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From chen...@apache.org
Subject svn commit: r1399397 - in /incubator/ctakes/trunk: ./ ctakes-clinical-pipeline/ ctakes-distribution/ ctakes-distribution/.settings/ ctakes-distribution/src/ ctakes-distribution/src/main/ ctakes-distribution/src/main/assembly/ ctakes-distribution/src/ma...
Date Wed, 17 Oct 2012 19:15:01 GMT
Author: chenpei
Date: Wed Oct 17 19:15:00 2012
New Revision: 1399397

URL: http://svn.apache.org/viewvc?rev=1399397&view=rev
Log:
-Reverted to use Lucene 3.0.2 instead of 3.5.0
-Moved the exec:cvd/cpe profiles to the parent pom
-Added new ctakes-distribution module 

Added:
    incubator/ctakes/trunk/ctakes-distribution/
    incubator/ctakes/trunk/ctakes-distribution/.project
    incubator/ctakes/trunk/ctakes-distribution/.settings/
    incubator/ctakes/trunk/ctakes-distribution/.settings/org.eclipse.core.resources.prefs
    incubator/ctakes/trunk/ctakes-distribution/.settings/org.eclipse.m2e.core.prefs
    incubator/ctakes/trunk/ctakes-distribution/RELEASE_NOTES.html
    incubator/ctakes/trunk/ctakes-distribution/pom.xml
    incubator/ctakes/trunk/ctakes-distribution/src/
    incubator/ctakes/trunk/ctakes-distribution/src/main/
    incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/
    incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml
    incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/src.xml
    incubator/ctakes/trunk/ctakes-distribution/src/main/bin/
    incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.bat
    incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.sh
    incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.bat
    incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.sh
Modified:
    incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml
    incubator/ctakes/trunk/pom.xml

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml?rev=1399397&r1=1399396&r2=1399397&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml Wed Oct 17 19:15:00 2012
@@ -7,7 +7,6 @@
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
 		<version>3.0.0-SNAPSHOT</version>
-		<relativePath>..</relativePath>
 	</parent>
 
 
@@ -69,143 +68,5 @@
 			<artifactId>ctakes-dependency-parser</artifactId>
 		</dependency>
 	</dependencies>
-	<profiles>
-		<profile>
-			<id>runCPE</id>
-			<activation>
-				<property>
-					<name>runCPE</name>
-				</property>
-			</activation>
-			<build>
-				<plugins>
-					<plugin>
-						<groupId>org.codehaus.mojo</groupId>
-						<artifactId>exec-maven-plugin</artifactId>
-						<version>1.2.1</version>
-						<configuration>
-							<includeProjectDependencies>true</includeProjectDependencies>
-							<includePluginDependencies>true</includePluginDependencies>
-							<executableDependency>
-								<groupId>org.apache.ctakes</groupId>
-								<artifactId>ctakes-clinical-pipeline</artifactId>
-							</executableDependency>
-							<executions>
-								<execution>
-									<goals>
-										<goal>exec</goal>
-									</goals>
-									<configuration></configuration>
-								</execution>
-							</executions>
-							<executable>java</executable>
-							<longClasspath>false</longClasspath>
-							<arguments>
-								<argument>-Djava.util.logging.config.file=${UIMA_HOME}/Logger.properties</argument>
-								<argument>-Xms512M</argument>
-								<argument>-Xmx1024M</argument>
-								<argument>-classpath</argument>
-								<classpath />
-								<argument>org.apache.uima.tools.cpm.CpmFrame</argument>
-							</arguments>
-						</configuration>
-						<dependencies>
-							<!-- System lib dependencies is causing a world of pain. Remove these 
-								when they're uploaded to Maven Central -->
-							<dependency>
-								<groupId>net.sourceforge.openai</groupId>
-								<artifactId>fsm</artifactId>
-								<version>0.1a</version>
-								<scope>system</scope>
-								<systemPath>${project.basedir}/../ctakes-core/lib/OpenAI_FSM.jar</systemPath>
-							</dependency>
-							<dependency>
-								<groupId>findstruct</groupId>
-								<artifactId>findstruct</artifactId>
-								<version>0.0.1</version>
-								<scope>system</scope>
-								<systemPath>${project.basedir}/../ctakes-core/lib/FindStructAPI.jar</systemPath>
-							</dependency>
-							<dependency>
-								<groupId>sqlWrapper</groupId>
-								<artifactId>sqlWrapper</artifactId>
-								<version>0.0.1</version>
-								<scope>system</scope>
-								<systemPath>${project.basedir}/../ctakes-core/lib/SQLWrapper.jar</systemPath>
-							</dependency>
-						</dependencies>
-					</plugin>
-				</plugins>
-			</build>
-		</profile>
-		<profile>
-			<id>runCVD</id>
-			<activation>
-				<property>
-					<name>runCVD</name>
-				</property>
-			</activation>
-			<build>
-				<plugins>
-					<plugin>
-						<groupId>org.codehaus.mojo</groupId>
-						<artifactId>exec-maven-plugin</artifactId>
-						<version>1.2.1</version>
-						<configuration>
-							<includeProjectDependencies>true</includeProjectDependencies>
-							<includePluginDependencies>true</includePluginDependencies>
-							<executableDependency>
-								<groupId>org.apache.ctakes</groupId>
-								<artifactId>ctakes-clinical-pipeline</artifactId>
-							</executableDependency>
-							<executions>
-								<execution>
-									<goals>
-										<goal>exec</goal>
-									</goals>
-									<configuration></configuration>
-								</execution>
-							</executions>
-							<executable>java</executable>
-							<longClasspath>false</longClasspath>
-							<arguments>
-								<argument>-Djava.util.logging.config.file=${UIMA_HOME}/Logger.properties</argument>
-								<argument>-Xms512M</argument>
-								<argument>-Xmx1024M</argument>
-								<argument>-classpath</argument>
-								<classpath />
-								<argument>org.apache.uima.tools.cvd.CVD</argument>
-							</arguments>
-						</configuration>
-						<dependencies>
-							<!-- System lib dependencies is causing a world of pain. Remove these 
-								when they're uploaded to Maven Central -->
-							<dependency>
-								<groupId>net.sourceforge.openai</groupId>
-								<artifactId>fsm</artifactId>
-								<version>0.1a</version>
-								<scope>system</scope>
-								<systemPath>${project.basedir}/../ctakes-core/lib/OpenAI_FSM.jar</systemPath>
-							</dependency>
-							<dependency>
-								<groupId>findstruct</groupId>
-								<artifactId>findstruct</artifactId>
-								<version>0.0.1</version>
-								<scope>system</scope>
-								<systemPath>${project.basedir}/../ctakes-core/lib/FindStructAPI.jar</systemPath>
-							</dependency>
-							<dependency>
-								<groupId>sqlWrapper</groupId>
-								<artifactId>sqlWrapper</artifactId>
-								<version>0.0.1</version>
-								<scope>system</scope>
-								<systemPath>${project.basedir}/../ctakes-core/lib/SQLWrapper.jar</systemPath>
-							</dependency>
-						</dependencies>
-					</plugin>
-				</plugins>
-			</build>
-		</profile>
-	</profiles>
 
 </project>

Added: incubator/ctakes/trunk/ctakes-distribution/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-distribution/.project?rev=1399397&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/.project (added)
+++ incubator/ctakes/trunk/ctakes-distribution/.project Wed Oct 17 19:15:00 2012
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>ctakes-distribution</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+</projectDescription>

Added: incubator/ctakes/trunk/ctakes-distribution/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-distribution/.settings/org.eclipse.core.resources.prefs?rev=1399397&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/.settings/org.eclipse.core.resources.prefs (added)
+++ incubator/ctakes/trunk/ctakes-distribution/.settings/org.eclipse.core.resources.prefs Wed Oct 17 19:15:00 2012
@@ -0,0 +1,3 @@
+#Wed Oct 17 12:26:27 EDT 2012
+eclipse.preferences.version=1
+encoding/<project>=UTF-8

Added: incubator/ctakes/trunk/ctakes-distribution/.settings/org.eclipse.m2e.core.prefs
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-distribution/.settings/org.eclipse.m2e.core.prefs?rev=1399397&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/.settings/org.eclipse.m2e.core.prefs (added)
+++ incubator/ctakes/trunk/ctakes-distribution/.settings/org.eclipse.m2e.core.prefs Wed Oct 17 19:15:00 2012
@@ -0,0 +1,5 @@
+#Wed Oct 17 12:26:20 EDT 2012
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

Added: incubator/ctakes/trunk/ctakes-distribution/RELEASE_NOTES.html
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-distribution/RELEASE_NOTES.html?rev=1399397&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/RELEASE_NOTES.html (added)
+++ incubator/ctakes/trunk/ctakes-distribution/RELEASE_NOTES.html Wed Oct 17 19:15:00 2012
@@ -0,0 +1,20 @@
+<!--
+    ***************************************************************
+    * Licensed to the Apache Software Foundation (ASF) under one
+    * or more contributor license agreements.  See the NOTICE file
+    * distributed with this work for additional information
+    * regarding copyright ownership.  The ASF licenses this file
+    * to you under the Apache License, Version 2.0 (the
+    * "License"); you may not use this file except in compliance
+    * with the License.  You may obtain a copy of the License at
+    *
+    *   http://www.apache.org/licenses/LICENSE-2.0
+    * 
+    * Unless required by applicable law or agreed to in writing,
+    * software distributed under the License is distributed on an
+    * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    * KIND, either express or implied.  See the License for the
+    * specific language governing permissions and limitations
+    * under the License.
+    ***************************************************************
+--> 

Added: incubator/ctakes/trunk/ctakes-distribution/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-distribution/pom.xml?rev=1399397&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/pom.xml (added)
+++ incubator/ctakes/trunk/ctakes-distribution/pom.xml Wed Oct 17 19:15:00 2012
@@ -0,0 +1,157 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<artifactId>ctakes-distribution</artifactId>
+	<name>Apache cTAKES Distribution</name>
+	<parent>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes</artifactId>
+		<version>3.0.0-SNAPSHOT</version>
+	</parent>
+	<packaging>pom</packaging>
+
+	<!-- Versions will automatically be updated by the release plugin -->
+	<dependencies>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-type-system</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-utils</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-context-tokenizer</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-dictionary-lookup</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-preprocessor</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-lvg</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-chunker</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-ne-contexts</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-pos-tagger</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-assertion</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-dependency-parser</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-clinical-pipeline</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-constituency-parser</artifactId>
+		</dependency>		
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-coreference</artifactId>
+		</dependency>			
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-drug-ner</artifactId>
+		</dependency>	
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-ne-contexts</artifactId>
+		</dependency>				
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-pad-term-spotter</artifactId>
+		</dependency>		
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-relation-extractor</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-side-effect</artifactId>
+		</dependency>		
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-smoking-status</artifactId>
+		</dependency>						
+	</dependencies>
+
+	<build>
+		<plugins>
+			<plugin>
+				<artifactId>maven-assembly-plugin</artifactId>
+				<executions>
+					<execution>
+						<id>bundle-project-sources</id>
+						<phase>package</phase>
+						<goals>
+							<goal>single</goal>
+						</goals>
+						<configuration>
+							<descriptors>
+								<descriptor>src/main/assembly/bin.xml</descriptor>
+								<descriptor>src/main/assembly/src.xml</descriptor>
+							</descriptors>
+							<!-- Tar package is only compatible with gnu tar, many file have more 
+								than 100 chars. Right now only javadoc files are too long. -->
+							<tarLongFileMode>gnu</tarLongFileMode>
+
+							<finalName>apache-ctakes-${project.version}-incubating</finalName>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<artifactId>maven-antrun-plugin</artifactId>
+				<version>1.6</version>
+				<executions>
+					<execution>
+						<id>generate checksums for binary artifacts</id>
+						<goals>
+							<goal>run</goal>
+						</goals>
+						<phase>verify</phase>
+						<configuration>
+							<target>
+								<checksum algorithm="sha1" format="MD5SUM">
+									<fileset dir="${project.build.directory}">
+										<include name="*.zip" />
+										<include name="*.gz" />
+									</fileset>
+								</checksum>
+								<checksum algorithm="md5" format="MD5SUM">
+									<fileset dir="${project.build.directory}">
+										<include name="*.zip" />
+										<include name="*.gz" />
+									</fileset>
+								</checksum>
+							</target>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
+		</plugins>
+	</build>
+</project>
\ No newline at end of file

Added: incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml?rev=1399397&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml (added)
+++ incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml Wed Oct 17 19:15:00 2012
@@ -0,0 +1,221 @@
+<assembly>
+	<id>bin</id>
+	<formats>
+		<format>tar.gz</format>
+		<format>zip</format>
+	</formats>
+
+	<includeBaseDirectory>true</includeBaseDirectory>
+	<baseDirectory>/apache-ctakes-${project.version}</baseDirectory>
+
+	<dependencySets>
+		<dependencySet>
+			<includes>
+				<include>org.apache.ctakes:ctakes-assertion</include>
+				<include>org.apache.ctakes:ctakes-chunker</include>
+				<include>org.apache.ctakes:ctakes-clinical-pipeline</include>
+				<include>org.apache.ctakes:ctakes-constituency-parser</include>
+				<include>org.apache.ctakes:ctakes-core</include>
+				<include>org.apache.ctakes:ctakes-coreference</include>
+				<include>org.apache.ctakes:ctakes-dependency-parser</include>
+				<include>org.apache.ctakes:ctakes-dictionary-lookup</include>
+				<include>org.apache.ctakes:ctakes-drug-ner</include>
+				<include>org.apache.ctakes:ctakes-lvg</include>
+				<include>org.apache.ctakes:ctakes-ne-contexts</include>
+				<include>org.apache.ctakes:ctakes-pad-term-spotter</include>
+				<include>org.apache.ctakes:ctakes-pos-tagger</include>
+				<include>org.apache.ctakes:ctakes-preprocessor</include>
+				<include>org.apache.ctakes:ctakes-relation-extractor</include>
+				<include>org.apache.ctakes:ctakes-side-effect</include>
+				<include>org.apache.ctakes:ctakes-smoking-status</include>
+				<!-- <include>org.apache.ctakes:ctakes-temporal</include> -->
+				<include>org.apache.ctakes:ctakes-type-system</include>
+				<include>org.apache.ctakes:ctakes-utils</include>
+			</includes>
+			<unpack>false</unpack>
+			<useProjectArtifact>false</useProjectArtifact>
+			<useTransitiveFiltering>true</useTransitiveFiltering>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>lib</outputDirectory>
+		</dependencySet>
+	</dependencySets>
+
+	<fileSets>
+
+		<fileSet>
+			<directory>../</directory>
+			<outputDirectory></outputDirectory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<includes>
+				<include>README</include>
+				<include>LICENSE</include>
+				<include>NOTICE</include>
+			</includes>
+		</fileSet>
+		<fileSet>
+			<directory>.</directory>
+			<outputDirectory></outputDirectory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<includes>
+				<include>RELEASE_NOTES.html</include>
+			</includes>
+		</fileSet>
+		<fileSet>
+			<directory>target</directory>
+			<outputDirectory></outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<includes>
+				<include>issuesFixed/**</include>
+			</includes>
+		</fileSet>
+
+		<fileSet>
+			<directory>src/main/bin</directory>
+			<fileMode>755</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>bin</outputDirectory>
+		</fileSet>
+
+		<!-- Copy all of the XML Descriptors. Temp Preserving this structure so 
+			that the relative paths still work. -->
+		<fileSet>
+			<directory>../ctakes-assertion/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-assertion/desc</outputDirectory>
+		</fileSet>
+		<fileSet>
+			<directory>../ctakes-chunker/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-chunker/desc</outputDirectory>
+		</fileSet>				
+		<fileSet>
+			<directory>../ctakes-clinical-pipeline/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-clinical-pipeline/desc</outputDirectory>
+		</fileSet>
+		<fileSet>
+			<directory>../ctakes-constituency-paraser/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-constituency-paraser/desc</outputDirectory>
+		</fileSet>	
+		<fileSet>
+			<directory>../ctakes-context-tokenizer/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-context-tokenizer/desc</outputDirectory>
+		</fileSet>	
+		<fileSet>
+			<directory>../ctakes-core/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-core/desc</outputDirectory>
+		</fileSet>							
+		<fileSet>
+			<directory>../ctakes-coreference/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-coreference/desc</outputDirectory>
+		</fileSet>						
+		<fileSet>
+			<directory>../ctakes-dependency-parser/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-dependency-parser/desc</outputDirectory>
+		</fileSet>	
+		<fileSet>
+			<directory>../ctakes-dictionary-lookup/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-dictionary-lookup/desc</outputDirectory>
+		</fileSet>	
+		<fileSet>
+			<directory>../ctakes-drug-ner/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-drug-ner/desc</outputDirectory>
+		</fileSet>		
+		<fileSet>
+			<directory>../ctakes-lvg/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-lvg/desc</outputDirectory>
+		</fileSet>
+		<fileSet>
+			<directory>../ctakes-ne-contexts/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-ne-contexts/desc</outputDirectory>
+		</fileSet>			
+		<fileSet>
+			<directory>../ctakes-pad-term-spotter/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-pad-term-spotter/desc</outputDirectory>
+		</fileSet>			
+		<fileSet>
+			<directory>../ctakes-pos-tagger/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-pos-tagger/desc</outputDirectory>
+		</fileSet>	
+		<fileSet>
+			<directory>../ctakes-preprocessor/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-preprocessor/desc</outputDirectory>
+		</fileSet>			
+		<fileSet>
+			<directory>../ctakes-relation-extractor/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-relation-extractor/desc</outputDirectory>
+		</fileSet>		
+		<fileSet>
+			<directory>../ctakes-side-effect/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-side-effect/desc</outputDirectory>
+		</fileSet>					
+		<fileSet>
+			<directory>../ctakes-smoking-status/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-smoking-status/desc</outputDirectory>
+		</fileSet>
+		<fileSet>
+			<directory>../ctakes-type-system/desc</directory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<outputDirectory>desc/ctakes-type-system/desc</outputDirectory>
+		</fileSet>													
+	</fileSets>
+</assembly>
\ No newline at end of file

Added: incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/src.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/src.xml?rev=1399397&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/src.xml (added)
+++ incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/src.xml Wed Oct 17 19:15:00 2012
@@ -0,0 +1,22 @@
+<assembly>
+  <id>src</id>
+  <formats>
+    <format>tar.gz</format>
+    <format>zip</format>
+  </formats>
+  
+  <baseDirectory>/apache-ctakes-${project.version}-incubating-src</baseDirectory>
+  
+  <fileSets>
+    <fileSet>
+      <directory>../</directory>
+      <outputDirectory></outputDirectory>
+      <excludes>
+        <exclude>**/target/**</exclude>
+        <exclude>**/.*/**</exclude>
+        <exclude>**/pom.xml.releaseBackup</exclude>
+        <exclude>**/release.properties</exclude>
+      </excludes>
+    </fileSet>
+  </fileSets>
+</assembly>
\ No newline at end of file

Added: incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.bat
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.bat?rev=1399397&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.bat (added)
+++ incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.bat Wed Oct 17 19:15:00 2012
@@ -0,0 +1,21 @@
+@REM
+@REM Licensed to the Apache Software Foundation (ASF) under one
+@REM or more contributor license agreements.  See the NOTICE file
+@REM distributed with this work for additional information
+@REM regarding copyright ownership.  The ASF licenses this file
+@REM to you under the Apache License, Version 2.0 (the
+@REM "License"); you may not use this file except in compliance
+@REM with the License.  You may obtain a copy of the License at
+@REM
+@REM   http://www.apache.org/licenses/LICENSE-2.0
+@REM
+@REM Unless required by applicable law or agreed to in writing,
+@REM software distributed under the License is distributed on an
+@REM "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+@REM KIND, either express or implied.  See the License for the
+@REM specific language governing permissions and limitations
+@REM under the License.
+@REM
+
+@REM Requires JAVA JDK 1.6+
+java -cp lib/;desc/ -Djava.util.logging.config.file=${UIMA_HOME}/Logger.properties -Xms512M -Xmx1024M org.apache.uima.tools.cpm.CpmFrame

Added: incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.sh
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.sh?rev=1399397&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.sh (added)
+++ incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.sh Wed Oct 17 19:15:00 2012
@@ -0,0 +1,21 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+#
+# Requires JAVA JDK 1.6+
+java -cp lib/:desc/ -Djava.util.logging.config.file=${UIMA_HOME}/Logger.properties -Xms512M -Xmx1024M org.apache.uima.tools.cpm.CpmFrame

Added: incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.bat
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.bat?rev=1399397&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.bat (added)
+++ incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.bat Wed Oct 17 19:15:00 2012
@@ -0,0 +1,21 @@
+@REM
+@REM Licensed to the Apache Software Foundation (ASF) under one
+@REM or more contributor license agreements.  See the NOTICE file
+@REM distributed with this work for additional information
+@REM regarding copyright ownership.  The ASF licenses this file
+@REM to you under the Apache License, Version 2.0 (the
+@REM "License"); you may not use this file except in compliance
+@REM with the License.  You may obtain a copy of the License at
+@REM
+@REM   http://www.apache.org/licenses/LICENSE-2.0
+@REM
+@REM Unless required by applicable law or agreed to in writing,
+@REM software distributed under the License is distributed on an
+@REM "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+@REM KIND, either express or implied.  See the License for the
+@REM specific language governing permissions and limitations
+@REM under the License.
+@REM
+
+@REM Requires JAVA JDK 1.6+
+java -cp lib/;desc/ -Djava.util.logging.config.file=${UIMA_HOME}/Logger.properties -Xms512M -Xmx1024M org.apache.uima.tools.cvd.CVD

Added: incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.sh
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.sh?rev=1399397&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.sh (added)
+++ incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.sh Wed Oct 17 19:15:00 2012
@@ -0,0 +1,21 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+#
+# Requires JAVA JDK 1.6+
+java -cp lib/:desc/ -Djava.util.logging.config.file=${UIMA_HOME}/Logger.properties -Xms512M -Xmx1024M org.apache.uima.tools.cvd.CVD

Modified: incubator/ctakes/trunk/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/pom.xml?rev=1399397&r1=1399396&r2=1399397&view=diff
==============================================================================
--- incubator/ctakes/trunk/pom.xml (original)
+++ incubator/ctakes/trunk/pom.xml Wed Oct 17 19:15:00 2012
@@ -9,9 +9,9 @@
 	<scm>
 		<!-- In child modules, Maven will append ${artifactId} to the following 
 			URLs -->
-		<connection>scm:svn:https://svn.apache.org/repos/asf/incubator/ctakes/</connection>
-		<developerConnection>scm:svn:https://svn.apache.org/repos/asf/incubator/ctakes/</developerConnection>
-		<url>https://svn.apache.org/repos/asf/incubator/ctakes/</url>
+		<connection>scm:svn:https://svn.apache.org/repos/asf/incubator/ctakes/trunk</connection>
+		<developerConnection>scm:svn:https://svn.apache.org/repos/asf/incubator/ctakes/trunk</developerConnection>
+		<url>https://svn.apache.org/repos/asf/incubator/ctakes/trunk</url>
 	</scm>
 	<properties>
 		<ctakes.version>3.0.0-SNAPSHOT</ctakes.version>
@@ -40,7 +40,8 @@
 		<module>ctakes-clinical-pipeline</module>
 		<module>ctakes-pad-term-spotter</module>
 		<module>ctakes-assertion</module>
-        <module>ctakes-temporal</module>
+		<module>ctakes-temporal</module>
+		<module>ctakes-distribution</module>
 	</modules>
 	<dependencyManagement>
 		<dependencies>
@@ -95,6 +96,20 @@
 			<dependency>
 				<groupId>org.apache.ctakes</groupId>
 				<artifactId>
+					ctakes-clinical-pipeline
+				</artifactId>
+				<version>${ctakes.version}</version>
+			</dependency>
+			<dependency>
+				<groupId>org.apache.ctakes</groupId>
+				<artifactId>
+					ctakes-pad-term-spotter
+				</artifactId>
+				<version>${ctakes.version}</version>
+			</dependency>
+			<dependency>
+				<groupId>org.apache.ctakes</groupId>
+				<artifactId>
 					ctakes-ne-contexts
 				</artifactId>
 				<version>${ctakes.version}</version>
@@ -155,6 +170,13 @@
 				</artifactId>
 				<version>${ctakes.version}</version>
 			</dependency>
+			<dependency>
+				<groupId>org.apache.ctakes</groupId>
+				<artifactId>
+					ctakes-distribution
+				</artifactId>
+				<version>${ctakes.version}</version>
+			</dependency>
 			<!-- cTAKES third party dependency versions -->
 			<dependency>
 				<groupId>jdom</groupId>
@@ -182,7 +204,7 @@
 			<dependency>
 				<groupId>org.apache.lucene</groupId>
 				<artifactId>lucene-core</artifactId>
-				<version>3.5.0</version>
+				<version>3.0.2</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.opennlp</groupId>
@@ -233,11 +255,11 @@
 				<artifactId>args4j</artifactId>
 				<version>2.0.16</version>
 			</dependency>
-            <dependency>
-                <groupId>com.lexicalscope.jewelcli</groupId>
-                <artifactId>jewelcli</artifactId>
-                <version>0.8.3</version>
-            </dependency>
+			<dependency>
+				<groupId>com.lexicalscope.jewelcli</groupId>
+				<artifactId>jewelcli</artifactId>
+				<version>0.8.3</version>
+			</dependency>
 			<dependency>
 				<groupId>commons-io</groupId>
 				<artifactId>commons-io</artifactId>
@@ -413,6 +435,8 @@
 						</execution>
 					</executions>
 					<configuration>
+						<includeProjectDependencies>true</includeProjectDependencies>
+						<includePluginDependencies>true</includePluginDependencies>
 						<mainClass>org.uimafit.util.JCasGenPomFriendly</mainClass>
 						<arguments>
 							<argument>${jcasgen.typesystem}
@@ -477,4 +501,213 @@
 			</plugins>
 		</pluginManagement>
 	</build>
+
+	<profiles>
+		<profile>
+			<id>runCPE</id>
+			<activation>
+				<property>
+					<name>runCPE</name>
+				</property>
+			</activation>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.codehaus.mojo</groupId>
+						<artifactId>exec-maven-plugin</artifactId>
+						<version>1.2.1</version>
+						<configuration>
+							<includeProjectDependencies>true</includeProjectDependencies>
+							<includePluginDependencies>true</includePluginDependencies>
+							<executableDependency>
+								<groupId>org.apache.ctakes</groupId>
+								<artifactId>ctakes-clinical-pipeline</artifactId>
+							</executableDependency>
+							<executions>
+								<execution>
+									<goals>
+										<goal>exec</goal>
+									</goals>
+									<configuration></configuration>
+								</execution>
+							</executions>
+							<executable>java</executable>
+							<longClasspath>false</longClasspath>
+							<arguments>
+								<argument>-Djava.util.logging.config.file=${UIMA_HOME}/Logger.properties</argument>
+								<argument>-Xms512M</argument>
+								<argument>-Xmx1024M</argument>
+								<argument>-classpath</argument>
+								<classpath />
+								<argument>org.apache.uima.tools.cpm.CpmFrame</argument>
+							</arguments>
+						</configuration>
+						<dependencies>
+							<!-- System lib dependencies is causing a world of pain. Remove these 
+								when they're uploaded to Maven Central -->
+							<dependency>
+								<groupId>net.sourceforge.openai</groupId>
+								<artifactId>fsm</artifactId>
+								<version>0.1a</version>
+								<scope>system</scope>
+								<systemPath>${project.basedir}/../ctakes-core/lib/OpenAI_FSM.jar</systemPath>
+							</dependency>
+							<dependency>
+								<groupId>findstruct</groupId>
+								<artifactId>findstruct</artifactId>
+								<version>0.0.1</version>
+								<scope>system</scope>
+								<systemPath>${project.basedir}/../ctakes-core/lib/FindStructAPI.jar</systemPath>
+							</dependency>
+							<dependency>
+								<groupId>sqlWrapper</groupId>
+								<artifactId>sqlWrapper</artifactId>
+								<version>0.0.1</version>
+								<scope>system</scope>
+								<systemPath>${project.basedir}/../ctakes-core/lib/SQLWrapper.jar</systemPath>
+							</dependency>
+							<dependency>
+								<groupId>org.mitre.medfacts</groupId>
+								<artifactId>medfacts-i2b2</artifactId>
+								<version>1.2</version>
+								<scope>system</scope>
+								<systemPath>${project.basedir}/../ctakes-assertion/lib/med-facts-i2b2-1.2-SNAPSHOT.jar</systemPath>
+							</dependency>
+							<dependency>
+								<groupId>org.mitre.medfacts</groupId>
+								<artifactId>medfacts-zoner</artifactId>
+								<version>1.1</version>
+								<scope>system</scope>
+								<systemPath>${project.basedir}/../ctakes-assertion/lib/med-facts-zoner-1.1.jar</systemPath>
+							</dependency>
+							<dependency>
+								<groupId>org.mitre.jcarafe.core</groupId>
+								<artifactId>jcarafe.core</artifactId>
+								<version>2.9.1</version>
+								<scope>system</scope>
+								<systemPath>${project.basedir}/../ctakes-assertion/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar</systemPath>
+							</dependency>
+							<dependency>
+								<groupId>org.mitre.jcarafe.ext</groupId>
+								<artifactId>jcarafe.ext</artifactId>
+								<version>2.9.1</version>
+								<scope>system</scope>
+								<systemPath>${project.basedir}/../ctakes-assertion/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar</systemPath>
+							</dependency>
+							<dependency>
+								<groupId>lvg2010dist</groupId>
+								<artifactId>lvg2010dist</artifactId>
+								<version>0.0.1</version>
+								<scope>system</scope>
+								<systemPath>${project.basedir}/../ctakes-lvg/lib/lvg2010dist.jar</systemPath>
+							</dependency>
+						</dependencies>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+		<profile>
+			<id>runCVD</id>
+			<activation>
+				<property>
+					<name>runCVD</name>
+				</property>
+			</activation>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.codehaus.mojo</groupId>
+						<artifactId>exec-maven-plugin</artifactId>
+						<version>1.2.1</version>
+						<configuration>
+							<includeProjectDependencies>true</includeProjectDependencies>
+							<includePluginDependencies>true</includePluginDependencies>
+							<executableDependency>
+								<groupId>org.apache.ctakes</groupId>
+								<artifactId>ctakes-clinical-pipeline</artifactId>
+							</executableDependency>
+							<executions>
+								<execution>
+									<goals>
+										<goal>exec</goal>
+									</goals>
+									<configuration></configuration>
+								</execution>
+							</executions>
+							<executable>java</executable>
+							<longClasspath>false</longClasspath>
+							<arguments>
+								<argument>-Djava.util.logging.config.file=${UIMA_HOME}/Logger.properties</argument>
+								<argument>-Xms512M</argument>
+								<argument>-Xmx1024M</argument>
+								<argument>-classpath</argument>
+								<classpath />
+								<argument>org.apache.uima.tools.cvd.CVD</argument>
+							</arguments>
+						</configuration>
+						<dependencies>
+							<!-- System lib dependencies is causing a world of pain. Remove these 
+								when they're uploaded to Maven Central -->
+							<dependency>
+								<groupId>net.sourceforge.openai</groupId>
+								<artifactId>fsm</artifactId>
+								<version>0.1a</version>
+								<scope>system</scope>
+								<systemPath>${project.basedir}/../ctakes-core/lib/OpenAI_FSM.jar</systemPath>
+							</dependency>
+							<dependency>
+								<groupId>findstruct</groupId>
+								<artifactId>findstruct</artifactId>
+								<version>0.0.1</version>
+								<scope>system</scope>
+								<systemPath>${project.basedir}/../ctakes-core/lib/FindStructAPI.jar</systemPath>
+							</dependency>
+							<dependency>
+								<groupId>sqlWrapper</groupId>
+								<artifactId>sqlWrapper</artifactId>
+								<version>0.0.1</version>
+								<scope>system</scope>
+								<systemPath>${project.basedir}/../ctakes-core/lib/SQLWrapper.jar</systemPath>
+							</dependency>
+							<dependency>
+								<groupId>org.mitre.medfacts</groupId>
+								<artifactId>medfacts-i2b2</artifactId>
+								<version>1.2</version>
+								<scope>system</scope>
+								<systemPath>${project.basedir}/../ctakes-assertion/lib/med-facts-i2b2-1.2-SNAPSHOT.jar</systemPath>
+							</dependency>
+							<dependency>
+								<groupId>org.mitre.medfacts</groupId>
+								<artifactId>medfacts-zoner</artifactId>
+								<version>1.1</version>
+								<scope>system</scope>
+								<systemPath>${project.basedir}/../ctakes-assertion/lib/med-facts-zoner-1.1.jar</systemPath>
+							</dependency>
+							<dependency>
+								<groupId>org.mitre.jcarafe.core</groupId>
+								<artifactId>jcarafe.core</artifactId>
+								<version>2.9.1</version>
+								<scope>system</scope>
+								<systemPath>${project.basedir}/../ctakes-assertion/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar</systemPath>
+							</dependency>
+							<dependency>
+								<groupId>org.mitre.jcarafe.ext</groupId>
+								<artifactId>jcarafe.ext</artifactId>
+								<version>2.9.1</version>
+								<scope>system</scope>
+								<systemPath>${project.basedir}/../ctakes-assertion/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar</systemPath>
+							</dependency>
+							<dependency>
+								<groupId>lvg2010dist</groupId>
+								<artifactId>lvg2010dist</artifactId>
+								<version>0.0.1</version>
+								<scope>system</scope>
+								<systemPath>${project.basedir}/../ctakes-lvg/lib/lvg2010dist.jar</systemPath>
+							</dependency>
+						</dependencies>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+	</profiles>
 </project>



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