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Felix Lohmeier 2020-07-09 19:02:48 +02:00 committed by GitHub
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#!/bin/bash
# bash-refine.sh, Felix Lohmeier, v1.0.0, 2020-07-09
# How to control OpenRefine 3.3+ with cURL (and jq) in Bash scripts
# https://gist.github.com/felixlohmeier/d76bd27fbc4b8ab6d683822cdf61f81d
# tested on Fedora 32 with OpenRefine 3.3, bash 5.0.17, curl 7.69.1 and jq 1.4
# license: MIT License https://choosealicense.com/licenses/mit/
# TODO: support for macOS
# TODO: example for setting metadata
# TODO: example for engine config (facets)
# make script executable from another directory
cd "$(dirname "${0}")" || exit 1
# ================================== CONFIG ================================== #
port="3333"
endpoint="http://localhost:${port}"
memory="1400M" # increase to available RAM
date="$(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 ============================== #
function refine_start() {
echo "start OpenRefine server..."
local dir
dir="$(readlink -f "${workspace}")"
${openrefine} -v warn -m "${memory}" -p "${port}" -d "${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!"
}
function refine_stats() {
# print server load
ps -o start,etime,%mem,%cpu,rss -p "${pid_server}"
}
function refine_kill() {
# kill OpenRefine immediately; SIGKILL (kill -9) prevents saving projects
{ kill -9 "${pid_server}" && wait "${pid_server}"; } 2>/dev/null
# delete temporary OpenRefine projects
(cd "${workspace}" && rm -rf ./*.project* && rm -f workspace.json)
}
function refine_check() {
if grep -i 'exception\|error' "${logfile}"; then
error "log contains warnings!"
else
log "checked log file, all good!"
fi
}
function refine_stop() {
echo "stop OpenRefine server and print server load..."
refine_stats
echo
refine_kill
echo "check log for any warnings..."
refine_check
}
function refine_csrf() {
# get CSRF token (introduced in OpenRefine 3.3)
if [[ "${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
}
function refine_store() {
# 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 ============================ #
function log() {
# log status message
echo "$(date +%H:%M:%S.%3N) [ client] $1"
}
function error() {
# log error message and exit
echo 1>&2 "ERROR: $1"
refine_kill; pkill -P $$; exit 1
}
function monitor() {
# store pid of last execution
pids[$1]="$!"
}
function monitoring() {
# 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 "%36s %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))"
}
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 ./*)
}
function init() {
# set trap, create directories and tee to log file
trap 'error "script interrupted!"' HUP INT QUIT TERM
mkdir -p "${workspace}"
exec &> >(tee -a "${logfile}")
}
# ======================= TEMPLATES FOR YOUR WORKFLOW ======================== #
# To increase readability, you may prefer to split up the code:
# - move all code below to a separate script (e.g. one for each workflow)
# - add the following lines at the beginning of the new file(s)
# #!/bin/bash
# . bash-refine.sh
# ================================= STARTUP ================================== #
checkpoint "Startup"
echo
# check requirements and download software if necessary
requirements
# override default config?
#port="3333"
#endpoint="http://localhost:${port}"
#memory="1400M"
#date="$(date +%Y%m%d_%H%M%S)"
#workspace="output/${date}"
#logfile="${workspace}/${date}.log"
# set trap, create directories and tee to log file
init
# start OpenRefine server
refine_start
echo
# ============================= MOCKUP TEST DATA ============================= #
mkdir -p input
cat << "DATA" > "input/example1.csv"
a,b,c
1,2,3
0,0,0
$,\,'
DATA
cat << "DATA" > "input/example2.tsv"
a b c
' \ $
0 0 0
3 2 1
DATA
cat << "DATA" > "input/example-operations-history.json"
[
{
"op": "core/column-addition",
"engineConfig": {
"mode": "row-based"
},
"newColumnName": "apply-from-file",
"columnInsertIndex": 2,
"baseColumnName": "b",
"expression": "grel:value.replace('2','TEST')",
"onError": "set-to-blank"
}
]
DATA
# ================================== IMPORT ================================== #
checkpoint "Import"
echo
# declare input
projects["from heredoc"]=""
projects["csv file example"]="input/example1.csv"
projects["tsv file example"]="input/example2.tsv"
projects["another csv example"]="input/example1.csv"
projects["yet another csv example"]="input/example1.csv"
# --------------------------- IMPORT FROM HEREDOC ---------------------------- #
# quoted heredoc ("DATA") will not be expanded by bash (no escaping needed)
# project id will be stored in as ${projects[csv file example]}
p="from heredoc"
f="" # optional filename, will be stored in OpenRefine project metadata
echo "import heredoc..."
if curl -fs --write-out "%{redirect_url}\n" \
--form project-file="@-$(if [[ -n $f ]]; then echo ";filename=${f}"; fi)" \
--form project-name="${p}" \
--form format="text/line-based/*sv" \
--form options='{
"encoding": "UTF-8",
"separator": " "
}' \
"${endpoint}/command/core/create-project-from-upload$(refine_csrf)" \
> "${workspace}/${p}.id" \
<< "DATA"
a b c
1 2 3
0 0 0
$ \ '
DATA
then
log "imported heredoc as ${p}"
else
error "import of ${p} failed!"
fi
refine_store "${p}" "${workspace}/${p}.id" || error "import of ${p} failed!"
echo
# ---------------------------- IMPORT FROM FILE ------------------------------ #
# project id will be stored in ${projects[tsv file example]}
p="tsv file example"
echo "import file ${projects[$p]} ..."
if curl -fs --write-out "%{redirect_url}\n" \
--form project-file="@${projects[$p]}" \
--form project-name="${p}" \
--form format="text/line-based/*sv" \
--form options='{
"encoding": "UTF-8",
"separator": "\t"
}' \
"${endpoint}/command/core/create-project-from-upload$(refine_csrf)" \
> "${workspace}/${p}.id"
then
log "imported ${projects[$p]} as ${p}"
else
error "import of ${projects[$p]} failed!"
fi
refine_store "${p}" "${workspace}/${p}.id" || error "import of ${p} failed!"
echo
# -------------------- IMPORT MULTIPLE FILES (PARALLEL) ---------------------- #
# project ids will be stored in ${projects[another csv example]} etc.
ps=( "csv file example" "another csv example" "yet another csv example" )
echo "import files" \
"$(for p in "${ps[@]}"; do printf "%s" "${projects[$p]} "; done)..."
for p in "${ps[@]}"; do
(if curl -fs --write-out "%{redirect_url}\n" \
--form project-file="@${projects[$p]}" \
--form project-name="${p}" \
--form format="line-based" \
--form options='{
"encoding": "UTF-8",
"separator": ","
}' \
"${endpoint}/command/core/create-project-from-upload$(refine_csrf)" \
> "${workspace}/${p}.id"
then
log "imported ${projects[$p]} as ${p}"
else
error "import of ${projects[$p]} failed!"
fi) &
monitor "${p}"
done
monitoring
for p in "${ps[@]}"; do
refine_store "${p}" "${workspace}/${p}.id" || error "import of ${p} failed!"
done
echo
# ================================ TRANSFORM ================================= #
checkpoint "Transform"
echo
# ------------------------ APPLY OPERATIONS FROM FILE ------------------------ #
p="csv file example"
f="input/example-operations-history.json"
echo "apply ${f} to ${p}..."
if curl -fs \
--data project="${projects[$p]}" \
--data-urlencode operations@"${f}" \
"${endpoint}/command/core/apply-operations$(refine_csrf)" > /dev/null
then
log "transformed ${p} (${projects[$p]})"
else
error "transform ${p} (${projects[$p]}) failed!"
fi
echo
# ---------------------- APPLY OPERATIONS FROM HEREDOC ----------------------- #
# quoted heredoc ("JSON") will not be expanded by bash (no escaping needed)
p="csv file example"
echo "add column apply-from-heredoc to ${p}..."
if curl -fs \
--data project="${projects[$p]}" \
--data-urlencode "operations@-" \
"${endpoint}/command/core/apply-operations$(refine_csrf)" > /dev/null \
<< "JSON"
[
{
"op": "core/column-addition",
"engineConfig": {
"mode": "row-based"
},
"newColumnName": "apply-from-heredoc",
"columnInsertIndex": 2,
"baseColumnName": "b",
"expression": "grel:value.replace('2','TEST')",
"onError": "set-to-blank"
}
]
JSON
then
log "transformed ${p} (${projects[$p]})"
else
error "transform ${p} (${projects[$p]}) failed!"
fi
echo
# ---------------- APPLY OPERATIONS FROM HEREDOC AND VARIABLES --------------- #
# unquoted heredocs with variable and multi-line expression (requires jq)
# \ must be used to quote the characters \, $, and `.
p="csv file example"
replace='TEST'
column="apply with variables"
echo "add column ${column} to ${p}..."
read -r -d '' expression << EXPRESSION
grel:value.replace(
'2',
'${replace}'
)
EXPRESSION
if curl -fs \
--data project="${projects[$p]}" \
--data-urlencode "operations@-" \
"${endpoint}/command/core/apply-operations$(refine_csrf)" > /dev/null \
<< JSON
[
{
"op": "core/column-addition",
"engineConfig": {
"mode": "row-based"
},
"newColumnName": "${column}",
"columnInsertIndex": 2,
"baseColumnName": "b",
"expression": $(echo "${expression}" | ${jq} -s -R '.'),
"onError": "set-to-blank"
}
]
JSON
then
log "transformed ${p} (${projects[$p]})"
else
error "transform ${p} (${projects[$p]}) failed!"
fi
echo
# ------ APPLY OPERATIONS FROM HEREDOC TO MULTIPLE PROJECTS (PARALLEL) ------ #
# quoted heredoc ("JSON") will not be expanded by bash (no escaping needed)
ps=( "another csv example" "yet another csv example" )
echo "add column apply-from-heredoc to" "${ps[@]}" "..."
for p in "${ps[@]}"; do
(if curl -fs \
--data project="${projects[$p]}" \
--data-urlencode "operations@-" \
"${endpoint}/command/core/apply-operations$(refine_csrf)" > /dev/null \
<< "JSON"
[
{
"op": "core/column-addition",
"engineConfig": {
"mode": "row-based"
},
"newColumnName": "apply-from-heredoc",
"columnInsertIndex": 2,
"baseColumnName": "b",
"expression": "grel:value.replace('2','TEST')",
"onError": "set-to-blank"
}
]
JSON
then
log "transformed ${p} (${projects[$p]})"
else
error "transform ${p} (${projects[$p]}) failed!"
fi) &
monitor "${p}"
done
monitoring
echo
# ------------- APPLY MULTIPLE OPERATIONS GENERATED FROM HEREDOC ------------- #
# unquoted heredoc (JSON) with variables and multiplied (requires jq)
# \ must be used to quote the characters \, $, and `.
p="csv file example"
columns=( "apply-from-file" "apply-from-heredoc" )
echo "delete columns" "${columns[@]}" "in ${p}..."
for column in "${columns[@]}"; do
cat << JSON >> "${workspace}/${p}.tmp"
[
{
"op": "core/column-removal",
"columnName": "${column}"
}
]
JSON
done
if "${jq}" -s add "${workspace}/${p}.tmp" | curl -fs \
--data project="${projects[$p]}" \
--data-urlencode operations@- \
"${endpoint}/command/core/apply-operations$(refine_csrf)" > /dev/null
then
log "transformed ${p} (${projects[$p]})"
rm "${workspace}/${p}.tmp"
else
error "transform ${p} (${projects[$p]}) failed!"
fi
echo
# ================================== EXPORT ================================== #
checkpoint "Export"
echo
# ----------------------------- EXPORT TO STDOUT ----------------------------- #
p="csv file example"
format="tsv"
echo "export ${p} in ${format} format..."
if curl -fs \
--data project="${projects[$p]}" \
--data format="tsv" \
--data engine='{"facets":[],"mode":"row-based"}' \
"${endpoint}/command/core/export-rows"
then
log "exported ${p} (${projects[$p]})"
else
error "export of ${p} (${projects[$p]}) failed!"
fi
echo
# ------------------------------ EXPORT TO FILE ------------------------------ #
p="csv file example"
format="csv"
echo "export ${p} to ${format} file..."
if curl -fs \
--data project="${projects[$p]}" \
--data format="${format}" \
--data engine='{"facets":[],"mode":"row-based"}' \
"${endpoint}/command/core/export-rows" \
> "${workspace}/${p}.${format}"
then
log "exported ${p} (${projects[$p]}) to ${workspace}/${p}.${format}"
else
error "export of ${p} (${projects[$p]}) failed!"
fi
echo
# ------------------------- TEMPLATING EXPORT TO FILE ------------------------ #
p="csv file example"
format="json"
echo "export ${p} to ${format} file using template..."
IFS= read -r -d '' template << "TEMPLATE"
{
"a": {{cells['a'].value.jsonize()}},
"b": {{cells['b'].value.jsonize()}},
"c": {{cells['c'].value.jsonize()}}
}
TEMPLATE
if echo "${template}" | head -c -2 | curl -fs \
--data project="${projects[$p]}" \
--data format="template" \
--data prefix="[
" \
--data suffix="
]" \
--data separator=",
" \
--data engine='{"facets":[],"mode":"row-based"}' \
--data-urlencode template@- \
"${endpoint}/command/core/export-rows" \
> "${workspace}/${p}.${format}"
then
log "exported ${p} (${projects[$p]}) to ${workspace}/${p}.${format}"
else
error "export of ${p} (${projects[$p]}) failed!"
fi
echo
# ------------------- EXPORT TO MULTIPLE FILES (PARALLEL) -------------------- #
ps=( "another csv example" "yet another csv example" )
format="tsv"
echo "export" "${ps[@]}" "to ${format} files..."
for p in "${ps[@]}"; do
(if curl -fs \
--data project="${projects[$p]}" \
--data format="${format}" \
--data engine='{"facets":[],"mode":"row-based"}' \
"${endpoint}/command/core/export-rows" \
> "${workspace}/${p}.${format}"
then
log "exported ${p} (${projects[$p]}) to ${workspace}/${p}.${format}"
else
error "export of ${p} (${projects[$p]}) failed!"
fi) &
monitor "${p}"
done
monitoring
echo
# ================================ UTILITIES ================================= #
checkpoint "Utilities"
echo
# ------------------------------ LIST PROJECTS ------------------------------- #
# get all project metadata and reshape json to print a list (requires jq)
echo "list projects..."
if curl -fs --get \
"${endpoint}/command/core/get-all-project-metadata" \
| "${jq}" -r '.projects | keys[] as $k | "\($k): \(.[$k] | .name)"'
then
: #log "printed list of projects"
else
error "getting list of projects failed!"
fi
echo
# ------------------------------- GET METADATA ------------------------------- #
# get project metadata and reshape json to include project id (requires jq)
p="csv file example"
echo "metadata for ${p}..."
if curl -fs --get \
--data project="${projects[$p]}" \
"${endpoint}/command/core/get-project-metadata" \
| "${jq}" "{ id: ${projects[$p]} } + ."
then
: #log "printed metadata of ${p} (${projects[$p]})"
else
error "getting metadata of ${p} (${projects[$p]}) failed!"
fi
echo
# ------------------------------ GET ROW COUNT ------------------------------- #
# get total number of rows
p="csv file example"
echo "total number of rows in ${p}..."
if curl -fs --get \
--data project="${projects[$p]}" \
--data limit=0 \
"${endpoint}/command/core/get-rows" \
| tr "," "\n" | grep total | cut -d ":" -f 2
then
: #log "printed row count of ${p} (${projects[$p]})"
else
error "getting row count of ${p} (${projects[$p]}) failed!"
fi
echo
# ------------------------------- GET COLUMNS -------------------------------- #
# get column names from project model (requires jq)
p="csv file example"
echo "column names of ${p}..."
if curl -fs --get \
--data project="${projects[$p]}" \
"${endpoint}/command/core/get-models" \
| "${jq}" -r '.columnModel | .columns[] | .name'
then
: #log "printed column names of ${p} (${projects[$p]})"
else
error "getting column names of ${p} (${projects[$p]}) failed!"
fi
echo
# -------------------------- GET OPERATIONS HISTORY -------------------------- #
# get operations history and reshape json to make it applicable (requires jq)
p="csv file example"
f="${workspace}/${p}_history.json"
echo "history of operations for ${p}..."
if curl -fs --get \
--data project="${projects[$p]}" \
"${endpoint}/command/core/get-operations" \
| "${jq}" '[ .entries[] | .operation ]' \
> "${f}"
then
log "saved ops history of ${p} (${projects[$p]}) to ${f}"
else
error "getting ops history of ${p} (${projects[$p]}) failed!"
fi
echo
# ---------------------------- GET IMPORT HISTORY ---------------------------- #
# get project metadata and filter import options history (requires jq)
p="csv file example"
echo "history of import for ${p}..."
if curl -fs --get \
--data project="${projects[$p]}" \
"${endpoint}/command/core/get-project-metadata" \
| "${jq}" ".importOptionMetadata[0]"
then
: #log "printed import history of ${p} (${projects[$p]})"
else
error "getting import history of ${p} (${projects[$p]}) failed!"
fi
echo
# ------------------------------ DELETE PROJECT ------------------------------ #
# delete a project (rarely needed for batch processing)
p="yet another csv example"
echo "delete project ${p}..."
if curl -fs \
--data project="${projects[$p]}" \
"${endpoint}/command/core/delete-project$(refine_csrf)" > /dev/null
then
log "deleted ${p} (${projects[$p]})"
else
error "deletion of ${p} (${projects[$p]}) failed!"
fi
echo
# ================================== FINISH ================================== #
checkpoint "Finish"
echo
# stop OpenRefine server
refine_stop
echo
# calculate run time based on checkpoints
checkpoint_stats
echo
# word count on all files in workspace
count_output

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@ -1,659 +0,0 @@
#!/bin/bash
# openrefine-bash-curl.sh, Felix Lohmeier, v0.5, 2020-07-07
# How to control OpenRefine 3.3+ with cURL (and jq) in Bash scripts
# https://gist.github.com/felixlohmeier/d76bd27fbc4b8ab6d683822cdf61f81d
# tested on Linux (Fedora 33), needs to be adapted to work on macOS
# TODO: example for engine config (facets)
# make script executable from another directory
cd "$(dirname "${0}")" || exit 1
# ================================== CONFIG ================================== #
# config
port="3333"
endpoint="http://localhost:${port}"
memory="1400M"
date="$(date +%Y%m%d_%H%M%S)"
workspace="${date}"
# =============================== REQUIREMENTS =============================== #
# check requirement java
java="$(command -v java 2> /dev/null)"
if [[ -z "${java}" ]] ; then
echo 1>&2 "ERROR: OpenRefine requires JAVA runtime environment (jre)" \
"https://openjdk.java.net/install/"
exit 1
fi
# check requirement cURL
curl="$(command -v curl 2> /dev/null)"
if [[ -z "${curl}" ]] ; then
echo 1>&2 "ERROR: This shell script requires cURL" \
"https://curl.haxx.se/download.html"
exit 1
fi
# install jq 1.4 (faster startup time than 1.5 and 1.6) in this directory
if [[ ! -f "jq" ]]; then
echo "Download jq..."
curl -L --output "jq" \
"https://github.com/stedolan/jq/releases/download/jq-1.4/jq-linux-x86_64"
chmod +x "jq"
echo
fi
jq="$(readlink -f jq)"
# install OpenRefine 3.3 in subdirectory openrefine
openrefine_url="https://github.com/OpenRefine/OpenRefine/releases/download/3.3/openrefine-linux-3.3.tar.gz"
if [[ ! -d "openrefine" ]]; then
echo "Download OpenRefine..."
mkdir -p "openrefine"
curl -L --output "$(basename ${openrefine_url})" "${openrefine_url}"
echo "Install OpenRefine in subdirectory openrefine..."
tar -xzf "$(basename ${openrefine_url})" -C openrefine --strip 1 --totals
rm -f "$(basename ${openrefine_url})"
# do not try to open OpenRefine in browser
sed -i '$ a JAVA_OPTIONS=-Drefine.headless=true' \
openrefine/refine.ini
# set autosave period from 5 minutes to 25 hours
sed -i 's/#REFINE_AUTOSAVE_PERIOD=60/REFINE_AUTOSAVE_PERIOD=1500/' \
openrefine/refine.ini
# set min java heap space to allocated memory
sed -i 's/-Xms$REFINE_MIN_MEMORY/-Xms$REFINE_MEMORY/' \
openrefine/refine
echo
fi
openrefine="$(readlink -f openrefine/refine)"
# =============================== ENVIRONMENT ================================ #
# start OpenRefine
function start() {
${openrefine} -v warn -m "${memory}" -p "${port}" -d "${workspace}" &
pid_server=${!}
timeout 30s bash -c "until curl -s \"${endpoint}\" \
| cat | grep -q -o 'OpenRefine' ; do sleep 1; done" \
|| { echo 1>&2 "ERROR: starting OpenRefine server failed!"; stop; exit 1; }
}
# stop OpenRefine
function stop() {
echo
# print system resources
ps -o start,etime,%mem,%cpu,rss -p "${pid_server}"
echo
# SIGKILL (kill -9) prevents saving OpenRefine projects
{ kill -9 "${pid_server}" && wait "${pid_server}"; } 2>/dev/null
# grep log for server exceptions
echo "check log for any warnings..."
if grep -i 'exception\|error' "${workspace}/${date}.log"; then
exit 1
else
log "no warnings, all good!"
fi
}
# cleanup handler
trap "stop;exit 1" HUP INT QUIT TERM
# get csrf token (introduced in OpenRefine 3.3)
function csrf() {
response=$(curl -fsS "${endpoint}/command/core/get-csrf-token")
if [[ "${response}" != '{"token":"'* ]]; then
echo 1>&2 "ERROR: getting CSRF token failed!"; return 1
else
echo "$response" | cut -d \" -f 4
fi
}
# check and store project ids from import in associative array p
declare -A ids
function store() {
if [[ $# -eq 2 ]]; then
ids[$1]=$(cut -d '=' -f 2 "$2")
else
echo 1>&2 "ERROR: invalid arguments supplied to import function"; return 1
fi
if [[ "${#ids[$1]}" != 13 ]]; then
echo 1>&2 "ERROR: returned project id is not valid"; return 1
else
rm "$2"
fi
}
# create directories
mkdir -p "${workspace}"
# logging
exec &> >(tee -a "${workspace}/${date}.log")
function log() {
echo "$(date +%H:%M:%S.%3N) [ client] $1"
}
function error() {
echo 1>&2 "ERROR: $1"; stop; exit 1
}
# ======================= TEMPLATES FOR YOUR WORKFLOW ======================== #
# ------------------------------- START SERVER ------------------------------- #
echo "start OpenRefine server..."
start
echo
# ----------------------------- IMPORT OPTION 1 ------------------------------ #
# create project from heredoc
# project id will be accessible as ${ids[example1]}
p="example1"
input="example1.csv"
filename="${input##*/})"
echo "import ${p}..."
if curl -fsS --write-out "%{redirect_url}\n" \
--form project-file="@-;filename=${input}" \
--form project-name="${p}" \
--form format="text/line-based/*sv" \
--form options='{"separator": " "}' \
"${endpoint}/command/core/create-project-from-upload?csrf_token=$(csrf)" \
> "${workspace}/${filename}.id" \
<< "DATA"
a b c
1 2 3
0 0 0
$ \ '
DATA
then
store "${p}" "${workspace}/${filename}.id" \
|| error "import of ${input} failed!" \
&& log "imported ${input} as ${p} (${ids[$p]})"
else
error "import of ${input} failed!"
fi
echo
# ----------------------------- IMPORT OPTION 2 ------------------------------ #
# mockup test data
cat << DATA > "${workspace}/test.csv"
z,x,y
3,2,1
0,0,0
DATA
# create project from file
# project id will be accessible as ${ids[example2]}
p="example2"
input="${workspace}/test.csv"
filename="${input##*/})"
echo "import ${p}..."
if curl -fsS --write-out "%{redirect_url}\n" \
--form project-file="@${input}" \
--form project-name="${p}" \
--form format="text/line-based/*sv" \
--form options='{"separator": ","}' \
"${endpoint}/command/core/create-project-from-upload?csrf_token=$(csrf)" \
> "${workspace}/${filename}.id"
then
store "${p}" "${workspace}/${filename}.id" \
|| error "import of ${input} failed!" \
&& log "imported ${input} as ${p} (${ids[$p]})"
else
error "import of ${input} failed!"
fi
echo
# ----------------------------- IMPORT OPTION 3 ------------------------------ #
# mockup test data
cat << DATA > "${workspace}/test2.csv"
r,s,t
1,1,1
2,2,2
DATA
# create projects from files (in parallel)
# project ids will be accessible as ${ids[test]} and ${ids[test2]}
inputs=( "${workspace}/test.csv" "${workspace}/test2.csv" )
echo "import files" "${inputs[@]}" "..."
pid=()
for i in "${!inputs[@]}"; do
filename="${inputs[$i]##*/}"
p="${filename%%.*}"
curl -fsS --write-out "%{redirect_url}\n" \
--form project-file="@${inputs[$i]}" \
--form project-name="${p}" \
--form format="text/line-based/*sv" \
--form options='{"separator": ","}' \
"${endpoint}/command/core/create-project-from-upload?csrf_token=$(csrf)" \
> "${workspace}/${filename}.id" &
pid+=("$!")
done
for i in "${!inputs[@]}"; do
filename="${inputs[$i]##*/}"
p="${filename%%.*}"
wait "${pid[$i]}"
if [[ $(wait "${pid[$i]}") -eq 0 ]]; then
store "${p}" "${workspace}/${filename}.id" \
|| error "import of ${input} failed!" \
&& log "imported ${inputs[$i]} as ${p} (${ids[$p]})"
else
error "import of ${inputs[$i]} failed!"
fi
done
echo
# ---------------------------- TRANSFORM OPTION 1 ---------------------------- #
# mockup test data
cat << DATA > "${workspace}/test.json"
[
{
"op": "core/column-addition",
"engineConfig": {
"mode": "row-based"
},
"newColumnName": "test",
"columnInsertIndex": 2,
"baseColumnName": "b",
"expression": "grel:value.replace('2','FILE')",
"onError": "set-to-blank"
}
]
DATA
# apply operation from file
p="example1"
input="${workspace}/test.json"
echo "add column test to ${p}..."
if curl -fsS \
--data project="${ids[$p]}" \
--data-urlencode operations@"${input}" \
"${endpoint}/command/core/apply-operations?csrf_token=$(csrf)" > /dev/null
then
log "transformed ${p} (${ids[$p]}) with ${input}"
else
error "transform ${p} (${ids[$p]}) with ${input} failed!"
fi
echo
# ---------------------------- TRANSFORM OPTION 2 ---------------------------- #
# apply operation from quoted heredoc
p="example1"
echo "add column test2 to ${p}..."
if curl -fsS \
--data project="${ids[$p]}" \
--data-urlencode "operations@-" \
"${endpoint}/command/core/apply-operations?csrf_token=$(csrf)" > /dev/null \
<< "JSON"
[
{
"op": "core/column-addition",
"engineConfig": {
"mode": "row-based"
},
"newColumnName": "test2",
"columnInsertIndex": 2,
"baseColumnName": "b",
"expression": "grel:value.replace('2','FOO')",
"onError": "set-to-blank"
}
]
JSON
then
log "transformed ${p} (${ids[$p]})"
else
error "transform ${p} (${ids[$p]}) failed!"
fi
echo
# ---------------------------- TRANSFORM OPTION 3 ---------------------------- #
# apply operation from unquoted heredoc (allows using bash variables)
p="example1"
new_column="test3"
base_column="b"
replace_value="BAR"
echo "add column ${new_column} to ${p}..."
if curl -fsS \
--data project="${ids[$p]}" \
--data-urlencode "operations@-" \
"${endpoint}/command/core/apply-operations?csrf_token=$(csrf)" > /dev/null \
<< JSON
[
{
"op": "core/column-addition",
"engineConfig": {
"mode": "row-based"
},
"newColumnName": "${new_column}",
"columnInsertIndex": 3,
"baseColumnName": "${base_column}",
"expression": "grel:value.replace('2','${replace_value}')",
"onError": "set-to-blank"
}
]
JSON
then
log "transformed ${p} (${ids[$p]})"
else
error "transform ${p} (${ids[$p]}) failed!"
fi
echo
# ---------------------------- TRANSFORM OPTION 4 ---------------------------- #
# apply operation from unquoted heredoc with multi-line expression (requires jq)
p="example1"
replace_value="!"
echo "add column test4 to ${p}..."
read -r -d '' expression << EXPRESSION
grel:value.replace(
'2',
'${replace_value}'
)
EXPRESSION
if curl -fsS \
--data project="${ids[$p]}" \
--data-urlencode "operations@-" \
"${endpoint}/command/core/apply-operations?csrf_token=$(csrf)" > /dev/null \
<< JSON
[
{
"op": "core/column-addition",
"engineConfig": {
"mode": "row-based"
},
"newColumnName": "test4",
"columnInsertIndex": 4,
"baseColumnName": "b",
"expression": $(echo "${expression}" | ${jq} -s -R '.'),
"onError": "set-to-blank"
}
]
JSON
then
log "transformed ${p} (${ids[$p]})"
else
error "transform ${p} (${ids[$p]}) failed!"
fi
echo
# ---------------------------- TRANSFORM OPTION 5 ---------------------------- #
# apply multiple operations generated on-the-fly (requires jq)
p="example1"
columns=( "test" "test2" "test3" )
echo "delete columns" "${columns[@]}" "in ${p}..."
payload=()
for column in "${columns[@]}"; do
payload+=( "$(cat << JSON
[
{
"op": "core/column-removal",
"columnName": "${column}"
}
]
JSON
)" )
done
if echo "${payload[@]}" | "${jq}" -s add | curl -fsS \
--data project="${ids[$p]}" \
--data-urlencode operations@- \
"${endpoint}/command/core/apply-operations?csrf_token=$(csrf)" > /dev/null
then
log "transformed ${p} (${ids[$p]})"
else
error "transform ${p} (${ids[$p]}) failed!"
fi
echo
# ----------------------------- EXPORT OPTION 1 ------------------------------ #
# export to stdout
p="example1"
echo "export ${p}..."
if curl -fsS \
--data project="${ids[$p]}" \
--data format="tsv" \
--data engine='{"facets":[],"mode":"row-based"}' \
"${endpoint}/command/core/export-rows"
then
#log "printed export of ${p} (${ids[$p]})"
:
else
error "export of ${p} (${ids[$p]}) failed!"
fi
echo
# ----------------------------- EXPORT OPTION 2 ------------------------------ #
# export to file
p="example1"
output="${workspace}/${p}.csv"
echo "export ${p} to file..."
if curl -fsS \
--data project="${ids[$p]}" \
--data format="csv" \
--data engine='{"facets":[],"mode":"row-based"}' \
"${endpoint}/command/core/export-rows" \
> "${output}"
then
log "${p} (${ids[$p]}) saved to file ${output}"
else
error "export of ${p} (${ids[$p]}) failed!"
fi
echo
# ----------------------------- EXPORT OPTION 3 ------------------------------ #
# templating export to stdout
p="example2"
echo "export ${p} using template..."
IFS= read -r -d '' template << TEMPLATE
{
"z": {{cells['z'].value.jsonize()}},
"y": {{cells['y'].value.jsonize()}}
}
TEMPLATE
if echo "${template}" | head -c -2 | curl -fsS \
--data project="${ids[$p]}" \
--data format="template" \
--data prefix="[
" \
--data suffix="
]" \
--data separator=",
" \
--data engine='{"facets":[],"mode":"row-based"}' \
--data-urlencode template@- \
"${endpoint}/command/core/export-rows"
then
echo
#log "printed export of ${p} (${ids[$p]})"
else
error "export of ${p} (${ids[$p]}) failed!"
fi
echo
# ----------------------------- EXPORT OPTION 4 ------------------------------ #
# templating export to file
p="example2"
output="${workspace}/${p}.json"
echo "export ${p} to file using template..."
IFS= read -r -d '' template << TEMPLATE
{
"z": {{cells['z'].value.jsonize()}},
"y": {{cells['y'].value.jsonize()}}
}
TEMPLATE
if echo "${template}" | head -c -2 | curl -fsS \
--data project="${ids[$p]}" \
--data format="template" \
--data prefix="[
" \
--data suffix="
]" \
--data separator=",
" \
--data engine='{"facets":[],"mode":"row-based"}' \
--data-urlencode template@- \
"${endpoint}/command/core/export-rows" \
> "${output}"
then
log "${p} (${ids[$p]}) saved to ${output}"
else
error "export of ${p} (${ids[$p]}) failed!"
fi
echo
# ----------------------------- EXPORT OPTION 5 ------------------------------ #
# export projects to files (in parallel)
ps=( "example1" "example2" )
format="tsv"
echo "export" "${ps[@]}" "to files..."
pid=()
for p in "${ps[@]}"; do
curl -fs \
--data project="${ids[$p]}" \
--data format="${format}" \
--data engine='{"facets":[],"mode":"row-based"}' \
"${endpoint}/command/core/export-rows" \
> "${workspace}/${p}.${format}" &
pid+=("$!")
done
for i in "${!ps[@]}"; do
p="${ps[$i]}"
wait "${pid[$i]}"
if [[ $(wait "${pid[$i]}") -eq 0 ]]; then
log "${p} (${ids[$p]}) saved to ${workspace}/${p}.${format}"
else
error "export of ${p} (${ids[$p]}) failed!"
fi
done
echo
# ------------------------------ LIST PROJECTS ------------------------------- #
# print id and name for each project (requires jq)
echo "list projects..."
if curl -fsS --get \
"${endpoint}/command/core/get-all-project-metadata" \
| "${jq}" -r '.projects | keys[] as $k | "\($k): \(.[$k] | .name)"'
then
#log "printed list of projects"
:
else
error "list projects failed!"
fi
echo
# ------------------------------- GET METADATA ------------------------------- #
# print metadata (requires jq)
p="example1"
echo "metadata for ${p}..."
if curl -fsS --get \
--data project="${ids[$p]}" \
"${endpoint}/command/core/get-project-metadata" \
| "${jq}" "{ id: ${ids[$p]} } + ."
then
#log "printed metadata of ${p} (${ids[$p]})"
:
else
error "getting metadata of ${p} (${ids[$p]}) failed!"
fi
echo
# ------------------------------ GET ROW COUNT ------------------------------- #
# print total number of rows (requires jq)
p="example1"
echo "total number of rows in ${p}..."
if curl -fsS --get \
--data project="${ids[$p]}" \
"${endpoint}/command/core/get-rows" \
| "${jq}" -r '.total'
then
#log "printed row count of ${p} (${ids[$p]})"
:
else
error "getting rowcount of ${p} (${ids[$p]}) failed!"
fi
echo
# ------------------------------- GET COLUMNS -------------------------------- #
# print columns (requires jq)
p="example1"
echo "column names of ${p}..."
if curl -fsS --get \
--data project="${ids[$p]}" \
"${endpoint}/command/core/get-models" \
| "${jq}" -r '.columnModel | .columns[] | .name'
then
#log "printed column names of ${p} (${ids[$p]})"
:
else
error "getting columns of ${p} (${ids[$p]}) failed!"
fi
echo
# -------------------------- GET OPERATIONS HISTORY -------------------------- #
# save operations history to file (requires jq)
p="example1"
output="${workspace}/${p}_history.json"
echo "history of operations for ${p}..."
if curl -fsS --get \
--data project="${ids[$p]}" \
"${endpoint}/command/core/get-operations" \
| "${jq}" '[ .entries[] | .operation ]' \
> "${output}"
then
log "ops history of ${p} (${ids[$p]}) saved to ${output}"
else
error "getting ops history of ${p} (${ids[$p]}) failed!"
fi
echo
# ---------------------------- GET IMPORT HISTORY ---------------------------- #
# print import options history (requires jq)
p="example2"
echo "history of import for ${p}..."
if curl -fsS --get \
--data project="${ids[$p]}" \
"${endpoint}/command/core/get-project-metadata" \
| "${jq}" ".importOptionMetadata[0]"
then
#log "printed import history of ${p} (${ids[$p]})"
:
else
error "getting imp history of ${p} (${ids[$p]}) failed!"
fi
echo
# ---------------------------------- DELETE ---------------------------------- #
# delete project
p="example1"
echo "delete project ${p}..."
if curl -fsS \
--data project="${ids[$p]}" \
"${endpoint}/command/core/delete-project?csrf_token=$(csrf)" > /dev/null
then
log "deleted ${p} (${ids[$p]})"
else
error "deletion of ${p} (${ids[$p]}) failed!"
fi
echo
# ------------------------------- STOP SERVER -------------------------------- #
echo "stop OpenRefine server..."
stop