mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-08-31 01:02:04 +08:00
Nicola Soranzo
96 lines
2.6 KiB
Bash
Executable File
96 lines
2.6 KiB
Bash
Executable File
#!/usr/bin/env bash
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# Configure this script in a cron job to run some common cleanup operations
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# Set the Environment variable GALAXY_CONFIG_FILE to use a custom galaxy config file.
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set -e
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display_help(){
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scriptname=$(basename "$0")
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printf "./$scriptname [--help] [--no-dry-run] [--days 10]
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Will run the galaxy cleanup scripts in the recommend order. By default a 'dry-run' is started. Specify --no-dry-run to do the actual cleanup.
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--help Show this help
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--dry-run|--no-dry-run Dry run(default), will only print out what the scripts would have done. Specify --no-dry-run to do the actual cleanup.
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--days Number of days to use as a cut off; do not act on objects updated more recently than this
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"
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}
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# number of days to use as a cut off; do not act on objects updated more recently than this
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DAYS=10
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DRYRUN=true
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while :
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do
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case "$1" in
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--no-dry-run)
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DRYRUN=false
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shift
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;;
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--dry-run ) # default
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DRYRUN=true
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shift
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;;
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--days )
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DAYS="$2"
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shift; shift
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;;
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-h )
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display_help
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exit 1
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;;
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--help )
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display_help
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exit 1
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;;
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"")
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break
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;;
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*)
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shift
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;;
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esac
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done
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cd "$(dirname "$0")"/..
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. scripts/common_startup_functions.sh
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setup_python
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set_galaxy_config_file_var
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if [ "$DRYRUN" = true ]; then
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MODE="--info_only"
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else
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MODE="-r"
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fi
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MAINTENANCE_LOG=maintenance.log
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COMMANDS=(
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"python scripts/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --delete_userless_histories >> $MAINTENANCE_LOG"
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"python scripts/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --purge_histories >> $MAINTENANCE_LOG"
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"python scripts/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --purge_datasets >> $MAINTENANCE_LOG"
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"python scripts/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --purge_folders >> $MAINTENANCE_LOG"
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"python scripts/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --delete_datasets >> $MAINTENANCE_LOG"
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"python scripts/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --purge_datasets >> $MAINTENANCE_LOG")
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printf "\nDry run: $DRYRUN\nDays: $DAYS\n\n"
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echo "Will run following commands and output in $MAINTENANCE_LOG"
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for (( i = 0; i < ${#COMMANDS[@]} ; i++ )); do
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echo "${COMMANDS[$i]}"
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done
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if [ "$DRYRUN" = false ]; then
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echo "python scripts/set_user_disk_usage.py >> $MAINTENANCE_LOG"
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fi
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# Run the commands
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for (( i = 0; i < ${#COMMANDS[@]} ; i++ )); do
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eval "${COMMANDS[$i]}"
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done
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if [ "$DRYRUN" = false ]; then
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python scripts/set_user_disk_usage.py >> $MAINTENANCE_LOG
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fi
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