563 lines
16 KiB
Bash
Executable File
563 lines
16 KiB
Bash
Executable File
#!/bin/bash
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# bash-refine v1.3.4: templates.sh, Felix Lohmeier, 2020-11-04
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# https://gist.github.com/felixlohmeier/d76bd27fbc4b8ab6d683822cdf61f81d
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# license: MIT License https://choosealicense.com/licenses/mit/
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# TODO: example for setting metadata
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# TODO: example for engine config (facets)
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# ======================= TEMPLATES FOR YOUR WORKFLOW ======================== #
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# The following code shows several options for import, transform and export
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# use the templates to write your own scripts or execute this file for a demo
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# =============================== ENVIRONMENT ================================ #
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# source the main script
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source "${BASH_SOURCE%/*}/bash-refine.sh" || exit 1
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# make script executable from another directory
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cd "${BASH_SOURCE%/*}/" || exit 1
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### override default config?
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#endpoint="http://localhost:3333"
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#memory="1400M" # increase to available RAM
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#csrf=true # set to false for OpenRefine < 3.3
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#date="$(date +%Y%m%d_%H%M%S)"
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#workdir="${BASH_SOURCE%/*}/output/${date}"
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#logfile="${BASH_SOURCE%/*}/log/${date}.log"
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#jq="${BASH_SOURCE%/*}/lib/jq" # path to executable
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#refine="${BASH_SOURCE%/*}/lib/openrefine/refine" # path to executable
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# check requirements, set trap, create workdir and tee to logfile
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init
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# ================================= STARTUP ================================== #
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checkpoint "Startup"; echo
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# start OpenRefine server
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refine_start; echo
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# ============================= MOCKUP TEST DATA ============================= #
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mkdir -p input
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cat << "DATA" > "input/example1.csv"
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a,b,c
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1,2,3
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0,0,0
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$,\,'
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DATA
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cat << "DATA" > "input/example2.tsv"
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a b c
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' \ $
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0 0 0
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3 2 1
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DATA
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cat << "DATA" > "input/example-operations-history.json"
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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": "apply-from-file",
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"columnInsertIndex": 2,
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"baseColumnName": "b",
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"expression": "grel:value.replace('2','TEST')",
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"onError": "set-to-blank"
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}
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]
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DATA
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# ================================== IMPORT ================================== #
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checkpoint "Import"; echo
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# declare input
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projects["from heredoc"]=""
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projects["csv file example"]="input/example1.csv"
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projects["tsv file example"]="input/example2.tsv"
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projects["another csv example"]="input/example1.csv"
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projects["yet another csv example"]="input/example1.csv"
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# --------------------------- IMPORT FROM HEREDOC ---------------------------- #
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# quoted heredoc ("DATA") will not be expanded by bash (no escaping needed)
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# project id will be stored in as ${projects[csv file example]}
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p="from heredoc"
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f="" # optional filename, will be stored in OpenRefine project metadata
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echo "import heredoc..."
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if curl -fs --write-out "%{redirect_url}\n" \
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--form project-file="@-$(if [[ -n $f ]]; then echo ";filename=${f}"; fi)" \
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--form project-name="${p}" \
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--form format="text/line-based/*sv" \
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--form options='{
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"encoding": "UTF-8",
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"separator": " "
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}' \
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"${endpoint}/command/core/create-project-from-upload$(refine_csrf)" \
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> "${workdir}/${p}.id" \
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<< "DATA"
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a b c
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1 2 3
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0 0 0
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$ \ '
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DATA
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then
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log "imported heredoc as ${p}"
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else
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error "import of ${p} failed!"
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fi
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refine_store "${p}" "${workdir}/${p}.id" || error "import of ${p} failed!"
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echo
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# ---------------------------- IMPORT FROM FILE ------------------------------ #
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# project id will be stored in ${projects[tsv file example]}
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p="tsv file example"
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echo "import file ${projects[$p]} ..."
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if curl -fs --write-out "%{redirect_url}\n" \
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--form project-file="@${projects[$p]}" \
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--form project-name="${p}" \
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--form format="text/line-based/*sv" \
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--form options='{
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"encoding": "UTF-8",
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"separator": "\t"
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}' \
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"${endpoint}/command/core/create-project-from-upload$(refine_csrf)" \
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> "${workdir}/${p}.id"
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then
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log "imported ${projects[$p]} as ${p}"
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else
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error "import of ${projects[$p]} failed!"
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fi
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refine_store "${p}" "${workdir}/${p}.id" || error "import of ${p} failed!"
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echo
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# -------------------- IMPORT MULTIPLE FILES (PARALLEL) ---------------------- #
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# project ids will be stored in ${projects[another csv example]} etc.
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ps=( "csv file example" "another csv example" "yet another csv example" )
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echo "import files" \
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"$(for p in "${ps[@]}"; do printf "%s" "${projects[$p]} "; done)..."
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for p in "${ps[@]}"; do
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(if curl -fs --write-out "%{redirect_url}\n" \
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--form project-file="@${projects[$p]}" \
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--form project-name="${p}" \
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--form format="line-based" \
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--form options='{
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"encoding": "UTF-8",
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"separator": ","
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}' \
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"${endpoint}/command/core/create-project-from-upload$(refine_csrf)" \
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> "${workdir}/${p}.id"
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then
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log "imported ${projects[$p]} as ${p}"
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else
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error "import of ${projects[$p]} failed!"
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fi) &
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monitor "${p}"
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done
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monitoring
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for p in "${ps[@]}"; do
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refine_store "${p}" "${workdir}/${p}.id" || error "import of ${p} failed!"
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done
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echo
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# ================================ TRANSFORM ================================= #
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checkpoint "Transform"; echo
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# ------------------------ APPLY OPERATIONS FROM FILE ------------------------ #
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p="csv file example"
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f="input/example-operations-history.json"
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echo "apply ${f} to ${p}..."
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if curl -fs \
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--data project="${projects[$p]}" \
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--data-urlencode operations@"${f}" \
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"${endpoint}/command/core/apply-operations$(refine_csrf)" > /dev/null
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then
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log "transformed ${p} (${projects[$p]})"
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else
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error "transform ${p} (${projects[$p]}) failed!"
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fi
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echo
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# ---------------------- APPLY OPERATIONS FROM HEREDOC ----------------------- #
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# quoted heredoc ("JSON") will not be expanded by bash (no escaping needed)
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p="csv file example"
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echo "add column apply-from-heredoc to ${p}..."
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if curl -fs \
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--data project="${projects[$p]}" \
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--data-urlencode "operations@-" \
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"${endpoint}/command/core/apply-operations$(refine_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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"engineConfig": {
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"mode": "row-based"
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},
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"newColumnName": "apply-from-heredoc",
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"columnInsertIndex": 2,
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"baseColumnName": "b",
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"expression": "grel:value.replace('2','TEST')",
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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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then
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log "transformed ${p} (${projects[$p]})"
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else
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error "transform ${p} (${projects[$p]}) failed!"
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fi
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echo
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# ---------------- APPLY OPERATIONS FROM HEREDOC AND VARIABLES --------------- #
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# unquoted heredocs with variable and multi-line expression (requires jq)
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# \ must be used to quote the characters \, $, and `.
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p="csv file example"
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replace='TEST'
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column="apply with variables"
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echo "add column ${column} to ${p}..."
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read -r -d '' expression << EXPRESSION
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grel:value.replace(
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'2',
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'${replace}'
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)
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EXPRESSION
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if curl -fs \
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--data project="${projects[$p]}" \
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--data-urlencode "operations@-" \
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"${endpoint}/command/core/apply-operations$(refine_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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"engineConfig": {
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"mode": "row-based"
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},
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"newColumnName": "${column}",
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"columnInsertIndex": 2,
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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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then
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log "transformed ${p} (${projects[$p]})"
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else
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error "transform ${p} (${projects[$p]}) failed!"
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fi
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echo
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# ------ APPLY OPERATIONS FROM HEREDOC TO MULTIPLE PROJECTS (PARALLEL) ------ #
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# quoted heredoc ("JSON") will not be expanded by bash (no escaping needed)
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ps=( "another csv example" "yet another csv example" )
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echo "add column apply-from-heredoc to" "${ps[@]}" "..."
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for p in "${ps[@]}"; do
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(if curl -fs \
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--data project="${projects[$p]}" \
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--data-urlencode "operations@-" \
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"${endpoint}/command/core/apply-operations$(refine_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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"engineConfig": {
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"mode": "row-based"
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},
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"newColumnName": "apply-from-heredoc",
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"columnInsertIndex": 2,
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"baseColumnName": "b",
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"expression": "grel:value.replace('2','TEST')",
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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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then
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log "transformed ${p} (${projects[$p]})"
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else
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error "transform ${p} (${projects[$p]}) failed!"
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fi) &
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monitor "${p}"
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done
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monitoring
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echo
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# ------------- APPLY MULTIPLE OPERATIONS GENERATED FROM HEREDOC ------------- #
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# unquoted heredoc (JSON) with variables and multiplied (requires jq)
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# \ must be used to quote the characters \, $, and `.
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p="csv file example"
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columns=( "apply-from-file" "apply-from-heredoc" )
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echo "delete columns" "${columns[@]}" "in ${p}..."
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for column in "${columns[@]}"; do
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cat << JSON >> "${workdir}/${p}.tmp"
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[
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{
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"op": "core/column-removal",
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"columnName": "${column}"
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}
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]
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JSON
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done
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if "${jq}" -s add "${workdir}/${p}.tmp" | curl -fs \
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--data project="${projects[$p]}" \
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--data-urlencode operations@- \
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"${endpoint}/command/core/apply-operations$(refine_csrf)" > /dev/null
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then
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log "transformed ${p} (${projects[$p]})"
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rm "${workdir}/${p}.tmp"
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else
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error "transform ${p} (${projects[$p]}) failed!"
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fi
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echo
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# ================================== EXPORT ================================== #
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checkpoint "Export"; echo
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# ----------------------------- EXPORT TO STDOUT ----------------------------- #
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p="csv file example"
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format="tsv"
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echo "export ${p} in ${format} format..."
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if curl -fs \
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--data project="${projects[$p]}" \
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--data format="tsv" \
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--data engine='{"facets":[],"mode":"row-based"}' \
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"${endpoint}/command/core/export-rows"
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then
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log "exported ${p} (${projects[$p]})"
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else
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error "export of ${p} (${projects[$p]}) failed!"
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fi
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echo
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# ------------------------------ EXPORT TO FILE ------------------------------ #
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p="csv file example"
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format="csv"
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echo "export ${p} to ${format} file..."
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if curl -fs \
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--data project="${projects[$p]}" \
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--data format="${format}" \
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--data engine='{"facets":[],"mode":"row-based"}' \
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"${endpoint}/command/core/export-rows" \
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> "${workdir}/${p}.${format}"
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then
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log "exported ${p} (${projects[$p]}) to ${workdir}/${p}.${format}"
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else
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error "export of ${p} (${projects[$p]}) failed!"
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fi
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echo
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# ------------------------- TEMPLATING EXPORT TO FILE ------------------------ #
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p="csv file example"
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format="json"
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echo "export ${p} to ${format} file using template..."
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IFS= read -r -d '' template << "TEMPLATE"
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{
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"a": {{cells['a'].value.jsonize()}},
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"b": {{cells['b'].value.jsonize()}},
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"c": {{cells['c'].value.jsonize()}}
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}
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TEMPLATE
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if echo "${template}" | head -c -2 | curl -fs \
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--data project="${projects[$p]}" \
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--data format="template" \
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--data prefix="[
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" \
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--data suffix="
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]" \
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--data separator=",
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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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"${endpoint}/command/core/export-rows" \
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> "${workdir}/${p}.${format}"
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then
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log "exported ${p} (${projects[$p]}) to ${workdir}/${p}.${format}"
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else
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error "export of ${p} (${projects[$p]}) failed!"
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fi
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echo
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# ------------------- EXPORT TO MULTIPLE FILES (PARALLEL) -------------------- #
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ps=( "another csv example" "yet another csv example" )
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format="tsv"
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echo "export" "${ps[@]}" "to ${format} files..."
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for p in "${ps[@]}"; do
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(if curl -fs \
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--data project="${projects[$p]}" \
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--data format="${format}" \
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--data engine='{"facets":[],"mode":"row-based"}' \
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"${endpoint}/command/core/export-rows" \
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> "${workdir}/${p}.${format}"
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then
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log "exported ${p} (${projects[$p]}) to ${workdir}/${p}.${format}"
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else
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error "export of ${p} (${projects[$p]}) failed!"
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fi) &
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monitor "${p}"
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done
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monitoring
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echo
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# ------------------------------ EXPORT PROJECT ------------------------------ #
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p="csv file example"
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format="openrefine.tar.gz"
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echo "export ${p} to ${format} file..."
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if curl -fs \
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--data project="${projects[$p]}" \
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"${endpoint}/command/core/export-project" \
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> "${workdir}/${p}.${format}"
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then
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log "exported ${p} (${projects[$p]}) to ${workdir}/${p}.${format}"
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else
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error "export of ${p} (${projects[$p]}) failed!"
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fi
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echo
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# ================================ UTILITIES ================================= #
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checkpoint "Utilities"; echo
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# ------------------------------ LIST PROJECTS ------------------------------- #
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# get all project metadata and reshape json to print a list (requires jq)
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echo "list projects..."
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if curl -fs --get \
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"${endpoint}/command/core/get-all-project-metadata" \
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| "${jq}" -r '.projects | keys[] as $k | "\($k): \(.[$k] | .name)"'
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then
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: #log "printed list of projects"
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else
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error "getting list of projects failed!"
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fi
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echo
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# ------------------------------- GET METADATA ------------------------------- #
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# get project metadata and reshape json to include project id (requires jq)
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p="csv file example"
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echo "metadata for ${p}..."
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if curl -fs --get \
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--data project="${projects[$p]}" \
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"${endpoint}/command/core/get-project-metadata" \
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| "${jq}" "{ id: ${projects[$p]} } + ."
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then
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: #log "printed metadata of ${p} (${projects[$p]})"
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else
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error "getting metadata of ${p} (${projects[$p]}) failed!"
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fi
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echo
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# ------------------------------ GET ROW COUNT ------------------------------- #
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# get total number of rows
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p="csv file example"
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echo "total number of rows in ${p}..."
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if curl -fs --get \
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--data project="${projects[$p]}" \
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--data limit=0 \
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"${endpoint}/command/core/get-rows" \
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| tr "," "\n" | grep total | cut -d ":" -f 2
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then
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: #log "printed row count of ${p} (${projects[$p]})"
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else
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error "getting row count of ${p} (${projects[$p]}) failed!"
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fi
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echo
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# ------------------------------- GET COLUMNS -------------------------------- #
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# get column names from project model (requires jq)
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p="csv file example"
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echo "column names of ${p}..."
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if curl -fs --get \
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--data project="${projects[$p]}" \
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"${endpoint}/command/core/get-models" \
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| "${jq}" -r '.columnModel | .columns[] | .name'
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then
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: #log "printed column names of ${p} (${projects[$p]})"
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else
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error "getting column names of ${p} (${projects[$p]}) failed!"
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fi
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echo
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# -------------------------- GET OPERATIONS HISTORY -------------------------- #
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# get operations history and reshape json to make it applicable (requires jq)
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p="csv file example"
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f="${workdir}/${p}_history.json"
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echo "history of operations for ${p}..."
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if curl -fs --get \
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--data project="${projects[$p]}" \
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"${endpoint}/command/core/get-operations" \
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| "${jq}" '[ .entries[] | .operation ]' \
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> "${f}"
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then
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log "saved ops history of ${p} (${projects[$p]}) to ${f}"
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else
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error "getting ops history of ${p} (${projects[$p]}) failed!"
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fi
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echo
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# ---------------------------- GET IMPORT HISTORY ---------------------------- #
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# get project metadata and filter import options history (requires jq)
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p="csv file example"
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echo "history of import for ${p}..."
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if curl -fs --get \
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--data project="${projects[$p]}" \
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"${endpoint}/command/core/get-project-metadata" \
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| "${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 workdir
|
|
count_output
|