Return-Path: X-Original-To: apmail-ctakes-commits-archive@www.apache.org Delivered-To: apmail-ctakes-commits-archive@www.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id 5142711A36 for ; Wed, 16 Jul 2014 14:47:02 +0000 (UTC) Received: (qmail 24940 invoked by uid 500); 16 Jul 2014 14:47:01 -0000 Delivered-To: apmail-ctakes-commits-archive@ctakes.apache.org Received: (qmail 24903 invoked by uid 500); 16 Jul 2014 14:47:01 -0000 Mailing-List: contact commits-help@ctakes.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: dev@ctakes.apache.org Delivered-To: mailing list commits@ctakes.apache.org Received: (qmail 24892 invoked by uid 99); 16 Jul 2014 14:47:01 -0000 Received: from athena.apache.org (HELO athena.apache.org) (140.211.11.136) by apache.org (qpsmtpd/0.29) with ESMTP; Wed, 16 Jul 2014 14:47:01 +0000 X-ASF-Spam-Status: No, hits=-2000.0 required=5.0 tests=ALL_TRUSTED X-Spam-Check-By: apache.org Received: from [140.211.11.4] (HELO eris.apache.org) (140.211.11.4) by apache.org (qpsmtpd/0.29) with ESMTP; Wed, 16 Jul 2014 14:46:58 +0000 Received: from eris.apache.org (localhost [127.0.0.1]) by eris.apache.org (Postfix) with ESMTP id 85252238890D; Wed, 16 Jul 2014 14:46:38 +0000 (UTC) Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: svn commit: r1611031 - in /ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal: ae/ eval/ Date: Wed, 16 Jul 2014 14:46:38 -0000 To: commits@ctakes.apache.org From: tmill@apache.org X-Mailer: svnmailer-1.0.9 Message-Id: <20140716144638.85252238890D@eris.apache.org> X-Virus-Checked: Checked by ClamAV on apache.org Author: tmill Date: Wed Jul 16 14:46:37 2014 New Revision: 1611031 URL: http://svn.apache.org/r1611031 Log: CTAKES-199: Multiple changes to temporal structure to allow for coreference data. Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventCoreferenceAnnotator.java ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKRelations.java ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventCoreference.java ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations.java ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventCoreferenceAnnotator.java URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventCoreferenceAnnotator.java?rev=1611031&r1=1611030&r2=1611031&view=diff ============================================================================== --- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventCoreferenceAnnotator.java (original) +++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventCoreferenceAnnotator.java Wed Jul 16 14:46:37 2014 @@ -8,13 +8,13 @@ import java.util.Collection; import java.util.HashSet; import java.util.List; -import org.apache.ctakes.coreference.ae.features.DistSemFeatureExtractor; -import org.apache.ctakes.coreference.ae.features.DistanceFeatureExtractor; -import org.apache.ctakes.coreference.ae.features.StringMatchingFeatureExtractor; -import org.apache.ctakes.coreference.ae.features.TokenFeatureExtractor; -import org.apache.ctakes.coreference.ae.features.UMLSFeatureExtractor; import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator; import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor; +import org.apache.ctakes.temporal.ae.feature.coreference.DistSemFeatureExtractor; +import org.apache.ctakes.temporal.ae.feature.coreference.DistanceFeatureExtractor; +import org.apache.ctakes.temporal.ae.feature.coreference.StringMatchingFeatureExtractor; +import org.apache.ctakes.temporal.ae.feature.coreference.TokenFeatureExtractor; +import org.apache.ctakes.temporal.ae.feature.coreference.UMLSFeatureExtractor; import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation; import org.apache.ctakes.typesystem.type.relation.CoreferenceRelation; import org.apache.ctakes.typesystem.type.relation.RelationArgument; Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKRelations.java URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKRelations.java?rev=1611031&r1=1611030&r2=1611031&view=diff ============================================================================== --- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKRelations.java (original) +++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKRelations.java Wed Jul 16 14:46:37 2014 @@ -114,7 +114,7 @@ public class EvaluationOfClearTKRelation File xmlDirectory, org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMLFormat xmlFormat, File xmiDirectory) { - super(baseDirectory, rawTextDirectory, xmlDirectory, xmlFormat, xmiDirectory, null, false, false, defaultParams); + super(baseDirectory, rawTextDirectory, xmlDirectory, xmlFormat, xmiDirectory, null, null, false, false, defaultParams); } private void setExtractEventTime(boolean eventTime) { Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventCoreference.java URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventCoreference.java?rev=1611031&r1=1611030&r2=1611031&view=diff ============================================================================== --- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventCoreference.java (original) +++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventCoreference.java Wed Jul 16 14:46:37 2014 @@ -16,8 +16,8 @@ import java.util.Stack; import org.apache.ctakes.core.resource.FileLocator; import org.apache.ctakes.core.util.DocumentIDAnnotationUtil; -import org.apache.ctakes.coreference.ae.CoreferenceChainAnnotator; import org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments; +import org.apache.ctakes.temporal.ae.CoreferenceChainAnnotator; import org.apache.ctakes.temporal.ae.EventCoreferenceAnnotator; import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings; import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation; Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java?rev=1611031&r1=1611030&r2=1611031&view=diff ============================================================================== --- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java (original) +++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java Wed Jul 16 14:46:37 2014 @@ -152,6 +152,7 @@ EvaluationOfTemporalRelations_ImplBase{ options.getXMLFormat(), options.getXMIDirectory(), options.getTreebankDirectory(), + options.getCoreferenceDirectory(), options.getClosure(), options.getPrintErrors(), options.getPrintFormattedRelations(), @@ -198,6 +199,7 @@ EvaluationOfTemporalRelations_ImplBase{ XMLFormat xmlFormat, File xmiDirectory, File treebankDirectory, + File coreferenceDirectory, boolean useClosure, boolean printErrors, boolean printRelations, @@ -212,6 +214,7 @@ EvaluationOfTemporalRelations_ImplBase{ xmlFormat, xmiDirectory, treebankDirectory, + coreferenceDirectory, printErrors, printRelations, params); @@ -478,33 +481,6 @@ EvaluationOfTemporalRelations_ImplBase{ return result; } - private static Collection correctArgOrder( - Collection systemRelations, - Collection goldRelations) { - Set 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; - } - - // @SuppressWarnings("unchecked") // private static Collection getDuplicateRelations( // Collection goldRelations, 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=1611031&r1=1611030&r2=1611031&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 Wed Jul 16 14:46:37 2014 @@ -218,6 +218,7 @@ EvaluationOfTemporalRelations_ImplBase{ xmlFormat, xmiDirectory, treebankDirectory, + null, printErrors, printRelations, params); @@ -487,32 +488,77 @@ EvaluationOfTemporalRelations_ImplBase{ } */ - // private static Collection removeNonGoldRelations( - // Collection systemRelations, - // Collection goldRelations, Function getSpan) { - // //remove non-gold pairs from system relations: - // Set goodSys = Sets.newHashSet(); - // Set goldspans = new HashSet(); - // - // for (BinaryTextRelation relation : goldRelations) { - // goldspans.add(((SPAN_TYPE) getSpan.apply(relation))); - // } - // - // for (BinaryTextRelation relation : systemRelations) { - // if (goldspans.contains(((SPAN_TYPE) getSpan.apply(relation)))) { - // goodSys.add(relation); - // } - // } - // - // return goodSys; - // } - +// private static Collection removeNonGoldRelations( +// Collection systemRelations, +// Collection goldRelations, Function getSpan) { +// //remove non-gold pairs from system relations: +// Set goodSys = Sets.newHashSet(); +// Set goldspans = new HashSet(); +// +// for (BinaryTextRelation relation : goldRelations) { +// goldspans.add(((SPAN_TYPE) getSpan.apply(relation))); +// } +// +// for (BinaryTextRelation relation : systemRelations) { +// if (goldspans.contains(((SPAN_TYPE) getSpan.apply(relation)))) { +// goodSys.add(relation); +// } +// } +// +// return goodSys; +// } + // private static boolean matchSpan(Annotation arg1, Annotation arg2) { // boolean result = false; -// if(arg1==null || arg2 == null) return result; // result = arg1.getBegin() == arg2.getBegin() && arg1.getEnd() == arg2.getEnd(); // return result; // } + +// protected static Collection correctArgOrder( +// Collection systemRelations, +// Collection goldRelations) { +// Set 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; +// } + + +// @SuppressWarnings("unchecked") +// private static Collection getDuplicateRelations( +// Collection goldRelations, +// Function getSpan) { +// Set duplicateRelations = Sets.newHashSet(); +// //build a multimap that map gold span to gold relation +// Multimap spanToRelation = HashMultimap.create(); +// for (BinaryTextRelation relation : goldRelations) { +// spanToRelation.put((SPAN) getSpan.apply(relation), relation); +// } +// for (SPAN span: spanToRelation.keySet()){ +// Collection relations = spanToRelation.get(span); +// if(relations.size()>1){//if same span maps to multiple relations +// duplicateRelations.addAll(relations); +// } +// } +// return duplicateRelations; +// } // private static Collection correctArgOrder( // Collection systemRelations, 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=1611031&r1=1611030&r2=1611031&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 Wed Jul 16 14:46:37 2014 @@ -20,6 +20,7 @@ package org.apache.ctakes.temporal.eval; import java.io.File; import java.util.Collection; +import java.util.Set; import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings; import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation; @@ -39,6 +40,7 @@ import org.uimafit.descriptor.Configurat import org.uimafit.util.JCasUtil; import com.google.common.collect.Lists; +import com.google.common.collect.Sets; import com.lexicalscope.jewel.cli.Option; public abstract class EvaluationOfTemporalRelations_ImplBase extends @@ -56,6 +58,10 @@ public abstract class EvaluationOfTempor @Option public boolean getClosure(); + + @Option + public boolean getClassificationOnly(); + } protected static boolean DEFAULT_BOTH_DIRECTIONS = false; @@ -72,11 +78,11 @@ public abstract class EvaluationOfTempor protected ParameterSettings params = null; protected boolean printRelations = false; - public EvaluationOfTemporalRelations_ImplBase(File baseDirectory, + public EvaluationOfTemporalRelations_ImplBase(File baseDirectory, File rawTextDirectory, File xmlDirectory, XMLFormat xmlFormat, - File xmiDirectory, File treebankDirectory, boolean printErrors, boolean printRelations, ParameterSettings params) { + File xmiDirectory, File treebankDirectory, File coreferenceDirectory, boolean printErrors, boolean printRelations, ParameterSettings params) { super(baseDirectory, rawTextDirectory, xmlDirectory, xmlFormat, xmiDirectory, - treebankDirectory); + treebankDirectory, coreferenceDirectory); this.params = params; this.printRelations = printRelations; this.printErrors = printErrors; @@ -148,6 +154,38 @@ public abstract class EvaluationOfTempor } } } + + protected static Collection correctArgOrder( + Collection systemRelations, + Collection goldRelations) { + Set 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 relations) { Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java?rev=1611031&r1=1611030&r2=1611031&view=diff ============================================================================== --- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java (original) +++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java Wed Jul 16 14:46:37 2014 @@ -20,6 +20,7 @@ package org.apache.ctakes.temporal.eval; import java.io.File; import java.io.FileInputStream; +import java.io.FileNotFoundException; import java.io.FileOutputStream; import java.io.FilenameFilter; import java.io.IOException; @@ -147,6 +148,9 @@ public abstract class Evaluation_ImplBas @Option(longName = "treebank", defaultToNull=true) public File getTreebankDirectory(); + @Option(longName = "coreference", defaultToNull=true) + public File getCoreferenceDirectory(); + @Option public boolean getUseGoldTrees(); @@ -181,6 +185,8 @@ public abstract class Evaluation_ImplBas protected File treebankDirectory; + protected File coreferenceDirectory; + protected boolean printErrors = false; protected boolean printOverlapping = false; @@ -195,7 +201,8 @@ public abstract class Evaluation_ImplBas File xmlDirectory, XMLFormat xmlFormat, File xmiDirectory, - File treebankDirectory) { + File treebankDirectory, + File coreferenceDirectory) { super(baseDirectory); this.rawTextDirectory = rawTextDirectory; this.xmlDirectory = xmlDirectory; @@ -203,6 +210,18 @@ public abstract class Evaluation_ImplBas this.xmiDirectory = xmiDirectory; this.xmiExists = this.xmiDirectory.exists() && this.xmiDirectory.listFiles().length > 0; this.treebankDirectory = treebankDirectory; + this.coreferenceDirectory = coreferenceDirectory; + } + + public Evaluation_ImplBase( + File baseDirectory, + File rawTextDirectory, + File xmlDirectory, + XMLFormat xmlFormat, + File xmiDirectory, + File treebankDirectory) { + this(baseDirectory, rawTextDirectory, xmlDirectory, xmlFormat, + xmiDirectory, treebankDirectory, null); } public void setI2B2Output(String outDir){ @@ -225,7 +244,7 @@ public abstract class Evaluation_ImplBas this.xmiExists = true; } - private List getFilesFor(List patientSets) { + private List getFilesFor(List patientSets) throws FileNotFoundException { List files = new ArrayList(); if (this.rawTextDirectory == null && this.xmlFormat == XMLFormat.Anafora) { @@ -260,13 +279,13 @@ public abstract class Evaluation_ImplBas System.err.println("Text file in training has no corresponding xml -- skipping: " + train); } } - File xmlText = new File(testDir, pt+".xml"); + File xmlTest = new File(testDir, pt+".xml"); File test = new File(testDir, pt+".xml.txt"); - if(test.exists()){ - if(xmlText.exists()){ + if(xmlTest.exists()){ + if(test.exists()){ files.add(test); }else{ - System.err.println("Text file in test has no corresponding xml -- skipping: " + test); + throw new FileNotFoundException("Could not find the test text file -- for cTAKES usage you must copy the text files into the xml directory for the test set."); } } assert !(train.exists() && test.exists()); @@ -286,11 +305,21 @@ public abstract class Evaluation_ImplBas }else{ // look for equivalent in xml directory: File xmlFile = new File(xmlDirectory, file.getName()); - if(xmlFile.exists()){ - files.add(file); - }else{ - System.err.println("Missing patient file : " + xmlFile); - } + if(xmlFile.exists()){ + if(coreferenceDirectory != null){ + // verify that coref version of xml exists + File corefFile = new File(coreferenceDirectory, file.getName()+".Coreference.gold.completed.xml"); + if(corefFile.exists() && xmlFile.exists()){ + files.add(file); + }else{ + System.err.println("Missing coref patient file : " + corefFile); + } + }else{ + files.add(file); + } + }else{ + System.err.println("Missing patient file : " + xmlFile); + } } } } @@ -357,6 +386,13 @@ public abstract class Evaluation_ImplBas break; } + if(this.coreferenceDirectory != null){ + aggregateBuilder.add( + THYMEAnaforaXMLReader.getDescription(this.coreferenceDirectory), + CAS.NAME_DEFAULT_SOFA, + GOLD_VIEW_NAME); + } + // identify segments if(this.xmlFormat == XMLFormat.I2B2){ aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(SimpleSegmentAnnotator.class)); @@ -425,6 +461,7 @@ public abstract class Evaluation_ImplBas UmlsDictionaryLookupAnnotator.createAnnotatorDescription() ); + /* // add lvg annotator String[] XeroxTreebankMap = { "adj|JJ", @@ -487,6 +524,8 @@ public abstract class Evaluation_ImplBas new File(LvgCmdApiResourceImpl.class.getResource( "/org/apache/ctakes/lvg/data/config/lvg.properties").toURI()))); aggregateBuilder.add(lvgAnnotator); + */ + aggregateBuilder.add(LvgAnnotator.createAnnotatorDescription()); // add dependency parser aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ClearNLPDependencyParserAE.class)); @@ -502,7 +541,9 @@ public abstract class Evaluation_ImplBas // add ctakes constituency parses to system view aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ConstituencyParser.class, ConstituencyParser.PARAM_MODEL_FILENAME, - "org/apache/ctakes/constituency/parser/models/sharpacq-3.1.bin")); + "org/apache/ctakes/constituency/parser/models/thyme.bin")); +// "org/apache/ctakes/constituency/parser/models/sharp-3.1.bin")); +// "org/apache/ctakes/constituency/parser/models/thymeNotempeval.bin")); // aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(BerkeleyParserWrapper.class, // BerkeleyParserWrapper.PARAM_MODEL_FILENAME, //