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From james-mas...@apache.org
Subject svn commit: r1501907 - /ctakes/sandbox/ctakes-2.5-with-resources-merged/
Date Wed, 10 Jul 2013 18:46:27 GMT
Author: james-masanz
Date: Wed Jul 10 18:46:24 2013
New Revision: 1501907

URL: http://svn.apache.org/r1501907
Log:
initial import of this into sandbox

Added:
    ctakes/sandbox/ctakes-2.5-with-resources-merged/.classpath   (with props)
    ctakes/sandbox/ctakes-2.5-with-resources-merged/.classpath-orig
    ctakes/sandbox/ctakes-2.5-with-resources-merged/.project   (with props)
    ctakes/sandbox/ctakes-2.5-with-resources-merged/.project-orig
    ctakes/sandbox/ctakes-2.5-with-resources-merged/LICENSE
    ctakes/sandbox/ctakes-2.5-with-resources-merged/MODIFICATIONS.JAMES.txt   (with props)
    ctakes/sandbox/ctakes-2.5-with-resources-merged/NOTICE
    ctakes/sandbox/ctakes-2.5-with-resources-merged/README
    ctakes/sandbox/ctakes-2.5-with-resources-merged/build.xml   (with props)
    ctakes/sandbox/ctakes-2.5-with-resources-merged/cTAKES.jar   (with props)
    ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCPE.bat
    ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCPE.sh
    ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCVD - Java 1.5 - using bin.bat
    ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCVD.bat
    ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCVD.sh

Added: ctakes/sandbox/ctakes-2.5-with-resources-merged/.classpath
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-2.5-with-resources-merged/.classpath?rev=1501907&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-2.5-with-resources-merged/.classpath (added)
+++ ctakes/sandbox/ctakes-2.5-with-resources-merged/.classpath Wed Jul 10 18:46:24 2013
@@ -0,0 +1,49 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry exported="true" kind="lib" path="cTAKESdesc"/>
+	<classpathentry kind="src" path="auto_generatesrc"/>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="lib" path="lib/uima-tools.jar"/>
+	<classpathentry kind="lib" path="lib/uima-examples.jar"/>
+	<classpathentry kind="lib" path="lib/uima-document-annotation.jar"/>
+	<classpathentry kind="lib" path="lib/uima-cpe.jar"/>
+	<classpathentry kind="lib" path="lib/uima-core.jar"/>
+	<classpathentry kind="lib" path="lib/uima-adapter-vinci.jar"/>
+	<classpathentry kind="lib" path="lib/uima-adapter-soap.jar"/>
+	<classpathentry kind="lib" path="lib/lvg2010dist.jar"/>
+	<classpathentry kind="lib" path="lib/jVinci.jar"/>
+	<classpathentry kind="lib" path="lib/hppc-0.3.1.jar"/>
+	<classpathentry kind="lib" path="lib/args4j-2.0.16.jar"/>
+	<classpathentry kind="lib" path="lib/junit.jar"/>
+	<classpathentry kind="lib" path="lib/Jama-1.0.2.jar"/>
+	<classpathentry kind="lib" path="lib/libsvm-2.91.jar"/>
+	<classpathentry kind="lib" path="lib/xercesImpl-2.6.2.jar"/>
+	<classpathentry kind="lib" path="lib/clearparser-0.33.jar"/>
+	<classpathentry kind="lib" path="lib/cleartk-util-0.8.1.jar"/>
+	<classpathentry kind="lib" path="lib/commons-io-2.0.1.jar"/>
+	<classpathentry kind="lib" path="lib/commons-lang-2.4.jar"/>
+	<classpathentry kind="lib" path="lib/commons-logging-1.1.1.jar"/>
+	<classpathentry kind="lib" path="lib/commons-cli-1.2.jar"/>
+	<classpathentry kind="lib" path="lib/commons-lang-2.6.jar"/>
+	<classpathentry kind="lib" path="lib/jackson-core-asl-1.5.0.jar"/>
+	<classpathentry kind="lib" path="lib/jackson-mapper-asl-1.5.0.jar"/>
+	<classpathentry kind="lib" path="lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar"/>
+	<classpathentry kind="lib" path="lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar"/>
+	<classpathentry kind="lib" path="lib/med-facts-i2b2-1.2-SNAPSHOT.jar"/>
+	<classpathentry kind="lib" path="lib/med-facts-zoner-1.1.jar"/>
+	<classpathentry kind="lib" path="lib/sbinary_2.9.0-0.4.0.jar"/>
+	<classpathentry kind="lib" path="lib/scala-library-2.9.0.jar"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7"/>
+	<classpathentry exported="true" kind="lib" path="resources"/>
+	<classpathentry kind="lib" path="lib/jdom.jar"/>
+	<classpathentry kind="lib" path="lib/log4j-1.2.15.jar"/>
+	<classpathentry kind="lib" path="lib/lucene-core-3.0.2.jar"/>
+	<classpathentry kind="lib" path="lib/OpenAI_FSM.jar"/>
+	<classpathentry kind="lib" path="lib/opennlp-maxent-3.0.2-incubating.jar"/>
+	<classpathentry kind="lib" path="lib/opennlp-tools-1.5.2-incubating.jar"/>
+	<classpathentry kind="lib" path="lib/SQLWrapper.jar"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
+	<classpathentry kind="lib" path="lib/FindStructAPI.jar"/>
+	<classpathentry kind="lib" path="lib/uimafit-1.4.0.jar"/>
+	<classpathentry kind="output" path="bin"/>
+</classpath>

Propchange: ctakes/sandbox/ctakes-2.5-with-resources-merged/.classpath
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: ctakes/sandbox/ctakes-2.5-with-resources-merged/.classpath-orig
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-2.5-with-resources-merged/.classpath-orig?rev=1501907&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-2.5-with-resources-merged/.classpath-orig (added)
+++ ctakes/sandbox/ctakes-2.5-with-resources-merged/.classpath-orig Wed Jul 10 18:46:24 2013
@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<classpath>
+	<classpathentry kind="src" path="auto_generatesrc"/>
+	<classpathentry kind="src" path="src"/>
+				<classpathentry exported="true" kind="lib" path="lib/uima-tools.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/uima-examples.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/uima-document-annotation.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/uima-cpe.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/uima-core.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/uima-adapter-vinci.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/uima-adapter-soap.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/lvg2010dist.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/jVinci.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/hppc-0.3.1.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/args4j-2.0.16.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/junit.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/Jama-1.0.2.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/libsvm-2.91.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/xercesImpl-2.6.2.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/uimafit-1.2.0.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/clearparser-0.33.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/cleartk-util-0.8.1.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/commons-io-2.0.1.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/commons-lang-2.4.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/commons-logging-1.1.1.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/commons-cli-1.2.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/commons-lang-2.6.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/jackson-core-asl-1.5.0.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/jackson-mapper-asl-1.5.0.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/med-facts-i2b2-1.2-SNAPSHOT.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/med-facts-zoner-1.1.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/sbinary_2.9.0-0.4.0.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/scala-library-2.9.0.jar"/>
+			
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="lib" path="resources"/>
+	<classpathentry kind="lib" path="lib/jdom.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/log4j-1.2.15.jar"/>
+	<classpathentry kind="lib" path="lib/lucene-core-3.0.2.jar"/>
+	<classpathentry kind="lib" path="lib/OpenAI_FSM.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/opennlp-maxent-3.0.2-incubating.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/opennlp-tools-1.5.2-incubating.jar"/>
+	<classpathentry kind="lib" path="lib/SQLWrapper.jar"/>
+	
+	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
+	
+	<classpathentry kind="lib" path="lib/FindStructAPI.jar"/>
+	
+	<classpathentry kind="output" path="bin"/>
+</classpath>

Added: ctakes/sandbox/ctakes-2.5-with-resources-merged/.project
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-2.5-with-resources-merged/.project?rev=1501907&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-2.5-with-resources-merged/.project (added)
+++ ctakes/sandbox/ctakes-2.5-with-resources-merged/.project Wed Jul 10 18:46:24 2013
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>ctakes-2.5-with-resources-merged</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.apache.uima.pear.UimaNature</nature>
+	</natures>
+</projectDescription>

Propchange: ctakes/sandbox/ctakes-2.5-with-resources-merged/.project
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: ctakes/sandbox/ctakes-2.5-with-resources-merged/.project-orig
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-2.5-with-resources-merged/.project-orig?rev=1501907&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-2.5-with-resources-merged/.project-orig (added)
+++ ctakes/sandbox/ctakes-2.5-with-resources-merged/.project-orig Wed Jul 10 18:46:24 2013
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<projectDescription>
+	<name>cTAKES</name>
+	<comment/>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.apache.uima.pear.UimaNature</nature>
+	</natures>
+</projectDescription>

Added: ctakes/sandbox/ctakes-2.5-with-resources-merged/LICENSE
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-2.5-with-resources-merged/LICENSE?rev=1501907&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-2.5-with-resources-merged/LICENSE (added)
+++ ctakes/sandbox/ctakes-2.5-with-resources-merged/LICENSE Wed Jul 10 18:46:24 2013
@@ -0,0 +1,202 @@
+
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+                        http://www.apache.org/licenses/
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+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
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+      "Contribution" shall mean any work of authorship, including
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+      communication on electronic mailing lists, source code control systems,
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+   4. Redistribution. You may reproduce and distribute copies of the
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+      meet the following conditions:
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+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
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+      (c) You must retain, in the Source form of any Derivative Works
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+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
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+      Contributor provides its Contributions) on an "AS IS" BASIS,
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+      unless required by applicable law (such as deliberate and grossly
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Added: ctakes/sandbox/ctakes-2.5-with-resources-merged/MODIFICATIONS.JAMES.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-2.5-with-resources-merged/MODIFICATIONS.JAMES.txt?rev=1501907&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-2.5-with-resources-merged/MODIFICATIONS.JAMES.txt (added)
+++ ctakes/sandbox/ctakes-2.5-with-resources-merged/MODIFICATIONS.JAMES.txt Wed Jul 10 18:46:24
2013
@@ -0,0 +1,10 @@
+
+Copied over full LVG from my working 1.0.5 copy
+
+Updated UMLS password and user ID (then removed them before posting into SVN)
+
+Created additional runcTAKES bat file to use Java 1.5 on my system
+
+Ran a CPE and created some output under cTAKESdesc/cpddesc
+
+Created  cTAKESdesc/typesystem/common_type_system-plus-specifics.xml

Propchange: ctakes/sandbox/ctakes-2.5-with-resources-merged/MODIFICATIONS.JAMES.txt
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: ctakes/sandbox/ctakes-2.5-with-resources-merged/NOTICE
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-2.5-with-resources-merged/NOTICE?rev=1501907&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-2.5-with-resources-merged/NOTICE (added)
+++ ctakes/sandbox/ctakes-2.5-with-resources-merged/NOTICE Wed Jul 10 18:46:24 2013
@@ -0,0 +1,19 @@
+
+Some material in the UMLS Metathesaurus is from copyrighted sources of
+the respective copyright holders. Users of the UMLS Metathesaurus are 
+solely responsible for compliance with any copyright, patent or 
+trademark restrictions and are referred to the copyright, patent or 
+trademark notices appearing in the original sources, all of which are 
+hereby incorporated by reference.
+
+This material includes SNOMED Clinical Terms® (SNOMED CT®) which is 
+used by permission of the International Health Terminology Standards 
+Development Organisation (IHTSDO). All rights reserved. SNOMED CT®, 
+was originally created by The College of American Pathologists. 
+"SNOMED" and "SNOMED CT" are registered trademarks of the IHTSDO.
+
+cTAKES includes the following vocabularies from the UMLS Metathesaurus:
+ - SNOMED CT
+ - NCI Thesaurus http://ncit.nci.nih.gov/
+ - Medical Subject Headings http://www.nlm.nih.gov/mesh/
+ - RxNorm http://www.nlm.nih.gov/research/umls/rxnorm/

Added: ctakes/sandbox/ctakes-2.5-with-resources-merged/README
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-2.5-with-resources-merged/README?rev=1501907&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-2.5-with-resources-merged/README (added)
+++ ctakes/sandbox/ctakes-2.5-with-resources-merged/README Wed Jul 10 18:46:24 2013
@@ -0,0 +1,67 @@
+Contents
+- Introduction
+- Running the clinical documents pipeline 
+	- AggregateCdaProcessor.xml  for CDA documents conforming to the provided DTD.
+	- AggregatePlaintextProcessor.xml  for plaintext documents.
+
+
+ 
+############
+Introduction
+############
+
+This project is the top-level, main project for processing a clinical document
+through the entire pipeline, including sentence detection, part of speech tagging, 
+chunking, named entity recognition, context detection, and negation detection.
+
+
+############################################################################
+Running the clinical documents pipeline
+############################################################################
+
+The pipeline can process two types of documents
+ - plaintext files
+ - Clinical Document Architecture (CDA) XML files that conform to the DTD provided 
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%
+AggregateCdaProcessor.xml  for CDA documents conforming to the provided DTD.
+
+The file cTAKESdesc/analysis_engine/AggregateCdaProcessor.xml is the aggregate
+analysis engine to use to run the entire pipeline, including the 
+CdaCasInitialzer analysis engine, which reads CDA documents that conform
+to the DTD provided, and create Segment annotations based on the sections
+within the CDA document.
+
+Open this file using the Component Descriptor Editor as described in the tutorial.
+Click on the tab labeled "Aggregate" to observe that the Component Engine Flow (pipeline)

+defined by this descriptor includes CdaCasInitialzer as the first component.
+Observe that part of speech tagging (POSTagger) comes before chunking (Chunker), etc.
+ 
+Click on the tab labeled "Parameter Settings" to view the parameters set in this
+descriptor.  The ChunkCreatorClass is set to edu.mayo.bmi.uima.chunker.PhraseTypeChunkCreator
+so that each phrase type gets its own type of annotation, rather than having all
+chunks be of type Chunk.  
+
+The parameters are:
+- ChunkerCreatorClass - the full class name of an implementation of the 
+                        interface edu.mayo.bmi.uima.chunker.ChunkerCreator
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+AggregatePlaintextProcessor.xml  for plaintext documents.
+
+The file cTAKESdesc/analysis_engine/AggregatePlaintextProcessor.xml is the aggregate
+analysis engine to use to run the entire pipeline, including the 
+SimpleSegmentAnnotator analysis engine, which creates a Segment annotation that
+wraps the entire plaintext document.  Other annotators in the pipeline require
+at least 1 Segment annotation.
+
+Click on the tab labeled "Parameter Settings" to view the parameters set in this
+descriptor.  The ChunkCreatorClass is set to edu.mayo.bmi.uima.chunker.PhraseTypeChunkCreator
+so that each phrase type gets its own type of annotation, rather than having all
+chunks be of type Chunk.  
+
+The parameters are:
+- SegmentID - the identifier or name to assign to the Segment annotation 
+- ChunkerCreatorClass - the full class name of an implementation of the 
+                        interface edu.mayo.bmi.uima.chunker.ChunkerCreator

Added: ctakes/sandbox/ctakes-2.5-with-resources-merged/build.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-2.5-with-resources-merged/build.xml?rev=1501907&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-2.5-with-resources-merged/build.xml (added)
+++ ctakes/sandbox/ctakes-2.5-with-resources-merged/build.xml Wed Jul 10 18:46:24 2013
@@ -0,0 +1,102 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<project default="cTAKES-2.5" name="Create Runnable Jar for cTAKES">
+      <target name="cTAKES-2.5">
+        <mkdir dir="bin"/>
+   				<path id="_ctakes.cp">
+            <pathelement location="lib/uima-tools.jar"/>
+            <pathelement location="lib/uima-examples.jar"/>
+            <pathelement location="lib/uima-document-annotation.jar"/>
+            <pathelement location="lib/uima-cpe.jar"/>
+            <pathelement location="lib/uima-core.jar"/>
+            <pathelement location="lib/uima-adapter-vinci.jar"/>
+            <pathelement location="lib/uima-adapter-soap.jar"/>
+            <pathelement location="lib/opennlp-tools-1.5.2-incubating.jar"/>
+            <pathelement location="lib/opennlp-maxent-3.0.2-incubating.jar"/>
+            <pathelement location="lib/OpenAI_FSM.jar"/>
+            <pathelement location="lib/lvg2010dist.jar"/>
+            <pathelement location="lib/lucene-core-3.0.2.jar"/>
+            <pathelement location="lib/Jama-1.0.2.jar"/>
+            <pathelement location="lib/SQLWrapper.jar"/>
+            <pathelement location="lib/log4j-1.2.15.jar"/>
+            <pathelement location="lib/jVinci.jar"/>
+            <pathelement location="lib/jdom.jar"/>
+            <pathelement location="lib/hppc-0.3.1.jar"/>
+            <pathelement location="lib/args4j-2.0.16.jar"/>
+            <pathelement location="lib/junit.jar"/>
+            <pathelement location="lib/libsvm-2.91.jar"/>
+            <!-- <pathelement location="lib/liblinear-1.51.jar"/> -->
+            <pathelement location="lib/xercesImpl-2.6.2.jar"/>
+            <pathelement location="lib/FindStructAPI.jar"/>
+            <pathelement location="lib/uimafit-1.2.0.jar" />
+            <pathelement location="lib/clearparser-0.33.jar"/>
+            <pathelement location="lib/cleartk-util-0.8.1.jar"/>
+            <pathelement location="lib/commons-io-2.0.1.jar"/>
+            <pathelement location="lib/commons-lang-2.4.jar"/>
+            <pathelement location="lib/commons-logging-1.1.1.jar"/>
+            <pathelement location="lib/commons-cli-1.2.jar"/>
+            <pathelement location="lib/commons-lang-2.6.jar"/>
+            <pathelement location="lib/jackson-core-asl-1.5.0.jar"/>
+            <pathelement location="lib/jackson-mapper-asl-1.5.0.jar"/>
+            <pathelement location="lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar"/>
+            <pathelement location="lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar"/>
+            <pathelement location="lib/med-facts-i2b2-1.2-SNAPSHOT.jar"/>
+            <pathelement location="lib/med-facts-zoner-1.1.jar"/>
+            <pathelement location="lib/sbinary_2.9.0-0.4.0.jar"/>
+            <pathelement location="lib/scala-library-2.9.0.jar"/>
+	    			</path>
+
+        <javac destdir="bin" debug="true">
+            <src path="auto_generatesrc" />
+            <src path="src" />
+            <classpath refid="_ctakes.cp" />
+        </javac>
+
+        <jar destfile="cTAKES.jar">
+            <manifest>
+                <attribute name="Main-Class" value="edu.mayo.bmi.ctakes.main.cTAKESCPEGUI"/>
+                <attribute name="Class-Path" value="."/>
+            </manifest>
+            <fileset dir="bin"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/uima-tools.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/uima-examples.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/uima-document-annotation.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/uima-cpe.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/uima-core.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/uima-adapter-vinci.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/uima-adapter-soap.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/opennlp-tools-1.5.2-incubating.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/opennlp-maxent-3.0.2-incubating.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/OpenAI_FSM.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/lvg2010dist.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/lucene-core-3.0.2.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/Jama-1.0.2.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/SQLWrapper.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/log4j-1.2.15.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/jVinci.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/jdom.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/hppc-0.3.1.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/args4j-2.0.16.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/junit.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/libsvm-2.91.jar"/>
+            <!-- <zipfileset excludes="META-INF/*.SF" src="lib/liblinear-1.51.jar"/>
-->
+            <zipfileset excludes="META-INF/*.SF" src="lib/xercesImpl-2.6.2.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/FindStructAPI.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/uimafit-1.2.0.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/clearparser-0.33.jar"/>
+	           <zipfileset excludes="META-INF/*.SF" src="lib/cleartk-util-0.8.1.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/commons-io-2.0.1.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/commons-lang-2.4.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/commons-logging-1.1.1.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/commons-cli-1.2.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/commons-lang-2.6.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/jackson-core-asl-1.5.0.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/jackson-mapper-asl-1.5.0.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/med-facts-i2b2-1.2-SNAPSHOT.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/med-facts-zoner-1.1.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/sbinary_2.9.0-0.4.0.jar"/>
+            <zipfileset excludes="META-INF/*.SF" src="lib/scala-library-2.9.0.jar"/>
+        </jar>
+    </target>
+</project>

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Added: ctakes/sandbox/ctakes-2.5-with-resources-merged/cTAKES.jar
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Added: ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCPE.bat
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCPE.bat?rev=1501907&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCPE.bat (added)
+++ ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCPE.bat Wed Jul 10 18:46:24 2013
@@ -0,0 +1,2 @@
+java  -Xms1024M -Xmx2048M -cp resources;cTAKESdesc;cTAKES.jar edu.mayo.bmi.ctakes.main.cTAKESCPEGUI
+

Added: ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCPE.sh
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCPE.sh?rev=1501907&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCPE.sh (added)
+++ ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCPE.sh Wed Jul 10 18:46:24 2013
@@ -0,0 +1,2 @@
+java  -Xms1024M -Xmx2048M  -cp resources:cTAKESdesc:cTAKES.jar edu.mayo.bmi.ctakes.main.cTAKESCPEGUI
+

Added: ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCVD - Java 1.5 - using bin.bat
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCVD%20-%20Java%201.5%20-%20using%20bin.bat?rev=1501907&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCVD - Java 1.5 - using bin.bat
(added)
+++ ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCVD - Java 1.5 - using bin.bat
Wed Jul 10 18:46:24 2013
@@ -0,0 +1,10 @@
+
+pause
+start cmdjava1.5
+pause
+echo %PATH%
+pause
+java -Xms1024M -Xmx2048M  -cp resources;bin;cTAKESdesc;cTAKES.jar edu.mayo.bmi.ctakes.main.cTAKESCVDGUI
+
+
+pause

Added: ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCVD.bat
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCVD.bat?rev=1501907&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCVD.bat (added)
+++ ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCVD.bat Wed Jul 10 18:46:24 2013
@@ -0,0 +1,2 @@
+java -Xms1024M -Xmx2048M  -cp resources;cTAKESdesc;cTAKES.jar edu.mayo.bmi.ctakes.main.cTAKESCVDGUI
+

Added: ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCVD.sh
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCVD.sh?rev=1501907&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCVD.sh (added)
+++ ctakes/sandbox/ctakes-2.5-with-resources-merged/runctakesCVD.sh Wed Jul 10 18:46:24 2013
@@ -0,0 +1,2 @@
+java  -Xms1024M -Xmx2048M  -cp resources:cTAKESdesc:cTAKES.jar edu.mayo.bmi.ctakes.main.cTAKESCVDGUI
+



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