JarCasting
JarCasting JarCasting

MongoDb Data Access Layer

Modules POM for bluima project, including common dependencies and repositories

License

License
Categories

Categories

MongoDB Data Databases
GroupId

GroupId

ch.epfl.bbp.nlp
ArtifactId

ArtifactId

bluima_mongodb
Last Version

Last Version

1.0.1
Release Date

Release Date
Type

Type

jar
Description

Description

MongoDb Data Access Layer
Modules POM for bluima project, including common dependencies and repositories
Project Organization

Project Organization

Bluebrain Project

Download bluima_mongodb

Filename Size
bluima_mongodb-1.0.1.pom
bluima_mongodb-1.0.1.jar 27 KB
bluima_mongodb-1.0.1-sources.jar 15 KB
bluima_mongodb-1.0.1-javadoc.jar 82 KB
Browse

How to add to project

<!-- https://jarcasting.com/artifacts/ch.epfl.bbp.nlp/bluima_mongodb/ -->
<dependency>
    <groupId>ch.epfl.bbp.nlp</groupId>
    <artifactId>bluima_mongodb</artifactId>
    <version>1.0.1</version>
</dependency>
// https://jarcasting.com/artifacts/ch.epfl.bbp.nlp/bluima_mongodb/
implementation 'ch.epfl.bbp.nlp:bluima_mongodb:1.0.1'
// https://jarcasting.com/artifacts/ch.epfl.bbp.nlp/bluima_mongodb/
implementation ("ch.epfl.bbp.nlp:bluima_mongodb:1.0.1")
'ch.epfl.bbp.nlp:bluima_mongodb:jar:1.0.1'
<dependency org="ch.epfl.bbp.nlp" name="bluima_mongodb" rev="1.0.1">
  <artifact name="bluima_mongodb" type="jar" />
</dependency>
@Grapes(
@Grab(group='ch.epfl.bbp.nlp', module='bluima_mongodb', version='1.0.1')
)
libraryDependencies += "ch.epfl.bbp.nlp" % "bluima_mongodb" % "1.0.1"
[ch.epfl.bbp.nlp/bluima_mongodb "1.0.1"]

Dependencies

compile (13)

Group / Artifact Type Version
ch.epfl.bbp.nlp : bluima_utils jar 1.0.1
org.mongodb : mongo-java-driver jar 2.8.0
ch.epfl.bbp.nlp : bluima_typesystem jar 1.0.1
ch.epfl.bbp.nlp : blue_commons jar 1.0.1
com.google.guava : guava jar 18.0
org.apache.commons : commons-math3 jar 3.0
org.apache.uima : ruta-core jar 2.1.0
org.apache.uima : RegularExpressionAnnotator jar 2.3.2-BBP
org.apache.uima : SnowballAnnotator jar 2.3.1
org.apache.uima : ConceptMapper jar 2.3.1
org.slf4j : jcl-over-slf4j jar 1.6.5
ch.qos.logback : logback-classic jar 1.0.6
org.slf4j : slf4j-api jar 1.6.5

test (1)

Group / Artifact Type Version
junit : junit jar 4.12

Project Modules

There are no modules declared in this project.

Bluima:: UIMA components at BlueBrain

Build Status

About

Bluima is a natural language processing (NLP) pipeline focusing on the extraction of neuroscientific content and based on the UIMA framework. Bluima builds upon models from biomedical NLP (BioNLP) like specialized tokenizers and lemmatizers. It adds further models and tools specific to neuroscience (e.g. named entity recognizer for neuron or brain region mentions) and provides collection readers for neuroscientific corpora.

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

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 includes all dependencies can be deployed on any computer with a JRE (e.g. cluster).

To release to nexus: mvnt clean deploy -Dgpg.passphrase="si......" -P release

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

ch.epfl.bbp.nlp

The Blue Brain Project

Open Source Software produced and used by the Blue Brain Project

Versions

Version
1.0.1
1.0.0