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From tm...@apache.org
Subject svn commit: r1625365 [4/10] - 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-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java Tue Sep 16 19:57:19 2014
@@ -41,19 +41,20 @@ import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.net.MalformedURLException;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.URL;
 
+import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
 import org.apache.uima.UIMAFramework;
+import org.apache.uima.UimaContext;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.CASException;
-import org.apache.uima.cas.FSIterator;
 import org.apache.uima.cas.impl.XmiCasSerializer;
 import org.apache.uima.collection.CasConsumerDescription;
-import org.apache.uima.collection.CasConsumer_ImplBase;
-import org.apache.uima.examples.SourceDocumentInformation;
+import org.apache.uima.fit.component.CasConsumer_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.resource.ResourceProcessException;
@@ -63,9 +64,6 @@ import org.apache.uima.util.XMLInputSour
 import org.apache.uima.util.XMLSerializer;
 import org.xml.sax.SAXException;
 
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
-import org.apache.ctakes.typesystem.type.structured.DocumentID;
-
 /**
  * A simple CAS consumer that writes the CAS to XMI format.
  * <p>
@@ -80,14 +78,15 @@ public class XmiWriterCasConsumerCtakes 
    * output files will be written.
    */
   public static final String PARAM_OUTPUTDIR = "OutputDirectory";
-
+  @ConfigurationParameter(name = PARAM_OUTPUTDIR, description = "Output directory to write xmi files", mandatory = true)
   private File mOutputDir;
 
   private int mDocNum;
 
-  public void initialize() throws ResourceInitializationException {
+  @Override
+  public void initialize(UimaContext context) throws ResourceInitializationException{
+    super.initialize(context);
     mDocNum = 0;
-    mOutputDir = new File((String) getConfigParameterValue(PARAM_OUTPUTDIR));
     if (!mOutputDir.exists()) {
       mOutputDir.mkdirs();
     }
@@ -99,21 +98,21 @@ public class XmiWriterCasConsumerCtakes 
    * 
    * @param aCAS
    *          a CAS which has been populated by the TAEs
-   * 
-   * @throws ResourceProcessException
-   *           if there is an error in processing the Resource
+ * @throws AnalysisEngineProcessException 
    * 
    * @see org.apache.uima.collection.base_cpm.CasObjectProcessor#processCas(org.apache.uima.cas.CAS)
    */
-  public void processCas(CAS aCAS) throws ResourceProcessException {
+  @Override
+  public void process(CAS aCAS) throws AnalysisEngineProcessException {
     String modelFileName = null;
 
     JCas jcas;
     try {
-      jcas = aCAS.getJCas();
-    } catch (CASException e) {
-      throw new ResourceProcessException(e);
-    }
+		jcas = aCAS.getJCas();
+	} catch (CASException e1) {
+		e1.printStackTrace();
+		throw new AnalysisEngineProcessException(e1);
+	}
     
     String originalFileName = DocumentIDAnnotationUtil.getDocumentID(jcas);
     File outFile = null;
@@ -148,9 +147,9 @@ public class XmiWriterCasConsumerCtakes 
     try {
       writeXmi(jcas.getCas(), outFile, modelFileName);
     } catch (IOException e) {
-      throw new ResourceProcessException(e);
+      throw new AnalysisEngineProcessException(e);
     } catch (SAXException e) {
-      throw new ResourceProcessException(e);
+      throw new AnalysisEngineProcessException(e);
     }
   }
 

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextReader.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextReader.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextReader.java Tue Sep 16 19:57:19 2014
@@ -37,8 +37,8 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.util.Progress;
 import org.apache.uima.util.ProgressImpl;
-import org.uimafit.component.JCasCollectionReader_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.component.JCasCollectionReader_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
 import org.xml.sax.SAXException;
 
 /**

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XMIReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XMIReader.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XMIReader.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XMIReader.java Tue Sep 16 19:57:19 2014
@@ -32,8 +32,8 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.util.Progress;
 import org.apache.uima.util.ProgressImpl;
-import org.uimafit.component.JCasCollectionReader_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.component.JCasCollectionReader_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
 import org.xml.sax.SAXException;
 
 /**

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/CtakesFileNamer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/CtakesFileNamer.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/CtakesFileNamer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/CtakesFileNamer.java Tue Sep 16 19:57:19 2014
@@ -19,15 +19,13 @@ package org.apache.ctakes.core.util;
  * under the License.
  */
 
-import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
 import org.apache.uima.UimaContext;
+import org.apache.uima.fit.component.initialize.ConfigurationParameterInitializer;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.ConfigurationParameterFactory;
+import org.apache.uima.fit.factory.initializable.Initializable;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.component.initialize.ConfigurationParameterInitializer;
-import org.uimafit.component.xwriter.XWriterFileNamer;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.ConfigurationParameterFactory;
-import org.uimafit.factory.initializable.Initializable;
 
 /**
  * This is a very simple implementation of XWriterFileNamer that generates file names based on a
@@ -36,24 +34,22 @@ import org.uimafit.factory.initializable
  * @author Philip Ogren
  */
 
-public class CtakesFileNamer implements XWriterFileNamer, Initializable {
+public class CtakesFileNamer implements Initializable {
 
         /**
          * The parameter name for the configuration parameter that specifies a fixed prefix for all
          * returned file names.
          */
-        public static final String PARAM_PREFIX = ConfigurationParameterFactory
-                        .createConfigurationParameterName(CtakesFileNamer.class, "prefix");
-        @ConfigurationParameter(description = "specify a prefix that is prepended to all returned file names", defaultValue="")
+        public static final String PARAM_PREFIX = "prefix";
+        @ConfigurationParameter(name = PARAM_PREFIX, description = "specify a prefix that is prepended to all returned file names", defaultValue="")
         private String prefix;
 
         /**
          * The parameter name for the configuration parameter that specifies a fixed suffix for all
          * returned file names.
          */
-        public static final String PARAM_SUFFIX = ConfigurationParameterFactory
-                        .createConfigurationParameterName(CtakesFileNamer.class, "suffix");
-        @ConfigurationParameter(description = "specify a suffix that is appended to all returned file names", defaultValue="")
+        public static final String PARAM_SUFFIX = "suffix";
+        @ConfigurationParameter(name = PARAM_SUFFIX, description = "specify a suffix that is appended to all returned file names", defaultValue="")
         private String suffix;
 
         int i = 1;

Modified: ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorTest.java (original)
+++ ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorTest.java Tue Sep 16 19:57:19 2014
@@ -31,11 +31,11 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 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 SentenceDetectorAnnotatorTest {
 
@@ -90,11 +90,11 @@ public class SentenceDetectorAnnotatorTe
     AggregateBuilder aggregateBuilder = new AggregateBuilder();
 
     // identify segments; use simple segment annotator on non-mayo notes
-    // aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(SegmentsFromBracketedSectionTagsAnnotator.class));
-    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(CDASegmentAnnotator.class));
+    // aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(SegmentsFromBracketedSectionTagsAnnotator.class));
+    aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(CDASegmentAnnotator.class));
 
     // identify sentences
-    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+    aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(
         SentenceDetector.class,
         SentenceDetector.SD_MODEL_FILE_PARAM,
         "org/apache/ctakes/core/sentdetect/sd-med-model.zip",
@@ -108,11 +108,11 @@ public class SentenceDetectorAnnotatorTe
     AggregateBuilder aggregateBuilder = new AggregateBuilder();
 
     // identify segments; use simple segment annotator on non-mayo notes
-    // aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(SegmentsFromBracketedSectionTagsAnnotator.class));
-    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(SimpleSegmentAnnotator.class));
+    // aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(SegmentsFromBracketedSectionTagsAnnotator.class));
+    aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(SimpleSegmentAnnotator.class));
 
     // identify sentences
-    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+    aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(
         SentenceDetector.class,
         SentenceDetector.SD_MODEL_FILE_PARAM,
         "org/apache/ctakes/core/sentdetect/sd-med-model.zip"

Modified: ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotatorTests.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotatorTests.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotatorTests.java (original)
+++ ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotatorTests.java Tue Sep 16 19:57:19 2014
@@ -31,9 +31,9 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.junit.Test;
-import org.uimafit.factory.JCasFactory;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.factory.JCasFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class SimpleSegmentAnnotatorTests {
 

Modified: ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/TestCDASegmentAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/TestCDASegmentAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/TestCDASegmentAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/TestCDASegmentAnnotator.java Tue Sep 16 19:57:19 2014
@@ -21,19 +21,19 @@ package org.apache.ctakes.core.ae;
 import junit.framework.Assert;
 
 import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.uima.analysis_engine.AnalysisEngine;
+import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
-import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.collection.CollectionReaderDescription;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+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.JCasIterable;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.metadata.TypeSystemDescription;
 import org.cleartk.util.cr.FilesCollectionReader;
 import org.junit.Test;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.util.JCasUtil;
 
 public class TestCDASegmentAnnotator {
 
@@ -44,14 +44,14 @@ public class TestCDASegmentAnnotator {
 		TypeSystemDescription typeSystem = TypeSystemDescriptionFactory
 				.createTypeSystemDescription();
 
-		CollectionReader reader = CollectionReaderFactory
-				.createCollectionReader(FilesCollectionReader.class,
+		CollectionReaderDescription reader = CollectionReaderFactory
+				.createReaderDescription(FilesCollectionReader.class,
 						typeSystem, FilesCollectionReader.PARAM_ROOT_FILE,
 						INPUT_FILE);
 
-		AnalysisEngine sectionAnnotator = AnalysisEngineFactory
-				.createPrimitive(CDASegmentAnnotator.class, typeSystem);
-		AnalysisEngine dumpOutput = AnalysisEngineFactory.createPrimitive(
+		AnalysisEngineDescription sectionAnnotator = AnalysisEngineFactory
+				.createEngineDescription(CDASegmentAnnotator.class, typeSystem);
+		AnalysisEngineDescription dumpOutput = AnalysisEngineFactory.createEngineDescription(
 				DumpOutputAE.class, typeSystem);
 		// SimplePipeline.runPipeline(reader, sectionAnnotator, dumpOutput);
 		JCasIterable casIter = new JCasIterable(reader, sectionAnnotator,
@@ -63,8 +63,7 @@ public class TestCDASegmentAnnotator {
 		int section_begin = 0;
 		int section_end = 0;
 
-		while (casIter.hasNext()) {
-			JCas jCas = casIter.next();
+		for(JCas jCas : casIter){
 			for (Segment segment : JCasUtil.select(jCas, Segment.class)) {
 				if (expected_hpi_section.equalsIgnoreCase(segment.getId())) {
 					section_exists = true;

Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java Tue Sep 16 19:57:19 2014
@@ -60,10 +60,10 @@ import org.apache.uima.jcas.cas.FSList;
 import org.apache.uima.jcas.cas.NonEmptyFSList;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.metadata.TypeSystemDescription;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
-import org.uimafit.pipeline.SimplePipeline;
+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;
 
 public class ODIEVectorFileWriter extends JCasAnnotator_ImplBase {
 
@@ -458,12 +458,12 @@ public class ODIEVectorFileWriter extend
 //																			 "../assertion/desc/medfactsTypeSystem.xml");
 //		TypeSystemDescription corefTypeSystem = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath();
 		try {
-			CollectionReader xmiReader = CollectionReaderFactory.createCollectionReader(XMIReader.class, 
+			CollectionReader xmiReader = CollectionReaderFactory.createReader(XMIReader.class, 
 //					typeSystem, 
 					XMIReader.PARAM_FILES, 
 					paths);
 			
-			AnalysisEngine consumer = AnalysisEngineFactory.createPrimitive(ODIEVectorFileWriter.class,
+			AnalysisEngine consumer = AnalysisEngineFactory.createEngine(ODIEVectorFileWriter.class,
 //					typeSystem,
 					ODIEVectorFileWriter.PARAM_VECTORS, true,
 					ODIEVectorFileWriter.PARAM_TREES, false,

Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java Tue Sep 16 19:57:19 2014
@@ -32,24 +32,23 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.cas.CASRuntimeException;
 import org.apache.uima.cas.impl.XmiCasSerializer;
 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.factory.ConfigurationParameterFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.apache.uima.resource.metadata.TypeSystemDescription;
 import org.apache.uima.util.XMLSerializer;
-import org.cleartk.util.Options_ImplBase;
+import org.kohsuke.args4j.CmdLineException;
+import org.kohsuke.args4j.CmdLineParser;
 import org.kohsuke.args4j.Option;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.factory.ConfigurationParameterFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
-import org.uimafit.pipeline.SimplePipeline;
 import org.xml.sax.ContentHandler;
 import org.xml.sax.SAXException;
 
 public class PreprocessAndWriteXmi {
-	public static class Options extends Options_ImplBase {
+	public static class Options {
 
 		@Option(name = "-t", 
 				aliases = "--textRoot", 
@@ -75,10 +74,12 @@ public class PreprocessAndWriteXmi {
 	 * @param args
 	 * @throws IOException 
 	 * @throws UIMAException 
+	 * @throws CmdLineException 
 	 */
-	public static void main(String[] args) throws UIMAException, IOException {
+	public static void main(String[] args) throws UIMAException, IOException, CmdLineException {
 		Options options = new Options();
-		options.parseOptions(args);
+		CmdLineParser parser = new CmdLineParser(options);
+		parser.parseArgument(args);
 
 		File outputRoot = options.outputRoot;
 		String inputRoot = options.textRoot;
@@ -86,14 +87,14 @@ public class PreprocessAndWriteXmi {
 //			TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath("../common-type-system/desc/common_type_system.xml", 
 //																			 "../assertion/desc/medfactsTypeSystem.xml");
 
-		AnalysisEngine ae = AnalysisEngineFactory.createAnalysisEngineFromPath("desc/analysis_engine/ODIESvmVectorCreator.xml");
+		AnalysisEngine ae = AnalysisEngineFactory.createEngineFromPath("desc/analysis_engine/ODIESvmVectorCreator.xml");
 
-		CollectionReader reader = CollectionReaderFactory.createCollectionReaderFromPath(
+		CollectionReader reader = CollectionReaderFactory.createReaderFromPath(
 				"../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml",
 				FilesInDirectoryCollectionReader.PARAM_INPUTDIR,
 				inputRoot);
 
-		AnalysisEngine serializer = AnalysisEngineFactory.createPrimitive(
+		AnalysisEngine serializer = AnalysisEngineFactory.createEngine(
 				PreprocessAndWriteXmi.SerializeDocumentToXMI.class,
 //				typeSystem,
 				PreprocessAndWriteXmi.SerializeDocumentToXMI.PARAM_OUTPUT_DIRECTORY, 
@@ -103,10 +104,9 @@ public class PreprocessAndWriteXmi {
 	}
 
 	public static class SerializeDocumentToXMI extends JCasAnnotator_ImplBase {
-		public static final String PARAM_OUTPUT_DIRECTORY = ConfigurationParameterFactory
-		.createConfigurationParameterName(SerializeDocumentToXMI.class, "outputDirectory");
+		public static final String PARAM_OUTPUT_DIRECTORY = "OutputDirectory";
 
-		@ConfigurationParameter(mandatory = true, description = "Specifies the output directory in which to write xmi files")
+		@ConfigurationParameter(name = PARAM_OUTPUT_DIRECTORY, mandatory = true, description = "Specifies the output directory in which to write xmi files")
 		private File outputDirectory;
 
 		@Override

Modified: ctakes/trunk/ctakes-dependency-parser/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dependency-parser/pom.xml?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dependency-parser/pom.xml (original)
+++ ctakes/trunk/ctakes-dependency-parser/pom.xml Tue Sep 16 19:57:19 2014
@@ -69,10 +69,6 @@
 			<groupId>org.cleartk</groupId>
 			<artifactId>cleartk-util</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>
@@ -94,6 +90,10 @@
 			<groupId>commons-logging</groupId>
 			<artifactId>commons-logging</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.uima</groupId>
+			<artifactId>uimafit-core</artifactId>
+		</dependency>
 	</dependencies>
 	<description>This wraps the ClearNLP dependency parser and semantic role labeler into a UIMA friendly annotator</description>
 </project>

Modified: ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPDependencyParserAE.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPDependencyParserAE.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPDependencyParserAE.java (original)
+++ ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPDependencyParserAE.java Tue Sep 16 19:57:19 2014
@@ -34,11 +34,11 @@ 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.descriptor.TypeCapability;
-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.descriptor.TypeCapability;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.googlecode.clearnlp.component.AbstractComponent;
 import com.googlecode.clearnlp.dependency.DEPFeat;
@@ -74,29 +74,31 @@ import com.googlecode.clearnlp.reader.Ab
 		})
 public class ClearNLPDependencyParserAE extends JCasAnnotator_ImplBase {
 
-	final String language = AbstractReader.LANG_EN;
-	public Logger logger = Logger.getLogger(getClass().getName());
-	
-	// Default model values
-	public static final String DEFAULT_MODEL_FILE_NAME = "org/apache/ctakes/dependency/parser/models/dependency/mayo-en-dep-1.3.0.jar";
-	public static final String ENG_LEMMATIZER_DATA_FILE = "org/apache/ctakes/dependency/parser/models/lemmatizer/dictionary-1.3.1.jar";
-	
-	
-	// Configuration Parameters 
-	public static final String PARAM_PARSER_MODEL_FILE_NAME = "ParserModelFileName";
-	@ConfigurationParameter(
-			name = PARAM_PARSER_MODEL_FILE_NAME,
-			description = "This parameter provides the file name of the dependency parser model required " +
+  final String language = AbstractReader.LANG_EN;
+  public Logger logger = Logger.getLogger(getClass().getName());
+
+  // Default model values
+  public static final String DEFAULT_MODEL_FILE_NAME = "org/apache/ctakes/dependency/parser/models/dependency/mayo-en-dep-1.3.0.jar";
+  public static final String ENG_LEMMATIZER_DATA_FILE = "org/apache/ctakes/dependency/parser/models/lemmatizer/dictionary-1.3.1.jar";
+
+
+  // Configuration Parameters 
+  public static final String PARAM_PARSER_MODEL_FILE_NAME = "ParserModelFileName";
+  @ConfigurationParameter(
+		  name = PARAM_PARSER_MODEL_FILE_NAME,
+		  description = "This parameter provides the file name of the dependency parser model required " +
 					      "by the factory method provided by ClearNLPUtil.  If not specified, this " +
-					      "analysis engine will use a default model from the resources directory")
-	protected URI parserModelUri;
+					      "analysis engine will use a default model from the resources directory",
+		  defaultValue = DEFAULT_MODEL_FILE_NAME)
+  protected URI parserModelUri;
 
   public static final String PARAM_LEMMATIZER_DATA_FILE = "LemmatizerDataFile";
 
   @ConfigurationParameter(
       name = PARAM_LEMMATIZER_DATA_FILE,
       description = "This parameter provides the data file required for the MorphEnAnalyzer. If not "
-          + "specified, this analysis engine will use a default model from the resources directory")
+          + "specified, this analysis engine will use a default model from the resources directory",
+      defaultValue = ENG_LEMMATIZER_DATA_FILE)
   protected URI lemmatizerDataFile;
 
 	public static final String PARAM_USE_LEMMATIZER = "UseLemmatizer";
@@ -163,6 +165,6 @@ public class ClearNLPDependencyParserAE 
 	}
 	
 	public static AnalysisEngineDescription createAnnotatorDescription() throws ResourceInitializationException{
-	  return AnalysisEngineFactory.createPrimitiveDescription(ClearNLPDependencyParserAE.class);
+	  return AnalysisEngineFactory.createEngineDescription(ClearNLPDependencyParserAE.class);
 	}
 }

Modified: ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPSemanticRoleLabelerAE.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPSemanticRoleLabelerAE.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPSemanticRoleLabelerAE.java (original)
+++ ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPSemanticRoleLabelerAE.java Tue Sep 16 19:57:19 2014
@@ -43,10 +43,10 @@ import org.apache.uima.jcas.cas.EmptyFSL
 import org.apache.uima.jcas.cas.FSList;
 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.descriptor.TypeCapability;
-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.descriptor.TypeCapability;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.googlecode.clearnlp.component.AbstractComponent;
 import com.googlecode.clearnlp.dependency.DEPArc;
@@ -99,19 +99,22 @@ final String language = AbstractReader.L
 
   @ConfigurationParameter(
 		  name = PARAM_PARSER_MODEL_FILE_NAME,
-		  description = "This parameter provides the file name of the semantic role labeler model required by the factory method provided by ClearNLPUtil.")
+		  description = "This parameter provides the file name of the semantic role labeler model required by the factory method provided by ClearNLPUtil.",
+		  defaultValue = DEFAULT_SRL_MODEL_FILE_NAME)
   private String parserModelFileName;
 
   public static final String PARAM_LEMMATIZER_DATA_FILE = "LemmatizerDataFile";
   
   @ConfigurationParameter(
 		  name = PARAM_PRED_MODEL_FILE_NAME,
-		  description = "This parameter provides the file name of the semantic role labeler model required by the factory method provided by ClearNLPUtil.")
+		  description = "This parameter provides the file name of the semantic role labeler model required by the factory method provided by ClearNLPUtil.",
+		  defaultValue = DEFAULT_PRED_MODEL_FILE_NAME)
   private String parserPredFileName;
 
   @ConfigurationParameter(
 		  name = PARAM_ROLE_MODEL_FILE_NAME,
-		  description = "This parameter provides the file name of the semantic role labeler model required by the factory method provided by ClearNLPUtil.")
+		  description = "This parameter provides the file name of the semantic role labeler model required by the factory method provided by ClearNLPUtil.",
+		  defaultValue = DEFAULT_ROLE_MODEL_FILE_NAME)
   private String parserRoleFileName;
 
   

Modified: ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/WriteClearNLPDescriptors.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/WriteClearNLPDescriptors.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/WriteClearNLPDescriptors.java (original)
+++ ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/WriteClearNLPDescriptors.java Tue Sep 16 19:57:19 2014
@@ -18,27 +18,28 @@
  */
 package org.apache.ctakes.dependency.parser.ae.util;
 
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+
 import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE;
 import org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE;
-import org.apache.uima.UIMAException;
-import org.apache.uima.UIMAFramework;
-import org.apache.uima.analysis_engine.AnalysisEngineDescription;
-import org.apache.uima.resource.ResourceInitializationException;
-import org.apache.uima.resource.metadata.TypeSystemDescription;
-import org.apache.uima.util.InvalidXMLException;
-import org.apache.uima.util.XMLInputSource;
-import org.apache.uima.util.XMLParser;
-import org.cleartk.util.Options_ImplBase;
-import org.kohsuke.args4j.Option;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
-import org.xml.sax.SAXException;
+import org.apache.uima.UIMAException;
+import org.apache.uima.UIMAFramework;
+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.fit.factory.TypeSystemDescriptionFactory;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.apache.uima.resource.metadata.TypeSystemDescription;
+import org.apache.uima.util.InvalidXMLException;
+import org.apache.uima.util.XMLInputSource;
+import org.apache.uima.util.XMLParser;
+import org.kohsuke.args4j.CmdLineException;
+import org.kohsuke.args4j.CmdLineParser;
+import org.kohsuke.args4j.Option;
+import org.xml.sax.SAXException;
 
 
 
@@ -55,7 +56,7 @@ public class WriteClearNLPDescriptors {
 	public static final String DEP_NAME="ClearNLPDependencyParser";
 	public static final String SRL_NAME="ClearNLPSRL";
 
-	public static class Options extends Options_ImplBase {
+	public static class Options {
 		@Option(name = "-o",
 				aliases = "--outputRoot",
 				usage = "specify the directory to write out descriptor files",
@@ -74,20 +75,22 @@ public class WriteClearNLPDescriptors {
 	 * @param args
 	 * @throws IOException 
 	 * @throws UIMAException 
-	 * @throws SAXException 
+	 * @throws SAXException 
+	 * @throws CmdLineException 
 	 */
-	public static void main(String[] args) throws IOException, UIMAException, SAXException {
+	public static void main(String[] args) throws IOException, UIMAException, SAXException, CmdLineException {
 		Options options = new Options();
-		options.parseOptions(args);
+		CmdLineParser parser = new CmdLineParser(options);
+		parser.parseArgument(args);
 
 		TypeSystemDescription typeSystem = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath("../../../ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml");
 
-		AnalysisEngineDescription ClearNLPSRLDesc = AnalysisEngineFactory.createPrimitiveDescription(
+		AnalysisEngineDescription ClearNLPSRLDesc = AnalysisEngineFactory.createEngineDescription(
 				ClearNLPSemanticRoleLabelerAE.class,
 				typeSystem
 				);
 
-		AnalysisEngineDescription ClearNLPDepParserDesc = AnalysisEngineFactory.createPrimitiveDescription(
+		AnalysisEngineDescription ClearNLPDepParserDesc = AnalysisEngineFactory.createEngineDescription(
 				ClearNLPDependencyParserAE.class,
 				typeSystem
 				);

Modified: ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/XMIReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/XMIReader.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/XMIReader.java (original)
+++ ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/XMIReader.java Tue Sep 16 19:57:19 2014
@@ -32,8 +32,8 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.util.Progress;
 import org.apache.uima.util.ProgressImpl;
-import org.uimafit.component.JCasCollectionReader_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.component.JCasCollectionReader_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
 import org.xml.sax.SAXException;
 
 

Modified: ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/AnnotationDepUtils.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/AnnotationDepUtils.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/AnnotationDepUtils.java (original)
+++ ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/AnnotationDepUtils.java Tue Sep 16 19:57:19 2014
@@ -29,7 +29,7 @@ import org.apache.ctakes.utils.tree.Simp
 import org.apache.log4j.Logger;
 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;
 
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;

Modified: ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyUtility.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyUtility.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyUtility.java (original)
+++ ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyUtility.java Tue Sep 16 19:57:19 2014
@@ -27,7 +27,7 @@ import org.apache.uima.cas.FSIterator;
 import org.apache.uima.cas.text.AnnotationIndex;
 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;
 
 import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;

Modified: ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/SRLUtility.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/SRLUtility.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/SRLUtility.java (original)
+++ ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/SRLUtility.java Tue Sep 16 19:57:19 2014
@@ -19,7 +19,7 @@
 package org.apache.ctakes.dependency.parser.util;
 
 import org.apache.uima.jcas.tcas.Annotation;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.util.JCasUtil;
 
 import org.apache.ctakes.typesystem.type.textsem.Predicate;
 import org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation;

Modified: ctakes/trunk/ctakes-dependency-parser/src/test/java/org/apache/ctakes/dependency/parser/ae/util/TestClearNLPAnalysisEngines.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dependency-parser/src/test/java/org/apache/ctakes/dependency/parser/ae/util/TestClearNLPAnalysisEngines.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dependency-parser/src/test/java/org/apache/ctakes/dependency/parser/ae/util/TestClearNLPAnalysisEngines.java (original)
+++ ctakes/trunk/ctakes-dependency-parser/src/test/java/org/apache/ctakes/dependency/parser/ae/util/TestClearNLPAnalysisEngines.java Tue Sep 16 19:57:19 2014
@@ -18,33 +18,25 @@
  */
 package org.apache.ctakes.dependency.parser.ae.util;
 
-import java.io.File;
-import java.io.IOException;
-import java.net.URI;
-
-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.jcas.JCas;
-import org.apache.uima.resource.metadata.TypeSystemDescription;
-import org.cleartk.util.Options_ImplBase;
-import org.cleartk.util.cr.FilesCollectionReader;
-import org.junit.Test;
-import org.kohsuke.args4j.Option;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
-import org.uimafit.pipeline.SimplePipeline;
-import org.uimafit.util.JCasUtil;
-import org.xml.sax.SAXException;
-
 import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE;
 import org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE;
 import org.apache.ctakes.dependency.parser.util.DependencyUtility;
 import org.apache.ctakes.dependency.parser.util.SRLUtility;
-import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+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.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.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.resource.metadata.TypeSystemDescription;
+import org.cleartk.util.cr.FilesCollectionReader;
+import org.junit.Test;
+import org.kohsuke.args4j.Option;
 
 /**
  * This class illustrates the pipeline needed to run the ClearNLP dependency parser and SRL systems
@@ -61,7 +53,7 @@ public class TestClearNLPAnalysisEngines
 	//public static final String DEP_DUMMY_MODEL_FILE = "org/apache/ctakes/dependency/parser/models/dependency/dummy.dep.mod.jar";
 	//public static final String SRL_DUMMY_MODEL_FILE = "org/apache/ctakes/dependency/parser/models/srl/dummy.srl.mod.jar";
 	public static String INPUT_FILE = "../ctakes-clinical-pipeline/src/test/data/plaintext/testpatient_plaintext_1.txt";
-	public static class Options extends Options_ImplBase {
+	public static class Options {
 		
 		@Option(name = "-d",
 				aliases = "--depModelFile",
@@ -83,7 +75,7 @@ public class TestClearNLPAnalysisEngines
 		public String inputFile = INPUT_FILE;
 	}
 
-	
+
 	/**
 	 * Simple inner class for dumping out ClearNLP output
 	 * @author lbecker
@@ -110,7 +102,7 @@ public class TestClearNLPAnalysisEngines
 		
 		TypeSystemDescription typeSystem = TypeSystemDescriptionFactory.createTypeSystemDescription();
 		
-		CollectionReader reader1 = CollectionReaderFactory.createCollectionReader(
+		CollectionReader reader1 = CollectionReaderFactory.createReader(
 				FilesCollectionReader.class,
 				typeSystem,
 				FilesCollectionReader.PARAM_ROOT_FILE,
@@ -122,19 +114,19 @@ public class TestClearNLPAnalysisEngines
 		
 		// Create dependency parsers analysis engine with the default models
 		// The dummy models from ClearParser haven't been updated to work with ClearNLP.
-		AnalysisEngine ClearNLPDepParser = AnalysisEngineFactory.createPrimitive(
+		AnalysisEngine ClearNLPDepParser = AnalysisEngineFactory.createEngine(
 				ClearNLPDependencyParserAE.class,
 				typeSystem
 				);
 	
 				
 		// Create analysis engine for SRL
-		AnalysisEngine ClearNLPSRL = AnalysisEngineFactory.createPrimitive(
+		AnalysisEngine ClearNLPSRL = AnalysisEngineFactory.createEngine(
 				ClearNLPSemanticRoleLabelerAE.class,
 				typeSystem
 				);
 		
-		AnalysisEngine dumpClearNLPOutput = AnalysisEngineFactory.createPrimitive(
+		AnalysisEngine dumpClearNLPOutput = AnalysisEngineFactory.createEngine(
 				DumpClearNLPOutputAE.class,
 				typeSystem);
 		

Modified: ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/AbstractJCasTermAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/AbstractJCasTermAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/AbstractJCasTermAnnotator.java (original)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/AbstractJCasTermAnnotator.java Tue Sep 16 19:57:19 2014
@@ -251,7 +251,7 @@ abstract public class AbstractJCasTermAn
    protected void getAnnotationsInWindow( final JCas jcas, final Annotation window,
                                           final List<FastLookupToken> allTokens,
                                           final List<Integer> lookupTokenIndices ) {
-      final List<BaseToken> allBaseTokens = org.uimafit.util.JCasUtil.selectCovered( jcas, BaseToken.class, window );
+      final List<BaseToken> allBaseTokens = org.apache.uima.fit.util.JCasUtil.selectCovered( jcas, BaseToken.class, window );
       for ( BaseToken baseToken : allBaseTokens ) {
          if ( baseToken instanceof NewlineToken ) {
             continue;

Modified: ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DirectLookupInitializerImpl.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DirectLookupInitializerImpl.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DirectLookupInitializerImpl.java (original)
+++ ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DirectLookupInitializerImpl.java Tue Sep 16 19:57:19 2014
@@ -34,7 +34,7 @@ import org.apache.uima.cas.text.Annotati
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.JFSIndexRepository;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.fit.util.JCasUtil;
 
 import java.util.*;
 

Modified: ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/FirstTokenPermLookupInitializerImpl.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/FirstTokenPermLookupInitializerImpl.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/FirstTokenPermLookupInitializerImpl.java (original)
+++ ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/FirstTokenPermLookupInitializerImpl.java Tue Sep 16 19:57:19 2014
@@ -230,7 +230,7 @@ public class FirstTokenPermLookupInitial
    public List<LookupToken> getSortedLookupTokens( final JCas jcas,
                                                    final Annotation covering ) throws AnnotatorInitializationException {
       final List<LookupToken> ltList = new ArrayList<>();
-      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-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java (original)
+++ ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java Tue Sep 16 19:57:19 2014
@@ -34,8 +34,8 @@ import org.apache.log4j.Logger;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.ExternalResourceFactory;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.ExternalResourceFactory;
 
 /**
  * UIMA annotator that identified entities based on lookup.
@@ -115,7 +115,7 @@ public class UmlsDictionaryLookupAnnotat
 	
 	public static AnalysisEngineDescription createAnnotatorDescription() throws ResourceInitializationException{
 	  try {
-      return AnalysisEngineFactory.createPrimitiveDescription(UmlsDictionaryLookupAnnotator.class,
+      return AnalysisEngineFactory.createEngineDescription(UmlsDictionaryLookupAnnotator.class,
           UMLSADDR_PARAM,
           "https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser",
           UMLSVENDOR_PARAM,

Modified: ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/ExampleHelloWorldAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/ExampleHelloWorldAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/ExampleHelloWorldAnnotator.java (original)
+++ ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/ae/ExampleHelloWorldAnnotator.java Tue Sep 16 19:57:19 2014
@@ -28,10 +28,10 @@ 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;
 
 public class ExampleHelloWorldAnnotator extends JCasAnnotator_ImplBase {
 
@@ -75,7 +75,7 @@ public class ExampleHelloWorldAnnotator 
 	public static AnalysisEngineDescription createAnnotatorDescription(
 			boolean saveAnn, boolean printAnn)
 			throws ResourceInitializationException {
-		return AnalysisEngineFactory.createPrimitiveDescription(
+		return AnalysisEngineFactory.createEngineDescription(
 				ExampleHelloWorldAnnotator.class,
 				ExampleHelloWorldAnnotator.PARAM_SAVE_ANN, saveAnn,
 				ExampleHelloWorldAnnotator.PARAM_PRINT_ANN, printAnn);
@@ -83,7 +83,7 @@ public class ExampleHelloWorldAnnotator 
 
 	public static AnalysisEngineDescription createAnnotatorDescription()
 			throws ResourceInitializationException {
-		return AnalysisEngineFactory.createPrimitiveDescription(
+		return AnalysisEngineFactory.createEngineDescription(
 				ExampleHelloWorldAnnotator.class,
 				ExampleHelloWorldAnnotator.PARAM_SAVE_ANN, true,
 				ExampleHelloWorldAnnotator.PARAM_PRINT_ANN, true);

Modified: ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipelines/ExampleAggregatePipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipelines/ExampleAggregatePipeline.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipelines/ExampleAggregatePipeline.java (original)
+++ ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipelines/ExampleAggregatePipeline.java Tue Sep 16 19:57:19 2014
@@ -6,10 +6,10 @@ import org.apache.ctakes.clinicalpipelin
 import org.apache.ctakes.examples.ae.ExampleHelloWorldAnnotator;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.uima.jcas.JCas;
-import org.uimafit.factory.AggregateBuilder;
-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.JCasFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
 
 /**
  * Example of a running a pipeline programatically w/o uima xml descriptor xml files

Modified: ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgAnnotator.java (original)
+++ ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgAnnotator.java Tue Sep 16 19:57:19 2014
@@ -54,11 +54,11 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.JFSIndexRepository;
 import org.apache.uima.jcas.cas.FSList;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.descriptor.ExternalResource;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.ExternalResourceFactory;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.descriptor.ExternalResource;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.ExternalResourceFactory;
 
 /**
  * UIMA annotator that uses the UMLS LVG package to find the canonical form of
@@ -562,7 +562,7 @@ public class LvgAnnotator extends JCasAn
 
 	public static AnalysisEngineDescription createAnnotatorDescription() throws ResourceInitializationException {
 	  try {
-      return AnalysisEngineFactory.createPrimitiveDescription(LvgAnnotator.class,
+      return AnalysisEngineFactory.createEngineDescription(LvgAnnotator.class,
           LvgAnnotator.PARAM_USE_CMD_CACHE,
           false,
           LvgAnnotator.PARAM_USE_LEMMA_CACHE,

Modified: ctakes/trunk/ctakes-lvg/src/main/test/org/apache/ctakes/lvg/test/TestLvgAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-lvg/src/main/test/org/apache/ctakes/lvg/test/TestLvgAnnotator.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-lvg/src/main/test/org/apache/ctakes/lvg/test/TestLvgAnnotator.java (original)
+++ ctakes/trunk/ctakes-lvg/src/main/test/org/apache/ctakes/lvg/test/TestLvgAnnotator.java Tue Sep 16 19:57:19 2014
@@ -35,10 +35,10 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.junit.Test;
-import org.uimafit.factory.AggregateBuilder;
-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.JCasFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class TestLvgAnnotator {
   public static final String note = "" +

Modified: ctakes/trunk/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/ClearNLPPOSTaggerAE.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/ClearNLPPOSTaggerAE.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/ClearNLPPOSTaggerAE.java (original)
+++ ctakes/trunk/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/ClearNLPPOSTaggerAE.java Tue Sep 16 19:57:19 2014
@@ -29,10 +29,10 @@ 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.uimafit.descriptor.TypeCapability;
-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.descriptor.TypeCapability;
+import org.apache.uima.fit.util.JCasUtil;
 
 import com.googlecode.clearnlp.component.AbstractComponent;
 import com.googlecode.clearnlp.dependency.DEPNode;

Modified: ctakes/trunk/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/POSTagger.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/POSTagger.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/POSTagger.java (original)
+++ ctakes/trunk/ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/POSTagger.java Tue Sep 16 19:57:19 2014
@@ -66,12 +66,12 @@ 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.descriptor.ConfigurationParameter;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.TypePrioritiesFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
-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.factory.TypePrioritiesFactory;
+import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
+import org.apache.uima.fit.util.JCasUtil;
 
 public class POSTagger extends JCasAnnotator_ImplBase {
 
@@ -141,7 +141,7 @@ public class POSTagger extends JCasAnnot
 
 	public static AnalysisEngineDescription createAnnotatorDescription()
 			throws ResourceInitializationException {
-		return AnalysisEngineFactory.createPrimitiveDescription(
+		return AnalysisEngineFactory.createEngineDescription(
 				POSTagger.class, TypeSystemDescriptionFactory
 						.createTypeSystemDescription(), TypePrioritiesFactory
 						.createTypePriorities(Segment.class, Sentence.class,
@@ -150,7 +150,7 @@ public class POSTagger extends JCasAnnot
 
 	public static AnalysisEngineDescription createAnnotatorDescription(
 			String model) throws ResourceInitializationException {
-		return AnalysisEngineFactory.createPrimitiveDescription(
+		return AnalysisEngineFactory.createEngineDescription(
 				POSTagger.class, TypeSystemDescriptionFactory
 						.createTypeSystemDescription(), TypePrioritiesFactory
 						.createTypePriorities(Segment.class, Sentence.class,

Modified: ctakes/trunk/ctakes-relation-extractor-res/src/main/resources/org/apache/ctakes/relationextractor/models/degree_of/model.jar
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor-res/src/main/resources/org/apache/ctakes/relationextractor/models/degree_of/model.jar?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
Binary files - no diff available.

Modified: ctakes/trunk/ctakes-relation-extractor-res/src/main/resources/org/apache/ctakes/relationextractor/models/location_of/model.jar
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor-res/src/main/resources/org/apache/ctakes/relationextractor/models/location_of/model.jar?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
Binary files - no diff available.

Modified: ctakes/trunk/ctakes-relation-extractor-res/src/main/resources/org/apache/ctakes/relationextractor/models/modifier_extractor/model.jar
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor-res/src/main/resources/org/apache/ctakes/relationextractor/models/modifier_extractor/model.jar?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
Binary files - no diff available.

Modified: ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/DegreeOfRelationExtractorAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/DegreeOfRelationExtractorAnnotator.xml?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/DegreeOfRelationExtractorAnnotator.xml (original)
+++ ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/DegreeOfRelationExtractorAnnotator.xml Tue Sep 16 19:57:19 2014
@@ -37,28 +37,28 @@
                 <mandatory>false</mandatory>
             </configurationParameter>
             <configurationParameter>
-                <name>org.cleartk.classifier.CleartkAnnotator.classifierFactoryClassName</name>
+                <name>classifierFactoryClassName</name>
                 <description>provides the full name of the ClassifierFactory class to be used.</description>
                 <type>String</type>
                 <multiValued>false</multiValued>
                 <mandatory>false</mandatory>
             </configurationParameter>
             <configurationParameter>
-                <name>org.cleartk.classifier.CleartkAnnotator.dataWriterFactoryClassName</name>
+                <name>dataWriterFactoryClassName</name>
                 <description>provides the full name of the DataWriterFactory class to be used.</description>
                 <type>String</type>
                 <multiValued>false</multiValued>
                 <mandatory>false</mandatory>
             </configurationParameter>
             <configurationParameter>
-                <name>org.cleartk.classifier.CleartkAnnotator.isTraining</name>
+                <name>isTraining</name>
                 <description>determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.</description>
                 <type>Boolean</type>
                 <multiValued>false</multiValued>
                 <mandatory>false</mandatory>
             </configurationParameter>
             <configurationParameter>
-                <name>org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath</name>
+                <name>classifierJarPath</name>
                 <type>String</type>
                 <multiValued>false</multiValued>
                 <mandatory>false</mandatory>
@@ -66,25 +66,25 @@
         </configurationParameters>
         <configurationParameterSettings>
             <nameValuePair>
-                <name>org.cleartk.classifier.CleartkAnnotator.classifierFactoryClassName</name>
+                <name>classifierFactoryClassName</name>
                 <value>
-                    <string>org.cleartk.classifier.jar.JarClassifierFactory</string>
+                    <string>org.cleartk.ml.jar.JarClassifierFactory</string>
                 </value>
             </nameValuePair>
             <nameValuePair>
-                <name>org.cleartk.classifier.CleartkAnnotator.dataWriterFactoryClassName</name>
+                <name>dataWriterFactoryClassName</name>
                 <value>
-                    <string>org.cleartk.classifier.jar.DefaultDataWriterFactory</string>
+                    <string>org.cleartk.ml.jar.DefaultDataWriterFactory</string>
                 </value>
             </nameValuePair>
             <nameValuePair>
                 <name>ProbabilityOfKeepingANegativeExample</name>
                 <value>
-                    <float>1.0</float>
+                    <float>0.5</float>
                 </value>
             </nameValuePair>
             <nameValuePair>
-                <name>org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath</name>
+                <name>classifierJarPath</name>
                 <value>
                     <string>/org/apache/ctakes/relationextractor/models/degree_of/model.jar</string>
                 </value>
@@ -95,6 +95,7 @@
                 <import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
             </imports>
         </typeSystemDescription>
+        <typePriorities/>
         <fsIndexCollection/>
         <capabilities/>
         <operationalProperties>

Modified: ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/LocationOfRelationExtractorAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/LocationOfRelationExtractorAnnotator.xml?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/LocationOfRelationExtractorAnnotator.xml (original)
+++ ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/LocationOfRelationExtractorAnnotator.xml Tue Sep 16 19:57:19 2014
@@ -37,28 +37,28 @@
                 <mandatory>false</mandatory>
             </configurationParameter>
             <configurationParameter>
-                <name>org.cleartk.classifier.CleartkAnnotator.classifierFactoryClassName</name>
+                <name>classifierFactoryClassName</name>
                 <description>provides the full name of the ClassifierFactory class to be used.</description>
                 <type>String</type>
                 <multiValued>false</multiValued>
                 <mandatory>false</mandatory>
             </configurationParameter>
             <configurationParameter>
-                <name>org.cleartk.classifier.CleartkAnnotator.dataWriterFactoryClassName</name>
+                <name>dataWriterFactoryClassName</name>
                 <description>provides the full name of the DataWriterFactory class to be used.</description>
                 <type>String</type>
                 <multiValued>false</multiValued>
                 <mandatory>false</mandatory>
             </configurationParameter>
             <configurationParameter>
-                <name>org.cleartk.classifier.CleartkAnnotator.isTraining</name>
+                <name>isTraining</name>
                 <description>determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.</description>
                 <type>Boolean</type>
                 <multiValued>false</multiValued>
                 <mandatory>false</mandatory>
             </configurationParameter>
             <configurationParameter>
-                <name>org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath</name>
+                <name>classifierJarPath</name>
                 <type>String</type>
                 <multiValued>false</multiValued>
                 <mandatory>false</mandatory>
@@ -66,25 +66,25 @@
         </configurationParameters>
         <configurationParameterSettings>
             <nameValuePair>
-                <name>org.cleartk.classifier.CleartkAnnotator.classifierFactoryClassName</name>
+                <name>classifierFactoryClassName</name>
                 <value>
-                    <string>org.cleartk.classifier.jar.JarClassifierFactory</string>
+                    <string>org.cleartk.ml.jar.JarClassifierFactory</string>
                 </value>
             </nameValuePair>
             <nameValuePair>
-                <name>org.cleartk.classifier.CleartkAnnotator.dataWriterFactoryClassName</name>
+                <name>dataWriterFactoryClassName</name>
                 <value>
-                    <string>org.cleartk.classifier.jar.DefaultDataWriterFactory</string>
+                    <string>org.cleartk.ml.jar.DefaultDataWriterFactory</string>
                 </value>
             </nameValuePair>
             <nameValuePair>
                 <name>ProbabilityOfKeepingANegativeExample</name>
                 <value>
-                    <float>1.0</float>
+                    <float>0.5</float>
                 </value>
             </nameValuePair>
             <nameValuePair>
-                <name>org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath</name>
+                <name>classifierJarPath</name>
                 <value>
                     <string>/org/apache/ctakes/relationextractor/models/location_of/model.jar</string>
                 </value>
@@ -95,6 +95,7 @@
                 <import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
             </imports>
         </typeSystemDescription>
+        <typePriorities/>
         <fsIndexCollection/>
         <capabilities/>
         <operationalProperties>

Modified: ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/ModifierExtractorAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/ModifierExtractorAnnotator.xml?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/ModifierExtractorAnnotator.xml (original)
+++ ctakes/trunk/ctakes-relation-extractor/desc/analysis_engine/ModifierExtractorAnnotator.xml Tue Sep 16 19:57:19 2014
@@ -30,28 +30,28 @@
         <vendor>org.apache.ctakes.relationextractor.ae</vendor>
         <configurationParameters>
             <configurationParameter>
-                <name>org.cleartk.classifier.CleartkAnnotator.classifierFactoryClassName</name>
+                <name>classifierFactoryClassName</name>
                 <description>provides the full name of the ClassifierFactory class to be used.</description>
                 <type>String</type>
                 <multiValued>false</multiValued>
                 <mandatory>false</mandatory>
             </configurationParameter>
             <configurationParameter>
-                <name>org.cleartk.classifier.CleartkAnnotator.dataWriterFactoryClassName</name>
+                <name>dataWriterFactoryClassName</name>
                 <description>provides the full name of the DataWriterFactory class to be used.</description>
                 <type>String</type>
                 <multiValued>false</multiValued>
                 <mandatory>false</mandatory>
             </configurationParameter>
             <configurationParameter>
-                <name>org.cleartk.classifier.CleartkAnnotator.isTraining</name>
+                <name>isTraining</name>
                 <description>determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.</description>
                 <type>Boolean</type>
                 <multiValued>false</multiValued>
                 <mandatory>false</mandatory>
             </configurationParameter>
             <configurationParameter>
-                <name>org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath</name>
+                <name>classifierJarPath</name>
                 <type>String</type>
                 <multiValued>false</multiValued>
                 <mandatory>false</mandatory>
@@ -59,19 +59,19 @@
         </configurationParameters>
         <configurationParameterSettings>
             <nameValuePair>
-                <name>org.cleartk.classifier.CleartkAnnotator.classifierFactoryClassName</name>
+                <name>classifierFactoryClassName</name>
                 <value>
-                    <string>org.cleartk.classifier.jar.JarClassifierFactory</string>
+                    <string>org.cleartk.ml.jar.JarClassifierFactory</string>
                 </value>
             </nameValuePair>
             <nameValuePair>
-                <name>org.cleartk.classifier.CleartkAnnotator.dataWriterFactoryClassName</name>
+                <name>dataWriterFactoryClassName</name>
                 <value>
-                    <string>org.cleartk.classifier.jar.DefaultDataWriterFactory</string>
+                    <string>org.cleartk.ml.jar.DefaultDataWriterFactory</string>
                 </value>
             </nameValuePair>
             <nameValuePair>
-                <name>org.cleartk.classifier.jar.GenericJarClassifierFactory.classifierJarPath</name>
+                <name>classifierJarPath</name>
                 <value>
                     <string>/org/apache/ctakes/relationextractor/models/modifier_extractor/model.jar</string>
                 </value>
@@ -82,6 +82,7 @@
                 <import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
             </imports>
         </typeSystemDescription>
+        <typePriorities/>
         <fsIndexCollection/>
         <capabilities/>
         <operationalProperties>



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