1 | #!/bin/sh -xvf |
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2 | #Perform the ON-OFF analysis |
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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 | dateSelected= |
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33 | #use -sim option to simulate processing (debug the script as if...) |
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34 | simulationMode=Off |
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35 | while [ $# -gt 0 ] |
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36 | do |
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37 | case "$1" in |
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38 | -src) sourceRadio=$2; shift;; |
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39 | -date) dateSelected=$2; shift;; |
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40 | -sim) simulationMode=On;; |
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41 | -h) |
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42 | echo >&2 \ |
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43 | "usage: $0 -src souce -date YYYYMMDD [-freq freq in MHz (default ${freqBAOCalib})] [-sim to trig simulation mode]" |
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44 | exit 1;; |
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45 | *) break;; # terminate while loop |
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46 | esac |
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47 | shift |
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48 | done |
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49 | |
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50 | if [ ${simulationMode} = "On" ]; then |
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51 | $ECHO "INFO ${scriptName} running in SIMUL mode" |
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52 | fi |
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53 | |
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54 | if [ "<${sourceRadio}>" = "<>" ]; then |
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55 | $ECHO "FATAL: You have forgotten to select the source option (-src)" |
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56 | exit 1 |
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57 | fi |
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58 | |
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59 | case ${sourceRadio} in |
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60 | Abell85) $ECHO "INFO (${scriptName}): process ${sourceRadio}";; |
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61 | Abell2440) $ECHO "INFO (${scriptName}): process ${sourceRadio}";; |
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62 | Abell1205) $ECHO "INFO (${scriptName}): process ${sourceRadio}";; |
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63 | *) ECHO "FATAL (${scriptName}): process ${sourceRadio} not yet foreseen" |
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64 | exit 1;; |
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65 | esac |
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66 | |
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67 | srclower=`${ECHO} ${sourceRadio} | ${TR} "[:upper:]" "[:lower:]" ` |
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68 | |
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69 | #Path to public backupable path |
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70 | publicpath="/afs/in2p3.fr/home/c/campagne/public" |
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71 | |
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72 | |
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73 | #temporary files to synchronize scripts |
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74 | tmppublicpath=${TMPPUBLICPATH} |
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75 | #wakeup the NFS disk |
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76 | $LS -l ${tmppublicpath} > /dev/null |
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77 | #clean previous spurious files |
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78 | $RM -f ${tmppublicpath}/*.finished |
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79 | |
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80 | #Path where the job will do temporary IO |
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81 | if [ ${ENVIRONMENT} = "INTERACTIVE" ]; then |
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82 | iojobpath="/sps/baoradio/AmasNancay/JEC" |
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83 | $MKDIR -p $iojobpath |
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84 | $ECHO "Usage in INTERACTIVE may be destructive... To be used with great care !!!!" |
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85 | exit 0; |
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86 | elif [ ${ENVIRONMENT} = "BATCH" ] ; then |
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87 | iojobpath=${TMPBATCH} |
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88 | else |
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89 | $ECHO "FATAL (${scriptName}): environment is ${ENVIRONMENT} not allowed" |
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90 | exit 1 |
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91 | fi |
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92 | cd ${iojobpath} |
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93 | |
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94 | localpath="${sourceRadio}" |
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95 | $MKDIR -p ./${localpath} |
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96 | cd ./${localpath} |
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97 | |
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98 | #save the top directory |
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99 | topDir=`pwd` |
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100 | |
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101 | #Path of the utility scripts |
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102 | scriptpath="/afs/in2p3.fr/home/c/campagne/private/work/AmasNancay" |
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103 | |
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104 | #JEC 1/10/11 Use generic baodaqstatus name |
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105 | #get the daq current irod status |
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106 | #tag=`${DATE} +%F` |
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107 | #OUT1=${publicpath}/baodaqstatus-${tag}.txt |
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108 | OUT1=${publicpath}/baodaqstatus-current.txt |
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109 | |
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110 | if [ ! -e ${OUT1} -o ! -r ${OUT1} ]; then |
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111 | $ECHO "FATAL (${scriptName}): ${OUT1} has a problem" |
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112 | exit 1 |
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113 | # $ECHO "We should bring the DAQ status more up to date, this take 1 or 2sec..." |
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114 | # $RM -f ${tmppublicpath}/statusdaq.finished |
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115 | # ${scriptpath}/statusdaq.sh > ${OUT1} |
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116 | # while [ ! -f "${tmppublicpath}/statusdaq.finished" ]; do |
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117 | # sleep 30 |
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118 | # done |
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119 | # $RM ${tmppublicpath}/statusdaq.finished |
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120 | #protect against remove/rewriting |
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121 | # $CHMOD -v 444 ${OUT1} |
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122 | fi |
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123 | |
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124 | |
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125 | |
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126 | $ECHO "You have selected sourceRadio = ${sourceRadio} [date = ${dateSelected}]" |
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127 | tableau=( `$GREP -i "${dateSelected}${srclower}" ${OUT1} | $AWK '( NF==4 ) { print $2 }' ` ) |
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128 | IFS=' |
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129 | ' |
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130 | tableau=( $( $PRINTF "%s\n" "${tableau[@]}" | $AWK 'x[$0]++ == 0' ) ) |
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131 | IFS=$DefaultIFS |
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132 | |
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133 | |
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134 | for i in ${tableau[@]} |
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135 | do |
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136 | # |
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137 | # start a "fresh" session |
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138 | cd ${topDir} |
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139 | $LS | $XARGS -i $RM -rf {} |
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140 | |
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141 | $ECHO "DEBUG: (${scriptName}) irods root dir $i" |
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142 | dateDAQ=`$ECHO ${i} | $AWK '{split($0,a,"/"); print a[6];}' | $AWK "{sub(/${srclower}/,\"\"); print}"` |
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143 | |
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144 | $ECHO "DEBUG: (${scriptName}): we are in directory `pwd` the topDir=${topDir}" |
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145 | $LS -lrt |
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146 | |
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147 | |
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148 | #JEC 1/10/11 Use generic baodaqstatus name |
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149 | #Look if the date has changed since beginning of the job! |
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150 | # curtag=`${DATE} +%F` |
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151 | # if [ "<${curtag}>" != "<${tag}>" ]; then |
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152 | # tag=${curtag} |
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153 | #it is necessary to update the daq status as the day has changed during the processing... (batch can take a long time...) |
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154 | # OUT1=${publicpath}/baodaqstatus-${curtag}.txt |
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155 | # $ECHO "We should bring the DAQ status more up to date, this take 1 or 2sec..." |
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156 | # $RM -f ${tmppublicpath}/statusdaq.finished |
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157 | # ${scriptpath}/statusdaq.sh > ${OUT1} |
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158 | # while [ ! -f "${tmppublicpath}/statusdaq.finished" ]; do |
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159 | # sleep 30 |
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160 | # done |
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161 | # $RM ${tmppublicpath}/statusdaq.finished |
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162 | #protect against remove/rewriting |
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163 | # $CHMOD -v 444 ${OUT1} |
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164 | # fi |
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165 | # |
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166 | # look if the gain & calibration files exist |
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167 | # |
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168 | gainDone=`ils ${i} 2>&1 | $GREP -i "gain_.*\.fits" | $WC -l` |
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169 | if [ ! ${gainDone} -gt 0 ]; then |
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170 | $ECHO "FATAL (${scriptName}): gain file DOES NOT exist skip `basename $i` " |
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171 | continue |
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172 | fi |
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173 | |
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174 | ###### |
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175 | $ECHO ">>>>>>>>>>>>> ANALYSIS Part of ${sourceRadio} ${dateDAQ}" |
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176 | #go to the .../source/date-sourcelowercase directory |
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177 | #download Off/datacycle<> and On/datacycle<> directories |
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178 | $MKDIR -p ${topDir}/${dateDAQ}${srclower} |
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179 | cd ${topDir}/${dateDAQ}${srclower} |
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180 | aboveOnOffDir=`pwd` |
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181 | $ECHO "DEBUG (${scriptName}): we are in directory: <`pwd`>" |
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182 | # |
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183 | mode="Off" |
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184 | $ECHO "DEBUG (${scriptName}): START download the ${mode} data fits files" |
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185 | inFileDirectory="./${mode}" |
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186 | $MKDIR -p ${inFileDirectory} |
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187 | listOfDataCycle=( `ils ${i}/${mode} 2>&1 | $GREP -i "datacycle"|$AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.10n` ) |
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188 | IFS=' |
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189 | ' |
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190 | listOfDataCycle=( $( $PRINTF "%s\n" "${listOfDataCycle[@]}" | $AWK 'x[$0]++ == 0' ) ) |
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191 | IFS=$DefaultIFS |
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192 | |
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193 | firstCycleOff=`$ECHO ${listOfDataCycle[0]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'` |
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194 | nCyclesOff=`expr ${#listOfDataCycle[*]} - 1` |
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195 | |
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196 | if [ ${nCyclesOff} -eq -1 ]; then |
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197 | continue |
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198 | fi |
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199 | |
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200 | lastCycleOff=`$ECHO ${listOfDataCycle[${nCyclesOff}]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'` |
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201 | |
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202 | listOfDataCycle=( "${listOfDataCycle[@]/#/${i}/${mode}/}" ) |
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203 | |
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204 | |
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205 | for j in ${listOfDataCycle[@]} |
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206 | do |
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207 | irodsDownDir="${j}" |
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208 | OUT=./getInFits.$$ |
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209 | iget -r -f -K ${irodsDownDir} ${inFileDirectory} > ${OUT} 2>&1 |
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210 | igetStatus=`$GREP "^ERROR" ${OUT}` |
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211 | if [ "<$igetStatus>" != "<>" ]; then |
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212 | $ECHO "FATAL (${scriptName}): error while iget fits files:" |
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213 | $ECHO $igetStatus |
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214 | $ECHO " ==> skip this run $sourceRadio $dateDAQ" |
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215 | continue |
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216 | fi |
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217 | $RM -f ${OUT} |
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218 | done |
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219 | $ECHO "DEBUG (${scriptName}): END download the ${mode} data fits files" |
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220 | # |
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221 | mode="On" |
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222 | $ECHO "DEBUG (${scriptName}): START download the ${mode} data fits files" |
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223 | inFileDirectory="./${mode}" |
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224 | $MKDIR -p ${inFileDirectory} |
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225 | |
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226 | listOfDataCycle=( `ils ${i}/${mode} 2>&1 | $GREP -i "datacycle" |$AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.10n` ) |
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227 | IFS=' |
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228 | ' |
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229 | listOfDataCycle=( $( $PRINTF "%s\n" "${listOfDataCycle[@]}" | $AWK 'x[$0]++ == 0' ) ) |
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230 | IFS=$DefaultIFS |
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231 | |
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232 | firstCycleOn=`$ECHO ${listOfDataCycle[0]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'` |
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233 | nCyclesOn=`expr ${#listOfDataCycle[*]} - 1` |
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234 | |
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235 | if [ ${nCyclesOn} -eq -1 ]; then |
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236 | continue |
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237 | fi |
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238 | |
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239 | lastCycleOn=`$ECHO ${listOfDataCycle[${nCyclesOn}]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'` |
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240 | |
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241 | listOfDataCycle=( "${listOfDataCycle[@]/#/${i}/${mode}/}" ) |
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242 | |
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243 | # |
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244 | #Check if there is the same number of cycles in Off and On mode |
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245 | # |
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246 | #first cycle = max(firstCycleOn, firstCycleOff) |
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247 | #last cycle = min(lastCycleOn,lastCycleOff) |
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248 | |
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249 | if [ ${firstCycleOn} -eq ${firstCycleOff} -a ${lastCycleOn} -eq ${lastCycleOff} ]; then |
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250 | firstCycle=${firstCycleOff} |
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251 | lastCycle=${lastCycleOff} |
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252 | else |
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253 | $ECHO "INFO (${scriptName}): missmatch between Off and On mode" |
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254 | $ECHO "${firstCycleOn} != ${firstCycleOff} OR ${lastCycleOn} != ${lastCycleOff}" |
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255 | firstCycle=${firstCycleOff} |
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256 | if [ ${firstCycleOn} -gt ${firstCycle} ]; then |
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257 | firstCycle=${firstCycleOn} |
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258 | fi |
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259 | lastCycle=${lastCycleOff} |
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260 | if [ ${lastCycleOn} -lt ${lastCycle} ]; then |
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261 | lastCycle=${lastCycleOn} |
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262 | fi |
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263 | fi |
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264 | $ECHO "INFO (${scriptName}): use cycles [${firstCycle}, ${lastCycle}]" |
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265 | |
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266 | |
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267 | for j in ${listOfDataCycle[@]} |
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268 | do |
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269 | irodsDownDir="${j}" |
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270 | OUT=./getInFits.$$ |
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271 | iget -r -f -K ${irodsDownDir} ${inFileDirectory} > ${OUT} 2>&1 |
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272 | igetStatus=`$GREP "^ERROR" ${OUT}` |
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273 | if [ "<$igetStatus>" != "<>" ]; then |
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274 | $ECHO "FATAL (${scriptName}): error while iget fits files:" |
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275 | $ECHO $igetStatus |
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276 | $ECHO " ==> skip this run $sourceRadio $dateDAQ" |
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277 | continue |
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278 | fi |
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279 | $RM -f ${OUT} |
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280 | done |
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281 | $ECHO "DEBUG (${scriptName}): END download the ${mode} data fits files" |
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282 | #Get sca file |
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283 | $ECHO "DEBUG (${scriptName}): START call getscafiles.sh ${sourceRadio} ${dateDAQ}" |
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284 | OUT1=./getScaStatus.$$ |
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285 | $RM -f ${tmppublicpath}/getscafiles.finished |
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286 | ${scriptpath}/getscafiles.sh ${sourceRadio} ${dateDAQ} > ${OUT1} 2>&1 |
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287 | while [ ! -f "${tmppublicpath}/getscafiles.finished" ]; do |
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288 | $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/getscafiles.finished" |
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289 | date +%T |
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290 | sleep 30 |
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291 | done |
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292 | $RM ${tmppublicpath}/getscafiles.finished |
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293 | $ECHO "DEBUG (${scriptName}): END" |
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294 | # |
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295 | getScaStatus=`$GREP "^\(FATAL\|ERROR\)" ${OUT1}` |
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296 | # |
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297 | if [ "<${getScaStatus}>" != "<>" ]; then |
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298 | $ECHO "FATAL (${scriptName}): error to get sca file for $sourceRadio $dateDAQ" |
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299 | $ECHO "DEBUG (${scriptName}): START with cat ${OUT1}" |
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300 | $CAT ${OUT1} |
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301 | $ECHO "DEBUG (${scriptName}): END" |
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302 | continue |
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303 | fi |
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304 | $RM -f ${OUT1} |
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305 | |
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306 | scaFile=`$FIND . -name "sca*.sum.trans" | $XARGS -i basename {}` |
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307 | |
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308 | |
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309 | #prepare job submission |
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310 | cd ${aboveOnOffDir} |
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311 | #the default spectra name is medfiltmtx, otherwise use -specname <a_string> |
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312 | |
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313 | logFile="analyse_RAWDATA_${sourceRadio}_${dateDAQ}.log" |
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314 | $ECHO "DEBUG (${scriptName}): execute the analysis... should not take long. `date`" |
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315 | if [ ${simulationMode} = "On" ]; then |
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316 | $ECHO "SIMUL: ${scriptpath}/Objs/analyse -act rawOnOff -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir datacycle -numcycle ${firstCycle},${lastCycle} -debug 1 >& ${logFile}" |
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317 | cat > ${logFile} <<EOF |
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318 | Ok rawOnOff finished |
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319 | EOF |
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320 | else |
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321 | ${scriptpath}/Objs/analyse -act rawOnOff -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir datacycle -numcycle ${firstCycle},${lastCycle} -debug 1 >& ${logFile} |
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322 | fi |
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323 | $ECHO "DEBUG (${scriptName}): analysis finished `date`. Look for errors before saving to Irods" |
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324 | rcstatus=`$GREP -i "Ok rawOnOff finished" ${logFile} | $WC -l` |
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325 | if [ ${rcstatus} -eq 0 ]; then |
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326 | $ECHO "INFO (${scriptName}): analysis problem for ${sourceRadio} ${dateDAQ}" |
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327 | $ECHO " START logfile" |
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328 | $CAT ${logFile} |
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329 | $ECHO " END logFile" |
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330 | #clean and leave |
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331 | cd ${aboveOnOffDir} |
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332 | $LS | $XARGS -i $RM -rf {} |
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333 | continue |
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334 | fi |
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335 | #Save into Irods |
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336 | $ECHO "DEBUG (${scriptName}): START save output files" |
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337 | $LS ${aboveOnOffDir} |
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338 | #use -f option for iput ONLY to force override |
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339 | if [ ${simulationMode} = "On" ]; then |
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340 | $ECHO "SIMUL: here we look for output files and put them in Irods" |
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341 | else |
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342 | $LS -lrth |
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343 | $FIND . -name "dataRaw_*" -print | $XARGS -i iput -f -v -K {} ${i} |
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344 | $FIND . -name "diffOnOffRaw_*" -print | $XARGS -i iput -f -v -K {} ${i} |
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345 | fi |
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346 | #save analysis logfile |
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347 | $LS -l ${tmppublicpath} > /dev/null |
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348 | $CP ${logFile} ${tmppublicpath} |
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349 | $ECHO "DEBUG (${scriptName}): END save output files" |
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350 | #clean up to avoid scratch SIZE EXCEED LIMIT |
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351 | cd ${aboveOnOffDir} |
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352 | $LS | $XARGS -i $RM -rf {} |
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353 | |
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354 | done |
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355 | |
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356 | exit 0 |
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