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From tm...@apache.org
Subject svn commit: r1625365 [10/10] - 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/...
Date Tue, 16 Sep 2014 19:57:25 GMT
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java
Tue Sep 16 19:57:19 2014
@@ -27,11 +27,9 @@ import org.apache.ctakes.temporal.ae.Eve
 import org.apache.ctakes.temporal.ae.EventTimeRelationAnnotator;
 import org.apache.uima.analysis_engine.AnalysisEngine;
 import org.apache.uima.collection.CollectionReader;
-import org.uimafit.component.xwriter.XWriter;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.pipeline.SimplePipeline;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
 
 import com.lexicalscope.jewel.cli.CliFactory;
 import com.lexicalscope.jewel.cli.Option;
@@ -72,7 +70,7 @@ public class FullTemporalExtractionPipel
   public static void main(String[] args) throws Exception {
     FullOptions options = CliFactory.parseArguments(FullOptions.class, args);
     
-    CollectionReader collectionReader = CollectionReaderFactory.createCollectionReaderFromPath(
+    CollectionReader collectionReader = CollectionReaderFactory.createReaderFromPath(
         "../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml",
         FilesInDirectoryCollectionReader.PARAM_INPUTDIR,
         options.getInputDirectory());
@@ -85,7 +83,7 @@ public class FullTemporalExtractionPipel
       aggregateBuilder.add(EventEventRelationAnnotator.createAnnotatorDescription(options.getEventEventRelationModelDirectory()
+ File.separator + "model.jar"));
     }
     
-    //aggregateBuilder.createAggregateDescription().toXML(new FileWriter("desc/analysis_engine/TemporalAggregateUMLSPipeline.xml"));
+    //aggregateBuilder.createEngineDescription().toXML(new FileWriter("desc/analysis_engine/TemporalAggregateUMLSPipeline.xml"));
     AnalysisEngine xWriter = getXMIWriter(options.getOutputDirectory());
     
     SimplePipeline.runPipeline(

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java
Tue Sep 16 19:57:19 2014
@@ -18,44 +18,23 @@
  */
 package org.apache.ctakes.temporal.pipelines;
 
-import java.io.File;
-
 import org.apache.ctakes.chunker.ae.Chunker;
-import org.apache.ctakes.chunker.ae.DefaultChunkCreator;
-import org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster;
 import org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory;
 import org.apache.ctakes.constituency.parser.ae.ConstituencyParser;
 import org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator;
 import org.apache.ctakes.core.ae.SentenceDetector;
 import org.apache.ctakes.core.ae.SimpleSegmentAnnotator;
 import org.apache.ctakes.core.ae.TokenizerAnnotatorPTB;
-import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.ctakes.core.resource.FileResourceImpl;
-import org.apache.ctakes.core.resource.JdbcConnectionResourceImpl;
-import org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl;
+import org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes;
 import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
 import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE;
 import org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE;
-import org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator;
-import org.apache.ctakes.lvg.ae.LvgAnnotator;
-import org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl;
 import org.apache.ctakes.postagger.POSTagger;
-import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.CopyNPChunksToLookupWindowAnnotations;
-import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.RemoveEnclosedLookupWindows;
-import org.apache.ctakes.typesystem.type.syntax.BaseToken;
-import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.ctakes.typesystem.type.textspan.Sentence;
 import org.apache.uima.analysis_engine.AnalysisEngine;
-import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.component.xwriter.XWriter;
-import org.uimafit.component.xwriter.XWriterFileNamer;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.ExternalResourceFactory;
-import org.uimafit.factory.TypePrioritiesFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
 
 import com.lexicalscope.jewel.cli.Option;
 
@@ -81,8 +60,8 @@ public abstract class TemporalExtraction
     AggregateBuilder aggregateBuilder = new AggregateBuilder();
     aggregateBuilder.add(ClinicalPipelineFactory.getDefaultPipeline());
     // add semantic role labeler
-    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ClearNLPSemanticRoleLabelerAE.class));
-    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ConstituencyParser.class));
+    aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(ClearNLPSemanticRoleLabelerAE.class));
+    aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(ConstituencyParser.class));
     return aggregateBuilder;
   }
   
@@ -93,7 +72,7 @@ public abstract class TemporalExtraction
      * 
      */
     // identify segments; use simple segment annotator on non-mayo notes
-    // aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(SegmentsFromBracketedSectionTagsAnnotator.class));
+    // aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(SegmentsFromBracketedSectionTagsAnnotator.class));
     
     aggregateBuilder.add(SimpleSegmentAnnotator.createAnnotatorDescription());
     aggregateBuilder.add(SentenceDetector.createAnnotatorDescription());
@@ -102,26 +81,17 @@ public abstract class TemporalExtraction
     aggregateBuilder.add(POSTagger.createAnnotatorDescription());
     aggregateBuilder.add(Chunker.createAnnotatorDescription());
     aggregateBuilder.add(ClearNLPDependencyParserAE.createAnnotatorDescription());
-    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ClearNLPSemanticRoleLabelerAE.class));
-    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ConstituencyParser.class));
+    aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(ClearNLPSemanticRoleLabelerAE.class));
+    aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(ConstituencyParser.class));
 
     return aggregateBuilder;
   }
   
   protected static AnalysisEngine getXMIWriter(String outputDirectory) throws ResourceInitializationException{
-    return AnalysisEngineFactory.createPrimitive(
-        XWriter.class,
-        XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
-        outputDirectory,
-        XWriter.PARAM_FILE_NAMER_CLASS_NAME,
-        DocIDFileNamer.class.getName()
+    return AnalysisEngineFactory.createEngine(
+        XmiWriterCasConsumerCtakes.class,
+        XmiWriterCasConsumerCtakes.PARAM_OUTPUTDIR,
+        outputDirectory
         );
   }
-  
-  public static class DocIDFileNamer implements XWriterFileNamer {
-    @Override
-    public String nameFile(JCas jCas) {
-      return DocumentIDAnnotationUtil.getDocumentID(jCas);
-    }
-  }
 }

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TimeExtractionPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TimeExtractionPipeline.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TimeExtractionPipeline.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TimeExtractionPipeline.java
Tue Sep 16 19:57:19 2014
@@ -24,9 +24,9 @@ import org.apache.ctakes.core.cr.FilesIn
 import org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator;
 import org.apache.uima.analysis_engine.AnalysisEngine;
 import org.apache.uima.collection.CollectionReader;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.pipeline.SimplePipeline;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
 
 import com.lexicalscope.jewel.cli.CliFactory;
 import com.lexicalscope.jewel.cli.Option;
@@ -52,7 +52,7 @@ public class TimeExtractionPipeline exte
 		
 		TimexOptions options = CliFactory.parseArguments(TimexOptions.class, args);
 
-		CollectionReader collectionReader = CollectionReaderFactory.createCollectionReaderFromPath(
+		CollectionReader collectionReader = CollectionReaderFactory.createReaderFromPath(
 				"../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml",
 				FilesInDirectoryCollectionReader.PARAM_INPUTDIR,
 				options.getInputDirectory());

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CheckKnowtatorAnnotations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CheckKnowtatorAnnotations.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CheckKnowtatorAnnotations.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CheckKnowtatorAnnotations.java
Tue Sep 16 19:57:19 2014
@@ -20,6 +20,7 @@ package org.apache.ctakes.temporal.utils
 
 import java.io.File;
 import java.util.ArrayList;
+import java.util.Iterator;
 import java.util.List;
 
 import org.apache.ctakes.core.ae.SentenceDetector;
@@ -30,14 +31,14 @@ import org.apache.ctakes.temporal.eval.E
 import org.apache.ctakes.typesystem.type.syntax.BaseToken;
 import org.apache.ctakes.typesystem.type.textsem.EventMention;
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
-import org.cleartk.util.ViewURIUtil;
+import org.cleartk.util.ViewUriUtil;
 import org.cleartk.util.ae.UriToDocumentTextAnnotator;
 import org.cleartk.util.cr.UriCollectionReader;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.util.JCasUtil;
 
 import com.lexicalscope.jewel.cli.CliFactory;
 import com.lexicalscope.jewel.cli.Option;
@@ -71,30 +72,31 @@ public class CheckKnowtatorAnnotations {
     CollectionReader reader = UriCollectionReader.getCollectionReaderFromFiles(files);
     AggregateBuilder builder = new AggregateBuilder();
     builder.add(UriToDocumentTextAnnotator.getDescription());
-    builder.add(AnalysisEngineFactory.createPrimitiveDescription(
+    builder.add(AnalysisEngineFactory.createEngineDescription(
         THYMEKnowtatorXMLReader.class,
         THYMEKnowtatorXMLReader.PARAM_KNOWTATOR_XML_DIRECTORY,
         options.getKnowtatorXMLDirectory()));
-    builder.add(AnalysisEngineFactory.createPrimitiveDescription(SegmentsFromBracketedSectionTagsAnnotator.class));
-    builder.add(AnalysisEngineFactory.createPrimitiveDescription(
+    builder.add(AnalysisEngineFactory.createEngineDescription(SegmentsFromBracketedSectionTagsAnnotator.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));
-    for (JCas jCas : new JCasIterable(reader, builder.createAggregate())) {
+    builder.add(AnalysisEngineFactory.createEngineDescription(TokenizerAnnotatorPTB.class));
+    for (Iterator<JCas> casIter = new JCasIterator(reader, builder.createAggregate());
casIter.hasNext();){
+      JCas jCas = casIter.next();
       for (EventMention event : JCasUtil.select(jCas, EventMention.class)) {
         List<BaseToken> tokens = JCasUtil.selectCovered(jCas, BaseToken.class, event);
         if (tokens.size() > 1) {
           System.err.printf(
               "Multi-token event \"%s\" in %s\n",
               event.getCoveredText(),
-              ViewURIUtil.getURI(jCas));
+              ViewUriUtil.getURI(jCas));
         }
         if (event.getCoveredText().contains(" ")) {
           System.err.printf(
               "Whitespace in event \"%s\" in %s\n",
               event.getCoveredText(),
-              ViewURIUtil.getURI(jCas));
+              ViewUriUtil.getURI(jCas));
         }
       }
     }

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/RunCorpusDiagnostics.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/RunCorpusDiagnostics.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/RunCorpusDiagnostics.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/RunCorpusDiagnostics.java
Tue Sep 16 19:57:19 2014
@@ -35,14 +35,14 @@ import org.apache.ctakes.typesystem.type
 import org.apache.ctakes.utils.struct.CounterMap;
 import org.apache.uima.UIMAException;
 import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.cleartk.util.ae.UriToDocumentTextAnnotator;
 import org.cleartk.util.cr.UriCollectionReader;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.util.JCasUtil;
 
 import com.lexicalscope.jewel.cli.CliFactory;
 import com.lexicalscope.jewel.cli.Option;
@@ -75,14 +75,14 @@ public class RunCorpusDiagnostics {
 		CollectionReader reader = UriCollectionReader.getCollectionReaderFromFiles(getFilesFor(options.getRawTextDirectory(),
trainItems));
 		AggregateBuilder aggregateBuilder = new AggregateBuilder();
 		aggregateBuilder.add(UriToDocumentTextAnnotator.getDescription());
-		aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+		aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(
 				XMIReader.class,
 				XMIReader.PARAM_XMI_DIRECTORY,
 				options.getXMIDirectory()));
 
 		CounterMap<String> timeClassCounts = new CounterMap<String>();
 		
-		JCasIterable casIter = new JCasIterable(reader, aggregateBuilder.createAggregate());
+		JCasIterator casIter = new JCasIterator(reader, aggregateBuilder.createAggregate());
 		while(casIter.hasNext()){
 			JCas jcas = casIter.next();
 			JCas goldView = jcas.getView(Evaluation_ImplBase.GOLD_VIEW_NAME);

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/SMOTEplus.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/SMOTEplus.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/SMOTEplus.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/SMOTEplus.java
Tue Sep 16 19:57:19 2014
@@ -24,8 +24,8 @@ import java.util.Comparator;
 import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.List;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.Instance;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.Instance;
 import com.google.common.collect.HashBasedTable;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Table;

Modified: ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java
Tue Sep 16 19:57:19 2014
@@ -39,14 +39,14 @@ import org.apache.uima.UIMAException;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
 import org.junit.Test;
-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.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;
 
 public class BackwardsTimeAnnotatorTest {
 
@@ -65,9 +65,9 @@ public class BackwardsTimeAnnotatorTest 
 		AggregateBuilder builder = new AggregateBuilder();
 		builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
 		builder.add(AnalysisEngineFactory
-				.createPrimitiveDescription(CopyNPChunksToLookupWindowAnnotations.class));
+				.createEngineDescription(CopyNPChunksToLookupWindowAnnotations.class));
 		builder.add(AnalysisEngineFactory
-				.createPrimitiveDescription(RemoveEnclosedLookupWindows.class));
+				.createEngineDescription(RemoveEnclosedLookupWindows.class));
 		// Commented out the Dictionary lookup for the test
 		// Uncomment and set -Dctakes.umlsuser and -Dctakes.umlspw env params if
 		// needed

Modified: ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java
Tue Sep 16 19:57:19 2014
@@ -40,14 +40,14 @@ import org.apache.ctakes.typesystem.type
 import org.apache.log4j.Logger;
 import org.apache.uima.UIMAException;
 import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
 import org.junit.Test;
-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.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 ContextualModalityAnnotatorTest {
@@ -67,9 +67,9 @@ public class ContextualModalityAnnotator
 		AggregateBuilder builder = new AggregateBuilder();
 		builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
 		builder.add(AnalysisEngineFactory
-				.createPrimitiveDescription(CopyNPChunksToLookupWindowAnnotations.class));
+				.createEngineDescription(CopyNPChunksToLookupWindowAnnotations.class));
 		builder.add(AnalysisEngineFactory
-				.createPrimitiveDescription(RemoveEnclosedLookupWindows.class));
+				.createEngineDescription(RemoveEnclosedLookupWindows.class));
 		// Commented out the Dictionary lookup for the test
 		// Uncomment and set -Dctakes.umlsuser and -Dctakes.umlspw env params if
 		// needed
@@ -90,7 +90,7 @@ public class ContextualModalityAnnotator
 		builder.add(DocTimeRelAnnotator
 				.createAnnotatorDescription("/org/apache/ctakes/temporal/ae/doctimerel/model.jar"));
 
-		//builder.createAggregateDescription().toXML(new FileWriter("desc/analysis_engine/TemporalAggregateUMLSPipeline.xml"));
+		//builder.createEngineDescription().toXML(new FileWriter("desc/analysis_engine/TemporalAggregateUMLSPipeline.xml"));
 		
 		SimplePipeline.runPipeline(jcas, builder.createAggregateDescription());
 

Modified: ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java
Tue Sep 16 19:57:19 2014
@@ -41,15 +41,15 @@ import org.apache.log4j.Logger;
 import org.apache.uima.UIMAException;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
 import org.junit.Test;
-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 com.google.common.collect.Lists;
 
@@ -70,9 +70,9 @@ public class DocTimeRelAnnotatorTest {
 		AggregateBuilder builder = new AggregateBuilder();
 		builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
 		builder.add(AnalysisEngineFactory
-				.createPrimitiveDescription(CopyNPChunksToLookupWindowAnnotations.class));
+				.createEngineDescription(CopyNPChunksToLookupWindowAnnotations.class));
 		builder.add(AnalysisEngineFactory
-				.createPrimitiveDescription(RemoveEnclosedLookupWindows.class));
+				.createEngineDescription(RemoveEnclosedLookupWindows.class));
 		// Commented out the Dictionary lookup for the test
 		// Uncomment and set -Dctakes.umlsuser and -Dctakes.umlspw env params if
 		// needed
@@ -86,7 +86,7 @@ public class DocTimeRelAnnotatorTest {
 		builder.add(EventAnnotator
 				.createAnnotatorDescription("/org/apache/ctakes/temporal/ae/eventannotator/model.jar"));
 		//link event to eventMention
-		builder.add(AnalysisEngineFactory.createPrimitiveDescription(AddEvent.class));
+		builder.add(AnalysisEngineFactory.createEngineDescription(AddEvent.class));
 		// Add Document Time Relative Annotator
 		builder.add(DocTimeRelAnnotator
 				.createAnnotatorDescription("/org/apache/ctakes/temporal/ae/doctimerel/model.jar"));

Modified: ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventAnnotatorTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventAnnotatorTest.java
(original)
+++ ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventAnnotatorTest.java
Tue Sep 16 19:57:19 2014
@@ -37,14 +37,14 @@ import org.apache.ctakes.typesystem.type
 import org.apache.log4j.Logger;
 import org.apache.uima.UIMAException;
 import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
 import org.junit.Test;
-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.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;
 
 public class EventAnnotatorTest {
 
@@ -63,9 +63,9 @@ public class EventAnnotatorTest {
 		AggregateBuilder builder = new AggregateBuilder();
 		builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
 		builder.add(AnalysisEngineFactory
-				.createPrimitiveDescription(CopyNPChunksToLookupWindowAnnotations.class));
+				.createEngineDescription(CopyNPChunksToLookupWindowAnnotations.class));
 		builder.add(AnalysisEngineFactory
-				.createPrimitiveDescription(RemoveEnclosedLookupWindows.class));
+				.createEngineDescription(RemoveEnclosedLookupWindows.class));
 		// Commented out the Dictionary lookup for the test
 		// Uncomment and set -Dctakes.umlsuser and -Dctakes.umlspw env params if
 		// needed
@@ -87,12 +87,9 @@ public class EventAnnotatorTest {
 					+ mention.getConfidence());
 			temp.add(mention.getCoveredText());
 		}
-		assertEquals(6, temp.size());
+		assertEquals(3, temp.size());
 		assertTrue(temp.contains("old"));
 		assertTrue(temp.contains("referred"));
-		assertTrue(temp.contains("cancer"));
-		assertTrue(temp.contains("till"));
 		assertTrue(temp.contains("blood"));
-		assertTrue(temp.contains("stool"));
 	}
 }

Modified: ctakes/trunk/ctakes-type-system/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-type-system/pom.xml?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-type-system/pom.xml (original)
+++ ctakes/trunk/ctakes-type-system/pom.xml Tue Sep 16 19:57:19 2014
@@ -34,10 +34,6 @@
 			<groupId>org.apache.uima</groupId>
 			<artifactId>uimaj-core</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.uimafit</groupId>
-			<artifactId>uimafit</artifactId>
-		</dependency>
 		<!-- we excluded spring-context in the parent pom, include it here -->
 		<dependency>
 			<groupId>org.springframework</groupId>
@@ -52,6 +48,10 @@
         	<artifactId>junit</artifactId>
         <scope>test</scope>
       </dependency>
+		<dependency>
+			<groupId>org.apache.uima</groupId>
+			<artifactId>uimafit-core</artifactId>
+		</dependency>
 	</dependencies>
 
 	<build>

Added: ctakes/trunk/ctakes-type-system/src/main/resources/META-INF/org.apache.uima.fit/types.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-type-system/src/main/resources/META-INF/org.apache.uima.fit/types.txt?rev=1625365&view=auto
==============================================================================
--- ctakes/trunk/ctakes-type-system/src/main/resources/META-INF/org.apache.uima.fit/types.txt
(added)
+++ ctakes/trunk/ctakes-type-system/src/main/resources/META-INF/org.apache.uima.fit/types.txt
Tue Sep 16 19:57:19 2014
@@ -0,0 +1,9 @@
+classpath*:org/apache/ctakes/typesystem/types/TypeSystem.xml
+classpath*:org/apache/ctakes/assertion/types/TypeSystem.xml
+classpath*:org/apache/ctakes/assertion/zoner/types/TypeSystem.xml
+classpath*:org/apache/ctakes/constituency/parser/types/LabeledTree.xml
+classpath*:org/apache/ctakes/coreference/types/TypeSystem.xml
+classpath*:org/apache/ctakes/drugner/types/TypeSystem.xml
+classpath*:org/apache/ctakes/padtermspotter/types/TypeSystem.xml
+classpath*:org/apache/ctakes/smokingstatus/types/TypeSystem.xml
+classpath*:org/apache/ctakes/sideeffect/types/TypeSystem.xml
\ No newline at end of file

Modified: ctakes/trunk/ctakes-utils/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-utils/pom.xml?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-utils/pom.xml (original)
+++ ctakes/trunk/ctakes-utils/pom.xml Tue Sep 16 19:57:19 2014
@@ -58,5 +58,14 @@
 			<groupId>org.apache.lucene</groupId>
 			<artifactId>lucene-analyzers-common</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.uima</groupId>
+			<artifactId>uimaj-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.uima</groupId>
+			<artifactId>uimaj-tools</artifactId>
+			<version>2.6.0</version>
+		</dependency>
 	</dependencies>
 </project>

Modified: ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/lookup/ae/FirstTokenPermLookupInitializerImpl.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/lookup/ae/FirstTokenPermLookupInitializerImpl.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/lookup/ae/FirstTokenPermLookupInitializerImpl.java
(original)
+++ ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/lookup/ae/FirstTokenPermLookupInitializerImpl.java
Tue Sep 16 19:57:19 2014
@@ -284,7 +284,7 @@ public class FirstTokenPermLookupInitial
    public List<LookupToken> getSortedLookupTokens( final JCas jcas,
                                                    final Annotation covering ) throws AnnotatorInitializationException
{
       final List<LookupToken> ltList = new ArrayList<LookupToken>();
-      final List<BaseToken> inputList = org.uimafit.util.JCasUtil.selectCovered( jcas,
BaseToken.class, covering );
+      final List<BaseToken> inputList = org.apache.uima.fit.util.JCasUtil.selectCovered(
jcas, BaseToken.class, covering );
       for ( BaseToken bta : inputList ) {
          final boolean isNonLookup = bta instanceof NewlineToken
                || bta instanceof PunctuationToken

Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/TestUtils.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/TestUtils.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/TestUtils.java
(original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/TestUtils.java
Tue Sep 16 19:57:19 2014
@@ -31,9 +31,9 @@ import org.apache.uima.resource.Resource
 import org.apache.uima.util.InvalidXMLException;
 import org.apache.uima.util.XMLInputSource;
 import org.apache.uima.util.XMLParser;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
 
 import com.google.common.base.Strings;
 
@@ -75,7 +75,7 @@ public class TestUtils {
 				"desc/analysis_engine/SentenceDetectorAnnotator.xml");
 		addDescriptor(builder,
 				"../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml");
-		builder.add(AnalysisEngineFactory.createPrimitiveDescription(
+		builder.add(AnalysisEngineFactory.createEngineDescription(
 				DBConsumer.class, "analysisBatch", dbAnalysisBatch,
 				"storeDocText", false, "storeCAS", true));
 		AnalysisEngine engine = builder.createAggregate();
@@ -85,7 +85,7 @@ public class TestUtils {
 	public static CollectionReader getFractureDemoCollectionReader()
 			throws ResourceInitializationException {
 		CollectionReader colReader = CollectionReaderFactory
-				.createCollectionReader(
+				.createReader(
 						DBCollectionReader.class,
 						"queryGetDocumentKeys",
 						String.format(queryGetDocumentKeys,

Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DBCollectionReaderTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DBCollectionReaderTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DBCollectionReaderTest.java
(original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DBCollectionReaderTest.java
Tue Sep 16 19:57:19 2014
@@ -30,7 +30,7 @@ import org.apache.uima.collection.metada
 import org.apache.uima.jcas.JCas;
 import org.junit.Assert;
 import org.junit.Test;
-import org.uimafit.factory.JCasFactory;
+import org.apache.uima.fit.factory.JCasFactory;
 import org.xml.sax.SAXException;
 
 public class DBCollectionReaderTest {

Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotatorTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotatorTest.java
(original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotatorTest.java
Tue Sep 16 19:57:19 2014
@@ -25,7 +25,7 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.junit.Assert;
 import org.junit.Test;
-import org.uimafit.factory.JCasFactory;
+import org.apache.uima.fit.factory.JCasFactory;
 
 /**
  * TODO get rid of hard-coded path to Types.xml - load from classpath

Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DictionaryLookupAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DictionaryLookupAnnotatorTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DictionaryLookupAnnotatorTest.java
(original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DictionaryLookupAnnotatorTest.java
Tue Sep 16 19:57:19 2014
@@ -37,8 +37,8 @@ import org.apache.uima.util.XMLInputSour
 import org.apache.uima.util.XMLParser;
 import org.junit.Assert;
 import org.junit.Test;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.JCasFactory;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.JCasFactory;
 
 /**
  * TODO get rid of hard-coded path to Types.xml - load from classpath

Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/NamedEntityRegexTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/NamedEntityRegexTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/NamedEntityRegexTest.java
(original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/NamedEntityRegexTest.java
Tue Sep 16 19:57:19 2014
@@ -31,7 +31,7 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.junit.Assert;
 import org.junit.Test;
-import org.uimafit.factory.JCasFactory;
+import org.apache.uima.fit.factory.JCasFactory;
 
 /**
  * TODO get rid of hard-coded path to Types.xml - load from classpath

Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SegmentRegexTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SegmentRegexTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SegmentRegexTest.java
(original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SegmentRegexTest.java
Tue Sep 16 19:57:19 2014
@@ -34,7 +34,7 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.junit.Assert;
 import org.junit.Test;
-import org.uimafit.factory.JCasFactory;
+import org.apache.uima.fit.factory.JCasFactory;
 
 /**
  * TODO get rid of hard-coded path to Types.xml - load from classpath

Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java
(original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java
Tue Sep 16 19:57:19 2014
@@ -42,7 +42,7 @@ import org.springframework.beans.factory
 import org.springframework.context.ConfigurableApplicationContext;
 import org.springframework.context.access.ContextSingletonBeanFactoryLocator;
 import org.springframework.jdbc.core.JdbcTemplate;
-import org.uimafit.factory.JCasFactory;
+import org.apache.uima.fit.factory.JCasFactory;
 
 import com.google.common.collect.Lists;
 

Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SentenceDetectorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SentenceDetectorTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SentenceDetectorTest.java
(original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SentenceDetectorTest.java
Tue Sep 16 19:57:19 2014
@@ -34,7 +34,7 @@ import org.apache.uima.util.XMLInputSour
 import org.apache.uima.util.XMLParser;
 import org.junit.Assert;
 import org.junit.Test;
-import org.uimafit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AggregateBuilder;
 
 /**
  * TODO get rid of hard-coded path to Types.xml - load from classpath

Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SparseDataExporterTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SparseDataExporterTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SparseDataExporterTest.java
(original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SparseDataExporterTest.java
Tue Sep 16 19:57:19 2014
@@ -35,7 +35,7 @@ import org.apache.uima.util.InvalidXMLEx
 import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
-import org.uimafit.pipeline.SimplePipeline;
+import org.apache.uima.fit.pipeline.SimplePipeline;
 
 public class SparseDataExporterTest {
 	static final String instanceClassQuery = "select note_id,  fracture, case when note_set
= 'train' then 1 else 0 end train from %sfracture_demo";

Modified: ctakes/trunk/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/pom.xml?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/pom.xml (original)
+++ ctakes/trunk/pom.xml Tue Sep 16 19:57:19 2014
@@ -483,22 +483,6 @@
 				<version>2.4.0</version>
 			</dependency>
 			<dependency>
-				<groupId>org.uimafit</groupId>
-				<artifactId>uimafit</artifactId>
-				<version>1.4.0</version>
-				<exclusions>
-					<exclusion>
-						<groupId>commons-io</groupId>
-						<artifactId>commons-io</artifactId>
-					</exclusion>
-					<!--  uima fit is pulling in spring 3.1.0, we want spring 3.1.2 -->
-					<exclusion>
-						<groupId>org.springframework</groupId>
-						<artifactId>spring-context</artifactId>
-					</exclusion>
-				</exclusions>
-			</dependency>
-			<dependency>
 				<groupId>tw.edu.ntu.csie</groupId>
 				<artifactId>libsvm</artifactId>
 				<version>3.1</version>
@@ -511,8 +495,8 @@
 			<!-- import a consistent set of versions for all ClearTK modules -->
 			<dependency>
 				<groupId>org.cleartk</groupId>
-				<artifactId>cleartk-release</artifactId>
-				<version>1.4.1</version>
+				<artifactId>cleartk</artifactId>
+				<version>2.0.0</version>
 				<type>pom</type>
 				<scope>import</scope>
 			</dependency>
@@ -600,7 +584,12 @@
 				<groupId>com.googlecode.clearnlp</groupId>
 				<artifactId>clearnlp</artifactId>
 				<version>1.3.1</version>
-			</dependency>			
+			</dependency>
+			<dependency>
+				<groupId>org.apache.uima</groupId>
+				<artifactId>uimafit-core</artifactId>
+				<version>2.1.0</version>
+			</dependency>
 		</dependencies>
 	</dependencyManagement>
 	<build>



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