<commit_before>Bluima:: UIMA components at BlueBrain
=====================================

[![Build Status](https://travis-ci.org/BlueBrain/bluima.svg?branch=master)](https://travis-ci.org/BlueBrain/bluima)


### Papers

* Richardet, Renaud, <NAME>, and <NAME>.
  "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"


### 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)<commit_msg>minor improvement to README.md<commit_after>Bluima:: UIMA components at BlueBrain
=====================================

[![Build Status](https://travis-ci.org/BlueBrain/bluima.svg?branch=master)](https://travis-ci.org/BlueBrain/bluima)


### Papers

* Richardet, Renaud, <NAME>, and <NAME>.
  "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)
{'fraction_non_alphanumeric': 0.12841308461746417, 'fraction_numerical': 0.011895106785617735, 'mean_word_length': 4.006765899864682, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 31, 'https://': 4, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 6, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4273852', 'n_tokens_mistral': 1272, 'n_tokens_neox': 1185, 'n_words': 388}