/**
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
* KIND, either express or implied. See the License for the
* specific language governing permissions and limitations
* under the License.
*/
package org.apache.ctakes.temporal.ae;
import java.io.File;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
import org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor;
import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
import org.apache.ctakes.relationextractor.ae.features.TokenFeaturesExtractor;
import org.apache.ctakes.temporal.ae.feature.CheckSpecialWordRelationExtractor;
import org.apache.ctakes.temporal.ae.feature.DependencyPathFeaturesExtractor;
import org.apache.ctakes.temporal.ae.feature.NearbyVerbTenseRelationExtractor;
import org.apache.ctakes.temporal.ae.feature.NearestFlagFeatureExtractor;
import org.apache.ctakes.temporal.ae.feature.SectionHeaderRelationExtractor;
//import org.apache.ctakes.temporal.ae.feature.TemporalAttributeFeatureExtractor;
//import org.apache.ctakes.temporal.ae.feature.treekernel.EventTimeFlatTreeFeatureExtractor;
//import org.apache.ctakes.temporal.ae.feature.treekernel.EventVerbRelationTreeExtractor;
import org.apache.ctakes.temporal.ae.feature.treekernel.TemporalPETExtractor;
//import org.apache.ctakes.temporal.ae.feature.treekernel.TemporalPathExtractor;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
import org.apache.ctakes.typesystem.type.relation.RelationArgument;
import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textsem.TimeMention;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
import org.apache.uima.resource.ResourceInitializationException;
import org.cleartk.classifier.CleartkAnnotator;
import org.cleartk.classifier.DataWriter;
import org.cleartk.classifier.jar.DefaultDataWriterFactory;
import org.cleartk.classifier.jar.DirectoryDataWriterFactory;
import org.cleartk.classifier.jar.GenericJarClassifierFactory;
import org.uimafit.factory.AnalysisEngineFactory;
import org.uimafit.util.JCasUtil;
import com.google.common.collect.Lists;
public class EventTimeRelationAnnotator extends RelationExtractorAnnotator {
public static AnalysisEngineDescription createDataWriterDescription(
Class<? extends DataWriter<String>> dataWriterClass,
File outputDirectory,
double probabilityOfKeepingANegativeExample) throws ResourceInitializationException {
return AnalysisEngineFactory.createPrimitiveDescription(
EventTimeRelationAnnotator.class,
CleartkAnnotator.PARAM_IS_TRAINING,
true,
DefaultDataWriterFactory.PARAM_DATA_WRITER_CLASS_NAME,
dataWriterClass,
DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
outputDirectory,
RelationExtractorAnnotator.PARAM_PROBABILITY_OF_KEEPING_A_NEGATIVE_EXAMPLE,
// not sure why this has to be cast; something funny going on in uimaFIT maybe?
(float) probabilityOfKeepingANegativeExample);
}
public static AnalysisEngineDescription createAnnotatorDescription(String modelPath)
throws ResourceInitializationException {
return AnalysisEngineFactory.createPrimitiveDescription(
EventTimeRelationAnnotator.class,
CleartkAnnotator.PARAM_IS_TRAINING,
false,
GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
modelPath);
}
/**
* @deprecated use String path instead of File.
* ClearTK will automatically Resolve the String to an InputStream.
* This will allow resources to be read within from a jar as well as File.
*/
public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
throws ResourceInitializationException {
return AnalysisEngineFactory.createPrimitiveDescription(
EventTimeRelationAnnotator.class,
CleartkAnnotator.PARAM_IS_TRAINING,
false,
GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
new File(modelDirectory, "model.jar"));
}
@Override
protected List<RelationFeaturesExtractor> getFeatureExtractors() {
return Lists.newArrayList(
new TokenFeaturesExtractor()
, new PartOfSpeechFeaturesExtractor()
// , new TemporalAttributeFeatureExtractor()
// , new EventTimeFlatTreeFeatureExtractor()
, new TemporalPETExtractor()
// , new TemporalPathExtractor()
// , new EventVerbRelationTreeExtractor()
, new SectionHeaderRelationExtractor()
, new NearbyVerbTenseRelationExtractor()
, new CheckSpecialWordRelationExtractor()
, new NearestFlagFeatureExtractor()
, new DependencyPathFeaturesExtractor()
// , new DependencyFeatureExtractor()
);
}
@Override
protected Class<? extends Annotation> getCoveringClass() {
return Sentence.class;
}
@Override
public List<IdentifiedAnnotationPair> getCandidateRelationArgumentPairs(
JCas jCas,
Annotation sentence) {
List<IdentifiedAnnotationPair> pairs = Lists.newArrayList();
for (EventMention event : JCasUtil.selectCovered(jCas, EventMention.class, sentence)) {
// ignore subclasses like Procedure and Disease/Disorder
if (event.getClass().equals(EventMention.class)) {
for (TimeMention time : JCasUtil.selectCovered(jCas, TimeMention.class, sentence)) {
pairs.add(new IdentifiedAnnotationPair(event, time));
}
}
}
//only use gold pairs:
// for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)) {
// Annotation arg1 = relation.getArg1().getArgument();
// Annotation arg2 = relation.getArg2().getArgument();
// EventMention event = null;
// TimeMention time = null;
// if(arg1 instanceof EventMention){
// event = (EventMention) arg1;
// }else if(arg1 instanceof TimeMention){
// time = (TimeMention) arg1;
// }
// if(arg2 instanceof EventMention){
// event = (EventMention) arg2;
// }else if(arg2 instanceof TimeMention){
// time = (TimeMention) arg2;
// }
// if(event != null && time != null){
// pairs.add(new IdentifiedAnnotationPair(event, time));
// }
// }
return pairs;
}
@Override
protected void createRelation(JCas jCas, IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2, String predictedCategory) {
RelationArgument relArg1 = new RelationArgument(jCas);
relArg1.setArgument(arg1);
relArg1.setRole("Arg1");
relArg1.addToIndexes();
RelationArgument relArg2 = new RelationArgument(jCas);
relArg2.setArgument(arg2);
relArg2.setRole("Arg2");
relArg2.addToIndexes();
TemporalTextRelation relation = new TemporalTextRelation(jCas);
relation.setArg1(relArg1);
relation.setArg2(relArg2);
relation.setCategory(predictedCategory);
relation.addToIndexes();
}
@Override
protected String getRelationCategory(
Map<List<Annotation>, BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) {
BinaryTextRelation relation = relationLookup.get(Arrays.asList(arg1, arg2));
String category = null;
if (relation != null) {
category = relation.getCategory();
} else {
relation = relationLookup.get(Arrays.asList(arg2, arg1));
if (relation != null) {
if(relation.getCategory().equals("OVERLAP")){
category = relation.getCategory();
}else{
category = relation.getCategory() + "-1";
}
}
}
if (category == null && coin.nextDouble() <= this.probabilityOfKeepingANegativeExample) {
category = NO_RELATION_CATEGORY;
}
return category;
}
}