1 | #!/bin/sh -xvf |
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2 | #download SCA file, proceed to introspection, and upload results |
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3 | DATE=/bin/date |
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4 | GREP=/bin/grep |
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5 | AWK=/bin/awk |
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6 | ECHO=/bin/echo |
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7 | WC=/usr/bin/wc |
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8 | CAT=/bin/cat |
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9 | PRINTF=/usr/bin/printf |
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10 | FIND=/usr/bin/find |
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11 | MKDIR=/bin/mkdir |
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12 | XARGS=/usr/bin/xargs |
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13 | SORT=/bin/sort |
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14 | RM=/bin/rm |
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15 | TR=/usr/bin/tr |
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16 | CP=/bin/cp |
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17 | LS=/bin/ls |
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18 | CHMOD=/bin/chmod |
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19 | |
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20 | DefaultIFS=$' \t\n' |
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21 | IFS=$DefaultIFS |
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22 | |
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23 | #set Irods environment |
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24 | . /usr/local/shared/bin/irods_env.sh -noverbose |
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25 | |
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26 | scriptName="`basename $0`" |
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27 | $ECHO "Processing script ${scriptName} at `date`" |
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28 | #which source to analyse |
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29 | |
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30 | #Process cmd line args: the -src option is mandatory (source name as Abell85) |
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31 | sourceRadio= |
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32 | freqBAOCalib=1346 |
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33 | bwBAOCalib=6.25 |
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34 | #use -sim option to simulate processing (debug the script as if...) |
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35 | simulationMode=Off |
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36 | while [ $# -gt 0 ] |
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37 | do |
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38 | case "$1" in |
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39 | -src) sourceRadio=$2; shift;; |
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40 | -freq) freqBAOCalib=$2; shift;; |
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41 | -bwd) bwBAOCalib=$2; shift;; |
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42 | -sim) simulationMode=On;; |
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43 | -h) |
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44 | echo >&2 \ |
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45 | "usage: $0 -src souce [-freq freq in MHz (default ${freqBAOCalib})] [-bwd bandwidth in MHz (default ${bwBAOCalib})]" |
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46 | exit 1;; |
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47 | *) break;; # terminate while loop |
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48 | esac |
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49 | shift |
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50 | done |
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51 | |
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52 | if [ ${simulationMode} = "On" ]; then |
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53 | $ECHO "INFO ${scriptName} running in SIMUL mode" |
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54 | fi |
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55 | |
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56 | if [ "<${sourceRadio}>" = "<>" ]; then |
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57 | $ECHO "FATAL: You have forgotten to select the source option (-src)" |
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58 | exit 1 |
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59 | fi |
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60 | |
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61 | case ${sourceRadio} in |
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62 | Abell85) $ECHO "INFO (${scriptName}): process ${sourceRadio}";; |
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63 | Abell2440) $ECHO "INFO (${scriptName}): process ${sourceRadio}";; |
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64 | Abell1205) $ECHO "INFO (${scriptName}): process ${sourceRadio}";; |
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65 | *) ECHO "FATAL (${scriptName}): process ${sourceRadio} not yet foreseen" |
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66 | exit 1;; |
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67 | esac |
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68 | |
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69 | srclower=`${ECHO} ${sourceRadio} | ${TR} "[:upper:]" "[:lower:]" ` |
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70 | |
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71 | #Path to public backupable path |
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72 | publicpath="/afs/in2p3.fr/home/c/campagne/public" |
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73 | |
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74 | |
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75 | #temporary files to synchronize scripts |
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76 | tmppublicpath=${TMPPUBLICPATH} |
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77 | #wakeup the NFS disk |
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78 | $LS -l ${tmppublicpath} > /dev/null |
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79 | #clean previous spurious files |
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80 | $RM -f ${tmppublicpath}/*.finished |
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81 | |
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82 | #Path where the job will do temporary IO |
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83 | if [ ${ENVIRONMENT} = "INTERACTIVE" ]; then |
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84 | iojobpath="/sps/baoradio/AmasNancay/JEC" |
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85 | $MKDIR -p $iojobpath |
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86 | $ECHO "Usage in INTERACTIVE may be destructive... To be used with great care !!!!" |
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87 | exit 0; |
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88 | elif [ ${ENVIRONMENT} = "BATCH" ] ; then |
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89 | iojobpath=${TMPBATCH} |
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90 | else |
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91 | $ECHO "FATAL (${scriptName}): environment is ${ENVIRONMENT} not allowed" |
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92 | exit 1 |
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93 | fi |
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94 | cd ${iojobpath} |
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95 | |
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96 | localpath="${sourceRadio}" |
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97 | $MKDIR -p ./${localpath} |
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98 | cd ./${localpath} |
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99 | |
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100 | #save the top directory |
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101 | topDir=`pwd` |
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102 | |
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103 | #Path of the utility scripts |
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104 | scriptpath=${SCRIPTPATH} |
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105 | |
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106 | #JEC 1/10/11 Use generic baodaqstatus name |
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107 | OUT1=${publicpath}/baodaqstatus-current.txt |
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108 | # |
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109 | #get the daq current irod status |
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110 | #tag=`${DATE} +%F` |
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111 | #OUT1=${publicpath}/baodaqstatus-${tag}.txt |
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112 | # |
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113 | if [ ! -e ${OUT1} -o ! -r ${OUT1} ]; then |
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114 | $ECHO "FATAL (${scriptName}): ${OUT1} has a problem" |
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115 | exit 1 |
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116 | # $ECHO "We should bring the DAQ status more up to date, this take 1 or 2sec..." |
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117 | # $RM -f ${tmppublicpath}/statusdaq.finished |
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118 | # ${scriptpath}/statusdaq.sh > ${OUT1} |
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119 | # while [ ! -f "${tmppublicpath}/statusdaq.finished" ]; do |
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120 | # sleep 30 |
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121 | # done |
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122 | # $RM ${tmppublicpath}/statusdaq.finished |
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123 | #protect against remove/rewriting |
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124 | # $CHMOD -v 444 ${OUT1} |
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125 | fi |
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126 | |
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127 | |
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128 | #Nb: if we want to implement a loop on sources we have to take care of srclower... |
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129 | |
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130 | $ECHO "You have selected sourceRadio = $sourceRadio" |
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131 | tableau=( `$GREP -i ${sourceRadio} ${OUT1} | $AWK '( NF==4 ) { print $2 }' ` ) |
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132 | IFS=' |
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133 | ' |
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134 | tableau=( $( $PRINTF "%s\n" "${tableau[@]}" | $AWK 'x[$0]++ == 0' ) ) |
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135 | IFS=$DefaultIFS |
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136 | |
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137 | |
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138 | for i in ${tableau[@]} |
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139 | do |
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140 | # |
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141 | # start a "fresh" session |
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142 | cd ${topDir} |
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143 | $LS | $XARGS -i $RM -rf {} |
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144 | |
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145 | |
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146 | $ECHO "DEBUG: (${scriptName}) irods root dir $i" |
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147 | dateDAQ=`$ECHO ${i} | $AWK '{split($0,a,"/"); print a[6];}' | $AWK "{sub(/${srclower}/,\"\"); print}"` |
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148 | |
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149 | $ECHO "DEBUG: (${scriptName}): we are in directory `pwd` the topDir=${topDir}" |
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150 | $LS -lrt |
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151 | |
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152 | |
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153 | #JEC 1/10/11 Use generic baodaqstatus name |
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154 | #Look if the date has changed since beginning of the job! |
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155 | # curtag=`${DATE} +%F` |
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156 | # if [ "<${curtag}>" != "<${tag}>" ]; then |
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157 | # tag=${curtag} |
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158 | #it is necessary to update the daq status as the day has changed during the processing... (batch can take a long time...) |
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159 | # OUT1=${publicpath}/baodaqstatus-${curtag}.txt |
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160 | # $ECHO "We should bring the DAQ status more up to date, this take 1 or 2sec..." |
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161 | # $RM -f ${tmppublicpath}/statusdaq.finished |
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162 | # ${scriptpath}/statusdaq.sh > ${OUT1} |
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163 | # while [ ! -f "${tmppublicpath}/statusdaq.finished" ]; do |
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164 | # sleep 30 |
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165 | # done |
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166 | # $RM ${tmppublicpath}/statusdaq.finished |
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167 | #protect against remove/rewriting |
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168 | # $CHMOD -v 444 ${OUT1} |
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169 | # fi |
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170 | # |
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171 | # look if the calibration files already exist |
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172 | # |
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173 | alreadyDone=`ils ${i} 2>&1 | $GREP -i "calib_.*\.txt" | $WC -l` |
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174 | if [ ${alreadyDone} -gt 0 ]; then |
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175 | $ECHO "INFO (${scriptName}): calibration coef files already exist" |
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176 | continue |
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177 | fi |
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178 | # |
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179 | somethingTodo=1 |
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180 | input4calibOff=`ils ${i}/Off 2>&1 | $GREP -i "calibcycle" | $AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.11n` |
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181 | input4calibOn=`ils ${i}/On 2>&1 | $GREP -i "calibcycle" | $AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.11n` |
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182 | # |
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183 | if [ "<${input4calibOff}>" != "<>" -a "<${input4calibOn}>" != "<>" ]; then |
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184 | #look at the content of the calibcycle directory as may be the previous batch job has crashed |
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185 | tableauOff=( `$ECHO ${input4calibOff}` ) |
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186 | IFS=' |
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187 | ' |
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188 | tableauOff=( $( $PRINTF "%s\n" "${tableauOff[@]}" | $AWK 'x[$0]++ == 0' ) ) |
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189 | IFS=$DefaultIFS |
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190 | # |
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191 | nTotFilesOff=0 |
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192 | for j in ${tableauOff[@]} |
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193 | do |
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194 | nFiles=`ils ${i}/Off/${j} | $GREP -i "medfiltmtx" | $WC -l` |
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195 | nTotFilesOff=`expr ${nTotFilesOff} + ${nFiles}` |
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196 | done |
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197 | # |
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198 | tableauOn=( `$ECHO ${input4calibOn}` ) |
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199 | IFS=' |
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200 | ' |
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201 | tableauOn=( $( $PRINTF "%s\n" "${tableauOn[@]}" | $AWK 'x[$0]++ == 0' ) ) |
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202 | IFS=$DefaultIFS |
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203 | # |
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204 | nTotFilesOn=0 |
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205 | for j in ${tableauOn[@]} |
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206 | do |
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207 | nFiles=`ils ${i}/On/${j} | $GREP -i "medfiltmtx" | $WC -l` |
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208 | nTotFilesOn=`expr ${nTotFilesOn} + ${nFiles}` |
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209 | done |
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210 | diffOnOff=`expr ${nTotFilesOff} - ${nTotFilesOn}` |
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211 | if [ ${diffOnOff} -lt 0 ]; then |
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212 | zero=0 |
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213 | diffOnOff=`expr ${zero} - ${diffOnOff}` |
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214 | fi |
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215 | #allow up to 5 files differences |
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216 | if [ ${nTotFilesOff} -gt 0 -a ${nTotFilesOn} -gt 0 ]; then |
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217 | somethingTodo=0 |
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218 | $ECHO "DEBUG (${scriptName}): $sourceRadio $dateDAQ has <${nTotFilesOff}> Off-files and <${nTotFilesOn}> On-files but OK" |
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219 | else |
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220 | $ECHO "INFO (${scriptName}): $sourceRadio $dateDAQ has <${nTotFilesOff}> Off-files and <${nTotFilesOn}> On-files => one should rebuild has something is wrong" |
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221 | fi |
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222 | # |
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223 | fi |
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224 | if [ ${somethingTodo} -eq 1 ]; then |
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225 | # |
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226 | $ECHO ">>>>>>>>>>>>>>>> Do $sourceRadio $dateDAQ CALIBOFF" |
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227 | $RM -f ${tmppublicpath}/proc_script.finished |
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228 | if [ ${simulationMode} = "On" ]; then |
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229 | $ECHO "SIMUL: ${scriptpath}/proc_script.sh $sourceRadio $dateDAQ CALIBOFF" |
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230 | else |
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231 | ${scriptpath}/proc_script.sh $sourceRadio $dateDAQ CALIBOFF |
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232 | while [ ! -e "${tmppublicpath}/proc_script.finished" ]; do |
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233 | $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/proc_script.finished" |
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234 | date +%T |
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235 | sleep 60 |
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236 | done |
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237 | fi |
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238 | $ECHO "INFO (${scriptName}): proc_script has finished" |
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239 | $ECHO ">>>>>>>>>>>> Done $sourceRadio $dateDAQ CALIBOFF" |
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240 | $ECHO ">>>>>>>>>>>>>>>> Do $sourceRadio $dateDAQ CALIBON" |
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241 | $RM ${tmppublicpath}/proc_script.finished |
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242 | |
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243 | if [ ${simulationMode} = "On" ]; then |
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244 | $ECHO "SIMUL: ${scriptpath}/proc_script.sh $sourceRadio $dateDAQ CALIBON" |
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245 | else |
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246 | ${scriptpath}/proc_script.sh $sourceRadio $dateDAQ CALIBON |
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247 | while [ ! -e "${tmppublicpath}/proc_script.finished" ]; do |
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248 | $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/proc_script.finished" |
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249 | date +%T |
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250 | sleep 60 |
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251 | done |
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252 | fi |
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253 | $ECHO "INFO (${scriptName}): proc_script has finished" |
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254 | $RM ${tmppublicpath}/proc_script.finished |
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255 | #Todo see if there is errors in the log file before copy |
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256 | $ECHO ">>>>>>>>>>>> Done $sourceRadio $dateDAQ CALIBON" |
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257 | ###### |
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258 | else |
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259 | ###### |
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260 | $ECHO ">>>>>>>>>>>>> ANALYSIS Part of ${sourceRadio} ${dateDAQ}" |
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261 | #go to the .../source/date-sourcelowercase directory |
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262 | #download Off/calibcycle<> and On/calibcycle<> directories |
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263 | $MKDIR -p ${topDir}/${dateDAQ}${srclower} |
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264 | cd ${topDir}/${dateDAQ}${srclower} |
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265 | aboveOnOffDir=`pwd` |
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266 | $ECHO "DEBUG (${scriptName}): we are in directory: <`pwd`>" |
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267 | # |
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268 | mode="Off" |
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269 | $ECHO "DEBUG (${scriptName}): START download the ${mode} calib fits files" |
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270 | inFileDirectory="./${mode}" |
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271 | $MKDIR -p ${inFileDirectory} |
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272 | listOfCalibCycle=( `ils ${i}/${mode} 2>&1 | $GREP -i "calibcycle"|$AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.11n` ) |
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273 | IFS=' |
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274 | ' |
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275 | listOfCalibCycle=( $( $PRINTF "%s\n" "${listOfCalibCycle[@]}" | $AWK 'x[$0]++ == 0' ) ) |
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276 | IFS=$DefaultIFS |
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277 | |
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278 | firstCycleOff=`$ECHO ${listOfCalibCycle[0]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'` |
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279 | nCyclesOff=`expr ${#listOfCalibCycle[*]} - 1` |
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280 | |
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281 | lastCycleOff=`$ECHO ${listOfCalibCycle[${nCyclesOff}]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'` |
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282 | |
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283 | listOfCalibCycle=( "${listOfCalibCycle[@]/#/${i}/${mode}/}" ) |
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284 | |
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285 | |
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286 | for j in ${listOfCalibCycle[@]} |
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287 | do |
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288 | irodsDownDir="${j}" |
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289 | OUT=./getInFits.$$ |
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290 | iget -r -f -K ${irodsDownDir} ${inFileDirectory} > ${OUT} 2>&1 |
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291 | igetStatus=`$GREP "^ERROR" ${OUT}` |
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292 | if [ "<$igetStatus>" != "<>" ]; then |
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293 | $ECHO "FATAL (${scriptName}): error while iget fits files:" |
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294 | $ECHO $igetStatus |
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295 | $ECHO " ==> skip this run $sourceRadio $dateDAQ" |
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296 | continue |
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297 | fi |
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298 | $RM -f ${OUT} |
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299 | done |
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300 | $ECHO "DEBUG (${scriptName}): END download the ${mode} calib fits files" |
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301 | # |
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302 | mode="On" |
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303 | $ECHO "DEBUG (${scriptName}): START download the ${mode} calib fits files" |
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304 | inFileDirectory="./${mode}" |
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305 | $MKDIR -p ${inFileDirectory} |
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306 | |
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307 | listOfCalibCycle=( `ils ${i}/${mode} 2>&1 | $GREP -i "calibcycle" |$AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.11n` ) |
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308 | IFS=' |
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309 | ' |
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310 | listOfCalibCycle=( $( $PRINTF "%s\n" "${listOfCalibCycle[@]}" | $AWK 'x[$0]++ == 0' ) ) |
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311 | IFS=$DefaultIFS |
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312 | |
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313 | firstCycleOn=`$ECHO ${listOfCalibCycle[0]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'` |
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314 | nCyclesOn=`expr ${#listOfCalibCycle[*]} - 1` |
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315 | |
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316 | lastCycleOn=`$ECHO ${listOfCalibCycle[${nCyclesOn}]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'` |
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317 | |
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318 | listOfCalibCycle=( "${listOfCalibCycle[@]/#/${i}/${mode}/}" ) |
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319 | |
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320 | |
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321 | # |
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322 | #Check if there is the same number of cycles in Off and On mode |
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323 | # |
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324 | #first cycle = max(firstCycleOn, firstCycleOff) |
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325 | #last cycle = min(lastCycleOn,lastCycleOff) |
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326 | |
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327 | if [ ${firstCycleOn} -eq ${firstCycleOff} -a ${lastCycleOn} -eq ${lastCycleOff} ]; then |
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328 | firstCycle=${firstCycleOff} |
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329 | lastCycle=${lastCycleOff} |
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330 | else |
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331 | $ECHO "INFO (${scriptName}): missmatch between Off and On mode" |
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332 | $ECHO "${firstCycleOn} != ${firstCycleOff} OR ${lastCycleOn} != ${lastCycleOff}" |
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333 | firstCycle=${firstCycleOff} |
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334 | if [ ${firstCycleOn} -gt ${firstCycle} ]; then |
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335 | firstCycle=${firstCycleOn} |
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336 | fi |
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337 | lastCycle=${lastCycleOff} |
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338 | if [ ${lastCycleOn} -lt ${lastCycle} ]; then |
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339 | lastCycle=${lastCycleOn} |
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340 | fi |
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341 | fi |
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342 | $ECHO "INFO (${scriptName}): use cycles [${firstCycle}, ${lastCycle}]" |
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343 | |
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344 | |
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345 | for j in ${listOfCalibCycle[@]} |
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346 | do |
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347 | irodsDownDir="${j}" |
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348 | OUT=./getInFits.$$ |
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349 | iget -r -f -K ${irodsDownDir} ${inFileDirectory} > ${OUT} 2>&1 |
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350 | igetStatus=`$GREP "^ERROR" ${OUT}` |
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351 | if [ "<$igetStatus>" != "<>" ]; then |
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352 | $ECHO "FATAL (${scriptName}): error while iget fits files:" |
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353 | $ECHO $igetStatus |
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354 | $ECHO " ==> skip this run $sourceRadio $dateDAQ" |
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355 | continue |
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356 | fi |
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357 | $RM -f ${OUT} |
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358 | done |
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359 | $ECHO "DEBUG (${scriptName}): END download the ${mode} calib fits files" |
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360 | #Get sca file |
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361 | $ECHO "DEBUG (${scriptName}): START call getscafiles.sh ${sourceRadio} ${dateDAQ}" |
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362 | OUT1=./getScaStatus.$$ |
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363 | $RM -f ${tmppublicpath}/getscafiles.finished |
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364 | ${scriptpath}/getscafiles.sh ${sourceRadio} ${dateDAQ} > ${OUT1} 2>&1 |
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365 | while [ ! -f "${tmppublicpath}/getscafiles.finished" ]; do |
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366 | $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/getscafiles.finished" |
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367 | date +%T |
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368 | sleep 30 |
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369 | done |
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370 | $RM ${tmppublicpath}/getscafiles.finished |
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371 | $ECHO "DEBUG (${scriptName}): END" |
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372 | # |
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373 | getScaStatus=`$GREP "^\(FATAL\|ERROR\)" ${OUT1}` |
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374 | # |
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375 | if [ "<${getScaStatus}>" != "<>" ]; then |
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376 | $ECHO "FATAL (${scriptName}): error to get sca file for $sourceRadio $dateDAQ" |
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377 | $ECHO "DEBUG (${scriptName}): START with cat ${OUT1}" |
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378 | $CAT ${OUT1} |
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379 | $ECHO "DEBUG (${scriptName}): END" |
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380 | continue |
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381 | fi |
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382 | $RM -f ${OUT1} |
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383 | |
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384 | scaFile=`$FIND . -name "sca*.sum.trans" | $XARGS -i basename {}` |
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385 | |
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386 | #prepare job submission |
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387 | cd ${aboveOnOffDir} |
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388 | #the default spectra name is medfiltmtx, otherwise use -specname <a_string> |
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389 | |
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390 | logFile="analyse_CALIB_${sourceRadio}_${dateDAQ}.log" |
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391 | $ECHO "DEBUG (${scriptName}): execute the analysis... should not take long. `date`" |
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392 | if [ ${simulationMode} = "On" ]; then |
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393 | $ECHO "SIMUL: ${scriptpath}/Objs/analyse -act calib -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir calibcycle -numcycle ${firstCycle},${lastCycle} -calibopt mean -debuglev 1 -freqBAOCalib ${freqBAOCalib} -bwBAOCalib ${bwBAOCalib} >& ${logFile}" |
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394 | cat > ${logFile} <<EOF |
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395 | Ok calibration finished |
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396 | EOF |
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397 | else |
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398 | ${scriptpath}/Objs/analyse -act calib -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir calibcycle -numcycle ${firstCycle},${lastCycle} -calibopt mean -debuglev 1 -freqBAOCalib ${freqBAOCalib} -bwBAOCalib ${bwBAOCalib} >& ${logFile} |
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399 | fi |
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400 | $ECHO "DEBUG (${scriptName}): analysis finished `date`. Look for errors before saving to Irods" |
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401 | rcstatus=`$GREP -i "Ok calibration finished" ${logFile} | $WC -l` |
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402 | if [ ${rcstatus} -eq 0 ]; then |
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403 | $ECHO "INFO (${scriptName}): analysis problem for ${sourceRadio} ${dateDAQ}" |
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404 | $ECHO " START logfile" |
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405 | $CAT ${logFile} |
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406 | $ECHO " END logFile" |
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407 | #clean and leave |
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408 | cd ${aboveOnOffDir} |
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409 | $LS | $XARGS -i $RM -rf {} |
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410 | continue |
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411 | fi |
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412 | #Save into Irods |
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413 | $ECHO "DEBUG (${scriptName}): START save output files" |
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414 | $LS ${aboveOnOffDir} |
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415 | #use -f option for iput ONLY to force override |
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416 | if [ ${simulationMode} = "On" ]; then |
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417 | $ECHO "SIMUL: here we look for calib file and put them in Irods" |
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418 | else |
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419 | $FIND . -name "calib_*" -print | $XARGS -i iput -v -K {} ${i} |
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420 | fi |
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421 | #save analysis logfile |
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422 | $LS -l ${tmppublicpath} > /dev/null |
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423 | $CP ${logFile} ${tmppublicpath} |
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424 | $ECHO "DEBUG (${scriptName}): END save output files" |
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425 | #clean up to avoid scratch SIZE EXCEED LIMIT |
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426 | cd ${aboveOnOffDir} |
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427 | $LS | $XARGS -i $RM -rf {} |
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428 | fi |
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429 | done |
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430 | |
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431 | exit 0 |
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