| 1 | #!/bin/bash
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| 2 |
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| 3 | today=`date +%F`
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| 4 | logfile=/home/`whoami`/DataCheck/log/CheckRaw$today.log
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| 5 |
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| 6 | skipmd5sum="no" # fill md5 sums in any case
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| 7 | skipmd5sum="iffilled" # fill md5 sum only if they are not yet in db
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| 8 | #skipmd5sum="yes" # do not fill md5 sums in any case
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| 9 |
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| 10 | doupdate="yes" # update all entries
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| 11 | doupdate="no" # fill only entries which are not yet existing
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| 12 |
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| 13 | fillonly="ifzipped" # fill only entries which are not yet existing + where zipped file is availabl
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| 14 |
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| 15 | echo "" >> $logfile 2>&1
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| 16 | echo "" >> $logfile 2>&1
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| 17 | echo "" >> $logfile 2>&1
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| 18 | echo `date`"executing "$0"..." >> $logfile 2>&1
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| 19 | echo "=====> doupdate: "$doupdate >> $logfile 2>&1
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| 20 | echo "=====> skipmd5sum: "$skipmd5sum >> $logfile 2>&1
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| 21 | echo "=====> fillonly: "$fillonly >> $logfile 2>&1
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| 22 |
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| 23 | password=`cat /home/fact/DataCheck/.pw`
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| 24 | if [ "$password" == "" ]
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| 25 | then
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| 26 | echo "please insert password in .pw file"
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| 27 | fi
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| 28 |
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| 29 | # path to FACT++ version
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| 30 | factpath=/home/fact/FACT++.2012.01.19
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| 31 |
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| 32 | # setup to use ftools
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| 33 | export HEADAS=/opt/heasoft-6.11/x86_64-unknown-linux-gnu-libc2.13-0/
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| 34 | source $HEADAS/headas-init.sh
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| 35 |
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| 36 | # get last 2 nights
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| 37 | dates=( `date +%Y/%m/%d --date="-12hour"` `date +%Y/%m/%d --date="-36hour"` )
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| 38 |
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| 39 | # do rsync for rawfiles of these dates
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| 40 | for date in ${dates[@]}
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| 41 | do
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| 42 | echo "" >> $logfile 2>&1
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| 43 | echo "" >> $logfile 2>&1
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| 44 | echo "" >> $logfile 2>&1
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| 45 | rawdir=/loc_data/raw/$date
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| 46 | runnumber=`echo $date | sed -e 's/\///g'`
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| 47 | echo `date`": processing files in "$rawdir >> $logfile 2>&1
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| 48 | # check if data are available from that night
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| 49 | if ! [ -d $rawdir ]
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| 50 | then
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| 51 | echo `date`": no data available in "$rawdir >> $logfile 2>&1
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| 52 | continue
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| 53 | fi
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| 54 |
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| 55 | # find all fits-files starting with the oldest file
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| 56 | echo `date`": finding files to be zipped in $rawdir..." >> $logfile 2>&1
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| 57 | fitsfiles=`find $rawdir -type f -name '*.fits'| sort `
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| 58 |
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| 59 | # loop to zip files
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| 60 | echo `date`": checking files in $rawdir..." >> $logfile 2>&1
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| 61 | for file in $fitsfiles
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| 62 | do
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| 63 | echo "" >> $logfile 2>&1
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| 64 | echo "checking file "$file >> $logfile 2>&1
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| 65 | # check if raw file was changed in the last 30 minutes
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| 66 | isnew=`find $file -cmin -30`
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| 67 | if [ "$isnew" != "" ]
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| 68 | then
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| 69 | echo $file" is not older than 30 min => continue" >> $logfile 2>&1
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| 70 | continue
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| 71 | fi
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| 72 |
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| 73 | # check if it is drs file
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| 74 | isnew=`ls $file | grep drs`
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| 75 | if [ "$isnew" != "" ]
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| 76 | then
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| 77 | echo $file" is a drs file => continue" >> $logfile 2>&1
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| 78 | continue
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| 79 | fi
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| 80 |
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| 81 | # check if file is already finished
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| 82 | # original file on daq (if data was taken on daq
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| 83 | origfile=`echo $file | sed -e 's/loc_data/daq/'`
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| 84 | if [ -e $origfile ]
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| 85 | then
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| 86 | # get time of last modification as seconds since Epoch for both files
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| 87 | timeorig=`stat -c %Y $origfile`
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| 88 | timecopy=`stat -c %Y $file`
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| 89 | # compare times
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| 90 | if ! [ $timeorig -eq $timecopy ]
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| 91 | then
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| 92 | # if times are not the same, the file is still open => no zip
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| 93 | echo `date`": file "$file" not yet closed => continue" >> $logfile 2>&1
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| 94 | continue
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| 95 | fi
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| 96 | else
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| 97 | # if the origfile doesn't exist, the data was probably written not on daq but on data
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| 98 | echo `date`": file "$file" was probably taken on data and not daq " >> $logfile 2>&1
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| 99 | fi
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| 100 |
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| 101 | # get run and file number form filename
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| 102 | runnumbererror="no"
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| 103 | numbererror="no"
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| 104 | 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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| 105 | runnumberfromname=`echo $numberfromname | cut -d_ -f1`
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| 106 | filenumberfromname=`echo $numberfromname | cut -d_ -f2 | sed -e 's/^0//g' -e 's/^0//g'`
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| 107 | if [ "$runnumber" != "$runnumberfromname" ]
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| 108 | then
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| 109 | runnumbererror="yes"
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| 110 | echo "ERROR: for file "$file" runnumber from date and filename don't agree ("$runnumber" - "$runnumberfromname")"
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| 111 | echo "ERROR: for file "$file" runnumber from date and filename don't agree ("$runnumber" - "$runnumberfromname")" >> $logfile 2>&1
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| 112 | fi
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| 113 |
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| 114 | # check if entry already exists
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| 115 | query3="SELECT fRunNumber FROM RunInfo WHERE Concat(fRunNumber, '_', LPAD(fFileNumber, 3, 0))='"$numberfromname"'"
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| 116 | echo "Q3:"$query3 >> $logfile 2>&1 2>&1
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| 117 | result3=`/usr/bin/mysql -u operator --host=fact01.fact.local --password=$password FactData -e "$query3" 2>> $logfile`
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| 118 |
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| 119 | # only proceed with file
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| 120 | # if information is not yet in database
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| 121 | # and no update is wished ($doupdate)
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| 122 | if [ "$result3" != "" ] && [ "$doupdate" == "no" ]
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| 123 | then
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| 124 | echo $file" has been inserted already => continue " >> $logfile 2>&1
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| 125 | continue
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| 126 | fi
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| 127 |
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| 128 | # check if entry has already checksums
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| 129 | query5="SELECT fRunNumber FROM RunInfo WHERE Concat(fRunNumber, '_', LPAD(fFileNumber, 3, 0))='"$numberfromname"'"
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| 130 | query5=$query5" AND NOT ISNULL(fMd5sumRaw) AND NOT ISNULL(fMd5sumRawZip)"
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| 131 | echo "Q5:"$query5 >> $logfile 2>&1
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| 132 | result5=`/usr/bin/mysql -u operator --host=fact01.fact.local --password=$password FactData -e "$query5" 2>> $logfile`
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| 133 |
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| 134 | # get md5sums of raw and zip file
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| 135 | # to safe time for tests and update this can be skipped ($skipmd5sum)
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| 136 | md5sum=
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| 137 | md5sumzip=
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| 138 | if [ "$skipmd5sum" == "no" ] || [ "$skipmd5sum" == "iffilled" ]
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| 139 | then
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| 140 | #echo "skip: "$skipmd5sum >> $logfile 2>&1
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| 141 | #echo "res5: -"$result5"-" >> $logfile 2>&1
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| 142 | #if [ "$skipmd5sum" == "no" ] || [ "$result5$skipmd5sum" == "iffilled" ]
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| 143 | if [ "$skipmd5sum" == "no" ] || [ "$result5" == "" ]
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| 144 | then
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| 145 | zipfile=`echo $file | sed -e 's/raw/zipraw/' -e 's/fits/fits.gz/'`
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| 146 | # only do the md5sum if the zipfile is already available
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| 147 | if ls $zipfile >/dev/null >> $logfile 2>&1
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| 148 | then
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| 149 | echo "calculation md5sum for raw..." >> $logfile 2>&1
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| 150 | md5sum=`md5sum $file | cut -d' ' -f1`
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| 151 | echo "calculation md5sum for zipraw..." >> $logfile 2>&1
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| 152 | md5sumzip=`md5sum $zipfile | cut -d' ' -f1`
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| 153 | fi
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| 154 | fi
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| 155 | fi
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| 156 | if [ "$result3" == "" ] && [ "$md5sum" == "" ] && [ "$fillonly" == "ifzipped" ]
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| 157 | then
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| 158 | echo $file" is still missing zip => do not insert yet => continue " >> $logfile 2>&1
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| 159 | continue
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| 160 | fi
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| 161 |
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| 162 | runtype=
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| 163 | # check if fits file is corrupted
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| 164 | numfitserrors=0
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| 165 | checkfitsfile=`fverify $file 2>> $logfile | grep '0 error(s)'`
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| 166 | if [ "$checkfitsfile" == "" ]
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| 167 | then
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| 168 | numfitserrors=1
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| 169 | fi
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| 170 |
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| 171 | if [ $numfitserrors -eq 0 ]
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| 172 | then
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| 173 | # get run and file number from file
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| 174 | runnumberfromfile=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep NIGHT | grep -E -o '20[1-9][0-9][01][0-9][0-3][0-9]'`
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| 175 | filenumberfromfileorig=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep RUNID | grep -E -o '[0-9]{1,3}'`
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| 176 | numberfromfile=$runnumberfromfile"_"`printf %03d $filenumberfromfileorig`
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| 177 | # compare numbers
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| 178 | if [ "$numberfromfile" != "$numberfromname" ]
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| 179 | then
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| 180 | numbererror="yes"
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| 181 | echo "ERROR: for file "$file" number from filename and file don't agree ("$numberfromname" -"$numberfromfile")"
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| 182 | echo "ERROR: for file "$file" number from filename and file don't agree ("$numberfromname" -"$numberfromfile")" >> $logfile 2>&1
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| 183 | fi
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| 184 |
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| 185 | # check if this run has drs file
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| 186 | drsfile=`echo $file | sed -e 's/fits/drs.fits/'`
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| 187 | numdrsfiles=`ls $drsfile 2>/dev/null | wc -l`
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| 188 |
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| 189 | # get other variables from header
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| 190 | runtype=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep RUNTYPE | grep -E -o "['][a-z-]+[']" | sed -e "s/'//g"`
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| 191 | roi=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep NROI | grep -v NROITM | grep -E -o '[0-9]{1,4}'`
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| 192 | roitm=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep NROITM | grep -E -o '[0-9]{1,4}'`
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| 193 | numevents=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep Events | grep -E -o '[0-9]+'`
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| 194 | numphys=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRG ' | grep -E -o '[0-9]+'`
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| 195 | numext1=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGEXT1' | grep -E -o '[ ][0-9]+[ ]' | sed -e 's/\ //g'`
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| 196 | numext2=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGEXT2' | grep -E -o '[ ][0-9]+[ ]' | sed -e 's/\ //g'`
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| 197 | numelp=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGLPE' | grep -E -o '[0-9]+'`
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| 198 | numilp=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGLPI' | grep -E -o '[0-9]+'`
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| 199 | numoth=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGMISC' | grep -E -o '[0-9]+'`
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| 200 | numped=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGPED' | grep -E -o '[0-9]+'`
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| 201 | numtime=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGTIM' | grep -E -o '[0-9]+'`
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| 202 | # in newest data start time is in DATE-OBS
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| 203 | # in older data start time is in TSTART
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| 204 | # in the beginning TSTART was empty
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| 205 | runstart=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep DATE-OBS | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 206 | runstart2=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep TSTART | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 207 | if [ "$runstart" == "" ]
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| 208 | then
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| 209 | if [ "$runstart2" == "" ]
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| 210 | then
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| 211 | runstart=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep DATE | grep -v 'DATE-' | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 212 | else
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| 213 | runstart=$runstart2
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| 214 | fi
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| 215 | fi
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| 216 | # in newest data start time is in DATE-END
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| 217 | # in older data start time is in TSTOP
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| 218 | # in the beginning TSTOP was empty
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| 219 | runstop=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep DATE-END | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 220 | runstop2=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep TSTOP | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 221 | if [ "$runstop" == "" ]
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| 222 | then
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| 223 | if [ "$runstop2" == "" ]
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| 224 | then
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| 225 | runstop=`stat $file 2>/dev/null | grep Modify | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9][ ][0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{9}'`
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| 226 | else
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| 227 | runstop=$runstop2
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| 228 | fi
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| 229 | fi
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| 230 | fi
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| 231 |
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| 232 | # set runtype to 'unknown' if no runtype could be queried
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| 233 | if [ "$runtype" == "" ]
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| 234 | then
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| 235 | runtype="n/a"
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| 236 | fi
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| 237 | # on 15.11.2011 the runtypes had different names
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| 238 | if [ "$date" == "2011/11/15" ]
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| 239 | then
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| 240 | if [ "$runtype" == "drs-calib" ]
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| 241 | then
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| 242 | runtype="drs-gain"
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| 243 | fi
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| 244 | if [ "$runtype" == "drs-time-calib" ]
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| 245 | then
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| 246 | runtype="drs-time"
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| 247 | fi
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| 248 | if [ "$runtype" == "pedestal" ]
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| 249 | then
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| 250 | runtype="drs-pedestal"
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| 251 | fi
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| 252 | if [ "$runtype" == "light-pulser" ]
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| 253 | then
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| 254 | runtype="light-pulser-ext"
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| 255 | fi
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| 256 | if [ "$runtype" == "pedestal-on" ]
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| 257 | then
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| 258 | runtype="pedestal"
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| 259 | fi
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| 260 | fi
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| 261 | # get runtype
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| 262 | query2="SELECT fRunTypeKEY FROM RunType WHERE fRunTypeName='"$runtype"'"
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| 263 | echo "Q2:"$query2 >> $logfile 2>&1
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| 264 | result2=( `/usr/bin/mysql -u operator --host=fact01.fact.local --password=$password FactData -e "$query2" 2>> $logfile` )
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| 265 | if [ ${#result2} -eq 0 ]
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| 266 | then
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| 267 | echo $numberfromname": Could not query fRunTypeKey for runtype "$runtype
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| 268 | echo $numberfromname": Could not query fRunTypeKey for runtype "$runtype >> $logfile 2>&1
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| 269 | continue
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| 270 | fi
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| 271 |
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| 272 | # insert or update depending on whether run exists
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| 273 | if [ "$result3" == "" ]
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| 274 | then
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| 275 | query4="INSERT"
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| 276 | querymid=" fRunNumber="$runnumber", fFileNumber="$filenumberfromname", "
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| 277 | querystop=
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| 278 | else
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| 279 | query4="UPDATE"
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| 280 | querymid=
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| 281 | querystop=" WHERE fRunNumber="$runnumber" AND fFileNumber="$filenumberfromname
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| 282 | fi
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| 283 | query4=$query4" RunInfo SET "$querymid" fRunTypeKey="${result2[1]}
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| 284 | if [ $numfitserrors -eq 0 ]
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| 285 | then
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| 286 | query4=$query4", fNumEvents="$numevents", fROI="$roi", fROITimeMarker="$roitm
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| 287 | query4=$query4", fRunStart='"$runstart"', fRunStop='"$runstop"'"
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| 288 | if [ "$numphys" != "" ]
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| 289 | then
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| 290 | query4=$query4", fNumPhysicsTrigger="$numphys
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| 291 | fi
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| 292 | if [ "$numext1" != "" ]
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| 293 | then
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| 294 | query4=$query4", fNumExt1Trigger="$numext1
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| 295 | fi
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| 296 | if [ "$numext2" != "" ]
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| 297 | then
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| 298 | query4=$query4", fNumExt2Trigger="$numext2
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| 299 | fi
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| 300 | if [ "$numelp" != "" ]
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| 301 | then
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| 302 | query4=$query4", fNumELPTrigger="$numelp
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| 303 | fi
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| 304 | if [ "$numilp" != "" ]
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| 305 | then
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| 306 | query4=$query4", fNumILPTrigger="$numilp
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| 307 | fi
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| 308 | if [ "$numped" != "" ]
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| 309 | then
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| 310 | query4=$query4", fNumPedestalTrigger="$numped
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| 311 | fi
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| 312 | if [ "$numtime" != "" ]
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| 313 | then
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| 314 | query4=$query4", fNumTimeTrigger="$numtime
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| 315 | fi
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| 316 | if [ "$numoth" != "" ]
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| 317 | then
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| 318 | query4=$query4", fNumOtherTrigger="$numoth
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| 319 | fi
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| 320 | fi
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| 321 | if [ "$md5sum" != "" ]
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| 322 | then
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| 323 | query4=$query4", fMd5sumRaw='"$md5sum"', fMd5sumRawZip='"$md5sumzip"'"
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| 324 | query4=$query4", fHasDrsFile="$numdrsfiles
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| 325 | fi
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| 326 | query4=$query4", fFitsFileErrors="$numfitserrors
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| 327 | query4=$query4" "$querystop
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| 328 | echo "Q4:"$query4 >> $logfile 2>&1
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| 329 | if ! /usr/bin/mysql -u operator --host=fact01.fact.local --password=$password FactData -e "$query4" >> $logfile 2>&1
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| 330 | then
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| 331 | echo "insert/update of "$numfromfile" to mysql failed" >> $logfile 2>&1
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| 332 | fi
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| 333 |
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| 334 | # print summary for debug
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| 335 | echo "*******" >> $logfile 2>&1
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| 336 | echo "summary for file "$file >> $logfile 2>&1
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| 337 | echo "*******" >> $logfile 2>&1
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| 338 | echo " errors: "$numfitserrors" (1 means errors exist)" >> $logfile 2>&1
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| 339 | echo " number of drs files: "$numdrsfiles >> $logfile 2>&1
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| 340 | echo " runnumber error: "$runnumbererror >> $logfile 2>&1
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| 341 | echo " number error: "$numbererror >> $logfile 2>&1
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| 342 | echo " roi: "$roi >> $logfile 2>&1
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| 343 | echo " roitm: "$roitm >> $logfile 2>&1
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| 344 | echo " runtype: "$runtype >> $logfile 2>&1
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| 345 | echo " numevents: "$numevents >> $logfile 2>&1
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| 346 | echo " md5sum: "$md5sum >> $logfile 2>&1
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| 347 | echo " md5sum(zip): "$md5sumzip >> $logfile 2>&1
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| 348 | echo " start: "$runstart >> $logfile 2>&1
|
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| 349 | echo " stop: "$runstop >> $logfile 2>&1
|
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| 350 |
|
|---|
| 351 | # missing
|
|---|
| 352 | # check wether entry has been made (status table)
|
|---|
| 353 | done
|
|---|
| 354 | done
|
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| 355 |
|
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| 356 |
|
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