This commit is contained in:
Felix Lohmeier
GitHub
parent
bf14449df9
commit
2df9d33ec4
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@ -1,5 +1,5 @@
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#!/bin/bash
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# openrefine-bash-curl.sh, Felix Lohmeier, v0.2, 2020-07-03
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# openrefine-bash-curl.sh, Felix Lohmeier, v0.3, 2020-07-03
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# How to control OpenRefine 3.3+ with cURL (and jq) in Bash scripts
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# https://gist.github.com/felixlohmeier/d76bd27fbc4b8ab6d683822cdf61f81d
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# tested on Linux (Fedora 33), needs to be adapted to work on macOS
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@ -17,7 +17,7 @@ memory="1400M"
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date="$(date +%Y%m%d_%H%M%S)"
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workspace="${date}"
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# ========================== REQUIREMENTS #=================================== #
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# ========================== REQUIREMENTS ==================================== #
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# check requirement java
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java="$(command -v java 2> /dev/null)"
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@ -69,10 +69,7 @@ openrefine="$(readlink -f openrefine/refine)"
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# ============================ ENVIRONMENT =================================== #
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function log() {
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echo "$(date +%H:%M:%S.%3N) [ client] $1"
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}
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# start OpenRefine
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function start() {
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${openrefine} -v warn -m "${memory}" -p "${port}" -d "${workspace}" &
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pid_server=${!}
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@ -81,6 +78,7 @@ function start() {
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|| { echo 1>&2 "ERROR: starting OpenRefine server failed!"; stop; exit 1; }
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}
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# stop OpenRefine
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function stop() {
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echo
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# print system resources
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@ -89,38 +87,50 @@ function stop() {
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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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# grep log for server exceptions
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grep -i 'exception\|error' "${workspace}/${date}.log" \
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&& exit 1 || log "no warnings, all good!"
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echo "check log for any warnings..."
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if grep -i 'exception\|error' "${workspace}/${date}.log"; then
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exit 1
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else
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log "no warnings, all good!"
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fi
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}
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# cleanup handler
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trap "stop;exit 1" SIGHUP SIGINT SIGQUIT SIGTERM
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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 [[ "${response}" != '{"token":"'* ]]; then
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echo 1>&2 "ERROR: getting CSRF token failed!"; stop; exit 1
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echo 1>&2 "ERROR: getting CSRF token failed!"; return 1
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else
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echo "$response" | cut -d \" -f 4
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fi
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}
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function import() {
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p[$project]=$(echo "$1" | cut -d '=' -f 2)
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# error handling: exit if import failed
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if [[ "${#p[$project]}" != 13 ]]; then
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echo 1>&2 "$1"; stop; exit 1
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# check and store project ids from import in associative array p
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declare -A p
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function store() {
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if [[ $# -eq 2 ]]; then
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p[$1]=$(cut -d '=' -f 2 "$2")
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else
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log "loaded as project id ${p[$project]}"
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echo 1>&2 "ERROR: invalid arguments supplied to import function"; return 1
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fi
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if [[ "${#p[$1]}" != 13 ]]; then
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echo 1>&2 "ERROR: returned project id is not valid"; return 1
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else
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rm "$2"
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fi
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}
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# create workspace
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# create directories
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mkdir -p "${workspace}"
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# simple logging
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# logging
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exec &> >(tee -a "${workspace}/${date}.log")
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# declare associative array for projects
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declare -A p
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function log() {
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echo "$(date +%H:%M:%S.%3N) [ client] $1"
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}
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# =================== TEMPLATES FOR YOUR WORKFLOW ============================ #
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@ -133,22 +143,31 @@ echo
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# ------------------------- IMPORT OPTION 1 ---------------------------------- #
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# create project from heredoc
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project="example1" # project id will be accessible as ${p[example1]}
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# project id will be accessible as ${p[example1]}
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project="example1"
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input="example1.csv"
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filename="${input##*/})"
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echo "import ${project}..."
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import "$(curl -fsS --write-out "%{redirect_url}\n" \
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--form project-file="@-;filename=example1.csv" \
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if curl -fsS --write-out "%{redirect_url}\n" \
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--form project-file="@-;filename=${input}" \
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--form project-name="${project}" \
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--form format="text/line-based/*sv" \
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--form options='{"separator": " "}' \
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"${endpoint}/command/core/create-project-from-upload?csrf_token=$(csrf)" \
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> "${workspace}/${filename}.id" \
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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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)"
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echo
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then
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store "${project}" "${workspace}/${filename}.id" \
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|| { echo 1>&2 "ERROR: import of ${input} failed!"; stop; exit 1; } \
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&& log "imported ${input} as ${p[$project]}"; echo
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else
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echo 1>&2 "ERROR: import of ${input} failed!"; stop; exit 1
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fi
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# -------------------------- IMPORT OPTION 2 --------------------------------- #
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@ -160,14 +179,64 @@ z,x,y
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DATA
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# create project from file
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project="example2" # project id will be accessible as ${p[example2]}
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echo "import ${project} from file..."
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import "$(curl -fsS --write-out "%{redirect_url}\n" \
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--form project-file="@${workspace}/test.csv" \
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# project id will be accessible as ${p[example2]}
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project="example2"
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input="${workspace}/test.csv"
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filename="${input##*/})"
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echo "import ${project}..."
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if curl -fsS --write-out "%{redirect_url}\n" \
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--form project-file="@${input}" \
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--form project-name="${project}" \
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--form format="text/line-based/*sv" \
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--form options='{"separator": ","}' \
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"${endpoint}/command/core/create-project-from-upload?csrf_token=$(csrf)")"
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"${endpoint}/command/core/create-project-from-upload?csrf_token=$(csrf)" \
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> "${workspace}/${filename}.id"
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then
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store "${project}" "${workspace}/${filename}.id" \
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|| { echo 1>&2 "ERROR: import of ${input} failed!"; stop; exit 1; } \
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&& log "imported ${input} as ${p[$project]}"; echo
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else
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echo 1>&2 "ERROR: import of ${input} failed!"; stop; exit 1
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fi
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# -------------------------- IMPORT OPTION 3 --------------------------------- #
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# mockup test data
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cat << DATA > "${workspace}/test2.csv"
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r,s,t
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1,1,1
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2,2,2
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DATA
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# create projects from files (in parallel)
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# project ids will be accessible as ${p[test]} and ${p[test2]}
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inputs=( "${workspace}/test.csv" "${workspace}/test2.csv" )
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echo "import files" "${input[@]}" "..."
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pid=()
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for i in "${!inputs[@]}"; do
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filename="${inputs[$i]##*/}"
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project="${filename%%.*}"
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curl -fsS --write-out "%{redirect_url}\n" \
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--form project-file="@${inputs[$i]}" \
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--form project-name="${project}" \
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--form format="text/line-based/*sv" \
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--form options='{"separator": ","}' \
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"${endpoint}/command/core/create-project-from-upload?csrf_token=$(csrf)" \
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> "${workspace}/${filename}.id" &
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pid+=("$!")
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done
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for i in "${!inputs[@]}"; do
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filename="${inputs[$i]##*/}"
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project="${filename%%.*}"
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wait "${pid[$i]}"
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if [[ $(wait "${pid[$i]}") -eq 0 ]]; then
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store "${project}" "${workspace}/${filename}.id" \
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|| { echo 1>&2 "ERROR: import of ${input} failed!"; stop; exit 1; } \
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&& log "imported ${input} as ${p[$project]}"
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else
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echo 1>&2 "ERROR: import of ${input} failed!"; stop; exit 1
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fi
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done
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echo
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# ------------------------ TRANSFORM OPTION 1 -------------------------------- #
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@ -190,23 +259,31 @@ cat << DATA > "${workspace}/test.json"
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DATA
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# apply operation from file
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project="example1"
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input="${workspace}/test.json"
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echo "add column test..."
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curl -fsS \
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--data project="${p[example1]}" \
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--data-urlencode operations@"${workspace}/test.json" \
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"${endpoint}/command/core/apply-operations?csrf_token=$(csrf)" \
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|| { stop; exit 1; }
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echo; echo
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if curl -fsS \
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--data project="${p[$project]}" \
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--data-urlencode operations@"${input}" \
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"${endpoint}/command/core/apply-operations?csrf_token=$(csrf)" > /dev/null
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then
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log "transformed ${p[$project]} with ${input}"
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echo
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else
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echo 1>&2 "ERROR: transform ${p[$project]} with ${input} failed!"
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stop; exit 1
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fi
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# ------------------------ TRANSFORM OPTION 2 -------------------------------- #
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# apply operation from quoted heredoc
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project="example1"
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echo "add column test2..."
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curl -fsS \
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--data project="${p[example1]}" \
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if curl -fsS \
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--data project="${p[$project]}" \
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--data-urlencode "operations@-" \
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"${endpoint}/command/core/apply-operations?csrf_token=$(csrf)" \
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<< "JSON" || { stop; exit 1; }
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"${endpoint}/command/core/apply-operations?csrf_token=$(csrf)" > /dev/null \
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<< "JSON"
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[
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{
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"op": "core/column-addition",
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@ -221,20 +298,26 @@ curl -fsS \
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}
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]
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JSON
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echo; echo
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then
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log "transformed ${p[$project]}"
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echo
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else
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echo 1>&2 "ERROR: transform ${p[$project]} failed!"; stop; exit 1
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fi
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# ------------------------ TRANSFORM OPTION 3 -------------------------------- #
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# apply operation from unquoted heredoc (allows using bash variables)
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echo "add column test3..."
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project="example1"
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new_column="test3"
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base_column="b"
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replace_value="BAR"
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curl -fsS \
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--data project="${p[example1]}" \
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echo "add column test3..."
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if curl -fsS \
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--data project="${p[$project]}" \
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--data-urlencode "operations@-" \
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"${endpoint}/command/core/apply-operations?csrf_token=$(csrf)" \
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<< JSON || { stop; exit 1; }
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"${endpoint}/command/core/apply-operations?csrf_token=$(csrf)" > /dev/null \
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<< JSON
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[
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{
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"op": "core/column-addition",
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@ -249,24 +332,30 @@ curl -fsS \
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}
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]
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JSON
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echo; echo
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then
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log "transformed ${p[$project]}"
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echo
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else
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echo 1>&2 "ERROR: transform ${p[$project]} failed!"; stop; exit 1
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fi
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# ------------------------ TRANSFORM OPTION 4 -------------------------------- #
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# apply operation from unquoted heredoc with multi-line expression (requires jq)
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echo "add column test4..."
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project="example1"
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replace_value="!"
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echo "add column test4..."
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read -r -d '' expression << EXPRESSION
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grel:value.replace(
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'2',
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'${replace_value}'
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)
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EXPRESSION
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curl -fsS \
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--data project="${p[example1]}" \
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if curl -fsS \
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--data project="${p[$project]}" \
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--data-urlencode "operations@-" \
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"${endpoint}/command/core/apply-operations?csrf_token=$(csrf)" \
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<< JSON || { stop; exit 1; }
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"${endpoint}/command/core/apply-operations?csrf_token=$(csrf)" > /dev/null \
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<< JSON
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[
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{
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"op": "core/column-addition",
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@ -281,13 +370,19 @@ curl -fsS \
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}
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]
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JSON
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echo; echo
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then
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log "transformed ${p[$project]}"
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echo
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else
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echo 1>&2 "ERROR: transform ${p[$project]} failed!"; stop; exit 1
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fi
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# ------------------------ TRANSFORM OPTION 5 -------------------------------- #
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# apply multiple operations generated on-the-fly (requires jq)
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echo "delete columns..."
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project="example1"
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columns=( "test" "test2" "test3" )
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echo "delete columns..."
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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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@ -300,43 +395,56 @@ for column in "${columns[@]}"; do
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JSON
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)" )
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done
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echo "${payload[@]}" | "${jq}" -s add | curl -fsS \
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--data project="${p[example1]}" \
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if echo "${payload[@]}" | "${jq}" -s add | curl -fsS \
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--data project="${p[$project]}" \
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--data-urlencode operations@- \
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"${endpoint}/command/core/apply-operations?csrf_token=$(csrf)" \
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|| { stop; exit 1; }
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echo; echo
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"${endpoint}/command/core/apply-operations?csrf_token=$(csrf)" > /dev/null
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then
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log "transformed ${p[$project]}"
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echo
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else
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echo 1>&2 "ERROR: transform ${p[$project]} failed!"; stop; exit 1
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fi
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# -------------------------- EXPORT OPTION 1 --------------------------------- #
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# export to stdout
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project="example1"
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echo "export example1..."
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curl -fsS \
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--data project="${p[example1]}" \
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if curl -fsS \
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--data project="${p[$project]}" \
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--data format="tsv" \
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--data engine='{"facets":[],"mode":"row-based"}' \
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"${endpoint}/command/core/export-rows" \
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|| { stop; exit 1; }
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echo
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"${endpoint}/command/core/export-rows"
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then
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echo
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else
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echo 1>&2 "ERROR: export of ${p[$project]} failed!"; stop; exit 1
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fi
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# -------------------------- EXPORT OPTION 2 --------------------------------- #
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# export to file
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project="example1"
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output="${workspace}/example1.csv"
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echo "export example1..."
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curl -fsS \
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--data project="${p[example1]}" \
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if curl -fsS \
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--data project="${p[$project]}" \
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--data format="csv" \
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--data engine='{"facets":[],"mode":"row-based"}' \
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"${endpoint}/command/core/export-rows" \
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> "${output}" \
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|| { stop; exit 1; } \
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&& log "saved to file ${output}"
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echo
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> "${output}"
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then
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log "${p[$project]} saved to file ${output}"
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echo
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else
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echo 1>&2 "ERROR: export of ${p[$project]} failed!"; stop; exit 1
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fi
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# -------------------------- EXPORT OPTION 3 --------------------------------- #
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# templating export to stdout
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project="example2"
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echo "export example2 using template..."
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IFS= read -r -d '' template << TEMPLATE
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{
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@ -344,8 +452,8 @@ IFS= read -r -d '' template << TEMPLATE
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"y": {{cells['y'].value.jsonize()}}
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}
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TEMPLATE
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echo "${template}" | head -c -2 | curl -fsS \
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--data project="${p[example2]}" \
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if echo "${template}" | head -c -2 | curl -fsS \
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--data project="${p[$project]}" \
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--data format="template" \
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--data prefix="[
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" \
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@ -355,13 +463,17 @@ echo "${template}" | head -c -2 | curl -fsS \
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" \
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--data engine='{"facets":[],"mode":"row-based"}' \
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--data-urlencode template@- \
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"${endpoint}/command/core/export-rows" \
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|| { stop; exit 1; }
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echo; echo
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"${endpoint}/command/core/export-rows"
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then
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echo; echo
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else
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echo 1>&2 "ERROR: export of ${p[$project]} failed!"; stop; exit 1
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fi
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# -------------------------- EXPORT OPTION 4 --------------------------------- #
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# templating export to file
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project="example2"
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output="${workspace}/example2.json"
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echo "export example2 using template..."
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IFS= read -r -d '' template << TEMPLATE
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@ -370,8 +482,8 @@ IFS= read -r -d '' template << TEMPLATE
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"y": {{cells['y'].value.jsonize()}}
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}
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TEMPLATE
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echo "${template}" | head -c -2 | curl -fsS \
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--data project="${p[example2]}" \
|
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if echo "${template}" | head -c -2 | curl -fsS \
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--data project="${p[$project]}" \
|
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--data format="template" \
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--data prefix="[
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" \
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|
|
@ -382,14 +494,17 @@ echo "${template}" | head -c -2 | curl -fsS \
|
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--data engine='{"facets":[],"mode":"row-based"}' \
|
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--data-urlencode template@- \
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"${endpoint}/command/core/export-rows" \
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> "${output}" \
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|| { stop; exit 1; } \
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&& log "saved to file ${output}"
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echo; echo
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> "${output}"
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||||
then
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||||
log "${p[$project]} saved to ${output}"
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||||
echo
|
||||
else
|
||||
echo 1>&2 "ERROR: export of ${p[$project]} failed!"; stop; exit 1
|
||||
fi
|
||||
|
||||
# -------------------------- EXPORT OPTION 5 --------------------------------- #
|
||||
|
||||
# export projects to files (example for parallel execution)
|
||||
# export projects to files (in parallel)
|
||||
projects=( "example1" "example2" )
|
||||
format="tsv"
|
||||
echo "export ${projects[*]} to files..."
|
||||
|
|
@ -403,10 +518,13 @@ for project in "${projects[@]}"; do
|
|||
> "${workspace}/${project}.${format}" &
|
||||
pid+=("$!")
|
||||
done
|
||||
for i in "${!projects[@]}"; do
|
||||
wait "${pid[$i]}" \
|
||||
|| { echo 1>&2 "ERROR: export of ${projects[$i]} failed!"; stop; exit 1; } \
|
||||
&& log "${projects[$i]} saved to file ${workspace}/${projects[$i]}.${format}"
|
||||
for i in "${!projects[@]}"; do
|
||||
project="${projects[$i]}"
|
||||
if [[ $(wait "${pid[$i]}") -eq 0 ]]; then
|
||||
log "${p[$project]} saved to ${workspace}/${project}.${format}"
|
||||
else
|
||||
echo 1>&2 "ERROR: export of ${p[$project]} failed!"; stop; exit 1
|
||||
fi
|
||||
done
|
||||
echo
|
||||
|
||||
|
|
@ -414,79 +532,107 @@ echo
|
|||
|
||||
# print id and name for each project (requires jq)
|
||||
echo "list projects..."
|
||||
curl -fsS --get \
|
||||
if curl -fsS --get \
|
||||
"${endpoint}/command/core/get-all-project-metadata" \
|
||||
| "${jq}" -r '.projects | keys[] as $k | "\($k): \(.[$k] | .name)"' \
|
||||
|| { stop; exit 1; }
|
||||
echo
|
||||
| "${jq}" -r '.projects | keys[] as $k | "\($k): \(.[$k] | .name)"'
|
||||
then
|
||||
echo
|
||||
else
|
||||
echo 1>&2 "ERROR: list projects failed!"; stop; exit 1
|
||||
fi
|
||||
|
||||
# -------------------------- GET METADATA ------------------------------------ #
|
||||
|
||||
# print metadata (requires jq)
|
||||
project="example1"
|
||||
echo "metadata for project example1..."
|
||||
curl -fsS --get \
|
||||
--data project="${p[example1]}" \
|
||||
if curl -fsS --get \
|
||||
--data project="${p[$project]}" \
|
||||
"${endpoint}/command/core/get-project-metadata" \
|
||||
| "${jq}" "{ id: ${p[example1]} } + ." \
|
||||
|| { stop; exit 1; }
|
||||
echo
|
||||
| "${jq}" "{ id: ${p[$project]} } + ."
|
||||
then
|
||||
echo
|
||||
else
|
||||
echo 1>&2 "ERROR: getting metadata of ${p[$project]} failed!"; stop; exit 1
|
||||
fi
|
||||
|
||||
# ---------------------------- GET ROWS -------------------------------------- #
|
||||
# -------------------------- GET ROWCOUNT ------------------------------------ #
|
||||
|
||||
# print total number of rows (requires jq)
|
||||
project="example1"
|
||||
echo "total number of rows in project example1..."
|
||||
curl -fsS --get \
|
||||
--data project="${p[example1]}" \
|
||||
if curl -fsS --get \
|
||||
--data project="${p[$project]}" \
|
||||
"${endpoint}/command/core/get-rows" \
|
||||
| "${jq}" -r '.total' \
|
||||
|| { stop; exit 1; }
|
||||
echo
|
||||
| "${jq}" -r '.total'
|
||||
then
|
||||
echo
|
||||
else
|
||||
echo 1>&2 "ERROR: getting rowcount of ${p[$project]} failed!"; stop; exit 1
|
||||
fi
|
||||
|
||||
# -------------------------- GET COLUMNS ------------------------------------- #
|
||||
|
||||
# print columns (requires jq)
|
||||
project="example1"
|
||||
echo "column names of project example1..."
|
||||
curl -fsS --get \
|
||||
--data project="${p[example1]}" \
|
||||
if curl -fsS --get \
|
||||
--data project="${p[$project]}" \
|
||||
"${endpoint}/command/core/get-models" \
|
||||
| "${jq}" -r '.columnModel | .columns[] | .name' \
|
||||
|| { stop; exit 1; }
|
||||
echo
|
||||
| "${jq}" -r '.columnModel | .columns[] | .name'
|
||||
then
|
||||
echo
|
||||
else
|
||||
echo 1>&2 "ERROR: getting columns of ${p[$project]} failed!"; stop; exit 1
|
||||
fi
|
||||
|
||||
# ---------------------- GET OPERATIONS HISTORY ------------------------------ #
|
||||
|
||||
# save operations history to file (requires jq)
|
||||
project="example1"
|
||||
output="${workspace}/example1_history.json"
|
||||
echo "operations history for project example1..."
|
||||
curl -fsS --get \
|
||||
--data project="${p[example1]}" \
|
||||
echo "history of operations for project example1..."
|
||||
if curl -fsS --get \
|
||||
--data project="${p[$project]}" \
|
||||
"${endpoint}/command/core/get-operations" \
|
||||
| "${jq}" '[ .entries[] | .operation ]' \
|
||||
> "${output}" \
|
||||
|| { stop; exit 1; } \
|
||||
&& log "saved to file ${output}"
|
||||
echo
|
||||
> "${output}"
|
||||
then
|
||||
log "ops history of ${p[$project]} saved to ${output}"
|
||||
echo
|
||||
else
|
||||
echo 1>&2 "ERROR: getting ops history of ${p[$project]} failed!"; stop; exit 1
|
||||
fi
|
||||
|
||||
# ------------------------ GET IMPORT History -------------------------------- #
|
||||
|
||||
# print import options history (requires jq)
|
||||
echo "print import options history for project example2..."
|
||||
curl -fsS --get \
|
||||
--data project="${p[example2]}" \
|
||||
project="example2"
|
||||
echo "history of import for project example2..."
|
||||
if curl -fsS --get \
|
||||
--data project="${p[$project]}" \
|
||||
"${endpoint}/command/core/get-project-metadata" \
|
||||
| "${jq}" ".importOptionMetadata[0]" \
|
||||
|| { stop; exit 1; }
|
||||
echo
|
||||
| "${jq}" ".importOptionMetadata[0]"
|
||||
then
|
||||
echo
|
||||
else
|
||||
echo 1>&2 "ERROR: getting imp history of ${p[$project]} failed!"; stop; exit 1
|
||||
fi
|
||||
|
||||
# ------------------------- DELETE project ----------------------------------- #
|
||||
|
||||
# delete project
|
||||
project="example1"
|
||||
echo "delete project example1..."
|
||||
curl -fsS \
|
||||
--data project="${p[example1]}" \
|
||||
"${endpoint}/command/core/delete-project?csrf_token=$(csrf)" \
|
||||
|| { stop; exit 1; }
|
||||
echo; echo
|
||||
if curl -fsS \
|
||||
--data project="${p[$project]}" \
|
||||
"${endpoint}/command/core/delete-project?csrf_token=$(csrf)"
|
||||
then
|
||||
log "${p[$project]} deleted"
|
||||
echo
|
||||
else
|
||||
echo 1>&2 "ERROR: deletion of ${p[$project]} failed!"; stop; exit 1
|
||||
fi
|
||||
|
||||
# --------------------------- STOP SERVER ------------------------------------ #
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue