starting exec on gitlab

d70f8533 · Yvonne Firing · d70f8533 · d70f8533 · d70f8533 · d70f8533
Commit d70f8533 authored 5 years ago by Yvonne Firing
20 changed files
--- a/jcr/sedexec_old2
+++ b/jcr/sedexec_old2
+#/bin/csh -f
+
+set stream  = $1
+set infile = "../scs_raw/${stream}.ACO"
+set otfile = "./${stream}.ACO"
+echo infile $infile
+echo otfile $otfile
+echo $MACHTYPE
+
+if ($MACHTYPE == 'x86_64-suse-linux') then
+  set sedcom = "sed -u"
+else if ($MACHTYPE == 'x86_64') then
+  set sedcom = "sed -u"
+else if ($MACHTYPE == 'i386') then
+  set sedcom = "sed -l"
+else
+  set sedcom = "sed"
+endif
+
+echo $sedcom
+
+ps -ef | grep tail | grep ${stream} | sed 's/ /Q/' | sed 's/^.*Q//' | sed 's/^ *//' | sed 's/ .*$//' >! wk$$
+foreach i (`cat wk$$`)
+kill -9 ${i}
+end
+/bin/rm wk$$
+
+if (-e ${otfile}) then
+/bin/rm ${otfile}
+endif
+
+tail -c 10000000000 -f ${infile} | ${sedcom}  's/, *,/,NaN,/g' | ${sedcom}  's/://g' | ${sedcom} 's/,/ /g' >! ${otfile} &
--- a/jcr/sedexec_startall
+++ b/jcr/sedexec_startall
+#
+
+foreach i (`cat /local/users/pstar/cruise/data/exec/jcr/list`)
+sedexec $i
+end
--- a/jcr/sedexec_stopall
+++ b/jcr/sedexec_stopall
+#
+pushd scs_sed
+foreach i (`cat /local/users/pstar/cruise/data/exec/jcr/list`)
+ps -ef | grep tail | grep ${i} | sed 's/ /Q/' | sed 's/^.*Q//' | sed 's/^ *//' | sed 's/ .*$//' >! wk$$
+foreach i (`cat wk$$`)
+kill -9 ${i}
+end
+/bin/rm wk$$
+end
+
+popd
--- a/jcr/sedscript
+++ b/jcr/sedscript
+s/\x0D//g
+s/$/,/
+s/,A,/,NaN,/g
+s/,V,/,NaN,/g
+s/,A...,/,NaN,/g
+s/GJ00,$/NaN,/
+s/, *,/,NaN,/g
+s/, *,/,NaN,/g
+s/,M,/,NaN,/g
+s/,U,/,NaN,/g
+s/://g
+s/,/ /g
+s/;/ /g
+s/</ /g
+s/>/ /g
+s/=/ /g
+s/\?/ /g
+s/@/ /g
+s/B/ /g
--- a/lad_linkscript_ix
+++ b/lad_linkscript_ix
+#!/bin/csh 
+# copy the raw .000 ladcp data into cruise/data/ladcp/raw/
+# then make links to those files using the filename format expected by IX processing
+
+cd /local/users/pstar/cruise/data/ladcp/rawdata
+
+rsync -av /mnt/data/jcr/current/ladcp/* . 
+
+#make links for IX
+foreach i (`ls JR18002_*.000`)
+   set num = `awk -v nm="$i" 'BEGIN {print substr(nm,index(nm,".000")-3,3)}'`
+   set linkfile = ${num}DL000.000
+   if(! -e ../ix/raw/$num) then
+      echo Making directory $num for raw file $i
+      mkdir -p ../ix/raw/$num
+   endif
+   cd ../ix/raw/$num
+   if (! -e $linkfile) then
+      echo Making link $linkfile for raw file $i
+      ln -s ../../../rawdata/$i $linkfile
+   endif
+   cd ../../../rawdata
+end
+
+cd ../..
--- a/mexec_cruise_backup
+++ b/mexec_cruise_backup
+# backup mexec cruise directory from workstation to external hard drive using rsync
+# usage: > mexec_cruise_backup drivename
+# e.g. > mexec_cruise_backup jr16002a
+# the external hard drives must be named/mounted as $cruise$letter
+# e.g. for cruise jr16002: jr16002a, jr16002b, etc.
+
+# setup
+set target = $1
+set thiscruise = `echo $target | sed s'/.$//'` 
+set target1 = /run/media/pstar/${target}/this_is_${target}
+set root =  /local/users/pstar/cruise
+set now = `date +%Y%m%d%H%M%S`
+set backuplog = $root/data/other_backups/backup_log_${now}
+
+if (-e ${target1}) then
+  set backupdir = /run/media/pstar/${target}/${thiscruise}/backup_${now}
+  set location = /run/media/pstar/${target}
+else
+  echo "disk ${target} not found"
+exit
+endif
+
+if (-e $backuplog) then
+  echo " "
+exit
+else
+  touch $backuplog
+endif
+
+if (-e $backupdir) then
+  echo " "
+  exit
+else
+  mkdir $backupdir
+endif
+
+pushd $root
+
+echo "disk ${target} found at ${location}" >> $backuplog
+
+# dot login and cshrc
+echo -------------        >> $backuplog
+echo Date `date`          >> $backuplog
+echo copying login and cshrc  >> $backuplog
+echo ------               >> $backuplog
+#/bin/cp -p ~/.login  $root/data/other_backups/dot_login
+#/bin/cp -p ~/.cshrc  $root/data/other_backups/dot_cshrc
+echo -------------        >> $backuplog
+echo Date `date`          >> $backuplog
+echo done login and cshrc  >> $backuplog
+echo ------               >> $backuplog
+
+# software
+echo -------------        >> $backuplog
+echo Date `date`          >> $backuplog
+echo start copying mexec software >> $backuplog
+echo ------               >> $backuplog
+cd $root
+rsync -a sw/mexec/ ${backupdir}/
+echo -------------        >> $backuplog
+echo Date `date`          >> $backuplog
+echo done copying mexec software >> $backuplog
+echo ------               >> $backuplog
+
+# backup everything in data
+echo -------------        >> $backuplog
+echo Date `date`          >> $backuplog
+echo start copy to disk of data   >> $backuplog
+echo ------               >> $backuplog
+cd $root
+rsync -aL --exclude legwork --exclude scs_raw --exclude jcrfs --exclude netcdf_files_rawdir_ship data ${backupdir}
+echo -------------        >> $backuplog
+echo Date `date`          >> $backuplog
+echo done copy to disk of data   >> $backuplog
+echo ------               >> $backuplog
+
+echo general_sw, legdata and legwork not backed up
+
+popd
+
--- a/modsal_unix
+++ b/modsal_unix
+#!/bin/csh
+#
+#Script by DADES on cruise jr302 to make mac files readable in unix.
+
+#cd data
+#cd ctd
+cd ctd
+cd BOTTLE_SAL
+foreach i (`ls /local/users/pstar/cruise/data/ctd/BOTTLE_SAL/sal_jr302_???.csv`)
+mac2unix -n $i ${i}_linux
+echo " " >> ${i}_linux
+end
+
+foreach i (`ls /local/users/pstar/cruise/data/ctd/BOTTLE_SAL/sal_jr302_????.csv`)
+mac2unix -n $i ${i}_linux
+echo " " >> ${i}_linux
+end
+
+rm sal_jr302_01.csv
+cat *linux >>! sal_jr302_01.csv
+
+
--- a/nut_linkscript
+++ b/nut_linkscript
+#!/bin/csh -f
+#
+#Script by BAK on cruise jc032 to create symbolic links.
+#Modified by CPA on di346 for nutrient data
+#Set to import all files from Drobo each time script is run to ensure
+#most up to date files are kept on nosea1  
+#The assumption is that the raw files are named
+#in a way that identifies the instrument, eg
+# ctd_jc032_001_ctm.cnv
+#
+#
+# The initial foreach command will need to be modified for each cruise.
+
+
+# modded bak jr302 8 jun 2014 to use rsync
+cd
+cd cruise/data
+cd ctd
+cd BOTTLE_NUT 
+
+rsync -av jcrfs_nut/J*csv .
+
+
+foreach i (`ls JR302nut???.csv`)
+#echo $i
+set num = `echo $i | awk '{print substr($1,9,3)}'`
+#echo $num
+#set cruise = `echo $i | awk '{print substr($1,9,5)}'`
+set cruise = 'jr302'
+#echo $cruise
+
+set linkfile = nut_${cruise}_${num}.csv
+#echo $linkfile
+
+if (! -e $linkfile) then
+  echo Making link $linkfile for raw file $i
+  ln -s $i $linkfile
+endif
+end
+
--- a/oxy_linkscript
+++ b/oxy_linkscript
+#!/bin/csh -f
+#
+#Script by BAK on cruise jc032 to create symbolic links.
+#Modified by BGW for cruise di346
+#Modified by CPA to import oxygen files from /Drobo 
+#The assumption is that the raw files are named
+#in a way that identifies the instrument, eg
+# ctd_jc032_001_ctm.cnv
+#
+#
+# The initial foreach command will need to be modified for each cruise.
+#cd data
+#cd ctd
+# modded bak di368
+# modded bak jr302 8 jun 2014 to use rsync
+
+cd ~/cruise/data
+cd ctd
+cd BOTTLE_OXY 
+
+rsync -av legwork/oxygen/oxygen calculation_JR18002_*.xls .
+
+foreach i (`ls oxygen_calculation_JR18002_*.csv`)
+#echo $i
+set num = `echo $i | awk '{print substr($1,9,3)}'`
+set cruise = 'jr16002'
+#echo $num
+
+set linkfile = oxy_${cruise}_${num}.csv
+#echo $linkfile
+
+if (! -e $linkfile) then
+  echo Making link $linkfile for raw file $i
+  ln -s $i $linkfile
+endif
+end
--- a/oxy_linkscript_jr302
+++ b/oxy_linkscript_jr302
+#!/bin/csh -f
+#
+#Script by BAK on cruise jc032 to create symbolic links.
+#Modified by BGW for cruise di346
+#Modified by CPA to import oxygen files from /Drobo 
+#The assumption is that the raw files are named
+#in a way that identifies the instrument, eg
+# ctd_jc032_001_ctm.cnv
+#
+#
+# The initial foreach command will need to be modified for each cruise.
+#cd data
+#cd ctd
+# modded bak di368
+# modded bak jr302 8 jun 2014 to use rsync
+cd
+cd cruise/data
+cd ctd
+cd BOTTLE_OXY 
+
+rsync -av jcrfs_oxy/* .
+
+
+
+foreach i (`ls JR302OXY???.csv`)
+#echo $i
+set num = `echo $i | awk '{print substr($1,9,3)}'`
+set cruise = 'jr302'
+#echo $num
+
+set linkfile = oxy_${cruise}_${num}.csv
+#echo $linkfile
+
+if (! -e $linkfile) then
+  echo Making link $linkfile for raw file $i
+  ln -s $i $linkfile
+endif
+end
--- a/oxy_linkscript_jr302_unc
+++ b/oxy_linkscript_jr302_unc
+#!/bin/csh -f
+#
+#Script by BAK on cruise jc032 to create symbolic links.
+#Modified by BGW for cruise di346
+#Modified by CPA to import oxygen files from /Drobo 
+#The assumption is that the raw files are named
+#in a way that identifies the instrument, eg
+# ctd_jc032_001_ctm.cnv
+#
+#
+# The initial foreach command will need to be modified for each cruise.
+#cd data
+#cd ctd
+# modded bak di368
+# modded bak jr302 8 jun 2014 to use rsync
+cd
+cd cruise/data
+cd ctd
+cd BOTTLE_OXY 
+
+#rsync -av jcrfs_oxy/* .
+
+
+
+foreach i (`ls unc/JR302OXY???.csv`)
+#echo $i
+set num = `echo $i | awk '{print substr($1,13,3)}'`
+set cruise = 'jr302'
+#echo $num
+
+set linkfile = oxy_${cruise}_${num}_unc.csv
+#echo $linkfile
+
+if (! -e $linkfile) then
+  echo Making link $linkfile for raw file $i
+  ln -s $i $linkfile
+endif
+end
--- a/sam_linkscript
+++ b/sam_linkscript
+#!/bin/csh -f
+#
+#Script by BAK on cruise jc032 to create symbolic links.
+#Modified by BGW for cruise di346
+#Modified by CPA to import oxygen files from /Drobo 
+#modified by YLF jr18002 to sync and link various sample data files
+#
+#The assumption is that the raw files are named
+#in a way that identifies the instrument, eg
+# ctd_jc032_001_ctm.cnv
+#
+#
+# The initial foreach command will need to be modified for each cruise.
+#cd data
+#cd ctd
+# modded bak di368
+# modded bak jr302 8 jun 2014 to use rsync
+
+cd ~/cruise/data/ctd
+
+set lpre = '../../legwork/scientific_work_areas'
+set cruise = 'jr18002'
+set CRUISE = 'JR18002'
+
+cd BOTTLE_OXY 
+rsync -av legoxy/Cast*.csv .
+cd ..
+
+#nuts, cfcs, co2
+cd ..
+
--- a/synclists
+++ b/synclists
+#!/bin/csh 
+# jr302 bak
+cd
+cd data
+cd ctd
+#rsync -av samlist_jr302_???_co2.csv ../legwork/jr302_co2
+#rsync -av samlist_jr302_???_ch4.csv ../legwork/jr302_ch4
+#rsync -av samlist_jr302_???_nuts.csv ../legwork/jr302_nut
+#rsync -av startend_jr302_??? ../legwork/jr302_surfactant
+# jr302 at end of crusie when legwork is no longer available
+rsync -av samlist_jr302_???_co2.csv ../from_legwork/jr302_co2
+rsync -av samlist_jr302_???_ch4.csv ../from_legwork/jr302_ch4
+rsync -av samlist_jr302_???_nuts.csv ../from_legwork/jr302_nut
+rsync -av startend_jr302_??? ../from_legwork/jr302_surfactant
--- a/techsas_linkscript
+++ b/techsas_linkscript
+#!/bin/csh -f
+#
+# script by bak 3 dec 2014 for cook to allow for techsas files to be sorted into a directory
+#
+# modded by bak at nocs on eriu for dy031 15 may 2015, modded to run as a crontab task
+#* * * * 1,2,3,4,5,6,7 /local/users/pstar/cruise/data/exec/techsas_linkscript >> & /dev/null
+
+
+cd /local/users/pstar #~/h # cludge on eriu when pstar home directory is wrong
+cd cruise
+cd data
+cd techsas
+cd netcdf_files_links
+
+set now = `date +%Y%m%d%H%M%S`
+set link_log = /local/users/pstar/cruise/data/techsas/techsas_link_logs/techsas_link_log_${now}
+echo " " >>! $link_log
+echo `date` >>! $link_log
+
+foreach techfile (`/bin/ls ../netcdf_files_rawdir/*/*`)
+  set i1 = `echo $techfile | awk '{print index($1,"/")}'`
+  set i2 = `echo $techfile  $i1| awk '{print substr($1,$2+1)}'`
+  set i3 = `echo $i2 | awk '{print index($1,"/")}'`
+  set i4 = `echo $i2  $i3| awk '{print substr($1,$2+1)}'`
+  set i5 = `echo $i4 | awk '{print index($1,"/")}'`
+  set linkfile = `echo $i4  $i5| awk '{print substr($1,$2+1)}'`
+  if (! -e $linkfile) then
+    if ( -s $techfile) then
+      set sss = ` /bin/ls -l $techfile`
+      set ss2 = `echo $sss | awk '{print $5}'`
+      if ($ss2 > 10000) then
+        echo "  making link $linkfile for raw file $techfile " >>! $link_log
+        ln -s $techfile $linkfile
+      else
+        echo "  ignoring $linkfile length $ss2 is less than 10k bytes " >>! $link_log
+      endif
+    else
+      echo "  ignoring $linkfile has zero length " >>! $link_log
+    endif
+  endif
+end
+
--- a/techsas_linkscript_mac
+++ b/techsas_linkscript_mac
+#!/bin/csh -f
+#
+# script by bak 3 dec 2014 for cook to allow for techsas files to be sorted into a directory
+#
+# modded by bak at nocs on eriu for dy031 15 may 2015, modded to run as a crontab task
+#* * * * 1,2,3,4,5,6,7 /local/users/pstar/cruise/data/exec/techsas_linkscript >> & /dev/null
+
+
+cd /local/users/pstar #~/h # cludge on eriu when pstar home directory is wrong
+cd cruise/data/techsas
+cd netcdf_files_links_mac
+
+set now = `date +%Y%m%d%H%M%S`
+set link_log = /local/users/pstar/cruise/data/techsas/techsas_link_logs/techsas_link_log_mac_${now}
+echo " " >>! $link_log
+echo `date` >>! $link_log
+
+foreach i (`/bin/ls ../netcdf_files_rawdir_mac/*/*`)
+ set i1 = `echo $i | awk '{print index($1,"/")}'`
+ set i2 = `echo $i  $i1| awk '{print substr($1,$2+1)}'`
+set i3 = `echo $i2 | awk '{print index($1,"/")}'`
+set i4 = `echo $i2  $i3| awk '{print substr($1,$2+1)}'`
+set i5 = `echo $i4 | awk '{print index($1,"/")}'`
+set i6 = `echo $i4  $i5| awk '{print substr($1,$2+1)}'`
+set i7 = `echo $i | awk '{print substr($1,1,22)}'`
+set i8 = `echo $i | awk '{print substr($1,23,length($1))}'`
+set i9 = `echo $i7$i8`
+
+set linkfile = $i6
+set techfile = $i9
+
+if (! -e $linkfile) then
+ if ( -s $i) then
+   set sss = ` /bin/ls -l $i`
+   set ss2 = `echo $sss | awk '{print $5}'`
+   echo $sss
+   echo $ss2
+      if ($ss2 > 10000) then
+         echo "  making link $linkfile for raw file $i " >>! $link_log
+            ln -s $techfile $linkfile
+      else
+         echo "  ignoring $linkfile length $ss2 is less than 10k bytes " >>! $link_log
+      endif
+ else
+   echo "  ignoring $linkfile has zero length " >>! $link_log
+ endif
+endif
+end
+
--- a/vmadcp_linkscript
+++ b/vmadcp_linkscript
+#!/bin/csh -f
+#
+#foreach i (`ls rawdata/*JC32*`)
+
+# overhaul on jr302 may 2014, to fit with new python codas
+# may need modification on cook/discovery to handle os75 and os150
+cd /local/users/pstar/cruise/data/vmadcp/
+
+echo "synchronising raw data"
+rsync -av ../jcrfs/current/adcp/ jr17001_os75/vmdas_data/
+# jcrfs is link to raw data on jrlb
+
+echo "making links to individual sequence directories"
+cd jr17001_os75/vmdas_data
+foreach i (`ls *.*`) # list all *.* to avoid collecting N1R directory
+set num = `echo $i | awk -F'.' '{print substr($1,length($1)-9,3)}'`
+
+set linkdir = rawdata{$num}
+
+if (! -e $linkdir) then
+  echo making $linkdir
+  mkdir $linkdir
+endif
+
+set rfile = $i
+set lfile = $i
+cd $linkdir
+if (! -e $lfile) then
+  echo linking ${lfile} to ${rfile}
+  ln -s ../${rfile} ${lfile}
+endif
+cd ..
+
+end
--- a/vmadcp_linkscript_jc145
+++ b/vmadcp_linkscript_jc145
+#!/bin/csh -f
+#
+# This script assumes that a mount to adcp data has been setup and files are named like
+# /local/users/pstar/cruise/data/vmadcp/jc145_os75/rawraw/OS075_JC145004_000000.ENR  
+# or mostly
+# /local/users/pstar/cruise/data/vmadcp/jc145_os75/rawraw/ADCP75_BTon_nosync010_000000.ENR
+# note unfortunately on this cruise the names didn't change for BToff files, 
+# however BT status is determined separately
+#
+# Go through loop once for each adcp
+
+set cruise = jc145
+set CRUISE = JC145
+    
+foreach adp ('75' '150')
+  echo $adp
+  cd /local/users/pstar/cruise/data/vmadcp
+  cd ${cruise}_os${adp}
+
+  echo "Synchronising raw data for the $adp"
+  rsync -av /mnt/adcp${adp}/${CRUISE}/raw_data/ rawraw
+
+# --------------------------------------------------
+# These next steps were needed as naming of files was not correct
+  cd rawdata
+  foreach fl (`ls ../rawraw/ADCP${adp}_BT*`)
+    set bb = `echo $fl | awk '{print substr($1,length($1)-13,length($1))}'`
+    set fl2 = OS${adp}_JC145_${bb}
+    if (! -e $fl2) then
+      ln -s $fl $fl2
+    endif
+  end
+  cd ..
+# --------------------------------------------------
+
+end
+
+#JC145 only: now deal with the initial (transit) files, one sequence at a time because
+#the sequences will have to be renumbered
+cd /local/users/pstar/cruise/data/vmadcp/jc145_os75/rawdata
+foreach fl (`ls ../rawraw/OS75_JC145001*`)
+  set bb = `echo $fl | awk '{print substr($1,length($1)-9,length($1))}'`
+  set fl2 = OS75_JC145_901_${bb}
+  if (! -e $fl2) then
+    ln -s $fl $fl2
+  endif
+end
+foreach fl (`ls ../rawraw/OS75_JC145002*`)
+  set bb = `echo $fl | awk '{print substr($1,length($1)-9,length($1))}'`
+  set fl2 = OS75_JC145_902_${bb}
+  if (! -e $fl2) then
+    ln -s $fl $fl2
+  endif
+end
+cd /local/users/pstar/cruise/data/vmadcp/jc145_os150/rawdata
+foreach fl (`ls ../rawraw/OS150_JC145001*`)
+  set bb = `echo $fl | awk '{print substr($1,length($1)-9,length($1))}'`
+  set fl2 = OS150_JC145_901_${bb}
+  if (! -e $fl2) then
+    ln -s $fl $fl2
+  endif
+end
+foreach fl (`ls ../rawraw/OS150_JC145002*`)
+  set bb = `echo $fl | awk '{print substr($1,length($1)-9,length($1))}'`
+  set fl2 = OS150_JC145_902_${bb}
+  if (! -e $fl2) then
+    ln -s $fl $fl2
+  endif
+end
--- a/vmadcp_linkscript_jc145a
+++ b/vmadcp_linkscript_jc145a
+#!/bin/csh -f
+#
+# This script assumes that a mount to adcp data has been setup and files are named like
+# /local/users/pstar/Acoustics/OS75kHz/raw_data/OS075_DY039004_000000.ENR  
+# /local/users/pstar/Acoustics/OS150kHz/raw_data/OS150_DY039002_000000.LOG
+# Works on dy039 might may need to modify on next cruise
+#
+# Go through loop once for each adcp
+foreach adp ('75' '150')
+  cd /local/users/pstar/cruise/data
+  cd va$adp
+  if ($adp == '75') then  
+	  set adpx = '075'
+	  echo $adpx
+  else if ($adp == '150') then
+	  set adpx = '150'
+	  echo $adpx
+  endif  
+
+  echo "Synchronising raw data for the v$adp"
+#  rsync -av /local/users/pstar/Acoustics/OS${adp}kHz/raw_data/OS${adpx}* rawdata
+  rsync -av /mnt/adcp${adp}/JC145/raw_data/OS* rawraw
+
+# --------------------------------------------------
+# These next steps were needed as nameing of files was not correct and need to add an extra underscore
+  cd rawdata
+  foreach fl (`ls ../rawraw/*`)
+    #set aa = `echo $fl | awk '{print substr($1,11,11)}'`
+    set aa = `echo $fl | awk '{print substr($1,11,length($1)-24)}'`
+    #set bb = `echo $fl | awk '{print substr($1,22,14)}'`
+    set bb = `echo $fl | awk '{print substr($1,length($1)-13,length($1))}'`
+    set fl2 = ${aa}_${bb}
+    echo $fl
+    echo $fl2
+    if (! -e $fl2) then
+      ln -s $fl $fl2
+    endif
+  end
+  cd ..
+# --------------------------------------------------
+
+  echo "Creating directories for OS$adp"
+  foreach i (`ls rawdata/*`)
+    set num = `echo $i | awk -F'_' '{print substr($3,length($3)-2,3)}'`
+# Extract file extension, e.g. for i = rawdata/OS150_DY039005_000000.ENX, num = 'ENR'
+    set fname = `echo $i | awk '{print substr($1,9,26)}'`
+    set movedir = rawdata{$num}
+
+# Create new directory like 'rawdataENX' if does nto already exist
+   if (! -e $movedir) then
+     echo making $movedir
+     mkdir $movedir
+   endif
+
+# Now create links from new directories to original files in rawdata with corresponding suffix
+   set rfile = ../${i}
+   set lfile = ${movedir}/${fname}
+   if (! -e ${lfile}) then
+     echo linking ${lfile} to ${rfile}
+     ln -s ${rfile} ${lfile}
+   endif
+   end
+end
+
+
--- a/vmadcp_linkscript_jr302
+++ b/vmadcp_linkscript_jr302
+#!/bin/csh -f
+#
+#foreach i (`ls rawdata/*JC32*`)
+
+# overhaul on jr302 may 2014, to fit with new python codas
+# may need modification on cook/discovery to handle os75 and os150
+cd /local/users/pstar/cruise/data/vmadcp
+
+echo "synchronising raw data"
+rsync -av jcrfs_adcp75/* raw_os75
+# jcrfs_adcp75 is link to raw data on jrlb
+# raw_os75 is link to directory in codas_shared available in virtual box.
+# raw_os75 -> codas_shared/vmdas_data/jr281_os75      so raw directory must already be configured in codas_shared
+
+echo "making links in old codas directory"
+foreach i (`ls raw_os75/*.*`) # list all *.* to avoid collecting N1R directory
+#set num = `echo $i | awk -F'_' '{print substr($2,length($2)-2,3)}'`
+# this extracts the file extension, e.g. for i = rawdata/D344os150001_000000.ENR, num is then set as ENR, ZBS 19.10.2009
+set num = `echo $i | awk -F'.' '{print substr($1,length($1)-9,3)}'`
+set fname = `echo $i | awk '{print substr($1,10,19)}'` # start at char 10 allows for removing raw_os75/ 
+
+cd /local/users/pstar/cruise/data/vmadcp/v75
+
+set linkdir = rawdata{$num}
+
+if (! -e $linkdir) then
+  echo making $linkdir
+  mkdir $linkdir
+endif
+
+
+set rfile = ../../${i}
+set lfile = ${linkdir}/${fname}
+if (! -e ${lfile}) then
+  echo linking ${lfile} to ${rfile}
+  ln -s ${rfile} ${lfile}
+endif
+
+end
--- a/vmadcp_movescript
+++ b/vmadcp_movescript
+#!/bin/csh -f
+#
+#foreach i (`ls rawdata/*JC32*`)
+foreach i (`ls rawdata/*`)
+#set num = `echo $i | awk -F'_' '{print substr($2,length($2)-2,3)}'`
+# this extracts the file extension, e.g. for i = rawdata/D344os150001_000000.ENR, num is then set as ENR, ZBS 19.10.2009
+set num = `echo $i | awk -F'.' '{print substr($1,length($1)-9,3)}'`
+
+set movedir = rawdata{$num}
+
+if (! -e $movedir) then
+  echo making $movedir
+  mkdir $movedir
+endif
+
+echo moving $i to $movedir
+mv {$i} {$movedir}
+
+end