release v1.13: improved use of sudo in docker version, pinned version of openrefine-client, improved README
This commit is contained in:
Felix Lohmeier
parent
f6c8ee9d98
commit
b259cf571c
46
README.md
46
README.md
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@ -19,7 +19,11 @@ If you prefer a containerized approach, see a [variation of this script for Dock
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### Install
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Download the script and grant file permissions to execute: `wget https://github.com/felixlohmeier/openrefine-batch/raw/master/openrefine-batch.sh && chmod +x openrefine-batch.sh`
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Download the script and grant file permissions to execute:
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```
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wget https://github.com/felixlohmeier/openrefine-batch/raw/master/openrefine-batch.sh
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chmod +x openrefine-batch.sh
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```
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That's all. The script will automatically download copies of OpenRefine and the python client on first run and will tell you if something (python, java) is missing.
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@ -288,8 +292,14 @@ A variation of the shell script orchestrates a [docker container for OpenRefine]
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**Install**
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1. Install [Docker](https://docs.docker.com/engine/installation/#on-linux) and **a)** [configure Docker to start on boot](https://docs.docker.com/engine/installation/linux/linux-postinstall/#configure-docker-to-start-on-boot) or **b)** start Docker on demand each time you use the script: `sudo systemctl start docker`
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2. Download the script and grant file permissions to execute: `wget https://github.com/felixlohmeier/openrefine-batch/raw/master/openrefine-batch-docker.sh && chmod +x openrefine-batch-docker.sh`
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1. Install [Docker](https://docs.docker.com/engine/installation/#on-linux)
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* **a)** [configure Docker to start on boot](https://docs.docker.com/engine/installation/linux/linux-postinstall/#configure-docker-to-start-on-boot)
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* or **b)** start Docker on demand each time you use the script: `sudo systemctl start docker`
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2. Download the script and grant file permissions to execute:
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```
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wget https://github.com/felixlohmeier/openrefine-batch/raw/master/openrefine-batch-docker.sh
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chmod +x openrefine-batch-docker.sh
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```
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**Usage**
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@ -298,10 +308,36 @@ mkdir input
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cp INPUTFILES input/
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mkdir config
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cp CONFIGFILES config/
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sudo ./openrefine-batch-docker.sh -a input/ -b config/ -c OUTPUT/
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./openrefine-batch-docker.sh -a input/ -b config/ -c OUTPUT/
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```
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Why `sudo`? Non-root users can only access the Unix socket of the Docker daemon by using `sudo`. If you created a Docker group in [Post-installation steps for Linux](https://docs.docker.com/engine/installation/linux/linux-postinstall/) then you may call the script without `sudo`.
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The script may ask you for sudo privileges. Why `sudo`? Non-root users can only access the Unix socket of the Docker daemon by using `sudo`. If you created a Docker group in [Post-installation steps for Linux](https://docs.docker.com/engine/installation/linux/linux-postinstall/) then you may call the script without `sudo`.
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**Example**
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[Example Powerhouse Museum](examples/powerhouse-museum)
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download example data
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```
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wget https://github.com/opencultureconsulting/openrefine-batch/archive/master.zip
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unzip master.zip openrefine-batch-master/examples/*
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mv openrefine-batch-master/examples .
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rm -f master.zip
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```
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execute openrefine-batch-docker.sh
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```
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./openrefine-batch-docker.sh \
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-a examples/powerhouse-museum/input/ \
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-b examples/powerhouse-museum/config/ \
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-c examples/powerhouse-museum/output/ \
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-f tsv \
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-i processQuotes=false \
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-i guessCellValueTypes=true \
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-RX
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```
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### Todo
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@ -1,23 +1,32 @@
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#!/bin/bash
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# openrefine-batch-docker.sh, Felix Lohmeier, v1.12, 2019-07-29
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# openrefine-batch-docker.sh, Felix Lohmeier, v1.13, 2019-08-06
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# https://github.com/felixlohmeier/openrefine-batch
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# check system requirements
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DOCKER="$(which docker 2> /dev/null)"
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DOCKER="$(command -v docker 2> /dev/null)"
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if [ -z "$DOCKER" ] ; then
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echo 1>&2 "This action requires you to have 'docker' installed and present in your PATH. You can download it for free at http://www.docker.com/"
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exit 1
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fi
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DOCKERINFO="$(docker info 2>/dev/null | grep 'Server Version')"
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if [ -z "$DOCKERINFO" ] ; then
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echo 1>&2 "This action requires you to start the docker daemon. Try 'sudo systemctl start docker' or 'sudo start docker'. If the docker daemon is already running then maybe some security privileges are missing to run docker commands. Try to run the script with 'sudo ./openrefine-batch-docker.sh ...'"
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exit 1
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if [ -z "$DOCKERINFO" ]
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then
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echo "command 'docker info' failed, trying again with sudo..."
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DOCKERINFO="$(sudo docker info 2>/dev/null | grep 'Server Version')"
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echo "OK"
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docker=(sudo docker)
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if [ -z "$DOCKERINFO" ] ; then
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echo 1>&2 "This action requires you to start the docker daemon. Try 'sudo systemctl start docker' or 'sudo start docker'. If the docker daemon is already running then maybe some security privileges are missing to run docker commands.'"
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exit 1
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fi
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else
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docker=(docker)
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fi
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# help screen
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function usage () {
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cat <<EOF
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Usage: sudo ./openrefine-batch-docker.sh [-a INPUTDIR] [-b TRANSFORMDIR] [-c OUTPUTDIR] ...
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Usage: ./openrefine-batch-docker.sh [-a INPUTDIR] [-b TRANSFORMDIR] [-c OUTPUTDIR] ...
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== basic arguments ==
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-a INPUTDIR path to directory with source files (leave empty to transform only ; multiple files may be imported into a single project by providing a zip or tar.gz archive, cf. https://github.com/OpenRefine/OpenRefine/wiki/Importers )
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@ -81,7 +90,7 @@ rm -f master.zip
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example 1 (input, transform, export to tsv)
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sudo ./openrefine-batch-docker.sh \
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./openrefine-batch-docker.sh \
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-a examples/powerhouse-museum/input/ \
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-b examples/powerhouse-museum/config/ \
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-c examples/powerhouse-museum/output/ \
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@ -92,7 +101,7 @@ sudo ./openrefine-batch-docker.sh \
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example 2 (input, transform, templating export)
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sudo ./openrefine-batch-docker.sh -a examples/powerhouse-museum/input/ -b examples/powerhouse-museum/config/ -c examples/powerhouse-museum/output/ -f tsv -i processQuotes=false -i guessCellValueTypes=true -RX -t template='{ "Record ID" : {{jsonize(cells["Record ID"].value)}}, "Object Title" : {{jsonize(cells["Object Title"].value)}}, "Registration Number" : {{jsonize(cells["Registration Number"].value)}}, "Description." : {{jsonize(cells["Description."].value)}}, "Marks" : {{jsonize(cells["Marks"].value)}}, "Production Date" : {{jsonize(cells["Production Date"].value)}}, "Provenance (Production)" : {{jsonize(cells["Provenance (Production)"].value)}}, "Provenance (History)" : {{jsonize(cells["Provenance (History)"].value)}}, "Categories" : {{jsonize(cells["Categories"].value)}}, "Persistent Link" : {{jsonize(cells["Persistent Link"].value)}}, "Height" : {{jsonize(cells["Height"].value)}}, "Width" : {{jsonize(cells["Width"].value)}}, "Depth" : {{jsonize(cells["Depth"].value)}}, "Diameter" : {{jsonize(cells["Diameter"].value)}}, "Weight" : {{jsonize(cells["Weight"].value)}}, "License info" : {{jsonize(cells["License info"].value)}} }' -t rowSeparator=',' -t prefix='{ "rows" : [ ' -t suffix='] }' -t splitToFiles=true
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./openrefine-batch-docker.sh -a examples/powerhouse-museum/input/ -b examples/powerhouse-museum/config/ -c examples/powerhouse-museum/output/ -f tsv -i processQuotes=false -i guessCellValueTypes=true -RX -t template='{ "Record ID" : {{jsonize(cells["Record ID"].value)}}, "Object Title" : {{jsonize(cells["Object Title"].value)}}, "Registration Number" : {{jsonize(cells["Registration Number"].value)}}, "Description." : {{jsonize(cells["Description."].value)}}, "Marks" : {{jsonize(cells["Marks"].value)}}, "Production Date" : {{jsonize(cells["Production Date"].value)}}, "Provenance (Production)" : {{jsonize(cells["Provenance (Production)"].value)}}, "Provenance (History)" : {{jsonize(cells["Provenance (History)"].value)}}, "Categories" : {{jsonize(cells["Categories"].value)}}, "Persistent Link" : {{jsonize(cells["Persistent Link"].value)}}, "Height" : {{jsonize(cells["Height"].value)}}, "Width" : {{jsonize(cells["Width"].value)}}, "Depth" : {{jsonize(cells["Depth"].value)}}, "Diameter" : {{jsonize(cells["Diameter"].value)}}, "Weight" : {{jsonize(cells["Weight"].value)}}, "License info" : {{jsonize(cells["License info"].value)}} }' -t rowSeparator=',' -t prefix='{ "rows" : [ ' -t suffix='] }' -t splitToFiles=true
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EOF
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exit 1
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}
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@ -200,8 +209,8 @@ memoryload=()
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cleanup()
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{
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echo "cleanup..."
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docker stop -t=5000 ${uuid}
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docker rm ${uuid}
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${docker[*]} stop -t=5000 ${uuid}
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${docker[*]} rm ${uuid}
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rm -r -f "${outputdir:?}"/workspace*.json
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# delete duplicates from copied projects
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if [ -n "$crossprojects" ]; then
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@ -218,11 +227,11 @@ echo "=== $checkpoints. ${checkpointname[$((checkpoints + 1))]} ==="
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echo ""
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echo "starting time: $(date --date=@${checkpointdate[$((checkpoints + 1))]})"
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echo ""
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sudo docker run -d --name=${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine:${version} -i 0.0.0.0 -m ${ram} -d /data
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${docker[*]} run -d --name=${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine:${version} -i 0.0.0.0 -m ${ram} -d /data
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# wait until server is available
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until sudo docker run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
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until ${docker[*]} run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.4 --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
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# show server logs
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docker attach ${uuid} &
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${docker[*]} attach ${uuid} &
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echo ""
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# import all files
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@ -237,7 +246,7 @@ if [ -n "$inputfiles" ]; then
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for inputfile in "${inputfiles[@]}" ; do
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echo "import ${inputfile}..."
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# run client with input command
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sudo docker run --rm --link ${uuid} -v ${inputdir}:/data:z felixlohmeier/openrefine-client -H ${uuid} -c $inputfile $inputformat ${inputoptions[@]}
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${docker[*]} run --rm --link ${uuid} -v ${inputdir}:/data:z felixlohmeier/openrefine-client:v0.3.4 -H ${uuid} -c $inputfile $inputformat ${inputoptions[@]}
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# show allocated system resources
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ps -o start,etime,%mem,%cpu,rss -C java --sort=start
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memoryload+=($(ps --no-headers -o rss -C java))
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@ -245,11 +254,11 @@ if [ -n "$inputfiles" ]; then
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# restart server to clear memory
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if [ "$restartfile" = "true" ]; then
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echo "save project and restart OpenRefine server..."
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docker stop -t=5000 ${uuid}
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docker rm ${uuid}
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sudo docker run -d --name=${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine:${version} -i 0.0.0.0 -m ${ram} -d /data
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until sudo docker run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
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docker attach ${uuid} &
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${docker[*]} stop -t=5000 ${uuid}
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${docker[*]} rm ${uuid}
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${docker[*]} run -d --name=${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine:${version} -i 0.0.0.0 -m ${ram} -d /data
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until ${docker[*]} run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.4 --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
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${docker[*]} attach ${uuid} &
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echo ""
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fi
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done
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@ -267,7 +276,7 @@ if [ -n "$jsonfiles" ] || [ "$export" = "true" ]; then
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# get project ids
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echo "get project ids..."
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sudo docker run --rm --link ${uuid} felixlohmeier/openrefine-client -H ${uuid} -l > "${outputdir}/projects.tmp"
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${docker[*]} run --rm --link ${uuid} felixlohmeier/openrefine-client:v0.3.4 -H ${uuid} -l > "${outputdir}/projects.tmp"
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projectids=($(cut -c 2-14 "${outputdir}/projects.tmp"))
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projectnames=($(cut -c 17- "${outputdir}/projects.tmp"))
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cat "${outputdir}/projects.tmp" && rm "${outputdir:?}/projects.tmp"
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@ -280,11 +289,11 @@ if [ -n "$jsonfiles" ] || [ "$export" = "true" ]; then
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rsync -a --exclude='*.project/history' "${crossdir}"/*.project "${outputdir}"
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# restart server to advertise copied projects
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echo "restart OpenRefine server to advertise copied projects..."
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docker stop -t=5000 ${uuid}
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docker rm ${uuid}
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sudo docker run -d --name=${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine:${version} -i 0.0.0.0 -m ${ram} -d /data
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until sudo docker run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
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docker attach ${uuid} &
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${docker[*]} stop -t=5000 ${uuid}
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${docker[*]} rm ${uuid}
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${docker[*]} run -d --name=${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine:${version} -i 0.0.0.0 -m ${ram} -d /data
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until ${docker[*]} run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.4 --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
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${docker[*]} attach ${uuid} &
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echo ""
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fi
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@ -303,7 +312,7 @@ if [ -n "$jsonfiles" ] || [ "$export" = "true" ]; then
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for jsonfile in "${jsonfiles[@]}" ; do
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echo "transform ${jsonfile}..."
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# run client with apply command
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sudo docker run --rm --link ${uuid} -v ${configdir}:/data:z felixlohmeier/openrefine-client -H ${uuid} -f ${jsonfile} ${projectids[i]}
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${docker[*]} run --rm --link ${uuid} -v ${configdir}:/data:z felixlohmeier/openrefine-client:v0.3.4 -H ${uuid} -f ${jsonfile} ${projectids[i]}
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# allocated system resources
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ps -o start,etime,%mem,%cpu,rss -C java --sort=start
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memoryload+=($(ps --no-headers -o rss -C java))
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@ -311,11 +320,11 @@ if [ -n "$jsonfiles" ] || [ "$export" = "true" ]; then
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# restart server to clear memory
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if [ "$restarttransform" = "true" ]; then
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echo "save project and restart OpenRefine server..."
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docker stop -t=5000 ${uuid}
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docker rm ${uuid}
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sudo docker run -d --name=${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine:${version} -i 0.0.0.0 -m ${ram} -d /data
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until sudo docker run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
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docker attach ${uuid} &
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${docker[*]} stop -t=5000 ${uuid}
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${docker[*]} rm ${uuid}
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${docker[*]} run -d --name=${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine:${version} -i 0.0.0.0 -m ${ram} -d /data
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until ${docker[*]} run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.4 --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
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${docker[*]} attach ${uuid} &
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fi
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echo ""
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done
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filename=${projectnames[i]%.*}
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echo "export to file ${filename}.${exportformat}..."
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# run client with export command
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sudo docker run --rm --link ${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine-client -H ${uuid} -E --output="${filename}.${exportformat}" "${templating[@]}" ${projectids[i]}
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${docker[*]} run --rm --link ${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine-client:v0.3.4 -H ${uuid} -E --output="${filename}.${exportformat}" "${templating[@]}" ${projectids[i]}
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# show allocated system resources
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ps -o start,etime,%mem,%cpu,rss -C java --sort=start
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memoryload+=($(ps --no-headers -o rss -C java))
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@ -344,11 +353,11 @@ if [ -n "$jsonfiles" ] || [ "$export" = "true" ]; then
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# restart server to clear memory
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if [ "$restartfile" = "true" ]; then
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echo "restart OpenRefine server..."
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docker stop -t=5000 ${uuid}
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docker rm ${uuid}
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sudo docker run -d --name=${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine:${version} -i 0.0.0.0 -m ${ram} -d /data
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until sudo docker run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
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docker attach ${uuid} &
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${docker[*]} stop -t=5000 ${uuid}
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${docker[*]} rm ${uuid}
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${docker[*]} run -d --name=${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine:${version} -i 0.0.0.0 -m ${ram} -d /data
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until ${docker[*]} run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.4 --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
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${docker[*]} attach ${uuid} &
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fi
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echo ""
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@ -1,5 +1,5 @@
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#!/bin/bash
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# openrefine-batch.sh, Felix Lohmeier, v1.12, 2019-07-29
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# openrefine-batch.sh, Felix Lohmeier, v1.13, 2019-08-06
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# https://github.com/felixlohmeier/openrefine-batch
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# declare download URLs for OpenRefine and OpenRefine client
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