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 ${scriptName} at `date`" |
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28 | |
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29 | #$ECHO "SHOULD BE RETUNED FOR THE inPath cmd line of analyse.cc (Sorry...): 21/7/11 by JEC" |
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30 | #exit 1 |
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31 | |
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32 | #Process cmd line args: the -src option is mandatory (source name as Abell85) |
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33 | sourceRadio= |
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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 | -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 [-sim]" |
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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 ${scriptName} running in SIMUL mode" |
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52 | fi |
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53 | |
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54 | |
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55 | if [ "<${sourceRadio}>" = "<>" ]; then |
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56 | $ECHO "FATAL: You have forgotten to select the source option (-src)" |
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57 | exit 1 |
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58 | fi |
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59 | |
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60 | case ${sourceRadio} in |
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61 | Abell85) $ECHO "INFO (${scriptName}): process ${sourceRadio}";; |
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62 | Abell2440) $ECHO "INFO (${scriptName}): process ${sourceRadio}";; |
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63 | Abell1205) $ECHO "INFO (${scriptName}): process ${sourceRadio}";; |
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64 | *) ECHO "FATAL (${scriptName}): process ${sourceRadio} not yet foreseen" |
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65 | exit 1;; |
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66 | esac |
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67 | |
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68 | |
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69 | srclower=`${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 | $LS -l ${tmppublicpath} > /dev/null |
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78 | |
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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 | elif [ ${ENVIRONMENT} = "BATCH" ] ; then |
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85 | iojobpath=${TMPBATCH} |
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86 | else |
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87 | $ECHO "FATAL (${scriptName}): environment is ${ENVIRONMENT} not allowed" |
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88 | exit 1 |
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89 | fi |
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90 | cd ${iojobpath} |
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91 | |
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92 | localpath="${sourceRadio}" |
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93 | $MKDIR -p ./${localpath} |
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94 | cd ./${localpath} |
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95 | |
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96 | #save the top directory |
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97 | topDir=`pwd` |
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98 | |
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99 | #Path of the utility scripts |
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100 | scriptpath="/afs/in2p3.fr/home/c/campagne/private/work/AmasNancay" |
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101 | |
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102 | |
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103 | #get the daq current irod status |
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104 | tag=`${DATE} +%F` |
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105 | OUT1=${publicpath}/baodaqstatus-${tag}.txt |
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106 | |
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107 | if [ ! -e ${OUT1} -o ! -r ${OUT1} ]; then |
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108 | $ECHO "We should bring the DAQ status more up to date, this take 1 or 2sec..." |
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109 | $RM -f ${tmppublicpath}/statusdaq.finished |
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110 | ${scriptpath}/statusdaq.sh > ${OUT1} |
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111 | while [ ! -f "${tmppublicpath}/statusdaq.finished" ]; do |
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112 | sleep 30 |
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113 | done |
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114 | $RM ${tmppublicpath}/statusdaq.finished |
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115 | #protect against remove/rewriting |
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116 | $CHMOD -v 444 ${OUT1} |
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117 | fi |
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118 | |
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119 | # |
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120 | #We forbib to perform the gain for all the sources in one shot! |
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121 | # |
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122 | #if [ ! "<${sourceRadio}>" = "All" ]; then |
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123 | $ECHO "You have selected sourceRadio = $sourceRadio" |
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124 | tableau=( `$GREP -i ${sourceRadio} ${OUT1} | $AWK '( NF==4 ) { print $2 }' ` ) |
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125 | #else |
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126 | # tableau=( `$CAT ${OUT1} | $AWK '( NF==4 ) { print $2 }'` ) |
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127 | #fi |
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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 | $ECHO "DEBUG (${scriptName}): irods root dir $i" |
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137 | dateDAQ=`$ECHO ${i} | $AWK '{split($0,a,"/"); print a[6];}' | $AWK "{sub(/${srclower}/,\"\"); print}"` |
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138 | #Look if the date has changed since beginning of the job! |
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139 | curtag=`${DATE} +%F` |
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140 | if [ "<${curtag}>" != "<${tag}>" ]; then |
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141 | tag=${curtag} |
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142 | #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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143 | OUT1=${publicpath}/baodaqstatus-${curtag}.txt |
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144 | $ECHO "We should bring the DAQ status more up to date, this take 1 or 2sec..." |
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145 | $RM -f ${tmppublicpath}/statusdaq.finished |
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146 | ${scriptpath}/statusdaq.sh > ${OUT1} |
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147 | while [ ! -f "${tmppublicpath}/statusdaq.finished" ]; do |
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148 | sleep 30 |
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149 | done |
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150 | $RM ${tmppublicpath}/statusdaq.finished |
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151 | #protect against remove/rewriting |
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152 | $CHMOD -v 444 ${OUT1} |
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153 | fi |
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154 | # |
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155 | # look if the fits file of the gains already exists |
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156 | alreadyDone=`ils ${i} 2>&1 | $GREP -i "gain_.*\.fits" | $WC -l` |
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157 | if [ ${alreadyDone} -gt 0 ]; then |
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158 | $ECHO "INFO (${scriptName}): Fits file for gains already exists" |
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159 | continue |
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160 | fi |
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161 | # Something should be done... |
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162 | #look if the files for the input to gain computations have been done |
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163 | somethingTodo=1 |
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164 | input4gainOk1=`ils ${i}/Off 2>&1 | $GREP -i "^ERROR" | $WC -l` |
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165 | input4gainOk2=`ils ${i}/Off 2>&1 | $GREP -i "gaincycle"` |
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166 | if [ $input4gainOk1 -eq 0 -a "<${input4gainOk2}>" != "<>" ]; then |
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167 | gaincycle=`$ECHO ${input4gainOk2} | $AWK '($1 == "C-"){print $2}'| $XARGS -i basename {}` |
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168 | input4gainOk3=`ils ${i}/Off/${gaincycle} 2>&1 | $GREP -i "medfiltmtx" | $WC -l` |
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169 | if [ $input4gainOk3 -gt 0 ]; then |
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170 | somethingTodo=0 |
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171 | fi |
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172 | fi |
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173 | if [ $somethingTodo -eq 1 ]; then |
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174 | # |
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175 | $ECHO ">>>>>>>>>>>>>>>> Do proc_script $sourceRadio $dateDAQ GAIN" |
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176 | $RM -f ${tmppublicpath}/proc_script.finished |
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177 | if [ ${simulationMode} = "On" ]; then |
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178 | $ECHO "SIMUL: ${scriptpath}/proc_script.sh $sourceRadio $dateDAQ GAIN" |
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179 | else |
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180 | ${scriptpath}/proc_script.sh $sourceRadio $dateDAQ GAIN |
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181 | while [ ! -e "${tmppublicpath}/proc_script.finished" ]; do |
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182 | $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/proc_script.finished" |
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183 | date +%T |
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184 | sleep 60 |
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185 | done |
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186 | fi |
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187 | $ECHO "INFO (${scriptName}): proc_script has finished" |
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188 | $RM ${tmppublicpath}/proc_script.finished |
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189 | #Todo see if there is errors in the log file before copy |
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190 | $ECHO ">>>>>>>>>>>>>>>> Done proc_script $sourceRadio $dateDAQ GAIN" |
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191 | ###### |
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192 | fi |
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193 | ###### |
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194 | $ECHO ">>>>>>>>>>>>> ANALYSIS Part of ${sourceRadio} ${dateDAQ}" |
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195 | #go to the .../source/date-sourcelowercase directory |
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196 | $MKDIR -p ${topDir}/${dateDAQ}${srclower} |
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197 | cd ${topDir}/${dateDAQ}${srclower} |
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198 | aboveOnOffDir=`pwd` |
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199 | $ECHO "DEBUG (${scriptName}): we are in directory: <`pwd`>" |
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200 | # So the input files are there, so the fits file can be determined |
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201 | mode="Off" |
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202 | spectraGenDirName=`$ECHO ${gaincycle} | $AWK '{match($0,"[a-zA-Z]+",arr); print arr[0]}'` |
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203 | cycleNumber=`$ECHO ${gaincycle} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'` |
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204 | #care: the gaincycle variable contains the cycle number |
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205 | $ECHO "DEBUG (${scriptName}): START download the fits files" |
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206 | inFileDirectory="./${mode}" |
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207 | $MKDIR -p ${inFileDirectory} |
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208 | irodsDownDir="${i}/${mode}/${gaincycle}" |
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209 | OUT=./getInFits.$$ |
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210 | iget -r -f -K ${irodsDownDir} ${inFileDirectory} > ${OUT} 2>&1 |
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211 | $LS ${inFileDirectory}/${gaincycle} |
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212 | igetStatus=`$GREP "^ERROR" ${OUT}` |
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213 | if [ "<$igetStatus>" != "<>" ]; then |
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214 | $ECHO "FATAL (${scriptName}): error while iget fits files:" |
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215 | $ECHO $igetStatus |
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216 | continue |
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217 | fi |
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218 | $RM -f ${OUT} |
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219 | $ECHO "DEBUG (${scriptName}): END download the fits files" |
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220 | #Get sca files |
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221 | $ECHO "DEBUG (${scriptName}): START call getscafiles.sh ${sourceRadio} ${dateDAQ}" |
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222 | OUT1=./getScaStatus.$$ |
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223 | $RM -f ${tmppublicpath}/getscafiles.finished |
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224 | ${scriptpath}/getscafiles.sh ${sourceRadio} ${dateDAQ} > ${OUT1} 2>&1 |
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225 | while [ ! -f "${tmppublicpath}/getscafiles.finished" ]; do |
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226 | $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/getscafiles.finished" |
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227 | date +%T |
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228 | sleep 30 |
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229 | done |
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230 | $RM ${tmppublicpath}/getscafiles.finished |
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231 | $ECHO "DEBUG (${scriptName}): END" |
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232 | # |
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233 | getScaStatus=`$GREP "^\(FATAL\|ERROR\)" ${OUT1}` |
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234 | # |
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235 | if [ "<${getScaStatus}>" != "<>" ]; then |
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236 | $ECHO "FATAL (${scriptName}): error to get sca file for $sourceRadio $dateDAQ" |
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237 | $ECHO "DEBUG (${scriptName}): START with cat ${OUT1}" |
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238 | $CAT ${OUT1} |
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239 | $ECHO "DEBUG (${scriptName}): END" |
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240 | continue |
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241 | fi |
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242 | $RM -f ${OUT1} |
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243 | $ECHO "DEBUG (${scriptName}): where am i `pwd`" |
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244 | $LS -lrt |
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245 | |
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246 | scaFile=`$FIND . -name "sca*.sum.trans" | $XARGS -i basename {}` |
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247 | # |
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248 | #the default spectra name is medfiltmtx, otherwise use -specname <a_string> |
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249 | logFile="analyse_GAIN_${sourceRadio}_${dateDAQ}.log" |
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250 | $ECHO "DEBUG (${scriptName}): execute the analysis... should not take long. `date`" |
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251 | if [ ${simulationMode} = "On" ]; then |
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252 | $ECHO "SIMUL: ${scriptpath}/Objs/analyse -act gain -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir ${spectraGenDirName} -mode ${mode} -numcycle ${cycleNumber},${cycleNumber} -debug 1 >& ${logFile}" |
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253 | cat > ${logFile} <<EOF |
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254 | Ok gain finished |
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255 | EOF |
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256 | |
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257 | else |
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258 | ${scriptpath}/Objs/analyse -act gain -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir ${spectraGenDirName} -mode ${mode} -numcycle ${cycleNumber},${cycleNumber} -debuglev 1 >& ${logFile} |
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259 | fi |
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260 | # |
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261 | $ECHO "DEBUG (${scriptName}): analysis finished `date`. Look for errors before saving to Irods" |
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262 | rcstatus=`$GREP -i "OK gain finished" ${logFile} | $WC -l` |
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263 | if [ ${rcstatus} -eq 0 ]; then |
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264 | $ECHO "INFO (${scriptName}): analysis problem for ${sourceRadio} ${dateDAQ}" |
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265 | $ECHO " START logfile" |
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266 | $CAT ${logFile} |
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267 | $ECHO " END logFile" |
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268 | #clean and leave |
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269 | cd ${aboveOnOffDir} |
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270 | $RM -rf ./* |
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271 | continue |
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272 | fi |
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273 | #Save into Irods |
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274 | $ECHO "DEBUG (${scriptName}): START save output files" |
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275 | $LS ${aboveOnOffDir} |
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276 | #use -f option of iput ONLY to force override |
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277 | if [ ${simulationMode} = "On" ]; then |
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278 | $ECHO "SIMUL: here we look for gain file and put them in Irods" |
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279 | else |
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280 | $FIND . -name "gain_*" -print | $XARGS -i iput -v -K {} ${i} |
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281 | fi |
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282 | #save analysis logfile |
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283 | $LS -l ${tmppublicpath} > /dev/null |
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284 | $CP ${logFile} ${tmppublicpath} |
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285 | $ECHO "DEBUG (${scriptName}): END save output files" |
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286 | #clean |
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287 | cd ${aboveOnOffDir} |
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288 | $RM -rf ./* |
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289 | done |
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290 | |
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291 | exit 0 |
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