GrowthRing

GrowthRing is a collections of attempts to visualize how a document grows over revisions. It contains:

• a multiple sequence alignment tool for texts, written in Scala.

• an interactive demo of text de-identification.

This software was in part used for a research paper presented in PACLIC 2014: k-repeating substrings: a string-algorithmic approach to privacy-preserving publishing of textual data. (paper, slides)

How to use

sbt and Java Development Kit (JDK) are required both for building and using this application. Latest release is built with sbt 1.10.0 and openjdk 21.0.3.

This application has a number of parameters that are set by a configuration file (or by Java properties). See src/main/resources/reference.conf for the default values and .conf files at the top level of the repository for other examples.`

Using the web interface

1. sbt "~WarStart # see https://index.scala-lang.org/earldouglas/sbt-war

2. xdg-open http://localhost:8080 # or open http://localhost:8080 on your browser

Using the multiple sequence aligner

1. sbt assembly

2. java -Dconfig.file=msa.conf -jar target/scala-*/growthring-assembly-*.jar < sample_input.txt | dot /dev/stdin -Tpdf -o sample_output.pdf

Using the de-identifier

1. sbt assembly

2. java -Dconfig.file=anonym.conf -jar target/scala-*/growthring-assembly-*.jar < sample_input.txt > sample_output.txt

Using SAIS

Note: instructions below have not been tested for years and probably need updating.

Better performance might be achieved by SAIS, which you need to install as separate a native library separately.

1. Use the command below to get the shared library version of SAIS. You may need to add -fPIC to CFLAGS in the Makefile.

   • make && ld -shared sais.o -o libsais.so

2. Put libsais.so into any directory included by LD_LIBRARY_PATH (or current directory).

3. Use java -Xss50M -Dconfig.file=sais.conf -jar target/scala-*/growthring-assembly-*.jar or otherwise specify -Dorg.whym.growthring.repeatsMethod=sais.

Launching as an App Engine app (devserver)

Note: instructions below have not been tested for years and probably need updating.

1. sbt publishM2

2. mvn -f pom-gae.xml appengine:devserver

3. xdg-open http://localhost:8080 # or open http://localhost:8080 on your browser

How to compile

The above procedures will automatically invoke compilation, but if you specifically want to compile:

• Build sources with sbt compile.

Credits

• Yusuke Matsubara <whym@whym.org>

• See https://meta.wikimedia.org/wiki/Talk:Vision/ja for credits of the texts contained in sample_input.txt