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From c...@apache.org
Subject svn commit: r1634983 [3/3] - in /ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal: ae/ ae/feature/ eval/ pipelines/
Date Tue, 28 Oct 2014 21:01:07 GMT
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfSelfEventTimeRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfSelfEventTimeRelations.java?rev=1634983&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfSelfEventTimeRelations.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfSelfEventTimeRelations.java Tue Oct 28 21:01:06 2014
@@ -0,0 +1,984 @@
+/**
+ * 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.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.HashMap;
+//import java.util.HashSet;
+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.EventTimeRelationAnnotator;
+import org.apache.ctakes.temporal.ae.EventTimeSelfRelationAnnotator;
+//import org.apache.ctakes.temporal.ae.EventTimeSyntacticAnnotator;
+//import org.apache.ctakes.temporal.ae.EventTimeRelationAnnotator;
+//import org.apache.ctakes.temporal.ae.EventEventRelationAnnotator;
+import org.apache.ctakes.temporal.ae.baselines.RecallBaselineEventTimeRelationAnnotator;
+import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings;
+import org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.RemoveNonContainsRelations.RemoveGoldAttributes;
+//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.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.AnalysisEngineProcessException;
+import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.CASException;
+import org.apache.uima.collection.CollectionReader;
+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.ml.jar.JarClassifierBuilder;
+import org.cleartk.ml.liblinear.LibLinearStringOutcomeDataWriter;
+//import org.cleartk.ml.libsvm.LibSvmStringOutcomeDataWriter;
+//import org.cleartk.ml.tksvmlight.TkSvmLightStringOutcomeDataWriter;
+import org.cleartk.ml.tksvmlight.model.CompositeKernel;
+import org.cleartk.ml.tksvmlight.model.CompositeKernel.ComboOperator;
+import org.cleartk.eval.AnnotationStatistics;
+import org.cleartk.util.ViewUriUtil;
+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 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;
+
+public class EvaluationOfSelfEventTimeRelations 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();
+	}
+
+	//  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("target/eval/thyme/");
+			if(!workingDir.exists()) workingDir.mkdirs();
+			if(options.getUseTmp()){
+				File tempModelDir = File.createTempFile("temporal", null, workingDir);
+				tempModelDir.delete();
+				tempModelDir.mkdir();
+				workingDir = tempModelDir;
+			}
+			EvaluationOfSelfEventTimeRelations evaluation = new EvaluationOfSelfEventTimeRelations(
+					workingDir,
+					options.getRawTextDirectory(),
+					options.getXMLDirectory(),
+					options.getXMLFormat(),
+					options.getXMIDirectory(),
+					options.getTreebankDirectory(),
+					options.getCoreferenceDirectory(),
+					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/event-time");
+			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();
+			params.stats = evaluation.trainAndRetrainAndTest(training, testing);//training);//
+			//      System.err.println(options.getKernelParams() == null ? params : options.getKernelParams());
+			System.err.println("No closure on gold::Closure on System::Recall Mode");
+			System.err.println(params.stats);
+
+			//do closure on gold, but not on system, to calculate precision
+			evaluation.skipTrain = true;
+			recallModeEvaluation = false;
+			params.stats = evaluation.trainAndRetrainAndTest(training, testing);//training);//
+			//      System.err.println(options.getKernelParams() == null ? params : options.getKernelParams());
+			System.err.println("No closure on System::Closure on Gold::Precision Mode");
+			System.err.println(params.stats);
+
+			//do closure on train, but not on test, to calculate plain results
+			evaluation.skipTrain = true;
+			evaluation.useClosure = false;
+			params.stats = evaluation.trainAndRetrainAndTest(training, testing);//training);//
+			//      System.err.println(options.getKernelParams() == null ? params : options.getKernelParams());
+			System.err.println("Closure on train::No closure on Test::Plain Mode");
+			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();
+		}
+	}
+
+	public AnnotationStatistics<String> trainAndRetrainAndTest(List<Integer> trainItems, List<Integer> testItems) 
+			throws Exception {
+		File trainDirectory = new File(this.baseDirectory, "train");
+		File retrainDirectory = new File(this.baseDirectory, "retrain_and_test");
+		trainDirectory.mkdirs();
+		retrainDirectory.mkdir();
+		this.train(this.getCollectionReader(trainItems), trainDirectory);
+		this.preTest(this.getCollectionReader(trainItems), trainDirectory, retrainDirectory);
+		return this.test(this.getCollectionReader(testItems), retrainDirectory);
+	}
+
+	//  private ParameterSettings params;
+	private boolean baseline;
+	protected boolean useClosure;
+	protected boolean useGoldAttributes;
+	protected boolean skipTrain=false;
+	//  protected boolean printRelations = false;
+
+	public EvaluationOfSelfEventTimeRelations(
+			File baseDirectory,
+			File rawTextDirectory,
+			File xmlDirectory,
+			XMLFormat xmlFormat,
+			File xmiDirectory,
+			File treebankDirectory,
+			File coreferenceDirectory,
+			boolean useClosure,
+			boolean printErrors,
+			boolean printRelations,
+			boolean baseline,
+			boolean useGoldAttributes,
+			String kernelParams,
+			ParameterSettings params){
+		super(
+				baseDirectory,
+				rawTextDirectory,
+				xmlDirectory,
+				xmlFormat,
+				xmiDirectory,
+				treebankDirectory,
+				coreferenceDirectory,
+				printErrors,
+				printRelations,
+				params);
+		this.params = params;
+		this.useClosure = useClosure;
+		this.printErrors = printErrors;
+		this.printRelations = printRelations;
+		this.useGoldAttributes = useGoldAttributes;
+		this.baseline = baseline;
+		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;
+		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.createPrimitiveDescription(AddTransitiveContainsRelations.class));
+			//			aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(AddContain2Overlap.class));
+			//			aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveBeforeAndOnRelations.class));
+		}
+		//		aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveNonContainsRelations.class));
+		//		aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(AddFlippedOverlap.class));//add flipped overlap instances to training data
+
+		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveEventEventRelations.class));
+		aggregateBuilder.add(EventTimeRelationAnnotator.createDataWriterDescription(
+				LibLinearStringOutcomeDataWriter.class,
+				//				LIBSVMStringOutcomeDataWriter.class,
+				//				TKSVMlightStringOutcomeDataWriter.class,
+				//        TKLIBSVMStringOutcomeDataWriter.class,
+				//        SVMlightStringOutcomeDataWriter.class,        
+				new File(directory,"event-time"),
+				params.probabilityOfKeepingANegativeExample));
+		//		aggregateBuilder.add(EventEventRelationAnnotator.createDataWriterDescription(
+		//				LIBSVMStringOutcomeDataWriter.class,
+		//				new File(directory,"event-event"), 
+		//				params.probabilityOfKeepingANegativeExample));
+		SimplePipeline.runPipeline(collectionReader, aggregateBuilder.createAggregate());
+		String[] optArray;
+
+		if(this.kernelParams == null){
+			ArrayList<String> svmOptions = new ArrayList<>();
+			svmOptions.add("-c"); svmOptions.add(""+params.svmCost);        // svm cost
+			svmOptions.add("-t"); svmOptions.add(""+params.svmKernelIndex); // kernel index 
+			svmOptions.add("-d"); svmOptions.add("3");                      // degree parameter for polynomial
+			svmOptions.add("-g"); svmOptions.add(""+params.svmGamma);
+			if(params.svmKernelIndex==ParameterSettings.SVM_KERNELS.indexOf("tk")){
+				svmOptions.add("-S"); svmOptions.add(""+params.secondKernelIndex);   // second kernel index (similar to -t) for composite kernel
+				String comboFlag = (params.comboOperator == ComboOperator.SUM ? "+" : params.comboOperator == ComboOperator.PRODUCT ? "*" : params.comboOperator == ComboOperator.TREE_ONLY ? "T" : "V");
+				svmOptions.add("-C"); svmOptions.add(comboFlag);
+				svmOptions.add("-L"); svmOptions.add(""+params.lambda);
+				svmOptions.add("-T"); svmOptions.add(""+params.tkWeight);
+				svmOptions.add("-N"); svmOptions.add("3");   // normalize trees and features
+			}
+			optArray = svmOptions.toArray(new String[]{});
+		}else{
+			optArray = this.kernelParams;
+			for(int i = 0; i < optArray.length; i+=2){
+				optArray[i] = "-" + optArray[i];
+			}
+		}
+
+		//    HideOutput hider = new HideOutput();
+		JarClassifierBuilder.trainAndPackage(new File(directory,"event-time"), "-w3","2","-w4","18","-w5","13","-w6","21","-w7","87","-w8","19","-c", optArray[1]);//"0.05");//"-h","0","-c", "1000");//optArray);
+		//		JarClassifierBuilder.trainAndPackage(new File(directory,"event-event"), "-h","0","-c", "1000");
+		//    hider.restoreOutput();
+		//    hider.close();
+	}
+
+	@Override
+	protected AnnotationStatistics<String> test(CollectionReader collectionReader, File directory)
+			throws Exception {
+		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);
+		}
+
+		aggregateBuilder.add(
+				AnalysisEngineFactory.createEngineDescription(RemoveEventEventRelations.class),
+				CAS.NAME_DEFAULT_SOFA,
+				GOLD_VIEW_NAME);
+
+		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveRelations.class));
+		aggregateBuilder.add(EventTimeRelationAnnotator.createEngineDescription(new File(directory,"event-time")));
+
+		if(this.i2b2Output != null){
+			aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(WriteI2B2XML.class, WriteI2B2XML.PARAM_OUTPUT_DIR, this.i2b2Output), "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
+					);
+			aggregateBuilder.add(
+					AnalysisEngineFactory.createEngineDescription(RemoveEventEventRelations.class),
+					GOLD_VIEW_NAME,
+					CAS.NAME_DEFAULT_SOFA
+					);
+			outf =  new File("target/eval/thyme/SystemError_eventTime_recall_dev.txt");
+		}else if (!recallModeEvaluation && this.useClosure){
+			outf =  new File("target/eval/thyme/SystemError_eventTime_precision_dev.txt");
+		}else{
+			outf =  new File("target/eval/thyme/SystemError_eventTime_plain_dev.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);
+
+			//newly add
+			//			systemRelations = removeNonGoldRelations(systemRelations, goldRelations, getSpan);//for removing non-gold pairs
+			//			systemRelations = correctArgOrder(systemRelations, goldRelations);//change the argument order of "OVERLAP" relation, if the order is flipped
+			//find duplicates in gold relations:
+			//			Collection<BinaryTextRelation> duplicateGoldRelations = getDuplicateRelations(goldRelations, getSpan);
+			//			if(!duplicateGoldRelations.isEmpty()){
+			//				System.err.println("******Duplicate gold relations in : " + ViewURIUtil.getURI(jCas).toString());
+			//				for (BinaryTextRelation rel : duplicateGoldRelations){
+			//					System.err.println("Duplicate : "+ formatRelation(rel));
+			//				}
+			//			}
+			//end newly add
+
+			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;
+	}
+
+	private void preTest(CollectionReader collectionReader, File directory, File retrainDirectory) throws Exception {
+		if(this.skipTrain) return;
+		AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
+//		aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class,TimeMention.class));
+
+		aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class, TimeMention.class, TemporalTextRelation.class));
+//		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveEventEventRelations.class));
+		//		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(
+		//				RemoveCrossSentenceRelations.class,
+		//				RemoveCrossSentenceRelations.PARAM_SENTENCE_VIEW,
+		//				CAS.NAME_DEFAULT_SOFA,
+		//				RemoveCrossSentenceRelations.PARAM_RELATION_VIEW,
+		//				GOLD_VIEW_NAME));
+
+
+//		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveRelations.class));
+		//annotate on system-generated events, for event-time relations
+		aggregateBuilder.add(EventTimeSelfRelationAnnotator.createEngineDescription(new File(directory,"event-time")));
+
+		//		//re-train:
+		//overwrite system-generated relations by gold temporal relations:
+//		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(OverwriteTemporalRelationToSystem.class));
+
+		//add closure for system output
+		aggregateBuilder.add(
+				AnalysisEngineFactory.createEngineDescription(AddClosure.class),//AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveContainsRelations.class),
+				GOLD_VIEW_NAME,
+				CAS.NAME_DEFAULT_SOFA
+				);
+		aggregateBuilder.add(
+				AnalysisEngineFactory.createEngineDescription(RemoveEventEventRelations.class),
+				GOLD_VIEW_NAME,
+				CAS.NAME_DEFAULT_SOFA
+				);
+
+		//		aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class, TimeMention.class, BinaryTextRelation.class));//could not copy over, because it will remove all system generated relations
+		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveCrossSentenceRelations.class));
+		
+		if(!this.useGoldAttributes){
+			aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveGoldAttributes.class));
+		}
+
+		//		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveEventEventRelations.class));
+		aggregateBuilder.add(EventTimeSelfRelationAnnotator.createDataWriterDescription(
+				LibLinearStringOutcomeDataWriter.class,
+				//				LIBSVMStringOutcomeDataWriter.class,
+				//				TKSVMlightStringOutcomeDataWriter.class,
+				//        TKLIBSVMStringOutcomeDataWriter.class,
+				//        SVMlightStringOutcomeDataWriter.class,        
+				new File(retrainDirectory,"event-time"),
+				params.probabilityOfKeepingANegativeExample));
+		//		aggregateBuilder.add(EventEventRelationAnnotator.createDataWriterDescription(
+		//				LIBSVMStringOutcomeDataWriter.class,
+		//				new File(directory,"event-event"), 
+		//				params.probabilityOfKeepingANegativeExample));
+		SimplePipeline.runPipeline(collectionReader, aggregateBuilder.createAggregate());
+		String[] optArray;
+
+		if(this.kernelParams == null){
+			ArrayList<String> svmOptions = new ArrayList<>();
+			svmOptions.add("-c"); svmOptions.add(""+params.svmCost);        // svm cost
+			svmOptions.add("-t"); svmOptions.add(""+params.svmKernelIndex); // kernel index 
+			svmOptions.add("-d"); svmOptions.add("3");                      // degree parameter for polynomial
+			svmOptions.add("-g"); svmOptions.add(""+params.svmGamma);
+			if(params.svmKernelIndex==ParameterSettings.SVM_KERNELS.indexOf("tk")){
+				svmOptions.add("-S"); svmOptions.add(""+params.secondKernelIndex);   // second kernel index (similar to -t) for composite kernel
+				String comboFlag = (params.comboOperator == ComboOperator.SUM ? "+" : params.comboOperator == ComboOperator.PRODUCT ? "*" : params.comboOperator == ComboOperator.TREE_ONLY ? "T" : "V");
+				svmOptions.add("-C"); svmOptions.add(comboFlag);
+				svmOptions.add("-L"); svmOptions.add(""+params.lambda);
+				svmOptions.add("-T"); svmOptions.add(""+params.tkWeight);
+				svmOptions.add("-N"); svmOptions.add("3");   // normalize trees and features
+			}
+			optArray = svmOptions.toArray(new String[]{});
+		}else{
+			optArray = this.kernelParams;
+			for(int i = 0; i < optArray.length; i+=2){
+				optArray[i] = "-" + optArray[i];
+			}
+		}
+
+		//    HideOutput hider = new HideOutput();
+		JarClassifierBuilder.trainAndPackage(new File(retrainDirectory,"event-time"), "-w1","0.6","-c", optArray[1]);//"-w1","0.6","-w3","28","-w4","8","-w5","2","-w6","9","-w7","9","-w8","12","-c", optArray[1]);//"0.05");//"-h","0","-c", "1000");//optArray);
+		//		JarClassifierBuilder.trainAndPackage(new File(directory,"event-event"), "-h","0","-c", "1000");
+		//    hider.restoreOutput();
+		//    hider.close();
+		// TODO Auto-generated method stub
+
+	}
+
+
+	public static class RemoveEventEventRelations extends JCasAnnotator_ImplBase {
+		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 relationView;
+			try {
+				relationView = jCas.getView(this.relationViewName);
+			} catch (CASException e) {
+				throw new AnalysisEngineProcessException(e);
+			}
+
+			for(BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(relationView, BinaryTextRelation.class))){
+				//	    	  if(relation.getCategory().equals("CONTAINS")){
+				RelationArgument arg1 = relation.getArg1();
+				RelationArgument arg2 = relation.getArg2();
+				if(arg1.getArgument() instanceof TimeMention && arg2.getArgument() instanceof EventMention ||
+						arg1.getArgument() instanceof EventMention && arg2.getArgument() instanceof TimeMention){
+					// these are the kind we keep.
+					continue;
+				}
+				//	    		  if(arg1.getArgument() instanceof EventMention && arg2.getArgument() instanceof EventMention){
+				arg1.removeFromIndexes();
+				arg2.removeFromIndexes();
+				relation.removeFromIndexes();
+			}
+			//	      }
+
+		}
+	}
+
+	public static class OverwriteTemporalRelationToSystem extends JCasAnnotator_ImplBase {
+
+		@Override
+		public void process(JCas jCas) throws AnalysisEngineProcessException {
+			JCas systemView;
+			JCas goldView;
+			try {
+				systemView = jCas.getView(CAS.NAME_DEFAULT_SOFA);
+				goldView = jCas.getView(GOLD_VIEW_NAME);
+			} catch (CASException e) {
+				throw new AnalysisEngineProcessException(e);
+			}
+			
+			Map<List<Integer>, TemporalTextRelation> goldRelationLookup = new HashMap<>();
+			
+			for(TemporalTextRelation relation: JCasUtil.select(goldView, TemporalTextRelation.class)){
+				Annotation arg1 = relation.getArg1().getArgument();
+				Annotation arg2 = relation.getArg2().getArgument();
+				
+				//populate gold relation hashmap:
+				goldRelationLookup.put(Arrays.asList(arg1.getBegin(),arg1.getEnd(),arg2.getBegin(),arg2.getEnd()), relation);
+			}
+			
+			//iterate system relations to update any conflicts with gold
+			for(TemporalTextRelation relation: JCasUtil.select(systemView, TemporalTextRelation.class)){
+				Annotation arg1 = relation.getArg1().getArgument();
+				Annotation arg2 = relation.getArg2().getArgument();
+				String sysLabel = relation.getCategory();
+				int arg1Beg = arg1.getBegin();
+				int arg1End = arg1.getEnd();
+				int arg2Beg = arg2.getBegin();
+				int arg2End = arg2.getEnd();
+				TemporalTextRelation goldRel = goldRelationLookup.get(Arrays.asList(arg1Beg,arg1End,arg2Beg,arg2End));
+				String goldLabel = null;
+				if(goldRel != null){
+					goldLabel = goldRel.getCategory();
+					if(!goldLabel.equals(sysLabel)){
+						relation.setCategory(goldLabel);
+					}
+				}else{//gold relation is not found
+					goldRel = goldRelationLookup.get(Arrays.asList(arg2Beg,arg2End, arg1Beg,arg1End));
+					if(goldRel != null){
+						RelationArgument tempArg = (RelationArgument) relation.getArg1().clone();
+						relation.setArg1((RelationArgument) relation.getArg2().clone());
+						relation.setArg2(tempArg);
+						goldLabel = goldRel.getCategory();
+						relation.setCategory(goldLabel);
+					}
+				}
+			}
+
+		}
+	}
+
+
+	public static class RemoveCrossSentenceRelations extends 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 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 AddContain2Overlap extends 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 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);
+	//					}
+	//				}
+	//			}
+	//		}
+	//
+	//	}
+}

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations.java?rev=1634983&r1=1634982&r2=1634983&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations.java Tue Oct 28 21:01:06 2014
@@ -349,7 +349,7 @@ EvaluationOfTemporalRelations_ImplBase{
 
 		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(RemoveRelations.class));
 		aggregateBuilder.add(this.baseline ? RecallBaselineEventTimeRelationAnnotator.createAnnotatorDescription(directory) :
-			EventTimeRelationAnnotator.createAnnotatorDescription(new File(directory,EVENT_TIME)));
+			EventTimeRelationAnnotator.createEngineDescription(new File(directory,EVENT_TIME)));
 		aggregateBuilder.add(EventEventRelationAnnotator.createAnnotatorDescription(new File(directory,EVENT_EVENT)));
 		aggregateBuilder.add(EventDischargeTimeAnnotator.createAnnotatorDescription(new File(directory,EVENT_DISCHARGE)));
 		aggregateBuilder.add(EventAdmissionTimeAnnotator.createAnnotatorDescription(new File(directory,EVENT_ADMISSION)));

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java?rev=1634983&r1=1634982&r2=1634983&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java Tue Oct 28 21:01:06 2014
@@ -47,204 +47,242 @@ import com.lexicalscope.jewel.cli.Option
 public abstract class EvaluationOfTemporalRelations_ImplBase extends
 Evaluation_ImplBase<AnnotationStatistics<String>> {
 
-  static interface TempRelOptions extends Evaluation_ImplBase.Options{
-    @Option
-    public boolean getTest();
-
-    @Option
-    public boolean getPrintFormattedRelations();
-
-    @Option
-    public boolean getBaseline();
-
-    @Option
-    public boolean getClosure();
-
-    @Option
-    public boolean getClassificationOnly();
-
-  }
-
-  protected static boolean DEFAULT_BOTH_DIRECTIONS = false;
-  protected static float DEFAULT_DOWNSAMPLE = 1.0f;
-  protected static double DEFAULT_SVM_C = 1.0;
-  protected static double DEFAULT_SVM_G = 1.0;
-  protected static double DEFAULT_TK = 0.5;
-  protected static double DEFAULT_LAMBDA = 0.5;
-
-  protected static ParameterSettings defaultParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS, DEFAULT_DOWNSAMPLE, "linear",
-      DEFAULT_SVM_C, DEFAULT_SVM_G, "polynomial", ComboOperator.SUM, DEFAULT_TK, DEFAULT_LAMBDA);
-
-
-  protected ParameterSettings params = null;
-  protected boolean printRelations = false;
-
-  public EvaluationOfTemporalRelations_ImplBase(File baseDirectory,
-      File rawTextDirectory, File xmlDirectory, XMLFormat xmlFormat,
-      File xmiDirectory, File treebankDirectory, File coreferenceDirectory, boolean printErrors, boolean printRelations, ParameterSettings params) {
-    super(baseDirectory, rawTextDirectory, xmlDirectory, xmlFormat, xmiDirectory,
-        treebankDirectory, coreferenceDirectory);
-    this.params = params;
-    this.printRelations = printRelations;
-    this.printErrors =  printErrors;
-  }
-
-  public EvaluationOfTemporalRelations_ImplBase(File baseDirectory,
-      File rawTextDirectory, File xmlDirectory, XMLFormat xmlFormat,
-      File xmiDirectory, File treebankDirectory, boolean printErrors, boolean printRelations, ParameterSettings params) {
-    super(baseDirectory, rawTextDirectory, xmlDirectory, xmlFormat, xmiDirectory,
-        treebankDirectory);
-    this.params = params;
-    this.printRelations = printRelations;
-    this.printErrors =  printErrors;
-  }
-
-  public static class PreserveEventEventRelations extends 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 {
-      for(BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(jCas, BinaryTextRelation.class))){
-        RelationArgument arg1 = relation.getArg1();
-        RelationArgument arg2 = relation.getArg2();
-        if(arg1.getArgument() instanceof EventMention && arg2.getArgument() instanceof EventMention && relation instanceof TemporalTextRelation){
-          // these are the kind we keep.
-          continue;
-        }
-        arg1.removeFromIndexes();
-        arg2.removeFromIndexes();
-        relation.removeFromIndexes();
-      }
-    }   
-  }
-
-  public static class RemoveNonContainsRelations extends JCasAnnotator_ImplBase {
-    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 relationView = null;
-
-      try {
-        relationView = jCas.getView(relationViewName);
-      } catch (CASException e) {
-        e.printStackTrace();
-      }
-      for (BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(
-          relationView,
-          BinaryTextRelation.class))) {
-        if (!relation.getCategory().startsWith("CONTAINS")) {
-          relation.getArg1().removeFromIndexes();
-          relation.getArg2().removeFromIndexes();
-          relation.removeFromIndexes();
-        }
-      }
-    }
-
-    public static class RemoveGoldAttributes extends JCasAnnotator_ImplBase {
-      @Override
-      public void process(JCas jCas) throws AnalysisEngineProcessException {
-        for(EventMention event : JCasUtil.select(jCas, EventMention.class)){
-          if(event.getEvent() != null && event.getEvent().getProperties() != null){
-            event.getEvent().getProperties().setContextualAspect("UNK");
-            event.getEvent().getProperties().setContextualModality("UNK");
-          }
-        }
-        for(TimeMention timex : JCasUtil.select(jCas, TimeMention.class)){
-          timex.setTimeClass("UNK");
-        }
-      }
-    }
-  }
-
-  protected static Collection<BinaryTextRelation> correctArgOrder(
-      Collection<BinaryTextRelation> systemRelations,
-      Collection<BinaryTextRelation> goldRelations) {
-    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(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.
-          continue;
-        }
-      }
-      goodSys.add(sysrel);
-    }
-
-    return goodSys;
-  }
-
-  private static boolean matchSpan(Annotation arg1, Annotation arg2) {
-    boolean result = false;
-    result = arg1.getBegin() == arg2.getBegin() && arg1.getEnd() == arg2.getEnd();
-    return result;
-  }
-
-  protected 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);
-    }
-  }
-
-  protected static String formatRelation(BinaryTextRelation relation) {
-    IdentifiedAnnotation arg1 = (IdentifiedAnnotation)relation.getArg1().getArgument();
-    IdentifiedAnnotation arg2 = (IdentifiedAnnotation)relation.getArg2().getArgument();
-    String arg1Type ="E";
-    String arg2Type ="T";
-    if(arg1 instanceof TimeMention) arg1Type = "T";
-    if(arg2 instanceof EventMention) arg2Type = "E";
-    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!%d-%d!%s), %s(type=%d!%d-%d!%s)) in ...%s...",
-        relation.getCategory(),
-        arg1.getCoveredText(),
-        arg1.getTypeID(),
-        //add extra
-        arg1.getBegin(),
-        arg1.getEnd(),
-        arg1Type,
-
-        arg2.getCoveredText(),
-        arg2.getTypeID(),
-        //add extra
-        arg2.getBegin(),
-        arg2.getEnd(),
-        arg2Type,
-        text.substring(begin, end).replaceAll("[\r\n]", " "));
-  }
+	static interface TempRelOptions extends Evaluation_ImplBase.Options{
+		@Option
+		public boolean getTest();
+
+		@Option
+		public boolean getPrintFormattedRelations();
+
+		@Option
+		public boolean getBaseline();
+
+		@Option
+		public boolean getClosure();
+
+		@Option
+		public boolean getClassificationOnly();
+
+	}
+
+	protected static boolean DEFAULT_BOTH_DIRECTIONS = false;
+	protected static float DEFAULT_DOWNSAMPLE = 1.0f;
+	protected static double DEFAULT_SVM_C = 1.0;
+	protected static double DEFAULT_SVM_G = 1.0;
+	protected static double DEFAULT_TK = 0.5;
+	protected static double DEFAULT_LAMBDA = 0.5;
+
+	protected static ParameterSettings defaultParams = new ParameterSettings(DEFAULT_BOTH_DIRECTIONS, DEFAULT_DOWNSAMPLE, "linear",
+			DEFAULT_SVM_C, DEFAULT_SVM_G, "polynomial", ComboOperator.SUM, DEFAULT_TK, DEFAULT_LAMBDA);
+
+
+	protected ParameterSettings params = null;
+	protected boolean printRelations = false;
+
+	public EvaluationOfTemporalRelations_ImplBase(File baseDirectory,
+			File rawTextDirectory, File xmlDirectory, XMLFormat xmlFormat,
+			File xmiDirectory, File treebankDirectory, File coreferenceDirectory, boolean printErrors, boolean printRelations, ParameterSettings params) {
+		super(baseDirectory, rawTextDirectory, xmlDirectory, xmlFormat, xmiDirectory,
+				treebankDirectory, coreferenceDirectory);
+		this.params = params;
+		this.printRelations = printRelations;
+		this.printErrors =  printErrors;
+	}
+
+	public EvaluationOfTemporalRelations_ImplBase(File baseDirectory,
+			File rawTextDirectory, File xmlDirectory, XMLFormat xmlFormat,
+			File xmiDirectory, File treebankDirectory, boolean printErrors, boolean printRelations, ParameterSettings params) {
+		super(baseDirectory, rawTextDirectory, xmlDirectory, xmlFormat, xmiDirectory,
+				treebankDirectory);
+		this.params = params;
+		this.printRelations = printRelations;
+		this.printErrors =  printErrors;
+	}
+
+	public static class PreserveEventEventRelations extends 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 {
+			for(BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(jCas, BinaryTextRelation.class))){
+				RelationArgument arg1 = relation.getArg1();
+				RelationArgument arg2 = relation.getArg2();
+				if(arg1.getArgument() instanceof EventMention && arg2.getArgument() instanceof EventMention && relation instanceof TemporalTextRelation){
+					// these are the kind we keep.
+					continue;
+				}
+				arg1.removeFromIndexes();
+				arg2.removeFromIndexes();
+				relation.removeFromIndexes();
+			}
+		}   
+	}
+
+	public static class RemoveNonContainsRelations extends JCasAnnotator_ImplBase {
+		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 relationView = null;
+
+			try {
+				relationView = jCas.getView(relationViewName);
+			} catch (CASException e) {
+				e.printStackTrace();
+			}
+			for (BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(
+					relationView,
+					BinaryTextRelation.class))) {
+				if (!relation.getCategory().startsWith("CONTAINS")) {
+					relation.getArg1().removeFromIndexes();
+					relation.getArg2().removeFromIndexes();
+					relation.removeFromIndexes();
+				}
+			}
+		}
+
+		public static class RemoveGoldAttributes extends JCasAnnotator_ImplBase {
+			@Override
+			public void process(JCas jCas) throws AnalysisEngineProcessException {
+				for(EventMention event : JCasUtil.select(jCas, EventMention.class)){
+					if(event.getEvent() != null && event.getEvent().getProperties() != null){
+						event.getEvent().getProperties().setContextualAspect("UNK");
+						event.getEvent().getProperties().setContextualModality("UNK");
+					}
+				}
+				for(TimeMention timex : JCasUtil.select(jCas, TimeMention.class)){
+					timex.setTimeClass("UNK");
+				}
+			}
+		}
+	}
+
+	protected static Collection<BinaryTextRelation> correctArgOrder(
+			Collection<BinaryTextRelation> systemRelations,
+			Collection<BinaryTextRelation> goldRelations) {
+		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(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.
+					continue;
+				}
+			}
+			goodSys.add(sysrel);
+		}
+
+		return goodSys;
+	}
+
+	private static boolean matchSpan(Annotation arg1, Annotation arg2) {
+		boolean result = false;
+		result = arg1.getBegin() == arg2.getBegin() && arg1.getEnd() == arg2.getEnd();
+		return result;
+	}
+
+	protected 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);
+		}
+	}
+
+	protected static String formatRelation(BinaryTextRelation relation) {
+		IdentifiedAnnotation arg1 = (IdentifiedAnnotation)relation.getArg1().getArgument();
+		IdentifiedAnnotation arg2 = (IdentifiedAnnotation)relation.getArg2().getArgument();
+		String arg1Type ="E";
+		String arg2Type ="T";
+		if(arg1 instanceof TimeMention) arg1Type = "T";
+		if(arg2 instanceof EventMention) arg2Type = "E";
+		String text = arg1.getCAS().getDocumentText();
+		int begin = Math.min(arg1.getBegin(), arg2.getBegin());
+		int end = Math.max(arg1.getEnd(), arg2.getEnd());
+		int begin1 = 0;
+		int end1 = 0;
+		int begin2 = 0;
+		int end2 = 0;
+		if(arg1.getBegin()< arg2.getBegin()){
+			begin1 = arg1.getBegin();
+			end1 = arg1.getEnd();
+			begin2 = arg2.getBegin();
+			end2 = arg2.getEnd();
+		}else{ //arg1 is after arg2
+			begin1 = arg2.getBegin();
+			end1 = arg2.getEnd();
+			begin2 = arg1.getBegin();
+			end2 = arg1.getEnd();
+		}
+		begin = Math.max(0, begin - 200);
+		end = Math.min(text.length(), end + 200);
+		StringBuilder between = new StringBuilder();
+		if(begin<begin1) between.append(text.substring(begin, begin1).replaceAll("[\r\n]", " "));
+		between.append(" [" + text.substring(begin1, end1) + "] ");
+		if(begin2<=end1){
+			between.append(text.substring(begin,begin1).replaceAll("[\r\n]", " ")+" ["+ text.substring(begin1,begin2)+" [");
+			if(end1<end2){
+				between.append(text.substring(begin2,end1) + "]" + text.substring(end1,end2) + "]" +  text.substring(end2,end));
+			}else{
+				between.append(text.substring(begin2,end2) + "]" + text.substring(end2,end1) + "]" +  text.substring(end1,end));
+			}
+
+		}else if(begin2-end1 <=400){
+			between.append(text.substring(end1, begin2).replaceAll("[\r\n]", " "));
+		}else{
+			between.append(text.substring(end1, end1+200).replaceAll("[\r\n]", " ")+ "...");
+			int extra = (begin2-end1-400)/10;
+			for (int i = 1; i<extra; i++){
+				between.append(".");
+			}
+			between.append(text.substring(begin2-200, begin2).replaceAll("[\r\n]", " "));
+		}
+		between.append(" [" + text.substring(begin2, end2)+ "] ");
+		if(end2 < end)  between.append(text.substring(end2, end).replaceAll("[\r\n]", " ") );
+		return String.format(
+				"%s(%s(type=%d!%d-%d!%s), %s(type=%d!%d-%d!%s)) in ...%s...",
+				relation.getCategory(),
+				arg1.getCoveredText(),
+				arg1.getTypeID(),
+				//add extra
+				arg1.getBegin(),
+				arg1.getEnd(),
+				arg1Type,
+
+				arg2.getCoveredText(),
+				arg2.getTypeID(),
+				//add extra
+				arg2.getBegin(),
+				arg2.getEnd(),
+				arg2Type,
+				between.toString());
+	}
 
 }

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java?rev=1634983&r1=1634982&r2=1634983&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java Tue Oct 28 21:01:06 2014
@@ -69,13 +69,13 @@ public class FullTemporalExtractionPipel
     @Option(
         shortName = "r",
         description = "Specify the path to the directory where the trained event-time relation model is located",
-        defaultValue="target/eval/temporal-relations/event-time/train_and_test/")
+        defaultValue="target/eval/thyme/train_and_test/event-time/")
     public String getEventTimeRelationModelDirectory();
 
     @Option(
         shortName = "s",
         description = "Specify the path to the directory where the trained event-event relation model is located",
-        defaultToNull=true) // add in default value once we have a satisfying trained model
+        defaultValue="target/eval/thyme/train_and_test/event-event/") // add in default value once we have a satisfying trained model
     public String getEventEventRelationModelDirectory();  
     
     @Option(
@@ -102,7 +102,7 @@ public class FullTemporalExtractionPipel
     aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(CopyPropertiesToTemporalEventAnnotator.class));
     aggregateBuilder.add(DocTimeRelAnnotator.createAnnotatorDescription(options.getDoctimerelModelDirectory() + File.separator + "model.jar"));
     aggregateBuilder.add(BackwardsTimeAnnotator.createAnnotatorDescription(options.getTimeModelDirectory() + File.separator + "model.jar"));
-    aggregateBuilder.add(EventTimeRelationAnnotator.createAnnotatorDescription(options.getEventTimeRelationModelDirectory() + File.separator + "model.jar"));
+    aggregateBuilder.add(EventTimeRelationAnnotator.createEngineDescription(options.getEventTimeRelationModelDirectory() + File.separator + "model.jar"));
     if(options.getEventEventRelationModelDirectory()!=null){
       aggregateBuilder.add(EventEventRelationAnnotator.createAnnotatorDescription(options.getEventEventRelationModelDirectory() + File.separator + "model.jar"));
     }



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