(fMd5sumRawZip)"
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| 259 | printprocesslog "DEBUG check if md5sums are alreay in DB. QUERY:"$query5
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| 260 | result5=`/usr/bin/mysql -u operator --host=fact01.fact.local --password=$password FactData -e "$query5"`
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| 261 |
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| 262 | # get md5sums of raw and zip file
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| 263 | # to safe time for tests and update this can be skipped ($skipmd5sum)
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| 264 | md5sum=
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| 265 | md5sumzip=
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| 266 | if [ "$skipmd5sum" == "no" ] || [ "$skipmd5sum" == "iffilled" ]
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| 267 | then
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| 268 | #echo "skip: "$skipmd5sum >> $logfile 2>&1
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| 269 | #echo "res5: -"$result5"-" >> $logfile 2>&1
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| 270 | #if [ "$skipmd5sum" == "no" ] || [ "$result5$skipmd5sum" == "iffilled" ]
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| 271 | if [ "$skipmd5sum" == "no" ] || [ "$result5" == "" ]
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| 272 | then
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| 273 | #zipfile=`echo $file | sed -e 's/raw/zipraw/' -e 's/fits/fits.gz/'`
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| 274 | # only do the md5sum if the zipfile is already available
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| 275 | if ls $file >/dev/null 2>&1
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| 276 | then
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| 277 | printprocesslog "INFO calculation md5sum for rawfile "$rawfile
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| 278 | md5sum=`md5sum $rawfile | cut -d' ' -f1`
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| 279 | printprocesslog "INFO calculation md5sum for zipfile "$file
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| 280 | md5sumzip=`md5sum $file | cut -d' ' -f1`
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| 281 | fi
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| 282 | fi
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| 283 | fi
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| 284 |
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| 285 | # insert or update depending on whether run exists
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| 286 | if [ "$result3" == "" ]
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| 287 | then
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| 288 | query4="INSERT"
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| 289 | querymid=" fRunNumber="$runnumber", fFileNumber="$filenumberfromname", "
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| 290 | querystop=
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| 291 | else
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| 292 | query4="UPDATE"
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| 293 | querymid=
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| 294 | querystop=" WHERE fRunNumber="$runnumber" AND fFileNumber="$filenumberfromname
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| 295 | fi
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| 296 | query4=$query4" RunInfo SET "$querymid" fRunTypeKey="${result2[1]}
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| 297 | if [ $numfitserrors -eq 0 ]
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| 298 | then
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| 299 | query4=$query4", fRunStart='"$runstart"', fRunStop='"$runstop"'"
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| 300 | if [ "$numevents" != "" ]
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| 301 | then
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| 302 | query4=$query4", fNumEvents="$numevent
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| 303 | fi
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| 304 | if [ "$roi" != "" ]
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| 305 | then
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| 306 | query4=$query4", fROI="$roi
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| 307 | fi
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| 308 | if [ "$roitm" != "" ]
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| 309 | then
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| 310 | query4=$query4", fROITimeMarker="$roitm
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| 311 | fi
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| 312 | if [ "$numphys" != "" ]
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| 313 | then
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| 314 | query4=$query4", fNumPhysicsTrigger="$numphys
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| 315 | fi
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| 316 | if [ "$numext1" != "" ]
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| 317 | then
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| 318 | query4=$query4", fNumExt1Trigger="$numext1
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| 319 | fi
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| 320 | if [ "$numext2" != "" ]
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| 321 | then
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| 322 | query4=$query4", fNumExt2Trigger="$numext2
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| 323 | fi
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| 324 | if [ "$numelp" != "" ]
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| 325 | then
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| 326 | query4=$query4", fNumELPTrigger="$numelp
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| 327 | fi
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| 328 | if [ "$numilp" != "" ]
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| 329 | then
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| 330 | query4=$query4", fNumILPTrigger="$numilp
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| 331 | fi
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| 332 | if [ "$numped" != "" ]
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| 333 | then
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| 334 | query4=$query4", fNumPedestalTrigger="$numped
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| 335 | fi
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| 336 | if [ "$numtime" != "" ]
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| 337 | then
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| 338 | query4=$query4", fNumTimeTrigger="$numtime
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| 339 | fi
|
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| 340 | if [ "$numoth" != "" ]
|
|---|
| 341 | then
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| 342 | query4=$query4", fNumOtherTrigger="$numoth
|
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| 343 | fi
|
|---|
| 344 | fi
|
|---|
| 345 | if [ "$md5sum" != "" ]
|
|---|
| 346 | then
|
|---|
| 347 | query4=$query4", fMd5sumRaw='"$md5sum"', fMd5sumRawZip='"$md5sumzip"'"
|
|---|
| 348 | query4=$query4", fHasDrsFile="$numdrsfiles
|
|---|
| 349 | fi
|
|---|
| 350 | if [ "$step" != "" ]
|
|---|
| 351 | then
|
|---|
| 352 | query4=$query4", fDrsStep="$step
|
|---|
| 353 | fi
|
|---|
| 354 | query4=$query4", fFitsFileErrors="$numfitserrors
|
|---|
| 355 | query4=$query4" "$querystop
|
|---|
| 356 | printprocesslog "INFO insert/update entry in DB. QUERY: "$query4
|
|---|
| 357 | if ! /usr/bin/mysql -u operator --host=fact01.fact.local --password=$password FactData -e "$query4"
|
|---|
| 358 | then
|
|---|
| 359 | printprocesslog "ERROR insert/update of "$numfromfile" to mysql failed."
|
|---|
| 360 | finish
|
|---|
| 361 | fi
|
|---|
| 362 | done
|
|---|
| 363 | done
|
|---|
| 364 |
|
|---|
| 365 | finish
|
|---|
| 366 |
|
|---|
