1 | #!/bin/bash
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2 |
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3 | # missing
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4 | # entry in status table
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5 |
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6 | # options:
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7 | skipmd5sum="no" # fill md5 sums in any case
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8 | skipmd5sum="iffilled" # fill md5 sum only if they are not yet in db # default
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9 | #skipmd5sum="yes" # do not fill md5 sums in any case
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10 |
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11 | doupdate="yes" # update all entries
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12 | #doupdate="no" # fill only entries which are not yet existing #default
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13 |
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14 | source `dirname $0`/Sourcefile.sh
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15 | printprocesslog "INFO starting $0 with options doupdate="$doupdate" and skipmd5sum="$skipmd5sum
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16 |
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17 | # setup to use ftools
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18 | source $HEADAS/headas-init.sh
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19 |
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20 | pwfile=`dirname $0`/.pw
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21 | password=`cat $pwfile 2>/dev/null`
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22 | if [ "$password" == "" ]
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23 | then
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24 | echo "please insert password in $pwfile"
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25 | printprocesslog "ERROR password for DB access in $pwfile missing"
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26 | finish
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27 | fi
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28 |
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29 | # check if software is available
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30 | if ! ls $factpath/fitsdump >/dev/null 2>&1
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31 | then
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32 | printprocesslog "ERROR "$factpath"/fitsdump is not available."
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33 | finish
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34 | fi
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35 |
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36 | # get last 3 nights
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37 | dates=( `date +%Y/%m/%d --date="-12hour"` `date +%Y/%m/%d --date="-36hour"` )
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38 | #dates=( `find /loc_data/zipraw/ -mindepth 3 -type d | sort | sed -e 's/\/loc_data\/zipraw\///g'` ) #all available dates in /loc_data/zipraw
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39 | #dates=( "2012/02/19" )
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40 |
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41 | # do check for rawfiles of these dates
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42 | for date in ${dates[@]}
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43 | do
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44 | ziprawdir=/loc_data/zipraw/$date
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45 | # check if data are available from that night
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46 | if ! [ -d $ziprawdir ]
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47 | then
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48 | printprocesslog "INFO "$ziprawdir" does not exist."
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49 | continue
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50 | else
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51 | printprocesslog "INFO processing "$ziprawdir"..."
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52 | fi
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53 |
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54 | # find all fits.gz files starting with the oldest file
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55 | printprocesslog "INFO finding files to be checked in $ziprawdir..."
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56 | fitsgzfiles=`find $ziprawdir -type f -name '*.fits.gz'| sort `
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57 |
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58 | # get runnumber from date
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59 | runnumber=`echo $date | sed -e 's/\///g'`
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60 |
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61 | # loop to check files
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62 | for file in $fitsgzfiles
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63 | do
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64 | printprocesslog "INFO checking file "$file
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65 | #echo "INFO checking file "$file
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66 |
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67 | # raw and original file
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68 | rawfile=`echo $file | sed -e 's/zipraw/raw/' -e 's/fits[.]gz/fits/'`
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69 | origfile=`echo $rawfile | sed -e 's/loc_data/daq/'`
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70 |
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71 | # check if raw file was changed in the last 30 minutes
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72 | isnew=`find $file -cmin -30`
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73 | if [ "$isnew" != "" ]
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74 | then
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75 | printprocesslog "INFO "$file" is not older than 30 min. -> continue"
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76 | continue
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77 | fi
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78 |
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79 | # check if it is drs file
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80 | isnew=`ls $file | grep drs`
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81 | if [ "$isnew" != "" ]
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82 | then
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83 | printprocesslog "INFO "$file" is a drs file. -> continue"
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84 | continue
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85 | fi
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86 |
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87 | # check if file is already finished
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88 | # original file on daq (if data was taken on daq
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89 | if [ -e $origfile ]
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90 | then
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91 | # get time of last modification as seconds since Epoch for both files
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92 | timeorig=`stat -c %Y $origfile`
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93 | timecopy=`stat -c %Y $rawfile`
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94 | # compare times
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95 | if ! [ $timeorig -eq $timecopy ]
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96 | then
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97 | # if times are not the same, the file is still open => no check
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98 | printprocesslog "INFO file "$rawfile" not yet closed. -> continue"
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99 | continue
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100 | fi
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101 | else
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102 | # if the origfile doesn't exist, the data was probably written not on daq but on data
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103 | printprocesslog "INFO file "$rawfile" was probably taken on data and not daq."
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104 | fi
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105 |
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106 | # get run and file number form filename
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107 | runnumbererror="no"
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108 | numbererror="no"
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109 | 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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110 | runnumberfromname=`echo $numberfromname | cut -d_ -f1`
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111 | filenumberfromname=`echo $numberfromname | cut -d_ -f2 | sed -e 's/^0//g' -e 's/^0//g'`
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112 | if [ "$runnumber" != "$runnumberfromname" ]
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113 | then
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114 | runnumbererror="yes"
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115 | printprocesslog "ERROR for file "$file": runnumber from date ("$runnumber") and filename ("$runnumberfromname") don't agree."
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116 | fi
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117 |
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118 | # check if entry already exists
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119 | query3="SELECT fNight FROM RunInfo WHERE Concat(fNight, '_', LPAD(fRunID, 3, 0))='"$numberfromname"'"
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120 | printprocesslog "DEBUG check if entry already exists in DB. QUERY: "$query3
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121 | result3=`/usr/bin/mysql -u operator --host=fact01.fact.local --password=$password FactData -e "$query3"`
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122 |
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123 | # only proceed with file
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124 | # if information is not yet in database
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125 | # and no update is wished ($doupdate)
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126 | if [ "$result3" != "" ] && [ "$doupdate" == "no" ]
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127 | then
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128 | printprocesslog "INFO "$file" has been inserted already. -> continue "
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129 | continue
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130 | fi
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131 |
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132 | runtype=
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133 | # check if fits file is corrupted
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134 | numfitserrors=0
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135 | #checkfitsfile=`fverify $rawfile 2>/dev/null | grep '0 error(s)'`
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136 | numfitserrors=`fverify $rawfile 2>/dev/null | grep -o '[0-9][ ]error(s)' | grep -E -o '[0-9]'`
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137 | #if [ "$checkfitsfile" == "" ]
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138 | if [ $numfitserrors -gt 0 ]
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139 | then
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140 | printprocesslog "WARN "$rawfile" has "$numfitserrors" fitserror(s). "
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141 | #numfitserrors=1
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142 | fi
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143 |
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144 | if [ $numfitserrors -eq 0 ]
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145 | then
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146 | # get run and file number from file
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147 | runnumberfromfile=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep NIGHT | grep -E -o '20[1-9][0-9][01][0-9][0-3][0-9]'`
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148 | filenumberfromfileorig=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep RUNID | grep -E -o '[0-9]{1,3}'`
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149 | if [ "$runnumberfromfile" = "" ] || [ "$filenumberfromfileorig" = "" ]
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150 | then
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151 | printprocesslog "ERROR couldn't get run or file number from file name ("$file")."
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152 | fi
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153 | numberfromfile=$runnumberfromfile"_"`printf %03d $filenumberfromfileorig`
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154 | # compare numbers
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155 | if [ "$numberfromfile" != "$numberfromname" ]
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156 | then
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157 | numbererror="yes"
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158 | printprocesslog "ERROR for file "$file": number from filename ("$numberfromname") and file ("$numberfromfile") don't agree."
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159 | fi
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160 |
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161 | # check if this run has drs file
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162 | # in case file is available, get STEP from header
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163 | # in the very beginning only drs-files were existing
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164 | # in the beginning the keywords DRSCALIB and STEP were not existing
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165 | numdrsfiles=
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166 | step=
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167 | drsfile=`echo $file | sed -e 's/fits/drs.fits/'`
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168 | numdrsfiles=`ls $drsfile 2>/dev/null | wc -l`
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169 | drscalib=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep DRSCALIB | grep -E -o "['][TF][']" | sed -e "s/'//g"`
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170 | if [ "$drscalib" == "T" ]
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171 | then
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172 | step=`$factpath/fitsdump -h -t Events $drsfile 2>/dev/null | grep STEP | grep -E -o "['][012][']" | sed -e "s/'//g"`
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173 | if ! [ $numdrsfiles -eq 1 ]
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174 | then
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175 | printprocesslog "ERROR for file "$file" number of drsfiles ("$numdrsfiles") and information from header ("$drscalib") don't agree."
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176 | fi
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177 | else
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178 | if ! [ "$drscalib" == "F" ]
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179 | then
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180 | printprocesslog "WARN for file "$file" DRSCALIB is neither T nor F."
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181 | fi
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182 | fi
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183 |
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184 | # get other variables from header
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185 | runtype=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep RUNTYPE | grep -E -o "['][a-z0-9._-]+[']" | sed -e "s/'//g" -e "s/_/-/g" -e "s/[.]//g"`
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186 | #echo "runtype for file "$file": "$runtype
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187 | roi=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep NROI | grep -v NROITM | grep -E -o '[0-9]{1,4}'`
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188 | roitm=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep NROITM | grep -E -o '[0-9]{1,4}'`
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189 | numevents=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep Events | grep -E -o '[0-9]+'`
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190 | numphys=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRG ' | grep -E -o '[0-9]+'`
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191 | numext1=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGEXT1' | grep -E -o '[ ][0-9]+[ ]' | sed -e 's/\ //g'`
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192 | numext2=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGEXT2' | grep -E -o '[ ][0-9]+[ ]' | sed -e 's/\ //g'`
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193 | numelp=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGLPE' | grep -E -o '[0-9]+'`
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194 | numilp=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGLPI' | grep -E -o '[0-9]+'`
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195 | numoth=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGMISC' | grep -E -o '[0-9]+'`
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196 | numped=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGPED' | grep -E -o '[0-9]+'`
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197 | numtime=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'NTRGTIM' | grep -E -o '[0-9]+'`
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198 | compiled=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'COMPILED' | grep -E -o "['][a-zA-Z]+[ ][ 12][0-9][ ]20[0-9][0-9][ ][0-2][0-9]:[0-5][0-9]:[0-5][0-9][']" | sed -e "s/'//g"`
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199 | if ! [ "$compiled" == "" ]
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200 | then
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201 | compiletime=`date +'%F %H:%M:%S' --date="${compiled}" `
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202 | else
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203 | compiletime=
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204 | fi
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205 | revnum=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep 'REVISION' | grep -E -o "['][0-9]+[:]?[0-9]*[MSP]*[']" | sed -e "s/'//g"`
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206 | # in newest data start time is in DATE-OBS
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207 | # in older data start time is in TSTART
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208 | # in the beginning TSTART was empty
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209 | runstart=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep DATE-OBS | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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210 | runstart2=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep TSTART | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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211 | if [ "$runstart" == "" ]
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212 | then
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213 | if [ "$runstart2" == "" ]
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214 | then
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215 | runstart=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep DATE | grep -v 'DATE-' | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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216 | else
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217 | runstart=$runstart2
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218 | fi
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219 | fi
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220 | # in newest data start time is in DATE-END
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221 | # in older data start time is in TSTOP
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222 | # in the beginning TSTOP was empty
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223 | runstop=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep DATE-END | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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224 | runstop2=`$factpath/fitsdump -h -t Events $file 2>/dev/null | grep TSTOP | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9]T[0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{6}'`
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225 | if [ "$runstop" == "" ]
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226 | then
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227 | if [ "$runstop2" == "" ]
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228 | then
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229 | runstop=`stat $file 2>/dev/null | grep Modify | grep -E -o '20[1-9][0-9][\-][01][0-9][\-][0-3][0-9][ ][0-2][0-9]:[0-6][0-9]:[0-6][0-9][.][0-9]{9}'`
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230 | else
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231 | runstop=$runstop2
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232 | fi
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233 | fi
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234 | fi
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235 |
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236 | # set runtype to 'unknown', if no runtype could be retrieved from file
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237 | if [ "$runtype" == "" ]
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238 | then
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239 | runtype="n/a"
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240 | fi
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241 | # on 15.11.2011 the runtypes had different names
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242 | if [ "$date" == "2011/11/15" ]
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243 | then
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244 | if [ "$runtype" == "drs-calib" ]
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245 | then
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246 | runtype="drs-gain"
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247 | fi
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248 | if [ "$runtype" == "drs-time-calib" ]
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249 | then
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250 | runtype="drs-time"
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251 | fi
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252 | if [ "$runtype" == "pedestal" ]
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253 | then
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254 | runtype="drs-pedestal"
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255 | fi
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256 | if [ "$runtype" == "light-pulser" ]
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257 | then
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258 | runtype="light-pulser-ext"
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259 | fi
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260 | if [ "$runtype" == "pedestal-on" ]
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261 | then
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262 | runtype="pedestal"
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263 | fi
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264 | fi
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265 | # get runtype
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266 | query2="SELECT fRunTypeKEY FROM RunType WHERE fRunTypeName='"$runtype"'"
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267 | printprocesslog "DEBUG get run type from DB. QUERY:"$query2
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268 | result2=( `/usr/bin/mysql -u operator --host=fact01.fact.local --password=$password FactData -e "$query2"` )
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269 | if [ ${#result2} -eq 0 ]
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270 | then
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271 | printprocesslog "ERROR "$numberfromname": Could not query fRunTypeKey for runtype "$runtype" ."
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272 | continue
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273 | fi
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274 |
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275 | # check if entry has already checksums
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276 | query5="SELECT fNight FROM RunInfo WHERE Concat(fNight, '_', LPAD(fRunID, 3, 0))='"$numberfromname"'"
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277 | query5=$query5" AND NOT ISNULL(fMd5sumRaw) AND NOT ISNULL(fMd5sumRawZip)"
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278 | printprocesslog "DEBUG check if md5sums are alreay in DB. QUERY:"$query5
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279 | result5=`/usr/bin/mysql -u operator --host=fact01.fact.local --password=$password FactData -e "$query5"`
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280 |
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281 | # get md5sums of raw and zip file
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282 | # to safe time for tests and update this can be skipped ($skipmd5sum)
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283 | md5sum=
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284 | md5sumzip=
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285 | if [ "$skipmd5sum" == "no" ] || [ "$skipmd5sum" == "iffilled" ]
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286 | then
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287 | #echo "skip: "$skipmd5sum >> $logfile 2>&1
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288 | #echo "res5: -"$result5"-" >> $logfile 2>&1
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289 | #if [ "$skipmd5sum" == "no" ] || [ "$result5$skipmd5sum" == "iffilled" ]
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290 | if [ "$skipmd5sum" == "no" ] || [ "$result5" == "" ]
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291 | then
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292 | #zipfile=`echo $file | sed -e 's/raw/zipraw/' -e 's/fits/fits.gz/'`
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293 | # only do the md5sum if the zipfile is already available
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294 | if ls $file >/dev/null 2>&1
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295 | then
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296 | printprocesslog "INFO calculation md5sum for rawfile "$rawfile
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297 | md5sum=`md5sum $rawfile | cut -d' ' -f1`
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298 | printprocesslog "INFO calculation md5sum for zipfile "$file
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299 | md5sumzip=`md5sum $file | cut -d' ' -f1`
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300 | fi
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301 | fi
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302 | fi
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303 |
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304 | # insert or update depending on whether run exists
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305 | if [ "$result3" == "" ]
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306 | then
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307 | query4="INSERT"
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308 | querymid=" fNight="$runnumber", fRunID="$filenumberfromname", "
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309 | querystop=
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310 | else
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311 | query4="UPDATE"
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312 | querymid=
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313 | querystop=" WHERE fNight="$runnumber" AND fRunID="$filenumberfromname
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314 | fi
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315 | query4=$query4" RunInfo SET "$querymid" fRunTypeKey="${result2[1]}
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316 | if [ $numfitserrors -eq 0 ]
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317 | then
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318 | query4=$query4", fRunStart='"$runstart"', fRunStop='"$runstop"'"
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319 | if [ "$numevents" != "" ]
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320 | then
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321 | query4=$query4", fNumEvents="$numevents
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322 | fi
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323 | if [ "$roi" != "" ]
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324 | then
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325 | query4=$query4", fROI="$roi
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326 | fi
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327 | if [ "$roitm" != "" ]
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328 | then
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329 | query4=$query4", fROITimeMarker="$roitm
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330 | fi
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331 | if [ "$numphys" != "" ]
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332 | then
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333 | query4=$query4", fNumPhysicsTrigger="$numphys
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334 | fi
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335 | if [ "$numext1" != "" ]
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336 | then
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337 | query4=$query4", fNumExt1Trigger="$numext1
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338 | fi
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339 | if [ "$numext2" != "" ]
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340 | then
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341 | query4=$query4", fNumExt2Trigger="$numext2
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342 | fi
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343 | if [ "$numelp" != "" ]
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344 | then
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345 | query4=$query4", fNumELPTrigger="$numelp
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346 | fi
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347 | if [ "$numilp" != "" ]
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348 | then
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349 | query4=$query4", fNumILPTrigger="$numilp
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350 | fi
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351 | if [ "$numped" != "" ]
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352 | then
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353 | query4=$query4", fNumPedestalTrigger="$numped
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354 | fi
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355 | if [ "$numtime" != "" ]
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356 | then
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357 | query4=$query4", fNumTimeTrigger="$numtime
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358 | fi
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359 | if [ "$numoth" != "" ]
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360 | then
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361 | query4=$query4", fNumOtherTrigger="$numoth
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362 | fi
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363 | fi
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364 | if [ "$md5sum" != "" ]
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365 | then
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366 | query4=$query4", fMd5sumRaw='"$md5sum"', fMd5sumRawZip='"$md5sumzip"'"
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367 | fi
|
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368 | if [ "$numdrsfiles" != "" ]
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369 | then
|
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370 | query4=$query4", fHasDrsFile="$numdrsfiles
|
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371 | fi
|
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372 | if [ "$step" != "" ]
|
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373 | then
|
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374 | query4=$query4", fDrsStep="$step
|
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375 | fi
|
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376 | if [ "$compiletime" != "" ]
|
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377 | then
|
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378 | query4=$query4", fCompileTime='"$compiletime"'"
|
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379 | fi
|
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380 | if [ "$revnum" != "" ]
|
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381 | then
|
---|
382 | query4=$query4", fRevisionNumber='"$revnum"'"
|
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383 | fi
|
---|
384 | query4=$query4", fFitsFileErrors="$numfitserrors
|
---|
385 | query4=$query4" "$querystop
|
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386 | printprocesslog "INFO insert/update entry in DB. QUERY: "$query4
|
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387 | if ! /usr/bin/mysql -u operator --host=fact01.fact.local --password=$password FactData -e "$query4"
|
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388 | then
|
---|
389 | printprocesslog "ERROR insert/update of "$numfromfile" to mysql failed."
|
---|
390 | finish
|
---|
391 | fi
|
---|
392 | done
|
---|
393 | done
|
---|
394 |
|
---|
395 | finish
|
---|
396 |
|
---|