Merge pull request #4916 from scholtalbers/add_maintenance_script

Add maintenance script..

scripts/common_startup_variables.sh

@@ -0,0 +1,38 @@
+#!/usr/bin/env bash
+
+# This file is sourced in the maintenance.sh script and could be sourced in ./run.sh or ./run_reports.sh
+SCRIPTLOCATION="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+# If there is a file that defines a shell environment specific to this
+# instance of Galaxy, source the file.
+if [ -z $GALAXY_LOCAL_ENV_FILE ];
+then
+  GALAXY_LOCAL_ENV_FILE="$SCRIPTLOCATION/../config/local_env.sh"
+fi
+
+if [ -f $GALAXY_LOCAL_ENV_FILE ];
+then
+  echo "Activating local env file: $GALAXY_LOCAL_ENV_FILE"
+  . $GALAXY_LOCAL_ENV_FILE
+fi
+
+# If there is a .venv/ directory, assume it contains a virtualenv that we
+# should run this instance in.
+GALAXY_VIRTUAL_ENV="${GALAXY_VIRTUAL_ENV:-$SCRIPTLOCATION/../.venv}"
+if [ -d "$GALAXY_VIRTUAL_ENV" -a -z "$skip_venv" ];
+then
+  [ -n "$PYTHONPATH" ] && { echo 'Unsetting $PYTHONPATH'; unset PYTHONPATH; }
+  echo "Activating virtualenv at $GALAXY_VIRTUAL_ENV"
+  . "$GALAXY_VIRTUAL_ENV/bin/activate"
+fi
+if [ -z "$GALAXY_CONFIG_FILE" ]; then
+  if [ -f "$SCRIPTLOCATION/../universe_wsgi.ini" ]; then
+    GALAXY_CONFIG_FILE=universe_wsgi.ini
+  elif [ -f "$SCRIPTLOCATION/../config/galaxy.ini" ]; then
+    GALAXY_CONFIG_FILE=config/galaxy.ini
+  else
+    GALAXY_CONFIG_FILE=config/galaxy.ini.sample
+  fi
+  export GALAXY_CONFIG_FILE
+fi
+
+echo "GALAXY_CONFIG_FILE: ${GALAXY_CONFIG_FILE}"

scripts/maintenance.sh

@@ -0,0 +1,91 @@
+#!/usr/bin/env bash
+
+# Configure this script in a cron job to run some common cleanup operations
+# Set the Environment variable GALAXY_CONFIG_FILE to use a custom galaxy config file.
+
+set -e
+
+display_help(){
+  scriptname=`basename $0`
+  printf "./$scriptname [--help] [--no-dry-run] [--days 10] 
+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.
+
+--help                  Show this help
+--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.
+--days                  Number of days to use as a cut off; do not act on objects updated more recently than this
+"
+}
+
+# number of days to use as a cut off; do not act on objects updated more recently than this
+DAYS=10
+DRYRUN=true
+
+while :
+do
+  case "$1" in
+    --no-dry-run)
+      DRYRUN=false
+      shift
+      ;;
+    --dry-run ) # default
+      DRYRUN=true
+      shift
+      ;;
+    --days )
+      DAYS="$2"
+      shift; shift
+      ;;
+    -h )
+      display_help
+      exit 1
+      ;;
+    --help )
+      display_help
+      exit 1
+      ;;
+    "")
+      break
+      ;;
+    *)
+      shift
+      ;;
+  esac
+done
+
+SCRIPTLOCATION="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+source ${SCRIPTLOCATION}/common_startup_variables.sh
+
+if [ "$DRYRUN" = true ]; then
+  MODE="--info_only"
+else
+  MODE="-r"
+fi
+
+MAINTENANCE_LOG="$SCRIPTLOCATION/../maintenance.log"
+COMMANDS=(
+"python $SCRIPTLOCATION/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --delete_userless_histories >> $MAINTENANCE_LOG"
+"python $SCRIPTLOCATION/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --purge_histories >> $MAINTENANCE_LOG"
+"python $SCRIPTLOCATION/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --purge_datasets >> $MAINTENANCE_LOG"
+"python $SCRIPTLOCATION/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --purge_folders >> $MAINTENANCE_LOG"
+"python $SCRIPTLOCATION/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --delete_datasets >> $MAINTENANCE_LOG"
+"python $SCRIPTLOCATION/cleanup_datasets/cleanup_datasets.py $GALAXY_CONFIG_FILE -d $DAYS $MODE --purge_datasets >> $MAINTENANCE_LOG")
+
+printf "\nDry run: $DRYRUN\nDays: $DAYS\n\n"
+echo "Will run following commands and output in $MAINTENANCE_LOG"
+for (( i = 0; i < ${#COMMANDS[@]} ; i++ )); do
+  echo "${COMMANDS[$i]}"
+done
+
+if [ "$DRYRUN" = false ]; then
+  echo "python $SCRIPTLOCATION/set_user_disk_usage.py >> $MAINTENANCE_LOG"
+fi
+
+# Run the commands
+cd $SCRIPTLOCATION/../
+for (( i = 0; i < ${#COMMANDS[@]} ; i++ )); do
+  eval "${COMMANDS[$i]}"
+done
+
+if [ "$DRYRUN" = false ]; then
+  python $SCRIPTLOCATION/set_user_disk_usage.py >> $MAINTENANCE_LOG
+fi