| 1 | #!/bin/bash
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| 2 |
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| 3 | # this script has been written to run on La Palma on the machine data
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| 4 | # i.e. paths are only working on this machine
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| 5 | # the script starts from the zipped files
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| 6 | # this causes a delay until files are in the database
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| 7 | # because they have to be rsynced and zipped first (see RsyncRawData.sh, ZipRawData.sh)
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| 8 |
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| 9 | # missing
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| 10 | # entry in status table
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| 11 |
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| 12 | # options:
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| 13 | skipmd5sum="no" # fill md5 sums in any case
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| 14 | skipmd5sum="iffilled" # fill md5 sum only if they are not yet in db # default
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| 15 | #skipmd5sum="yes" # do not fill md5 sums in any case
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| 16 |
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| 17 | doupdate="yes" # update all entries
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| 18 | doupdate="no" # fill only entries which are not yet existing #default
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| 19 |
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| 20 | source `dirname $0`/Sourcefile.sh
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| 21 | printprocesslog "INFO starting $0 with options doupdate="$doupdate" and skipmd5sum="$skipmd5sum
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| 22 |
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| 23 | # setup to use ftools
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| 24 | source $HEADAS/headas-init.sh
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| 25 |
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| 26 | pwfile=`dirname $0`/.pw
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| 27 | password=`cat $pwfile 2>/dev/null`
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| 28 | if [ "$password" == "" ]
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| 29 | then
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| 30 | echo "please insert password in $pwfile"
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| 31 | printprocesslog "ERROR password for DB access in $pwfile missing"
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| 32 | finish
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| 33 | fi
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| 34 |
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| 35 | # check if software is available
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| 36 | if ! ls $factpath/fitsdump >/dev/null 2>&1
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| 37 | then
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| 38 | printprocesslog "ERROR "$factpath"/fitsdump is not available."
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| 39 | finish
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| 40 | fi
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| 41 |
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| 42 | # check if paths are available
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| 43 | if ! ls /daq/raw >/dev/null 2>&1
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| 44 | then
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| 45 | printprocesslog "ERROR /daq/raw is not available."
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| 46 | finish
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| 47 | fi
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| 48 | if ! ls /loc_data/raw >/dev/null 2>&1
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| 49 | then
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| 50 | printprocesslog "ERROR /loc_data/raw is not available."
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| 51 | finish
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| 52 | fi
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| 53 | if ! ls /loc_data/zipraw >/dev/null 2>&1
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| 54 | then
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| 55 | printprocesslog "ERROR /loc_data/zipraw is not available."
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| 56 | finish
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| 57 | fi
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| 58 |
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| 59 | # get last 3 nights
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| 60 | dates=( `date +%Y/%m/%d --date="-12hour"` `date +%Y/%m/%d --date="-36hour"` `date +%Y/%m/%d --date="-60hour"` )
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| 61 | #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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| 62 |
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| 63 | # do check for rawfiles of these dates
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| 64 | for date in ${dates[@]}
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| 65 | do
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| 66 | ziprawdir=/loc_data/zipraw/$date
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| 67 | # check if data are available from that night
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| 68 | if ! [ -d $ziprawdir ]
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| 69 | then
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| 70 | printprocesslog "INFO "$ziprawdir" does not exist."
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| 71 | continue
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| 72 | else
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| 73 | printprocesslog "INFO processing "$ziprawdir"..."
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| 74 | fi
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| 75 |
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| 76 | # find all fits.gz files starting with the oldest file
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| 77 | printprocesslog "INFO finding files to be checked in $ziprawdir..."
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| 78 | fitsgzfiles=`find $ziprawdir -type f -name '*.fits.gz'| sort `
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| 79 |
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| 80 | # get runnumber from date
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| 81 | runnumber=`echo $date | sed -e 's/\///g'`
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| 82 |
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| 83 | # loop to check files
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| 84 | for file in $fitsgzfiles
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| 85 | do
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| 86 | printprocesslog "INFO checking file "$file
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| 87 | #echo "INFO checking file "$file
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| 88 |
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| 89 | # raw and original file
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| 90 | rawfile=`echo $file | sed -e 's/zipraw/raw/' -e 's/fits[.]gz/fits/'`
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| 91 | origfile=`echo $rawfile | sed -e 's/loc_data/daq/'`
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| 92 |
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| 93 | # check if raw file was changed in the last 30 minutes
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| 94 | isnew=`find $file -cmin -30`
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| 95 | if [ "$isnew" != "" ]
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| 96 | then
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| 97 | printprocesslog "INFO "$file" is not older than 30 min. -> continue"
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| 98 | continue
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| 99 | fi
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| 100 |
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| 101 | # check if it is drs file
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| 102 | isnew=`ls $file | grep drs`
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| 103 | if [ "$isnew" != "" ]
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| 104 | then
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| 105 | printprocesslog "INFO "$file" is a drs file. -> continue"
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| 106 | continue
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| 107 | fi
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| 108 |
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| 109 | # check if file is already finished
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| 110 | # original file on daq (if data was taken on daq
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| 111 | if [ -e $origfile ]
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| 112 | then
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| 113 | # get time of last modification as seconds since Epoch for both files
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| 114 | timeorig=`stat -c %Y $origfile`
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| 115 | timecopy=`stat -c %Y $rawfile`
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| 116 | # compare times
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| 117 | if ! [ $timeorig -eq $timecopy ]
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| 118 | then
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| 119 | # if times are not the same, the file is still open => no check
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| 120 | printprocesslog "INFO file "$rawfile" not yet closed. -> continue"
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| 121 | continue
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| 122 | fi
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| 123 | else
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| 124 | # if the origfile doesn't exist, the data was probably written not on daq but on data
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| 125 | printprocesslog "INFO file "$rawfile" was probably taken on data and not daq."
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| 126 | fi
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| 127 |
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| 128 | # get run and file number form filename
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| 129 | runnumbererror="no"
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| 130 | numbererror="no"
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| 131 | 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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| 132 | runnumberfromname=`echo $numberfromname | cut -d_ -f1`
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| 133 | filenumberfromname=`echo $numberfromname | cut -d_ -f2 | sed -e 's/^0//g' -e 's/^0//g'`
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| 134 | if [ "$runnumber" != "$runnumberfromname" ]
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| 135 | then
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| 136 | runnumbererror="yes"
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| 137 | printprocesslog "ERROR for file "$file": runnumber from date ("$runnumber") and filename ("$runnumberfromname") don't agree."
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| 138 | fi
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| 139 |
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| 140 | # check if entry already exists
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| 141 | query="SELECT fNight FROM RunInfo WHERE Concat(fNight, '_', LPAD(fRunID, 3, 0))='"$numberfromname"'"
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| 142 | printprocesslog "DEBUG check if entry already exists in DB. QUERY: "$query
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| 143 | #result3=`/usr/bin/mysql -u operator --host=fact01.fact.local --password=$password FactData -e "$query3"`
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| 144 | result3=`sendquery`
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| 145 |
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| 146 | # only proceed with file
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| 147 | # if information is not yet in database
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| 148 | # and no update is wished ($doupdate)
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| 149 | if [ "$result3" != "" ] && [ "$doupdate" == "no" ]
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| 150 | then
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| 151 | printprocesslog "INFO "$file" has been inserted already. -> continue "
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| 152 | continue
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| 153 | fi
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| 154 |
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| 155 | runtype=
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| 156 | # check if fits file is corrupted
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| 157 | numfitserrors=0
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| 158 | #checkfitsfile=`fverify $rawfile 2>/dev/null | grep '0 error(s)'`
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| 159 | numfitserrors=`fverify $rawfile 2>/dev/null | grep -o '[0-9][ ]error(s)' | grep -E -o '[0-9]'`
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| 160 | #if [ "$checkfitsfile" == "" ]
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| 161 | if [ $numfitserrors -gt 0 ]
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| 162 | then
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| 163 | printprocesslog "WARN "$rawfile" has "$numfitserrors" fitserror(s). "
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| 164 | #numfitserrors=1
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| 165 | fi
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| 166 |
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| 167 | if [ $numfitserrors -eq 0 ]
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| 168 | then
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| 169 | # get run and file number from file
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| 170 | runnumberfromfile=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep NIGHT | grep -E -o '20[1-9][0-9][01][0-9][0-3][0-9]'`
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| 171 | filenumberfromfileorig=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep RUNID | grep -E -o '[0-9]{1,3}'`
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| 172 | if [ "$runnumberfromfile" = "" ] || [ "$filenumberfromfileorig" = "" ]
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| 173 | then
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| 174 | printprocesslog "ERROR couldn't get run or file number from file name ("$file")."
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| 175 | fi
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| 176 | numberfromfile=$runnumberfromfile"_"`printf %03d $filenumberfromfileorig`
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| 177 | # compare numbers
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| 178 | if [ "$numberfromfile" != "$numberfromname" ]
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| 179 | then
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| 180 | numbererror="yes"
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| 181 | printprocesslog "ERROR for file "$file": number from filename ("$numberfromname") and file ("$numberfromfile") don't agree."
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| 182 | fi
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| 183 |
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| 184 | # check if this run has drs file
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| 185 | # in case file is available, get STEP from header
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| 186 | # in the very beginning only drs-files were existing
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| 187 | # in the beginning the keywords DRSCALIB and STEP were not existing
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| 188 | numdrsfiles=
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| 189 | step=
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| 190 | drsfile=`echo $file | sed -e 's/fits/drs.fits/'`
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| 191 | numdrsfiles=`ls $drsfile 2>/dev/null | wc -l`
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| 192 | drscalib=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep DRSCALIB | grep -E -o "['][TF][']" | sed -e "s/'//g"`
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| 193 | if [ "$drscalib" == "T" ]
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| 194 | then
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| 195 | step=`$factpath/fitsdump -h -t Events $drsfile 2>/dev/null | grep STEP | grep -E -o "['][012][']" | sed -e "s/'//g"`
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| 196 | if ! [ $numdrsfiles -eq 1 ]
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| 197 | then
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| 198 | printprocesslog "ERROR for file "$file" number of drsfiles ("$numdrsfiles") and information from header ("$drscalib") don't agree."
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| 199 | fi
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| 200 | else
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| 201 | if ! [ "$drscalib" == "F" ]
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| 202 | then
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| 203 | printprocesslog "WARN for file "$file" DRSCALIB is neither T nor F."
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| 204 | fi
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| 205 | fi
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| 206 |
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| 207 | # get other variables from header
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| 208 | runtype=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep RUNTYPE | grep -E -o "['][a-z0-9._-]+[']" | sed -e "s/'//g" -e "s/_/-/g" -e "s/[.]//g"`
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| 209 | #echo "runtype for file "$file": "$runtype
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| 210 | roi=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep NROI | grep -v NROITM | grep -E -o '[0-9]{1,4}'`
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| 211 | roitm=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep NROITM | grep -E -o '[0-9]{1,4}'`
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| 212 | numevents=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep Events | grep -E -o '[0-9]+'`
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| 213 | numphys=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRG ' | grep -E -o '[0-9]+'`
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| 214 | numext1=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGEXT1' | grep -E -o '[ ][0-9]+[ ]' | sed -e 's/\ //g'`
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| 215 | numext2=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGEXT2' | grep -E -o '[ ][0-9]+[ ]' | sed -e 's/\ //g'`
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| 216 | numelp=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGLPE' | grep -E -o '[0-9]+'`
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| 217 | numilp=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGLPI' | grep -E -o '[0-9]+'`
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| 218 | numoth=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGMISC' | grep -E -o '[0-9]+'`
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| 219 | numped=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGPED' | grep -E -o '[0-9]+'`
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| 220 | numtime=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGTIM' | grep -E -o '[0-9]+'`
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| 221 | compiled=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'COMPILED' | grep -E -o "['][a-zA-Z]+[ ][ 12][0-9][ ]20[0-9][0-9][ ][0-2][0-9]:[0-5][0-9]:[0-5][0-9][']" | sed -e "s/'//g"`
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| 222 | if ! [ "$compiled" == "" ]
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| 223 | then
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| 224 | compiletime=`date +'%F %H:%M:%S' --date="${compiled}" `
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| 225 | else
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| 226 | compiletime=
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| 227 | fi
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| 228 | revnum=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'REVISION' | grep -E -o "['][0-9]+[:]?[0-9]*[MSP]*[']" | sed -e "s/'//g"`
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| 229 | # in newest data start time is in DATE-OBS
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| 230 | # in older data start time is in TSTART
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| 231 | # in the beginning TSTART was empty
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| 232 | runstart=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep DATE-OBS | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 233 | runstart2=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep TSTART | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 234 | if [ "$runstart" == "" ]
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| 235 | then
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| 236 | if [ "$runstart2" == "" ]
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| 237 | then
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| 238 | runstart=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep DATE | grep -v 'DATE-' | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 239 | else
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| 240 | runstart=$runstart2
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| 241 | fi
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| 242 | fi
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| 243 | # in newest data start time is in DATE-END
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| 244 | # in older data start time is in TSTOP
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| 245 | # in the beginning TSTOP was empty
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| 246 | runstop=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep DATE-END | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 247 | runstop2=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep TSTOP | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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| 248 | if [ "$runstop" == "" ]
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| 249 | then
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| 250 | if [ "$runstop2" == "" ]
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| 251 | then
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| 252 | runstop=`stat $file 2>/dev/null | grep Modify | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9][ ][0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{9}'`
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| 253 | else
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| 254 | runstop=$runstop2
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| 255 | fi
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| 256 | fi
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| 257 | fi
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| 258 |
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| 259 | # set runtype to 'unknown', if no runtype could be retrieved from file
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| 260 | if [ "$runtype" == "" ]
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| 261 | then
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| 262 | runtype="n/a"
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| 263 | fi
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| 264 | # on 15.11.2011 the runtypes had different names
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| 265 | if [ "$date" == "2011/11/15" ]
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| 266 | then
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| 267 | if [ "$runtype" == "drs-calib" ]
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| 268 | then
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| 269 | runtype="drs-gain"
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| 270 | fi
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| 271 | if [ "$runtype" == "drs-time-calib" ]
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| 272 | then
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| 273 | runtype="drs-time"
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| 274 | fi
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| 275 | if [ "$runtype" == "pedestal" ]
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| 276 | then
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| 277 | runtype="drs-pedestal"
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| 278 | fi
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| 279 | if [ "$runtype" == "light-pulser" ]
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| 280 | then
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| 281 | runtype="light-pulser-ext"
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| 282 | fi
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| 283 | if [ "$runtype" == "pedestal-on" ]
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| 284 | then
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| 285 | runtype="pedestal"
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| 286 | fi
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| 287 | fi
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| 288 | # get runtype
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| 289 | query="SELECT fRunTypeKEY FROM RunType WHERE fRunTypeName='"$runtype"'"
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| 290 | printprocesslog "DEBUG get run type from DB. QUERY:"$query
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| 291 | #result2=( `/usr/bin/mysql -u operator --host=fact01.fact.local --password=$password FactData -e "$query2"` )
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| 292 | result2=( `sendquery` )
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| 293 | if [ ${#result2} -eq 0 ]
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| 294 | then
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| 295 | printprocesslog "ERROR "$numberfromname": Could not query fRunTypeKey for runtype "$runtype" ."
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| 296 | continue
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| 297 | fi
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| 298 |
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| 299 | # check if entry has already checksums
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| 300 | query="SELECT fNight FROM RunInfo WHERE Concat(fNight, '_', LPAD(fRunID, 3, 0))='"$numberfromname"'"
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| 301 | query=$query" AND NOT ISNULL(fMd5sumRaw) AND NOT ISNULL(fMd5sumRawZip)"
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| 302 | printprocesslog "DEBUG check if md5sums are alreay in DB. QUERY:"$query
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| 303 | #result5=`/usr/bin/mysql -u operator --host=fact01.fact.local --password=$password FactData -e "$query5"`
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| 304 | result5=`sendquery`
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| 305 |
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| 306 | # get md5sums of raw and zip file
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| 307 | # to safe time for tests and update this can be skipped ($skipmd5sum)
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| 308 | md5sum=
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| 309 | md5sumzip=
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| 310 | if [ "$skipmd5sum" == "no" ] || [ "$skipmd5sum" == "iffilled" ]
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| 311 | then
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| 312 | #echo "skip: "$skipmd5sum >> $logfile 2>&1
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| 313 | #echo "res5: -"$result5"-" >> $logfile 2>&1
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| 314 | #if [ "$skipmd5sum" == "no" ] || [ "$result5$skipmd5sum" == "iffilled" ]
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| 315 | if [ "$skipmd5sum" == "no" ] || [ "$result5" == "" ]
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| 316 | then
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| 317 | #zipfile=`echo $file | sed -e 's/raw/zipraw/' -e 's/fits/fits.gz/'`
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| 318 | # only do the md5sum if the zipfile is already available
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| 319 | if ls $file >/dev/null 2>&1
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| 320 | then
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| 321 | printprocesslog "INFO calculation md5sum for rawfile "$rawfile
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| 322 | md5sum=`md5sum $rawfile | cut -d' ' -f1`
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| 323 | printprocesslog "INFO calculation md5sum for zipfile "$file
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| 324 | md5sumzip=`md5sum $file | cut -d' ' -f1`
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| 325 | fi
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| 326 | fi
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| 327 | fi
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| 328 |
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| 329 | # insert or update depending on whether run exists
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| 330 | if [ "$result3" == "" ]
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| 331 | then
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| 332 | query="INSERT"
|
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| 333 | querymid=" fNight="$runnumber", fRunID="$filenumberfromname", "
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| 334 | querystop=
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| 335 | else
|
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| 336 | query="UPDATE"
|
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| 337 | querymid=
|
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| 338 | querystop=" WHERE fNight="$runnumber" AND fRunID="$filenumberfromname
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| 339 | fi
|
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| 340 | query=$query" RunInfo SET "$querymid" fRunTypeKey="${result2[0]}
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| 341 | if [ $numfitserrors -eq 0 ]
|
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| 342 | then
|
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| 343 | query=$query", fRunStart='"$runstart"', fRunStop='"$runstop"'"
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| 344 | if [ "$numevents" != "" ]
|
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| 345 | then
|
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| 346 | query=$query", fNumEvents="$numevents
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|---|
| 347 | fi
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|---|
| 348 | if [ "$roi" != "" ]
|
|---|
| 349 | then
|
|---|
| 350 | query=$query", fROI="$roi
|
|---|
| 351 | fi
|
|---|
| 352 | if [ "$roitm" != "" ]
|
|---|
| 353 | then
|
|---|
| 354 | query=$query", fROITimeMarker="$roitm
|
|---|
| 355 | fi
|
|---|
| 356 | if [ "$numphys" != "" ]
|
|---|
| 357 | then
|
|---|
| 358 | query=$query", fNumPhysicsTrigger="$numphys
|
|---|
| 359 | fi
|
|---|
| 360 | if [ "$numext1" != "" ]
|
|---|
| 361 | then
|
|---|
| 362 | query=$query", fNumExt1Trigger="$numext1
|
|---|
| 363 | fi
|
|---|
| 364 | if [ "$numext2" != "" ]
|
|---|
| 365 | then
|
|---|
| 366 | query=$query", fNumExt2Trigger="$numext2
|
|---|
| 367 | fi
|
|---|
| 368 | if [ "$numelp" != "" ]
|
|---|
| 369 | then
|
|---|
| 370 | query=$query", fNumELPTrigger="$numelp
|
|---|
| 371 | fi
|
|---|
| 372 | if [ "$numilp" != "" ]
|
|---|
| 373 | then
|
|---|
| 374 | query=$query", fNumILPTrigger="$numilp
|
|---|
| 375 | fi
|
|---|
| 376 | if [ "$numped" != "" ]
|
|---|
| 377 | then
|
|---|
| 378 | query=$query", fNumPedestalTrigger="$numped
|
|---|
| 379 | fi
|
|---|
| 380 | if [ "$numtime" != "" ]
|
|---|
| 381 | then
|
|---|
| 382 | query=$query", fNumTimeTrigger="$numtime
|
|---|
| 383 | fi
|
|---|
| 384 | if [ "$numoth" != "" ]
|
|---|
| 385 | then
|
|---|
| 386 | query=$query", fNumOtherTrigger="$numoth
|
|---|
| 387 | fi
|
|---|
| 388 | fi
|
|---|
| 389 | if [ "$md5sum" != "" ]
|
|---|
| 390 | then
|
|---|
| 391 | query=$query", fMd5sumRaw='"$md5sum"', fMd5sumRawZip='"$md5sumzip"'"
|
|---|
| 392 | fi
|
|---|
| 393 | if [ "$numdrsfiles" != "" ]
|
|---|
| 394 | then
|
|---|
| 395 | query=$query", fHasDrsFile="$numdrsfiles
|
|---|
| 396 | fi
|
|---|
| 397 | if [ "$step" != "" ]
|
|---|
| 398 | then
|
|---|
| 399 | query=$query", fDrsStep="$step
|
|---|
| 400 | fi
|
|---|
| 401 | if [ "$compiletime" != "" ]
|
|---|
| 402 | then
|
|---|
| 403 | query=$query", fCompileTime='"$compiletime"'"
|
|---|
| 404 | fi
|
|---|
| 405 | if [ "$revnum" != "" ]
|
|---|
| 406 | then
|
|---|
| 407 | query=$query", fRevisionNumber='"$revnum"'"
|
|---|
| 408 | fi
|
|---|
| 409 | query=$query", fFitsFileErrors="$numfitserrors
|
|---|
| 410 | query=$query" "$querystop
|
|---|
| 411 | printprocesslog "INFO insert/update entry in DB. QUERY: "$query
|
|---|
| 412 | # send query to DB
|
|---|
| 413 | sendquery >/dev/null
|
|---|
| 414 | #if ! /usr/bin/mysql -u operator --host=fact01.fact.local --password=$password FactData -e "$query4"
|
|---|
| 415 | #then
|
|---|
| 416 | # printprocesslog "ERROR insert/update of "$numfromfile" to mysql failed."
|
|---|
| 417 | # finish
|
|---|
| 418 | #fi
|
|---|
| 419 | done
|
|---|
| 420 | done
|
|---|
| 421 |
|
|---|
| 422 | finish
|
|---|
| 423 |
|
|---|
