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release v1.8, updated OpenRefine version (dev snapshot 2017-10-28)
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@felixlohmeier
felixlohmeier committed Oct 28, 2017
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129 changes: 79 additions & 50 deletions README.md
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Expand Up @@ -39,7 +39,7 @@ cp CONFIGFILES config/
* you may use hard symlinks instead of cp: `ln INPUTFILE input/`

**CONFIGFILES**
* JSON files with [OpenRefine transformation rules)](http://kb.refinepro.com/2012/06/google-refine-json-and-my-notepad-or.html)
* JSON files with [OpenRefine transformation rules](http://kb.refinepro.com/2012/06/google-refine-json-and-my-notepad-or.html)

**OUTPUT/**
* path to directory where results and temporary data should be stored
Expand All @@ -50,6 +50,17 @@ cp CONFIGFILES config/

[Example Powerhouse Museum](examples/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/ \
Expand All @@ -61,12 +72,10 @@ cp CONFIGFILES config/
-RX
```

clone or [download GitHub repository](https://github.com/felixlohmeier/openrefine-batch/archive/master.zip) to get example data

### Help Screen

```
[14:45 felix ~/openrefine-batch]$ ./openrefine-batch.sh
[11:36 felix ~/openrefine-batch]$ ./openrefine-batch.sh
Usage: ./openrefine-batch.sh [-a INPUTDIR] [-b TRANSFORMDIR] [-c OUTPUTDIR] ...
== basic arguments ==
Expand Down Expand Up @@ -109,118 +118,138 @@ Usage: ./openrefine-batch.sh [-a INPUTDIR] [-b TRANSFORMDIR] [-c OUTPUTDIR] ...
== example ==
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
clone or download GitHub repository to get example data:
https://github.com/felixlohmeier/openrefine-batch/archive/master.zip
```

### Logging

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

```
[00:41 felix ~/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
[11:36 felix ~/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-2017-10-26.tar.gz 100%[=====================================================================================================================>] 66,34M 5,62MB/s in 12s
openrefine-linux-2017-10-2 100%[=====================================>] 66,34M 5,62MB/s in 12s
Install OpenRefine in subdirectory openrefine...
Total bytes read: 79861760 (77MiB, 128MiB/s)
Total bytes read: 79861760 (77MiB, 129MiB/s)
Download OpenRefine client...
openrefine-client_0-3-1_linux-64bit 100%[=====================================================================================================================>] 5,39M 5,08MB/s in 1,1s
openrefine-client_0-3-1_li 100%[=====================================>] 5,39M 5,17MB/s in 1,0s
Input directory: /home/felix/owncloud/Business/projekte/openrefine/openrefine-batch/examples/powerhouse-museum/input
Input directory: /home/felix/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/owncloud/Business/projekte/openrefine/openrefine-batch/examples/powerhouse-museum/config
Config directory: /home/felix/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/owncloud/Business/projekte/openrefine/openrefine-batch/examples/powerhouse-museum/output
OpenRefine workspace: /home/felix/openrefine-batch/examples/powerhouse-museum/output
Export to workspace: true
Export format: tsv
restart after file: false
restart after transform: false
=== 1. Launch OpenRefine ===
starting time: Sa 28. Okt 00:42:33 CEST 2017
starting time: Sa 28. Okt 11:38:19 CEST 2017
Starting OpenRefine at 'http://127.0.0.1:3333/'
00:42:33.199 [ refine_server] Starting Server bound to '127.0.0.1:3333' (0ms)
00:42:33.200 [ refine_server] refine.memory size: 2048M JVM Max heap: 2058354688 (1ms)
00:42:33.206 [ refine_server] Initializing context: '/' from '/home/felix/owncloud/Business/projekte/openrefine/openrefine-batch/openrefine/webapp' (6ms)
00:42:33.418 [ refine] Starting OpenRefine 2017-10-26 [TRUNK]... (212ms)
00:42:33.424 [ FileProjectManager] Failed to load workspace from any attempted alternatives. (6ms)
00:42:35.993 [ refine] Running in headless mode (2569ms)
11:38:19.275 [ refine_server] Starting Server bound to '127.0.0.1:3333' (0ms)
11:38:19.275 [ refine_server] refine.memory size: 2048M JVM Max heap: 2058354688 (0ms)
11:38:19.281 [ refine_server] Initializing context: '/' from '/home/felix/openrefine-batch/openrefine/webapp' (6ms)
11:38:19.478 [ refine] Starting OpenRefine 2017-10-28 [TRUNK]... (197ms)
11:38:19.484 [ FileProjectManager] Failed to load workspace from any attempted alternatives. (6ms)
11:38:22.010 [ refine] Running in headless mode (2526ms)
=== 2. Import all files ===
starting time: Sa 28. Okt 00:42:36 CEST 2017
starting time: Sa 28. Okt 11:38:22 CEST 2017
import phm-collection.tsv...
00:42:36.393 [ refine] POST /command/core/create-project-from-upload (400ms)
New project: 1721413008439
00:42:40.731 [ refine] GET /command/core/get-rows (4338ms)
11:38:22.479 [ refine] POST /command/core/create-project-from-upload (469ms)
New project: 1530205635037
11:38:26.474 [ refine] GET /command/core/get-rows (3995ms)
Number of rows: 75814
STARTED ELAPSED %MEM %CPU RSS
00:42:32 00:07 5.7 220 937692
11:38:18 00:07 5.8 214 946616
=== 3. Prepare transform & export ===
starting time: Sa 28. Okt 00:42:40 CEST 2017
starting time: Sa 28. Okt 11:38:26 CEST 2017
get project ids...
00:42:40.866 [ refine] GET /command/core/get-all-project-metadata (135ms)
1721413008439: phm-collection.tsv
11:38:26.589 [ refine] GET /command/core/get-all-project-metadata (115ms)
1530205635037: phm-collection.tsv
=== 4. Transform phm-collection.tsv ===
starting time: Sa 28. Okt 00:42:40 CEST 2017
starting time: Sa 28. Okt 11:38:26 CEST 2017
transform phm-transform.json...
00:42:40.963 [ refine] GET /command/core/get-models (97ms)
00:42:40.967 [ refine] POST /command/core/apply-operations (4ms)
11:38:26.684 [ refine] GET /command/core/get-models (95ms)
11:38:26.687 [ refine] POST /command/core/apply-operations (3ms)
STARTED ELAPSED %MEM %CPU RSS
00:42:32 00:29 7.1 142 1162720
11:38:18 00:28 7.2 139 1169204
=== 5. Export phm-collection.tsv ===
starting time: Sa 28. Okt 00:43:02 CEST 2017
starting time: Sa 28. Okt 11:38:47 CEST 2017
export to file phm-collection.tsv...
00:43:02.555 [ refine] GET /command/core/get-models (21588ms)
00:43:02.557 [ refine] GET /command/core/get-all-project-metadata (2ms)
00:43:02.561 [ refine] POST /command/core/export-rows/phm-collection.tsv.tsv (4ms)
11:38:47.214 [ refine] GET /command/core/get-models (20527ms)
11:38:47.217 [ refine] GET /command/core/get-all-project-metadata (3ms)
11:38:47.221 [ refine] POST /command/core/export-rows/phm-collection.tsv.tsv (4ms)
STARTED ELAPSED %MEM %CPU RSS
00:42:32 00:53 7.1 81.1 1164684
11:38:18 00:50 7.2 81.2 1170760
output (number of lines / size in bytes):
167017 60619468 /home/felix/owncloud/Business/projekte/openrefine/openrefine-batch/examples/powerhouse-museum/output/phm-collection.tsv
167017 60619468 /home/felix/openrefine-batch/examples/powerhouse-museum/output/phm-collection.tsv
cleanup...
00:43:26.161 [ ProjectManager] Saving all modified projects ... (23600ms)
00:43:29.586 [ project_utilities] Saved project '1721413008439' (3425ms)
11:39:12.562 [ ProjectManager] Saving all modified projects ... (25341ms)
11:39:15.953 [ project_utilities] Saved project '1530205635037' (3391ms)
=== Statistics ===
starting time and run time of each step:
Start process Sa 28. Okt 00:42:33 CEST 2017 (00:00:00)
Launch OpenRefine Sa 28. Okt 00:42:33 CEST 2017 (00:00:03)
Import all files Sa 28. Okt 00:42:36 CEST 2017 (00:00:04)
Prepare transform & export Sa 28. Okt 00:42:40 CEST 2017 (00:00:00)
Transform phm-collection.tsv Sa 28. Okt 00:42:40 CEST 2017 (00:00:22)
Export phm-collection.tsv Sa 28. Okt 00:43:02 CEST 2017 (00:00:28)
End process Sa 28. Okt 00:43:30 CEST 2017 (00:00:00)
total run time: 00:00:57 (hh:mm:ss)
highest memory load: 1137 MB
Start process Sa 28. Okt 11:38:19 CEST 2017 (00:00:00)
Launch OpenRefine Sa 28. Okt 11:38:19 CEST 2017 (00:00:03)
Import all files Sa 28. Okt 11:38:22 CEST 2017 (00:00:04)
Prepare transform & export Sa 28. Okt 11:38:26 CEST 2017 (00:00:00)
Transform phm-collection.tsv Sa 28. Okt 11:38:26 CEST 2017 (00:00:21)
Export phm-collection.tsv Sa 28. Okt 11:38:47 CEST 2017 (00:00:30)
End process Sa 28. Okt 11:39:17 CEST 2017 (00:00:00)
total run time: 00:00:58 (hh:mm:ss)
highest memory load: 1143 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](https://github.com/felixlohmeier/OpenRefine/wiki>) 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
Expand Down
16 changes: 11 additions & 5 deletions openrefine-batch-docker.sh
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@@ -1,5 +1,5 @@
#!/bin/bash
# openrefine-batch.sh, Felix Lohmeier, v1.7, 2017-10-28
# openrefine-batch-docker.sh, Felix Lohmeier, v1.8, 2017-10-28
# https://github.com/felixlohmeier/openrefine-batch

# check system requirements
Expand Down Expand Up @@ -59,6 +59,15 @@ Usage: sudo ./openrefine-batch-docker.sh [-a INPUTDIR] [-b TRANSFORMDIR] [-c OUT
== example ==
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
sudo ./openrefine-batch-docker.sh \
-a examples/powerhouse-museum/input/ \
-b examples/powerhouse-museum/config/ \
Expand All @@ -68,16 +77,13 @@ sudo ./openrefine-batch-docker.sh \
-i guessCellValueTypes=true \
-RX
clone or download GitHub repository to get example data:
https://github.com/felixlohmeier/openrefine-batch/archive/master.zip
EOF
exit 1
}

# defaults
ram="2048M"
version="2.7"
version="dev"
restartfile="true"
restarttransform="true"
export="true"
Expand Down
16 changes: 11 additions & 5 deletions openrefine-batch.sh
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@@ -1,9 +1,9 @@
#!/bin/bash
# openrefine-batch.sh, Felix Lohmeier, v1.7, 2017-10-28
# openrefine-batch.sh, Felix Lohmeier, v1.8, 2017-10-28
# https://github.com/felixlohmeier/openrefine-batch

# declare download URLs for OpenRefine and OpenRefine client
openrefine_URL="https://github.com/opencultureconsulting/openrefine-batch/raw/master/src/openrefine-linux-2017-10-26.tar.gz"
openrefine_URL="https://github.com/opencultureconsulting/openrefine-batch/raw/master/src/openrefine-linux-2017-10-28.tar.gz"
client_URL="https://github.com/opencultureconsulting/openrefine-batch/raw/master/src/openrefine-client_0-3-1_linux-64bit"

# check system requirements
Expand Down Expand Up @@ -83,6 +83,15 @@ Usage: ./openrefine-batch.sh [-a INPUTDIR] [-b TRANSFORMDIR] [-c OUTPUTDIR] ...
== example ==
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/ \
Expand All @@ -92,9 +101,6 @@ Usage: ./openrefine-batch.sh [-a INPUTDIR] [-b TRANSFORMDIR] [-c OUTPUTDIR] ...
-i guessCellValueTypes=true \
-RX
clone or download GitHub repository to get example data:
https://github.com/felixlohmeier/openrefine-batch/archive/master.zip
EOF
exit 1
}
Expand Down

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