ctakes-commits mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From c...@apache.org
Subject svn commit: r1799256 - in /ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn: ae/JointRelationTokenBasedAnnotator.java eval/EvaluationOfNeuralJointRelations.java
Date Mon, 19 Jun 2017 18:38:39 GMT
Author: clin
Date: Mon Jun 19 18:38:39 2017
New Revision: 1799256

URL: http://svn.apache.org/viewvc?rev=1799256&view=rev
Log:
add a joint model for both EE and ET relations.

Added:
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/JointRelationTokenBasedAnnotator.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EvaluationOfNeuralJointRelations.java

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/JointRelationTokenBasedAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/JointRelationTokenBasedAnnotator.java?rev=1799256&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/JointRelationTokenBasedAnnotator.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/JointRelationTokenBasedAnnotator.java Mon Jun 19 18:38:39 2017
@@ -0,0 +1,536 @@
+package org.apache.ctakes.temporal.nn.ae;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+
+import org.apache.ctakes.core.resource.FileLocator;
+import org.apache.ctakes.core.util.OntologyConceptUtil;
+import org.apache.ctakes.temporal.ae.TemporalRelationExtractorAnnotator.IdentifiedAnnotationPair;
+import org.apache.ctakes.temporal.nn.ae.EventTimeTokenBasedAnnotator.OutputMode;
+import org.apache.ctakes.temporal.nn.data.ArgContextProvider;
+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.syntax.BaseToken;
+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.AnalysisEngineProcessException;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.Instance;
+import org.cleartk.util.ViewUriUtil;
+
+import com.google.common.collect.Lists;
+/**
+ * a joint annotator for annotating both event-time and event-event relations using neural models.
+ * @author chenlin
+ *
+ */
+public class JointRelationTokenBasedAnnotator extends CleartkAnnotator<String> {
+
+	public static final String NO_RELATION_CATEGORY = "none";
+	private static TimeMention coveringTimex;
+	public static Map<String, Integer> timex_idx;
+
+	//output modes:
+	//"TokenSeq": original token sequence
+	//"TokenTimeclass": original token sequence + timeClass tag
+	//"TokenTimeclassPosSeq": original token sequence + timeClass + pos seq tag
+	//"timeclass": <timex_timeClass>
+	//"timeclassPosSeq": <timex_timeClass_POStags>
+	//"posSeq": <timex_jj_nn>
+	//"singleTag": <timex>
+	//"indexTags": <timex_0>
+	public static OutputMode timexMode;
+
+	private BufferedReader reader;
+	private static FileWriter fstream;
+	private static BufferedWriter out;
+
+	public JointRelationTokenBasedAnnotator() {
+		timexMode = OutputMode.TokenSeq; //set the mode here
+		if(timexMode == OutputMode.IndexTags){
+			timex_idx = new HashMap<>();
+		}
+	}
+
+	public Map<String, Integer> TimexIdxReader(InputStream in) throws IOException{
+		reader = new BufferedReader(new InputStreamReader(in));
+		Map<String, Integer> timex_index = new HashMap<>();
+		String line = null;
+		while((line = reader.readLine()) != null){
+			line = line.trim();
+			int sep = line.lastIndexOf("|");
+			String timex = line.substring(0, sep);
+			Integer idx = Integer.parseInt(line.substring(sep+1));
+			timex_index.put(timex, idx);
+		}
+		reader.close();
+		return timex_index;
+	}
+
+	public static void TimexIdxWriter() throws IOException{
+		fstream = new FileWriter("target/eval/thyme/train_and_test/event-event/timex_idx.txt");
+		out = new BufferedWriter(fstream);
+
+		Iterator<Entry<String, Integer>> it = timex_idx.entrySet().iterator();
+		while (it.hasNext()) {
+
+			// the key/value pair is stored here in pairs
+			Map.Entry<String, Integer> pairs = it.next();
+			out.write(pairs.getKey() + "|" + pairs.getValue() + "\n");
+		}
+		out.close();
+	}
+	@Override
+	public void process(JCas jCas) throws AnalysisEngineProcessException {
+		if(timexMode == OutputMode.IndexTags && !this.isTraining()){
+			final String timexIdxMapFile = "target/eval/thyme/train_and_test/event-event/timex_idx.txt";
+			try {
+				timex_idx = TimexIdxReader(FileLocator.getAsStream(timexIdxMapFile));
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
+		}
+
+		//		Map<EventMention, Collection<EventMention>> coveringMap =
+		//				JCasUtil.indexCovering(jCas, EventMention.class, EventMention.class);
+
+		// get all gold relation lookup
+		Map<List<Annotation>, BinaryTextRelation> relationLookup;
+		relationLookup = new HashMap<>();
+		if (this.isTraining()) {
+			relationLookup = new HashMap<>();
+			for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)) {
+				Annotation arg1 = relation.getArg1().getArgument();
+				Annotation arg2 = relation.getArg2().getArgument();
+				// The key is a list of args so we can do bi-directional lookup
+				List<Annotation> key = Arrays.asList(arg1, arg2);
+				if(relationLookup.containsKey(key)){
+					String reln = relationLookup.get(key).getCategory();
+					System.err.println("Error in: "+ ViewUriUtil.getURI(jCas).toString());
+					System.err.println("Error! This attempted relation " + relation.getCategory() + 
+							" already has a relation " + reln + " at this span: " + 
+							arg1.getCoveredText() + " -- " + arg2.getCoveredText());
+				} else {
+					relationLookup.put(key, relation);
+				}
+			}
+		}
+
+		for(Sentence sentence : JCasUtil.select(jCas, Sentence.class)) {
+			// collect all relevant relation arguments from the sentence
+			List<IdentifiedAnnotationPair> candidatePairs = getCandidateRelationArgumentPairs(jCas, sentence);
+
+			// walk through the pairs of annotations
+			for (IdentifiedAnnotationPair pair : candidatePairs) {
+				IdentifiedAnnotation arg1 = pair.getArg1();
+				IdentifiedAnnotation arg2 = pair.getArg2();
+
+				String context;
+				String cuis;
+				if(arg2.getBegin() < arg1.getBegin()) {
+					// ... event2 ... event1 ... scenario
+					if(timexMode == OutputMode.TokenSeq){
+						String arg2tag = "e2";
+						if(arg2 instanceof TimeMention){
+							arg2tag="t";
+						}
+						context = ArgContextProvider.getTokenContext(jCas, sentence, arg2, arg2tag, arg1, "e1", 2); 
+
+					}else{
+						context = getTokenTimexContext(jCas, sentence, arg2, "e2", arg1, "e1", 2);
+					}
+				} else {
+					// ... event1 ... event2 ... scenario
+					if(timexMode == OutputMode.TokenSeq){
+						String arg2tag ="e2";
+						if(arg2 instanceof TimeMention){
+							arg2tag="t";
+						}
+						context = ArgContextProvider.getTokenContext(jCas, sentence, arg1, "e1", arg2, arg2tag, 2);
+					}else{
+						context = getTokenTimexContext(jCas, sentence, arg1, "e1", arg2, "e2", 2);
+					}
+				}
+
+				//get CUIs for two arguments
+				//				Set<String> CUIs = getCuiDtrel(jCas, arg1);
+				//				CUIs.addAll(getCuiDtrel(jCas, arg2));
+				//
+				//				cuis = String.join(" ", CUIs);
+
+				//derive features based on context:
+				List<Feature> feats = new ArrayList<>();
+				String[] tokens = context.split(" ");
+				//				String[] tokens = (context + "|" + cuis).split(" ");
+				for (String token: tokens){
+					feats.add(new Feature(token.toLowerCase()));
+				}
+
+				// during training, feed the features to the data writer
+				if(this.isTraining()) {
+					String category = getRelationCategory(relationLookup, arg1, arg2);
+
+					// drop some portion of negative examples during training
+					// if(category == null && coin.nextDouble() <= 0.5) {
+					//   continue; // skip this negative example
+					// }
+
+					if(category == null) {
+						category = NO_RELATION_CATEGORY;
+					} else{
+						category = category.toLowerCase();
+					}
+					this.dataWriter.write(new Instance<>(category, feats));
+				} else {
+					String predictedCategory = this.classifier.classify(feats);
+
+					// add a relation annotation if a true relation was predicted
+					if (predictedCategory != null && !predictedCategory.equals(NO_RELATION_CATEGORY)) {
+
+						// if we predict an inverted relation, reverse the order of the
+						// arguments
+						//if for event-time relations:
+						if(arg1 instanceof TimeMention || arg2 instanceof TimeMention){
+							if(predictedCategory.endsWith("-1")) {
+								predictedCategory = predictedCategory.substring(0, predictedCategory.length() - 2);
+								if(arg1 instanceof TimeMention){
+									IdentifiedAnnotation temp = arg1;
+									arg1 = arg2;
+									arg2 = temp;
+								}
+							} else {
+								if(arg1 instanceof EventMention){
+									IdentifiedAnnotation temp = arg1;
+									arg1 = arg2;
+									arg2 = temp;
+								}
+							}
+
+							//							createRelation(jCas, arg1, arg2, predictedCategory.toUpperCase(), 0.0);
+						}else{//if for event-event relations:		
+							if (predictedCategory.endsWith("-1")) {
+								predictedCategory = predictedCategory.substring(0, predictedCategory.length() - 2);
+								IdentifiedAnnotation temp = arg1;
+								arg1 = arg2;
+								arg2 = temp;
+							}
+
+							//							createRelation(jCas, arg1, arg2, predictedCategory.toUpperCase(), 0.0);
+						}
+
+						createRelation(jCas, arg1, arg2, predictedCategory.toUpperCase(), 0.0);
+					}
+				}
+			}
+
+		}
+		if(timexMode== OutputMode.IndexTags && !this.isTraining()){//in test time update the hashmap file for each cas
+			try {
+				TimexIdxWriter();
+			} catch (IOException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+		}
+	}
+
+	private static Set<String> getCuiDtrel(JCas jCas, IdentifiedAnnotation arg) {
+		Set<String> CuiDtr = new HashSet<>();
+
+		List<EventMention> events = new ArrayList<>();
+		events.addAll(JCasUtil.selectCovering(jCas, EventMention.class, arg));
+		List<EventMention> realEvents = Lists.newArrayList();
+		String dtrel = null;
+		for( EventMention event : events){
+			if(!event.getClass().equals(EventMention.class)){//find all non-gold events
+				realEvents.add(event);
+			}else{
+				dtrel = event.getEvent().getProperties().getDocTimeRel();
+			}
+		}
+
+		if(dtrel != null && !dtrel.equals("AFTER")){
+			events = realEvents;
+			for(EventMention event : events){
+				for(String cui: OntologyConceptUtil.getCuis( event )){
+					CuiDtr.add(cui);
+				}	
+			}
+		}
+		return CuiDtr;
+	}
+
+	//	private static boolean hasBiggerSpan(EventMention event1, IdentifiedAnnotation arg1) {
+	//		if(event1.getBegin()<=arg1.getBegin() && event1.getEnd()>arg1.getEnd()){
+	//			return true;
+	//		}
+	//		if(event1.getBegin()<arg1.getBegin() && event1.getEnd()>=arg1.getEnd()){
+	//			return true;
+	//		}
+	//		return false;
+	//	}
+
+	public static String getTokenTimexContext(JCas jCas, Sentence sentence, IdentifiedAnnotation arg1, String leftType,
+			IdentifiedAnnotation arg2, String rightType, int contextSize) {
+		List<String> tokens = new ArrayList<>();
+		//select prior context:
+		List<TimeMention> preTimex = JCasUtil.selectCovered(jCas, TimeMention.class, sentence.getBegin(), arg1.getBegin());
+		List<TimeMention> betweenTimex = JCasUtil.selectCovered(jCas, TimeMention.class, arg1.getEnd(), arg2.getBegin());
+		List<TimeMention> afterTimex = JCasUtil.selectCovered(jCas, TimeMention.class, arg2.getEnd(), sentence.getEnd());
+
+		tokens = addTimex2TokenSequence(jCas, tokens, JCasUtil.selectPreceding(jCas, BaseToken.class, arg1, contextSize), preTimex, sentence);
+		//get arg1:
+		tokens.add("<" + leftType + ">");
+		if (arg1 instanceof TimeMention){
+			String timeTag = generateTimeTag(jCas, (TimeMention)arg1);
+			tokens.add(timeTag);
+		}else{
+			tokens.add(arg1.getCoveredText());
+			//          tokens.add(getEventProperty((EventMention)arg1));
+		}
+		tokens.add("</" + leftType + ">");
+		tokens = addTimex2TokenSequence(jCas, tokens, JCasUtil.selectBetween(jCas, BaseToken.class, arg1, arg2), betweenTimex, sentence);
+		//arg2
+		tokens.add("<" + rightType + ">");
+		if (arg2 instanceof TimeMention){
+			String timeTag = generateTimeTag(jCas, (TimeMention)arg2);
+			tokens.add(timeTag);
+		}else{
+			tokens.add(arg2.getCoveredText());
+			//          tokens.add(getEventProperty((EventMention)arg2));
+		}
+		tokens.add("</" + rightType + ">");
+		tokens = addTimex2TokenSequence(jCas, tokens, JCasUtil.selectFollowing(jCas, BaseToken.class, arg2, contextSize), afterTimex, sentence);
+
+
+		return String.join(" ", tokens).replaceAll("[\r\n]", " ");
+	}
+
+	private static String generateTimeTag(JCas jCas, TimeMention timex) {
+		String timeTag = "<timex";
+		if(timexMode == OutputMode.IndexTags){
+			timeTag = timeTag+"_";
+			int idx = 0;
+			String timeWord = timex.getCoveredText().toLowerCase().replaceAll("[\r\n]", " ");
+			if(timex_idx.containsKey(timeWord)){
+				idx = timex_idx.get(timeWord);         
+			}else{
+				idx = timex_idx.size();
+				timex_idx.put(timeWord, idx);
+			}
+			timeTag = timeTag+ idx+">";
+		}else if(timexMode == OutputMode.Timeclass){
+			timeTag = "<timex_"+timex.getTimeClass()+">";
+		}else if(timexMode == OutputMode.TimeclassPosSeq){
+			timeTag = "<timex_"+timex.getTimeClass();
+			for(BaseToken token : JCasUtil.selectCovered(jCas, BaseToken.class, timex)){
+				timeTag = timeTag+"_"+token.getPartOfSpeech();
+			}
+			timeTag = timeTag+">";
+		}else if(timexMode == OutputMode.PosSeq){
+			timeTag = "<timex";
+			for(BaseToken token : JCasUtil.selectCovered(jCas, BaseToken.class, timex)){
+				timeTag = timeTag+"_"+token.getPartOfSpeech();
+			}
+			timeTag = timeTag+">";
+		}else if(timexMode == OutputMode.SingleTag){
+			timeTag = timeTag+">";
+		}else if(timexMode == OutputMode.TokenTimeclass){
+			timeTag = timex.getCoveredText()+" <timex_"+timex.getTimeClass()+">";
+		}else if(timexMode == OutputMode.TokenTimeclassPosSeq){
+			timeTag = timex.getCoveredText()+" <timex_"+timex.getTimeClass();
+			for(BaseToken token : JCasUtil.selectCovered(jCas, BaseToken.class, timex)){
+				timeTag = timeTag+"_"+token.getPartOfSpeech();
+			}
+			timeTag = timeTag+">";
+		}else if(timexMode == OutputMode.NoTag){
+			timeTag="";
+		}
+		return timeTag;
+	}
+
+	private static List<String> addTimex2TokenSequence(JCas jCas, List<String> tokens, List<BaseToken> tokenSequences, List<TimeMention> listOfTimex, Sentence sent) {
+		coveringTimex = null;
+		for (BaseToken baseToken : tokenSequences){
+			if(baseToken.getEnd() <= sent.getEnd() && sent.getBegin() <= baseToken.getBegin()){
+				TimeMention currentTimex = findCoveringTimex(baseToken, listOfTimex);
+				if(currentTimex == null){
+					if(coveringTimex != null ){
+						coveringTimex = null;
+					}
+					tokens.add(baseToken.getCoveredText()); 
+				}else{//current timex is not null
+					if( currentTimex != coveringTimex){
+						String timeTag = generateTimeTag(jCas, currentTimex);
+						tokens.add(timeTag);
+						coveringTimex = currentTimex;
+					}
+				}
+			}
+		}
+		return tokens;
+	}
+
+	private static TimeMention findCoveringTimex(BaseToken baseToken, List<TimeMention> timexs) {
+		for(TimeMention timex : timexs){
+			if(timex.getBegin()<= baseToken.getBegin() && timex.getEnd() >= baseToken.getEnd()){
+				return timex;
+			}
+		}
+		return null;
+	}
+
+
+	/**
+	 * original way of getting label
+	 * @param relationLookup
+	 * @param arg1
+	 * @param arg2
+	 * @return
+	 */
+	protected String getRelationCategory(
+			Map<List<Annotation>, BinaryTextRelation> relationLookup,
+			IdentifiedAnnotation arg1,
+			IdentifiedAnnotation arg2) {
+
+		BinaryTextRelation relation = relationLookup.get(Arrays.asList(arg1, arg2));
+		String category = null;
+		//for event-time relations:
+		if(arg1 instanceof TimeMention || arg2 instanceof TimeMention){
+
+			if (relation != null) {
+				category = relation.getCategory();
+				if(arg1 instanceof EventMention){
+					category = category + "-1";
+				}
+			} else {
+				relation = relationLookup.get(Arrays.asList(arg2, arg1));
+				if (relation != null) {
+					category = relation.getCategory();
+					if(arg2 instanceof EventMention){
+						category = category + "-1";
+					}
+				}
+			}
+		}else{
+
+			//for event-event relations:
+			if (relation != null) {
+				if (arg2.getBegin() < arg1.getBegin()) {
+					category = relation.getCategory() + "-1";
+				} else {
+					category = relation.getCategory();
+				}
+			} else {
+				relation = relationLookup.get(Arrays.asList(arg2, arg1));
+				if (relation != null) {
+					if(arg2.getBegin() < arg1.getBegin()){
+						category = relation.getCategory();
+					} else {
+						category = relation.getCategory() + "-1";
+					}
+				}
+			}
+		}
+
+		return category;
+	}
+
+	//	protected String getRelationCategory2(Map<List<Annotation>, BinaryTextRelation> relationLookup,
+	//			IdentifiedAnnotation arg1,
+	//			IdentifiedAnnotation arg2) {
+	//
+	//		// gold view representation (i.e. only contains relations)
+	//		BinaryTextRelation arg1ContainsArg2 = relationLookup.get(Arrays.asList(arg1, arg2));
+	//		BinaryTextRelation arg2ContainsArg1 = relationLookup.get(Arrays.asList(arg2, arg1));
+	//
+	//		// now translate to position dependent representation (i.e. contains and contains-1)
+	//		if(arg1ContainsArg2 != null) {
+	//			// still need to know whether it's arg1 ... arg2 or arg2 ... arg1
+	//			// because that determines whether it's contains or contains-1
+	//			if(arg1.getBegin() < arg2.getBegin()) {
+	//				return arg1ContainsArg2.getCategory();
+	//			} else {
+	//				return arg1ContainsArg2.getCategory() + "-1";
+	//			}
+	//		} else if(arg2ContainsArg1 != null) {
+	//			if(arg1.getBegin() < arg2.getBegin()) {
+	//				return arg2ContainsArg1.getCategory() + "-1";
+	//			} else {
+	//				return arg2ContainsArg1.getCategory();
+	//			}
+	//		} else {
+	//			return null;      
+	//		}
+	//	}
+
+	protected void createRelation(JCas jCas, IdentifiedAnnotation arg1,
+			IdentifiedAnnotation arg2, String predictedCategory, double confidence) {
+		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.setConfidence(confidence);
+		relation.addToIndexes();
+	}
+
+	private static List<IdentifiedAnnotationPair> getCandidateRelationArgumentPairs(JCas jCas, Sentence sentence) {
+
+		List<IdentifiedAnnotationPair> pairs = Lists.newArrayList();
+		List<EventMention> events = new ArrayList<>(JCasUtil.selectCovered(jCas, EventMention.class, sentence));
+		// filter events
+		List<EventMention> realEvents = Lists.newArrayList();
+		for( EventMention event : events){
+			if(event.getClass().equals(EventMention.class)){
+				realEvents.add(event);
+			}
+		}
+		events = realEvents;
+
+		int eventNum = events.size();
+		for (int i = 0; i < eventNum-1; i++) {
+			for(int j = i+1; j < eventNum; j++) {
+				EventMention eventA = events.get(i);
+				EventMention eventB = events.get(j);
+				pairs.add(new IdentifiedAnnotationPair(eventA, eventB));
+			}
+		}
+
+		for (EventMention event: events){
+			for (TimeMention time : JCasUtil.selectCovered(jCas, TimeMention.class, sentence)) {
+				pairs.add(new IdentifiedAnnotationPair(event, time));
+			}
+		}
+
+		return pairs;
+	}
+}

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EvaluationOfNeuralJointRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EvaluationOfNeuralJointRelations.java?rev=1799256&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EvaluationOfNeuralJointRelations.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EvaluationOfNeuralJointRelations.java Mon Jun 19 18:38:39 2017
@@ -0,0 +1,1065 @@
+/**
+ * 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.nn.eval;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.net.URI;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Deque;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments;
+import org.apache.ctakes.temporal.ae.DocTimeRelAnnotator;
+import org.apache.ctakes.temporal.ae.EventEventRelationAnnotator;
+import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings;
+import org.apache.ctakes.temporal.keras.KerasStringOutcomeDataWriter;
+import org.apache.ctakes.temporal.keras.ScriptStringFeatureDataWriter;
+import org.apache.ctakes.temporal.nn.ae.JointRelationTokenBasedAnnotator;
+import org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase;
+import org.apache.ctakes.temporal.eval.Evaluation_ImplBase;
+import org.apache.ctakes.temporal.eval.I2B2Data;
+import org.apache.ctakes.temporal.eval.THYMEData;
+//import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteI2B2XML;
+//import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMLFormat;
+import org.apache.ctakes.temporal.utils.AnnotationIdCollection;
+import org.apache.ctakes.temporal.utils.TLinkTypeArray2;
+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.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.CASException;
+import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.apache.uima.util.FileUtils;
+import org.cleartk.eval.AnnotationStatistics;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.jar.DefaultDataWriterFactory;
+import org.cleartk.ml.jar.DirectoryDataWriterFactory;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
+import org.cleartk.ml.jar.JarClassifierBuilder;
+import org.cleartk.ml.liblinear.LibLinearStringOutcomeDataWriter;
+//import org.cleartk.ml.libsvm.tk.TkLibSvmStringOutcomeDataWriter;
+//import org.cleartk.ml.libsvm.LIBSVMStringOutcomeDataWriter;
+//import org.cleartk.ml.tksvmlight.TKSVMlightStringOutcomeDataWriter;
+import org.cleartk.ml.tksvmlight.model.CompositeKernel.ComboOperator;
+import org.cleartk.util.ViewUriUtil;
+
+import com.google.common.base.Function;
+import com.google.common.collect.HashMultimap;
+import com.google.common.collect.Lists;
+import com.google.common.collect.Maps;
+import com.google.common.collect.Multimap;
+import com.google.common.collect.Sets;
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+
+/**
+ * This is the evaluation code to evaluate a joint neural model for predicting temporal relations, including event-time and event-event relations.
+ * @author chenlin
+ *
+ */
+public class EvaluationOfNeuralJointRelations extends
+EvaluationOfTemporalRelations_ImplBase{
+	static interface TempRelOptions extends Evaluation_ImplBase.Options{
+		@Option
+		public boolean getPrintFormattedRelations();
+
+		@Option
+		public boolean getBaseline();
+
+		@Option
+		public boolean getClosure();
+
+		@Option
+		public boolean getUseTmp();
+
+		@Option
+		public boolean getUseGoldAttributes();
+
+		@Option
+		public boolean getSkipTrain();
+
+		@Option
+		public boolean getWriteProbabilities();
+
+		@Option
+		public boolean getTestOnTrain();
+
+		@Option
+		public boolean getSkipWrite();
+	}
+
+	//  protected static boolean DEFAULT_BOTH_DIRECTIONS = false;
+	//  protected static float DEFAULT_DOWNSAMPLE = 1.0f;
+	//  private static double DEFAULT_SVM_C = 1.0;
+	//  private static double DEFAULT_SVM_G = 1.0;
+	//  private static double DEFAULT_TK = 0.5;
+	//  private static double DEFAULT_LAMBDA = 0.5;
+
+	//  defaultParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS, DEFAULT_DOWNSAMPLE, "tk",
+	//  		  DEFAULT_SVM_C, DEFAULT_SVM_G, "polynomial", ComboOperator.SUM, DEFAULT_TK, DEFAULT_LAMBDA);
+	protected static ParameterSettings flatParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS, DEFAULT_DOWNSAMPLE, "linear",
+			10.0, 1.0, "linear", ComboOperator.VECTOR_ONLY, DEFAULT_TK, DEFAULT_LAMBDA);
+	protected static ParameterSettings allBagsParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS, DEFAULT_DOWNSAMPLE, "tk", 
+			100.0, 0.1, "radial basis function", ComboOperator.SUM, 0.5, 0.5);
+	protected static ParameterSettings allParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS, DEFAULT_DOWNSAMPLE, "tk",
+			10.0, 1.0, "polynomial", ComboOperator.SUM, 0.1, 0.5);  // (0.3, 0.4 for tklibsvm)
+	protected static ParameterSettings ftParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS, DEFAULT_DOWNSAMPLE, "tk", 
+			1.0, 0.1, "radial basis function", ComboOperator.SUM, 0.5, 0.5);
+	private static Boolean recallModeEvaluation = true;
+
+	public static void main(String[] args) throws Exception {
+		TempRelOptions options = CliFactory.parseArguments(TempRelOptions.class, args);
+		List<Integer> trainItems = null;
+		List<Integer> devItems = null;
+		List<Integer> testItems = null;
+
+		List<Integer> patientSets = options.getPatients().getList();
+		if(options.getXMLFormat() == XMLFormat.I2B2){
+			trainItems = I2B2Data.getTrainPatientSets(options.getXMLDirectory());
+			devItems = I2B2Data.getDevPatientSets(options.getXMLDirectory());
+			testItems = I2B2Data.getTestPatientSets(options.getXMLDirectory());
+		}else{
+			trainItems = THYMEData.getPatientSets(patientSets, options.getTrainRemainders().getList());
+			devItems = THYMEData.getPatientSets(patientSets, options.getDevRemainders().getList());
+			testItems = THYMEData.getPatientSets(patientSets, options.getTestRemainders().getList());
+		}
+		ParameterSettings params = allParams;
+
+		//    possibleParams.add(defaultParams);
+
+		//    for(ParameterSettings params : possibleParams){
+		try{
+			File workingDir = new File("/Volumes/chip-nlp/Public/THYME/eval/thyme/");//"target/eval/thyme/");
+			if(!workingDir.exists()) workingDir.mkdirs();
+			if(options.getUseTmp()){
+				File tempModelDir = File.createTempFile("temporal", null, workingDir);
+				tempModelDir.delete();
+				tempModelDir.mkdir();
+				workingDir = tempModelDir;
+			}
+			EvaluationOfNeuralJointRelations evaluation = new EvaluationOfNeuralJointRelations(
+					workingDir,
+					options.getRawTextDirectory(),
+					options.getXMLDirectory(),
+					options.getXMLFormat(),
+					options.getSubcorpus(),
+					options.getXMIDirectory(),
+					options.getTreebankDirectory(),
+					options.getClosure(),
+					options.getPrintErrors(),
+					options.getPrintFormattedRelations(),
+					options.getBaseline(),
+					options.getUseGoldAttributes(),
+					options.getKernelParams(),
+					params);
+			//			evaluation.prepareXMIsFor(patientSets);
+			if(options.getI2B2Output()!=null) evaluation.setI2B2Output(options.getI2B2Output() + "/temporal-relations/joint");
+			if(options.getAnaforaOutput()!=null) evaluation.anaforaOutput = options.getAnaforaOutput();
+
+			List<Integer> training = trainItems;
+			List<Integer> testing = null;
+			if(options.getTest()){
+				training.addAll(devItems);
+				testing = testItems;
+			}else{
+				testing = devItems;
+			}
+			//do closure on system, but not on gold, to calculate recall
+			evaluation.skipTrain = options.getSkipTrain();
+			evaluation.skipWrite = options.getSkipWrite();
+			if(evaluation.skipTrain && options.getTest()){
+				evaluation.prepareXMIsFor(testing);
+			}else{
+				evaluation.prepareXMIsFor(patientSets);
+			}
+
+			//sort list:
+			Collections.sort(training);
+			Collections.sort(testing);
+
+			//test or train or test
+			evaluation.testOnTrain = options.getTestOnTrain();
+			if(evaluation.testOnTrain){
+				params.stats = evaluation.trainAndTest(training, training);
+			}else{//test on testing set
+				params.stats = evaluation.trainAndTest(training, testing);//training
+			}
+			System.err.println(params.stats);
+
+			if(options.getUseTmp()){
+				// won't work because it's not empty. should we be concerned with this or is it responsibility of 
+				// person invoking the tmp flag?
+				FileUtils.deleteRecursive(workingDir);
+			}
+		}catch(ResourceInitializationException e){
+			System.err.println("Error with parameter settings: " + params);
+			e.printStackTrace();
+		}
+	}
+
+	//  private ParameterSettings params;
+	protected boolean useClosure;
+	protected boolean useGoldAttributes;
+	protected boolean skipTrain=false;
+	public boolean skipWrite = false;
+	//  protected boolean printRelations = false;
+	protected boolean testOnTrain=false;
+
+	public EvaluationOfNeuralJointRelations(
+			File baseDirectory,
+			File rawTextDirectory,
+			File xmlDirectory,
+			XMLFormat xmlFormat,
+			Subcorpus subcorpus,
+			File xmiDirectory,
+			File treebankDirectory,
+			boolean useClosure,
+			boolean printErrors,
+			boolean printRelations,
+			boolean baseline,
+			boolean useGoldAttributes,
+			String kernelParams,
+			ParameterSettings params){
+		super(
+				baseDirectory,
+				rawTextDirectory,
+				xmlDirectory,
+				xmlFormat,
+				subcorpus,
+				xmiDirectory,
+				treebankDirectory,
+				printErrors,
+				printRelations,
+				params);
+		this.params = params;
+		this.useClosure = useClosure;
+		this.printErrors = printErrors;
+		this.printRelations = printRelations;
+		this.useGoldAttributes = useGoldAttributes;
+		this.kernelParams = kernelParams == null ? null : kernelParams.split(" ");
+	}
+
+	//  public EvaluationOfTemporalRelations(File baseDirectory, File rawTextDirectory,
+	//      File knowtatorXMLDirectory, File xmiDirectory) {
+	//
+	//    super(baseDirectory, rawTextDirectory, knowtatorXMLDirectory, xmiDirectory, null);
+	//    this.params = defaultParams;
+	//    this.printErrors = false;
+	//  }
+
+	@Override
+	protected void train(CollectionReader collectionReader, File directory) throws Exception {
+		//	  if(this.baseline) return;
+		if(this.skipTrain) return;
+		if(!this.skipWrite){
+			AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
+			aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class, TimeMention.class, BinaryTextRelation.class));
+			aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveCrossSentenceRelations.class));
+			if(!this.useGoldAttributes){
+				aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveGoldAttributes.class));
+			}
+			if (this.useClosure) {
+				aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(AddClosure.class));
+			}
+			aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveNonContainsRelations.class));
+			//		aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(AddFlippedOverlap.class));//add flipped overlap instances to training data
+
+			//		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveNonTLINKRelations.class));//remove non tlink relations, such as alinks
+
+			//		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(Overlap2Contains.class));
+
+			//		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(PreserveEventEventRelations.class));
+			//		aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveNonUMLSEvents.class));
+
+			//add unlabeled nearby system events as potential links: 
+			//		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(AddEEPotentialRelations.class));
+			//		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(AddPotentialRelations.class));	
+
+			//		aggregateBuilder.add(
+			//				AnalysisEngineFactory.createEngineDescription(EventEventTokenBasedAnnotator.class,//EventEventTokenBasedAnnotator.class,EventEventPathsBasedAnnotator.class, EventEventTokenAndPosBasedAnnotator, EventEventPathsBasedAnnotator
+			//						CleartkAnnotator.PARAM_IS_TRAINING,
+			//						true,
+			//						DefaultDataWriterFactory.PARAM_DATA_WRITER_CLASS_NAME,
+			//						KerasStringOutcomeDataWriter.class,
+			//						DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
+			//						new File(directory,"event-event"),
+			//						ScriptStringFeatureDataWriter.PARAM_SCRIPT_DIR,
+			//						"scripts/nn/"
+			//						) );
+
+			aggregateBuilder.add(
+					AnalysisEngineFactory.createEngineDescription(JointRelationTokenBasedAnnotator.class,//EventTimeTokenAndPathBasedAnnotator.class,//
+							CleartkAnnotator.PARAM_IS_TRAINING,
+							true,
+							DefaultDataWriterFactory.PARAM_DATA_WRITER_CLASS_NAME,
+							KerasStringOutcomeDataWriter.class,
+							DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
+							new File(directory,"joint"),
+							ScriptStringFeatureDataWriter.PARAM_SCRIPT_DIR,
+							"scripts/nn-joint/"
+							) );
+
+			SimplePipeline.runPipeline(collectionReader, aggregateBuilder.createAggregate());
+		}
+		//    HideOutput hider = new HideOutput();
+		JarClassifierBuilder.trainAndPackage(new File(directory,"joint"));
+
+	}
+
+	@Override
+	protected AnnotationStatistics<String> test(CollectionReader collectionReader, File directory)
+			throws Exception {
+		this.useClosure=false;
+		AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
+
+		aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class, TimeMention.class));
+
+		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(
+				RemoveCrossSentenceRelations.class,
+				RemoveCrossSentenceRelations.PARAM_SENTENCE_VIEW,
+				CAS.NAME_DEFAULT_SOFA,
+				RemoveCrossSentenceRelations.PARAM_RELATION_VIEW,
+				GOLD_VIEW_NAME));
+
+		if (!recallModeEvaluation && this.useClosure) { //closure for gold
+			aggregateBuilder.add(
+					AnalysisEngineFactory.createEngineDescription(AddClosure.class),//AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveContainsRelations.class),
+					CAS.NAME_DEFAULT_SOFA,
+					GOLD_VIEW_NAME);
+		}
+
+		//keep event event tlinks, remove the other relations
+		//		aggregateBuilder.add(
+		//				AnalysisEngineFactory.createEngineDescription(PreserveEventEventRelations.class),
+		//				CAS.NAME_DEFAULT_SOFA,
+		//				GOLD_VIEW_NAME);
+
+		//remove non-tlink relations, such as alinks
+		//		aggregateBuilder.add(
+		//				AnalysisEngineFactory.createEngineDescription(RemoveNonTLINKRelations.class),
+		//				CAS.NAME_DEFAULT_SOFA,
+		//				GOLD_VIEW_NAME);
+
+		//		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveNonUMLSEvents.class));
+
+
+
+		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveNonContainsRelations.class),
+				CAS.NAME_DEFAULT_SOFA,
+				GOLD_VIEW_NAME);
+
+		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveRelations.class));
+		AnalysisEngineDescription aed = null;
+		//		aed=AnalysisEngineFactory.createEngineDescription(EventEventTokenBasedAnnotator.class,//EventEventTokenBasedAnnotator.class,EventEventPathsBasedAnnotator.class, EventEventTokenAndPosBasedAnnotator
+		//				CleartkAnnotator.PARAM_IS_TRAINING,
+		//				false,
+		//				GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+		//				new File(new File(directory,"event-event"), "model.jar").getPath());
+		//		aed = EventEventRelationAnnotator.createAnnotatorDescription((new File(directory,"event-event/model.jar")).getAbsolutePath());
+		//		aggregateBuilder.add(aed);
+		aed = AnalysisEngineFactory.createEngineDescription(JointRelationTokenBasedAnnotator.class,
+				CleartkAnnotator.PARAM_IS_TRAINING,
+				false,
+				GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+				new File(new File(directory,"joint"), "model.jar").getPath());
+		aggregateBuilder.add(aed);
+
+//		aed = DocTimeRelAnnotator.createAnnotatorDescription(new File("target/eval/event-properties/train_and_test/docTimeRel/model.jar").getAbsolutePath());		
+//		aggregateBuilder.add(aed);
+
+		//		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(CrossSentenceTemporalRelationAnnotator.class));
+		//		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(WithinSentenceBeforeRelationAnnotator.class));
+
+		if(this.anaforaOutput != null){
+			aed = AnalysisEngineFactory.createEngineDescription(WriteAnaforaXML.class, WriteAnaforaXML.PARAM_OUTPUT_DIR, this.anaforaOutput);
+			aggregateBuilder.add(aed, "TimexView", CAS.NAME_DEFAULT_SOFA);
+		}
+
+		File outf = null;
+		if (recallModeEvaluation && this.useClosure) {//add closure for system output
+			aggregateBuilder.add(
+					AnalysisEngineFactory.createEngineDescription(AddClosure.class),//AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveContainsRelations.class),
+					GOLD_VIEW_NAME,
+					CAS.NAME_DEFAULT_SOFA
+					);
+			outf =  new File("target/eval/thyme/SystemError_eventEvent_recall_test.txt");
+		}else if (!recallModeEvaluation && this.useClosure){
+			outf =  new File("target/eval/thyme/SystemError_eventEvent_precision_test.txt");
+		}else{
+			outf =  new File("target/eval/thyme/SystemError_eventEvent_plain_test.txt");
+		}
+
+		PrintWriter outDrop =null;
+//		outDrop = new PrintWriter(new BufferedWriter(new FileWriter(outf, false)));
+
+		Function<BinaryTextRelation, ?> getSpan = new Function<BinaryTextRelation, HashableArguments>() {
+			public HashableArguments apply(BinaryTextRelation relation) {
+				return new HashableArguments(relation);
+			}
+		};
+		Function<BinaryTextRelation, String> getOutcome = AnnotationStatistics.annotationToFeatureValue("category");
+
+		AnnotationStatistics<String> stats = new AnnotationStatistics<>();
+		JCasIterator jcasIter =new JCasIterator(collectionReader, aggregateBuilder.createAggregate());
+		JCas jCas = null;
+		while(jcasIter.hasNext()) {
+			jCas = jcasIter.next();
+			JCas goldView = jCas.getView(GOLD_VIEW_NAME);
+			JCas systemView = jCas.getView(CAS.NAME_DEFAULT_SOFA);
+			Collection<BinaryTextRelation> goldRelations = JCasUtil.select(
+					goldView,
+					BinaryTextRelation.class);
+			Collection<BinaryTextRelation> systemRelations = JCasUtil.select(
+					systemView,
+					BinaryTextRelation.class);
+
+			stats.add(goldRelations, systemRelations, getSpan, getOutcome);
+			if(this.printRelations){
+				URI uri = ViewUriUtil.getURI(jCas);
+				String[] path = uri.getPath().split("/");
+				printRelationAnnotations(path[path.length - 1], systemRelations);
+			}
+			if(this.printErrors){
+				Map<HashableArguments, BinaryTextRelation> goldMap = Maps.newHashMap();
+				for (BinaryTextRelation relation : goldRelations) {
+					goldMap.put(new HashableArguments(relation), relation);
+				}
+				Map<HashableArguments, BinaryTextRelation> systemMap = Maps.newHashMap();
+				for (BinaryTextRelation relation : systemRelations) {
+					systemMap.put(new HashableArguments(relation), relation);
+				}
+				Set<HashableArguments> all = Sets.union(goldMap.keySet(), systemMap.keySet());
+				List<HashableArguments> sorted = Lists.newArrayList(all);
+				Collections.sort(sorted);
+				outDrop.println("Doc id: " + ViewUriUtil.getURI(jCas).toString());
+				for (HashableArguments key : sorted) {
+					BinaryTextRelation goldRelation = goldMap.get(key);
+					BinaryTextRelation systemRelation = systemMap.get(key);
+					if (goldRelation == null) {
+						outDrop.println("System added: " + formatRelation(systemRelation));
+					} else if (systemRelation == null) {
+						outDrop.println("System dropped: " + formatRelation(goldRelation));
+					} else if (!systemRelation.getCategory().equals(goldRelation.getCategory())) {
+						String label = systemRelation.getCategory();
+						outDrop.printf("System labeled %s for %s\n", label, formatRelation(goldRelation));
+					} else{
+						outDrop.println("Nailed it! " + formatRelation(systemRelation));
+					}
+				}
+			}
+		}
+//		outDrop.close();
+		return stats;
+	}
+
+	public static class RemoveNonUMLSEvents extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
+		public static final String PARAM_GOLD_VIEW = "GoldView";
+
+		@ConfigurationParameter(name = PARAM_GOLD_VIEW,mandatory=false)
+		private String goldViewName = CAS.NAME_DEFAULT_SOFA;
+
+		@Override
+		public void process(JCas jCas) throws AnalysisEngineProcessException {
+			JCas sysView;
+			JCas goldView;
+			try {
+				sysView = jCas.getView(CAS.NAME_DEFAULT_SOFA);
+				goldView = jCas.getView(PARAM_GOLD_VIEW);
+			} catch (CASException e) {
+				throw new AnalysisEngineProcessException(e);
+			}
+			for(TemporalTextRelation relation : Lists.newArrayList(JCasUtil.select(goldView, TemporalTextRelation.class))){
+				Annotation arg1 = relation.getArg1().getArgument();
+				Annotation arg2 = relation.getArg2().getArgument();
+				boolean arg1Valid = false;
+				boolean arg2Valid = false;
+				for (EventMention event : JCasUtil.selectCovered(sysView, EventMention.class, arg1)){
+					if(!event.getClass().equals(EventMention.class)){
+						arg1Valid = true;
+						break;
+					}
+				}
+				for (EventMention event : JCasUtil.selectCovered(sysView, EventMention.class, arg2)){
+					if(!event.getClass().equals(EventMention.class)){
+						arg2Valid = true;
+						break;
+					}
+				}
+				if(arg1Valid && arg2Valid){
+					// these are the kind we keep.
+					continue;
+				}
+				arg1.removeFromIndexes();
+				arg2.removeFromIndexes();
+				relation.removeFromIndexes();
+			}
+		}   
+	}
+
+
+	static void createRelation(JCas jCas, Annotation arg1,
+			Annotation arg2, String category) {
+		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(category);
+		relation.addToIndexes();
+
+	}
+
+
+	/*
+  private static String formatRelation(BinaryTextRelation relation) {
+	  IdentifiedAnnotation arg1 = (IdentifiedAnnotation)relation.getArg1().getArgument();
+	  IdentifiedAnnotation arg2 = (IdentifiedAnnotation)relation.getArg2().getArgument();
+	  String text = arg1.getCAS().getDocumentText();
+	  int begin = Math.min(arg1.getBegin(), arg2.getBegin());
+	  int end = Math.max(arg1.getBegin(), arg2.getBegin());
+	  begin = Math.max(0, begin - 50);
+	  end = Math.min(text.length(), end + 50);
+	  return String.format(
+			  "%s(%s(type=%d), %s(type=%d)) in ...%s...",
+			  relation.getCategory(),
+			  arg1.getCoveredText(),
+			  arg1.getTypeID(),
+			  arg2.getCoveredText(),
+			  arg2.getTypeID(),
+			  text.substring(begin, end).replaceAll("[\r\n]", " "));
+  }
+
+  private static void printRelationAnnotations(String fileName, Collection<BinaryTextRelation> relations) {
+
+	  for(BinaryTextRelation binaryTextRelation : relations) {
+
+		  Annotation arg1 = binaryTextRelation.getArg1().getArgument();
+		  Annotation arg2 = binaryTextRelation.getArg2().getArgument();
+
+		  String arg1Type = arg1.getClass().getSimpleName();
+		  String arg2Type = arg2.getClass().getSimpleName();
+
+		  int arg1Begin = arg1.getBegin();
+		  int arg1End = arg1.getEnd();
+		  int arg2Begin = arg2.getBegin();
+		  int arg2End = arg2.getEnd();
+
+		  String category = binaryTextRelation.getCategory();
+
+		  System.out.format("%s\t%s\t%s\t%d\t%d\t%s\t%d\t%d\n", 
+				  fileName, category, arg1Type, arg1Begin, arg1End, arg2Type, arg2Begin, arg2End);
+	  }
+  }
+	 */
+
+
+
+	//	@SuppressWarnings("unchecked")
+	//	private static <SPAN> Collection<BinaryTextRelation> getDuplicateRelations(
+	//			Collection<BinaryTextRelation> goldRelations,
+	//			Function<BinaryTextRelation, ?> getSpan) {
+	//		Set<BinaryTextRelation> duplicateRelations = Sets.newHashSet();
+	//		//build a multimap that map gold span to gold relation
+	//		Multimap<SPAN, BinaryTextRelation> spanToRelation = HashMultimap.create();
+	//		for (BinaryTextRelation relation : goldRelations) {
+	//			spanToRelation.put((SPAN) getSpan.apply(relation), relation);			
+	//		}
+	//		for (SPAN span: spanToRelation.keySet()){
+	//			Collection<BinaryTextRelation> relations = spanToRelation.get(span);
+	//			if(relations.size()>1){//if same span maps to multiple relations
+	//				duplicateRelations.addAll(relations);
+	//			}
+	//		}
+	//		return duplicateRelations;
+	//	}
+
+	//	private static Collection<BinaryTextRelation> removeNonGoldRelations(
+	//			Collection<BinaryTextRelation> systemRelations, Collection<BinaryTextRelation> goldRelations) {
+	//		//remove non-gold pairs from system relations:
+	//		Set<BinaryTextRelation> goodSys = Sets.newHashSet();
+	//
+	//		for(BinaryTextRelation sysrel : systemRelations){
+	//			Annotation sysArg1 = sysrel.getArg1().getArgument();
+	//			Annotation sysArg2 = sysrel.getArg2().getArgument();
+	//			for(BinaryTextRelation goldrel : goldRelations){
+	//				Annotation goldArg1 = goldrel.getArg1().getArgument();
+	//				Annotation goldArg2 = goldrel.getArg2().getArgument();
+	//				if(matchSpan(sysArg1, goldArg1) && matchSpan(sysArg2, goldArg2)){
+	//					goodSys.add(sysrel);
+	//					continue;
+	//				}else if (matchSpan(sysArg2, goldArg1) && matchSpan(sysArg1, goldArg2)){//the order of system pair was flipped 
+	//					if(sysrel.getCategory().equals("OVERLAP")){ //if the relation is overlap, and the arg order was flipped, then change back the order
+	//						RelationArgument tempArg = (RelationArgument) sysrel.getArg1().clone();
+	//						sysrel.setArg1((RelationArgument) sysrel.getArg2().clone());
+	//						sysrel.setArg2(tempArg);
+	//					}//for other types of relation, still maintain the type.
+	//					goodSys.add(sysrel);
+	//					continue;
+	//				}
+	//			}
+	//		}
+	//
+	//		return goodSys;
+	//	}
+
+
+
+
+	public static class RemoveNonTLINKRelations extends JCasAnnotator_ImplBase {
+		@Override
+		public void process(JCas jCas) throws AnalysisEngineProcessException {
+			for (BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(
+					jCas,
+					BinaryTextRelation.class))) {
+				if (!(relation instanceof TemporalTextRelation)) {
+					relation.getArg1().removeFromIndexes();
+					relation.getArg2().removeFromIndexes();
+					relation.removeFromIndexes();
+				}
+			}
+		}
+	}
+
+	public static class RemoveCrossSentenceRelations extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
+
+		public static final String PARAM_SENTENCE_VIEW = "SentenceView";
+
+		@ConfigurationParameter(name = PARAM_SENTENCE_VIEW,mandatory=false)
+		private String sentenceViewName = CAS.NAME_DEFAULT_SOFA;
+
+		public static final String PARAM_RELATION_VIEW = "RelationView";
+
+		@ConfigurationParameter(name = PARAM_RELATION_VIEW,mandatory=false)
+		private String relationViewName = CAS.NAME_DEFAULT_SOFA;
+
+		@Override
+		public void process(JCas jCas) throws AnalysisEngineProcessException {
+			JCas sentenceView, relationView;
+			try {
+				sentenceView = jCas.getView(this.sentenceViewName);
+				relationView = jCas.getView(this.relationViewName);
+			} catch (CASException e) {
+				throw new AnalysisEngineProcessException(e);
+			}
+
+			// map events and times to the sentences that contain them
+			Map<IdentifiedAnnotation, Integer> sentenceIndex = Maps.newHashMap();
+			int index = -1;
+			for (Sentence sentence : JCasUtil.select(sentenceView, Sentence.class)) {
+				++index;
+				for (EventMention event : JCasUtil.selectCovered(relationView, EventMention.class, sentence)) {
+					sentenceIndex.put(event, index);
+				}
+				for (TimeMention time : JCasUtil.selectCovered(relationView, TimeMention.class, sentence)) {
+					sentenceIndex.put(time, index);
+				}
+			}
+
+			// remove any relations that are in different sentences.
+			for (BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(
+					relationView,
+					BinaryTextRelation.class))) {
+				Integer sent1 = sentenceIndex.get(relation.getArg1().getArgument());
+				Integer sent2 = sentenceIndex.get(relation.getArg2().getArgument());
+				if (sent1 == null || sent2 == null || !sent1.equals(sent2)) {
+					relation.getArg1().removeFromIndexes();
+					relation.getArg2().removeFromIndexes();
+					relation.removeFromIndexes();
+				}
+			}
+		}
+	}
+
+
+	public static class RemoveRelations extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
+		@Override
+		public void process(JCas jCas) throws AnalysisEngineProcessException {
+			for (BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(
+					jCas,
+					BinaryTextRelation.class))) {
+				relation.getArg1().removeFromIndexes();
+				relation.getArg2().removeFromIndexes();
+				relation.removeFromIndexes();
+			}
+		}
+	}
+
+
+	public static class AddTransitiveContainsRelations extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
+
+		@Override
+		public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+			// collect many-to-many mappings of containment relations 
+			Multimap<Annotation, Annotation> isContainedIn = HashMultimap.create();
+			Multimap<Annotation, Annotation> contains = HashMultimap.create();
+			Set<BinaryTextRelation> containsRelations = Sets.newHashSet();
+			for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)) {
+				if (relation.getCategory().equals("CONTAINS")) {
+					containsRelations.add(relation);
+					Annotation arg1 = relation.getArg1().getArgument();
+					Annotation arg2 = relation.getArg2().getArgument();
+					contains.put(arg1, arg2);
+					isContainedIn.put(arg2, arg1);
+				}
+			}
+
+			// look for X -> Y -> Z containment chains and add X -> Z relations
+			Deque<Annotation> todo = new ArrayDeque<>(isContainedIn.keySet());
+			while (!todo.isEmpty()) {
+				Annotation next = todo.removeFirst();
+				for (Annotation parent : Lists.newArrayList(isContainedIn.get(next))) {
+					for (Annotation grandParent : Lists.newArrayList(isContainedIn.get(parent))) {
+						if (!isContainedIn.containsEntry(next, grandParent)) {
+							isContainedIn.put(next, grandParent);
+							contains.put(grandParent, next);
+
+							// once X -> Z has been added, we need to re-do all W where W -> X
+							for (Annotation child : contains.get(next)) {
+								todo.add(child);
+							}
+						}
+					}
+				}
+			}
+
+			// remove old relations
+			for (BinaryTextRelation relation : containsRelations) {
+				relation.getArg1().removeFromIndexes();
+				relation.getArg2().removeFromIndexes();
+				relation.removeFromIndexes();
+			}
+
+			// add new, transitive relations
+			for (Annotation contained : isContainedIn.keySet()) {
+				for (Annotation container : isContainedIn.get(contained)) {
+					RelationArgument arg1 = new RelationArgument(jCas);
+					arg1.setArgument(container);
+					RelationArgument arg2 = new RelationArgument(jCas);
+					arg2.setArgument(contained);
+					BinaryTextRelation relation = new BinaryTextRelation(jCas);
+					relation.setArg1(arg1);
+					relation.setArg2(arg2);
+					relation.setCategory("CONTAINS");
+					arg1.addToIndexes();
+					arg2.addToIndexes();
+					relation.addToIndexes();
+				}
+			}
+		}
+
+	}
+
+	public static class AddContain2Overlap extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
+
+		@Override
+		public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+			Set<BinaryTextRelation> containsRelations = Sets.newHashSet();
+			for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)) {
+				if (relation.getCategory().equals("CONTAINS")) {
+					containsRelations.add(relation);
+				}
+			}
+
+			for (BinaryTextRelation relation : containsRelations) {
+				RelationArgument arg1 = (RelationArgument) relation.getArg1().clone();
+				RelationArgument arg2 = (RelationArgument) relation.getArg2().clone();
+				BinaryTextRelation newrelation = new BinaryTextRelation(jCas);
+				newrelation.setArg1(arg1);
+				newrelation.setArg2(arg2);
+				newrelation.setCategory("OVERLAP");
+				arg1.addToIndexes();
+				arg2.addToIndexes();
+				newrelation.addToIndexes();
+			}
+		}
+	}
+
+	public static class AddFlippedOverlap extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
+
+		@Override
+		public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+			Set<BinaryTextRelation> overlapRelations = Sets.newHashSet();
+			Multimap<Annotation, Annotation> overlaps = HashMultimap.create();
+			for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)) {
+				if (relation.getCategory().equals("OVERLAP")) {
+					overlapRelations.add(relation);
+					Annotation arg1 = relation.getArg1().getArgument();
+					Annotation arg2 = relation.getArg2().getArgument();
+					overlaps.put(arg1, arg2);
+				}
+			}
+
+			for (BinaryTextRelation orelation : overlapRelations) {
+				Annotation argA = orelation.getArg1().getArgument();
+				Annotation argB = orelation.getArg2().getArgument();
+				//add overlap 
+				if (!overlaps.containsEntry(argB, argA)) {
+					//create a new flipped relation:
+					RelationArgument arg1 = new RelationArgument(jCas);
+					arg1.setArgument(argB);
+					RelationArgument arg2 = new RelationArgument(jCas);
+					arg2.setArgument(argA);
+					BinaryTextRelation relation = new BinaryTextRelation(jCas);
+					relation.setArg1(arg1);
+					relation.setArg2(arg2);
+					relation.setCategory("OVERLAP");
+					arg1.addToIndexes();
+					arg2.addToIndexes();
+					relation.addToIndexes();
+					overlaps.put(argB, argA);
+				}
+
+			}
+		}
+	}
+
+	public static class AddClosure extends JCasAnnotator_ImplBase {
+
+		@Override
+		public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+			Multimap<List<Annotation>, BinaryTextRelation> annotationsToRelation = HashMultimap.create();
+			for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)){
+				String relationType = relation.getCategory();
+				if(validTemporalType(relationType)){
+					Annotation arg1 = relation.getArg1().getArgument();
+					Annotation arg2 = relation.getArg2().getArgument();
+					annotationsToRelation.put(Arrays.asList(arg1, arg2), relation);
+				}
+			}
+			for (List<Annotation> span: Lists.newArrayList(annotationsToRelation.keySet())){
+				Collection<BinaryTextRelation> relations = annotationsToRelation.get(span);
+				if(relations.size()>1){//if same span maps to multiple relations
+					Set<String> types = Sets.newHashSet();
+					for(BinaryTextRelation relation: relations){
+						types.add(relation.getCategory());
+					}
+					if(types.size()>1){
+						for(BinaryTextRelation relation: Lists.newArrayList(relations)){
+							annotationsToRelation.remove(span, relation);
+							relation.getArg1().removeFromIndexes();
+							relation.getArg2().removeFromIndexes();
+							relation.removeFromIndexes();
+						}
+					}else if(types.size()==1){
+						for (int i =1; i< relations.size(); i++){
+							BinaryTextRelation relation = (BinaryTextRelation) relations.toArray()[i];
+							annotationsToRelation.remove(span, relation);
+							relation.getArg1().removeFromIndexes();
+							relation.getArg2().removeFromIndexes();
+							relation.removeFromIndexes();
+						}
+					}
+				}
+			}
+
+			ArrayList<BinaryTextRelation> temporalRelation = new ArrayList<>(annotationsToRelation.values());//new ArrayList<BinaryTextRelation>();
+			//			Map<List<Annotation>, BinaryTextRelation> temporalRelationLookup = new HashMap<List<Annotation>, BinaryTextRelation>();
+			//
+			//			for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)){
+			//				String relationType = relation.getCategory();
+			//				if(validTemporalType(relationType)){
+			//					Annotation arg1 = relation.getArg1().getArgument();
+			//			        Annotation arg2 = relation.getArg2().getArgument();
+			//			        BinaryTextRelation tempRelation = temporalRelationLookup.get(Arrays.asList(arg1, arg2));
+			//					if( tempRelation == null){
+			//						temporalRelation.add(relation);					
+			//				        temporalRelationLookup.put(Arrays.asList(arg1, arg2), relation);
+			//					}else{//if there is duplicate
+			//						relation.getArg1().removeFromIndexes();
+			//						relation.getArg2().removeFromIndexes();
+			//						relation.removeFromIndexes();
+			//					}
+			//					
+			//				}
+			//			}
+
+			if (!temporalRelation.isEmpty()){
+				TLinkTypeArray2 relationArray = new TLinkTypeArray2(temporalRelation, new AnnotationIdCollection(temporalRelation));
+
+				int addedCount = 0;
+				for (BinaryTextRelation relation : relationArray.getClosedTlinks(jCas)) {
+					RelationArgument arg1 = relation.getArg1();
+					RelationArgument arg2 = relation.getArg2();
+					String relationType = relation.getCategory();
+					if(relationType.equals("CONTAINED-BY")||relationType.equals("AFTER")){//ignore these two categories, because their reciprocal already exist.
+						continue;
+					}
+					//check if the inferred relation new:
+					Collection<BinaryTextRelation> relations = annotationsToRelation.get(Arrays.asList(arg1.getArgument(), arg2.getArgument()));
+					if(relations.isEmpty()){ //if haven't seen this inferred relation before, then add this relation
+						arg1.addToIndexes();
+						arg2.addToIndexes();
+						relation.addToIndexes();
+						addedCount++;
+					}		
+				}
+
+				System.out.println( "**************************************************************");
+				System.out.println( "Finally added closure relations: " + addedCount );
+				System.out.println( "**************************************************************");
+			}			
+
+		}
+
+		private static boolean validTemporalType(String relationType) {
+			if(relationType.equals("CONTAINS")||relationType.equals("OVERLAP")||relationType.equals("BEFORE")||relationType.equals("ENDS-ON")||relationType.equals("BEGINS-ON"))
+				return true;
+			return false;
+		}
+	}
+
+	//	public static class AddTransitiveBeforeAndOnRelations extends JCasAnnotator_ImplBase {
+	//
+	//		@Override
+	//		public void process(JCas jCas) throws AnalysisEngineProcessException {
+	//
+	//			// collect many-to-many mappings of containment relations 
+	//			Multimap<Annotation, Annotation> contains = HashMultimap.create();
+	//			Multimap<Annotation, Annotation> before = HashMultimap.create();
+	//			Multimap<Annotation, Annotation> endson = HashMultimap.create();
+	//			Multimap<Annotation, Annotation> beginson = HashMultimap.create();
+	//			Set<BinaryTextRelation> beforeRel = Sets.newHashSet();
+	//
+	//			for (BinaryTextRelation relation : JCasUtil.select(jCas, BinaryTextRelation.class)) {
+	//				if (relation.getCategory().equals("CONTAINS")) {
+	//					Annotation arg1 = relation.getArg1().getArgument();
+	//					Annotation arg2 = relation.getArg2().getArgument();
+	//					contains.put(arg1, arg2);
+	//				}else if (relation.getCategory().equals("BEFORE")) {
+	//					Annotation arg1 = relation.getArg1().getArgument();
+	//					Annotation arg2 = relation.getArg2().getArgument();
+	//					before.put(arg1, arg2);
+	//					beforeRel.add(relation);
+	//				}else if (relation.getCategory().equals("ENDS-ON")) {
+	//					Annotation arg1 = relation.getArg1().getArgument();
+	//					Annotation arg2 = relation.getArg2().getArgument();
+	//					endson.put(arg1, arg2);
+	//					if (!endson.containsEntry(arg2, arg1)) {
+	//						endson.put(arg2, arg1);
+	//					}
+	//				}else if (relation.getCategory().equals("BEGINS-ON")) {
+	//					Annotation arg1 = relation.getArg1().getArgument();
+	//					Annotation arg2 = relation.getArg2().getArgument();
+	//					beginson.put(arg1, arg2);
+	//					if (!beginson.containsEntry(arg2, arg1)) {
+	//						beginson.put(arg2, arg1);
+	//					}
+	//				}
+	//			}
+	//
+	//			// for A BEFORE B, check if A and B Contain anything
+	//			for (BinaryTextRelation brelation : beforeRel) {
+	//				Annotation argA = brelation.getArg1().getArgument();
+	//				Annotation argB = brelation.getArg2().getArgument();
+	//				//add contained before
+	//				for (Annotation childA : contains.get(argA)) {
+	//					for (Annotation childB : contains.get(argB)) {
+	//						if (!before.containsEntry(childA, childB)) {
+	//							//create a new before relation:
+	//							RelationArgument arg1 = new RelationArgument(jCas);
+	//							arg1.setArgument(childA);
+	//							RelationArgument arg2 = new RelationArgument(jCas);
+	//							arg2.setArgument(childB);
+	//							BinaryTextRelation relation = new BinaryTextRelation(jCas);
+	//							relation.setArg1(arg1);
+	//							relation.setArg2(arg2);
+	//							relation.setCategory("BEFORE");
+	//							arg1.addToIndexes();
+	//							arg2.addToIndexes();
+	//							relation.addToIndexes();
+	//							before.put(childA, childB);
+	//						}
+	//					}
+	//				}
+	//				//add ends-on A
+	//				for (Annotation endsOnA : endson.get(argA)) {
+	//					if (!before.containsEntry(endsOnA, argB)) {
+	//						//create a new before relation:
+	//						RelationArgument arg1 = new RelationArgument(jCas);
+	//						arg1.setArgument(endsOnA);
+	//						RelationArgument arg2 = new RelationArgument(jCas);
+	//						arg2.setArgument(argB);
+	//						BinaryTextRelation relation = new BinaryTextRelation(jCas);
+	//						relation.setArg1(arg1);
+	//						relation.setArg2(arg2);
+	//						relation.setCategory("BEFORE");
+	//						arg1.addToIndexes();
+	//						arg2.addToIndexes();
+	//						relation.addToIndexes();
+	//						before.put(endsOnA, argB);
+	//					}
+	//				}
+	//				//add begins-on B
+	//				for (Annotation beginsOnB : beginson.get(argB)) {
+	//					if (!before.containsEntry(argA, beginsOnB)) {
+	//						//create a new before relation:
+	//						RelationArgument arg1 = new RelationArgument(jCas);
+	//						arg1.setArgument(argA);
+	//						RelationArgument arg2 = new RelationArgument(jCas);
+	//						arg2.setArgument(beginsOnB);
+	//						BinaryTextRelation relation = new BinaryTextRelation(jCas);
+	//						relation.setArg1(arg1);
+	//						relation.setArg2(arg2);
+	//						relation.setCategory("BEFORE");
+	//						arg1.addToIndexes();
+	//						arg2.addToIndexes();
+	//						relation.addToIndexes();
+	//						before.put(argA, beginsOnB);
+	//					}
+	//				}
+	//			}
+	//		}
+	//
+	//	}
+}



Mime
View raw message