openrefine-batch/README.md at 93be203efed43dd68003b1ecf50695f0e3cfec3e

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OpenRefine batch processing (openrefine-batch.sh)

Shell script to run OpenRefine in batch mode (import, transform, export). This bash script automatically...

imports all data from a given directory into OpenRefine
transforms the data by applying OpenRefine transformation rules from all json files in another given directory and
finally exports the data in csv, tsv, html, xlsx or ods.

It orchestrates OpenRefine (server) and a python client that communicates with the OpenRefine API. By restarting the server after each process it reduces memory requirements to a minimum.

If you prefer a containerized approach, see a variation of this script for Docker below.

Typical Workflow

Step 1: Do some experiments with your data (or parts of it) in the graphical user interface of OpenRefine. If you are fine with all transformation rules, extract the json code and save it as file (e.g. transform.json).
Step 2: Put your data and the json file(s) in two different directories and execute the script. The script will automatically import all data files in OpenRefine projects, apply the transformation rules in the json files to each project and export all projects to files in the format specified (default: TSV - tab-separated values).

Install

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

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.

Usage

mkdir input
cp INPUTFILES input/
mkdir config
cp CONFIGFILES config/
./openrefine-batch.sh -a input/ -b config/ -c OUTPUT/

INPUTFILES

any data that OpenRefine supports. CSV, TSV and line-based files should work out of the box. XML, JSON, fixed-width, XSLX and ODS need one additional input parameter (see chapter Options below)
multiple slices of data may be transformed into a into a single file by providing a zip or tar.gz archive
you may use hard symlinks instead of cp: ln INPUTFILE input/

CONFIGFILES

JSON files with OpenRefine transformation rules

OUTPUT/

path to directory where results and temporary data should be stored
Transformed data will be stored in this directory in the format specified (default: TSV). Show results: ls OUTPUT/*.tsv
OpenRefine stores data in directories like "1234567890123.project". You may have a look at the results by starting OpenRefine with this workspace. Delete the directories if you do not need them: rm -r -f OUTPUT/*.project

Example

Example Powerhouse Museum

download example data

wget https://github.com/opencultureconsulting/openrefine-batch/archive/master.zip
unzip master.zip openrefine-batch-master/examples/*
mv openrefine-batch-master/examples .
rm -f master.zip

execute openrefine-batch.sh

./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

Help Screen

[felix@tux openrefine-batch]$ ./openrefine-batch.sh
Usage: ./openrefine-batch.sh [-a INPUTDIR] [-b TRANSFORMDIR] [-c OUTPUTDIR] ...

== basic arguments ==
    -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 )
    -b TRANSFORMDIR  path to directory with OpenRefine transformation rules (json files, cf. http://kb.refinepro.com/2012/06/google-refine-json-and-my-notepad-or.html ; leave empty to transform only)
    -c OUTPUTDIR     path to directory for exported files (and OpenRefine workspace)

== options ==
    -d CROSSDIR      path to directory with additional OpenRefine projects (will be copied to workspace before transformation step to support the cross function, cf. https://github.com/OpenRefine/OpenRefine/wiki/GREL-Other-Functions )
    -e EXPORTFORMAT  (csv, tsv, html, xls, xlsx, ods)
    -f INPUTFORMAT   (csv, tsv, xml, json, line-based, fixed-width, xlsx, ods)
    -i INPUTOPTIONS  several options provided by openrefine-client, see below...
    -m RAM           maximum RAM for OpenRefine java heap space (default: 2048M)
    -p PORT          PORT on which OpenRefine should listen (default: 3333)
    -t TEMPLATING    several options for templating export, see below...
    -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)
    -h               displays this help screen

== inputoptions (mandatory for xml, json, fixed-width, xslx, ods) ==
    -i recordPath=RECORDPATH (xml, json): please provide path in multiple arguments without slashes, e.g. /collection/record/ should be entered like this: -i recordPath=collection -i recordPath=record, default xml: record, default json: _ _
    -i columnWidths=COLUMNWIDTHS (fixed-width): please provide widths separated by comma (e.g. 7,5)
    -i sheets=SHEETS (xls, xlsx, ods): please provide sheets separated by comma (e.g. 0,1), default: 0 (first sheet)

== more inputoptions (optional, only together with inputformat) ==
    -i projectName=PROJECTNAME (all formats), default: filename
    -i limit=LIMIT (all formats), default: -1
    -i includeFileSources=true/false (all formats), default: false
    -i trimStrings=true/false (xml, json), default: false
    -i storeEmptyStrings=true/false (xml, json), default: true
    -i guessCellValueTypes=true/false (xml, csv, tsv, fixed-width, json), default: false
    -i encoding=ENCODING (csv, tsv, line-based, fixed-width), please provide short encoding name (e.g. UTF-8)
    -i ignoreLines=IGNORELINES (csv, tsv, line-based, fixed-width, xls, xlsx, ods), default: -1
    -i headerLines=HEADERLINES (csv, tsv, fixed-width, xls, xlsx, ods), default: 1, default fixed-width: 0
    -i skipDataLines=true/false (csv, tsv, line-based, fixed-width, xls, xlsx, ods), default: 0, default line-based: -1
    -i storeBlankRows=true/false (csv, tsv, line-based, fixed-width, xls, xlsx, ods), default: true
    -i processQuotes=true/false (csv, tsv), default: true
    -i storeBlankCellsAsNulls=true/false (csv, tsv, line-based, fixed-width, xls, xlsx, ods), default: true
    -i linesPerRow=LINESPERROW (line-based), default: 1

== templating options (alternative exportformat) ==
    -t template=TEMPLATE (mandatory; (big) text string that you enter in the *row template* textfield in the export/templating menu in the browser app)
    -t mode=row-based/record-based (engine mode, default: row-based)
    -t prefix=PREFIX (text string that you enter in the *prefix* textfield in the browser app)
    -t rowSeparator=ROWSEPARATOR (text string that you enter in the *row separator* textfield in the browser app)
    -t suffix=SUFFIX (text string that you enter in the *suffix* textfield in the browser app)
    -t filterQuery=REGEX (Simple RegEx text filter on filterColumn, e.g. ^12015$)
    -t filterColumn=COLUMNNAME (column name for filterQuery, default: name of first column)
    -t facets=FACETS (facets config in json format, may be extracted with browser dev tools in browser app)
    -t splitToFiles=true/false (will split each row/record into a single file; it specifies a presumably unique character series for splitting; prefix and suffix will be applied to all files
    -t suffixById=true/false (enhancement option for splitToFiles; will generate filename-suffix from values in key column)

== examples ==

download example data

wget https://github.com/opencultureconsulting/openrefine-batch/archive/master.zip
unzip master.zip openrefine-batch-master/examples/*
mv openrefine-batch-master/examples .
rm -f master.zip

example 1 (input, transform, export to tsv)

./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

example 2 (input, transform, templating export)

./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 -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

Logging

The script prints log messages from OpenRefine server and makes use of ps to show statistics for each step. Here is a sample:

[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     
Install OpenRefine in subdirectory openrefine...
Total bytes read: 139970560 (134MiB, 86MiB/s)

Download OpenRefine client...
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
Input format:            --format=tsv
Input options:           --processQuotes=false --guessCellValueTypes=true
Config directory:        /home/felix/git/openrefine-batch/examples/powerhouse-museum/config
Transformation rules:    phm-transform.json
Cross directory:         /dev/null
Cross projects:          
OpenRefine heap space:   2048M
OpenRefine port:         3333
OpenRefine workspace:    /home/felix/git/openrefine-batch/examples/powerhouse-museum/output
Export to workspace:     true
Export format:           tsv
Templating options:      
restart after file:      false
restart after transform: false

=== 1. Launch OpenRefine ===

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/'

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]
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: Mo 4. Jan 16:56:36 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
rows: 75814
 STARTED     ELAPSED %MEM %CPU   RSS
16:56:27       00:18  6.1  194 997020

=== 3. Prepare transform & export ===

starting time: Mo 4. Jan 16:56:46 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

=== 4. Transform phm-collection ===

starting time: Mo 4. Jan 16:56:46 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
 STARTED     ELAPSED %MEM %CPU   RSS
16:56:27       00:34  6.2  162 1026072


=== 5. Export phm-collection ===

starting time: Mo 4. Jan 16:57:02 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)
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


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)

=== 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)

total run time: 00:00:45 (hh:mm:ss)
highest memory load: 1153 MB

Performance gain with extended cross function

The original cross function expects normalized data (one foreign key per cell in base column). If you have multiple key values in one cell you need to split them first in multiple rows before you apply cross (and join results afterwards). This can be quite "expensive" if you work with bigger datasets.

There is a fork available that extend the cross function to support an integrated split and may provide a massive performance gain for this special use case.

Here is a code snippet to install this fork together with openrefine-batch.sh in a blank directory:

wget https://github.com/felixlohmeier/openrefine-batch/raw/master/openrefine-batch.sh && chmod +x openrefine-batch.sh
sed -i 's/.tar.gz/-with-pr1294.tar.gz/' openrefine-batch.sh
./openrefine-batch.sh

Docker

A variation of the shell script orchestrates a docker container for OpenRefine (server) and a docker container for the python client instead of native applications.

Install

Install Docker

a) configure Docker to start on boot
or b) start Docker on demand each time you use the script: sudo systemctl start docker

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

Usage

mkdir input
cp INPUTFILES input/
mkdir config
cp CONFIGFILES config/
./openrefine-batch-docker.sh -a input/ -b config/ -c OUTPUT/

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 then you may call the script without sudo.

Example

Example Powerhouse Museum

download example data

wget https://github.com/opencultureconsulting/openrefine-batch/archive/master.zip
unzip master.zip openrefine-batch-master/examples/*
mv openrefine-batch-master/examples .
rm -f master.zip

execute openrefine-batch-docker.sh

./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

Todo

howto for extracting input options from OpenRefine GUI with Firefox network monitor
provide more example data from other OpenRefine tutorials

Licensing

MIT License

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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