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openrefine-batch
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OpenRefine 3.4.1, openrefine-client 0.3.10

This commit is contained in:
Felix Lohmeier 2021-01-04 17:37:49 +01:00
parent 80fb37cb65
commit 4199fadc04
3 changed files with 69 additions and 62 deletions
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91
README.md
View File

@ -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.gz 100%[===============================================>] 101,13M 9,46MB/s in 19s
openrefine-linux-3.4.1.tar.gz 100%[============================================================================================>] 114,70M 8,49MB/s in 20s
Install OpenRefine in subdirectory openrefine...
Total bytes read: 125419520 (120MiB, 74MiB/s)
Total bytes read: 139970560 (134MiB, 86MiB/s)
Download OpenRefine client...
openrefine-client_0-3-9_linux 100%[===============================================>] 4,25M 2,61MB/s in 1,6s
openrefine-client_0-3-10_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
@ -184,94 +184,101 @@ restart after transform: false
=== 1. Launch OpenRefine ===
starting time: Sa 8. Aug 13:32:45 CEST 2020
starting time: Mo 4. Jan 16:56:28 CET 2021
Using refine.ini for configuration
openrefine/refine: line 810: [: 2048M: integer expression expected
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
/usr/bin/java -cp server/classes:server/target/lib/* -Drefine.headless=true -Xms2048M -Xmx2048M -Drefine.memory=2048M -Drefine.max_form_content_size=1048576 -Drefine.verbosity=info -Dpython.path=main/webapp/WEB-INF/lib/jython -Dpython.cachedir=/home/felix/.local/share/google/refine/cachedir -Drefine.data_dir=/home/felix/git/openrefine-batch/examples/powerhouse-museum/output -Drefine.webapp=main/webapp -Drefine.port=3333 -Drefine.host=127.0.0.1 -Drefine.autosave=1440 com.google.refine.Refine
Starting OpenRefine at 'http://127.0.0.1:3333/'
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)
16:56:28.993 [ refine_server] Starting Server bound to '127.0.0.1:3333' (0ms)
16:56:28.994 [ refine_server] refine.memory size: 2048M JVM Max heap: 2058354688 (1ms)
16:56:29.004 [ 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]
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)
16:56:29.690 [ refine] Starting OpenRefine 3.4.1 [437dc4d]... (686ms)
16:56:29.690 [ refine] initializing FileProjectManager with dir (0ms)
16:56:29.690 [ refine] /home/felix/git/openrefine-batch/examples/powerhouse-museum/output (0ms)
16:56:29.696 [ FileProjectManager] Failed to load workspace from any attempted alternatives. (6ms)
16:56:35.245 [ refine] Running in headless mode (5549ms)
=== 2. Import all files ===
starting time: Sa 8. Aug 13:32:53 CEST 2020
starting time: Mo 4. Jan 16:56:36 CET 2021
import phm-collection.tsv...
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
16:56:36.199 [ refine] GET /command/core/get-csrf-token (954ms)
16:56:36.339 [ refine] POST /command/core/create-project-from-upload (140ms)
16:56:45.999 [ refine] GET /command/core/get-models (9660ms)
16:56:46.105 [ refine] POST /command/core/get-rows (106ms)
id: 1841400347972
rows: 75814
STARTED ELAPSED %MEM %CPU RSS
13:32:45 00:16 6.0 201 993192
16:56:27 00:18 6.1 194 997020
=== 3. Prepare transform & export ===
starting time: Sa 8. Aug 13:33:01 CEST 2020
starting time: Mo 4. Jan 16:56:46 CET 2021
get project ids...
13:33:02.003 [ refine] GET /command/core/get-all-project-metadata (281ms)
1705197298924: phm-collection
16:56:46.383 [ refine] GET /command/core/get-csrf-token (278ms)
16:56:46.387 [ refine] GET /command/core/get-all-project-metadata (4ms)
1841400347972: phm-collection
=== 4. Transform phm-collection ===
starting time: Sa 8. Aug 13:33:02 CEST 2020
starting time: Mo 4. Jan 16:56:46 CET 2021
transform phm-transform.json...
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
16:56:46.594 [ refine] GET /command/core/get-csrf-token (207ms)
16:56:46.597 [ refine] GET /command/core/get-models (3ms)
16:56:46.607 [ refine] POST /command/core/apply-operations (10ms)
File /home/felix/git/openrefine-batch/examples/powerhouse-museum/config/phm-transform.json has been successfully applied to project 1841400347972
STARTED ELAPSED %MEM %CPU RSS
13:32:45 00:32 6.3 165 1037688
16:56:27 00:34 6.2 162 1026072
=== 5. Export phm-collection ===
starting time: Sa 8. Aug 13:33:17 CEST 2020
starting time: Mo 4. Jan 16:57:02 CET 2021
export to file phm-collection.tsv...
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)
16:57:02.322 [ refine] GET /command/core/get-csrf-token (15715ms)
16:57:02.325 [ refine] GET /command/core/get-models (3ms)
16:57:02.328 [ refine] GET /command/core/get-all-project-metadata (3ms)
16:57:02.331 [ refine] POST /command/core/export-rows/phm-collection.tsv (3ms)
Export to file /home/felix/git/openrefine-batch/examples/powerhouse-museum/output/phm-collection.tsv complete
STARTED ELAPSED %MEM %CPU RSS
13:32:45 00:35 6.7 168 1098564
16:56:27 00:37 7.2 169 1181160
output (number of lines / size in bytes):
75728 59431272 /home/felix/git/openrefine-batch/examples/powerhouse-museum/output/phm-collection.tsv
cleanup...
13:33:24.667 [ ProjectManager] Saving all modified projects ... (6660ms)
13:33:28.044 [ project_utilities] Saved project '1705197298924' (3377ms)
16:57:08.684 [ ProjectManager] Saving all modified projects ... (6353ms)
16:57:12.069 [ project_utilities] Saved project '1841400347972' (3385ms)
=== Statistics ===
starting time and run time of each step:
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)
Start process Mo 4. Jan 16:56:28 CET 2021 (00:00:00)
Launch OpenRefine Mo 4. Jan 16:56:28 CET 2021 (00:00:08)
Import all files Mo 4. Jan 16:56:36 CET 2021 (00:00:10)
Prepare transform & export Mo 4. Jan 16:56:46 CET 2021 (00:00:00)
Transform phm-collection Mo 4. Jan 16:56:46 CET 2021 (00:00:16)
Export phm-collection Mo 4. Jan 16:57:02 CET 2021 (00:00:11)
End process Mo 4. Jan 16:57:13 CET 2021 (00:00:00)
total run time: 00:00:44 (hh:mm:ss)
highest memory load: 1072 MB
total run time: 00:00:45 (hh:mm:ss)
highest memory load: 1153 MB
```
### Performance gain with extended cross function

24
openrefine-batch-docker.sh
View File

@ -1,5 +1,5 @@
#!/bin/bash
# openrefine-batch-docker.sh, Felix Lohmeier, v1.14, 2020-08-08
# openrefine-batch-docker.sh, Felix Lohmeier, v1.15, 2021-01-04
# https://github.com/felixlohmeier/openrefine-batch
# check system requirements
@ -40,7 +40,7 @@ Usage: ./openrefine-batch-docker.sh [-a INPUTDIR] [-b TRANSFORMDIR] [-c OUTPUTDI
-i INPUTOPTIONS several options provided by openrefine-client, see below...
-m RAM maximum RAM for OpenRefine java heap space (default: 2048M)
-t TEMPLATING several options for templating export, see below...
-v VERSION OpenRefine version (3.2, 3.1, 3.0, 2.8, 2.7, ...; default: 3.2)
-v VERSION OpenRefine version (3.4.1, 3.4, 3.3, 3.2, 3.1, 3.0, 2.8, 2.7, ...; default: 3.4.1)
-E do NOT export files
-R do NOT restart OpenRefine after each transformation (e.g. config file)
-X do NOT restart OpenRefine after each project (e.g. input file)
@ -108,7 +108,7 @@ EOF
# defaults
ram="2048M"
version="3.2"
version="3.4.1"
restartfile="true"
restarttransform="true"
export="true"
@ -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 ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.9 --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
until ${docker[*]} run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.10 --silent -N http://${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:v0.3.9 -H ${uuid} -c $inputfile $inputformat ${inputoptions[@]}
${docker[*]} run --rm --link ${uuid} -v ${inputdir}:/data:z felixlohmeier/openrefine-client:v0.3.10 -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 ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.9 --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
until ${docker[*]} run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.10 --silent -N http://${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:v0.3.9 -H ${uuid} -l > "${outputdir}/projects.tmp"
${docker[*]} run --rm --link ${uuid} felixlohmeier/openrefine-client:v0.3.10 -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 ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.9 --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
until ${docker[*]} run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.10 --silent -N http://${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:v0.3.9 -H ${uuid} -f ${jsonfile} ${projectids[i]}
${docker[*]} run --rm --link ${uuid} -v ${configdir}:/data:z felixlohmeier/openrefine-client:v0.3.10 -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 ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.9 --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
until ${docker[*]} run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.10 --silent -N http://${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:v0.3.9 -H ${uuid} -E --output="${filename}.${exportformat}" "${templating[@]}" ${projectids[i]}
${docker[*]} run --rm --link ${uuid} -v ${outputdir}:/data:z felixlohmeier/openrefine-client:v0.3.10 -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 ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.9 --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
until ${docker[*]} run --rm --link ${uuid} --entrypoint /usr/bin/curl felixlohmeier/openrefine-client:v0.3.10 --silent -N http://${uuid}:3333 | cat | grep -q -o "OpenRefine" ; do sleep 1; done
${docker[*]} attach ${uuid} &
fi
echo ""

16
openrefine-batch.sh
View File

@ -1,10 +1,10 @@
#!/bin/bash
# openrefine-batch.sh, Felix Lohmeier, v1.14, 2020-08-08
# openrefine-batch.sh, Felix Lohmeier, v1.15, 2021-01-04
# 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/v0.3.9/openrefine-client_0-3-9_linux"
openrefine_URL="https://github.com/OpenRefine/OpenRefine/releases/download/3.4.1/openrefine-linux-3.4.1.tar.gz"
client_URL="https://github.com/opencultureconsulting/openrefine-client/releases/download/v0.3.10/openrefine-client_0-3-10_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 $client_URL
chmod +x openrefine-client/openrefine-client_0-3-9_linux
chmod +x openrefine-client/openrefine-client_0-3-10_linux
echo ""
fi
@ -259,7 +259,7 @@ if [ -n "$inputfiles" ]; then
for inputfile in "${inputfiles[@]}" ; do
echo "import ${inputfile}..."
# run client with input command
openrefine-client/openrefine-client_0-3-9_linux -P ${port} -c ${inputdir}/${inputfile} $inputformat "${inputoptions[@]}"
openrefine-client/openrefine-client_0-3-10_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_0-3-9_linux -P ${port} -l > "${outputdir}/projects.tmp"
openrefine-client/openrefine-client_0-3-10_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_0-3-9_linux -P ${port} -f ${configdir}/${jsonfile} ${projectids[i]}
openrefine-client/openrefine-client_0-3-10_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_0-3-9_linux -P ${port} -E --output="${outputdir}/${filename}.${exportformat}" "${templating[@]}" ${projectids[i]}
openrefine-client/openrefine-client_0-3-10_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}))