Building

Python Set-Up

conda create -n word-embeddings-py3.7 python=3.7
conda activate word-embeddings-py3.7

Java Set-Up

export JAVA_HOME=/path/to/jdk1.8.0_131.jdk/Contents/Home

export UIMA_HOME=/path/to/apache-uima-2.9.0
export PATH=$PATH:$UIMA_HOME/bin

export CTAKES_HOME="/path/to/apache-ctakes-4.0.0"

export PIPELINE_ROOT=/path/to/ots-clinical-context-attributes/ml-feature-gen-uima-2.9.0

export UIMA_CLASSPATH=${PIPELINE_ROOT}/target/classes
export UIMA_CLASSPATH=$UIMA_CLASSPATH:${PIPELINE_ROOT}/lib
export UIMA_CLASSPATH=${UIMA_CLASSPATH}:${CTAKES_HOME}/lib:${CTAKES_HOME}/resources
export UIMA_CLASSPATH=${UIMA_CLASSPATH}:${PIPELINE_ROOT}/resources

export UIMA_DATAPATH=${PIPELINE_ROOT}/resources

export UIMA_JVM_OPTS="-Xms128M -Xmx2G"

cd ${PIPELINE_ROOT}/resources/openNlpModels
curl -Lfs --output 'en-token.bin' 'http://opennlp.sourceforge.net/models-1.5/en-token.bin'
curl -Lfs --output 'en-pos-maxent.bin' 'http://opennlp.sourceforge.net/models-1.5/en-pos-maxent.bin'

cd ${PIPELINE_ROOT}/resources/ctakesModels
curl -Lfs --output 'sd-med-model.zip' \
    'https://github.com/apache/ctakes/tree/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/sentdetect/sd-med-model.zip

cd ${PIPELINE_ROOT}
mvn package

Running

A sample scripts is available under:

• ml-feature-gen-uima-2.9.0/train.sh
• ml-feature-gen-uima-2.9.0/test.sh
• ml-feature-gen-uima-2.9.0/scripts/runAttr.sh

cp resources/pipeline.properties.TEMPLATE resources/pipeline.properties

export JAVA_HOME=/path/to/jdk1.8.0_131.jdk/Contents/Home
export VERSION=21.40.3

java -cp \
    resources:target/classes:target/ml-feature-gen-${VERSION}-SNAPSHOT-jar-with-dependencies.jar \
    edu.musc.tbic.uima.FeatureGen -h

java -cp \
    resources:target/classes:target/ml-feature-gen-${VERSION}-SNAPSHOT-jar-with-dependencies.jar \
    edu.musc.tbic.uima.FeatureGen \
    --pipeline-properties pipeline.properties