| 1 | #!/bin/bash
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| 2 |
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| 3 | # completely new version of the script
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| 4 | # running on newdaq to fill the information as fast as possible
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| 5 | # ftools is not used in this script anymore
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| 6 |
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| 7 | # todo
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| 8 | # tempfile for fitsdump -h output
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| 9 |
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| 10 | # option whether to fill all row or only those where information is missing
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| 11 | # $doupdate might be given as environment variable
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| 12 | if [ "$doupdate" = "" ]
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| 13 | then
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| 14 | doupdate="yes" # update all entries (needed when new fields have been added)
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| 15 | doupdate="no" # fill only entries which are not yet existing (default)
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| 16 | fi
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| 17 |
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| 18 | source `dirname $0`/../Sourcefile.sh
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| 19 | printprocesslog "INFO starting $0 with options doupdate="$doupdate #" and skipmd5sum="$skipmd5sum
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| 20 |
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| 21 | # check if software is available
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| 22 | if ! ls $factpath/fitsdump >/dev/null 2>&1
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| 23 | then
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| 24 | printprocesslog "ERROR "$factpath"/fitsdump is not available."
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| 25 | finish
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| 26 | fi
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| 27 |
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| 28 | # check if paths are available
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| 29 | if ! ls $rawdata >/dev/null 2>&1
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| 30 | then
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| 31 | printprocesslog "ERROR "$rawdata" is not available."
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| 32 | finish
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| 33 | fi
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| 34 |
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| 35 | # get dates
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| 36 | if [ "$certaindate" != "" ]
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| 37 | then
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| 38 | checkstring=`echo $certaindate | grep -E -o '^20[0-9][0-9]\/[01][0-9]\/[0-3][0-9]$'`
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| 39 | if [ "$checkstring" = "" ]
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| 40 | then
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| 41 | echo "Please give the variable certaindate in the correct format (YYYY/MM/DD)"
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| 42 | finish
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| 43 | fi
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| 44 | getdates $certaindate
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| 45 | else
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| 46 | # get all night
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| 47 | #getdates "all"
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| 48 | # get last 6 nights if hour between 7 and 19h, else only current night
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| 49 | getdates 6 7 19
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| 50 | fi
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| 51 |
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| 52 | # do check for rawfiles of these dates
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| 53 | for date in ${dates[@]}
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| 54 | do
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| 55 | # get runnumber from date
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| 56 | runnumber=`echo $date | sed -e 's/\///g'`
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| 57 |
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| 58 | night=
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| 59 | query="SELECT fNight FROM AuxDataInsertStatus WHERE fNight="$runnumber
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| 60 | night=`sendquery`
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| 61 | if [ "$night" == "" ] && ls $rawdata/$date >/dev/null 2>&1
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| 62 | then
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| 63 | printprocesslog "INFO insert "$runnumber" to AuxDataInsertStatus"
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| 64 | query="INSERT AuxDataInsertStatus SET fNight="$runnumber", fPriority="$runnumber
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| 65 | sendquery >/dev/null 2>&1
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| 66 | fi
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| 67 | rawdir=$rawdata/$date
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| 68 | # check if data are available from that night
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| 69 | if ! [ -d $rawdir ]
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| 70 | then
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| 71 | printprocesslog "INFO "$rawdir" does not exist."
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| 72 | continue
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| 73 | else
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| 74 | printprocesslog "INFO processing "$rawdir"..."
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| 75 | fi
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| 76 |
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| 77 | # find all fits.gz files starting with the oldest file
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| 78 | printprocesslog "INFO finding files to be checked in $rawdir..."
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| 79 | #fitsfiles=`ls $rawdir/*.fits 2>/dev/null | sort `
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| 80 | fitsfiles=( `find $rawdir -type f -regex '.*20[0-9][0-9][01][0-9][0-3][0-9][_][0-9][0-9][0-9][.]d?r?s?[.]?fits[.]?[g]?[f]?[z]?' 2>/dev/null | sort ` )
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| 81 |
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| 82 | # loop to check files
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| 83 | for file in ${fitsfiles[@]}
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| 84 | do
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| 85 | printprocesslog "INFO checking file "$file
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| 86 | #echo "INFO checking file "$file
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| 87 | filenotclosed="no"
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| 88 |
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| 89 | # check if it is drs file
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| 90 | isdrs=`ls $file | grep drs`
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| 91 | if [ "$isdrs" != "" ]
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| 92 | then
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| 93 | printprocesslog "INFO "$file" is a drs file. -> continue"
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| 94 | continue
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| 95 | fi
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| 96 |
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| 97 | # get run and file number form filename
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| 98 | 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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| 99 | runnumberfromname=`echo $numberfromname | cut -d_ -f1`
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| 100 | filenumberfromname=`echo $numberfromname | cut -d_ -f2 | sed -e 's/^0//g' -e 's/^0//g'`
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| 101 | if [ "$runnumber" != "$runnumberfromname" ]
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| 102 | then
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| 103 | printprocesslog "ERROR for file "$file": runnumber from date ("$runnumber") and filename ("$runnumberfromname") don't agree."
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| 104 | fi
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| 105 |
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| 106 | # check if entry already exists
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| 107 | query="SELECT fNight FROM RunInfo WHERE Concat(fNight, '_', LPAD(fRunID, 3, 0))='"$numberfromname"'"
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| 108 | printprocesslog "DEBUG check if entry already exists in DB. QUERY: "$query
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| 109 | #result3=`/usr/bin/mysql -u operator --host=fact01.fact.local --password=$password FactData -e "$query3"`
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| 110 | result3=`sendquery`
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| 111 |
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| 112 | # only proceed with file
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| 113 | # if information is not yet in database
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| 114 | # and no update is wished ($doupdate)
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| 115 | if [ "$result3" != "" ] && [ "$doupdate" == "no" ]
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| 116 | then
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| 117 | printprocesslog "INFO "$file" has been inserted already. -> continue "
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| 118 | continue
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| 119 | fi
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| 120 |
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| 121 | runtype=
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| 122 | # check if file was closed properly
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| 123 | if [ "`echo $file | grep -o drs`" == "drs" ]
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| 124 | then
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| 125 | nondrsfile=`echo $file | sed -e 's/[.]drs//g'`".fz" # fixme: maybe more flexible
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| 126 | tstop=`$factpath/fitsdump -h $nondrsfile 2>/dev/null | grep TSTOPI | grep -E -o '[0-9]+'`
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| 127 | checkstatus=$?
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| 128 | else
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| 129 | tstop=`$factpath/fitsdump -h $file 2>/dev/null | grep TSTOPI | grep -E -o '[0-9]+'`
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| 130 | checkstatus=$?
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| 131 | fi
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| 132 | #if [ $checkstatus -gt 0 ]
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| 133 | #then
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| 134 | # echo "WARN: getting tstop for file "$file" failed: tstop: -"$tstop"-"`date`
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| 135 | #fi
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| 136 | if [ "$tstop" == "0" ] || [ "$tstop" == "" ]
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| 137 | then
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| 138 | fileaccessed=`find $file -amin -30`
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| 139 | if ! [ "$fileaccessed" == "" ]
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| 140 | then
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| 141 | printprocesslog "INFO "$file" was accessed in the last 30 minutes => continue"
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| 142 | continue
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| 143 | else
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| 144 | printprocesslog "WARN "$file" has empty TSTOP but was not touched for 30 minutes"
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| 145 | filenotclosed="yes"
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| 146 | fi
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| 147 | fi
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| 148 |
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| 149 | numdrsfiles=
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| 150 | step=
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| 151 | if [ "$filenotclosed" == "no" ]
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| 152 | then
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| 153 | # get run and file number from file
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| 154 | runnumberfromfile=`$factpath/fitsdump -h $file 2>/dev/null | grep NIGHT | grep -E -o '20[1-9][0-9][01][0-9][0-3][0-9]'`
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| 155 | filenumberfromfileorig=`$factpath/fitsdump -h $file 2>/dev/null | grep RUNID | grep -E -o '[0-9]{1,3}'`
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| 156 | if [ "$runnumberfromfile" = "" ] || [ "$filenumberfromfileorig" = "" ]
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| 157 | then
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| 158 | printprocesslog "ERROR couldn't get run or file number from file name ("$file")."
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| 159 | fi
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| 160 | numberfromfile=$runnumberfromfile"_"`printf %03d $filenumberfromfileorig`
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| 161 | # compare numbers
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| 162 | if [ "$numberfromfile" != "$numberfromname" ]
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| 163 | then
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| 164 | printprocesslog "ERROR for file "$file": number from filename ("$numberfromname") and file ("$numberfromfile") don't agree."
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| 165 | fi
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| 166 |
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| 167 | # get checksums from header
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| 168 | checksum=`$factpath/fitsdump -h $file 2>/dev/null | grep CHECKSUM | grep -E -o '[a-zA-Z0-9]{16}'`
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| 169 | if [ "$checksum" == "" ]
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| 170 | then
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| 171 | printprocesslog "WARN checksum for file "$file" is empty."
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| 172 | fi
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| 173 | datasum=`$factpath/fitsdump -h $file 2>/dev/null | grep DATASUM | grep -E -o '[0-9]{1,10}'`
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| 174 | if [ "$datasum" == "" ]
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| 175 | then
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| 176 | printprocesslog "WARN datasum for file "$file" is empty."
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| 177 | fi
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| 178 |
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| 179 | # check if this run has drs file
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| 180 | # in case file is available, get STEP from header
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| 181 | # in the very beginning only drs-files were existing
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| 182 | # in the beginning the keywords DRSCALIB and STEP were not existing
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| 183 | drsfile=`echo $file | sed -e 's/fits.fz/drs.fits/'`
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| 184 | numdrsfiles=`ls $drsfile 2>/dev/null | wc -l`
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| 185 | drscalib=`$factpath/fitsdump -h $file 2>/dev/null | grep DRSCALIB | grep -E -o "[\ ][TF][\ ]" | sed -e "s/\ //g"`
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| 186 | if [ "$drscalib" == "T" ]
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| 187 | then
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| 188 | step=`$factpath/fitsdump -h $file 2>/dev/null | grep DRSSTEP | grep -E -o "[\ ][012][\ ]" | sed -e "s/\ //g"`
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| 189 | stepfromdrs=`$factpath/fitsdump -h $drsfile 2>/dev/null | grep STEP | grep -E -o "[\ ][012][\ ]?" | sed -e "s/\ //g"`
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| 190 | if [ "$stepfromdrs" != "$step" ]
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| 191 | then
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| 192 | printprocesslog "ERROR for file "$file" step from drsfile ("$stepfromdrs") and from file ("$step") do not agree."
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| 193 | if [ "$stepfromdrsfile" != "" ] && [ "$step" == "" ]
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| 194 | then
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| 195 | step=$stepfromdrsfile
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| 196 | printprocesslog "WARN setting drsstep from drsfile ("$stepfromdrs") although value differs from the one in file "$file"."
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| 197 | fi
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| 198 | fi
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| 199 | if ! [ $numdrsfiles -eq 1 ]
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| 200 | then
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| 201 | printprocesslog "ERROR for file "$file" number of drsfiles ("$numdrsfiles") and information from header ("$drscalib") don't agree."
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| 202 | fi
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| 203 | if [ "$step" = "" ]
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| 204 | then
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| 205 | printprocesslog "ERROR file "$file" has drsfiles ("$numdrsfiles"), but step ("$step") is empty."
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| 206 | fi
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| 207 | else
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| 208 | if ! [ "$drscalib" == "F" ]
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| 209 | then
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| 210 | printprocesslog "WARN for file "$file" DRSCALIB is neither T nor F."
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| 211 | fi
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| 212 | fi
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| 213 |
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| 214 | # get other variables from header
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| 215 | runtype=`$factpath/fitsdump -h $file 2>/dev/null | grep RUNTYPE | grep -E -o "['][a-z0-9._-]+[']" | sed -e "s/'//g" -e "s/_/-/g" -e "s/[.]//g"`
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| 216 | roi=`$factpath/fitsdump -h $file 2>/dev/null | grep NROI | grep -v NROITM | grep -E -o '[0-9]{1,4}'`
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| 217 | roitm=`$factpath/fitsdump -h $file 2>/dev/null | grep NROITM | grep -E -o '[0-9]{1,4}'`
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| 218 | numevents=`$factpath/fitsdump -h $file 2>/dev/null | grep Events | grep -E -o '[0-9]+'`
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| 219 | numphys=`$factpath/fitsdump -h $file 2>/dev/null | grep 'NTRG ' | grep -E -o '[0-9]+'`
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| 220 | numext1=`$factpath/fitsdump -h $file 2>/dev/null | grep 'NTRGEXT1' | grep -E -o '[ ][0-9]+[ ]' | sed -e 's/\ //g'`
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| 221 | numext2=`$factpath/fitsdump -h $file 2>/dev/null | grep 'NTRGEXT2' | grep -E -o '[ ][0-9]+[ ]' | sed -e 's/\ //g'`
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| 222 | numelp=`$factpath/fitsdump -h $file 2>/dev/null | grep 'NTRGLPE' | grep -E -o '[0-9]+'`
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| 223 | numilp=`$factpath/fitsdump -h $file 2>/dev/null | grep 'NTRGLPI' | grep -E -o '[0-9]+'`
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| 224 | numoth=`$factpath/fitsdump -h $file 2>/dev/null | grep 'NTRGMISC' | grep -E -o '[0-9]+'`
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| 225 | numped=`$factpath/fitsdump -h $file 2>/dev/null | grep 'NTRGPED' | grep -E -o '[0-9]+'`
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| 226 | numtime=`$factpath/fitsdump -h $file 2>/dev/null | grep 'NTRGTIM' | grep -E -o '[0-9]+'`
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| 227 | compiled=`$factpath/fitsdump -h $file 2>/dev/null | grep 'COMPILED' | grep -E -o "['][a-zA-Z]+[ ][ 12][0-9][ ]20[0-9][0-9][ ][0-2][0-9]:[0-5][0-9]:[0-5][0-9][']" | sed -e "s/'//g"`
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| 228 | if ! [ "$compiled" == "" ]
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| 229 | then
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| 230 | compiletime=`date +'%F %H:%M:%S' --date="${compiled}" `
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| 231 | else
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| 232 | compiletime=
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| 233 | fi
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| 234 | revnum=`$factpath/fitsdump -h $file 2>/dev/null | grep 'REVISION' | grep -E -o "['][0-9]+[:]?[0-9]*[MSP]*[']" | sed -e "s/'//g"`
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| 235 | # in newest data start time is in DATE-OBS
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| 236 | # in older data start time is in TSTART
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| 237 | # in the beginning TSTART was empty
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| 238 | runstart=`$factpath/fitsdump -h $file 2>/dev/null | grep DATE-OBS | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 239 | runstart2=`$factpath/fitsdump -h $file 2>/dev/null | grep TSTART | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 240 | if [ "$runstart" == "" ]
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| 241 | then
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| 242 | if [ "$runstart2" == "" ]
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| 243 | then
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| 244 | # for very old data, but gives problems for newer data
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| 245 | #runstart=`$factpath/fitsdump -h $file 2>/dev/null | grep DATE | grep -v 'DATE-' | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 246 | #runstart="0000-00-00 00:00:00"
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| 247 | runstart=
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| 248 | else
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| 249 | runstart=$runstart2
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| 250 | fi
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| 251 | fi
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| 252 | # in newest data start time is in DATE-END
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| 253 | # in older data start time is in TSTOP
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| 254 | # in the beginning TSTOP was empty
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| 255 | runstop=`$factpath/fitsdump -h $file 2>/dev/null | grep DATE-END | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 256 | runstop2=`$factpath/fitsdump -h $file 2>/dev/null | grep TSTOP | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 257 | if [ "$runstop" == "" ]
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| 258 | then
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| 259 | if [ "$runstop2" == "" ]
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| 260 | then
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| 261 | # for very old data, but gives problems for newer data
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| 262 | #runstop=`stat $file 2>/dev/null | grep Modify | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9][ ][0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{9}'`
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| 263 | #runstop="0000-00-00 00:00:00"
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| 264 | runstop=
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| 265 | else
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| 266 | runstop=$runstop2
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| 267 | fi
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| 268 | fi
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| 269 | fi
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| 270 |
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| 271 | # set runtype to 'unknown', if no runtype could be retrieved from file
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| 272 | if [ "$runtype" == "" ]
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| 273 | then
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| 274 | runtype="n/a"
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| 275 | fi
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| 276 | # on 15.11.2011 the runtypes had different names
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| 277 | if [ "$date" == "2011/11/15" ]
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| 278 | then
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| 279 | if [ "$runtype" == "drs-calib" ]
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| 280 | then
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| 281 | runtype="drs-gain"
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| 282 | fi
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| 283 | if [ "$runtype" == "drs-time-calib" ]
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| 284 | then
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| 285 | runtype="drs-time"
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| 286 | fi
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| 287 | if [ "$runtype" == "pedestal" ]
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| 288 | then
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| 289 | runtype="drs-pedestal"
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| 290 | fi
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| 291 | if [ "$runtype" == "light-pulser" ]
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| 292 | then
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| 293 | runtype="light-pulser-ext"
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| 294 | fi
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| 295 | if [ "$runtype" == "pedestal-on" ]
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| 296 | then
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| 297 | runtype="pedestal"
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| 298 | fi
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| 299 | fi
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| 300 | # get runtype
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| 301 | query="SELECT fRunTypeKEY FROM RunType WHERE fRunTypeName='"$runtype"'"
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| 302 | printprocesslog "DEBUG get run type from DB. QUERY:"$query
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| 303 | result2=( `sendquery` )
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| 304 | if [ ${#result2} -eq 0 ]
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| 305 | then
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| 306 | printprocesslog "ERROR "$numberfromname": Could not query fRunTypeKey for runtype "$runtype" ."
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| 307 | continue
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| 308 | fi
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| 309 |
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| 310 | # insert or update depending on whether run exists
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| 311 | if [ "$result3" == "" ]
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| 312 | then
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| 313 | query="INSERT"
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| 314 | querymid=" fNight="$runnumber", fRunID="$filenumberfromname", FileID="`echo $runnumber | cut -c 3-8``printf %03d $filenumberfromname`", "
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| 315 | querystop=
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| 316 | else
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| 317 | query="UPDATE"
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| 318 | querymid=
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| 319 | querystop=" WHERE fNight="$runnumber" AND fRunID="$filenumberfromname
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| 320 | fi
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| 321 | query=$query" RunInfo SET "$querymid" fRunTypeKey="${result2[0]}
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| 322 |
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| 323 | # some information is only available at the end of the run
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| 324 | # the fits header is updated then
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| 325 | if [ "$filenotclosed" == "no" ]
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| 326 | then
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| 327 | if [ "$runstart" == "" ]
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| 328 | then
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| 329 | query=$query", fRunStart=NULL"
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| 330 | else
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| 331 | query=$query", fRunStart='"$runstart"'"
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| 332 | fi
|
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| 333 | if [ "$runstop" == "" ]
|
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| 334 | then
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| 335 | query=$query", fRunStop=NULL"
|
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| 336 | else
|
|---|
| 337 | query=$query", fRunStop='"$runstop"'"
|
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| 338 | fi
|
|---|
| 339 | if [ "$numevents" != "" ]
|
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| 340 | then
|
|---|
| 341 | query=$query", fNumEvents="$numevents
|
|---|
| 342 | fi
|
|---|
| 343 | if [ "$numphys" != "" ]
|
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| 344 | then
|
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| 345 | query=$query", fNumPhysicsTrigger="$numphys
|
|---|
| 346 | fi
|
|---|
| 347 | if [ "$numext1" != "" ]
|
|---|
| 348 | then
|
|---|
| 349 | query=$query", fNumExt1Trigger="$numext1
|
|---|
| 350 | fi
|
|---|
| 351 | if [ "$numext2" != "" ]
|
|---|
| 352 | then
|
|---|
| 353 | query=$query", fNumExt2Trigger="$numext2
|
|---|
| 354 | fi
|
|---|
| 355 | if [ "$numelp" != "" ]
|
|---|
| 356 | then
|
|---|
| 357 | query=$query", fNumELPTrigger="$numelp
|
|---|
| 358 | fi
|
|---|
| 359 | if [ "$numilp" != "" ]
|
|---|
| 360 | then
|
|---|
| 361 | query=$query", fNumILPTrigger="$numilp
|
|---|
| 362 | fi
|
|---|
| 363 | if [ "$numped" != "" ]
|
|---|
| 364 | then
|
|---|
| 365 | query=$query", fNumPedestalTrigger="$numped
|
|---|
| 366 | fi
|
|---|
| 367 | if [ "$numtime" != "" ]
|
|---|
| 368 | then
|
|---|
| 369 | query=$query", fNumTimeTrigger="$numtime
|
|---|
| 370 | fi
|
|---|
| 371 | if [ "$numoth" != "" ]
|
|---|
| 372 | then
|
|---|
| 373 | query=$query", fNumOtherTrigger="$numoth
|
|---|
| 374 | fi
|
|---|
| 375 | fi
|
|---|
| 376 | if [ "$roi" != "" ]
|
|---|
| 377 | then
|
|---|
| 378 | query=$query", fROI="$roi
|
|---|
| 379 | fi
|
|---|
| 380 | if [ "$roitm" != "" ]
|
|---|
| 381 | then
|
|---|
| 382 | query=$query", fROITimeMarker="$roitm
|
|---|
| 383 | fi
|
|---|
| 384 | if [ "$checksum" != "" ]
|
|---|
| 385 | then
|
|---|
| 386 | query=$query", fCheckSum='"$checksum"'"
|
|---|
| 387 | fi
|
|---|
| 388 | if [ "$datasum" != "" ]
|
|---|
| 389 | then
|
|---|
| 390 | query=$query", fDataSum='"$datasum"'"
|
|---|
| 391 | fi
|
|---|
| 392 | if [ "$numdrsfiles" != "" ]
|
|---|
| 393 | then
|
|---|
| 394 | query=$query", fHasDrsFile="$numdrsfiles
|
|---|
| 395 | fi
|
|---|
| 396 | if [ "$step" != "" ]
|
|---|
| 397 | then
|
|---|
| 398 | query=$query", fDrsStep="$step
|
|---|
| 399 | fi
|
|---|
| 400 | if [ "$compiletime" != "" ]
|
|---|
| 401 | then
|
|---|
| 402 | query=$query", fCompileTime='"$compiletime"'"
|
|---|
| 403 | fi
|
|---|
| 404 | if [ "$revnum" != "" ]
|
|---|
| 405 | then
|
|---|
| 406 | query=$query", fRevisionNumber='"$revnum"'"
|
|---|
| 407 | fi
|
|---|
| 408 | #query=$query", fFitsFileErrors="$numfitserrors
|
|---|
| 409 | query=$query" "$querystop
|
|---|
| 410 | # send query to DB
|
|---|
| 411 | #echo $query
|
|---|
| 412 | sendquery >/dev/null
|
|---|
| 413 | done
|
|---|
| 414 | done
|
|---|
| 415 |
|
|---|
| 416 | finish
|
|---|
| 417 |
|
|---|
