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openrefine-batch
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OpenRefine 3.5.0

This commit is contained in:
Felix Lohmeier 2021-11-09 23:14:30 +01:00
parent a9c494856b
commit 4e32074d85
3 changed files with 54 additions and 56 deletions
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100
README.md
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@ -166,12 +166,12 @@ 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-3.4.1.tar.gz 100%[============================================================================================>] 114,70M 8,49MB/s in 20s
openrefine-linux-3.5.0.tar.gz 100%[=========================================================================================================================================>] 125,73M 9,50MB/s in 13s
Install OpenRefine in subdirectory openrefine...
Total bytes read: 139970560 (134MiB, 86MiB/s)
Total bytes read: 154163200 (148MiB, 87MiB/s)
Download OpenRefine client...
openrefine-client_0-3-10_linux 100%[============================================================================================>] 4,25M 2,61MB/s in 1,6s
openrefine-client_0-3-10_linux 100%[=========================================================================================================================================>] 4,25M 9,17MB/s in 0,5s
Input directory: /home/felix/git/openrefine-batch/examples/powerhouse-museum/input
Input files: phm-collection.tsv
@ -192,101 +192,99 @@ restart after transform: false
=== 1. Launch OpenRefine ===
starting time: Mo 4. Jan 16:56:28 CET 2021
starting time: Di 9. Nov 22:37:25 CET 2021
Using refine.ini for configuration
openrefine/refine: line 810: [: 2048M: integer expression expected
You have 15927M of free memory.
You have 15913M 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
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.interface=127.0.0.1 -Drefine.host=127.0.0.1 -Drefine.autosave=1440 com.google.refine.Refine
Starting OpenRefine at 'http://127.0.0.1:3333/'
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)
log4j:WARN No appenders could be found for logger (org.eclipse.jetty.util.log).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
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: Found binding in [jar:file:/home/felix/git/openrefine-batch/openrefine/webapp/WEB-INF/lib/slf4j-log4j12-1.7.30.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/home/felix/git/openrefine-batch/openrefine/server/target/lib/slf4j-log4j12-1.7.30.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]
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)
22:37:28.211 [ refine] Starting OpenRefine 3.5.0 [d4209a2]... (0ms)
22:37:28.213 [ refine] initializing FileProjectManager with dir (2ms)
22:37:28.213 [ refine] /home/felix/git/openrefine-batch/examples/powerhouse-museum/output (0ms)
22:37:28.223 [ FileProjectManager] Failed to load workspace from any attempted alternatives. (10ms)
=== 2. Import all files ===
starting time: Mo 4. Jan 16:56:36 CET 2021
starting time: Di 9. Nov 22:37:33 CET 2021
import phm-collection.tsv...
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
22:37:33.804 [ refine] GET /command/core/get-csrf-token (5581ms)
22:37:33.872 [ refine] POST /command/core/create-project-from-upload (68ms)
22:37:44.653 [ refine] GET /command/core/get-models (10781ms)
22:37:44.790 [ refine] POST /command/core/get-rows (137ms)
id: 2252508879578
rows: 75814
STARTED ELAPSED %MEM %CPU RSS
16:56:27 00:18 6.1 194 997020
22:37:25 00:19 10.2 202 1670620
=== 3. Prepare transform & export ===
starting time: Mo 4. Jan 16:56:46 CET 2021
starting time: Di 9. Nov 22:37:44 CET 2021
get project ids...
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
22:37:45.112 [ refine] GET /command/core/get-csrf-token (322ms)
22:37:45.115 [ refine] GET /command/core/get-all-project-metadata (3ms)
2252508879578: phm-collection
=== 4. Transform phm-collection ===
starting time: Mo 4. Jan 16:56:46 CET 2021
starting time: Di 9. Nov 22:37:45 CET 2021
transform phm-transform.json...
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
22:37:45.303 [ refine] GET /command/core/get-csrf-token (188ms)
22:37:45.308 [ refine] GET /command/core/get-models (5ms)
22:37:45.324 [ refine] POST /command/core/apply-operations (16ms)
File /home/felix/git/openrefine-batch/examples/powerhouse-museum/config/phm-transform.json has been successfully applied to project 2252508879578
STARTED ELAPSED %MEM %CPU RSS
16:56:27 00:34 6.2 162 1026072
22:37:25 00:34 11.9 175 1940600
=== 5. Export phm-collection ===
starting time: Mo 4. Jan 16:57:02 CET 2021
starting time: Di 9. Nov 22:37:59 CET 2021
export to file phm-collection.tsv...
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)
22:37:59.944 [ refine] GET /command/core/get-csrf-token (14620ms)
22:37:59.947 [ refine] GET /command/core/get-models (3ms)
22:37:59.951 [ refine] GET /command/core/get-all-project-metadata (4ms)
22:37:59.954 [ 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
16:56:27 00:37 7.2 169 1181160
22:37:25 00:38 12.4 181 2021388
output (number of lines / size in bytes):
75728 59431272 /home/felix/git/openrefine-batch/examples/powerhouse-museum/output/phm-collection.tsv
cleanup...
16:57:08.684 [ ProjectManager] Saving all modified projects ... (6353ms)
16:57:12.069 [ project_utilities] Saved project '1841400347972' (3385ms)
22:38:06.850 [ ProjectManager] Saving all modified projects ... (6896ms)
22:38:10.014 [ project_utilities] Saved project '2252508879578' (3164ms)
=== Statistics ===
starting time and run time of each step:
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)
Start process Di 9. Nov 22:37:25 CET 2021 (00:00:00)
Launch OpenRefine Di 9. Nov 22:37:25 CET 2021 (00:00:08)
Import all files Di 9. Nov 22:37:33 CET 2021 (00:00:11)
Prepare transform & export Di 9. Nov 22:37:44 CET 2021 (00:00:01)
Transform phm-collection Di 9. Nov 22:37:45 CET 2021 (00:00:14)
Export phm-collection Di 9. Nov 22:37:59 CET 2021 (00:00:11)
End process Di 9. Nov 22:38:10 CET 2021 (00:00:00)
total run time: 00:00:45 (hh:mm:ss)
highest memory load: 1153 MB
highest memory load: 1974 MB
```
### Docker

6
openrefine-batch-docker.sh
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@ -1,5 +1,5 @@
#!/bin/bash
# openrefine-batch-docker.sh, Felix Lohmeier, v1.15, 2021-01-04
# openrefine-batch-docker.sh, Felix Lohmeier, v1.16, 2021-11-09
# 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 (3.4.1, 3.4, 3.3, 3.2, 3.1, 3.0, 2.8, 2.7, ...; default: 3.4.1)
-v VERSION OpenRefine version (3.5.0, 3.4.1, 3.4, 3.3, 3.2, 3.1, 3.0, 2.8, 2.7, ...; default: 3.5.0)
-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="3.4.1"
version="3.5.0"
restartfile="true"
restarttransform="true"
export="true"

4
openrefine-batch.sh
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@ -1,9 +1,9 @@
#!/bin/bash
# openrefine-batch.sh, Felix Lohmeier, v1.15, 2021-01-04
# openrefine-batch.sh, Felix Lohmeier, v1.16, 2021-11-09
# https://github.com/felixlohmeier/openrefine-batch
# declare download URLs for OpenRefine and OpenRefine client
openrefine_URL="https://github.com/OpenRefine/OpenRefine/releases/download/3.4.1/openrefine-linux-3.4.1.tar.gz"
openrefine_URL="https://github.com/OpenRefine/OpenRefine/releases/download/3.5.0/openrefine-linux-3.5.0.tar.gz"
client_URL="https://github.com/opencultureconsulting/openrefine-client/releases/download/v0.3.10/openrefine-client_0-3-10_linux"
# check system requirements