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5. Data Management Topics : 5.1 backupScript.sh
5.1
backupScript.sh
The backupScript.sh is a user-modifiable script that is run automatically from the instrument and is responsible for copying the raw data, which can not be recreated. For the GS FLX+ System, the script copies the data from the instrument to an archive system. For the GS Junior System, the script copies the data from the Attendant PC to the archive system. The following are the critical files in the R_ directory that are be backed up by default.
•
dataRunParams.parse
•
imageLog.parse
•
runLog.parse
•
aaLog.txt
•
and all the PNG files under rawImages
The backup script is passed the full path of the R_ directory. It is run as the adminrig user and calls the “backupLog” command to inform the instrument control of the status of the backup. It is important that any modifications or additions be made in the marked section. The lines containing “backupLog” must be preserved. The RET_ERR variable passes the backup status to the GS Sequencer GUI Data tab and is set to 0 for success and 1 for error.
Below is an example backupScript.sh file content. The highlighted portion, between the sets of “========”, is provided as an illustration only.
 
#!/bin/bash
################################################################################
##
##    Filename:   backupScript.sh
##
##    Programmer: Bernard Puc
##
##    Description:
##
##          Runs at completion of the fluidics.
##
##    $Id: backupScript.sh,v 1.7 2005/01/20 15:59:23 bpuc Exp $
##
################################################################################
 
if [ $# -ne 1 ]
then
      echo "Need to specify a directory on the command line."
      echo "Exiting."
      exit 1
fi
 
#
#     Initialize the backup status variable as failed
#
RET_ERR=1
 
#
#     Update the backup status file
#
backupLog $1 "running" "permanent"
 
 
# =======================================
# =======================================
#
#     Add custom backup code here...
#
 
# The first argument is the fully qualified pathname of the Run directory
RUN_SRC=$1
 
# The destination directory "/mnt/backupServer" must already be configured via
# nfs, samba, etc.
DEST_SERVER=/mnt/backupServer
RUN_DEST=$DEST_SERVER/$RUN_SRC
 
# Copy all regular files (purposely allowing subdirectories to fail)
cp -p $RUN_SRC/* $RUN_DEST
if [ $? -ne 0 ]
then
      RET_ERR=1
else
      # Now explicitly copy subdirectory containing raw images
      cp -rp $RUN_SRC/rawImages $RUN_DEST
      if [ $? -ne 0 ]
      then
            RET_ERR=1
      fi
fi
 
# =======================================
# =======================================
 
#
#     Update the backup status file
#
if [ $RET_ERR -eq 0 ]
then
      backupLog $1 "complete" "permanent"
else
      backupLog $1 "failure" "permanent"
fi
 
#
#     End of script
#
exit 0