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openrefine-batch
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update openrefine-client to v0.3.9

This commit is contained in:
Felix Lohmeier 2020-08-08 13:43:00 +02:00
parent b259cf571c
commit 68dbc04c01
3 changed files with 61 additions and 60 deletions
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89
README.md
View File

@ -79,7 +79,7 @@ execute openrefine-batch.sh
### Help Screen
```
[23:10 felix ~/openrefine-batch]$ ./openrefine-batch.sh
[felix@tux openrefine-batch]$ ./openrefine-batch.sh
Usage: ./openrefine-batch.sh [-a INPUTDIR] [-b TRANSFORMDIR] [-c OUTPUTDIR] ...
== basic arguments ==
@ -158,12 +158,12 @@ The script prints log messages from OpenRefine server and makes use of `ps` to s
```
[felix@tux openrefine-batch]$ ./openrefine-batch.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
Download OpenRefine...
openrefine-linux-3.2.tar.g 100%[=====================================>] 101,13M 4,13MB/s in 27s
openrefine-linux-3.2.tar.gz 100%[===============================================>] 101,13M 9,46MB/s in 19s
Install OpenRefine in subdirectory openrefine...
Total bytes read: 125419520 (120MiB, 145MiB/s)
Total bytes read: 125419520 (120MiB, 74MiB/s)
Download OpenRefine client...
openrefine-client_0-3-4_li 100%[=====================================>] 4,69M 2,78MB/s in 1,7s
openrefine-client_0-3-9_linux 100%[===============================================>] 4,25M 2,61MB/s in 1,6s
Input directory: /home/felix/git/openrefine-batch/examples/powerhouse-museum/input
Input files: phm-collection.tsv
@ -184,93 +184,94 @@ restart after transform: false
=== 1. Launch OpenRefine ===
starting time: Mo 29. Jul 23:33:34 CEST 2019
starting time: Sa 8. Aug 13:32:45 CEST 2020
You have 15962M of free memory.
You have 15927M of free memory.
Your current configuration is set to use 2048M of memory.
OpenRefine can run better when given more memory. Read our FAQ on how to allocate more memory here:
https://github.com/OpenRefine/OpenRefine/wiki/FAQ:-Allocate-More-Memory
Starting OpenRefine at 'http://127.0.0.1:3333/'
23:33:34.277 [ refine_server] Starting Server bound to '127.0.0.1:3333' (0ms)
23:33:34.277 [ refine_server] refine.memory size: 2048M JVM Max heap: 2058354688 (0ms)
23:33:34.284 [ refine_server] Initializing context: '/' from '/home/felix/git/openrefine-batch/openrefine/webapp' (7ms)
13:32:46.213 [ refine_server] Starting Server bound to '127.0.0.1:3333' (0ms)
13:32:46.214 [ refine_server] refine.memory size: 2048M JVM Max heap: 2058354688 (1ms)
13:32:46.224 [ refine_server] Initializing context: '/' from '/home/felix/git/openrefine-batch/openrefine/webapp' (10ms)
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/home/felix/git/openrefine-batch/openrefine/server/target/lib/slf4j-log4j12-1.7.18.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/home/felix/git/openrefine-batch/openrefine/webapp/WEB-INF/lib/slf4j-log4j12-1.7.18.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
23:33:34.706 [ refine] Starting OpenRefine 3.2 [55c921b]... (422ms)
23:33:34.706 [ refine] initializing FileProjectManager with dir (0ms)
23:33:34.706 [ refine] /home/felix/git/openrefine-batch/examples/powerhouse-museum/output (0ms)
23:33:34.709 [ FileProjectManager] Failed to load workspace from any attempted alternatives. (3ms)
23:33:38.275 [ refine] Running in headless mode (3566ms)
13:32:46.937 [ refine] Starting OpenRefine 3.2 [55c921b]... (713ms)
13:32:46.937 [ refine] initializing FileProjectManager with dir (0ms)
13:32:46.937 [ refine] /home/felix/git/openrefine-batch/examples/powerhouse-museum/output (0ms)
13:32:46.947 [ FileProjectManager] Failed to load workspace from any attempted alternatives. (10ms)
13:32:52.249 [ refine] Running in headless mode (5302ms)
=== 2. Import all files ===
starting time: Mo 29. Jul 23:33:39 CEST 2019
starting time: Sa 8. Aug 13:32:53 CEST 2020
import phm-collection.tsv...
23:33:39.466 [ refine] POST /command/core/create-project-from-upload (1191ms)
23:33:44.326 [ refine] GET /command/core/get-models (4860ms)
23:33:44.409 [ refine] POST /command/core/get-rows (83ms)
id: 1675004209805
13:32:53.686 [ refine] POST /command/core/create-project-from-upload (1437ms)
13:33:01.606 [ refine] GET /command/core/get-models (7920ms)
13:33:01.722 [ refine] POST /command/core/get-rows (116ms)
id: 1705197298924
rows: 75814
23:33:44.495 [ refine] GET /command/core/get-models (86ms)
STARTED ELAPSED %MEM %CPU RSS
23:33:33 00:10 5.9 207 976248
13:32:45 00:16 6.0 201 993192
=== 3. Prepare transform & export ===
starting time: Mo 29. Jul 23:33:44 CEST 2019
starting time: Sa 8. Aug 13:33:01 CEST 2020
get project ids...
23:33:44.597 [ refine] GET /command/core/get-all-project-metadata (102ms)
1675004209805: phm-collection
13:33:02.003 [ refine] GET /command/core/get-all-project-metadata (281ms)
1705197298924: phm-collection
=== 4. Transform phm-collection ===
starting time: Mo 29. Jul 23:33:44 CEST 2019
starting time: Sa 8. Aug 13:33:02 CEST 2020
transform phm-transform.json...
23:33:44.712 [ refine] GET /command/core/get-models (115ms)
23:33:44.715 [ refine] POST /command/core/apply-operations (3ms)
13:33:02.187 [ refine] GET /command/core/get-models (184ms)
13:33:02.193 [ refine] POST /command/core/apply-operations (6ms)
File /home/felix/git/openrefine-batch/examples/powerhouse-museum/config/phm-transform.json has been successfully applied to project 1705197298924
STARTED ELAPSED %MEM %CPU RSS
23:33:33 00:20 6.8 164 1121200
13:32:45 00:32 6.3 165 1037688
=== 5. Export phm-collection ===
starting time: Mo 29. Jul 23:33:54 CEST 2019
starting time: Sa 8. Aug 13:33:17 CEST 2020
export to file phm-collection.tsv...
23:33:54.156 [ refine] GET /command/core/get-models (9441ms)
23:33:54.158 [ refine] GET /command/core/get-all-project-metadata (2ms)
23:33:54.161 [ refine] POST /command/core/export-rows/phm-collection.tsv (3ms)
13:33:18.001 [ refine] GET /command/core/get-models (15808ms)
13:33:18.005 [ refine] GET /command/core/get-all-project-metadata (4ms)
13:33:18.007 [ refine] POST /command/core/export-rows/phm-collection.tsv (2ms)
Export to file /home/felix/git/openrefine-batch/examples/powerhouse-museum/output/phm-collection.tsv complete
STARTED ELAPSED %MEM %CPU RSS
23:33:33 01:08 7.1 53.1 1160936
13:32:45 00:35 6.7 168 1098564
output (number of lines / size in bytes):
75728 59431272 /home/felix/git/openrefine-batch/examples/powerhouse-museum/output/phm-collection.tsv
cleanup...
23:34:44.740 [ ProjectManager] Saving all modified projects ... (50579ms)
23:34:46.677 [ project_utilities] Saved project '1675004209805' (1937ms)
13:33:24.667 [ ProjectManager] Saving all modified projects ... (6660ms)
13:33:28.044 [ project_utilities] Saved project '1705197298924' (3377ms)
=== Statistics ===
starting time and run time of each step:
Start process Mo 29. Jul 23:33:34 CEST 2019 (00:00:00)
Launch OpenRefine Mo 29. Jul 23:33:34 CEST 2019 (00:00:05)
Import all files Mo 29. Jul 23:33:39 CEST 2019 (00:00:05)
Prepare transform & export Mo 29. Jul 23:33:44 CEST 2019 (00:00:00)
Transform phm-collection Mo 29. Jul 23:33:44 CEST 2019 (00:00:10)
Export phm-collection Mo 29. Jul 23:33:54 CEST 2019 (00:00:53)
End process Mo 29. Jul 23:34:47 CEST 2019 (00:00:00)
Start process Sa 8. Aug 13:32:45 CEST 2020 (00:00:00)
Launch OpenRefine Sa 8. Aug 13:32:45 CEST 2020 (00:00:08)
Import all files Sa 8. Aug 13:32:53 CEST 2020 (00:00:08)
Prepare transform & export Sa 8. Aug 13:33:01 CEST 2020 (00:00:01)
Transform phm-collection Sa 8. Aug 13:33:02 CEST 2020 (00:00:15)
Export phm-collection Sa 8. Aug 13:33:17 CEST 2020 (00:00:12)
End process Sa 8. Aug 13:33:29 CEST 2020 (00:00:00)
total run time: 00:01:13 (hh:mm:ss)
highest memory load: 1133 MB
total run time: 00:00:44 (hh:mm:ss)
highest memory load: 1072 MB
```
### Performance gain with extended cross function

18
openrefine-batch-docker.sh
View File

@ -229,7 +229,7 @@ echo "starting time: $(date --date=@${checkpointdate[$((checkpoints + 1))]})"
echo ""
${docker[*]} run -d --name=${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine:${version} -i 0.0.0.0 -m ${ram} -d /data
# wait until server is available
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
until ${docker[*]} run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.9 --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
# show server logs
${docker[*]} attach ${uuid} &
echo ""
@ -246,7 +246,7 @@ if [ -n "$inputfiles" ]; then
for inputfile in "${inputfiles[@]}" ; do
echo "import ${inputfile}..."
# run client with input command
${docker[*]} run --rm --link ${uuid} -v ${inputdir}:/data:z felixlohmeier/openrefine-client:v0.3.4 -H ${uuid} -c $inputfile $inputformat ${inputoptions[@]}
${docker[*]} run --rm --link ${uuid} -v ${inputdir}:/data:z felixlohmeier/openrefine-client:v0.3.9 -H ${uuid} -c $inputfile $inputformat ${inputoptions[@]}
# show allocated system resources
ps -o start,etime,%mem,%cpu,rss -C java --sort=start
memoryload+=($(ps --no-headers -o rss -C java))
@ -257,7 +257,7 @@ if [ -n "$inputfiles" ]; then
${docker[*]} stop -t=5000 ${uuid}
${docker[*]} rm ${uuid}
${docker[*]} run -d --name=${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine:${version} -i 0.0.0.0 -m ${ram} -d /data
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
until ${docker[*]} run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.9 --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
${docker[*]} attach ${uuid} &
echo ""
fi
@ -276,7 +276,7 @@ if [ -n "$jsonfiles" ] || [ "$export" = "true" ]; then
# get project ids
echo "get project ids..."
${docker[*]} run --rm --link ${uuid} felixlohmeier/openrefine-client:v0.3.4 -H ${uuid} -l > "${outputdir}/projects.tmp"
${docker[*]} run --rm --link ${uuid} felixlohmeier/openrefine-client:v0.3.9 -H ${uuid} -l > "${outputdir}/projects.tmp"
projectids=($(cut -c 2-14 "${outputdir}/projects.tmp"))
projectnames=($(cut -c 17- "${outputdir}/projects.tmp"))
cat "${outputdir}/projects.tmp" && rm "${outputdir:?}/projects.tmp"
@ -292,7 +292,7 @@ if [ -n "$jsonfiles" ] || [ "$export" = "true" ]; then
${docker[*]} stop -t=5000 ${uuid}
${docker[*]} rm ${uuid}
${docker[*]} run -d --name=${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine:${version} -i 0.0.0.0 -m ${ram} -d /data
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
until ${docker[*]} run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.9 --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
${docker[*]} attach ${uuid} &
echo ""
fi
@ -312,7 +312,7 @@ if [ -n "$jsonfiles" ] || [ "$export" = "true" ]; then
for jsonfile in "${jsonfiles[@]}" ; do
echo "transform ${jsonfile}..."
# run client with apply command
${docker[*]} run --rm --link ${uuid} -v ${configdir}:/data:z felixlohmeier/openrefine-client:v0.3.4 -H ${uuid} -f ${jsonfile} ${projectids[i]}
${docker[*]} run --rm --link ${uuid} -v ${configdir}:/data:z felixlohmeier/openrefine-client:v0.3.9 -H ${uuid} -f ${jsonfile} ${projectids[i]}
# allocated system resources
ps -o start,etime,%mem,%cpu,rss -C java --sort=start
memoryload+=($(ps --no-headers -o rss -C java))
@ -323,7 +323,7 @@ if [ -n "$jsonfiles" ] || [ "$export" = "true" ]; then
${docker[*]} stop -t=5000 ${uuid}
${docker[*]} rm ${uuid}
${docker[*]} run -d --name=${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine:${version} -i 0.0.0.0 -m ${ram} -d /data
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
until ${docker[*]} run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.9 --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
${docker[*]} attach ${uuid} &
fi
echo ""
@ -343,7 +343,7 @@ if [ -n "$jsonfiles" ] || [ "$export" = "true" ]; then
filename=${projectnames[i]%.*}
echo "export to file ${filename}.${exportformat}..."
# run client with export command
${docker[*]} run --rm --link ${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine-client:v0.3.4 -H ${uuid} -E --output="${filename}.${exportformat}" "${templating[@]}" ${projectids[i]}
${docker[*]} run --rm --link ${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine-client:v0.3.9 -H ${uuid} -E --output="${filename}.${exportformat}" "${templating[@]}" ${projectids[i]}
# show allocated system resources
ps -o start,etime,%mem,%cpu,rss -C java --sort=start
memoryload+=($(ps --no-headers -o rss -C java))
@ -356,7 +356,7 @@ if [ -n "$jsonfiles" ] || [ "$export" = "true" ]; then
${docker[*]} stop -t=5000 ${uuid}
${docker[*]} rm ${uuid}
${docker[*]} run -d --name=${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine:${version} -i 0.0.0.0 -m ${ram} -d /data
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
until ${docker[*]} run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.9 --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
${docker[*]} attach ${uuid} &
fi
echo ""

14
openrefine-batch.sh
View File

@ -1,10 +1,10 @@
#!/bin/bash
# openrefine-batch.sh, Felix Lohmeier, v1.13, 2019-08-06
# openrefine-batch.sh, Felix Lohmeier, v1.14, 2020-08-08
# https://github.com/felixlohmeier/openrefine-batch
# declare download URLs for OpenRefine and OpenRefine client
openrefine_URL="https://github.com/OpenRefine/OpenRefine/releases/download/3.2/openrefine-linux-3.2.tar.gz"
client_URL="https://github.com/opencultureconsulting/openrefine-client/releases/download/v0.3.4/openrefine-client_0-3-4_linux-64bit"
client_URL="https://github.com/opencultureconsulting/openrefine-client/releases/download/v0.3.9/openrefine-client_0-3-9_linux"
# check system requirements
JAVA="$(which java 2> /dev/null)"
@ -34,7 +34,7 @@ if [ ! -d "openrefine-client" ]; then
echo "Download OpenRefine client..."
mkdir -p openrefine-client
wget -q -P openrefine-client $wget_opt $client_URL
chmod +x openrefine-client/openrefine-client_0-3-4_linux-64bit
chmod +x openrefine-client/openrefine-client_0-3-9_linux
echo ""
fi
@ -259,7 +259,7 @@ if [ -n "$inputfiles" ]; then
for inputfile in "${inputfiles[@]}" ; do
echo "import ${inputfile}..."
# run client with input command
openrefine-client/openrefine-client_0-3-4_linux-64bit -P ${port} -c ${inputdir}/${inputfile} $inputformat "${inputoptions[@]}"
openrefine-client/openrefine-client_0-3-9_linux -P ${port} -c ${inputdir}/${inputfile} $inputformat "${inputoptions[@]}"
# show allocated system resources
ps -o start,etime,%mem,%cpu,rss -p ${pid} --sort=start
memoryload+=($(ps --no-headers -o rss -p ${pid}))
@ -290,7 +290,7 @@ if [ -n "$jsonfiles" ] || [ "$export" = "true" ]; then
# get project ids
echo "get project ids..."
openrefine-client/openrefine-client_0-3-4_linux-64bit -P ${port} -l > "${outputdir}/projects.tmp"
openrefine-client/openrefine-client_0-3-9_linux -P ${port} -l > "${outputdir}/projects.tmp"
projectids=($(cut -c 2-14 "${outputdir}/projects.tmp"))
projectnames=($(cut -c 17- "${outputdir}/projects.tmp"))
cat "${outputdir}/projects.tmp" && rm "${outputdir:?}/projects.tmp"
@ -327,7 +327,7 @@ if [ -n "$jsonfiles" ] || [ "$export" = "true" ]; then
for jsonfile in "${jsonfiles[@]}" ; do
echo "transform ${jsonfile}..."
# run client with apply command
openrefine-client/openrefine-client_0-3-4_linux-64bit -P ${port} -f ${configdir}/${jsonfile} ${projectids[i]}
openrefine-client/openrefine-client_0-3-9_linux -P ${port} -f ${configdir}/${jsonfile} ${projectids[i]}
# allocated system resources
ps -o start,etime,%mem,%cpu,rss -p ${pid} --sort=start
memoryload+=($(ps --no-headers -o rss -p ${pid}))
@ -359,7 +359,7 @@ if [ -n "$jsonfiles" ] || [ "$export" = "true" ]; then
filename=${projectnames[i]%.*}
echo "export to file ${filename}.${exportformat}..."
# run client with export command
openrefine-client/openrefine-client_0-3-4_linux-64bit -P ${port} -E --output="${outputdir}/${filename}.${exportformat}" "${templating[@]}" ${projectids[i]}
openrefine-client/openrefine-client_0-3-9_linux -P ${port} -E --output="${outputdir}/${filename}.${exportformat}" "${templating[@]}" ${projectids[i]}
# show allocated system resources
ps -o start,etime,%mem,%cpu,rss -p ${pid} --sort=start
memoryload+=($(ps --no-headers -o rss -p ${pid}))