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Merge pull request #108 from JoshuaUrrutia/patch-5
Update files-list
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‎bin/files-list‎

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#!/usr/bin/env python
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"""
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Usage: files-list [OPTIONS] agave://SYSTEM/PATH
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Lists files on a Tapis storage system.
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The path must be specified as an agave URI.
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Example:
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files-list -l agave://tacc-data-user/path/to/dir
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Flags:
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-c, --cachedir Session cache directory.
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-l, --long Use long listing format
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"""
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from __future__ import print_function
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import argparse
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import sys
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from agavepy.agave import Agave
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from agavepy import utils
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parser = argparse.ArgumentParser(
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description="Lists files on a Tapis storage system. The path must be specified as an agave URI (i.e. agave://tacc-data-user/path/to/dir)")
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parser.add_argument(
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"-c",
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"--cachedir",
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default=utils.credentials_cache_dir(),
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help="Session cache directory.")
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parser.add_argument(
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"-l", "--long", action="store_true", help="Use long listing format.")
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parser.add_argument("filepath", help="Path to list")
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if __name__ == "__main__":
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try:
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args = parser.parse_args()
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cache_dir = args.cachedir
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long_format = args.long
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uri = args.filepath
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agave = Agave()
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agave.load_client(cache_dir)
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# Refresh tokens if necessary.
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agave.refresh_tokens()
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# Save out session cache
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if agave.client_name is not None:
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agave.save_configs(cache_dir)
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# Obtain uri - remove the prefix 'agave://'.
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uri = uri[len("agave://"):]
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# List files on remote system.
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agave.files_list(uri, long_format=long_format)
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sys.exit(0)
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except Exception as err:
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print(err)
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sys.exit(1)
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#!/bin/bash
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#
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# files-list
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#
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# author: opensource@tacc.cloud
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#
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# This script is part of the Agave API command line interface (CLI).
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# It retrieves a file listing on a remote system. If no jobs. Optionally, one can search by name, tag,
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# ontology, or start date
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#
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DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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source "$DIR/common.sh"
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# Script logic -- TOUCH THIS {{{
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# A list of all variables to prompt in interactive mode. These variables HAVE
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# to be named exactly as the longname option definition in usage().
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interactive_opts=(apisecret apikey)
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# Print usage
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usage() {
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echo -n "$(basename $0) [OPTION]... [PATH]
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List files on a remote system. If no system is specified, your default storage
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system will be used. By specifying a system, the path given will be resolved
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on that remote system. Note that the system id, not hostname must be given.
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Options:
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-z, --access_token Access token
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-S, --systemId Specify the system id
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-L, --long Print response in unix-style ls -l format
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-l, --limit Maximum number of results to return
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-o, --offset Number of results to skip from the start
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--filter Comma separated list of fields to return in the response
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-H, --hosturl URL of the service
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-d, --development Run in dev mode using default dev server
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-f, --force Skip all user interaction
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-i, --interactive Prompt for values
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-q, --quiet Quiet (no output)
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-v, --verbose Verbose output
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-V, --veryverbose Very verbose output
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-h, --help Display this help and exit
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--version Output version information and exit
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--rich Provide rich response
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"
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}
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##################################################################
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##################################################################
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# Begin Script Logic #
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##################################################################
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##################################################################
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source "$DIR/files-common.sh"
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main() {
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#echo -n
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#set -x
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if [ -n "$systemId" ]; then
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hosturl="${hosturl}listings/system/${systemId}/${args}"
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else
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hosturl="${hosturl}listings/${args}"
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fi
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cmd="curl -sk -H \"${authheader}\" '${hosturl}?pretty=true$(pagination)'"
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if ((veryverbose)); then
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[ "$piped" -eq 0 ] && log "Calling $cmd"
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fi
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response=`curl -sk -H "${authheader}" "${hosturl}?pretty=true$(pagination)"`
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if [[ $(jsonquery "$response" "status") = 'success' ]]; then
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result=$(format_api_json "$response")
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# success "$result"
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echo "$result";
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else
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errorresponse=$(jsonquery "$response" "message")
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err "$errorresponse"
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fi
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}
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format_api_json() {
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if ((veryverbose)); then
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json_prettyify "${1}"
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elif [[ $verbose -eq 1 ]]; then
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result=$(jsonquery "$1" "result" 1)
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json_prettyify "${result}"
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elif [[ $long -eq 1 ]]; then
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#lstng=$(lsify "$1" | awk '{ printf("%-10s %+12s %+18s %+32s %s\n", $1, $2, $3, $4, $5); }')
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lsify "$1" | column -t -s$'\t'
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elif [[ $rich -eq 1 ]]; then
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result=$(richify "$1")
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columnize "${result}"
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else
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result=$(jsonquery "$1" "result.[].name")
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echo "${result}"
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fi
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}
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lsify () {
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#jq '.result[] | {type,length,name,lastModified}'
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names=($(jsonquery "$1" "result.[].name"))
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#echo $names
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lengths=($(jsonquery "$1" "result.[].length"))
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#echo $lengths
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types=($(jsonquery "$1" "result.[].type"))
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#echo $types
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modifieds=($(jsonquery "$1" "result.[].lastModified"))
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#echo $modifieds
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pems=($(jsonquery "$1" "result.[].permissions"))
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thisyear=$(date +%Y)
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n=0
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for i in "${names[@]}"; do
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up=''
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if [[ "${pems[$n]}" == "ALL" ]]; then
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up='rwx------'
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elif [[ "${pems[$n]}" == "READ" ]]; then
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up='r--------'
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elif [[ "${pems[$n]}" == "WRITE" ]]; then
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up='-w-------'
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elif [[ "${pems[$n]}" == "EXECUTE" ]]; then
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up='--x------'
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elif [[ "${pems[$n]}" == "READ_WRITE" ]]; then
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up='rw-------'
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elif [[ "${pems[$n]}" == "READ_EXECUTE" ]]; then
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up='r-x------'
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elif [[ "${pems[$n]}" == "WRITE_EXECUTE" ]]; then
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up='-wx------'
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elif [[ "${pems[$n]}" == "EXECUTE" ]]; then
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up='--x------'
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fi
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if [[ "${types[$n]}" == "dir" ]]; then
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up="d${up}"
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else
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up="-${up}"
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fi
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formatteddate=$(format_iso8601_time "${modifieds[$n]}")
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echo -e "${up}\t${username}\t${lengths[$n]}\t${formatteddate}\t$i"
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# moddate=($(echo ${modifieds[$n]} | sed -e 's/T.*//' -e 's/-/ /g'))
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# tmon=$(month_of_year ${moddate[1]})
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# tday=$(echo ${moddate[1]} | sed 's/^0*//')
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# if [[ $thisyear = ${moddate[0]} ]]; then
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# modtime=$(echo ${modifieds[$n]} | sed -e 's/.*T//' -e 's/\:..\....-..\:..//')
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# echo -e "${up}\t${username}\t${lengths[$n]}\t${modtime}\t$i"
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# else
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# echo -e "${up}\t${username}\t${lengths[$n]}\t${tmon}\t${tday}\t${moddate[0]}\t$i"
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# fi
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# tmod=`date -d "$(echo ${modifieds[$n]} | sed -e 's/T//' -e 's/.000-05\:00\:00//' | sed -e )"`
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# echo -e "${up}\t${username}\t${lengths[$n]}\t${tmod}\t$i"
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n=$[n+1]
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done
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}
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##################################################################
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##################################################################
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# End Script Logic #
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##################################################################
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##################################################################
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# }}}
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# Parse command line options
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source "$DIR/options.sh"
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# Main loop {{{
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# Print help if no arguments were passed.
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#[[ $# -eq 0 ]] && set -- "--help"
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# Read the options and set stuff
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while [[ $1 = -?* ]]; do
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case $1 in
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-h|--help) usage >&2; safe_exit ;;
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--version) version; copyright; disclaimer; safe_exit ;;
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-z|--access_token) shift; access_token=$1 ;;
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-S|--systemId) shift; systemId=$1 ;;
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-L|--long) long=1;;
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-l|--limit) shift; limit=$1;;
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-o|--offset) shift; offset=$1;;
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--filter) shift; responsefilter=$1 ;;
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-H|--hosturl) shift; hosturl=$1;;
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-d|--development) development=1 ;;
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-v|--verbose) verbose=1 ;;
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-V|--veryverbose) veryverbose=1; verbose=1 ;;
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-q|--quiet) quiet=1 ;;
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-i|--interactive) interactive=1 ;;
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-f|--force) force=1 ;;
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--rich) rich=1 ;;
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--endopts) shift; break ;;
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*) die "invalid option: $1" ;;
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esac
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shift
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done
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# Store the remaining part as arguments.
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args+=("$@")
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# }}}
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# Run the script logic
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source "$DIR/runner.sh"

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