Add piscal manager scripts
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#!/bin/bash
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# piscal manager script
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usage="$(basename "$0") [-h]
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-d directory_name
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[-s|-c|-k]
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-p photosynthetic_type
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-u notify_url
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-t
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where:
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-h show this help text
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-d working directory name
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-s start job
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-c cleanup directory
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-k kill job
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-u url to notify on completion
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-p photosynthetic type
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-t suppress storage copy"
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# Initialize variables:
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# http://stackoverflow.com/a/246128/99492
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base_directory="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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directory_name=""
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photosynthetic_type="C3_photosynthesis_leafweb" #default
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task="get_status" # default task
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input_directory_name="input"
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pid_filename="piscal.pid"
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stderr_filename="piscal.err"
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cleaned_input_directory_name="output/clninput"
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output_directory_name="output/fitresult/touser"
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nottouser_directory_name="output/fitresult/nottouser"
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launcher="$base_directory/piscal_launcher.sh"
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# http://stackoverflow.com/a/14203146/99492
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# http://wiki.bash-hackers.org/howto/getopts_tutorial
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while getopts "hd:f:p:stcku:" opt; do
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#echo "$opt = $OPTARG"
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case "$opt" in
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h )
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echo "$usage"
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exit
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;;
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d )
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directory_name=$OPTARG
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;;
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p )
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photosynthetic_type=$OPTARG
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;;
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s )
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task="launch"
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;;
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t )
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suppress_storage_copy=true
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;;
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c )
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task="cleanup"
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;;
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k )
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task="kill"
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;;
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u )
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notify_url=$OPTARG
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;;
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\?) printf "illegal option: -%s\n" "$OPTARG" >&2
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echo "$usage" >&2
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exit 1
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;;
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esac
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done
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## Examine directories
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if [ -z "$directory_name" ]; then
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echo "directory name required (-d)"
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exit 1
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fi
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working_directory="$base_directory/$directory_name"
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if [ ! -d "$working_directory" ]; then
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echo "working directory $working_directory not found"
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exit 1
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fi
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input_directory="$working_directory/$input_directory_name"
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if [ ! -d "$input_directory" ]; then
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echo "input directory $input_directory not found"
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exit 1
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fi
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pid_path="$working_directory/$pid_filename"
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## Process task
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if [ "$task" = "launch" ]; then
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# verify process isn't running yet
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pid=$(head -n 1 $pid_path 2>/dev/null)
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# if the pid exists, check the process status using ps
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if ps -p $pid &>/dev/null; then
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# if it is in ps, then it's still running
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echo still running
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exit 1
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fi
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piscal_config_file="$working_directory"/piscal.cfg
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# write config file for piscal
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echo $photosynthetic_type > "$piscal_config_file"
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find "$input_directory" -maxdepth 1 -type f\
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-printf '%P\n'\
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>> "$piscal_config_file"
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command="$launcher -d $working_directory -f piscal.cfg"
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if [ "$suppress_storage_copy" = true ]; then
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command="$command -t"
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fi
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if [ -n "$notify_url" ]; then
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command="$command -u $notify_url"
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fi
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# launch it, sending error output to file
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nohup ${command} > $working_directory/$stderr_filename 2>&1 &
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# write the PID to a temp file to check for completion later
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echo $! > $pid_path
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echo started
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elif [ "$task" = "get_status" ] || [ "$task" = "get_status_cleaned_input" ]; then
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# if the pid doesn't exist, then process hasn't started
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if [ ! -f "$pid_path" ]; then
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echo "not started"
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exit
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fi
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pid=$(head -n 1 $pid_path 2>/dev/null)
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# if the pid exists, check the process status using ps
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if ps -p $pid > /dev/null; then
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# if it is in ps, then it's still running
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echo running
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else
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# otherwise, it is complete, check for runtime errors
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if [ -s "$working_directory/$stderr_filename" ]; then
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cat "$working_directory/$stderr_filename"
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exit 1
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fi
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output_directory="$working_directory/$output_directory_name"
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if [ ! -d "$output_directory" ]; then
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echo "output directory $output_directory not found"
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exit 1
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fi
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echo complete
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if [ "$task" = "get_status" ]; then
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echo "#touser"
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find "$output_directory"/* 2>/dev/null
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cleaned_input_directory="$working_directory/$cleaned_input_directory_name"
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echo "#clninput"
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find "$cleaned_input_directory"/* 2>/dev/null
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nottouser_directory="$working_directory/$nottouser_directory_name"
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echo "#nottouser"
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find "$nottouser_directory"/* 2>/dev/null
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exit 0
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fi
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fi
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elif [ "$task" = "cleanup" ]; then
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pid=$(head -n 1 $pid_path 2>/dev/null)
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# if the pid exists, check the process status using ps
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if ps -p $pid > /dev/null; then
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# if it is in ps, then it's still running
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echo still running
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exit 1
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fi
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rm -rf "$working_directory"
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elif [ "$task" = "kill" ]; then
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# if the pid doesn't exist, then process hasn't started
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if [ ! -f "$pid_path" ]; then
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echo "not started"
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exit 1
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fi
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pid=$(head -n 1 $pid_path 2>/dev/null)
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# if the pid exists, check the process status using ps
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if ps -p $pid > /dev/null; then
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# if it is in ps, then it's still running
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kill $pid
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fi
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echo killed
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fi
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