source: BAORadio/AmasNancay/trunk/hdrfitsextractor.sh @ 629

#!/bin/sh
#download SCA file, proceed to introspection, and upload results
DATE=/bin/date
GREP=/bin/grep
AWK=/bin/awk
ECHO=/bin/echo
WC=/usr/bin/wc
CAT=/bin/cat
PRINTF=/usr/bin/printf
MKDIR=/bin/mkdir
XARGS=/usr/bin/xargs
SORT=/bin/sort
RM=/bin/rm
defaultIFS=$IFS
SED=/bin/sed

#set Irods environment    
. /usr/local/shared/bin/irods_env.sh -noverbose

scriptName="`basename $0`"
$ECHO "Processing script ${scriptName} at `date`"

#which source to analyse
sourceRadio=$1

#Path to public backupable path
publicpath="/afs/in2p3.fr/home/c/campagne/public"


#Path where the job will do temporary IO
. ${SCRIPTPATH}/set_iojobpath.sh
iojobpath=$(set_iojobpath)
cd ${iojobpath}

localpath="${sourceRadio}"
$MKDIR -p ./${localpath}
cd ./${localpath}


#Path of the utility scripts
scriptpath=${SCRIPTPATH}


#JEC 1/10/11 Use generic baodaqstatus name 
#get the daq current irod status
#tag=`${DATE} +%F`
#OUT1=${publicpath}/baodaqstatus-${tag}.txt
OUT1=${publicpath}/baodaqstatus-current.txt

if [ ! -e ${OUT1}  -o ! -r ${OUT1} ]; then
    $ECHO "FATAL (${scriptName}): ${OUT1} has a problem"
    exit 1
fi

#if [ ! -e ${OUT1} ]; then
#    $ECHO "We should bring the DAQ status more up to date, this take 1 or 2sec..."
#    ${scriptpath}/statusdaq.sh > ${OUT1}
#fi

if [ ! "<${sourceRadio}>" = "<>" ]; then
    $ECHO "You have selected sourceRadio = $sourceRadio"
#    tableau=( `$GREP -i ${sourceRadio} ${OUT1} | $AWK '( NF==4 ) { print $2 }' ` )
    tableau=( `imeta qu -C status "=" hdrNOTDone | $AWK "/$sourceRadio/" | $AWK '{print $2}' ` )
else
#    tableau=( `$CAT ${OUT1} | $AWK '( NF==4 ) { print $2 }'`  )
    tableau=( `imeta qu -C status "=" hdrNOTDone | $AWK '{print $2}' | $SED '/^$/d' ` )
fi
IFS='
'
tableau=( $( $PRINTF "%s\n" "${tableau[@]}" | $AWK 'x[$0]++ == 0' ) )


workArea="headers"
$MKDIR -p ./${workArea}
cd ./${workArea}


nloop4dbg=0


for i in ${tableau[@]}
do
#look if the headers have been already extracted
  $ECHO "DEBUG (${scriptName}): irods root dir $i"
  for fibdir in Fiber1 Fiber2; do
      $ECHO "DEBUG (${scriptName}): Fiber $fibdir"
      status=`imeta ls -C ${i}/${fibdir} status | $AWK '/value/{print $2}'`
      $ECHO ${status}
##NB: care should be taken to the fact that ILS returns all the instance of the file (HPSS, disk...)
##    so one should use a trick to count unique instance
#      listOfsig=( `ils ${i}/${fibdir} | $GREP -i "signal" | $XARGS -i basename {} | $SORT -k1.7n` )
#      IFS='
#'
#      listOfsig=( $( $PRINTF "%s\n" "${listOfsig[@]}" | $AWK 'x[$0]++ == 0' ) )
#      nblinesSIG=${#listOfsig[@]}
#      listOfhdr=( `ils ${i}/${fibdir} | $GREP -i "header" | $XARGS -i basename {} | $SORT -k1.7n` )
#      IFS='
#'
#      listOfhdr=( $( $PRINTF "%s\n" "${listOfhdr[@]}" | $AWK 'x[$0]++ == 0' ) )
#      nblinesHDR=${#listOfhdr[@]}
#      $ECHO "(DEBUG) (${scriptName}:  test if $nblinesHDR != $nblinesSIG "
#      if [ $nblinesHDR != $nblinesSIG ]; then
       if [ "<$status>" != "<hdrDone>" ]; then
##do the header extraction
##build signal files list 
##loop on signal files
          listOfsig=( `ils ${i}/${fibdir} | $GREP -i "signal" | $XARGS -i basename {} | $SORT -k1.7n` )
          IFS='
'
          listOfsig=( $( $PRINTF "%s\n" "${listOfsig[@]}" | $AWK 'x[$0]++ == 0' ) )
          $ECHO "(DEBUG) (${scriptName}):  ${listOfsig[@]}"

          for sigfname in ${listOfsig[@]}
            do
            filename=$(basename $sigfname)
            extension=${filename##*.}
            filename=${filename%.*}
            number=`$ECHO $filename | $AWK '{len=length("signal");len=len+1;a=substr($1,len);print a}'`
            hdrname="header${number}.txt"
#look if header file already exists: if so skip it
            hdrIsthere=`ils ${i}/${fibdir}/${hdrname} 2>&1 | $GREP -i "^ERROR" | $WC -l`
            $ECHO "(DEBUG) (${scriptName}): look if ${hdrname}  exist (${hdrIsthere})"
            if [ $hdrIsthere -eq 0 ]; then 
                continue
            fi
#get the signal file
            $ECHO "DEBUG (${scriptName}): iget $sigfname (dgg = ${nloop4dbg})"
            OUT3=./igetlog${nloop4dbg}.$$
            iget -f -v -K ${i}/${fibdir}/${sigfname} . >${OUT3} 2>&1
            igetStatus=`$GREP "^ERROR" ${OUT3}`
            if [ "<$igetStatus>" != "<>" ]; then
                $ECHO "INFO (${scriptName}): error while iget:"
                $ECHO $igetStatus
                continue
            fi
            $RM $OUT3
#extract the header part of the  signal file
            $ECHO "DEBUG (${scriptName}): get header from ${sigfname} and put it in ${hdrname}"
            IFS=$defaultIFS
            while read -n80 L
              do
              [ "${L::3}" = "END" ] && break
              $ECHO $L
            done < ${sigfname} > ${hdrname}
            $RM ${sigfname}
            nhdrlines=`$WC -l ${hdrname} | $AWK '{print $1}' `
            if [  "${nhdrlines}" = "0"  ]; then
                $ECHO "WARNING (${scriptName}): ${sigfname} has no valid header"
            else
#transfert to irod the header
                $ECHO "INFO (${scriptName}): transfert ${hdrname} to ${i}/${fibdir}"
#use -f option ONLY to force override
                iput  -v -K ${hdrname} ${i}/${fibdir}
            fi
            $RM ${hdrname}
            nloop4dbg=$(expr $nloop4dbg + 1)
          done
          imeta mod -C ${i}/${fibdir} status hdrNOTDone v:hdrDone
      else
          $ECHO "INFO (${scriptName}): nothing to do for ${i}/${fibdir}"
      fi
  done
done