Merge pull request #6 from opencultureconsulting/dependabot/pip/binder/jupyter-server-proxy-3.2.1

Bump jupyter-server-proxy from 1.5.3 to 3.2.1 in /binder
2022-01-28 17:23:34 +01:00 · 2022-01-27 16:25:09 +00:00 · 2021-11-09 23:14:30 +01:00 · 2021-06-17 13:00:33 +02:00 · 2021-06-17 12:59:47 +02:00 · 2021-06-17 12:42:22 +02:00
7 changed files with 72 additions and 75 deletions
--- a/README.md
+++ b/README.md
@ -1,6 +1,6 @@
 ## OpenRefine batch processing (openrefine-batch.sh)

-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/66bf001c38194f5bb722f65f5e15f0ec)](https://www.codacy.com/app/mail_74/openrefine-batch?utm_source=github.com&utm_medium=referral&utm_content=opencultureconsulting/openrefine-batch&utm_campaign=badger)
+[![Codacy Badge](https://app.codacy.com/project/badge/Grade/ad8a97e42e634bbe87203ea48efb436e)](https://www.codacy.com/gh/opencultureconsulting/openrefine-batch/dashboard) [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/opencultureconsulting/openrefine-batch/master?urlpath=lab/tree/demo.ipynb)

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

@ -17,6 +17,14 @@ If you prefer a containerized approach, see a [variation of this script for Dock
 - **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](http://kb.refinepro.com/2012/06/google-refine-json-and-my-notepad-or.html) 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).

+### Demo via binder
+
+[![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/opencultureconsulting/openrefine-batch/master?urlpath=lab/tree/demo.ipynb)
+
+- free to use on-demand server with Jupyterlab and Bash Kernel
+- no registration needed, will start within a few minutes
+- [restricted](https://mybinder.readthedocs.io/en/latest/about/about.html#how-much-memory-am-i-given-when-using-binder) to 2 GB RAM and server will be deleted after 10 minutes of inactivity
+
 ### Install

 Download the script and grant file permissions to execute:
@ -158,12 +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
@ -184,114 +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
-```
-
-### 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
+highest memory load: 1974 MB
 ```

 ### Docker
@ -347,11 +340,6 @@ execute openrefine-batch-docker.sh
 -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
--- a/binder/apt.txt
+++ b/binder/apt.txt
@ -0,0 +1 @@
+openjdk-8-jre
--- a/binder/postBuild
+++ b/binder/postBuild
@ -0,0 +1,5 @@
+#!/bin/bash
+set -e
+
+# Install bash_kernel https://github.com/takluyver/bash_kernel
+python -m bash_kernel.install
--- a/binder/requirements.txt
+++ b/binder/requirements.txt
@ -0,0 +1,2 @@
+jupyter-server-proxy==3.2.1
+bash_kernel==0.7.2
--- a/demo.ipynb
+++ b/demo.ipynb
@ -0,0 +1 @@
+{"metadata":{"language_info":{"name":"bash","codemirror_mode":"shell","mimetype":"text/x-sh","file_extension":".sh"},"kernelspec":{"name":"bash","display_name":"Bash","language":"bash"}},"nbformat_minor":5,"nbformat":4,"cells":[{"cell_type":"markdown","source":"# Example Powerhouse Museum\n\nOutput will be stored in examples/powerhouse-museum/output/phm-collection.tsv","metadata":{}},{"cell_type":"code","source":"./openrefine-batch.sh \\\n-a examples/powerhouse-museum/input/ \\\n-b examples/powerhouse-museum/config/ \\\n-c examples/powerhouse-museum/output/ \\\n-f tsv \\\n-i processQuotes=false \\\n-i guessCellValueTypes=true \\\n-RX","metadata":{"trusted":true},"execution_count":null,"outputs":[]}]}
--- a/openrefine-batch-docker.sh
+++ b/openrefine-batch-docker.sh
@ -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"
--- a/openrefine-batch.sh
+++ b/openrefine-batch.sh
@ -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
Author	SHA1	Message	Date
Felix Lohmeier	2cc2378085	Merge pull request #6 from opencultureconsulting/dependabot/pip/binder/jupyter-server-proxy-3.2.1 Bump jupyter-server-proxy from 1.5.3 to 3.2.1 in /binder	2022-01-28 17:23:34 +01:00
dependabot[bot]	9e6e42261b	Bump jupyter-server-proxy from 1.5.3 to 3.2.1 in /binder Bumps [jupyter-server-proxy](https://github.com/jupyterhub/jupyter-server-proxy) from 1.5.3 to 3.2.1. - [Release notes](https://github.com/jupyterhub/jupyter-server-proxy/releases) - [Changelog](https://github.com/jupyterhub/jupyter-server-proxy/blob/main/CHANGELOG.md) - [Commits](https://github.com/jupyterhub/jupyter-server-proxy/compare/v1.5.3...v3.2.1) --- updated-dependencies: - dependency-name: jupyter-server-proxy dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>	2022-01-27 16:25:09 +00:00
Felix Lohmeier	4e32074d85	OpenRefine 3.5.0	2021-11-09 23:14:30 +01:00
Felix Lohmeier	a9c494856b	cleanup README	2021-06-17 13:00:33 +02:00
Felix Lohmeier	ca19d7ef16	add jupyter notebook	2021-06-17 12:59:47 +02:00
Felix Lohmeier	93be203efe	add binder config	2021-06-17 12:42:22 +02:00
Felix Lohmeier	2894b0194f	fix codacy badge	2021-02-12 13:38:33 +01:00
				`@ -0,0 +1 @@`
				{"metadata":{"language_info":{"name":"bash","codemirror_mode":"shell","mimetype":"text/x-sh","file_extension":".sh"},"kernelspec":{"name":"bash","display_name":"Bash","language":"bash"}},"nbformat_minor":5,"nbformat":4,"cells":[{"cell_type":"markdown","source":"# Example Powerhouse Museum\n\nOutput will be stored in examples/powerhouse-museum/output/phm-collection.tsv","metadata":{}},{"cell_type":"code","source":"./openrefine-batch.sh \\\n-a examples/powerhouse-museum/input/ \\\n-b examples/powerhouse-museum/config/ \\\n-c examples/powerhouse-museum/output/ \\\n-f tsv \\\n-i processQuotes=false \\\n-i guessCellValueTypes=true \\\n-RX","metadata":{"trusted":true},"execution_count":null,"outputs":[]}]}