224 lines
7.1 KiB
Bash
Executable File
224 lines
7.1 KiB
Bash
Executable File
#!/bin/bash
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# bash-refine v1.1.1: bash-refine.sh, Felix Lohmeier, 2020-07-22
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# https://gist.github.com/felixlohmeier/d76bd27fbc4b8ab6d683822cdf61f81d
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# license: MIT License https://choosealicense.com/licenses/mit/
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# TODO: support for macOS
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# ================================== CONFIG ================================== #
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endpoint="http://localhost:3333"
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memory="1400M" # increase to available RAM
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date="$(date +%Y%m%d_%H%M%S)"
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workspace="output/${date}"
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logfile="${workspace}/${date}.log"
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csrf=true # set to false for OpenRefine < 3.3
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jq="jq" # path to executable
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openrefine="openrefine/refine" # path to executable
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declare -A checkpoints # associative array for stats
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declare -A pids # associative array for monitoring background jobs
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declare -A projects # associative array for OpenRefine projects
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# =============================== REQUIREMENTS =============================== #
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function requirements {
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# check existence of java and cURL
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if [[ -z "$(command -v java 2> /dev/null)" ]] ; then
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echo 1>&2 "ERROR: OpenRefine requires JAVA runtime environment (jre)" \
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"https://openjdk.java.net/install/"
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exit 1
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fi
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if [[ -z "$(command -v curl 2> /dev/null)" ]] ; then
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echo 1>&2 "ERROR: This shell script requires cURL" \
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"https://curl.haxx.se/download.html"
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exit 1
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fi
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# download jq and OpenRefine if necessary
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if [[ -z "$(readlink -e "${jq}")" ]]; then
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echo "Download jq..."
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# jq 1.4 has much faster startup time than 1.5 and 1.6
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curl -L --output "${jq}" \
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"https://github.com/stedolan/jq/releases/download/jq-1.4/jq-linux-x86_64"
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chmod +x "${jq}"; echo
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fi
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if [[ -z "$(readlink -e "${openrefine}")" ]]; then
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echo "Download OpenRefine..."
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mkdir -p "$(dirname "${openrefine}")"
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curl -L --output openrefine.tar.gz \
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"https://github.com/OpenRefine/OpenRefine/releases/download/3.3/openrefine-linux-3.3.tar.gz"
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echo "Install OpenRefine in subdirectory $(dirname "${openrefine}")..."
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tar -xzf openrefine.tar.gz -C "$(dirname "${openrefine}")" --strip 1 --totals
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rm -f openrefine.tar.gz
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# do not try to open OpenRefine in browser
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sed -i '$ a JAVA_OPTIONS=-Drefine.headless=true' \
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"$(dirname "${openrefine}")"/refine.ini
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# set min java heap space to allocated memory
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sed -i 's/-Xms$REFINE_MIN_MEMORY/-Xms$REFINE_MEMORY/' \
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"$(dirname "${openrefine}")"/refine
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# set autosave period from 5 minutes to 25 hours
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sed -i 's/#REFINE_AUTOSAVE_PERIOD=60/REFINE_AUTOSAVE_PERIOD=1500/' \
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"$(dirname "${openrefine}")"/refine.ini
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echo
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fi
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}
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# ============================== OPENREFINE API ============================== #
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function refine_start {
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echo "start OpenRefine server..."
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local dir
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dir="$(readlink -f "${workspace}")"
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${openrefine} -v warn -m "${memory}" -p "${endpoint##*:}" -d "${dir}" &
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pid_server=${!}
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timeout 30s bash -c "until curl -s \"${endpoint}\" \
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| cat | grep -q -o 'OpenRefine' ; do sleep 1; done" \
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|| error "starting OpenRefine server failed!"
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}
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function refine_stats {
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# print server load
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ps -o start,etime,%mem,%cpu,rss -p "${pid_server}"
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}
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function refine_kill {
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# kill OpenRefine immediately; SIGKILL (kill -9) prevents saving projects
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{ kill -9 "${pid_server}" && wait "${pid_server}"; } 2>/dev/null
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# delete temporary OpenRefine projects
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(cd "${workspace}" && rm -rf ./*.project* && rm -f workspace.json)
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}
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function refine_check {
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if grep -i 'exception\|error' "${logfile}"; then
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error "log contains warnings!"
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else
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log "checked log file, all good!"
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fi
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}
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function refine_stop {
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echo "stop OpenRefine server and print server load..."
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refine_stats
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echo
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refine_kill
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echo "check log for any warnings..."
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refine_check
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}
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function refine_csrf {
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# get CSRF token (introduced in OpenRefine 3.3)
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if [[ "${csrf}" = true ]]; then
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local response
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response=$(curl -fs "${endpoint}/command/core/get-csrf-token")
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if [[ "${response}" != '{"token":"'* ]]; then
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error "getting CSRF token failed!"
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else
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echo "?csrf_token=$(echo "$response" | cut -d \" -f 4)"
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fi
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fi
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}
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function refine_store {
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# check and store project id from import in associative array projects
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if [[ $# = 2 ]]; then
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projects[$1]=$(cut -d '=' -f 2 "$2")
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else
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error "invalid arguments supplied to import function!"
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fi
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if [[ "${#projects[$1]}" != 13 ]]; then
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error "returned project id is not valid!"
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else
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rm "$2"
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fi
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# check if project contains at least one row (may be skipped to gain ~40ms)
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local rows
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rows=$(curl -fs --get \
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--data project="${projects[$p]}" \
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--data limit=0 \
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"${endpoint}/command/core/get-rows" \
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| tr "," "\n" | grep total | cut -d ":" -f 2)
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if [[ "$rows" = "0" ]]; then
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error "imported project contains 0 rows!"
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fi
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}
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# ============================ SCRIPT ENVIRONMENT ============================ #
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function log {
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# log status message
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echo "$(date +%H:%M:%S.%3N) [ client] $1"
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}
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function error {
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# log error message and exit
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echo 1>&2 "ERROR: $1"
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refine_kill; pkill -P $$; exit 1
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}
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function monitor {
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# store pid of last execution
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pids[$1]="$!"
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}
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function monitoring {
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# wait for stored pids, remove them from array and check log for errors
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for pid in "${!pids[@]}"; do
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wait "${pids[$pid]}" \
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|| error "${pid} (${projects[$pid]}) failed!" \
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&& unset pids["$pid"]
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done
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refine_check
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}
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function checkpoint {
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# store timestamp in associative array checkpoints and print checkpoint
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checkpoints[$1]=$(date +%s.%3N)
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printf '%*.*s %s %*.*s\n' \
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0 "$(((80-2-${#1})/2))" "$(printf '%0.1s' ={1..40})" \
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"${#checkpoints[@]}. $1" \
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0 "$(((80-1-${#1})/2))" "$(printf '%0.1s' ={1..40})"
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}
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function checkpoint_stats {
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# calculate run time based on checkpoints
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local k keys values i diffsec
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echo "starting time and run time (hh:mm:ss) of each step..."
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# sort keys by value and store in array key
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readarray -t keys < <(
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for k in "${!checkpoints[@]}"; do
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echo "${checkpoints[$k]}:::$k"
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done | sort | awk -F::: '{print $2}')
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# remove milliseconds from corresponding values and store in array values
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readarray -t values < <(
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for k in "${keys[@]}" ; do
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echo "${checkpoints[$k]%.*}"
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done)
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# add final timestamp for calculation
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values+=("$(date +%s)")
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# calculate and print run time for each step
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for i in "${!keys[@]}"; do
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diffsec=$(( values[$((i + 1))] - values[i] ))
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printf "%35s %s %s %s\n" "${keys[$i]}" "($((i + 1)))" \
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"$(date -d @"${values[$i]}")" \
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"($(date -d @${diffsec} -u +%H:%M:%S))"
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done
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# calculate and print total run time
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diffsec=$(( values[${#keys[@]}] - values[0] ))
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printf "%80s\n%80s\n" "----------" "($(date -d @${diffsec} -u +%H:%M:%S))"
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}
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function count_output {
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# word count on all files in workspace
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echo "files (number of lines / size in bytes) in ${workspace}..."
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(cd "${workspace}" && wc -c -l ./*)
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}
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function init {
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# check requirements and download software if necessary
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requirements
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# set trap, create directories and tee to log file
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trap 'error "script interrupted!"' HUP INT QUIT TERM
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mkdir -p "${workspace}"
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exec &> >(tee -i -a "${logfile}")
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}
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