ba-sachsen-pica/bash-refine.sh

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