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From chen...@apache.org
Subject svn commit: r1389618 [22/22] - 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-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ResolutionAnnotator.java (from r1388196, incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/ae/ResolutionAnnotator.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ResolutionAnnotator.java?p2=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ResolutionAnnotator.java&p1=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/ae/ResolutionAnnotator.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/ae/ResolutionAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ResolutionAnnotator.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.smoking.ae;
+package org.apache.ctakes.smokingstatus.ae;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -36,10 +36,11 @@ import org.apache.uima.analysis_engine.a
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.TOP;
 
-import edu.mayo.bmi.smoking.Const;
-import edu.mayo.bmi.uima.SmokingStatus.type.NonSmokerNamedEntityAnnotation;
-import edu.mayo.bmi.uima.SmokingStatus.type.SmokerNamedEntityAnnotation;
-import edu.mayo.bmi.uima.core.resource.FileResource;
+import org.apache.ctakes.smokingstatus.type.NonSmokerNamedEntityAnnotation;
+import org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation;
+
+import org.apache.ctakes.core.resource.FileResource;
+import org.apache.ctakes.smokingstatus.Const;
 import org.apache.ctakes.typesystem.type.syntax.WordToken;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
 import edu.mayo.bmi.uima.libsvm.type.NominalAttributeValue;

Copied: incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/SentenceAdjuster.java (from r1388196, incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/ae/SentenceAdjuster.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/SentenceAdjuster.java?p2=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/SentenceAdjuster.java&p1=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/ae/SentenceAdjuster.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/ae/SentenceAdjuster.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/SentenceAdjuster.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.smoking.ae;
+package org.apache.ctakes.smokingstatus.ae;
 
 import java.util.HashMap;
 import java.util.HashSet;

Copied: incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/cc/RecordResolutionCasConsumer.java (from r1388196, incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/cc/RecordResolutionCasConsumer.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/cc/RecordResolutionCasConsumer.java?p2=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/cc/RecordResolutionCasConsumer.java&p1=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/cc/RecordResolutionCasConsumer.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/cc/RecordResolutionCasConsumer.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/cc/RecordResolutionCasConsumer.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.smoking.cc;
+package org.apache.ctakes.smokingstatus.cc;
 
 import java.io.BufferedWriter;
 import java.io.File;
@@ -34,8 +34,9 @@ import org.apache.uima.resource.Resource
 import org.apache.uima.resource.ResourceProcessException;
 import org.apache.uima.util.ProcessTrace;
 
-import edu.mayo.bmi.smoking.patientLevel.PatientLevelSmokingStatus;
-import edu.mayo.bmi.smoking.type.SmokingDocumentClassification;
+import org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification;
+
+import org.apache.ctakes.smokingstatus.patientLevel.PatientLevelSmokingStatus;
 import org.apache.ctakes.typesystem.type.structured.DocumentID;
 
 public class RecordResolutionCasConsumer extends CasConsumer_ImplBase

Copied: incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/NamedEntityContextAnalyzer.java (from r1388092, incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/context/NamedEntityContextAnalyzer.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/NamedEntityContextAnalyzer.java?p2=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/NamedEntityContextAnalyzer.java&p1=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/context/NamedEntityContextAnalyzer.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/context/NamedEntityContextAnalyzer.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/NamedEntityContextAnalyzer.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.smoking.context;
+package org.apache.ctakes.smokingstatus.context;
 
 import java.util.ArrayList;
 import java.util.HashSet;
@@ -24,15 +24,15 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
 
+import org.apache.ctakes.core.fsm.adapters.TextTokenAdapter;
+import org.apache.ctakes.core.fsm.token.TextToken;
+import org.apache.ctakes.necontexts.ContextAnalyzer;
 import org.apache.log4j.Logger;
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.apache.uima.resource.ResourceInitializationException;
 
-import edu.mayo.bmi.fsm.token.TextToken;
-import edu.mayo.bmi.uima.context.ContextAnalyzer;
-import edu.mayo.bmi.uima.core.fsm.adapters.TextTokenAdapter;
 
 /**
  * This context analyzer provides code that is shared by the

Copied: incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/negation/NegationContextAnalyzer.java (from r1388092, incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/context/negation/NegationContextAnalyzer.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/negation/NegationContextAnalyzer.java?p2=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/negation/NegationContextAnalyzer.java&p1=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/context/negation/NegationContextAnalyzer.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/context/negation/NegationContextAnalyzer.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/context/negation/NegationContextAnalyzer.java Mon Sep 24 22:04:51 2012
@@ -16,18 +16,18 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.smoking.context.negation;
+package org.apache.ctakes.smokingstatus.context.negation;
 
 import java.util.List;
 import java.util.Set;
 
+import org.apache.ctakes.core.fsm.output.NegationIndicator;
+import org.apache.ctakes.core.fsm.token.TextToken;
+import org.apache.ctakes.necontexts.ContextHit;
+import org.apache.ctakes.smokingstatus.context.NamedEntityContextAnalyzer;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.jcas.tcas.Annotation;
 
-import edu.mayo.bmi.fsm.output.NegationIndicator;
-import edu.mayo.bmi.fsm.token.TextToken;
-import edu.mayo.bmi.uima.context.ContextHit;
-import edu.mayo.bmi.smoking.context.NamedEntityContextAnalyzer;
 import edu.mayo.bmi.fsm.smoking.machine.NegationFSM;
 
 public class NegationContextAnalyzer extends NamedEntityContextAnalyzer {

Copied: incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/NonSmokerNamedEntityLookupConsumerImpl.java (from r1388196, incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/uima/lookup/ae/NonSmokerNamedEntityLookupConsumerImpl.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/NonSmokerNamedEntityLookupConsumerImpl.java?p2=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/NonSmokerNamedEntityLookupConsumerImpl.java&p1=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/uima/lookup/ae/NonSmokerNamedEntityLookupConsumerImpl.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/uima/lookup/ae/NonSmokerNamedEntityLookupConsumerImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/NonSmokerNamedEntityLookupConsumerImpl.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.uima.lookup.ae;
+package org.apache.ctakes.smokingstatus.lookup.ae;
 
 import java.util.Collection;
 import java.util.Iterator;
@@ -27,13 +27,14 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.cas.FSArray;
 import org.apache.uima.jcas.JCas;
 
-import edu.mayo.bmi.dictionary.MetaDataHit;
-import edu.mayo.bmi.lookup.vo.LookupHit;
-import edu.mayo.bmi.uima.SmokingStatus.type.NonSmokerNamedEntityAnnotation;
+import org.apache.ctakes.smokingstatus.type.NonSmokerNamedEntityAnnotation;
+
+import org.apache.ctakes.dictionary.lookup.MetaDataHit;
+import org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl;
+import org.apache.ctakes.dictionary.lookup.ae.LookupConsumer;
+import org.apache.ctakes.dictionary.lookup.vo.LookupHit;
 import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
 import org.apache.ctakes.typesystem.type.constants.CONST;
-import edu.mayo.bmi.uima.lookup.ae.BaseLookupConsumerImpl;
-import edu.mayo.bmi.uima.lookup.ae.LookupConsumer;
 
 /**
  * copied from edu.may.bmi.uima.lookup.ae.NamedEntityLookupConsumerImpl in the "Dictionary Lookup" project

Copied: incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/SmokerNamedEntityLookupConsumerImpl.java (from r1388196, incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/uima/lookup/ae/SmokerNamedEntityLookupConsumerImpl.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/SmokerNamedEntityLookupConsumerImpl.java?p2=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/SmokerNamedEntityLookupConsumerImpl.java&p1=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/uima/lookup/ae/SmokerNamedEntityLookupConsumerImpl.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/uima/lookup/ae/SmokerNamedEntityLookupConsumerImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/SmokerNamedEntityLookupConsumerImpl.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.uima.lookup.ae;
+package org.apache.ctakes.smokingstatus.lookup.ae;
 
 import java.util.Collection;
 import java.util.Iterator;
@@ -27,9 +27,12 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FSArray;
 
-import edu.mayo.bmi.dictionary.MetaDataHit;
-import edu.mayo.bmi.lookup.vo.LookupHit;
-import edu.mayo.bmi.uima.SmokingStatus.type.SmokerNamedEntityAnnotation;
+import org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation;
+
+import org.apache.ctakes.dictionary.lookup.MetaDataHit;
+import org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl;
+import org.apache.ctakes.dictionary.lookup.ae.LookupConsumer;
+import org.apache.ctakes.dictionary.lookup.vo.LookupHit;
 import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
 import org.apache.ctakes.typesystem.type.constants.CONST;
 

Copied: incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/UnknownSmokerNamedEntityLookupConsumerImpl.java (from r1388196, incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/uima/lookup/ae/UnknownSmokerNamedEntityLookupConsumerImpl.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/UnknownSmokerNamedEntityLookupConsumerImpl.java?p2=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/UnknownSmokerNamedEntityLookupConsumerImpl.java&p1=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/uima/lookup/ae/UnknownSmokerNamedEntityLookupConsumerImpl.java&r1=1388196&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/uima/lookup/ae/UnknownSmokerNamedEntityLookupConsumerImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/UnknownSmokerNamedEntityLookupConsumerImpl.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.uima.lookup.ae;
+package org.apache.ctakes.smokingstatus.lookup.ae;
 
 import java.util.Collection;
 import java.util.Iterator;
@@ -27,9 +27,12 @@ import org.apache.uima.analysis_engine.A
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FSArray;
 
-import edu.mayo.bmi.dictionary.MetaDataHit;
-import edu.mayo.bmi.lookup.vo.LookupHit;
-import edu.mayo.bmi.uima.SmokingStatus.type.UnknownSmokerNamedEntityAnnotation;
+import org.apache.ctakes.smokingstatus.type.UnknownSmokerNamedEntityAnnotation;
+
+import org.apache.ctakes.dictionary.lookup.MetaDataHit;
+import org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl;
+import org.apache.ctakes.dictionary.lookup.ae.LookupConsumer;
+import org.apache.ctakes.dictionary.lookup.vo.LookupHit;
 import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
 import org.apache.ctakes.typesystem.type.constants.CONST;
 

Copied: incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/patientLevel/PatientLevelSmokingStatus.java (from r1388092, incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/patientLevel/PatientLevelSmokingStatus.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/patientLevel/PatientLevelSmokingStatus.java?p2=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/patientLevel/PatientLevelSmokingStatus.java&p1=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/patientLevel/PatientLevelSmokingStatus.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/patientLevel/PatientLevelSmokingStatus.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/patientLevel/PatientLevelSmokingStatus.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.smoking.patientLevel;
+package org.apache.ctakes.smokingstatus.patientLevel;
 
 import java.io.BufferedReader;
 import java.io.BufferedWriter;

Copied: incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/util/ClassifiableEntry.java (from r1388092, incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/util/ClassifiableEntry.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/util/ClassifiableEntry.java?p2=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/util/ClassifiableEntry.java&p1=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/util/ClassifiableEntry.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/util/ClassifiableEntry.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/util/ClassifiableEntry.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.smoking.util;
+package org.apache.ctakes.smokingstatus.util;
 
 public class ClassifiableEntry
 {

Copied: incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/util/TruthValue.java (from r1388092, incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/util/TruthValue.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/util/TruthValue.java?p2=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/util/TruthValue.java&p1=incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/util/TruthValue.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/edu/mayo/bmi/smoking/util/TruthValue.java (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/util/TruthValue.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.smoking.util;
+package org.apache.ctakes.smokingstatus.util;
 
 import java.util.List;
 

Modified: incubator/ctakes/trunk/ctakes-type-system/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-type-system/.project?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-type-system/.project (original)
+++ incubator/ctakes/trunk/ctakes-type-system/.project Mon Sep 24 22:04:51 2012
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <projectDescription>
-	<name>common-type-system</name>
+	<name>ctakes-type-system</name>
 	<comment></comment>
 	<projects>
 	</projects>

Copied: incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/kernel/Kernel.java (from r1388092, incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/chboston/cnlp/ctakes/kernel/Kernel.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/kernel/Kernel.java?p2=incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/kernel/Kernel.java&p1=incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/chboston/cnlp/ctakes/kernel/Kernel.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/chboston/cnlp/ctakes/kernel/Kernel.java (original)
+++ incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/kernel/Kernel.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.kernel;
+package org.apache.ctakes.typesystem.kernel;
 
 import libsvm.svm_node;
 

Copied: incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/kernel/LinearKernel.java (from r1388092, incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/chboston/cnlp/ctakes/kernel/LinearKernel.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/kernel/LinearKernel.java?p2=incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/kernel/LinearKernel.java&p1=incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/chboston/cnlp/ctakes/kernel/LinearKernel.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/chboston/cnlp/ctakes/kernel/LinearKernel.java (original)
+++ incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/kernel/LinearKernel.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.kernel;
+package org.apache.ctakes.typesystem.kernel;
 
 public class LinearKernel extends PolyKernel{
 	public LinearKernel(){

Copied: incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/kernel/PolyKernel.java (from r1388092, incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/chboston/cnlp/ctakes/kernel/PolyKernel.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/kernel/PolyKernel.java?p2=incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/kernel/PolyKernel.java&p1=incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/chboston/cnlp/ctakes/kernel/PolyKernel.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/chboston/cnlp/ctakes/kernel/PolyKernel.java (original)
+++ incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/kernel/PolyKernel.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.kernel;
+package org.apache.ctakes.typesystem.kernel;
 
 import java.util.concurrent.ConcurrentHashMap;
 

Copied: incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/kernel/RBFKernel.java (from r1388092, incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/chboston/cnlp/ctakes/kernel/RBFKernel.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/kernel/RBFKernel.java?p2=incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/kernel/RBFKernel.java&p1=incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/chboston/cnlp/ctakes/kernel/RBFKernel.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/chboston/cnlp/ctakes/kernel/RBFKernel.java (original)
+++ incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/kernel/RBFKernel.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.kernel;
+package org.apache.ctakes.typesystem.kernel;
 
 import libsvm.svm_node;
 

Copied: incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/util/FragmentUtils.java (from r1388092, incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/chboston/cnlp/util/FragmentUtils.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/util/FragmentUtils.java?p2=incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/util/FragmentUtils.java&p1=incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/chboston/cnlp/util/FragmentUtils.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/chboston/cnlp/util/FragmentUtils.java (original)
+++ incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/util/FragmentUtils.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.util;
+package org.apache.ctakes.typesystem.util;
 
 public class FragmentUtils {
 

Copied: incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/util/SimpleTree.java (from r1388092, incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/chboston/cnlp/util/SimpleTree.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/util/SimpleTree.java?p2=incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/util/SimpleTree.java&p1=incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/chboston/cnlp/util/SimpleTree.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/chboston/cnlp/util/SimpleTree.java (original)
+++ incubator/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/util/SimpleTree.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.util;
+package org.apache.ctakes.typesystem.util;
 
 import java.util.ArrayList;
 import java.util.regex.Matcher;

Modified: incubator/ctakes/trunk/ctakes-utils/scripts/knowtatorTools/cTakesNeToKnowtatorAnnotation (for Apache UIMA and cTAKES).launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/scripts/knowtatorTools/cTakesNeToKnowtatorAnnotation%20%28for%20Apache%20UIMA%20and%20cTAKES%29.launch?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/scripts/knowtatorTools/cTakesNeToKnowtatorAnnotation (for Apache UIMA and cTAKES).launch (original)
+++ incubator/ctakes/trunk/ctakes-utils/scripts/knowtatorTools/cTakesNeToKnowtatorAnnotation (for Apache UIMA and cTAKES).launch Mon Sep 24 22:04:51 2012
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/KnowtatorUtils/src/edu/mayo/bmi/uima/knowtatorutils/apache/app/cTakesNeToKnowtatorSHARPAnnotation.java"/>
+<listEntry value="/KnowtatorUtils/src/main/java/org/apache/ctakes/knowtatorutils/apache/app/cTakesNeToKnowtatorSHARPAnnotation.java"/>
 </listAttribute>
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
 <listEntry value="1"/>

Modified: incubator/ctakes/trunk/ctakes-utils/scripts/knowtatorTools/copyKnowtatorFiles.bat
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/scripts/knowtatorTools/copyKnowtatorFiles.bat?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/scripts/knowtatorTools/copyKnowtatorFiles.bat (original)
+++ incubator/ctakes/trunk/ctakes-utils/scripts/knowtatorTools/copyKnowtatorFiles.bat Mon Sep 24 22:04:51 2012
@@ -21,10 +21,10 @@ REM @ECHO OFF
 SETLOCAL ENABLEDELAYEDEXPANSION
 set UIMA_HOME=c:\tools\apache-uima
 SET CLASSPATH1=%UIMA_HOME%\lib\uima-core.jar;%UIMA_HOME%\lib\uima-cpe.jar;%UIMA_HOME%\lib\uima-tools.jar;%UIMA_HOME%\lib\uima-document-annotations.jar;%UIMA_HOME%\lib\uima-examples.jar;
-SET CLASSPATH2=chunker/bin;clinical documents pipeline/bin;context dependent tokenizer/bin;core/bin;dictionary lookup/bin;document preprocessor/bin;LVG/bin;NE contexts/bin;POS tagger/bin;core/lib/log4j-1.2.8.jar;
+SET CLASSPATH2=chunker/bin;ctakes-clinical-pipeline/bin;context dependent tokenizer/bin;core/bin;dictionary lookup/bin;document preprocessor/bin;LVG/bin;NE contexts/bin;POS tagger/bin;core/lib/log4j-1.2.8.jar;
 SET CLASSPATH3=core/lib/jdom.jar;core/lib/lucene-core-3.0.2.jar;core/lib/opennlp-tools-1.4.0.jar;core/lib/maxent-2.5.0.jar;core/lib/OpenAI_FSM.jar;core/lib/trove.jar;Drug NER/bin;Drug NER/resources;
 SET CLASSPATH4=LVG/lib/lvg2008dist.jar;document preprocessor/lib/xercesImpl.jar;document preprocessor/lib/xml-apis.jar;document preprocessor/lib/xmlParserAPIs.jar;smoking status/bin;smoking status/resources;
-SET CLASSPATH5=chunker/resources;clinical documents pipeline/resources;context dependent tokenizer/resources;core/resources;dictionary lookup/resources;document preprocessor/resources;LVG/resources;POS tagger/resources;KnowtatorUtils/bin;KnowtatorUtils/resourses;utils/lib/knowtator.jar;
+SET CLASSPATH5=chunker/resources;ctakes-clinical-pipeline/resources;context dependent tokenizer/resources;core/resources;dictionary lookup/resources;document preprocessor/resources;LVG/resources;POS tagger/resources;KnowtatorUtils/bin;KnowtatorUtils/resourses;utils/lib/knowtator.jar;
 SET CLASSPATH6=utils/lib/looks-2.1.3.jar;utils/lib/protege.jar
 
 FOR /F  %%G IN ('dir /b /on %1\Docset*') DO (

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.Constituency Parser.properties (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.Constituency Parser.properties)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.Constituency%20Parser.properties?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.Constituency%20Parser.properties&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.Constituency%20Parser.properties&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.Constituency Parser.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.Constituency Parser.properties Mon Sep 24 22:04:51 2012
@@ -18,6 +18,6 @@
 #
 
 project=Constituency Parser
-classpath=$main_root/bin;$main_root/../core/bin;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/trove.jar;$main_root/resources;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/jdom.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/resources;
-datapath=$main_root/resources;$main_root/../core/resources;
+classpath=$main_root/bin;$main_root/../ctakes-core/bin;$main_root/../ctakes-core/lib/opennlp-tools-1.4.3.jar;$main_root/../ctakes-core/lib/maxent-2.5.0.jar;$main_root/../ctakes-core/lib/trove.jar;$main_root/resources;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;$main_root/../ctakes-core/lib/jdom.jar;$main_root/../ctakes-core/lib/lucene-core-3.0.2.jar;$main_root/../ctakes-core/resources;
+datapath=$main_root/resources;$main_root/../ctakes-core/resources;
 aeDescriptor=desc/analysis_engine/AggregateParsingProcessor.xml
\ No newline at end of file

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.Drug NER.properties (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.Drug NER.properties)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.Drug%20NER.properties?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.Drug%20NER.properties&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.Drug%20NER.properties&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.Drug NER.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.Drug NER.properties Mon Sep 24 22:04:51 2012
@@ -18,6 +18,6 @@
 #
 
 project=Drug NER
-classpath=$main_root/bin;$main_root/resources;$main_root/../core/lib/jdom.jar;$main_root/../core/lib/junit.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/trove.jar;$main_root/../core/bin;$main_root/../dictionary lookup/bin;$main_root/../NE contexts/bin;$main_root/../context dependent tokenizer/bin;$main_root/../document preprocessor/bin;$main_root/../LVG/bin;$main_root/../clinical documents pipeline/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/resources;$main_root/../dictionary lookup/resources;$main_root/../POS tagger/resources;$main_root/../chunker/resources;$main_root/../chunker/bin;$main_root/../LVG/lib/lvg2008dist.jar;$main_root/../LVG/resources;$main_root/../POS tagger/bin;$main_root/../document preprocessor/resources;
-datapath=$main_root/resources;$main_root/../core/resources;$main_root/../dictionary lookup/resources;$main_root/../POS tagger/resources;$main_root/../chunker/resources;
+classpath=$main_root/bin;$main_root/resources;$main_root/../ctakes-core/lib/jdom.jar;$main_root/../ctakes-core/lib/junit.jar;$main_root/../ctakes-core/lib/maxent-2.5.0.jar;$main_root/../ctakes-core/lib/OpenAI_FSM.jar;$main_root/../ctakes-core/lib/opennlp-tools-1.4.3.jar;$main_root/../ctakes-core/lib/trove.jar;$main_root/../ctakes-core/bin;$main_root/../ctakes-dictionary-lookup/bin;$main_root/../ctakes-ne-contexts/bin;$main_root/../ctakes-context-tokenizer/bin;$main_root/../ctakes-preprocessor/bin;$main_root/../ctakes-lvg/bin;$main_root/../ctakes-clinical-pipeline/bin;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;$main_root/../ctakes-core/lib/lucene-core-3.0.2.jar;$main_root/../ctakes-core/resources;$main_root/../ctakes-dictionary-lookup/resources;$main_root/../ctakes-pos-tagger/resources;$main_root/../ctakes-chunker/resources;$main_root/../ctakes-chunker/bin;$main_root/../ctakes-lvg/lib/lvg2008dist.jar;$main_root/../ctakes-lvg/resources;$main_root/../ctakes-pos-tagger/bin;$m
 ain_root/../ctakes-preprocessor/resources;
+datapath=$main_root/resources;$main_root/../ctakes-core/resources;$main_root/../ctakes-dictionary-lookup/resources;$main_root/../ctakes-pos-tagger/resources;$main_root/../ctakes-chunker/resources;
 aeDescriptor=desc/analysis_engine/DrugAggregatePlaintextProcessor.xml
\ No newline at end of file

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.LVG.properties (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.LVG.properties)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.LVG.properties?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.LVG.properties&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.LVG.properties&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.LVG.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.LVG.properties Mon Sep 24 22:04:51 2012
@@ -18,6 +18,6 @@
 #
 
 project=LVG
-classpath=$main_root/bin;$main_root/resources;$main_root/../core/bin;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/trove.jar;$main_root/../core/resources;$main_root/lib/lvg2008dist.jar;$main_root/../core/lib/log4j-1.2.8.jar;
-datapath=$main_root/resources;$main_root/../core/resources;
+classpath=$main_root/bin;$main_root/resources;$main_root/../ctakes-core/bin;$main_root/../ctakes-core/lib/opennlp-tools-1.4.3.jar;$main_root/../ctakes-core/lib/maxent-2.5.0.jar;$main_root/../ctakes-core/lib/trove.jar;$main_root/../ctakes-core/resources;$main_root/lib/lvg2008dist.jar;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;
+datapath=$main_root/resources;$main_root/../ctakes-core/resources;
 aeDescriptor=desc/analysis_engine/AggregateAE.xml
\ No newline at end of file

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.NE contexts.properties (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.NE contexts.properties)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.NE%20contexts.properties?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.NE%20contexts.properties&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.NE%20contexts.properties&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.NE contexts.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.NE contexts.properties Mon Sep 24 22:04:51 2012
@@ -18,6 +18,6 @@
 #
 
 project=NE contexts
-classpath=$main_root/bin;$main_root/../core/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/OpenAI_FSM.jar;
+classpath=$main_root/bin;$main_root/../ctakes-core/bin;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;$main_root/../ctakes-core/lib/OpenAI_FSM.jar;
 datapath=$main_root/resources;
 aeDescriptor=desc/AggregateAE.xml
\ No newline at end of file

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.PAD term spotter.properties (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.PAD term spotter.properties)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.PAD%20term%20spotter.properties?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.PAD%20term%20spotter.properties&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.PAD%20term%20spotter.properties&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.PAD term spotter.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.PAD term spotter.properties Mon Sep 24 22:04:51 2012
@@ -18,6 +18,6 @@
 #
 
 project=PAD term spotter
-classpath=$main_root/bin;$main_root/resources;$main_root/../core/bin;$main_root/../core/lib/jdom.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/trove.jar;$main_root/../NE contexts/bin;$main_root/../dictionary lookup/bin;$main_root/../context dependent tokenizer/bin;$main_root/../chunker/bin;$main_root/../POS tagger/bin;$main_root/../clinical documents pipeline/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/resources;$main_root/../dictionary lookup/resources;$main_root/../POS tagger/resources;$main_root/../chunker/resources;
-datapath=$main_root/resources;$main_root/../core/resources;$main_root/../dictionary lookup/resources;$main_root/../POS tagger/resources;$main_root/../chunker/resources;
+classpath=$main_root/bin;$main_root/resources;$main_root/../ctakes-core/bin;$main_root/../ctakes-core/lib/jdom.jar;$main_root/../ctakes-core/lib/maxent-2.5.0.jar;$main_root/../ctakes-core/lib/opennlp-tools-1.4.3.jar;$main_root/../ctakes-core/lib/trove.jar;$main_root/../ctakes-ne-contexts/bin;$main_root/../ctakes-dictionary-lookup/bin;$main_root/../ctakes-context-tokenizer/bin;$main_root/../ctakes-chunker/bin;$main_root/../ctakes-pos-tagger/bin;$main_root/../ctakes-clinical-pipeline/bin;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;$main_root/../ctakes-core/lib/OpenAI_FSM.jar;$main_root/../ctakes-core/lib/lucene-core-3.0.2.jar;$main_root/../ctakes-core/resources;$main_root/../ctakes-dictionary-lookup/resources;$main_root/../ctakes-pos-tagger/resources;$main_root/../ctakes-chunker/resources;
+datapath=$main_root/resources;$main_root/../ctakes-core/resources;$main_root/../ctakes-dictionary-lookup/resources;$main_root/../ctakes-pos-tagger/resources;$main_root/../ctakes-chunker/resources;
 aeDescriptor=desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml
\ No newline at end of file

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.POS tagger.properties (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.POS tagger.properties)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.POS%20tagger.properties?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.POS%20tagger.properties&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.POS%20tagger.properties&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.POS tagger.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.POS tagger.properties Mon Sep 24 22:04:51 2012
@@ -18,6 +18,6 @@
 #
 
 project=POS tagger
-classpath=$main_root/bin;$main_root/../core/bin;$main_root/../core/lib/jdom.jar;$main_root/../core/lib/trove.jar;$main_root/../core/resources;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../core/lib/SQLWrapper.jar;$main_root/resources;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;
+classpath=$main_root/bin;$main_root/../ctakes-core/bin;$main_root/../ctakes-core/lib/jdom.jar;$main_root/../ctakes-core/lib/trove.jar;$main_root/../ctakes-core/resources;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;$main_root/../ctakes-core/lib/lucene-core-3.0.2.jar;$main_root/../ctakes-core/lib/OpenAI_FSM.jar;$main_root/../ctakes-core/lib/SQLWrapper.jar;$main_root/resources;$main_root/../ctakes-core/lib/maxent-2.5.0.jar;$main_root/../ctakes-core/lib/opennlp-tools-1.4.3.jar;
 datapath=$main_root/resources;
 aeDescriptor=desc/AggregateAE.xml
\ No newline at end of file

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.SideEffect.properties (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.SideEffect.properties)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.SideEffect.properties?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.SideEffect.properties&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.SideEffect.properties&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.SideEffect.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.SideEffect.properties Mon Sep 24 22:04:51 2012
@@ -18,6 +18,6 @@
 #
 
 project=SideEffect
-classpath=$main_root/bin;$main_root/../dictionary lookup/resources/lookup;$main_root/resources;$main_root/../Drug NER/bin;$main_root/../clinical documents pipeline/bin;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/lib/libsvm-2.91.jar;$main_root/../core/bin;$main_root/../core/lib/jdom.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/trove.jar;$main_root/../NE contexts/bin;$main_root/../dictionary lookup/bin;$main_root/../chunker/bin;$main_root/../POS tagger/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../context dependent tokenizer/bin;$main_root/../LVG/bin;$main_root/../LVG/lib/lvg2008dist.jar;$main_root/../core/resources;$main_root/../dictionary lookup/resources;$main_root/../chunker/resources;$main_root/../POS tagger/resources;$main_root/../LVG/resources;$main_root/../document preprocessor/bin;$main_root/../document preprocessor/resources;
-datapath=$main_root/../dictionary lookup/resources/lookup;$main_root/resources;$main_root/../core/resources;$main_root/../dictionary lookup/resources;$main_root/../chunker/resources;$main_root/../POS tagger/resources;$main_root/../LVG/resources;
+classpath=$main_root/bin;$main_root/../ctakes-dictionary-lookup/resources/lookup;$main_root/resources;$main_root/../ctakes-drug-ner/bin;$main_root/../ctakes-clinical-pipeline/bin;$main_root/../ctakes-core/lib/lucene-core-3.0.2.jar;$main_root/lib/libsvm-2.91.jar;$main_root/../ctakes-core/bin;$main_root/../ctakes-core/lib/jdom.jar;$main_root/../ctakes-core/lib/maxent-2.5.0.jar;$main_root/../ctakes-core/lib/opennlp-tools-1.4.3.jar;$main_root/../ctakes-core/lib/trove.jar;$main_root/../ctakes-ne-contexts/bin;$main_root/../ctakes-dictionary-lookup/bin;$main_root/../ctakes-chunker/bin;$main_root/../ctakes-pos-tagger/bin;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;$main_root/../ctakes-core/lib/OpenAI_FSM.jar;$main_root/../ctakes-context-tokenizer/bin;$main_root/../ctakes-lvg/bin;$main_root/../ctakes-lvg/lib/lvg2008dist.jar;$main_root/../ctakes-core/resources;$main_root/../ctakes-dictionary-lookup/resources;$main_root/../ctakes-chunker/resources;$main_root/../ctakes-pos-tagger/reso
 urces;$main_root/../ctakes-lvg/resources;$main_root/../ctakes-preprocessor/bin;$main_root/../ctakes-preprocessor/resources;
+datapath=$main_root/../ctakes-dictionary-lookup/resources/lookup;$main_root/resources;$main_root/../ctakes-core/resources;$main_root/../ctakes-dictionary-lookup/resources;$main_root/../ctakes-chunker/resources;$main_root/../ctakes-pos-tagger/resources;$main_root/../ctakes-lvg/resources;
 aeDescriptor=desc/analysis_engine/SideEffectAggregateTAE.xml
\ No newline at end of file

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.chunker.properties (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.chunker.properties)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.chunker.properties?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.chunker.properties&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.chunker.properties&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.chunker.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.chunker.properties Mon Sep 24 22:04:51 2012
@@ -18,5 +18,5 @@
 #
 
 project=chunker
-classpath=$main_root/bin;$main_root/../context dependent tokenizer/bin;$main_root/resources;$main_root/../LVG/bin;$main_root/../dictionary lookup/bin;$main_root/../NE contexts/bin;$main_root/../core/resources;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/trove.jar;$main_root/../core/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../POS tagger/bin;$main_root/../POS tagger/resources;$main_root/../document preprocessor/bin;
+classpath=$main_root/bin;$main_root/../ctakes-context-tokenizer/bin;$main_root/resources;$main_root/../ctakes-lvg/bin;$main_root/../ctakes-dictionary-lookup/bin;$main_root/../ctakes-ne-contexts/bin;$main_root/../ctakes-core/resources;$main_root/../ctakes-core/lib/opennlp-tools-1.4.3.jar;$main_root/../ctakes-core/lib/maxent-2.5.0.jar;$main_root/../ctakes-core/lib/trove.jar;$main_root/../ctakes-core/bin;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;$main_root/../ctakes-pos-tagger/bin;$main_root/../ctakes-pos-tagger/resources;$main_root/../ctakes-preprocessor/bin;
 aeDescriptor=desc/AggregateAE.xml
\ No newline at end of file

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.clinical documents pipeline.properties (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.clinical documents pipeline.properties)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.clinical%20documents%20pipeline.properties?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.clinical%20documents%20pipeline.properties&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.clinical%20documents%20pipeline.properties&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.clinical documents pipeline.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.clinical documents pipeline.properties Mon Sep 24 22:04:51 2012
@@ -17,6 +17,6 @@
 # under the License.
 #
 
-project=clinical documents pipeline
-classpath=$main_root/bin;$main_root/../context dependent tokenizer/bin;$main_root/resources;$main_root/../chunker/bin;$main_root/../chunker/resources;$main_root/../LVG/bin;$main_root/../LVG/lib/lvg2008dist.jar;$main_root/../LVG/resources;$main_root/../dictionary lookup/bin;$main_root/../dictionary lookup/resources;$main_root/../NE contexts/bin;$main_root/../core/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/trove.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/lib/jdom.jar;$main_root/../core/resources;$main_root/../POS tagger/bin;$main_root/../POS tagger/resources;$main_root/../document preprocessor/bin;$main_root/../document preprocessor/resources;
+project=ctakes-clinical-pipeline
+classpath=$main_root/bin;$main_root/../ctakes-context-tokenizer/bin;$main_root/resources;$main_root/../ctakes-chunker/bin;$main_root/../ctakes-chunker/resources;$main_root/../ctakes-lvg/bin;$main_root/../ctakes-lvg/lib/lvg2008dist.jar;$main_root/../ctakes-lvg/resources;$main_root/../ctakes-dictionary-lookup/bin;$main_root/../ctakes-dictionary-lookup/resources;$main_root/../ctakes-ne-contexts/bin;$main_root/../ctakes-core/bin;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;$main_root/../ctakes-core/lib/OpenAI_FSM.jar;$main_root/../ctakes-core/lib/opennlp-tools-1.4.3.jar;$main_root/../ctakes-core/lib/maxent-2.5.0.jar;$main_root/../ctakes-core/lib/trove.jar;$main_root/../ctakes-core/lib/lucene-core-3.0.2.jar;$main_root/../ctakes-core/lib/jdom.jar;$main_root/../ctakes-core/resources;$main_root/../ctakes-pos-tagger/bin;$main_root/../ctakes-pos-tagger/resources;$main_root/../ctakes-preprocessor/bin;$main_root/../ctakes-preprocessor/resources;
 aeDescriptor=desc/analysis_engine/AggregatePlaintextProcessor.xml
\ No newline at end of file

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.context dependent tokenizer.properties (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.context dependent tokenizer.properties)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.context%20dependent%20tokenizer.properties?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.context%20dependent%20tokenizer.properties&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.context%20dependent%20tokenizer.properties&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.context dependent tokenizer.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.context dependent tokenizer.properties Mon Sep 24 22:04:51 2012
@@ -18,6 +18,6 @@
 #
 
 project=context dependent tokenizer
-classpath=$main_root/bin;$main_root/../core/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/trove.jar;
-datapath=$main_root/resources;$main_root/../core/resources;
+classpath=$main_root/bin;$main_root/../ctakes-core/bin;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;$main_root/../ctakes-core/lib/OpenAI_FSM.jar;$main_root/../ctakes-core/lib/opennlp-tools-1.4.3.jar;$main_root/../ctakes-core/lib/maxent-2.5.0.jar;$main_root/../ctakes-core/lib/trove.jar;
+datapath=$main_root/resources;$main_root/../ctakes-core/resources;
 aeDescriptor=desc/analysis_engine/AggregateAE.xml
\ No newline at end of file

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.coref-resolver.properties (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.coref-resolver.properties)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.coref-resolver.properties?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.coref-resolver.properties&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.coref-resolver.properties&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.coref-resolver.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.coref-resolver.properties Mon Sep 24 22:04:51 2012
@@ -18,6 +18,6 @@
 #
 
 project=coref-resolver
-classpath=$main_root/bin;$main_root/../Constituency Parser/bin;$main_root/lib/Jama-1.0.2.jar;$main_root/lib/libsvm.jar;$main_root/../core/bin;$main_root/../context dependent tokenizer/bin;$main_root/../clinical documents pipeline/bin;$main_root/../chunker/bin;$main_root/../chunker/resources;$main_root/../LVG/bin;$main_root/../LVG/lib/lvg2008dist.jar;$main_root/../LVG/resources;$main_root/../dictionary lookup/bin;$main_root/../dictionary lookup/resources;$main_root/../NE contexts/bin;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/trove.jar;$main_root/resources;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/jdom.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/resources;$main_root/../POS tagger/bin;$main_root/../POS tagger/resources;$main_root/../document preprocessor/bin;$main_root/../document preprocessor/resources;
-datapath=$main_root/resources;$main_root/../core/resources;$main_root/../Constituency Parser/resources;
+classpath=$main_root/bin;$main_root/../Constituency Parser/bin;$main_root/lib/Jama-1.0.2.jar;$main_root/lib/libsvm.jar;$main_root/../ctakes-core/bin;$main_root/../ctakes-context-tokenizer/bin;$main_root/../ctakes-clinical-pipeline/bin;$main_root/../ctakes-chunker/bin;$main_root/../ctakes-chunker/resources;$main_root/../ctakes-lvg/bin;$main_root/../ctakes-lvg/lib/lvg2008dist.jar;$main_root/../ctakes-lvg/resources;$main_root/../ctakes-dictionary-lookup/bin;$main_root/../ctakes-dictionary-lookup/resources;$main_root/../ctakes-ne-contexts/bin;$main_root/../ctakes-core/lib/OpenAI_FSM.jar;$main_root/../ctakes-core/lib/opennlp-tools-1.4.3.jar;$main_root/../ctakes-core/lib/maxent-2.5.0.jar;$main_root/../ctakes-core/lib/trove.jar;$main_root/resources;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;$main_root/../ctakes-core/lib/jdom.jar;$main_root/../ctakes-core/lib/lucene-core-3.0.2.jar;$main_root/../ctakes-core/resources;$main_root/../ctakes-pos-tagger/bin;$main_root/../ctakes-pos-tag
 ger/resources;$main_root/../ctakes-preprocessor/bin;$main_root/../ctakes-preprocessor/resources;
+datapath=$main_root/resources;$main_root/../ctakes-core/resources;$main_root/../Constituency Parser/resources;
 aeDescriptor=desc/analysis_engine/CorefProcessor.xml

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.dependency parser.properties (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.dependency parser.properties)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.dependency%20parser.properties?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.dependency%20parser.properties&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.dependency%20parser.properties&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.dependency parser.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.dependency parser.properties Mon Sep 24 22:04:51 2012
@@ -18,5 +18,5 @@
 #
 
 project=dependency parser
-classpath=$main_root/bin;$main_root/clinical documents pipeline/bin;$main_root/../context dependent tokenizer/bin;$main_root/resources;$main_root/../chunker/bin;$main_root/../chunker/resources;$main_root/../LVG/bin;$main_root/../LVG/lib/lvg2008dist.jar;$main_root/../LVG/resources;$main_root/../dictionary lookup/bin;$main_root/../dictionary lookup/resources;$main_root/../NE contexts/bin;$main_root/../core/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/trove.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/lib/jdom.jar;$main_root/../core/resources;$main_root/../POS tagger/bin;$main_root/../POS tagger/resources;$main_root/../document preprocessor/bin;$main_root/../document preprocessor/resources;
+classpath=$main_root/bin;$main_root/ctakes-clinical-pipeline/bin;$main_root/../ctakes-context-tokenizer/bin;$main_root/resources;$main_root/../ctakes-chunker/bin;$main_root/../ctakes-chunker/resources;$main_root/../ctakes-lvg/bin;$main_root/../ctakes-lvg/lib/lvg2008dist.jar;$main_root/../ctakes-lvg/resources;$main_root/../ctakes-dictionary-lookup/bin;$main_root/../ctakes-dictionary-lookup/resources;$main_root/../ctakes-ne-contexts/bin;$main_root/../ctakes-core/bin;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;$main_root/../ctakes-core/lib/OpenAI_FSM.jar;$main_root/../ctakes-core/lib/opennlp-tools-1.4.3.jar;$main_root/../ctakes-core/lib/maxent-2.5.0.jar;$main_root/../ctakes-core/lib/trove.jar;$main_root/../ctakes-core/lib/lucene-core-3.0.2.jar;$main_root/../ctakes-core/lib/jdom.jar;$main_root/../ctakes-core/resources;$main_root/../ctakes-pos-tagger/bin;$main_root/../ctakes-pos-tagger/resources;$main_root/../ctakes-preprocessor/bin;$main_root/../ctakes-preprocessor/resources;
 aeDescriptor=desc/analysis_engine/ClearParserPlaintextAggregate.xml
\ No newline at end of file

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.dictionary lookup.properties (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.dictionary lookup.properties)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.dictionary%20lookup.properties?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.dictionary%20lookup.properties&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.dictionary%20lookup.properties&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.dictionary lookup.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.dictionary lookup.properties Mon Sep 24 22:04:51 2012
@@ -18,6 +18,6 @@
 #
 
 project=dictionary lookup
-classpath=$main_root/bin;$main_root/../core/bin;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/trove.jar;$main_root/resources;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/jdom.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/resources;
-datapath=$main_root/resources;$main_root/../core/resources;
+classpath=$main_root/bin;$main_root/../ctakes-core/bin;$main_root/../ctakes-core/lib/opennlp-tools-1.4.3.jar;$main_root/../ctakes-core/lib/maxent-2.5.0.jar;$main_root/../ctakes-core/lib/trove.jar;$main_root/resources;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;$main_root/../ctakes-core/lib/jdom.jar;$main_root/../ctakes-core/lib/lucene-core-3.0.2.jar;$main_root/../ctakes-core/resources;
+datapath=$main_root/resources;$main_root/../ctakes-core/resources;
 aeDescriptor=desc/analysis_engine/AggregateAE.xml
\ No newline at end of file

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.document preprocessor.properties (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.document preprocessor.properties)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.document%20preprocessor.properties?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.document%20preprocessor.properties&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.document%20preprocessor.properties&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.document preprocessor.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.document preprocessor.properties Mon Sep 24 22:04:51 2012
@@ -18,5 +18,5 @@
 #
 
 project=document preprocessor
-classpath=$main_root/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/bin;$main_root/resources;$main_root/lib/xercesImpl.jar;$main_root/lib/xml-apis.jar;$main_root/lib/xmlParserAPIs.jar;
+classpath=$main_root/bin;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;$main_root/../ctakes-core/bin;$main_root/resources;$main_root/lib/xercesImpl.jar;$main_root/lib/xml-apis.jar;$main_root/lib/xmlParserAPIs.jar;
 aeDescriptor=desc/AggregateAE.xml
\ No newline at end of file

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.java (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.java?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.java&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.java (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.utils.build;
+package org.apache.ctakes.utils.build;
 
 import java.io.File;
 import java.io.FileInputStream;
@@ -90,7 +90,7 @@ public class BuildPear {
 		Properties props = new Properties();
 		// set defaults in case file not found or properties file does not contain value
 		// Nearly all project rely on core, so add it to the classpath
-		final String classpathDefault = "$main_root/bin;$main_root/../core/bin;";
+		final String classpathDefault = "$main_root/bin;$main_root/../ctakes-core/bin;";
 		final String datapathDefault = "$main_root/resources;";
 		final String aeDescriptorDefault = "desc/AE.xml";
 		// Set default values in case properties file not found

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.smoking status.properties (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.smoking status.properties)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.smoking%20status.properties?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.smoking%20status.properties&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.smoking%20status.properties&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPear.smoking status.properties (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPear.smoking status.properties Mon Sep 24 22:04:51 2012
@@ -18,6 +18,6 @@
 #
 
 project=smoking status
-classpath=$main_root/bin;$main_root/resources;$main_root/desc;$main_root/../context dependent tokenizer/bin;$main_root/../clinical documents pipeline/bin;$main_root/../chunker/bin;$main_root/../chunker/resources;$main_root/../LVG/bin;$main_root/../LVG/lib/lvg2008dist.jar;$main_root/../LVG/resources;$main_root/../dictionary lookup/bin;$main_root/../dictionary lookup/resources;$main_root/../NE contexts/bin;$main_root/lib/libsvm-2.91.jar;$main_root/../core/bin;$main_root/../core/lib/log4j-1.2.8.jar;$main_root/../core/lib/OpenAI_FSM.jar;$main_root/../core/lib/opennlp-tools-1.4.3.jar;$main_root/../core/lib/maxent-2.5.0.jar;$main_root/../core/lib/trove.jar;$main_root/../core/lib/lucene-core-3.0.2.jar;$main_root/../core/lib/jdom.jar;$main_root/../core/resources;$main_root/../POS tagger/bin;$main_root/../POS tagger/resources;$main_root/../document preprocessor/bin;$main_root/../document preprocessor/resources;$main_root/../context dependent tokenizer/bin;
+classpath=$main_root/bin;$main_root/resources;$main_root/desc;$main_root/../ctakes-context-tokenizer/bin;$main_root/../ctakes-clinical-pipeline/bin;$main_root/../ctakes-chunker/bin;$main_root/../ctakes-chunker/resources;$main_root/../ctakes-lvg/bin;$main_root/../ctakes-lvg/lib/lvg2008dist.jar;$main_root/../ctakes-lvg/resources;$main_root/../ctakes-dictionary-lookup/bin;$main_root/../ctakes-dictionary-lookup/resources;$main_root/../ctakes-ne-contexts/bin;$main_root/lib/libsvm-2.91.jar;$main_root/../ctakes-core/bin;$main_root/../ctakes-core/lib/log4j-1.2.8.jar;$main_root/../ctakes-core/lib/OpenAI_FSM.jar;$main_root/../ctakes-core/lib/opennlp-tools-1.4.3.jar;$main_root/../ctakes-core/lib/maxent-2.5.0.jar;$main_root/../ctakes-core/lib/trove.jar;$main_root/../ctakes-core/lib/lucene-core-3.0.2.jar;$main_root/../ctakes-core/lib/jdom.jar;$main_root/../ctakes-core/resources;$main_root/../ctakes-pos-tagger/bin;$main_root/../ctakes-pos-tagger/resources;$main_root/../ctakes-preprocessor
 /bin;$main_root/../ctakes-preprocessor/resources;$main_root/../ctakes-context-tokenizer/bin;
 datapath=$main_root/resources;
 aeDescriptor=desc/analysis_engine/NullAnnotator.xml
\ No newline at end of file

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPipelinePears.java (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPipelinePears.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPipelinePears.java?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPipelinePears.java&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPipelinePears.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/BuildPipelinePears.java (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/BuildPipelinePears.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.utils.build;
+package org.apache.ctakes.utils.build;
 
 /**
  * This class is used to edu.mayo.bmi.utils.build the PEAR files for the pipeline.
@@ -61,7 +61,7 @@ public class BuildPipelinePears  {
 		  "dictionary lookup",
 		  "LVG",
 		  "NE contexts",
-		  "clinical documents pipeline", // install after all above ones, as depends on others
+		  "ctakes-clinical-pipeline", // install after all above ones, as depends on others
 		  "Drug NER",
 		  "PAD term spotter",
 		  "SideEffect",

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/InstallPearSilently.java (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/InstallPearSilently.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/InstallPearSilently.java?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/InstallPearSilently.java&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/InstallPearSilently.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/InstallPearSilently.java (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/InstallPearSilently.java Mon Sep 24 22:04:51 2012
@@ -39,7 +39,7 @@
  * under the License.
  */
 
-package edu.mayo.bmi.utils.build;
+package org.apache.ctakes.utils.build;
 //package org.apache.uima.tools.pear.install;
 
 import java.io.File;

Copied: incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/InstallPipelineFromPears.java (from r1388092, incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/InstallPipelineFromPears.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/InstallPipelineFromPears.java?p2=incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/InstallPipelineFromPears.java&p1=incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/InstallPipelineFromPears.java&r1=1388092&r2=1389618&rev=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/src/main/java/edu/mayo/bmi/utils/build/InstallPipelineFromPears.java (original)
+++ incubator/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/build/InstallPipelineFromPears.java Mon Sep 24 22:04:51 2012
@@ -16,7 +16,7 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-package edu.mayo.bmi.utils.build;
+package org.apache.ctakes.utils.build;
 
 import java.io.File;
 //package org.apache.uima.tools.pear.install;
@@ -66,7 +66,7 @@ public class InstallPipelineFromPears  {
 		  "dictionary lookup",
 		  "LVG",
 		  "NE contexts",
-		  "clinical documents pipeline", // install last as depends on others
+		  "ctakes-clinical-pipeline", // install last as depends on others
    };
   		
   

Modified: incubator/ctakes/trunk/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/pom.xml?rev=1389618&r1=1389617&r2=1389618&view=diff
==============================================================================
--- incubator/ctakes/trunk/pom.xml (original)
+++ incubator/ctakes/trunk/pom.xml Mon Sep 24 22:04:51 2012
@@ -45,6 +45,7 @@
 		<module>ctakes-relation-extractor</module>
 		<module>ctakes-clinical-pipeline</module>
 		<module>ctakes-pad-term-spotter</module>
+		<module>ctakes-assertion</module>		
 	</modules>
 	<dependencyManagement>
 		<dependencies>
@@ -106,6 +107,13 @@
 			<dependency>
 				<groupId>org.apache.ctakes</groupId>
 				<artifactId>
+					ctakes-assertion
+				</artifactId>
+				<version>${ctakes.version}</version>
+			</dependency>			
+			<dependency>
+				<groupId>org.apache.ctakes</groupId>
+				<artifactId>
 					ctakes-constituency-parser
 				</artifactId>
 				<version>${ctakes.version}</version>
@@ -396,7 +404,7 @@
 					</configuration>
 				</plugin>
 
-				<!-- All plugins below should really only be in common-type-system. However, 
+				<!-- All plugins below should really only be in ctakes-type-system. However, 
 					some cTAKES modules still declare their own type systems internally. So until 
 					those are fixed, this needs to stay in the parent pom. -->
 



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