#!/bin/bash --login

#---------------
#About this script
#stageFromAcaciaTar.sh : copies a tar object from Acacia and extracts it in the destination path

#---------------
#Requested resources:
#SBATCH --account=[yourProjectName]
#SBATCH --job-name=stageTar.rclone
#SBATCH --partition=copy
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --time=[requiredTime]
#SBATCH --export=NONE

#-----------------
#Loading the required modules
module load rclone/<version> #This example is performed with the use of the rclone. 

#-----------------
#Defining variables that will handle the names related to your access, buckets and stored objects in Acacia
profileName=<profileNameGivenToYourProfileOfAccessToAcacia>
bucketName=<bucketInAcaciaContainingTheData>
prefixPath=<prefixPathInBucketUsedToOrginiseTheData>
fullPathInAcacia="${profileName}:${bucketName}/${prefixPath}" #Note the colon(:) when using rclone

#-----------------
#Name of the file to be transferred and auxiliary dir to temporarily place it
tarFileName=<nameOfTheTarFileContainingInitialData>
auxiliaryDirForTars="$MYSCRATCH/tars"
echo "Checking that the auxiliary directory exists"
if ! [ -d $auxiliaryDirForTars ]; then
   echo "Trying to create the auxiliary directory as it does not exist"
   mkdir -p $auxiliaryDirForTars; exitcode=$?
   if [ $exitcode -ne 0 ]; then
      echo "The auxiliary directory $auxiliaryDirForTars does not exist and can't be created"
      echo "Exiting the script with non-zero code in order to inform job dependencies not to continue."
      exit 1
   fi
fi

#-----------------
#Working directory in scratch for the supercomputing job
workingDir="$MYSCRATCH/<workingDirectoryForSupercomputingJob>"
echo "Checking that the working directory exists"
if ! [ -d $workingDir ]; then
   echo "Trying to create the working directory as it does not exist"
   mkdir -p $workingDir; exitcode=$?
   if [ $exitcode -ne 0 ]; then
      echo "The working directory $workingDir does not exist and can't be created"
      echo "Exiting the script with non-zero code in order to inform job dependencies not to continue."
      exit 1
   fi
fi

#-----------------
#Check if Acacia definitions make sense, and if the object to transfer exist
echo "Checking that the profile exists"
rclone config show | grep "${profileName}" > /dev/null; exitcode=$?
if [ $exitcode -ne 0 ]; then
   echo "The given profileName=$profileName seems not to exist in the user configuration of rclone"
   echo "Exiting the script with non-zero code in order to inform job dependencies not to continue."
   exit 1
fi
echo "Checking that bucket exists and that you have read access"
rclone lsd "${profileName}:${bucketName}" > /dev/null; exitcode=$? #Note the colon(:) when using rclone
if [ $exitcode -ne 0 ]; then
   echo "The bucket name or the profile name may be wrong: ${profileName}:${bucketName}"
   echo "Exiting the script with non-zero code in order to inform job dependencies not to continue."
   exit 1
fi
echo "Checking if the file can be listed in Acacia"
listResult=$(rclone lsl "${fullPathInAcacia}/${tarFileName}")
if [ -z "$listResult" ]; then
   echo "Problems occurred during the listing of the file ${tarFileName}"
   echo "Check that the file exists in the fullPathInAcacia: ${fullPathInAcacia}/"
   echo "Exiting the script with non-zero code in order to inform job dependencies not to continue."
   exit 1
fi

#-----------------
#Perform the transfer of the tar file into the auxiliary directory and check for the transfer
echo "Performing the transfer ... "
srun rclone copy "${fullPathInAcacia}/${tarFileName}" "${auxiliaryDirForTars}/"; exitcode=$?
if [ $exitcode -ne 0 ]; then
   echo "Problems occurred during the transfer of file ${tarFileName}"
   echo "Check that the file exists in the fullPathInAcacia: ${fullPathInAcacia}/"
   echo "Exiting the script with non-zero code in order to inform job dependencies not to continue."
   exit 1
fi

#-----------------
#Perform untaring with desired options into the working directory
echo "Performing the untarring ... "
#tarOptions=( --strip-components 8 ) #Avoiding creation of some directories in the path
srun tar -xvzf "${auxiliaryDirForTars}/${tarFileName}" -C $workingDir "${tarOptions[@]}"; exitcode=$?
if [ $exitcode -ne 0 ]; then
   echo "Problems occurred during the untaring of file ${auxiliaryDirForTars}/${tarFileName}"
   echo "Exiting the script with non-zero code in order to inform job dependencies not to continue."
   exit 1
else
   echo "Removing the tar file as it has been successfully untarred"
   rm $auxiliaryDirForTars/$tarFileName #comment this line when debugging workflow
fi

#-----------------
## Final checks ....

#---------------
#Successfully finished
echo "Done"
exit 0

#!/bin/bash --login

#SBATCH --account=[yourProjectName]
#SBATCH --job-name=storeTar
#SBATCH --partition=copy
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --time=[requiredTime]
#SBATCH --export=NONE

#-----------------
#Loading the required modules
module load rclone/<version> #This example is performed with the use of the rclone. 

#-----------------
#Defining variables that will hold the names related to your access, buckets and objects to be stored in Acacia
profileName=<profileNameGivenToYourProfileOfAccessToAcacia>
bucketName=<bucketInAcaciaContainingTheData>
prefixPath=<prefixPathInBucketUsedToOrginiseTheData>
fullPathInAcacia="${profileName}:${bucketName}/${prefixPath}" #Note the colon(:) when using rclone

#-----------------
#Check if Acacia definitions make sense, and if you can transfer objects into the desired bucket
echo "Checking that the profile exists"
rclone config show | grep "${profileName}" > /dev/null; exitcode=$?
if [ $exitcode -ne 0 ]; then
   echo "The given profileName=$profileName seems not to exist in the user configuration of rclone"
   echo "Exiting the script with non-zero code in order to inform job dependencies not to continue."
   exit 1
fi
echo "Checking the bucket exists and that you have writing access"
rclone lsd "${profileName}:${bucketName}" > /dev/null; exitcode=$? #Note the colon(:) when using rclone
if [ $exitcode -ne 0 ]; then
   echo "The bucket intended to receive the data does not exist: ${profileName}:${bucketName}"
   echo "Trying to create it"
   rclone mkdir "${profileName}:${bucketName}"; exitcode=$?
   if [ $exitcode -ne 0 ]; then
      echo "Creation of bucket failed"
      echo "The bucket name or the profile name may be wrong: ${profileName}:${bucketName}"
      echo "Exiting the script with non-zero code in order to inform job dependencies not to continue."
      exit 1
   fi
fi
echo "Checking if a test file can be trasferred into the desired full path in Acacia"
testFile=test_file_${SLURM_JOBID}.txt
echo "File for test" > "${testFile}"
rclone copy "${testFile}" "${fullPathInAcacia}/"; exitcode=$?
if [ $exitcode -ne 0 ]; then
   echo "The test file $testFile cannot be transferred into ${fullPathInAcacia}"
   echo "Exiting the script with non-zero code in order to inform job dependencies not to continue."
   exit 1
fi
echo "Checking if the test file can be listed in Acacia"
listResult=$(rclone lsl "${fullPathInAcacia}/${testFile}")
if [ -z "$listResult" ]; then
   echo "Problems occurred during the listing of the test file ${testFile} in ${fullPathInAcacia}"
   echo "Exiting the script with non-zero code in order to inform job dependencies not to continue."
   exit 1
fi
echo "Removing test file from Acacia"
rclone delete "${fullPathInAcacia}/${testFile}"; exitcode=$?
if [ $exitcode -ne 0 ]; then
   echo "The test file $testFile cannot be removed from ${fullPathInAcacia}"
   echo "Exiting the script with non-zero code in order to inform job dependencies not to continue."
   exit 1
fi
rm $testFile

#----------------
#Defining the working dir and cd into it
workingDir="$MYSCRATCH/<workingDirectoryOfSupercomputingJob>"
echo "Checking that the working directory exists"
if ! [ -d $workingDir ]; then
   echo "The working directory $workingDir does not exist"
   echo "Exiting the script with non-zero code in order to inform job dependencies not to continue."
   exit 1
else
   cd $workingDir
fi

#----------------
#Defining what to tar and the name and place of the tarfile
whatToTar=( file1 dir1/ dir2/file2 dir3/file* ) #These are inside the working dir
tarFileName=case_A1-newData.tar.gz
auxiliaryDirForTars="$MYSCRATCH/tars"
echo "Checking that the auxiliary directory exists"
if ! [ -d $auxiliaryDirForTars ]; then
   echo "Trying to create the auxiliary directory as it does not exist"
   mkdir -p $auxiliaryDirForTars; exitcode=$?
   if [ $exitcode -ne 0 ]; then
      echo "The auxiliary directory $auxiliaryDirForTars does not exist and can't be created"
      echo "Exiting the script with non-zero code in order to inform job dependencies not to continue."
      exit 1
   fi
fi

#----------------
#Taring the indicated files and directories
srun tar -cvzf "${auxiliaryDirForTars}/${tarFileName}" "${whatToTar[@]}"; exitcode=$?
if [ $exitcode -ne 0 ]; then
   echo "Something went wrong when taring:"
   echo "tarFileName=${tarFileName}"
   echo "whatToTar=( ${whatToTar[@]} )"
   echo "Exiting the script with non-zero code in order to inform job dependencies not to continue."
   exit 1
fi

#-----------------
#Perform the transfer of the tar file into the working directory and check for the transfer
echo "Performing the transfer ... "
srun rclone copy "${auxiliaryDirForTars}/${tarFileName}" "${fullPathInAcacia}/"; exitcode=$?
if [ $exitcode -ne 0 ]; then
   echo "Problems occurred during the transfer of file ${tarFileName}"
   echo "Check that the file exists in ${workingDir}"
   echo "And that nothing is wrong with the fullPathInAcacia: ${fullPathInAcacia}/"
   echo "Exiting the script with non-zero code in order to inform job dependencies not to continue."
   exit 1
else
   echo "Removing the tar file from scratch as it was successfully transferred into Acacia"
   echo "Final place in Acacia: ${fullPathInAcacia}/${tarFileName}"
   rm "${auxiliaryDirForTars}/${tarFileName}" #Comment this line when debugging workflow
fi

#---------------
# Final checks ...

#---------------
#Successfully finished
echo "Done"
exit 0