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openrefine-batch
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openrefine-batch/openrefine-batch.sh

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#!/bin/bash
# openrefine-batch.sh, Felix Lohmeier, v1.5, 2017-10-26
# https://github.com/felixlohmeier/openrefine-batch
# declare download URLs for OpenRefine and OpenRefine client
openrefine_URL="https://github.com/felixlohmeier/OpenRefine/releases/download/2017-10-26%2Bpr1290/openrefine-linux-2017-10-26-pr1290.tar.gz"
client_URL="https://github.com/felixlohmeier/openrefine-client/releases/download/v0.3.1/openrefine-client_0-3-1_linux-64bit"
# check system requirements
JAVA="$(which java 2> /dev/null)"
if [ -z "$JAVA" ] ; then
echo 1>&2 "This action requires you to have 'Java JRE' installed. You can download it for free at https://java.com"
exit 1
fi
# check if wget supports option --show-progress (since wget 1.16)
wget --help | grep -q '\--show-progress' && wget_opt="--show-progress" || wget_opt=""
# autoinstall OpenRefine
if [ ! -d "openrefine" ]; then
echo "Download OpenRefine..."
mkdir -p openrefine
wget -q $wget_opt $openrefine_URL
echo "Install OpenRefine in subdirectory openrefine..."
tar -xzf "$(basename $openrefine_URL)" -C openrefine --strip 1 --totals
rm -f "$(basename $openrefine_URL)"
sed -i '$ a JAVA_OPTIONS=-Drefine.headless=true' openrefine/refine.ini
sed -i 's/#REFINE_AUTOSAVE_PERIOD=60/REFINE_AUTOSAVE_PERIOD=1440/' openrefine/refine.ini
sed -i 's/-Xms$REFINE_MIN_MEMORY/-Xms$REFINE_MEMORY/' openrefine/refine
echo ""
fi
# autoinstall OpenRefine client
if [ ! -d "openrefine-client" ]; then
echo "Download OpenRefine client..."
mkdir -p openrefine-client
wget -q -P openrefine-client $wget_opt $client_URL
chmod +x openrefine-client/openrefine-client_0-3-1_linux-64bit
echo ""
fi
# help screen
function usage () {
cat <<EOF
Usage: ./openrefine-batch.sh [-a INPUTDIR] [-b TRANSFORMDIR] [-c OUTPUTDIR] ...
== basic arguments ==
-a INPUTDIR path to directory with source files (leave empty to transform only ; multiple files may be imported into a single project by providing a zip or tar.gz archive, cf. https://github.com/OpenRefine/OpenRefine/wiki/Importers )
-b TRANSFORMDIR path to directory with OpenRefine transformation rules (json files, cf. http://kb.refinepro.com/2012/06/google-refine-json-and-my-notepad-or.html ; leave empty to transform only)
-c OUTPUTDIR path to directory for exported files (and OpenRefine workspace)
== options ==
-d CROSSDIR path to directory with additional OpenRefine projects (will be copied to workspace before transformation step to support the cross function, cf. https://github.com/OpenRefine/OpenRefine/wiki/GREL-Other-Functions )
-f INPUTFORMAT (csv, tsv, xml, json, line-based, fixed-width, xlsx, ods)
-i INPUTOPTIONS several options provided by openrefine-client, see below...
-m RAM maximum RAM for OpenRefine java heap space (default: 2048M)
-p PORT PORT on which OpenRefine should listen (default: 3333)
-E do NOT export files
-R do NOT restart OpenRefine after each transformation (e.g. config file)
-X do NOT restart OpenRefine after each project (e.g. input file)
-h displays this help screen
== inputoptions (mandatory for xml, json, fixed-width, xslx, ods) ==
-i recordPath=RECORDPATH (xml, json): please provide path in multiple arguments without slashes, e.g. /collection/record/ should be entered like this: --recordPath=collection --recordPath=record
-i columnWidths=COLUMNWIDTHS (fixed-width): please provide widths separated by comma (e.g. 7,5)
-i sheets=SHEETS (xlsx, ods): please provide sheets separated by comma (e.g. 0,1), default: 0 (first sheet)
== more inputoptions (optional, only together with inputformat) ==
-i projectName=PROJECTNAME (all formats)
-i limit=LIMIT (all formats), default: -1
-i includeFileSources=INCLUDEFILESOURCES (all formats), default: false
-i trimStrings=TRIMSTRINGS (xml, json), default: false
-i storeEmptyStrings=STOREEMPTYSTRINGS (xml, json), default: true
-i guessCellValueTypes=GUESSCELLVALUETYPES (xml, csv, tsv, fixed-width, json), default: false
-i encoding=ENCODING (csv, tsv, line-based, fixed-width), please provide short encoding name (e.g. UTF-8)
-i ignoreLines=IGNORELINES (csv, tsv, line-based, fixed-width, xlsx, ods), default: -1
-i headerLines=HEADERLINES (csv, tsv, fixed-width, xlsx, ods), default: 1
-i skipDataLines=SKIPDATALINES (csv, tsv, line-based, fixed-width, xlsx, ods), default: 0
-i storeBlankRows=STOREBLANKROWS (csv, tsv, line-based, fixed-width, xlsx, ods), default: true
-i processQuotes=PROCESSQUOTES (csv, tsv), default: true
-i storeBlankCellsAsNulls=STOREBLANKCELLSASNULLS (csv, tsv, line-based, fixed-width, xlsx, ods), default: true
-i linesPerRow=LINESPERROW (line-based), default: 1
== example ==
./openrefine-batch.sh \
-a examples/powerhouse-museum/input/ \
-b examples/powerhouse-museum/config/ \
-c examples/powerhouse-museum/output/ \
-f tsv \
-i processQuotes=false \
-i guessCellValueTypes=true \
-RX
clone or download GitHub repository to get example data:
https://github.com/felixlohmeier/openrefine-batch/archive/master.zip
EOF
exit 1
}
# defaults
ram="2048M"
port="3333"
restartfile="true"
restarttransform="true"
export="true"
inputdir=/dev/null
configdir=/dev/null
crossdir=/dev/null
# check input
NUMARGS=$#
if [ "$NUMARGS" -eq 0 ]; then
usage
fi
# get user input
options="a:b:c:d:f:i:m:p:ERXh"
while getopts $options opt; do
case $opt in
a ) inputdir=$(readlink -f ${OPTARG}); if [ -n "${inputdir// }" ] ; then inputfiles=($(find -L "${inputdir}"/* -type f -printf "%f\n" 2>/dev/null)); fi ;;
b ) configdir=$(readlink -f ${OPTARG}); if [ -n "${configdir// }" ] ; then jsonfiles=($(find -L "${configdir}"/* -type f -printf "%f\n" 2>/dev/null)); fi ;;
c ) outputdir=$(readlink -m ${OPTARG}); mkdir -p "${outputdir}" ;;
d ) crossdir=$(readlink -f ${OPTARG}); if [ -n "${crossdir// }" ] ; then crossprojects=($(find -L "${crossdir}"/* -maxdepth 0 -type d -printf "%f\n" 2>/dev/null)); fi ;;
f ) format="${OPTARG}" ; inputformat="--format=${OPTARG}" ;;
i ) inputoptions+=("--${OPTARG}") ;;
m ) ram=${OPTARG} ;;
p ) port=${OPTARG} ;;
E ) export="false" ;;
R ) restarttransform="false" ;;
X ) restartfile="false" ;;
h ) usage ;;
\? ) echo 1>&2 "Unknown option: -$OPTARG"; usage; exit 1;;
: ) echo 1>&2 "Missing option argument for -$OPTARG"; usage; exit 1;;
* ) echo 1>&2 "Unimplemented option: -$OPTARG"; usage; exit 1;;
esac
done
shift $(($OPTIND - 1))
# check for mandatory options
if [ -z "$outputdir" ]; then
echo 1>&2 "please provide path to directory for exported files (and OpenRefine workspace)"
echo 1>&2 "example: ./openrefine-batch.sh -c output/"
exit 1
fi
if [ "$format" = "xml" ] || [ "$format" = "json" ] && [ -z "$inputoptions" ]; then
echo 1>&2 "error: you specified the inputformat $format but did not provide mandatory input options"
echo 1>&2 "please provide recordpath in multiple arguments without slashes"
echo 1>&2 "example: ./openrefine-batch.sh ... -f $format -i recordPath=collection -i recordPath=record"
exit 1
fi
if [ "$format" = "fixed-width" ] && [ -z "$inputoptions" ]; then
echo 1>&2 "error: you specified the inputformat $format but did not provide mandatory input options"
echo 1>&2 "please provide column widths separated by comma (e.g. 7,5)"
echo 1>&2 "example: ./openrefine-batch.sh ... -f $format -i columnWidths=7,5"
exit 1
fi
if [ "$format" = "xlsx" ] || [ "$format" = "ods" ] && [ -z "$inputoptions" ]; then
echo 1>&2 "error: you specified the inputformat $format but did not provide mandatory input options"
echo 1>&2 "please provide sheets separated by comma (e.g. 0,1), default: 0 (first sheet)"
echo 1>&2 "example: ./openrefine-batch.sh ... -f $format -i sheets=0"
exit 1
fi
# print variables
echo "Input directory: $inputdir"
echo "Input files: ${inputfiles[*]}"
echo "Input format: $inputformat"
echo "Input options: ${inputoptions[*]}"
echo "Config directory: $configdir"
echo "Transformation rules: ${jsonfiles[*]}"
echo "Cross directory: $crossdir"
echo "Cross projects: ${crossprojects[*]}"
echo "OpenRefine heap space: $ram"
echo "OpenRefine port: $port"
echo "OpenRefine workspace: $outputdir"
echo "Export TSV to workspace: $export"
echo "restart after file: $restartfile"
echo "restart after transform: $restarttransform"
echo ""
# declare additional variables
checkpoints=${#checkpointdate[@]}
checkpointdate[$(($checkpoints + 1))]=$(date +%s)
checkpointname[$(($checkpoints + 1))]="Start process"
memoryload=()
# launch server
checkpoints=${#checkpointdate[@]}
checkpointdate[$(($checkpoints + 1))]=$(date +%s)
checkpointname[$(($checkpoints + 1))]="Launch OpenRefine"
echo "=== $checkpoints. ${checkpointname[$(($checkpoints + 1))]} ==="
echo ""
echo "starting time: $(date --date=@${checkpointdate[$(($checkpoints + 1))]})"
echo ""
openrefine/refine -p ${port} -d "${outputdir}" -m ${ram} &
pid=$!
# wait until server is available
until wget -q -O - http://localhost:${port} | cat | grep -q -o "OpenRefine" ; do sleep 1; done
echo ""
# import all files
if [ -n "$inputfiles" ]; then
checkpoints=${#checkpointdate[@]}
checkpointdate[$(($checkpoints + 1))]=$(date +%s)
checkpointname[$(($checkpoints + 1))]="Import all files"
echo "=== $checkpoints. ${checkpointname[$(($checkpoints + 1))]} ==="
echo ""
echo "starting time: $(date --date=@${checkpointdate[$(($checkpoints + 1))]})"
echo ""
for inputfile in "${inputfiles[@]}" ; do
echo "import ${inputfile}..."
# run client with input command
openrefine-client/openrefine-client_0-3-1_linux-64bit -P ${port} -c ${inputdir}/${inputfile} $inputformat "${inputoptions[@]}"
# show allocated system resources
ps -o start,etime,%mem,%cpu,rss -p ${pid} --sort=start
memoryload+=($(ps --no-headers -o rss -p ${pid}))
echo ""
# restart server to clear memory
if [ "$restartfile" = "true" ]; then
echo "save project and restart OpenRefine server..."
kill ${pid}
wait
echo ""
openrefine/refine -p ${port} -d "${outputdir}" -m ${ram} &
pid=$!
until wget -q -O - http://localhost:${port} | cat | grep -q -o "OpenRefine" ; do sleep 1; done
echo ""
fi
done
fi
# transform and export files
if [ -n "$jsonfiles" ] || [ "$export" = "true" ]; then
checkpoints=${#checkpointdate[@]}
checkpointdate[$(($checkpoints + 1))]=$(date +%s)
checkpointname[$(($checkpoints + 1))]="Prepare transform & export"
echo "=== $checkpoints. ${checkpointname[$(($checkpoints + 1))]} ==="
echo ""
echo "starting time: $(date --date=@${checkpointdate[$(($checkpoints + 1))]})"
echo ""
# get project ids
echo "get project ids..."
openrefine-client/openrefine-client_0-3-1_linux-64bit -P ${port} -l > "${outputdir}/projects.tmp"
projectids=($(cat "${outputdir}/projects.tmp" | cut -c 2-14))
projectnames=($(cat "${outputdir}/projects.tmp" | cut -c 17-))
cat "${outputdir}/projects.tmp" && rm "${outputdir:?}/projects.tmp"
echo ""
# provide additional OpenRefine projects for cross function
if [ -n "$crossprojects" ]; then
echo "provide additional projects for cross function..."
# copy given projects to workspace
rsync -a --exclude='*.project/history' "${crossdir}"/*.project "${outputdir}"
# restart server to advertise copied projects
echo "restart OpenRefine server to advertise copied projects..."
kill ${pid}
wait
echo ""
openrefine/refine -p ${port} -d "${outputdir}" -m ${ram} &
pid=$!
until wget -q -O - http://localhost:${port} | cat | grep -q -o "OpenRefine" ; do sleep 1; done
echo ""
fi
# loop for all projects
for ((i=0;i<${#projectids[@]};++i)); do
# apply transformation rules
if [ -n "$jsonfiles" ]; then
checkpoints=${#checkpointdate[@]}
checkpointdate[$(($checkpoints + 1))]=$(date +%s)
checkpointname[$(($checkpoints + 1))]="Transform ${projectnames[i]}"
echo "=== $checkpoints. ${checkpointname[$(($checkpoints + 1))]} ==="
echo ""
echo "starting time: $(date --date=@${checkpointdate[$(($checkpoints + 1))]})"
echo ""
for jsonfile in "${jsonfiles[@]}" ; do
echo "transform ${jsonfile}..."
# run client with apply command
openrefine-client/openrefine-client_0-3-1_linux-64bit -P ${port} -f ${configdir}/${jsonfile} ${projectids[i]}
# allocated system resources
ps -o start,etime,%mem,%cpu,rss -p ${pid} --sort=start
memoryload+=($(ps --no-headers -o rss -p ${pid}))
echo ""
# restart server to clear memory
if [ "$restarttransform" = "true" ]; then
echo "save project and restart OpenRefine server..."
kill ${pid}
wait
echo ""
openrefine/refine -p ${port} -d "${outputdir}" -m ${ram} &
pid=$!
until wget -q -O - http://localhost:${port} | cat | grep -q -o "OpenRefine" ; do sleep 1; done
fi
echo ""
done
fi
# export project to workspace
if [ "$export" = "true" ]; then
checkpoints=${#checkpointdate[@]}
checkpointdate[$(($checkpoints + 1))]=$(date +%s)
checkpointname[$(($checkpoints + 1))]="Export ${projectnames[i]}"
echo "=== $checkpoints. ${checkpointname[$(($checkpoints + 1))]} ==="
echo ""
echo "starting time: $(date --date=@${checkpointdate[$(($checkpoints + 1))]})"
echo ""
# get filename without extension
filename=${projectnames[i]%.*}
echo "export to file ${filename}.tsv..."
# run client with export command
openrefine-client/openrefine-client_0-3-1_linux-64bit -P ${port} -E --output="${outputdir}/${filename}.tsv" ${projectids[i]}
# show allocated system resources
ps -o start,etime,%mem,%cpu,rss -p ${pid} --sort=start
memoryload+=($(ps --no-headers -o rss -p ${pid}))
echo ""
fi
# restart server to clear memory
if [ "$restartfile" = "true" ]; then
echo "restart OpenRefine server..."
kill ${pid}
wait
echo ""
openrefine/refine -p ${port} -d "${outputdir}" -m ${ram} &
pid=$!
until wget -q -O - http://localhost:${port} | cat | grep -q -o "OpenRefine" ; do sleep 1; done
fi
echo ""
done
# list output files
if [ "$export" = "true" ]; then
echo "output (number of lines / size in bytes):"
wc -c -l "${outputdir}"/*.tsv
echo ""
fi
fi
# cleanup
echo "cleanup..."
kill ${pid}
wait
rm -r -f "${outputdir:?}"/workspace*.json
# delete duplicates from copied projects
if [ -n "$crossprojects" ]; then
for i in "${crossprojects[@]}" ; do rm -r -f "${outputdir}/${i}" ; done
fi
echo ""
# calculate and print checkpoints
echo "=== Statistics ==="
echo ""
checkpoints=${#checkpointdate[@]}
checkpointdate[$(($checkpoints + 1))]=$(date +%s)
checkpointname[$(($checkpoints + 1))]="End process"
echo "starting time and run time of each step:"
checkpoints=${#checkpointdate[@]}
checkpointdate[$(($checkpoints + 1))]=$(date +%s)
for i in $(seq 1 $checkpoints); do
diffsec="$((${checkpointdate[$(($i + 1))]} - ${checkpointdate[$i]}))"
printf "%35s $(date --date=@${checkpointdate[$i]}) ($(date -d@${diffsec} -u +%H:%M:%S))\n" "${checkpointname[$i]}"
done
echo ""
diffsec="$((${checkpointdate[$checkpoints]} - ${checkpointdate[1]}))"
echo "total run time: $(date -d@${diffsec} -u +%H:%M:%S) (hh:mm:ss)"
# calculate and print memory load
max=${memoryload[0]}
for n in "${memoryload[@]}" ; do
((n > max)) && max=$n
done
echo "highest memory load: $(($max / 1024)) MB"
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