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Merge pull request #23 from CCBR/issue_18
Issue 18
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| import sys, os | ||
| import subprocess | ||
| from pathlib import Path | ||
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| def main(): | ||
| # Path to your bash script | ||
| p = Path(__file__).absolute() | ||
| pp = str(p.parent) | ||
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| # script_path = 'parkit/scripts/parkit_folder2hpcdme' | ||
| script_path = os.path.join(pp, "scripts", "projark") # projark ... archive a ccbr project!! | ||
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| # Pass all arguments to the bash script | ||
| subprocess.run([script_path] + sys.argv[1:]) | ||
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| if __name__ == "__main__": | ||
| main() |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| #!/usr/bin/env bash | ||
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| SCRIPTNAME="$BASH_SOURCE" | ||
| SCRIPTDIRNAME=$(readlink -f $(dirname "$SCRIPTNAME")) | ||
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| # add "bin" to PATH | ||
| if [[ ":$PATH:" != *":${SCRIPTDIRNAME}:"* ]];then | ||
| export PATH=${PATH}:${SCRIPTDIRNAME} | ||
| fi | ||
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| # rely on redirect to be redirect to the python script | ||
| RESOURCEDIR=$(dirname "$SCRIPTDIRNAME") | ||
| TOOLDIR="$SCRIPTDIRNAME" | ||
| TOOLNAME="parkit" | ||
| # PARKIT="${TOOLDIR}/${TOOLNAME}" | ||
| PARKIT="parkit" | ||
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| # Check if --version is provided as the first argument | ||
| if [[ "$1" == "--version" ]]; then | ||
| echo "projark is using the following parkit version:" | ||
| ${PARKIT} --version | ||
| exit 0 | ||
| fi | ||
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| # Test if parkit is working | ||
| ${PARKIT} > /dev/null 2>&1 || { echo "${PARKIT} not found or cannot be run!"; exit 1; } | ||
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| ARGPARSE_DESCRIPTION="Wrapper for folder2hpcdme for quick CCBR project archiving!" | ||
| source ${RESOURCEDIR}/resources/argparse.bash || exit 1 | ||
| argparse "$@" <<EOF || exit 1 | ||
| parser.add_argument('--folder',required=True,help='Input folder path to archive') | ||
| parser.add_argument('--projectnumber',required=True,help='CCBR project number.. destination will be /CCBR_Archive/GRIDFTP/Project_CCBR-<projectnumber>') | ||
| parser.add_argument('--executor',required=False,default='slurm', help='slurm or local') | ||
| parser.add_argument('--rawdata',required=False,action='store_true', help='If tarball is rawdata and needs to go under folder Rawdata') | ||
| parser.add_argument('--cleanup',required=False,action='store_true', help='post transfer step to delete local files') | ||
| EOF | ||
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| # Destination path for archiving | ||
| TITLE="CCBR-${PROJECTNUMBER}" | ||
| DEST="/CCBR_Archive/GRIDFTP/Project_${TITLE}" | ||
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| # Check if SOURCE_CONDA_CMD is set | ||
| if [ -z "${SOURCE_CONDA_CMD}" ];then | ||
| echo "SOURCE_CONDA_CMD env variable must be set" | ||
| exit 1 | ||
| else | ||
| echo "SOURCE_CONDA_CMD is set to: $SOURCE_CONDA_CMD" | ||
| fi | ||
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| # Check if HPC_DM_UTILS is set | ||
| if [ -z "$HPC_DM_UTILS" ]; then | ||
| echo "HPC_DM_UTILS environment variable is not set." | ||
| exit 1 # Exit the script with an error code | ||
| else | ||
| echo "HPC_DM_UTILS is set to: $HPC_DM_UTILS" | ||
| fi | ||
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| # Call folder2hpcdme with necessary parameters | ||
| cmd="parkit_folder2hpcdme --folder \"$FOLDER\" --dest \"$DEST\" --projecttitle \"$TITLE\" --projectdesc \"$TITLE\" --executor \"$EXECUTOR\" --hpcdmutilspath $HPC_DM_UTILS --makereadme" | ||
| if [[ "${RAWDATA}" == "yes" ]];then | ||
| cmd="${cmd} --rawdata" | ||
| fi | ||
| if [[ "${CLEANUP}" == "yes" ]];then | ||
| cmd="${cmd} --cleanup" | ||
| fi | ||
| echo $cmd | ||
| eval "$cmd" | ||
| if [[ "$?" != "0" ]];then | ||
| exit 1 | ||
| fi | ||
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| # Exit with the same status code as folder2hpcdme | ||
| exit $? |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| 2.0.2 | ||
| 2.0.2-dev |
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