Bluima:: UIMA components at BlueBrain

Papers

• Richardet, Renaud, Jean-Cédric Chappelier, and Martin Telefont. "Bluima: a UIMA-based NLP Toolkit for Neuroscience." Unstructured Information Management Architecture (UIMA) (2013): 34. ceur-ws.org/Vol-1038/paper_7.pdf

Dependencies

• Java JDK 6 or higher (http://www.oracle.com/technetwork/java/javase/downloads/index.html)
• Maven 3 (http://maven.apache.org/download.html#Installation)

Configure

Setup BLUIMA_HOME, e.g. (in your .bash_profile):

export BLUIMA_HOME={absolute path to Bluima}

Build

> export MAVEN_OPTS="-Xmx4G -XX:MaxPermSize=256m"
> mvn clean install -Dblue_uima_home={PATH_TO_HOME}

Get yourself a coffee. Rinse and repeat above command if error is "could not download artifacts"

If gpg signing is not setup and you simply want to skip it then you can add -Dgpg.skip=true to the maven command line options.

Maven Tests

• The reference test environment is the command line.
• Run all tests > mvn clean test
• Skip tests while building > mvn install -Dmaven.test.skip=true

Eclipse

• Tested with 4.2 and latest m2e plugin
• Make sure you have built the codebase with the above step (mvn)
• Import the module bluima_bbp with: File -> Import... -> Existing Maven Projects
• Set BLUIMA_HOME in Eclipse
• Preferences: Java > Installed JRE > Edit
• -Xms1G -Xmx4G -Dbluima_home={absolute path to Bluima}
• Test your installation (see "Getting Started" below)
• Import other modules you need with: File -> Import... -> Existing Maven Projects

Release

> cd modules/bluima
> sh release.sh

The release can be deployed on any computer with a JRE (e.g. cluster).

Conventions (over configuration)

• Maven projects are named bluima_{project-name}
• Class naming conventions
• UIMA Analysis Engines are named Annotator
• UIMA Collection Readers are named CollectionReader
• UIMA Cas Consumers are named Writer
• JUnit tests are named {base-class}Test

Getting Started

• launch the class ch.epfl.bbp.uima.RunPipeline in project bluima_bbp
• select a pipeline to run, e.g. examples/1_simple/simple.pipeline

Feedback

• is welcome: renaud.richardet@epfl.ch