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From tm...@apache.org
Subject svn commit: r1625365 [3/10] - in /ctakes/trunk: ./ ctakes-assertion-zoner-res/src/main/resources/META-INF/org.apache.uima.fit/ ctakes-assertion-zoner-res/src/main/resources/META-INF/org.uimafit/ ctakes-assertion-zoner/ ctakes-assertion-zoner/src/main/j...
Date Tue, 16 Sep 2014 19:57:25 GMT
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionAboveLeftTreeExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionAboveLeftTreeExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionAboveLeftTreeExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionAboveLeftTreeExtractor.java Tue Sep 16 19:57:19 2014
@@ -28,13 +28,13 @@ import org.apache.ctakes.core.resource.F
 import org.apache.ctakes.utils.tree.SimpleTree;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.TreeFeature;
-import org.cleartk.classifier.feature.extractor.CleartkExtractorException;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.TreeFeature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 import org.cleartk.util.CleartkInitializationException;
 
-public class AssertionAboveLeftTreeExtractor implements SimpleFeatureExtractor {
+public class AssertionAboveLeftTreeExtractor implements FeatureExtractor1 {
   protected SemanticClasses sems = null;
 
   public AssertionAboveLeftTreeExtractor() throws CleartkInitializationException{

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionDependencyTreeExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionDependencyTreeExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionDependencyTreeExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionDependencyTreeExtractor.java Tue Sep 16 19:57:19 2014
@@ -28,18 +28,18 @@ import org.apache.ctakes.core.resource.F
 import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
 import org.apache.ctakes.utils.tree.SimpleTree;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.TreeFeature;
-import org.cleartk.classifier.feature.extractor.CleartkExtractorException;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.TreeFeature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 import org.cleartk.util.CleartkInitializationException;
-import org.uimafit.util.JCasUtil;
 
 import com.google.common.collect.Lists;
 
-public class AssertionDependencyTreeExtractor implements SimpleFeatureExtractor {
+public class AssertionDependencyTreeExtractor implements FeatureExtractor1 {
   protected SemanticClasses sems = null;
 
   public AssertionDependencyTreeExtractor() throws CleartkInitializationException {

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/BrownClusterFeatureFunction.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/BrownClusterFeatureFunction.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/BrownClusterFeatureFunction.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/BrownClusterFeatureFunction.java Tue Sep 16 19:57:19 2014
@@ -30,8 +30,8 @@ import javax.annotation.Nullable;
 
 import org.apache.ctakes.core.resource.FileLocator;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.function.FeatureFunction;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.function.FeatureFunction;
 
 import com.google.common.collect.Maps;
 

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ContextWordWindowExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ContextWordWindowExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ContextWordWindowExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ContextWordWindowExtractor.java Tue Sep 16 19:57:19 2014
@@ -29,14 +29,14 @@ import java.util.regex.Pattern;
 
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.extractor.CleartkExtractorException;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
-public class ContextWordWindowExtractor implements SimpleFeatureExtractor {
+public class ContextWordWindowExtractor implements FeatureExtractor1 {
 
 	private HashMap<String,Double> termVals = null;
 	private static final Pattern linePatt = Pattern.compile("^([^ ]+) : (.+)$");

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest.java Tue Sep 16 19:57:19 2014
@@ -21,39 +21,28 @@ package org.apache.ctakes.assertion.medf
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.Collections;
 import java.util.List;
 import java.util.Map;
-import org.apache.log4j.Logger;
 
-import org.apache.ctakes.core.ae.DocumentIdPrinterAnalysisEngine;
-import org.apache.ctakes.core.cr.XMIReader;
-import org.apache.ctakes.core.util.CtakesFileNamer;
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation;
 import org.apache.ctakes.typesystem.type.textsem.EntityMention;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.log4j.Logger;
 import org.apache.uima.UIMAException;
-import org.apache.uima.analysis_engine.AnalysisEngineDescription;
-import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.JCasFactory;
+import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.metadata.TypeSystemDescription;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor;
-import org.cleartk.classifier.feature.extractor.simple.CombinedExtractor;
-import org.cleartk.classifier.feature.extractor.simple.CoveredTextExtractor;
-import org.cleartk.classifier.feature.extractor.simple.NamingExtractor;
-import org.cleartk.classifier.feature.extractor.simple.TypePathExtractor;
-import org.uimafit.component.xwriter.XWriter;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.factory.JCasFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractor;
+import org.cleartk.ml.feature.extractor.CombinedExtractor1;
+import org.cleartk.ml.feature.extractor.CoveredTextExtractor;
+import org.cleartk.ml.feature.extractor.TypePathExtractor;
 
 public class CueWordTest
 {
@@ -98,8 +87,8 @@ public class CueWordTest
       sentenceToCoveredCuePhraseMap =
         JCasUtil.indexCovered(jcas, Sentence.class, AssertionCuePhraseAnnotation.class);
     
-    CombinedExtractor baseExtractorCuePhraseCategory =
-        new CombinedExtractor
+    CombinedExtractor1 baseExtractorCuePhraseCategory =
+        new CombinedExtractor1
           (
            new CoveredTextExtractor(),
            new TypePathExtractor(AssertionCuePhraseAnnotation.class, "cuePhrase"),

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest2.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest2.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest2.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest2.java Tue Sep 16 19:57:19 2014
@@ -21,39 +21,28 @@ package org.apache.ctakes.assertion.medf
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.Collections;
 import java.util.List;
 import java.util.Map;
-import org.apache.log4j.Logger;
 
-import org.apache.ctakes.core.ae.DocumentIdPrinterAnalysisEngine;
-import org.apache.ctakes.core.cr.XMIReader;
-import org.apache.ctakes.core.util.CtakesFileNamer;
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation;
 import org.apache.ctakes.typesystem.type.textsem.EntityMention;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.log4j.Logger;
 import org.apache.uima.UIMAException;
-import org.apache.uima.analysis_engine.AnalysisEngineDescription;
-import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.JCasFactory;
+import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.metadata.TypeSystemDescription;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.extractor.CleartkExtractor;
-import org.cleartk.classifier.feature.extractor.simple.CombinedExtractor;
-import org.cleartk.classifier.feature.extractor.simple.CoveredTextExtractor;
-import org.cleartk.classifier.feature.extractor.simple.NamingExtractor;
-import org.cleartk.classifier.feature.extractor.simple.TypePathExtractor;
-import org.uimafit.component.xwriter.XWriter;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.factory.JCasFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractor;
+import org.cleartk.ml.feature.extractor.CombinedExtractor1;
+import org.cleartk.ml.feature.extractor.CoveredTextExtractor;
+import org.cleartk.ml.feature.extractor.TypePathExtractor;
 
 public class CueWordTest2
 {
@@ -98,8 +87,8 @@ public class CueWordTest2
       sentenceToCoveredCuePhraseMap =
         JCasUtil.indexCovered(jcas, Sentence.class, AssertionCuePhraseAnnotation.class);
     
-    CombinedExtractor baseExtractorCuePhraseCategory =
-        new CombinedExtractor
+    CombinedExtractor1 baseExtractorCuePhraseCategory =
+        new CombinedExtractor1
           (
            new CoveredTextExtractor(),
            new TypePathExtractor(AssertionCuePhraseAnnotation.class, "cuePhrase"),

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/DependencyWordsFragmentExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/DependencyWordsFragmentExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/DependencyWordsFragmentExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/DependencyWordsFragmentExtractor.java Tue Sep 16 19:57:19 2014
@@ -28,11 +28,11 @@ import org.apache.ctakes.constituency.pa
 import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
 import org.apache.ctakes.utils.tree.SimpleTree;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
+import org.cleartk.ml.Feature;
 import org.cleartk.util.CleartkInitializationException;
-import org.uimafit.util.JCasUtil;
 
 public class DependencyWordsFragmentExtractor extends TreeFragmentFeatureExtractor {
 

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ExtractorListFeatureFunctionConverter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ExtractorListFeatureFunctionConverter.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ExtractorListFeatureFunctionConverter.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ExtractorListFeatureFunctionConverter.java Tue Sep 16 19:57:19 2014
@@ -21,17 +21,16 @@ package org.apache.ctakes.assertion.medf
 import java.util.ArrayList;
 import java.util.List;
 
-import org.cleartk.classifier.feature.extractor.CleartkExtractor;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
-import org.cleartk.classifier.feature.function.FeatureFunction;
-import org.cleartk.classifier.feature.function.FeatureFunctionExtractor;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
+import org.cleartk.ml.feature.function.FeatureFunction;
+import org.cleartk.ml.feature.function.FeatureFunctionExtractor;
 
 public class ExtractorListFeatureFunctionConverter {
-	public static List<FeatureFunctionExtractor> convert( List<? extends SimpleFeatureExtractor> extractors, FeatureFunction ff ) {
+	public static List<FeatureFunctionExtractor> convert( List<? extends FeatureExtractor1> extractors, FeatureFunction ff ) {
 
 		List<FeatureFunctionExtractor> featureFunctionExtractors = new ArrayList<FeatureFunctionExtractor>();
 		if (null!=extractors) {
-			for (SimpleFeatureExtractor extractor : extractors) {
+			for (FeatureExtractor1 extractor : extractors) {
 				featureFunctionExtractors.add(
 						new FeatureFunctionExtractor(extractor,ff)
 						);

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/FedaFeatureFunction.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/FedaFeatureFunction.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/FedaFeatureFunction.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/FedaFeatureFunction.java Tue Sep 16 19:57:19 2014
@@ -19,11 +19,10 @@
 package org.apache.ctakes.assertion.medfacts.cleartk.extractors;
 
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.List;
 
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.function.FeatureFunction;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.function.FeatureFunction;
 
 public class FedaFeatureFunction implements FeatureFunction {
 

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/NegationDependencyFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/NegationDependencyFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/NegationDependencyFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/NegationDependencyFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -25,15 +25,15 @@ import org.apache.ctakes.assertion.util.
 import org.apache.ctakes.dependency.parser.util.DependencyUtility;
 import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.extractor.CleartkExtractorException;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
 public class NegationDependencyFeatureExtractor implements
-		SimpleFeatureExtractor {
+		FeatureExtractor1 {
 
 	NegationManualDepContextAnalyzer conAnal = null;
 

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SRLFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SRLFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SRLFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SRLFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -28,16 +28,16 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textsem.SemanticArgument;
 import org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FSList;
 import org.apache.uima.jcas.cas.NonEmptyFSList;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.extractor.CleartkExtractorException;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
-public class SRLFeatureExtractor implements SimpleFeatureExtractor {
+public class SRLFeatureExtractor implements FeatureExtractor1 {
 
   @Override
   public List<Feature> extract(JCas jCas, Annotation entity)

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SurroundingExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SurroundingExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SurroundingExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SurroundingExtractor.java Tue Sep 16 19:57:19 2014
@@ -24,17 +24,16 @@ import java.util.List;
 import java.util.Map;
 
 import org.apache.ctakes.assertion.zoner.types.Zone;
-import org.apache.ctakes.typesystem.type.textsem.EntityMention;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.log4j.Logger;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.extractor.CleartkExtractorException;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
-public class SurroundingExtractor implements SimpleFeatureExtractor
+public class SurroundingExtractor implements FeatureExtractor1
 {
 	protected static final Logger logger = Logger.getLogger(SurroundingExtractor.class);
 	

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/TreeFragmentFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/TreeFragmentFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/TreeFragmentFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/TreeFragmentFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -30,8 +30,8 @@ import org.apache.ctakes.utils.tree.Frag
 import org.apache.ctakes.utils.tree.SimpleTree;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 import org.cleartk.util.CleartkInitializationException;
 
 /* 
@@ -40,7 +40,7 @@ import org.cleartk.util.CleartkInitializ
  * Model location is hardcoded as of right now.
  * TODO: Parameterize this so that, e.g., multiple projects could use this feature if necessary.
  */
-public abstract class TreeFragmentFeatureExtractor implements SimpleFeatureExtractor {
+public abstract class TreeFragmentFeatureExtractor implements FeatureExtractor1 {
 	public static final String PARAM_OUTPUTDIR = "outputDir";
 	public static final String PARAM_SEMDIR = "semDir";
 	protected HashSet<SimpleTree> frags = null;

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/UncertaintyFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/UncertaintyFeatureExtractor.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/UncertaintyFeatureExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/UncertaintyFeatureExtractor.java Tue Sep 16 19:57:19 2014
@@ -25,11 +25,11 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.feature.extractor.CleartkExtractorException;
-import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
 
-public class UncertaintyFeatureExtractor implements SimpleFeatureExtractor {
+public class UncertaintyFeatureExtractor implements FeatureExtractor1 {
 
   @Override
   public List<Feature> extract(JCas view, Annotation focusAnnotation)

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java Tue Sep 16 19:57:19 2014
@@ -43,13 +43,13 @@ import org.apache.ctakes.utils.tree.Simp
 import org.apache.log4j.Logger;
 import org.apache.uima.UIMAException;
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.kohsuke.args4j.CmdLineException;
 import org.kohsuke.args4j.CmdLineParser;
 import org.kohsuke.args4j.Option;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.util.JCasUtil;
 
 public class GenerateDependencyRepresentation {
   public static class Options {
@@ -93,12 +93,12 @@ public class GenerateDependencyRepresent
     for (int i = 0; i < paths.length; ++i) {
       paths[i] = trainFiles.get(i).getPath();
     }
-    CollectionReader reader = CollectionReaderFactory.createCollectionReader(
+    CollectionReader reader = CollectionReaderFactory.createReader(
             XMIReader.class,
             XMIReader.PARAM_FILES,
             paths);
        
-    JCasIterable casIter = new JCasIterable(reader);
+    JCasIterator casIter = new JCasIterator(reader);
     while(casIter.hasNext()){
       JCas jcas = casIter.next();
 //      String docId = DocumentIDAnnotationUtil.getDocumentID(jcas);

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java Tue Sep 16 19:57:19 2014
@@ -21,7 +21,6 @@ package org.apache.ctakes.assertion.pipe
 import static org.apache.ctakes.assertion.util.AssertionTreeUtils.extractAboveLeftConceptTree;
 
 import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.PrintStream;
 import java.util.Arrays;
@@ -40,13 +39,13 @@ import org.apache.ctakes.utils.tree.Simp
 import org.apache.log4j.Logger;
 import org.apache.uima.UIMAException;
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.kohsuke.args4j.CmdLineException;
 import org.kohsuke.args4j.CmdLineParser;
 import org.kohsuke.args4j.Option;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.util.JCasUtil;
 
 public class GenerateTreeRepresentation{
 
@@ -99,12 +98,12 @@ public class GenerateTreeRepresentation{
 	    for (int i = 0; i < paths.length; ++i) {
 	      paths[i] = trainFiles.get(i).getPath();
 	    }
-	    CollectionReader reader = CollectionReaderFactory.createCollectionReader(
+	    CollectionReader reader = CollectionReaderFactory.createReader(
 	            XMIReader.class,
 	            XMIReader.PARAM_FILES,
 	            paths);
 	       
-	    JCasIterable casIter = new JCasIterable(reader);
+	    JCasIterator casIter = new JCasIterator(reader);
 	    while(casIter.hasNext()){
 	    	JCas jcas = casIter.next();
 	    	processDocument(jcas);

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipeline.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipeline.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipeline.java Tue Sep 16 19:57:19 2014
@@ -21,19 +21,17 @@ package org.apache.ctakes.assertion.pipe
 
 import java.io.IOException;
 
+import org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader;
+import org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes;
+import org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader;
 import org.apache.uima.UIMAException;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.collection.CollectionReaderDescription;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
 import org.apache.uima.resource.metadata.TypeSystemDescription;
-import org.uimafit.component.xwriter.XWriter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
-import org.uimafit.pipeline.SimplePipeline;
-
-import org.apache.ctakes.assertion.cr.GoldEntityAndAttributeReader;
-import org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader;
-import org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader;
 
 /**
  * 
@@ -49,11 +47,11 @@ public class GoldEntityAndAttributeReade
 		
 		TypeSystemDescription typeSystemDescription = 
 				// use the uimafit method of finding available type system
-				// descriptor via META-INF/org.uimafit/types.txt 
+				// descriptor via META-INF/org.apache.uima.fit/types.txt 
 				// (found in ctakes-type-system/src/main/resources)
 			TypeSystemDescriptionFactory.createTypeSystemDescription();
 		
-		CollectionReaderDescription collectionReader = CollectionReaderFactory.createDescription(
+		CollectionReaderDescription collectionReader = CollectionReaderFactory.createReaderDescription(
 				FilesInDirectoryCollectionReader.class,
 				typeSystemDescription,
 				"InputDirectory",
@@ -62,7 +60,7 @@ public class GoldEntityAndAttributeReade
 				//"/work/medfacts/sharp/data/2012-10-16_full_data_set_updated/Seed_Corpus/sandbox/batch02_mayo/text"
 				);
 		
-//		AnalysisEngineDescription goldAnnotator = AnalysisEngineFactory.createPrimitiveDescription(
+//		AnalysisEngineDescription goldAnnotator = AnalysisEngineFactory.createEngineDescription(
 //				GoldEntityAndAttributeReader.class,
 //				typeSystemDescription,
 //				"InputDirectory",
@@ -70,7 +68,7 @@ public class GoldEntityAndAttributeReade
 //				"/Users/m081914/work/sharpattr/ctakes/ctakes-assertion/sharp_data/one/xml/");
 ////				"/work/medfacts/sharp/data/2012-10-16_full_data_set_updated/Seed_Corpus/sandbox/batch02_mayo/knowtator/");
 
-		AnalysisEngineDescription goldAnnotator = AnalysisEngineFactory.createPrimitiveDescription(
+		AnalysisEngineDescription goldAnnotator = AnalysisEngineFactory.createEngineDescription(
 				SHARPKnowtatorXMLReader.class,
 				typeSystemDescription,
 				"KnowtatorURI",
@@ -78,16 +76,14 @@ public class GoldEntityAndAttributeReade
 				"TextURI",
 				"/Users/m081914/work/sharpattr/ctakes/ctakes-assertion/sharp_data/one/Knowtator/text");
 		
-		AnalysisEngineDescription xWriter = AnalysisEngineFactory.createPrimitiveDescription(
-        XWriter.class,
+		AnalysisEngineDescription xWriter = AnalysisEngineFactory.createEngineDescription(
+        XmiWriterCasConsumerCtakes.class,
         typeSystemDescription,
-        XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
+        XmiWriterCasConsumerCtakes.PARAM_OUTPUTDIR,
 //        "/Users/m081914/work/data/sharp/Seed_Corpus/Mayo/UMLS_CEM/ss1_batch10/Knowtator XMI/",
-    	"/Users/m081914/work/sharpattr/ctakes/ctakes-assertion/sharp_data/one/Knowtator_XMI/",
+    	"/Users/m081914/work/sharpattr/ctakes/ctakes-assertion/sharp_data/one/Knowtator_XMI/"
         // "/work/medfacts/sharp/data/2012-10-09_full_data_set/batch02",
 //        "/work/medfacts/sharp/data/2012-10-16_full_data_set_updated/Seed_Corpus/sandbox/batch02_mayo/xmi",
-        XWriter.PARAM_FILE_NAMER_CLASS_NAME,
-        CtakesFileNamer.class.getName()
         );
     
 		SimplePipeline.runPipeline(collectionReader, goldAnnotator, xWriter);

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipelineForSeedCorpus.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipelineForSeedCorpus.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipelineForSeedCorpus.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipelineForSeedCorpus.java Tue Sep 16 19:57:19 2014
@@ -29,19 +29,20 @@ import org.apache.ctakes.assertion.cr.Mi
 import org.apache.ctakes.assertion.cr.NegExCorpusReader;
 import org.apache.ctakes.assertion.pipelines.SharpCorpusSplit.Subcorpus;
 import org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader;
+import org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes;
 import org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader;
 import org.apache.log4j.Logger;
 import org.apache.uima.UIMAException;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.collection.CollectionReaderDescription;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.resource.metadata.TypeSystemDescription;
-import org.uimafit.component.xwriter.XWriter;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
-import org.uimafit.pipeline.SimplePipeline;
+
 import com.google.common.base.Function;
 
 /**
@@ -135,13 +136,13 @@ public class GoldEntityAndAttributeReade
 			
 			TypeSystemDescription typeSystemDescription = 
 					// use the uimafit method of finding available type system
-					// descriptor via META-INF/org.uimafit/types.txt 
+					// descriptor via META-INF/org.apache.uima.fit/types.txt 
 					// (found in ctakes-type-system/src/main/resources)
 				TypeSystemDescriptionFactory.createTypeSystemDescription();
 			
 			AggregateBuilder aggregate = new AggregateBuilder();
 			
-			CollectionReaderDescription collectionReader = CollectionReaderFactory.createDescription(
+			CollectionReaderDescription collectionReader = CollectionReaderFactory.createReaderDescription(
 					FilesInDirectoryCollectionReader.class,
 					typeSystemDescription,
 					"InputDirectory",
@@ -149,7 +150,7 @@ public class GoldEntityAndAttributeReade
 					);
 			
 			// read the UMLS_CEM data from Knowtator
-			AnalysisEngineDescription goldAnnotator = AnalysisEngineFactory.createPrimitiveDescription(
+			AnalysisEngineDescription goldAnnotator = AnalysisEngineFactory.createEngineDescription(
 					SHARPKnowtatorXMLReader.class,
 					typeSystemDescription,
 					"TextDirectory", // 3/13/13 halgrim changed from "TextURI" trying to work with new SHARPKnowtatorXMLReader.java
@@ -159,18 +160,16 @@ public class GoldEntityAndAttributeReade
 			aggregate.add(goldAnnotator);
 
 			// write just the XMI version of what's in Knowtator UMLS_CEM
-			AnalysisEngineDescription xWriter = AnalysisEngineFactory.createPrimitiveDescription(
-					XWriter.class,
+			AnalysisEngineDescription xWriter = AnalysisEngineFactory.createEngineDescription(
+					XmiWriterCasConsumerCtakes.class,
 					typeSystemDescription,
-					XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
-					xmiDirectory.toString(),
-					XWriter.PARAM_FILE_NAMER_CLASS_NAME,
-					CtakesFileNamer.class.getName()
+					XmiWriterCasConsumerCtakes.PARAM_OUTPUTDIR,
+					xmiDirectory.toString()
 			);
 			aggregate.add(xWriter);
 
 			// fill in other values that are necessary for preprocessing
-			AnalysisEngineDescription preprocessAnnotator = AnalysisEngineFactory.createAnalysisEngineDescription(
+			AnalysisEngineDescription preprocessAnnotator = AnalysisEngineFactory.createEngineDescription(
 					"desc/analysis_engine/AttributeDiscoveryPreprocessor"
 					);
 			aggregate.add(preprocessAnnotator);
@@ -194,13 +193,11 @@ public class GoldEntityAndAttributeReade
 					subcorpusDirectory = trainDirectory;
 					break;
 				}
-				AnalysisEngineDescription xWriter2 = AnalysisEngineFactory.createPrimitiveDescription(
-						XWriter.class,
+				AnalysisEngineDescription xWriter2 = AnalysisEngineFactory.createEngineDescription(
+						XmiWriterCasConsumerCtakes.class,
 						typeSystemDescription,
-						XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
-						subcorpusDirectory,
-						XWriter.PARAM_FILE_NAMER_CLASS_NAME,
-						CtakesFileNamer.class.getName()
+						XmiWriterCasConsumerCtakes.PARAM_OUTPUTDIR,
+						subcorpusDirectory
 				);
 				aggregate.add(xWriter2);
 //				SimplePipeline.runPipeline(collectionReader, goldAnnotator, xWriter, xWriter2);
@@ -247,14 +244,14 @@ public class GoldEntityAndAttributeReade
 	    for(File batchDir : batches){
 	      TypeSystemDescription typeSystemDescription = 
 	          // use the uimafit method of finding available type system
-	          // descriptor via META-INF/org.uimafit/types.txt 
+	          // descriptor via META-INF/org.apache.uima.fit/types.txt 
 	          // (found in ctakes-type-system/src/main/resources)
 	        TypeSystemDescriptionFactory.createTypeSystemDescription();
 	      
 	      File textDirectory = new File(batchDir, "text");
 	      AggregateBuilder aggregate = new AggregateBuilder();
 	      
-	      CollectionReaderDescription collectionReader = CollectionReaderFactory.createDescription(
+	      CollectionReaderDescription collectionReader = CollectionReaderFactory.createReaderDescription(
 	          FilesInDirectoryCollectionReader.class,
 	          typeSystemDescription,
 	          "InputDirectory",
@@ -262,7 +259,7 @@ public class GoldEntityAndAttributeReade
 	          );
 	      
 	      // read the UMLS_CEM data from Knowtator
-	      AnalysisEngineDescription goldAnnotator = AnalysisEngineFactory.createPrimitiveDescription(
+	      AnalysisEngineDescription goldAnnotator = AnalysisEngineFactory.createEngineDescription(
 	          SHARPKnowtatorXMLReader.class,
 	          typeSystemDescription,
 	          "TextDirectory", // 3/13/13 halgrim changed from "TextURI" trying to work with new SHARPKnowtatorXMLReader.java
@@ -272,7 +269,7 @@ public class GoldEntityAndAttributeReade
 	      aggregate.add(goldAnnotator);
 
 	      // fill in other values that are necessary for preprocessing
-	      AnalysisEngineDescription preprocessAnnotator = AnalysisEngineFactory.createAnalysisEngineDescription(
+	      AnalysisEngineDescription preprocessAnnotator = AnalysisEngineFactory.createEngineDescription(
 	          "desc/analysis_engine/AttributeDiscoveryPreprocessor"
 	          );
 	      aggregate.add(preprocessAnnotator);
@@ -294,13 +291,11 @@ public class GoldEntityAndAttributeReade
 	        subcorpusDir = trainDirectory;
 	      }
 	      
-	       AnalysisEngineDescription xWriter = AnalysisEngineFactory.createPrimitiveDescription(
-	            XWriter.class,
+	       AnalysisEngineDescription xWriter = AnalysisEngineFactory.createEngineDescription(
+	            XmiWriterCasConsumerCtakes.class,
 	            typeSystemDescription,
-	            XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
-	            subcorpusDir,
-	            XWriter.PARAM_FILE_NAMER_CLASS_NAME,
-	            CtakesFileNamer.class.getName()
+	            XmiWriterCasConsumerCtakes.PARAM_OUTPUTDIR,
+	            subcorpusDir
 	        );
 	       aggregate.add(xWriter);
 	       SimplePipeline.runPipeline(collectionReader, aggregate.createAggregateDescription());
@@ -314,13 +309,13 @@ public class GoldEntityAndAttributeReade
 
 		TypeSystemDescription typeSystemDescription = 
 			// use the uimafit method of finding available type system
-			// descriptor via META-INF/org.uimafit/types.txt 
+			// descriptor via META-INF/org.apache.uima.fit/types.txt 
 			// (found in ctakes-type-system/src/main/resources)
 			TypeSystemDescriptionFactory.createTypeSystemDescription();
 
 		AggregateBuilder aggregate = new AggregateBuilder();
 
-		CollectionReaderDescription collectionReader = CollectionReaderFactory.createDescription(
+		CollectionReaderDescription collectionReader = CollectionReaderFactory.createReaderDescription(
 				I2B2Challenge2010CollectionReader.class,
 				typeSystemDescription,
 				"inputDir",
@@ -328,19 +323,17 @@ public class GoldEntityAndAttributeReade
 		);
 
 		// fill in other values that are necessary for preprocessing
-		AnalysisEngineDescription preprocessAnnotator = AnalysisEngineFactory.createAnalysisEngineDescription(
+		AnalysisEngineDescription preprocessAnnotator = AnalysisEngineFactory.createEngineDescription(
 				"desc/analysis_engine/AttributeDiscoveryPreprocessor"
 		);
 		aggregate.add(preprocessAnnotator);
 
 		if (preprocessedDirectory!=null) {
-			AnalysisEngineDescription xWriter2 = AnalysisEngineFactory.createPrimitiveDescription(
-					XWriter.class,
+			AnalysisEngineDescription xWriter2 = AnalysisEngineFactory.createEngineDescription(
+					XmiWriterCasConsumerCtakes.class,
 					typeSystemDescription,
-					XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
-					preprocessedDirectory,
-					XWriter.PARAM_FILE_NAMER_CLASS_NAME,
-					CtakesFileNamer.class.getName()
+					XmiWriterCasConsumerCtakes.PARAM_OUTPUTDIR,
+					preprocessedDirectory
 			);
 			aggregate.add(xWriter2);
 			//		SimplePipeline.runPipeline(collectionReader, goldAnnotator, xWriter, xWriter2);
@@ -359,25 +352,23 @@ public class GoldEntityAndAttributeReade
 		AggregateBuilder aggregate = new AggregateBuilder();
 
 		// input dir is hard-coded in AssertionConst
-		CollectionReaderDescription collectionReader = CollectionReaderFactory.createDescription(
+		CollectionReaderDescription collectionReader = CollectionReaderFactory.createReaderDescription(
 				NegExCorpusReader.class,
 				typeSystemDescription
 		);
 
 		// fill in other values that are necessary for preprocessing
-		AnalysisEngineDescription preprocessAnnotator = AnalysisEngineFactory.createAnalysisEngineDescription(
+		AnalysisEngineDescription preprocessAnnotator = AnalysisEngineFactory.createEngineDescription(
 				"desc/analysis_engine/AttributeDiscoveryPreprocessor"
 		);
 		aggregate.add(preprocessAnnotator);
 
 		if (preprocessedDirectory!=null) {
-			AnalysisEngineDescription xWriter2 = AnalysisEngineFactory.createPrimitiveDescription(
-					XWriter.class,
+			AnalysisEngineDescription xWriter2 = AnalysisEngineFactory.createEngineDescription(
+					XmiWriterCasConsumerCtakes.class,
 					typeSystemDescription,
-					XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
-					preprocessedDirectory,
-					XWriter.PARAM_FILE_NAMER_CLASS_NAME,
-					CtakesFileNamer.class.getName()
+					XmiWriterCasConsumerCtakes.PARAM_OUTPUTDIR,
+					preprocessedDirectory
 			);
 			aggregate.add(xWriter2);
 			//		SimplePipeline.runPipeline(collectionReader, goldAnnotator, xWriter, xWriter2);
@@ -400,7 +391,7 @@ public class GoldEntityAndAttributeReade
 		for (File inDir : splitMipacq.keySet() ) {
 			AggregateBuilder aggregate = new AggregateBuilder();
 
-			CollectionReaderDescription collectionReader = CollectionReaderFactory.createDescription(
+			CollectionReaderDescription collectionReader = CollectionReaderFactory.createReaderDescription(
 					FilesInDirectoryCollectionReader.class,
 					typeSystemDescription,
 					"InputDirectory",
@@ -408,7 +399,7 @@ public class GoldEntityAndAttributeReade
 					);
 
 			// read the UMLS_CEM data from Knowtator
-			AnalysisEngineDescription goldAnnotator = AnalysisEngineFactory.createPrimitiveDescription(
+			AnalysisEngineDescription goldAnnotator = AnalysisEngineFactory.createEngineDescription(
 					MiPACQKnowtatorXMLReader.class,
 					typeSystemDescription,
 					MiPACQKnowtatorXMLReader.PARAM_TEXT_DIRECTORY,
@@ -417,19 +408,17 @@ public class GoldEntityAndAttributeReade
 
 			aggregate.add(goldAnnotator);
 			// fill in other values that are necessary for preprocessing
-			AnalysisEngineDescription preprocessAnnotator = AnalysisEngineFactory.createAnalysisEngineDescription(
+			AnalysisEngineDescription preprocessAnnotator = AnalysisEngineFactory.createEngineDescription(
 					"desc/analysis_engine/AttributeDiscoveryPreprocessor"
 					);
 			aggregate.add(preprocessAnnotator);
 
 			if (preprocessedDirectory!=null) {
-				AnalysisEngineDescription xWriter2 = AnalysisEngineFactory.createPrimitiveDescription(
-						XWriter.class,
+				AnalysisEngineDescription xWriter2 = AnalysisEngineFactory.createEngineDescription(
+						XmiWriterCasConsumerCtakes.class,
 						typeSystemDescription,
-						XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
-						splitMipacq.get(inDir),
-						XWriter.PARAM_FILE_NAMER_CLASS_NAME,
-						CtakesFileNamer.class.getName()
+						XmiWriterCasConsumerCtakes.PARAM_OUTPUTDIR,
+						splitMipacq.get(inDir)
 						);
 				aggregate.add(xWriter2);
 				//		SimplePipeline.runPipeline(collectionReader, goldAnnotator, xWriter, xWriter2);

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/RunJudgeAttributeInstances.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/RunJudgeAttributeInstances.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/RunJudgeAttributeInstances.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/RunJudgeAttributeInstances.java Tue Sep 16 19:57:19 2014
@@ -28,19 +28,20 @@ import org.apache.ctakes.assertion.util.
 import org.apache.uima.UIMAException;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.collection.CollectionReaderDescription;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.resource.metadata.TypeSystemDescription;
-import org.cleartk.util.Options_ImplBase;
+import org.kohsuke.args4j.CmdLineException;
+import org.kohsuke.args4j.CmdLineParser;
 import org.kohsuke.args4j.Option;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
-import org.uimafit.pipeline.SimplePipeline;
 
 import scala.actors.threadpool.Arrays;
 
 public class RunJudgeAttributeInstances {
-	public static class Options extends Options_ImplBase {
+	public static class Options {
 		@Option(
 				name = "--input-dir",
 				usage = "where to read the fully-annotated xmi data from",
@@ -94,9 +95,11 @@ public class RunJudgeAttributeInstances 
 
 	/**
 	 * @param args
+	 * @throws CmdLineException 
 	 */
-	public static void main(String[] args) {
-		options.parseOptions(args);
+	public static void main(String[] args) throws CmdLineException {
+		CmdLineParser parser = new CmdLineParser(options);
+		parser.parseArgument(args);
 
 		TypeSystemDescription typeSystemDescription;
 		CollectionReaderDescription collectionReader = null;
@@ -111,19 +114,17 @@ public class RunJudgeAttributeInstances 
 		      paths[i] = items.get(i).getAbsolutePath();
 		    }
 			
-			collectionReader = CollectionReaderFactory.createDescription(
+			collectionReader = CollectionReaderFactory.createReaderDescription(
 			        XMIReader.class,
 			        TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath(),
 			        XMIReader.PARAM_FILES,
 			        paths);
 			
-			userInput = AnalysisEngineFactory.createPrimitiveDescription(
+			userInput = AnalysisEngineFactory.createEngineDescription(
 					JudgeAttributeInstances.class,
 					typeSystemDescription,
 					JudgeAttributeInstances.PARAM_OUTPUT_DIRECTORY_NAME,
-					options.outputDir,
-					JudgeAttributeInstances.PARAM_FILE_NAMER_CLASS_NAME,
-					CtakesFileNamer.class.getName()
+					options.outputDir
 			);			
 			
 		} catch (ResourceInitializationException e) {

Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionDepUtils.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionDepUtils.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionDepUtils.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionDepUtils.java Tue Sep 16 19:57:19 2014
@@ -29,7 +29,7 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.utils.tree.SimpleTree;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class AssertionDepUtils {
 

Modified: ctakes/trunk/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/Chunker.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/Chunker.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/Chunker.java (original)
+++ ctakes/trunk/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/Chunker.java Tue Sep 16 19:57:19 2014
@@ -35,10 +35,10 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 /**
  * This class provides a UIMA wrapper for the OpenNLP
@@ -168,11 +168,11 @@ public class Chunker extends JCasAnnotat
 	}
 	
 	public static AnalysisEngineDescription createAnnotatorDescription() throws ResourceInitializationException{
-	  return AnalysisEngineFactory.createPrimitiveDescription(Chunker.class);
+	  return AnalysisEngineFactory.createEngineDescription(Chunker.class);
 	}
 
 	 public static AnalysisEngineDescription createAnnotatorDescription(String modelFile) throws ResourceInitializationException{
-	    return AnalysisEngineFactory.createPrimitiveDescription(Chunker.class,
+	    return AnalysisEngineFactory.createEngineDescription(Chunker.class,
 	        Chunker.PARAM_CHUNKER_MODEL_FILE,
 	        modelFile);
 	  }

Modified: ctakes/trunk/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/adjuster/ChunkAdjuster.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/adjuster/ChunkAdjuster.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/adjuster/ChunkAdjuster.java (original)
+++ ctakes/trunk/ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/adjuster/ChunkAdjuster.java Tue Sep 16 19:57:19 2014
@@ -32,10 +32,10 @@ import org.apache.uima.analysis_engine.a
 import org.apache.uima.analysis_engine.annotator.AnnotatorProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 /**
  * UIMA annotator that uses a pattern and a rule about that pattern to adjust
@@ -284,7 +284,7 @@ public class ChunkAdjuster extends JCasA
 	}
 
 	public static AnalysisEngineDescription createAnnotatorDescription(String[] chunkPattern, int patternIndex) throws ResourceInitializationException{
-	  return AnalysisEngineFactory.createPrimitiveDescription(ChunkAdjuster.class, 
+	  return AnalysisEngineFactory.createEngineDescription(ChunkAdjuster.class, 
 	      ChunkAdjuster.PARAM_CHUNK_PATTERN,
 	      chunkPattern,
 	      ChunkAdjuster.PARAM_EXTEND_TO_INCLUDE_TOKEN,

Modified: ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java Tue Sep 16 19:57:19 2014
@@ -43,12 +43,12 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.JCasFactory;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.JCasFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
 import org.xml.sax.SAXException;
 
 public class ClinicalPipelineFactory {
@@ -56,8 +56,8 @@ public class ClinicalPipelineFactory {
   public static AnalysisEngineDescription getDefaultPipeline() throws ResourceInitializationException{
     AggregateBuilder builder = new AggregateBuilder();
     builder.add(getTokenProcessingPipeline());
-    builder.add(AnalysisEngineFactory.createPrimitiveDescription(CopyNPChunksToLookupWindowAnnotations.class));
-    builder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveEnclosedLookupWindows.class));
+    builder.add(AnalysisEngineFactory.createEngineDescription(CopyNPChunksToLookupWindowAnnotations.class));
+    builder.add(AnalysisEngineFactory.createEngineDescription(RemoveEnclosedLookupWindows.class));
     builder.add(UmlsDictionaryLookupAnnotator.createAnnotatorDescription());
     builder.add(ClearNLPDependencyParserAE.createAnnotatorDescription());
     builder.add(PolarityCleartkAnalysisEngine.createAnnotatorDescription());

Modified: ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java Tue Sep 16 19:57:19 2014
@@ -23,13 +23,14 @@ import java.io.File;
 import java.util.Date;
 
 import org.apache.ctakes.assertion.util.AssertionConst;
-import org.apache.ctakes.core.util.CtakesFileNamer;
+import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
-import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.collection.CollectionReaderDescription;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.CasIOUtil;
+import org.apache.uima.jcas.JCas;
 import org.cleartk.util.cr.FilesCollectionReader;
-import org.uimafit.component.xwriter.XWriter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.pipeline.SimplePipeline;
 
 /**
  * Run the plaintext clinical pipeline, using the dictionary of terms from UMLS.
@@ -53,24 +54,17 @@ public class ClinicalPipelineWithUmls {
 		//InputStream inStream = InputStreamCollectionReader.convertToByteArrayInputStream(documentText);
 		//CollectionReader collectionReader = InputStreamCollectionReader.getCollectionReader(inStream);
 		
-		CollectionReader collectionReader = FilesCollectionReader.getCollectionReader(AssertionConst.CORPUS_WO_GOLD_STD_TO_RUN_THROUGH_CTAKES);
+		CollectionReaderDescription collectionReader = FilesCollectionReader.getDescription(AssertionConst.CORPUS_WO_GOLD_STD_TO_RUN_THROUGH_CTAKES);
 
 		System.out.println("Reading from directory: " + AssertionConst.CORPUS_WO_GOLD_STD_TO_RUN_THROUGH_CTAKES);
 		System.out.println("Outputting to directory: " + AssertionConst.evalOutputDir);
 		
-		AnalysisEngineDescription pipelineIncludingUmlsDictionaries = AnalysisEngineFactory.createAnalysisEngineDescription(
+		AnalysisEngineDescription pipelineIncludingUmlsDictionaries = AnalysisEngineFactory.createEngineDescription(
 				"desc/analysis_engine/AggregatePlaintextUMLSProcessor");
 
-		AnalysisEngineDescription xWriter = AnalysisEngineFactory.createPrimitiveDescription(
-				XWriter.class,
-				XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
-				AssertionConst.evalOutputDir,
-	            XWriter.PARAM_XML_SCHEME_NAME,
-	            XWriter.XMI,
-	            XWriter.PARAM_FILE_NAMER_CLASS_NAME,
-	            CtakesFileNamer.class.getName());
-
-		SimplePipeline.runPipeline(collectionReader, pipelineIncludingUmlsDictionaries, xWriter);
+		for(JCas jCas : SimplePipeline.iteratePipeline(collectionReader, pipelineIncludingUmlsDictionaries)){
+			CasIOUtil.writeXmi(jCas, new File(AssertionConst.evalOutputDir, DocumentIDAnnotationUtil.getDocumentID(jCas) + ".xmi"));
+		}
 		
 	    System.out.println("Done at " + new Date());
 	}

Modified: ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java Tue Sep 16 19:57:19 2014
@@ -30,12 +30,12 @@ import org.apache.ctakes.core.util.Docum
 import org.apache.uima.UIMAException;
 import org.apache.uima.analysis_engine.AnalysisEngine;
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.util.JCasUtil;
 
 public abstract class BagOfAnnotationsGenerator<T extends Annotation,K> {
 
@@ -55,15 +55,15 @@ public abstract class BagOfAnnotationsGe
 	}
 	
 	public BagOfAnnotationsGenerator(String inputDir, String outputDir, String aePath) throws UIMAException, IOException {
-		reader = CollectionReaderFactory.createCollectionReaderFromPath("../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml", 
+		reader = CollectionReaderFactory.createReaderFromPath("../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml", 
 				FilesInDirectoryCollectionReader.PARAM_INPUTDIR, inputDir);
-		this.ae = AnalysisEngineFactory.createAnalysisEngineFromPath(aePath == null ? defaultAEPath : aePath);
+		this.ae = AnalysisEngineFactory.createEngineFromPath(aePath == null ? defaultAEPath : aePath);
 		this.outputDir = outputDir;
 		this.classOfT = getClassOfT();
 	}
 	
 	public void process() throws UIMAException, IOException{
-		JCasIterable casIter = new JCasIterable(reader, ae);
+		JCasIterator casIter = new JCasIterator(reader, ae);
 		while(casIter.hasNext()){
 			JCas jcas = casIter.next();
 			String docId = DocumentIDAnnotationUtil.getDocumentID(jcas);

Modified: ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java (original)
+++ ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java Tue Sep 16 19:57:19 2014
@@ -28,8 +28,8 @@ import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
 
 
 public class ConstituencyParser extends JCasAnnotator_ImplBase {

Modified: ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ParserEvaluationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ParserEvaluationAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ParserEvaluationAnnotator.java (original)
+++ ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ParserEvaluationAnnotator.java Tue Sep 16 19:57:19 2014
@@ -30,21 +30,19 @@ import opennlp.tools.parser.Parse;
 import opennlp.tools.parser.ParserModel;
 import opennlp.tools.parser.chunking.Parser;
 
-import org.apache.ctakes.constituency.parser.util.TreeUtils;
 import org.apache.ctakes.core.cr.LinesFromFileCollectionReader;
-import org.apache.ctakes.core.resource.FileLocator;
 import org.apache.ctakes.typesystem.type.syntax.TopTreebankNode;
 import org.apache.uima.UIMAException;
 import org.apache.uima.analysis_engine.AnalysisEngine;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 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.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.util.JCasUtil;
 
 public class ParserEvaluationAnnotator extends JCasAnnotator_ImplBase{
 
@@ -104,14 +102,14 @@ public class ParserEvaluationAnnotator e
 			System.exit(-1);
 		}
 		
-		CollectionReader reader = CollectionReaderFactory.createCollectionReader(LinesFromFileCollectionReader.class,
+		CollectionReader reader = CollectionReaderFactory.createReader(LinesFromFileCollectionReader.class,
 				LinesFromFileCollectionReader.PARAM_INPUT_FILE_NAME,
 				args[0]);
 		PrintWriter out = new PrintWriter(args[1]);
-		AnalysisEngine ae = AnalysisEngineFactory.createPrimitive(ParserEvaluationAnnotator.class, new Object[]{});
+		AnalysisEngine ae = AnalysisEngineFactory.createEngine(ParserEvaluationAnnotator.class, new Object[]{});
 		
 		JCas jcas = null;
-		JCasIterable casIter = new JCasIterable(reader, ae);
+		JCasIterator casIter = new JCasIterator(reader, ae);
 		while(casIter.hasNext()){
 			jcas = casIter.next();
 			Collection<TopTreebankNode> nodes = JCasUtil.select(jcas, TopTreebankNode.class);

Modified: ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/AnnotationTreeUtils.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/AnnotationTreeUtils.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/AnnotationTreeUtils.java (original)
+++ ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/AnnotationTreeUtils.java Tue Sep 16 19:57:19 2014
@@ -28,7 +28,7 @@ import org.apache.uima.jcas.tcas.Annotat
 import org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode;
 import org.apache.ctakes.typesystem.type.syntax.TopTreebankNode;
 import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.util.JCasUtil;
 
 
 public class AnnotationTreeUtils {

Modified: ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/CommandLineParserUtil.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/CommandLineParserUtil.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/CommandLineParserUtil.java (original)
+++ ctakes/trunk/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/CommandLineParserUtil.java Tue Sep 16 19:57:19 2014
@@ -31,12 +31,12 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.cas.FSIterator;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.metadata.TypeSystemDescription;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.ExternalResourceFactory;
-import org.uimafit.factory.JCasFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
-import org.uimafit.pipeline.SimplePipeline;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.ExternalResourceFactory;
+import org.apache.uima.fit.factory.JCasFactory;
+import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
 
 public class CommandLineParserUtil {
 
@@ -48,15 +48,15 @@ public class CommandLineParserUtil {
 	public static void main(String[] args) throws UIMAException, IOException {
 		TypeSystemDescription types = TypeSystemDescriptionFactory.createTypeSystemDescription();
 		
-//		AnalysisEngine ae = AnalysisEngineFactory.createAnalysisEngineFromPath("desc/analysis_engine/AggregateParsingProcessor.xml");
+//		AnalysisEngine ae = AnalysisEngineFactory.createEngineFromPath("desc/analysis_engine/AggregateParsingProcessor.xml");
 		AggregateBuilder builder = new AggregateBuilder();
-		builder.add(AnalysisEngineFactory.createPrimitiveDescription(SimpleSegmentAnnotator.class));
-	    builder.add(AnalysisEngineFactory.createPrimitiveDescription(
+		builder.add(AnalysisEngineFactory.createEngineDescription(SimpleSegmentAnnotator.class));
+	    builder.add(AnalysisEngineFactory.createEngineDescription(
 	            SentenceDetector.class,
 	            SentenceDetector.SD_MODEL_FILE_PARAM,
 	            "org/apache/ctakes/core/sentdetect/sd-med-model.zip"));
-		builder.add(AnalysisEngineFactory.createPrimitiveDescription(TokenizerAnnotatorPTB.class));
-		builder.add(AnalysisEngineFactory.createPrimitiveDescription(ConstituencyParser.class));
+		builder.add(AnalysisEngineFactory.createEngineDescription(TokenizerAnnotatorPTB.class));
+		builder.add(AnalysisEngineFactory.createEngineDescription(ConstituencyParser.class));
 		
 		AnalysisEngine ae = builder.createAggregate();
 		

Modified: ctakes/trunk/ctakes-context-tokenizer/src/main/java/org/apache/ctakes/contexttokenizer/ae/ContextDependentTokenizerAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-context-tokenizer/src/main/java/org/apache/ctakes/contexttokenizer/ae/ContextDependentTokenizerAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-context-tokenizer/src/main/java/org/apache/ctakes/contexttokenizer/ae/ContextDependentTokenizerAnnotator.java (original)
+++ ctakes/trunk/ctakes-context-tokenizer/src/main/java/org/apache/ctakes/contexttokenizer/ae/ContextDependentTokenizerAnnotator.java Tue Sep 16 19:57:19 2014
@@ -68,9 +68,9 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 /**
  * Finds tokens based on context.
@@ -230,6 +230,6 @@ public class ContextDependentTokenizerAn
 	}
 	
 	public static AnalysisEngineDescription createAnnotatorDescription() throws ResourceInitializationException{
-	  return AnalysisEngineFactory.createPrimitiveDescription(ContextDependentTokenizerAnnotator.class);
+	  return AnalysisEngineFactory.createEngineDescription(ContextDependentTokenizerAnnotator.class);
 	}
 }

Modified: ctakes/trunk/ctakes-core/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/pom.xml?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/pom.xml (original)
+++ ctakes/trunk/ctakes-core/pom.xml Tue Sep 16 19:57:19 2014
@@ -41,10 +41,6 @@
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-utils</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.uimafit</groupId>
-			<artifactId>uimafit</artifactId>
-		</dependency>
 		<!-- we excluded spring-context uimafit transitive dependency in the parent pom, include it here -->
 		<dependency>
 				<groupId>org.springframework</groupId>
@@ -107,7 +103,11 @@
 			<groupId>org.apache.uima</groupId>
 			<artifactId>uimaj-examples</artifactId> <!--  for XCasWriterCasConsumer -->
 		</dependency>
-		
-				
+
+
+		<dependency>
+			<groupId>org.apache.uima</groupId>
+			<artifactId>uimafit-core</artifactId>
+		</dependency>
 	</dependencies>
 </project>

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java Tue Sep 16 19:57:19 2014
@@ -41,8 +41,8 @@ import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
 
 /**
  * Creates segment annotations based on the ccda_sections.txt file Which is

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CopyAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CopyAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CopyAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CopyAnnotator.java Tue Sep 16 19:57:19 2014
@@ -32,9 +32,9 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.TOP;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.util.JCasUtil;
 
 
 /**

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java Tue Sep 16 19:57:19 2014
@@ -24,7 +24,7 @@ import org.apache.log4j.Logger;
 import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
-import org.uimafit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
 
 public class DocumentIdPrinterAnalysisEngine extends JCasAnnotator_ImplBase
 {

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java Tue Sep 16 19:57:19 2014
@@ -106,17 +106,17 @@ import org.apache.log4j.Logger;
 import org.apache.uima.analysis_engine.AnalysisEngine;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.cas.Feature;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.CasIOUtil;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FSArray;
 import org.apache.uima.jcas.cas.TOP;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.util.UriUtils;
 import org.jdom2.JDOMException;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.component.xwriter.XWriter;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
 
 import com.google.common.base.Charsets;
 import com.google.common.collect.Maps;
@@ -129,9 +129,10 @@ public class SHARPKnowtatorXMLReader ext
   public static final String PARAM_TEXT_DIRECTORY = "TextDirectory";
   @ConfigurationParameter(
       name = PARAM_TEXT_DIRECTORY,
+      mandatory = false,
       description = "directory containing the text files (if DocumentIDs are just filenames); "
           + "defaults to assuming that DocumentIDs are full file paths")
-  private File textDirectory;
+  private File textDirectory=null;
   
   public static final String PARAM_SET_DEFAULTS = "SetDefaults";
   @ConfigurationParameter(
@@ -1530,15 +1531,7 @@ public class SHARPKnowtatorXMLReader ext
           "usage: java %s path/to/Knowtator/text [path/to/Knowtator/text ...]",
           SHARPKnowtatorXMLReader.class.getName()));
     }
-    AnalysisEngine engine = AnalysisEngineFactory.createPrimitive(SHARPKnowtatorXMLReader.class);
-    
-    AnalysisEngine xWriter = AnalysisEngineFactory.createPrimitive(
-            XWriter.class,
-            XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
-	    	    "/tmp",
-	    	    XWriter.PARAM_FILE_NAMER_CLASS_NAME,
-	    	    CtakesFileNamer.class.getName()
-           );
+    AnalysisEngine engine = AnalysisEngineFactory.createEngine(SHARPKnowtatorXMLReader.class);
     
     for (String knowtatorTextDirectoryPath : args) {
       File knowtatorTextDirectory = new File(knowtatorTextDirectoryPath);
@@ -1550,7 +1543,7 @@ public class SHARPKnowtatorXMLReader ext
         documentID.addToIndexes();
         engine.process(jCas);
         documentID.setDocumentID(textFile.getName());
-        xWriter.process(jCas);
+        CasIOUtil.writeXmi(jCas, new File("/tmp", textFile.toURI().toString()));
       }
     }
 

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java Tue Sep 16 19:57:19 2014
@@ -53,10 +53,10 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.analysis_engine.annotator.AnnotatorProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 /**
  * Wraps the OpenNLP sentence detector in a UIMA annotator
@@ -250,7 +250,7 @@ public class SentenceDetector extends JC
 	}
 
 	public static AnalysisEngineDescription createAnnotatorDescription() throws ResourceInitializationException{
-	  return AnalysisEngineFactory.createPrimitiveDescription(SentenceDetector.class,
+	  return AnalysisEngineFactory.createEngineDescription(SentenceDetector.class,
 	      SentenceDetector.PARAM_SD_MODEL_FILE,
 	      "org/apache/ctakes/core/sentdetect/sd-med-model.zip");
 	}

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java Tue Sep 16 19:57:19 2014
@@ -24,9 +24,9 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
 
 /**
  * Creates a single segment annotation that spans the entire document. This is
@@ -65,11 +65,11 @@ public class SimpleSegmentAnnotator exte
 	}
 	
 	public static AnalysisEngineDescription createAnnotatorDescription() throws ResourceInitializationException{
-	  return AnalysisEngineFactory.createPrimitiveDescription(SimpleSegmentAnnotator.class);
+	  return AnalysisEngineFactory.createEngineDescription(SimpleSegmentAnnotator.class);
 	}
 	
 	public static AnalysisEngineDescription createAnnotatorDescription(String segmentID) throws ResourceInitializationException {
-    return AnalysisEngineFactory.createPrimitiveDescription(SimpleSegmentAnnotator.class,
+    return AnalysisEngineFactory.createEngineDescription(SimpleSegmentAnnotator.class,
         SimpleSegmentAnnotator.PARAM_SEGMENT_ID,
         segmentID);
 	}

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTB.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTB.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTB.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTB.java Tue Sep 16 19:57:19 2014
@@ -35,10 +35,10 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 /**
  * UIMA annotator that tokenizes based on Penn Treebank rules.
@@ -176,7 +176,7 @@ public class TokenizerAnnotatorPTB exten
 	}
 	
 	public static AnalysisEngineDescription createAnnotatorDescription() throws ResourceInitializationException{
-	  return AnalysisEngineFactory.createPrimitiveDescription(TokenizerAnnotatorPTB.class);
+	  return AnalysisEngineFactory.createEngineDescription(TokenizerAnnotatorPTB.class);
 	}
 }	
 



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