This commit is contained in:
Felix Lohmeier
GitHub
commit
115a62acfa
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#!/bin/bash
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# openrefine-bash-curl.sh, Felix Lohmeier, v0.1, 2020-06-29
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# How to control OpenRefine 3.3+ with cURL (and jq) in Bash scripts
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# tested on Linux (Fedora 33), needs to be adapted to work on macOS
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# make script executable from another directory
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cd "$(dirname "${0}")" || exit 1
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# ============================= CONFIG ======================================= #
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# config
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port="3333"
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endpoint="http://localhost:${port}"
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memory="1400M"
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date="$(date +%Y%m%d_%H%M%S)"
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workspace="${date}"
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# ============================= INSTALL ====================================== #
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# check requirement java
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JAVA="$(command -v java 2> /dev/null)"
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if [[ -z "${JAVA}" ]] ; then
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echo 1>&2 "ERROR: OpenRefine requires JAVA runtime environment (jre)" \
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"https://openjdk.java.net/install/"
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exit 1
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fi
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# check requirement cURL
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CURL="$(command -v curl 2> /dev/null)"
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if [[ -z "${CURL}" ]] ; then
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echo 1>&2 "ERROR: This shell script requires cURL" \
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"https://curl.haxx.se/download.html"
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exit 1
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fi
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# install jq 1.4 (faster startup time than 1.5 and 1.6) in this directory
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if [[ ! -f "jq" ]]; then
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echo "Download jq..."
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curl -L --output "jq" \
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"https://github.com/stedolan/jq/releases/download/jq-1.4/jq-linux-x86_64"
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chmod +x "jq"
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echo
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fi
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jq="$(readlink -f jq)"
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# install OpenRefine 3.3 in subdirectory openrefine
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openrefine_url="https://github.com/OpenRefine/OpenRefine/releases/download/3.3/openrefine-linux-3.3.tar.gz"
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if [[ ! -d "openrefine" ]]; then
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echo "Download OpenRefine..."
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mkdir -p "openrefine"
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curl -L --output "$(basename ${openrefine_url})" "${openrefine_url}"
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echo "Install OpenRefine in subdirectory openrefine..."
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tar -xzf "$(basename ${openrefine_url})" -C openrefine --strip 1 --totals
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rm -f "$(basename ${openrefine_url})"
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# do not try to open OpenRefine in browser
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sed -i '$ a JAVA_OPTIONS=-Drefine.headless=true' \
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openrefine/refine.ini
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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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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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openrefine/refine
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echo
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fi
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openrefine="$(readlink -f openrefine/refine)"
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# ============================ ENVIRONMENT =================================== #
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# wait for user input after each step
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function pause(){
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read -r -s -n 1 -p "Press any key to continue..."
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echo; echo
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}
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# safe cleanup handler
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function cleanup(){
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# SIGKILL (kill -9) prevents saving OpenRefine projects
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{ kill -9 "${pid_server}" && wait "${pid_server}"; } 2>/dev/null
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}
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trap "cleanup;exit 1" SIGHUP SIGINT SIGQUIT SIGTERM
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# create workspace
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mkdir -p "${workspace}"
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# simple logging
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exec &> >(tee -a "${workspace}/${date}.log")
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# =========================== START SERVER =================================== #
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# start OpenRefine server
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echo "start OpenRefine server..."
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${openrefine} -v warn -m "${memory}" -p "${port}" -d "${workspace}" &
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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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|| { echo 1>&2 "ERROR: starting OpenRefine server failed!"; cleanup; exit 1; }
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echo
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pause
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# =========================== CSRF TOKEN ===================================== #
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# get CSRF token (introduced in OpenRefine 3.3)
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function csrf(){
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response=$(curl -fsS "${endpoint}/command/core/get-csrf-token")
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if [[ "${response}" != '{"token":"'* ]]; then
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echo 1>&2 "ERROR: getting CSRF token failed!"; cleanup; exit 1
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else
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csrf=$(echo "$response" | cut -d \" -f 4)
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fi
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}
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# ============================= IMPORT ======================================= #
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# create example data from heredoc and store project id from response
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echo "import example data..."
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response=$(csrf; curl -fsS --write-out "%{redirect_url}\n" \
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--form project-file="@-;filename=example1.csv" \
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--form project-name="example1" \
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--form format="text/line-based/*sv" \
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"${endpoint}/command/core/create-project-from-upload?csrf_token=${csrf}" \
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<< "DATA"
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a,b,c
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1,2,3
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0,0,0
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$,\,'
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DATA
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) && p1=$(echo "$response" | cut -d '=' -f 2)
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# error handling: exit if import failed
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if [[ "${#p1}" != 13 ]]; then
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echo 1>&2 "$response"; cleanup; exit 1
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fi
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echo
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pause
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# create another project from file
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echo "import example data from file..."
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cat << DATA > "${workspace}/test.csv"
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z,x,y
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3,2,1
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0,0,0
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DATA
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response=$(csrf; curl -fsS --write-out "%{redirect_url}\n" \
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--form project-file="@${workspace}/test.csv" \
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--form project-name="example2" \
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--form format="text/line-based/*sv" \
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"${endpoint}/command/core/create-project-from-upload?csrf_token=${csrf}") \
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&& p2=$(echo "$response" | cut -d '=' -f 2)
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if [[ "${#p2}" != 13 ]]; then
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echo 1>&2 "$response"; cleanup; exit 1
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fi
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echo
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pause
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# ============================ TRANSFORM ===================================== #
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# export to stdout
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echo "export data..."
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curl -fsS \
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--data project="${p1}" \
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--data format="tsv" \
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"${endpoint}/command/core/export-rows" \
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|| { cleanup; exit 1; }
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echo
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pause
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# apply operation from quoted heredoc
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echo "add column test..."
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csrf; curl -fsS \
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--data-urlencode "operations@-" \
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"${endpoint}/command/core/apply-operations?project=${p1}&csrf_token=${csrf}" \
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<< "JSON" || { cleanup; exit 1; }
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[
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{
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"op": "core/column-addition",
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"engineConfig": {
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"mode": "row-based"
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},
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"newColumnName": "test",
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"columnInsertIndex": 2,
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"baseColumnName": "b",
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"expression": "grel:value.replace('2','FOO')",
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"onError": "set-to-blank"
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}
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]
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JSON
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echo; echo
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pause
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# export to stdout
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echo "export data (again)..."
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curl -fsS \
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--data project="${p1}" \
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--data format="tsv" \
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"${endpoint}/command/core/export-rows" \
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|| { cleanup; exit 1; }
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echo
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pause
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# apply operation from unquoted heredoc (allows using bash variables)
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echo "add column test2..."
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new_column="test2"
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base_column="b"
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replace_value="BAR"
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csrf; curl -fsS \
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--data-urlencode "operations@-" \
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"${endpoint}/command/core/apply-operations?project=${p1}&csrf_token=${csrf}" \
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<< JSON || { cleanup; exit 1; }
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[
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{
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"op": "core/column-addition",
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"engineConfig": {
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"mode": "row-based"
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},
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"newColumnName": "${new_column}",
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"columnInsertIndex": 3,
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"baseColumnName": "${base_column}",
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"expression": "grel:value.replace('2','${replace_value}')",
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"onError": "set-to-blank"
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}
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]
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JSON
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echo; echo
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pause
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# apply operation from unquoted heredoc with multi-line expression (requires jq)
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echo "add column test3..."
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replace_value="!"
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read -r -d '' expression <<- EXPR
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grel:value.replace(
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'2',
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'${replace_value}'
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)
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EXPR
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csrf; curl -fsS \
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--data-urlencode "operations@-" \
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"${endpoint}/command/core/apply-operations?project=${p1}&csrf_token=${csrf}" \
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<<- JSON || { cleanup; exit 1; }
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[
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{
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"op": "core/column-addition",
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"engineConfig": {
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"mode": "row-based"
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},
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"newColumnName": "test3",
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"columnInsertIndex": 4,
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"baseColumnName": "b",
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"expression": $(echo "${expression}" | ${jq} -s -R '.'),
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"onError": "set-to-blank"
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}
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]
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JSON
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echo; echo
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pause
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# export to stdout
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echo "export data (again)..."
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curl -fsS \
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--data project="${p1}" \
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--data format="tsv" \
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"${endpoint}/command/core/export-rows" \
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|| { cleanup; exit 1; }
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echo
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pause
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# apply multiple operations generated on-the-fly (requires jq)
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echo "delete columns..."
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columns=( "test" "test2" )
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payload=()
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for column in "${columns[@]}"; do
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payload+=( "$(cat <<- JSON
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[
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{
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"op": "core/column-removal",
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"columnName": "${column}"
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}
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]
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JSON
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)" )
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done
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csrf; echo "${payload[@]}" | "${jq}" -s add | curl -fsS \
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--data-urlencode operations@- \
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"${endpoint}/command/core/apply-operations?project=${p1}&csrf_token=${csrf}" \
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|| { cleanup; exit 1; }
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echo; echo
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pause
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# ============================== EXPORT ====================================== #
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# export to stdout
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echo "export data..."
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curl -fsS \
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--data project="${p1}" \
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--data format="tsv" \
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"${endpoint}/command/core/export-rows" \
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|| { cleanup; exit 1; }
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echo
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pause
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# export to stdout
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echo "export data..."
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curl -fsS \
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--data project="${p2}" \
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--data format="tsv" \
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"${endpoint}/command/core/export-rows" \
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|| { cleanup; exit 1; }
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echo
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pause
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# export projects to files (example for parallel execution)
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echo "export to files..."
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projects=( "${p1}" "${p2}" )
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pid=()
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for project in "${projects[@]}"; do
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echo "export project ${project} to file ${workspace}/${project}.tsv"
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curl -fs \
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--data project="${project}" \
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--data format="tsv" \
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"${endpoint}/command/core/export-rows" \
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> "${workspace}/${project}.tsv" &
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pid+=("$!")
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done
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for i in "${!projects[@]}"; do
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wait "${pid[$i]}" \
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|| { echo 1>&2 "ERROR: export of ${projects[$i]} failed!"; cleanup; exit 1; }
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done
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echo
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pause
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# ============================= METADATA ===================================== #
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# get metadata (requires jq)
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echo "show metadata for project ${p2}"
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curl -fsS \
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"${endpoint}/command/core/get-project-metadata?project=${p2}" \
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| "${jq}" "{ id: ${p1} } + ." \
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|| { cleanup; exit 1; }
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echo
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pause
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# get history (requires jq)
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echo "save operations history for project ${p1}" \
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"to file ${workspace}/${p1}_history.json"
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curl -fsS \
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"${endpoint}/command/core/get-operations?project=${p1}" \
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| "${jq}" '[ .entries[] | .operation ]' \
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> "${workspace}/${p1}_history.json" \
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|| { cleanup; exit 1; }
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echo
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pause
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# =========================== STOP SERVER ==================================== #
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# show allocated system resources
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echo "show system resources..."
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ps -o start,etime,%mem,%cpu,rss -p "${pid_server}"
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echo
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pause
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# stop OpenRefine server without saving projects to workspace
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echo "stop OpenRefine server..."
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cleanup
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echo
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pause
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# grep log for server exceptions
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echo "check log for any warnings..."
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grep -i 'exception\|error' "${workspace}/${date}.log" \
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&& exit 1 || echo "no warnings, all good!" && exit 0
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