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From chen...@apache.org
Subject svn commit: r1389618 [20/22] - in /incubator/ctakes/trunk: ./ ctakes-chunker/ ctakes-chunker/desc/ ctakes-chunker/resources/launch/ ctakes-chunker/src/main/java/edu/ ctakes-chunker/src/main/java/org/ ctakes-chunker/src/main/java/org/apache/ ctakes-chun...
Date Mon, 24 Sep 2012 22:05:23 GMT
Copied: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/MultiClassLIBSVMDataWriterFactory.java (from r1388092, incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/MultiClassLIBSVMDataWriterFactory.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/MultiClassLIBSVMDataWriterFactory.java?p2=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/MultiClassLIBSVMDataWriterFactory.java&p1=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/MultiClassLIBSVMDataWriterFactory.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/MultiClassLIBSVMDataWriterFactory.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/MultiClassLIBSVMDataWriterFactory.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.relationextractor.eval;
+package org.apache.ctakes.relationextractor.eval;
 
 import java.io.IOException;
 

Copied: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/PreprocessAndWriteXmi.java (from r1388196, incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/PreprocessAndWriteXmi.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/PreprocessAndWriteXmi.java?p2=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/PreprocessAndWriteXmi.java&p1=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/PreprocessAndWriteXmi.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/PreprocessAndWriteXmi.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/PreprocessAndWriteXmi.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.relationextractor.eval;
+package org.apache.ctakes.relationextractor.eval;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -40,7 +40,6 @@ import org.apache.uima.util.InvalidXMLEx
 import org.apache.uima.util.XMLInputSource;
 import org.apache.uima.util.XMLParser;
 import org.apache.uima.util.XMLSerializer;
-import org.chboston.cnlp.ctakes.relationextractor.cr.GoldEntityAndRelationReader;
 import org.cleartk.util.Options_ImplBase;
 import org.cleartk.util.ViewURIUtil;
 import org.cleartk.util.cr.FilesCollectionReader;
@@ -56,9 +55,11 @@ import org.uimafit.pipeline.SimplePipeli
 import org.xml.sax.ContentHandler;
 import org.xml.sax.SAXException;
 
-import edu.mayo.bmi.uima.core.cr.FilesInDirectoryCollectionReader;
+
+import org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader;
+import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.relationextractor.cr.GoldEntityAndRelationReader;
 import org.apache.ctakes.typesystem.type.structured.DocumentID;
-import edu.mayo.bmi.uima.core.util.DocumentIDAnnotationUtil;
 
 
 /**

Copied: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/PrintRelationStatistics.java (from r1388196, incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/PrintRelationStatistics.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/PrintRelationStatistics.java?p2=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/PrintRelationStatistics.java&p1=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/PrintRelationStatistics.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/PrintRelationStatistics.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/PrintRelationStatistics.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.relationextractor.eval;
+package org.apache.ctakes.relationextractor.eval;
 
 import java.io.File;
 import java.util.ArrayList;
@@ -63,7 +63,7 @@ public class PrintRelationStatistics {
         options.trainDirectory.getPath());
 
     Multiset<Integer> mentionsBetweenCounts = HashMultiset.create();
-    JCas jCas = JCasFactory.createJCasFromPath("../common-type-system/desc/common_type_system.xml");
+    JCas jCas = JCasFactory.createJCasFromPath("../ctakes-type-system/desc/common_type_system.xml");
     while (reader.hasNext()) {
       reader.getNext(jCas.getCas());
       JCas goldView = jCas.getView(GOLD_VIEW_NAME);

Copied: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java (from r1388196, incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/RelationExtractorEvaluation.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java?p2=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java&p1=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/RelationExtractorEvaluation.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/RelationExtractorEvaluation.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.relationextractor.eval;
+package org.apache.ctakes.relationextractor.eval;
 
 import java.io.File;
 import java.util.ArrayList;
@@ -37,10 +37,6 @@ import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.util.CasCopier;
 import org.apache.uima.util.Level;
-import org.chboston.cnlp.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator;
-import org.chboston.cnlp.ctakes.relationextractor.ae.EntityMentionPairRelationExtractorAnnotator;
-import org.chboston.cnlp.ctakes.relationextractor.ae.RelationExtractorAnnotator;
-import org.chboston.cnlp.ctakes.relationextractor.ae.RelationExtractorAnnotator.HashableArguments;
 import org.cleartk.classifier.CleartkAnnotator;
 import org.cleartk.classifier.DataWriterFactory;
 import org.cleartk.classifier.jar.DirectoryDataWriterFactory;
@@ -67,6 +63,10 @@ import com.google.common.base.Objects;
 import com.google.common.base.Objects.ToStringHelper;
 import com.google.common.collect.Ordering;
 
+import org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator;
+import org.apache.ctakes.relationextractor.ae.EntityMentionPairRelationExtractorAnnotator;
+import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
+import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.HashableArguments;
 import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
 import org.apache.ctakes.typesystem.type.relation.RelationArgument;
 import org.apache.ctakes.typesystem.type.textsem.EntityMention;
@@ -257,7 +257,7 @@ public class RelationExtractorEvaluation
     // return a reader that will load each of the XMI files
     return CollectionReaderFactory.createCollectionReader(
         XMIReader.class,
-        TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath("../common-type-system/desc/common_type_system.xml"),
+        TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath("../ctakes-type-system/desc/common_type_system.xml"),
         XMIReader.PARAM_FILES,
         paths);
   }

Copied: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/XMIReader.java (from r1388092, incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/XMIReader.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/XMIReader.java?p2=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/XMIReader.java&p1=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/XMIReader.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/eval/XMIReader.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/XMIReader.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.relationextractor.eval;
+package org.apache.ctakes.relationextractor.eval;
 
 import java.io.BufferedInputStream;
 import java.io.File;

Copied: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/ArgumentInfo.java (from r1388092, incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/knowtator/ArgumentInfo.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/ArgumentInfo.java?p2=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/ArgumentInfo.java&p1=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/knowtator/ArgumentInfo.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/knowtator/ArgumentInfo.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/ArgumentInfo.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.relationextractor.knowtator;
+package org.apache.ctakes.relationextractor.knowtator;
 
 /**
  * Information about a relation argument.

Copied: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/RelationInfo.java (from r1388092, incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/knowtator/RelationInfo.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/RelationInfo.java?p2=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/RelationInfo.java&p1=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/knowtator/RelationInfo.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/knowtator/RelationInfo.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/RelationInfo.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.relationextractor.knowtator;
+package org.apache.ctakes.relationextractor.knowtator;
 
 import java.util.HashSet;
 

Copied: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/Span.java (from r1388092, incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/knowtator/Span.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/Span.java?p2=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/Span.java&p1=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/knowtator/Span.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/knowtator/Span.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/Span.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.relationextractor.knowtator;
+package org.apache.ctakes.relationextractor.knowtator;
 
 import com.google.common.base.Objects;
 

Copied: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/XMLReader.java (from r1388092, incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/knowtator/XMLReader.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/XMLReader.java?p2=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/XMLReader.java&p1=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/knowtator/XMLReader.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/knowtator/XMLReader.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/XMLReader.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.relationextractor.knowtator;
+package org.apache.ctakes.relationextractor.knowtator;
 
 import java.util.ArrayList;
 import java.util.HashMap;

Copied: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/GoldEntityAndRelationReaderPipeline.java (from r1388092, incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/pipelines/GoldEntityAndRelationReaderPipeline.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/GoldEntityAndRelationReaderPipeline.java?p2=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/GoldEntityAndRelationReaderPipeline.java&p1=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/pipelines/GoldEntityAndRelationReaderPipeline.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/pipelines/GoldEntityAndRelationReaderPipeline.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/GoldEntityAndRelationReaderPipeline.java Mon Sep 24 22:04:51 2012
@@ -16,21 +16,21 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.relationextractor.pipelines;
+package org.apache.ctakes.relationextractor.pipelines;
 
 import java.io.IOException;
 
+import org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader;
+import org.apache.ctakes.relationextractor.cr.GoldEntityAndRelationReader;
 import org.apache.uima.UIMAException;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.collection.CollectionReaderDescription;
 import org.apache.uima.resource.metadata.TypeSystemDescription;
-import org.chboston.cnlp.ctakes.relationextractor.cr.GoldEntityAndRelationReader;
 import org.uimafit.component.xwriter.XWriter;
 import org.uimafit.factory.AnalysisEngineFactory;
 import org.uimafit.factory.CollectionReaderFactory;
 import org.uimafit.factory.TypeSystemDescriptionFactory;
 import org.uimafit.pipeline.SimplePipeline;
-import edu.mayo.bmi.uima.core.cr.FilesInDirectoryCollectionReader;
 
 /**
  * 
@@ -45,7 +45,7 @@ public class GoldEntityAndRelationReader
 	public static void main(String[] args) throws UIMAException, IOException {
 		
 		TypeSystemDescription typeSystemDescription = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath(
-				"/home/dima/workspaces/ctakes/common-type-system/desc/common_type_system.xml");
+				"/home/dima/workspaces/ctakes/ctakes-type-system/desc/common_type_system.xml");
 		
 		CollectionReaderDescription collectionReader = CollectionReaderFactory.createDescription(
 				FilesInDirectoryCollectionReader.class,

Copied: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationAnnotationAnalysis.java (from r1388092, incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/pipelines/RelationAnnotationAnalysis.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationAnnotationAnalysis.java?p2=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationAnnotationAnalysis.java&p1=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/pipelines/RelationAnnotationAnalysis.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/pipelines/RelationAnnotationAnalysis.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationAnnotationAnalysis.java Mon Sep 24 22:04:51 2012
@@ -16,15 +16,16 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.relationextractor.pipelines;
+package org.apache.ctakes.relationextractor.pipelines;
 
 import java.io.File;
 import java.util.Arrays;
 import java.util.List;
+
+import org.apache.ctakes.relationextractor.eval.XMIReader;
 import org.apache.uima.analysis_engine.AnalysisEngine;
 import org.apache.uima.collection.CollectionReader;
 import org.apache.uima.resource.metadata.TypeSystemDescription;
-import org.chboston.cnlp.ctakes.relationextractor.eval.XMIReader;
 import org.cleartk.util.Options_ImplBase;
 import org.kohsuke.args4j.Option;
 import org.uimafit.factory.AnalysisEngineFactory;
@@ -57,7 +58,7 @@ public class RelationAnnotationAnalysis 
 		options.parseOptions(args);
 
 		TypeSystemDescription typeSystemDescription = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath(
-				"../common-type-system/desc/common_type_system.xml");
+				"../ctakes-type-system/desc/common_type_system.xml");
 		
 		List<File> trainFiles = Arrays.asList(options.inputDirectory.listFiles());
     CollectionReader collectionReader = getCollectionReader(trainFiles, typeSystemDescription);

Copied: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorConsumer.java (from r1388196, incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/pipelines/RelationExtractorConsumer.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorConsumer.java?p2=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorConsumer.java&p1=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/pipelines/RelationExtractorConsumer.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/pipelines/RelationExtractorConsumer.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorConsumer.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.relationextractor.pipelines;
+package org.apache.ctakes.relationextractor.pipelines;
 
 import java.util.List;
 

Copied: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipeline.java (from r1388092, incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/pipelines/RelationExtractorPipeline.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipeline.java?p2=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipeline.java&p1=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/pipelines/RelationExtractorPipeline.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/pipelines/RelationExtractorPipeline.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipeline.java Mon Sep 24 22:04:51 2012
@@ -16,10 +16,11 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.relationextractor.pipelines;
+package org.apache.ctakes.relationextractor.pipelines;
 
 import java.io.IOException;
 
+import org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader;
 import org.apache.uima.UIMAException;
 import org.apache.uima.analysis_engine.AnalysisEngine;
 import org.apache.uima.collection.CollectionReader;
@@ -31,7 +32,6 @@ import org.uimafit.factory.AnalysisEngin
 import org.uimafit.factory.CollectionReaderFactory;
 import org.uimafit.factory.TypeSystemDescriptionFactory;
 import org.uimafit.pipeline.SimplePipeline;
-import edu.mayo.bmi.uima.core.cr.FilesInDirectoryCollectionReader;
 
 /**
  * A simple pipeline that runs relation extraction on all files in a directory and saves
@@ -65,10 +65,10 @@ public class RelationExtractorPipeline {
 		options.parseOptions(args);
 
 		TypeSystemDescription typeSystemDescription = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath(
-				"../common-type-system/desc/common_type_system.xml");
+				"../ctakes-type-system/desc/common_type_system.xml");
     
 		CollectionReader collectionReader = CollectionReaderFactory.createCollectionReaderFromPath(
-				"../core/desc/collection_reader/FilesInDirectoryCollectionReader.xml",
+				"../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml",
 				FilesInDirectoryCollectionReader.PARAM_INPUTDIR,
 				options.inputDirectory);
 

Copied: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java (from r1388092, incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java?p2=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java&p1=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java Mon Sep 24 22:04:51 2012
@@ -40,7 +40,7 @@
 * 
 * @author Dmitriy Dligach
 */
-package org.chboston.cnlp.ctakes.relationextractor.pipelines;
+package org.apache.ctakes.relationextractor.pipelines;
 
 import java.io.IOException;
 
@@ -69,7 +69,7 @@ public class RelationExtractorPipelineSi
 			String sampleSentence = "Abdomen: Soft, nontender without hepatosplenomegaly or masses";
 			
 			TypeSystemDescription typeSystemDescription = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath(
-					"../common-type-system/desc/common_type_system.xml");
+					"../ctakes-type-system/desc/common_type_system.xml");
 
 			JCas jCas = JCasFactory.createJCas(typeSystemDescription);
 			jCas.setDocumentText(sampleSentence);

Copied: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorTrain.java (from r1388092, incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/pipelines/RelationExtractorTrain.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorTrain.java?p2=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorTrain.java&p1=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/pipelines/RelationExtractorTrain.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/cnlp/ctakes/relationextractor/pipelines/RelationExtractorTrain.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorTrain.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.relationextractor.pipelines;
+package org.apache.ctakes.relationextractor.pipelines;
 
 import java.io.File;
 import java.io.FileOutputStream;
@@ -24,19 +24,19 @@ import java.io.IOException;
 import java.util.Arrays;
 import java.util.List;
 
+import org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator;
+import org.apache.ctakes.relationextractor.ae.EntityMentionPairRelationExtractorAnnotator;
+import org.apache.ctakes.relationextractor.ae.ModifierExtractorAnnotator;
+import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
+import org.apache.ctakes.relationextractor.eval.ModifierExtractorEvaluation;
+import org.apache.ctakes.relationextractor.eval.MultiClassLIBSVMDataWriterFactory;
+import org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation;
+import org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.ParameterSettings;
 import org.apache.uima.UIMAFramework;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.collection.CollectionReader;
 import org.apache.uima.util.XMLInputSource;
 import org.apache.uima.util.XMLParser;
-import org.chboston.cnlp.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator;
-import org.chboston.cnlp.ctakes.relationextractor.ae.EntityMentionPairRelationExtractorAnnotator;
-import org.chboston.cnlp.ctakes.relationextractor.ae.ModifierExtractorAnnotator;
-import org.chboston.cnlp.ctakes.relationextractor.ae.RelationExtractorAnnotator;
-import org.chboston.cnlp.ctakes.relationextractor.eval.ModifierExtractorEvaluation;
-import org.chboston.cnlp.ctakes.relationextractor.eval.MultiClassLIBSVMDataWriterFactory;
-import org.chboston.cnlp.ctakes.relationextractor.eval.RelationExtractorEvaluation;
-import org.chboston.cnlp.ctakes.relationextractor.eval.RelationExtractorEvaluation.ParameterSettings;
 import org.cleartk.classifier.DataWriterFactory;
 import org.cleartk.classifier.jar.GenericJarClassifierFactory;
 import org.cleartk.util.Options_ImplBase;

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/test/src/org/chboston/cnlp/ctakes/relationextractor/ae/NamedEntityFeaturesExtractorTest.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/test/src/org/chboston/cnlp/ctakes/relationextractor/ae/NamedEntityFeaturesExtractorTest.java?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/test/src/org/chboston/cnlp/ctakes/relationextractor/ae/NamedEntityFeaturesExtractorTest.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/test/src/org/chboston/cnlp/ctakes/relationextractor/ae/NamedEntityFeaturesExtractorTest.java Mon Sep 24 22:04:51 2012
@@ -16,14 +16,14 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package org.chboston.cnlp.ctakes.relationextractor.ae;
+package org.apache.ctakes.relationextractor.ae;
 
 import static org.junit.Assert.assertTrue;
 
 import java.util.List;
 
 import org.apache.uima.jcas.JCas;
-import org.chboston.cnlp.ctakes.relationextractor.ae.features.NamedEntityFeaturesExtractor;
+import org.apache.ctakes.relationextractor.ae.features.NamedEntityFeaturesExtractor;
 import org.cleartk.classifier.Feature;
 import org.junit.Test;
 import org.uimafit.factory.JCasFactory;
@@ -35,7 +35,7 @@ public class NamedEntityFeaturesExtracto
   @Test
   public void test() throws Exception {
     // create and populate a JCas with some EntityMention objects
-    JCas jCas = JCasFactory.createJCasFromPath("../common-type-system/desc/common_type_system.xml");
+    JCas jCas = JCasFactory.createJCasFromPath("../ctakes-type-system/desc/common_type_system.xml");
     jCas.setDocumentText("aaa bbb ccc ddd");
     EntityMention e1 = new EntityMention(jCas, 0, 3);
     e1.setTypeID(42);

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/AdjP2LookupWindow.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/AdjP2LookupWindow.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/AdjP2LookupWindow.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/AdjP2LookupWindow.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.core.ae.CopyAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.core.ae.CopyAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>AdjP to LookupWindow</name>
     <description>Copies Shallow Parse AdjP annotations to be used as lookup windows for dictionary lookup.</description>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffect.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffect.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffect.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffect.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.lookup.ae.DictionaryLookupAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>DictionaryLookupAnnotator</name>
     <description/>
@@ -32,7 +32,7 @@
     <configurationParameterSettings/>
     <typeSystemDescription>
       <imports>
-        <import location="../../../common-type-system/desc/common_type_system.xml"/>
+        <import location="../../../ctakes-type-system/desc/common_type_system.xml"/>
       </imports>
     </typeSystemDescription>
     <capabilities>
@@ -57,37 +57,37 @@
     <externalResourceDependency>
       <key>LookupDescriptor</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+      <interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
       <optional>false</optional>
     </externalResourceDependency>
     <externalResourceDependency>
       <key>SnomedIndexReader</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.core.resource.LuceneIndexReaderResource</interfaceName>
+      <interfaceName>org.apache.ctakes.core.resource.LuceneIndexReaderResource</interfaceName>
       <optional>false</optional>
     </externalResourceDependency>
     <externalResourceDependency>
       <key>CodesListIndexDirectory</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+      <interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
       <optional>true</optional>
     </externalResourceDependency>
     <externalResourceDependency>
       <key>RxnormIndexReader</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.core.resource.LuceneIndexReaderResource</interfaceName>
+      <interfaceName>org.apache.ctakes.core.resource.LuceneIndexReaderResource</interfaceName>
       <optional>false</optional>
     </externalResourceDependency>
     <externalResourceDependency>
       <key>OrangeBookIndexReader</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.core.resource.LuceneIndexReaderResource</interfaceName>
+      <interfaceName>org.apache.ctakes.core.resource.LuceneIndexReaderResource</interfaceName>
       <optional>false</optional>
     </externalResourceDependency>
     <externalResourceDependency>
       <key>CsvSE</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+      <interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
       <optional>false</optional>
     </externalResourceDependency>
   </externalResourceDependencies>
@@ -99,7 +99,7 @@
         <fileResourceSpecifier>
           <fileUrl>file:sideeffect/lookup/LookupDesc_sideEffect.xml</fileUrl>
         </fileResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
       </externalResource>
       <externalResource>
         <name>SnomedIndex</name>
@@ -138,7 +138,7 @@
             </configurationParameterSettings>
           </resourceMetaData>
         </configurableDataResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.LuceneIndexReaderResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl</implementationName>
       </externalResource>
       <externalResource>
         <name>CodesListIndexDirectory</name>
@@ -146,7 +146,7 @@
         <fileResourceSpecifier>
           <fileUrl>file:lookup/snomed-like_codes_sample</fileUrl>
         </fileResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
       </externalResource>
       <externalResource>
         <name>RxnormIndex</name>
@@ -185,7 +185,7 @@
             </configurationParameterSettings>
           </resourceMetaData>
         </configurableDataResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.LuceneIndexReaderResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl</implementationName>
       </externalResource>
       <externalResource>
         <name>OrangeBookIndex</name>
@@ -224,7 +224,7 @@
             </configurationParameterSettings>
           </resourceMetaData>
         </configurableDataResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.LuceneIndexReaderResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl</implementationName>
       </externalResource>
       <externalResource>
         <name>CsvSEFile</name>
@@ -232,7 +232,7 @@
         <fileResourceSpecifier>
           <fileUrl>file:sideeffect/lookup/additionalNE_dictionary.csv</fileUrl>
         </fileResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
       </externalResource>
     </externalResources>
     <externalResourceBindings>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffectUMLS.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffectUMLS.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffectUMLS.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffectUMLS.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.lookup.ae.UmlsDictionaryLookupAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>UmlsDictionaryLookupAnnotator</name>
     <description/>
@@ -128,31 +128,31 @@
     <externalResourceDependency>
       <key>LookupDescriptor</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+      <interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
       <optional>false</optional>
     </externalResourceDependency>
     <externalResourceDependency>
       <key>DbConnection</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.core.resource.JdbcConnectionResource</interfaceName>
+      <interfaceName>org.apache.ctakes.core.resource.JdbcConnectionResource</interfaceName>
       <optional>false</optional>
     </externalResourceDependency>
     <externalResourceDependency>
       <key>RxnormIndexReader</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.core.resource.LuceneIndexReaderResource</interfaceName>
+      <interfaceName>org.apache.ctakes.core.resource.LuceneIndexReaderResource</interfaceName>
       <optional>false</optional>
     </externalResourceDependency>
     <externalResourceDependency>
       <key>OrangeBookIndexReader</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.core.resource.LuceneIndexReaderResource</interfaceName>
+      <interfaceName>org.apache.ctakes.core.resource.LuceneIndexReaderResource</interfaceName>
       <optional>false</optional>
     </externalResourceDependency>
     <externalResourceDependency>
       <key>CsvSE</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.core.resource.FileResource</interfaceName>
+      <interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
       <optional>false</optional>
     </externalResourceDependency>
   </externalResourceDependencies>
@@ -164,7 +164,7 @@
         <fileResourceSpecifier>
           <fileUrl>file:sideeffect/lookup/LookupDesc_sideEffectUMLS.xml</fileUrl>
         </fileResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
       </externalResource>
       <externalResource>
         <name>DbConnectionResrc</name>
@@ -209,7 +209,7 @@
               <nameValuePair>
                 <name>URL</name>
                 <value>
-                  <string>jdbc:hsqldb:file:../dictionary lookup/resources/lookup/umls2011ab/umls</string>
+                  <string>jdbc:hsqldb:file:../ctakes-dictionary-lookup/resources/lookup/umls2011ab/umls</string>
                 </value>
               </nameValuePair>
               <nameValuePair>
@@ -227,7 +227,7 @@
             </configurationParameterSettings>
           </resourceMetaData>
         </configurableDataResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.JdbcConnectionResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.JdbcConnectionResourceImpl</implementationName>
       </externalResource>
       <externalResource>
         <name>RxnormIndex</name>
@@ -266,7 +266,7 @@
             </configurationParameterSettings>
           </resourceMetaData>
         </configurableDataResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.LuceneIndexReaderResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl</implementationName>
       </externalResource>
       <externalResource>
         <name>OrangeBookIndex</name>
@@ -305,7 +305,7 @@
             </configurationParameterSettings>
           </resourceMetaData>
         </configurableDataResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.LuceneIndexReaderResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl</implementationName>
       </externalResource>
       <externalResource>
         <name>CsvSEFile</name>
@@ -313,7 +313,7 @@
         <fileResourceSpecifier>
           <fileUrl>file:sideeffect/lookup/additionalNE_dictionary.csv</fileUrl>
         </fileResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
       </externalResource>
     </externalResources>
     <externalResourceBindings>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/LookupWindowAnnotator_sideEffect.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/LookupWindowAnnotator_sideEffect.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/LookupWindowAnnotator_sideEffect.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/LookupWindowAnnotator_sideEffect.xml Mon Sep 24 22:04:51 2012
@@ -24,10 +24,10 @@
   <primitive>false</primitive>
   <delegateAnalysisEngineSpecifiers>
     <delegateAnalysisEngine key="NP2LookupWindow">
-      <import location="../../../clinical documents pipeline/desc/analysis_engine/NP2LookupWindow.xml"/>
+      <import location="../../../ctakes-clinical-pipeline/desc/analysis_engine/NP2LookupWindow.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="DrugCNP2LookupWindow">
-      <import location="../../../Drug NER/desc/analysis_engine/DrugCNP2LookupWindow.xml"/>
+      <import location="../../../ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="VG2LookupWindow">
       <import location="VG2LookupWindow.xml"/>
@@ -36,13 +36,13 @@
       <import location="AdjP2LookupWindow.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="AdjustNPToIncludePPNP">
-      <import location="../../../chunker/desc/AdjustNounPhraseToIncludeFollowingPPNP.xml"/>
+      <import location="../../../ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingPPNP.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="MaxLookupWindows">
-      <import location="../../../clinical documents pipeline/desc/analysis_engine/MaxLookupWindows.xml"/>
+      <import location="../../../ctakes-clinical-pipeline/desc/analysis_engine/MaxLookupWindows.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="AdjustNPToIncludeNP">
-      <import location="../../../chunker/desc/AdjustNounPhraseToIncludeFollowingNP.xml"/>
+      <import location="../../../ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingNP.xml"/>
     </delegateAnalysisEngine>
   </delegateAnalysisEngineSpecifiers>
   <analysisEngineMetaData>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/PSESentenceAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/PSESentenceAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/PSESentenceAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/PSESentenceAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.sideeffect.ae.PSESentenceAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.sideeffect.ae.PSESentenceAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>PSESentenceAnnotator</name>
     <description>Annotate spans of the sentence(s) that contains signs/symptoms or disease and drugs. But disregard the particular section(s).</description>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SESentenceClassifierAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SESentenceClassifierAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SESentenceClassifierAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SESentenceClassifierAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.sideeffect.ae.SESentenceClassifierAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.sideeffect.ae.SESentenceClassifierAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>SESentenceClassifierAnnotator</name>
     <description>identify sentences containing side effect and causative drugs using both rules and libSVM</description>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SESentenceFeatureAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SESentenceFeatureAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SESentenceFeatureAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SESentenceFeatureAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.sideeffect.ae.SESentenceFeatureAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.sideeffect.ae.SESentenceFeatureAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>SESentenceFeatureAnnotator</name>
     <description>Annotate features from PSESentence</description>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE.xml Mon Sep 24 22:04:51 2012
@@ -24,37 +24,37 @@
   <primitive>false</primitive>
   <delegateAnalysisEngineSpecifiers>
     <delegateAnalysisEngine key="TokenizerAnnotator">
-      <import location="../../../core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
-      <import location="../../../context dependent tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="NegationAnnotator">
-      <import location="../../../NE contexts/desc/NegationAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="StatusAnnotator">
-      <import location="../../../NE contexts/desc/StatusAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SentenceDetectorAnnotator">
-      <import location="../../../core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="POSTagger">
-      <import location="../../../POS tagger/desc/POSTagger.xml"/>
+      <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="DrugMentionAnnotator">
-      <import location="../../../Drug NER/desc/analysis_engine/DrugMentionAnnotator.xml"/>
+      <import location="../../../ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="Chunker">
-      <import location="../../../chunker/desc/Chunker.xml"/>
+      <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SideEffectAnnotator">
       <import location="SideEffectAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SimpleSegmentWithTagsAnnotator">
-      <import location="../../../core/desc/analysis_engine/SimpleSegmentWithTagsAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SimpleSegmentWithTagsAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ExtractionPrepAnnotator">
-      <import location="../../../clinical documents pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml"/>
+      <import location="../../../ctakes-clinical-pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LookupWindowAnnotator">
       <import location="LookupWindowAnnotator_sideEffect.xml"/>
@@ -63,7 +63,7 @@
       <import location="DictionaryLookupAnnotator_sideEffect.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LvgAnnotator">
-      <import location="../../../LVG/desc/analysis_engine/LvgAnnotator.xml"/>
+      <import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
     </delegateAnalysisEngine>
   </delegateAnalysisEngineSpecifiers>
   <analysisEngineMetaData>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE_UMLS.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE_UMLS.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE_UMLS.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE_UMLS.xml Mon Sep 24 22:04:51 2012
@@ -24,37 +24,37 @@
   <primitive>false</primitive>
   <delegateAnalysisEngineSpecifiers>
     <delegateAnalysisEngine key="TokenizerAnnotator">
-      <import location="../../../core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
-      <import location="../../../context dependent tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="NegationAnnotator">
-      <import location="../../../NE contexts/desc/NegationAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="StatusAnnotator">
-      <import location="../../../NE contexts/desc/StatusAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SentenceDetectorAnnotator">
-      <import location="../../../core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="POSTagger">
-      <import location="../../../POS tagger/desc/POSTagger.xml"/>
+      <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="DrugMentionAnnotator">
-      <import location="../../../Drug NER/desc/analysis_engine/DrugMentionAnnotator.xml"/>
+      <import location="../../../ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="Chunker">
-      <import location="../../../chunker/desc/Chunker.xml"/>
+      <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SideEffectAnnotator">
       <import location="SideEffectAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SimpleSegmentWithTagsAnnotator">
-      <import location="../../../core/desc/analysis_engine/SimpleSegmentWithTagsAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SimpleSegmentWithTagsAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ExtractionPrepAnnotator">
-      <import location="../../../clinical documents pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml"/>
+      <import location="../../../ctakes-clinical-pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LookupWindowAnnotator">
       <import location="LookupWindowAnnotator_sideEffect.xml"/>
@@ -63,7 +63,7 @@
       <import location="DictionaryLookupAnnotator_sideEffectUMLS.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LvgAnnotator">
-      <import location="../../../LVG/desc/analysis_engine/LvgAnnotator.xml"/>
+      <import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
     </delegateAnalysisEngine>
   </delegateAnalysisEngineSpecifiers>
   <analysisEngineMetaData>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAggregate_CDA_TAE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAggregate_CDA_TAE.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAggregate_CDA_TAE.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAggregate_CDA_TAE.xml Mon Sep 24 22:04:51 2012
@@ -24,37 +24,37 @@
   <primitive>false</primitive>
   <delegateAnalysisEngineSpecifiers>
     <delegateAnalysisEngine key="TokenizerAnnotator">
-      <import location="../../../core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
-      <import location="../../../context dependent tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="NegationAnnotator">
-      <import location="../../../NE contexts/desc/NegationAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="StatusAnnotator">
-      <import location="../../../NE contexts/desc/StatusAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SentenceDetectorAnnotator">
-      <import location="../../../core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="POSTagger">
-      <import location="../../../POS tagger/desc/POSTagger.xml"/>
+      <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="DrugMentionAnnotator">
-      <import location="../../../Drug NER/desc/analysis_engine/DrugMentionAnnotator.xml"/>
+      <import location="../../../ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="Chunker">
-      <import location="../../../chunker/desc/Chunker.xml"/>
+      <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SideEffectAnnotator">
       <import location="SideEffectAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="CdaCasInitializer">
-      <import location="../../../document preprocessor/desc/CdaCasInitializer.xml"/>
+      <import location="../../../ctakes-preprocessor/desc/CdaCasInitializer.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ExtractionPrepAnnotator">
-      <import location="../../../clinical documents pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml"/>
+      <import location="../../../ctakes-clinical-pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LookupWindowAnnotator">
       <import location="LookupWindowAnnotator_sideEffect.xml"/>
@@ -63,7 +63,7 @@
       <import location="DictionaryLookupAnnotator_sideEffect.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LvgAnnotator">
-      <import location="../../../LVG/desc/analysis_engine/LvgAnnotator.xml"/>
+      <import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
     </delegateAnalysisEngine>
   </delegateAnalysisEngineSpecifiers>
   <analysisEngineMetaData>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAggregate_CDA_TAE_UMLS.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAggregate_CDA_TAE_UMLS.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAggregate_CDA_TAE_UMLS.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAggregate_CDA_TAE_UMLS.xml Mon Sep 24 22:04:51 2012
@@ -24,37 +24,37 @@
   <primitive>false</primitive>
   <delegateAnalysisEngineSpecifiers>
     <delegateAnalysisEngine key="TokenizerAnnotator">
-      <import location="../../../core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
-      <import location="../../../context dependent tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="NegationAnnotator">
-      <import location="../../../NE contexts/desc/NegationAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="StatusAnnotator">
-      <import location="../../../NE contexts/desc/StatusAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SentenceDetectorAnnotator">
-      <import location="../../../core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="POSTagger">
-      <import location="../../../POS tagger/desc/POSTagger.xml"/>
+      <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="DrugMentionAnnotator">
-      <import location="../../../Drug NER/desc/analysis_engine/DrugMentionAnnotator.xml"/>
+      <import location="../../../ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="Chunker">
-      <import location="../../../chunker/desc/Chunker.xml"/>
+      <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SideEffectAnnotator">
       <import location="SideEffectAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="CdaCasInitializer">
-      <import location="../../../document preprocessor/desc/CdaCasInitializer.xml"/>
+      <import location="../../../ctakes-preprocessor/desc/CdaCasInitializer.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ExtractionPrepAnnotator">
-      <import location="../../../clinical documents pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml"/>
+      <import location="../../../ctakes-clinical-pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LookupWindowAnnotator">
       <import location="LookupWindowAnnotator_sideEffect.xml"/>
@@ -63,7 +63,7 @@
       <import location="DictionaryLookupAnnotator_sideEffectUMLS.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LvgAnnotator">
-      <import location="../../../LVG/desc/analysis_engine/LvgAnnotator.xml"/>
+      <import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
     </delegateAnalysisEngine>
   </delegateAnalysisEngineSpecifiers>
   <analysisEngineMetaData>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAnnotator.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectAnnotator.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.sideeffect.ae.SideEffectAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.sideeffect.ae.SideEffectAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>side effect annotator</name>
     <description>Rule-based side effect annotator</description>
@@ -231,7 +231,7 @@
     <externalResourceDependency>
       <key>sideEffectTable</key>
       <description/>
-      <interfaceName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</interfaceName>
+      <interfaceName>org.apache.ctakes.core.resource.FileResourceImpl</interfaceName>
       <optional>false</optional>
     </externalResourceDependency>
   </externalResourceDependencies>
@@ -243,7 +243,7 @@
         <fileResourceSpecifier>
           <fileUrl>file:sideeffect/lookup/sideEffect_dictionary.txt</fileUrl>
         </fileResourceSpecifier>
-        <implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl</implementationName>
+        <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
       </externalResource>
     </externalResources>
     <externalResourceBindings>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregateTAE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregateTAE.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregateTAE.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregateTAE.xml Mon Sep 24 22:04:51 2012
@@ -24,34 +24,34 @@
   <primitive>false</primitive>
   <delegateAnalysisEngineSpecifiers>
     <delegateAnalysisEngine key="TokenizerAnnotator">
-      <import location="../../../core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SESentenceFeatureAnnotator">
       <import location="SESentenceFeatureAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
-      <import location="../../../context dependent tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="NegationAnnotator">
-      <import location="../../../NE contexts/desc/NegationAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SentDetectAnnotator">
-      <import location="../../../core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="StatusAnnotator">
-      <import location="../../../NE contexts/desc/StatusAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SimpleSegmentAnnotator">
-      <import location="../../../core/desc/analysis_engine/SimpleSegmentWithTagsAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SimpleSegmentWithTagsAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="POSTagger">
-      <import location="../../../POS tagger/desc/POSTagger.xml"/>
+      <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="DrugMentionAnnotator">
-      <import location="../../../Drug NER/desc/analysis_engine/DrugMentionAnnotator.xml"/>
+      <import location="../../../ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="Chunker">
-      <import location="../../../chunker/desc/Chunker.xml"/>
+      <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="PSESentenceAnnotator">
       <import location="PSESentenceAnnotator.xml"/>
@@ -63,7 +63,7 @@
       <import location="SideEffectAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ExtractionPrepAnnotator">
-      <import location="../../../clinical documents pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml"/>
+      <import location="../../../ctakes-clinical-pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LookupWindowAnnotator">
       <import location="LookupWindowAnnotator_sideEffect.xml"/>
@@ -72,7 +72,7 @@
       <import location="DictionaryLookupAnnotator_sideEffect.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LvgAnnotator">
-      <import location="../../../LVG/desc/analysis_engine/LvgAnnotator.xml"/>
+      <import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
     </delegateAnalysisEngine>
   </delegateAnalysisEngineSpecifiers>
   <analysisEngineMetaData>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregateTAE_UMLS.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregateTAE_UMLS.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregateTAE_UMLS.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregateTAE_UMLS.xml Mon Sep 24 22:04:51 2012
@@ -24,34 +24,34 @@
   <primitive>false</primitive>
   <delegateAnalysisEngineSpecifiers>
     <delegateAnalysisEngine key="TokenizerAnnotator">
-      <import location="../../../core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SESentenceFeatureAnnotator">
       <import location="SESentenceFeatureAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
-      <import location="../../../context dependent tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="NegationAnnotator">
-      <import location="../../../NE contexts/desc/NegationAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SentDetectAnnotator">
-      <import location="../../../core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="StatusAnnotator">
-      <import location="../../../NE contexts/desc/StatusAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SimpleSegmentAnnotator">
-      <import location="../../../core/desc/analysis_engine/SimpleSegmentWithTagsAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SimpleSegmentWithTagsAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="POSTagger">
-      <import location="../../../POS tagger/desc/POSTagger.xml"/>
+      <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="DrugMentionAnnotator">
-      <import location="../../../Drug NER/desc/analysis_engine/DrugMentionAnnotator.xml"/>
+      <import location="../../../ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="Chunker">
-      <import location="../../../chunker/desc/Chunker.xml"/>
+      <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="PSESentenceAnnotator">
       <import location="PSESentenceAnnotator.xml"/>
@@ -63,7 +63,7 @@
       <import location="SideEffectAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ExtractionPrepAnnotator">
-      <import location="../../../clinical documents pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml"/>
+      <import location="../../../ctakes-clinical-pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LookupWindowAnnotator">
       <import location="LookupWindowAnnotator_sideEffect.xml"/>
@@ -72,7 +72,7 @@
       <import location="DictionaryLookupAnnotator_sideEffect.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LvgAnnotator">
-      <import location="../../../LVG/desc/analysis_engine/LvgAnnotator.xml"/>
+      <import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
     </delegateAnalysisEngine>
   </delegateAnalysisEngineSpecifiers>
   <analysisEngineMetaData>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregate_CDA_TAE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregate_CDA_TAE.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregate_CDA_TAE.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregate_CDA_TAE.xml Mon Sep 24 22:04:51 2012
@@ -24,31 +24,31 @@
   <primitive>false</primitive>
   <delegateAnalysisEngineSpecifiers>
     <delegateAnalysisEngine key="TokenizerAnnotator">
-      <import location="../../../core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SESentenceFeatureAnnotator">
       <import location="SESentenceFeatureAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
-      <import location="../../../context dependent tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="NegationAnnotator">
-      <import location="../../../NE contexts/desc/NegationAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SentDetectAnnotator">
-      <import location="../../../core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="StatusAnnotator">
-      <import location="../../../NE contexts/desc/StatusAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="POSTagger">
-      <import location="../../../POS tagger/desc/POSTagger.xml"/>
+      <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="DrugMentionAnnotator">
-      <import location="../../../Drug NER/desc/analysis_engine/DrugMentionAnnotator.xml"/>
+      <import location="../../../ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="Chunker">
-      <import location="../../../chunker/desc/Chunker.xml"/>
+      <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="PSESentenceAnnotator">
       <import location="PSESentenceAnnotator.xml"/>
@@ -60,10 +60,10 @@
       <import location="SideEffectAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="CdaCasInitializer">
-      <import location="../../../document preprocessor/desc/CdaCasInitializer.xml"/>
+      <import location="../../../ctakes-preprocessor/desc/CdaCasInitializer.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ExtractionPrepAnnotator">
-      <import location="../../../clinical documents pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml"/>
+      <import location="../../../ctakes-clinical-pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LookupWindowAnnotator">
       <import location="LookupWindowAnnotator_sideEffect.xml"/>
@@ -72,7 +72,7 @@
       <import location="DictionaryLookupAnnotator_sideEffect.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LvgAnnotator">
-      <import location="../../../LVG/desc/analysis_engine/LvgAnnotator.xml"/>
+      <import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
     </delegateAnalysisEngine>
   </delegateAnalysisEngineSpecifiers>
   <analysisEngineMetaData>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregate_CDA_TAE_UMLS.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregate_CDA_TAE_UMLS.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregate_CDA_TAE_UMLS.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregate_CDA_TAE_UMLS.xml Mon Sep 24 22:04:51 2012
@@ -24,31 +24,31 @@
   <primitive>false</primitive>
   <delegateAnalysisEngineSpecifiers>
     <delegateAnalysisEngine key="TokenizerAnnotator">
-      <import location="../../../core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SESentenceFeatureAnnotator">
       <import location="SESentenceFeatureAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
-      <import location="../../../context dependent tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+      <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="NegationAnnotator">
-      <import location="../../../NE contexts/desc/NegationAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="SentDetectAnnotator">
-      <import location="../../../core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
+      <import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="StatusAnnotator">
-      <import location="../../../NE contexts/desc/StatusAnnotator.xml"/>
+      <import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="POSTagger">
-      <import location="../../../POS tagger/desc/POSTagger.xml"/>
+      <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="DrugMentionAnnotator">
-      <import location="../../../Drug NER/desc/analysis_engine/DrugMentionAnnotator.xml"/>
+      <import location="../../../ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="Chunker">
-      <import location="../../../chunker/desc/Chunker.xml"/>
+      <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="PSESentenceAnnotator">
       <import location="PSESentenceAnnotator.xml"/>
@@ -60,10 +60,10 @@
       <import location="SideEffectAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="CdaCasInitializer">
-      <import location="../../../document preprocessor/desc/CdaCasInitializer.xml"/>
+      <import location="../../../ctakes-preprocessor/desc/CdaCasInitializer.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="ExtractionPrepAnnotator">
-      <import location="../../../clinical documents pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml"/>
+      <import location="../../../ctakes-clinical-pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LookupWindowAnnotator">
       <import location="LookupWindowAnnotator_sideEffect.xml"/>
@@ -72,7 +72,7 @@
       <import location="DictionaryLookupAnnotator_sideEffectUMLS.xml"/>
     </delegateAnalysisEngine>
     <delegateAnalysisEngine key="LvgAnnotator">
-      <import location="../../../LVG/desc/analysis_engine/LvgAnnotator.xml"/>
+      <import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
     </delegateAnalysisEngine>
   </delegateAnalysisEngineSpecifiers>
   <analysisEngineMetaData>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/VG2LookupWindow.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/VG2LookupWindow.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/VG2LookupWindow.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/analysis_engine/VG2LookupWindow.xml Mon Sep 24 22:04:51 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.core.ae.CopyAnnotator</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.core.ae.CopyAnnotator</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>VG to LookupWindow</name>
     <description>Copies Shallow Parse VG annotations to be used as lookup windows for dictionary lookup.</description>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/cas_consumer/SideEffectCasConsumer.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/cas_consumer/SideEffectCasConsumer.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/cas_consumer/SideEffectCasConsumer.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/cas_consumer/SideEffectCasConsumer.xml Mon Sep 24 22:04:51 2012
@@ -21,7 +21,7 @@
 -->
 <casConsumerDescription xmlns="http://uima.apache.org/resourceSpecifier">
 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
-<implementationName>edu.mayo.bmi.uima.sideeffect.cc.SideEffectCasConsumer</implementationName>
+<implementationName>org.apache.ctakes.sideeffect.cc.SideEffectCasConsumer</implementationName>
 <processingResourceMetaData>
 <name>SideEffectCasConsumer</name>
 <description>Write results from SideEffectAnnotator. The output file name and delimiter are set by Parameters.



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