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From chen...@apache.org
Subject svn commit: r1480409 [1/2] - in /ctakes/trunk: ctakes-assertion-res/ ctakes-assertion-res/.settings/ ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/types/ ctakes-assertion-zoner-res/ ctakes-assertion-zoner-res/.settings/ ctakes-ass...
Date Wed, 08 May 2013 19:02:56 GMT
Author: chenpei
Date: Wed May  8 19:02:55 2013
New Revision: 1480409

URL: http://svn.apache.org/r1480409
Log:
CTAKES-183 - Move the resources/models from src/main/resources to their own projects {project}-res
1) The various TypeSystem.xml files doesn't/shouldn't need to be in the resource/models projects.  I think that was an oversight on my part last time.
2) I noticed that some of the projects have drivers or main classes which I assume a lot of folks are able to and plan to run pipelines directly from individual projects.  If this is true, then I think it is actually easier to leave it as is and default to have the corresponding -res dependency in the pom.xml.  Since it's maven controlled now, an external app can always add  <exclude ctakes-drug-ner-res/>.  This is just based on observation--  otherwise, each project will need to think about *-res during runtime if it's not in the pom.xml

Added:
    ctakes/trunk/ctakes-assertion-zoner/src/main/resources/
    ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/
    ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/
    ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/
    ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/
    ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/
    ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/
    ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml
    ctakes/trunk/ctakes-assertion/src/main/resources/
    ctakes/trunk/ctakes-assertion/src/main/resources/org/
    ctakes/trunk/ctakes-assertion/src/main/resources/org/apache/
    ctakes/trunk/ctakes-assertion/src/main/resources/org/apache/ctakes/
    ctakes/trunk/ctakes-assertion/src/main/resources/org/apache/ctakes/assertion/
    ctakes/trunk/ctakes-assertion/src/main/resources/org/apache/ctakes/assertion/types/
    ctakes/trunk/ctakes-assertion/src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml
    ctakes/trunk/ctakes-constituency-parser/src/main/resources/
    ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/
    ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/
    ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/ctakes/
    ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/
    ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/
    ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/types/
    ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml
    ctakes/trunk/ctakes-drug-ner/src/main/resources/
    ctakes/trunk/ctakes-drug-ner/src/main/resources/org/
    ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/
    ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/
    ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/
    ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/
    ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml
    ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/
    ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/
    ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/
    ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/
    ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/
    ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/types/
    ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/types/TypeSystem.xml
    ctakes/trunk/ctakes-side-effect/src/main/resources/
    ctakes/trunk/ctakes-side-effect/src/main/resources/org/
    ctakes/trunk/ctakes-side-effect/src/main/resources/org/apache/
    ctakes/trunk/ctakes-side-effect/src/main/resources/org/apache/ctakes/
    ctakes/trunk/ctakes-side-effect/src/main/resources/org/apache/ctakes/sideeffect/
    ctakes/trunk/ctakes-side-effect/src/main/resources/org/apache/ctakes/sideeffect/types/
    ctakes/trunk/ctakes-side-effect/src/main/resources/org/apache/ctakes/sideeffect/types/TypeSystem.xml
    ctakes/trunk/ctakes-smoking-status/src/main/resources/
    ctakes/trunk/ctakes-smoking-status/src/main/resources/org/
    ctakes/trunk/ctakes-smoking-status/src/main/resources/org/apache/
    ctakes/trunk/ctakes-smoking-status/src/main/resources/org/apache/ctakes/
    ctakes/trunk/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/
    ctakes/trunk/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/
    ctakes/trunk/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
Removed:
    ctakes/trunk/ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/types/
    ctakes/trunk/ctakes-assertion-zoner-res/src/main/resources/org/apache/
    ctakes/trunk/ctakes-assertion-zoner/pom.xml.backup01
    ctakes/trunk/ctakes-constituency-parser-res/src/main/resources/org/apache/ctakes/constituency/parser/types/
    ctakes/trunk/ctakes-pad-term-spotter-res/src/main/resources/org/apache/ctakes/padtermspotter/types/
    ctakes/trunk/ctakes-side-effect-res/src/main/resources/org/apache/ctakes/sideeffect/types/
    ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/
    ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/types/
Modified:
    ctakes/trunk/ctakes-assertion-res/.classpath
    ctakes/trunk/ctakes-assertion-res/.settings/org.eclipse.core.resources.prefs
    ctakes/trunk/ctakes-assertion-res/pom.xml
    ctakes/trunk/ctakes-assertion-zoner-res/.classpath
    ctakes/trunk/ctakes-assertion-zoner-res/.settings/org.eclipse.core.resources.prefs
    ctakes/trunk/ctakes-assertion-zoner-res/pom.xml
    ctakes/trunk/ctakes-assertion-zoner/.classpath
    ctakes/trunk/ctakes-assertion-zoner/pom.xml
    ctakes/trunk/ctakes-assertion/.classpath
    ctakes/trunk/ctakes-assertion/pom.xml
    ctakes/trunk/ctakes-chunker/pom.xml
    ctakes/trunk/ctakes-constituency-parser-res/.classpath
    ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.core.resources.prefs
    ctakes/trunk/ctakes-constituency-parser-res/pom.xml
    ctakes/trunk/ctakes-constituency-parser/.classpath
    ctakes/trunk/ctakes-constituency-parser/pom.xml
    ctakes/trunk/ctakes-core/pom.xml
    ctakes/trunk/ctakes-coreference/pom.xml
    ctakes/trunk/ctakes-dependency-parser/pom.xml
    ctakes/trunk/ctakes-dictionary-lookup/pom.xml
    ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml
    ctakes/trunk/ctakes-drug-ner-res/.classpath
    ctakes/trunk/ctakes-drug-ner-res/.settings/org.eclipse.core.resources.prefs
    ctakes/trunk/ctakes-drug-ner-res/pom.xml
    ctakes/trunk/ctakes-drug-ner/.classpath
    ctakes/trunk/ctakes-drug-ner/pom.xml
    ctakes/trunk/ctakes-lvg/pom.xml
    ctakes/trunk/ctakes-ne-contexts/pom.xml
    ctakes/trunk/ctakes-pad-term-spotter-res/pom.xml
    ctakes/trunk/ctakes-pad-term-spotter/.classpath
    ctakes/trunk/ctakes-pad-term-spotter/pom.xml
    ctakes/trunk/ctakes-pos-tagger/pom.xml
    ctakes/trunk/ctakes-side-effect-res/.classpath
    ctakes/trunk/ctakes-side-effect-res/.settings/org.eclipse.core.resources.prefs
    ctakes/trunk/ctakes-side-effect-res/pom.xml
    ctakes/trunk/ctakes-side-effect/.classpath
    ctakes/trunk/ctakes-side-effect/pom.xml
    ctakes/trunk/ctakes-smoking-status-res/.classpath
    ctakes/trunk/ctakes-smoking-status-res/.settings/org.eclipse.core.resources.prefs
    ctakes/trunk/ctakes-smoking-status-res/pom.xml
    ctakes/trunk/ctakes-smoking-status/.classpath
    ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml
    ctakes/trunk/ctakes-smoking-status/pom.xml
    ctakes/trunk/ctakes-temporal/.classpath

Modified: ctakes/trunk/ctakes-assertion-res/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-res/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-res/.classpath (original)
+++ ctakes/trunk/ctakes-assertion-res/.classpath Wed May  8 19:02:55 2013
@@ -17,12 +17,6 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>

Modified: ctakes/trunk/ctakes-assertion-res/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-res/.settings/org.eclipse.core.resources.prefs?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-res/.settings/org.eclipse.core.resources.prefs (original)
+++ ctakes/trunk/ctakes-assertion-res/.settings/org.eclipse.core.resources.prefs Wed May  8 19:02:55 2013
@@ -2,5 +2,4 @@ eclipse.preferences.version=1
 encoding//src/main/java=UTF-8
 encoding//src/main/resources=UTF-8
 encoding//src/test/java=UTF-8
-encoding//target/generated-sources/jcasgen=UTF-8
 encoding/<project>=UTF-8

Modified: ctakes/trunk/ctakes-assertion-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-res/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-res/pom.xml (original)
+++ ctakes/trunk/ctakes-assertion-res/pom.xml Wed May  8 19:02:55 2013
@@ -33,17 +33,6 @@
      <dependency>
 		<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-type-system</artifactId>
-	 </dependency>
+	 </dependency>	    	 
   </dependencies>
-	<build>
-		<plugins>
-			<plugin>
-				<groupId>org.cleartk</groupId>
-				<artifactId>jcasgen-maven-plugin</artifactId>
-				<configuration>
-					<typeSystem>src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml</typeSystem>
-				</configuration>
-			</plugin>
-		</plugins>
-	</build>    
 </project>
\ No newline at end of file

Modified: ctakes/trunk/ctakes-assertion-zoner-res/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner-res/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner-res/.classpath (original)
+++ ctakes/trunk/ctakes-assertion-zoner-res/.classpath Wed May  8 19:02:55 2013
@@ -11,12 +11,6 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
 	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
 		<attributes>
 			<attribute name="optional" value="true"/>

Modified: ctakes/trunk/ctakes-assertion-zoner-res/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner-res/.settings/org.eclipse.core.resources.prefs?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner-res/.settings/org.eclipse.core.resources.prefs (original)
+++ ctakes/trunk/ctakes-assertion-zoner-res/.settings/org.eclipse.core.resources.prefs Wed May  8 19:02:55 2013
@@ -2,5 +2,4 @@ eclipse.preferences.version=1
 encoding//src/main/java=UTF-8
 encoding//src/main/resources=UTF-8
 encoding//src/test/java=UTF-8
-encoding//target/generated-sources/jcasgen=UTF-8
 encoding/<project>=UTF-8

Modified: ctakes/trunk/ctakes-assertion-zoner-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner-res/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner-res/pom.xml (original)
+++ ctakes/trunk/ctakes-assertion-zoner-res/pom.xml Wed May  8 19:02:55 2013
@@ -33,17 +33,6 @@
      <dependency>
 		<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-type-system</artifactId>
-	 </dependency>
-  </dependencies>    
-	<build>
-		<plugins>
-			<plugin>
-				<groupId>org.cleartk</groupId>
-				<artifactId>jcasgen-maven-plugin</artifactId>
-				<configuration>
-					<typeSystem>src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml</typeSystem>
-				</configuration>
-			</plugin>
-		</plugins>
-	</build>  
+	 </dependency> 
+  </dependencies>
 </project>
\ No newline at end of file

Modified: ctakes/trunk/ctakes-assertion-zoner/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner/.classpath (original)
+++ ctakes/trunk/ctakes-assertion-zoner/.classpath Wed May  8 19:02:55 2013
@@ -1,26 +1,37 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

Modified: ctakes/trunk/ctakes-assertion-zoner/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner/pom.xml (original)
+++ ctakes/trunk/ctakes-assertion-zoner/pom.xml Wed May  8 19:02:55 2013
@@ -29,10 +29,10 @@
 		<version>3.1.0-SNAPSHOT</version>
 	</parent>
 	<dependencies>
-	    <dependency>
-	      <groupId>org.apache.ctakes</groupId>
-	      <artifactId>ctakes-assertion-zoner-res</artifactId>
-	    </dependency>    
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-assertion-zoner-res</artifactId>
+		</dependency>	    
 		<dependency>
 			<groupId>net.sf.mastif</groupId>
 			<artifactId>mastif-zoner</artifactId>
@@ -50,7 +50,16 @@
       <groupId>org.apache.ctakes</groupId>
       <artifactId>ctakes-core</artifactId>
     </dependency>
-
 	</dependencies>
-
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.cleartk</groupId>
+				<artifactId>jcasgen-maven-plugin</artifactId>
+				<configuration>
+					<typeSystem>src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml</typeSystem>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>  
 </project>

Added: ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml?rev=1480409&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml (added)
+++ ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml Wed May  8 19:02:55 2013
@@ -0,0 +1,66 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    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.
+
+-->
+<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <name>org.apache.ctakes.assertion.types.TypeSystem</name>
+  <description/>
+  <version>1.0</version>
+  <vendor/>
+  <types>
+    <typeDescription>
+      <name>org.apache.ctakes.assertion.zoner.types.Heading</name>
+      <description>a section heading</description>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+      <features>
+        <featureDescription>
+          <name>label</name>
+          <description/>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+      </features>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.assertion.zoner.types.Zone</name>
+      <description>A document Zone, including its heading</description>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+      <features>
+        <featureDescription>
+          <name>label</name>
+          <description/>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+      </features>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.assertion.zoner.types.Subzone</name>
+      <description/>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+      <features>
+        <featureDescription>
+          <name>label</name>
+          <description/>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+      </features>
+    </typeDescription>
+  </types>
+</typeSystemDescription>
+

Modified: ctakes/trunk/ctakes-assertion/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/.classpath (original)
+++ ctakes/trunk/ctakes-assertion/.classpath Wed May  8 19:02:55 2013
@@ -1,27 +1,38 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

Modified: ctakes/trunk/ctakes-assertion/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/pom.xml (original)
+++ ctakes/trunk/ctakes-assertion/pom.xml Wed May  8 19:02:55 2013
@@ -238,4 +238,15 @@
 			<artifactId>ctakes-chunker</artifactId>
 		</dependency>
 	</dependencies>	
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.cleartk</groupId>
+				<artifactId>jcasgen-maven-plugin</artifactId>
+				<configuration>
+					<typeSystem>src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml</typeSystem>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>    	
 </project>

Added: ctakes/trunk/ctakes-assertion/src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml?rev=1480409&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml (added)
+++ ctakes/trunk/ctakes-assertion/src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml Wed May  8 19:02:55 2013
@@ -0,0 +1,73 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    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.
+
+-->
+<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <name>org.apache.ctakes.assertion.types.TypeSystem</name>
+  <description/>
+  <version>1.0</version>
+  <vendor/>
+  <types>
+    <typeDescription>
+      <name>org.apache.ctakes.assertion.medfacts.types.Concept</name>
+      <description/>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+      <features>
+        <featureDescription>
+          <name>conceptType</name>
+          <description>the concept type -- one of problem, treatment, or test</description>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>conceptText</name>
+          <description/>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>externalId</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>originalEntityExternalId</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+      </features>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.assertion.medfacts.types.Assertion</name>
+      <description/>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+      <features>
+        <featureDescription>
+          <name>assertionType</name>
+          <description>assertion type -- one of present, absent, possible, conditional, hypothetical, or assocated_with_someone_else</description>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>associatedConcept</name>
+          <description/>
+          <rangeTypeName>org.apache.ctakes.assertion.medfacts.types.Concept</rangeTypeName>
+        </featureDescription>
+      </features>
+    </typeDescription>
+  </types>
+</typeSystemDescription>

Modified: ctakes/trunk/ctakes-chunker/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-chunker/pom.xml (original)
+++ ctakes/trunk/ctakes-chunker/pom.xml Wed May  8 19:02:55 2013
@@ -29,10 +29,10 @@
 		<version>3.1.0-SNAPSHOT</version>
 	</parent>
 	<dependencies>
-		<dependency>
+      	<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-chunker-res</artifactId>
-		</dependency>	    
+		</dependency>		      
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-type-system</artifactId>

Modified: ctakes/trunk/ctakes-constituency-parser-res/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser-res/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser-res/.classpath (original)
+++ ctakes/trunk/ctakes-constituency-parser-res/.classpath Wed May  8 19:02:55 2013
@@ -17,12 +17,6 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>

Modified: ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.core.resources.prefs?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.core.resources.prefs (original)
+++ ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.core.resources.prefs Wed May  8 19:02:55 2013
@@ -2,5 +2,4 @@ eclipse.preferences.version=1
 encoding//src/main/java=UTF-8
 encoding//src/main/resources=UTF-8
 encoding//src/test/java=UTF-8
-encoding//target/generated-sources/jcasgen=UTF-8
 encoding/<project>=UTF-8

Modified: ctakes/trunk/ctakes-constituency-parser-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser-res/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser-res/pom.xml (original)
+++ ctakes/trunk/ctakes-constituency-parser-res/pom.xml Wed May  8 19:02:55 2013
@@ -33,17 +33,7 @@
      <dependency>
 		<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-type-system</artifactId>
-	 </dependency>
+	 </dependency>	 
   </dependencies>
-	<build>
-		<plugins>
-			<plugin>
-				<groupId>org.cleartk</groupId>
-				<artifactId>jcasgen-maven-plugin</artifactId>
-				<configuration>
-					<typeSystem>src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml</typeSystem>
-				</configuration>
-			</plugin>
-		</plugins>
-	</build>  
+  
 </project>
\ No newline at end of file

Modified: ctakes/trunk/ctakes-constituency-parser/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser/.classpath (original)
+++ ctakes/trunk/ctakes-constituency-parser/.classpath Wed May  8 19:02:55 2013
@@ -1,28 +1,37 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/cTakes"/>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

Modified: ctakes/trunk/ctakes-constituency-parser/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser/pom.xml (original)
+++ ctakes/trunk/ctakes-constituency-parser/pom.xml Wed May  8 19:02:55 2013
@@ -28,11 +28,11 @@
 		<artifactId>ctakes</artifactId>
 		<version>3.1.0-SNAPSHOT</version>
 	</parent>
-	<dependencies>
+	<dependencies> 
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-constituency-parser-res</artifactId>
-		</dependency>	    
+		</dependency>	 	    
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-type-system</artifactId>
@@ -62,4 +62,15 @@
 			<artifactId>junit</artifactId>
 		</dependency>
 	</dependencies>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.cleartk</groupId>
+				<artifactId>jcasgen-maven-plugin</artifactId>
+				<configuration>
+					<typeSystem>src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml</typeSystem>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>  	
 </project>

Added: ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml?rev=1480409&view=auto
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml (added)
+++ ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml Wed May  8 19:02:55 2013
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    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.
+
+-->
+<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <name>org.apache.ctakes.constituency.parser.types.LabeledTree</name>
+  <description/>
+  <version>1.0</version>
+  <vendor/>
+  <types>
+    <typeDescription>
+      <name>org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree</name>
+      <description/>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+      <features>
+        <featureDescription>
+          <name>label</name>
+          <description/>
+          <rangeTypeName>uima.cas.Boolean</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>tree</name>
+          <description/>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+      </features>
+    </typeDescription>
+  </types>
+</typeSystemDescription>

Modified: ctakes/trunk/ctakes-core/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/pom.xml (original)
+++ ctakes/trunk/ctakes-core/pom.xml Wed May  8 19:02:55 2013
@@ -28,13 +28,12 @@
 		<artifactId>ctakes</artifactId>
 		<version>3.1.0-SNAPSHOT</version>
 	</parent>
-
 	<dependencies>
-		<dependency>
+	     <dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-core-res</artifactId>
-		</dependency>	    
-		<dependency>
+		</dependency>		    
+  		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-type-system</artifactId>
 		</dependency>

Modified: ctakes/trunk/ctakes-coreference/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/pom.xml (original)
+++ ctakes/trunk/ctakes-coreference/pom.xml Wed May  8 19:02:55 2013
@@ -28,12 +28,11 @@
 		<artifactId>ctakes</artifactId>
 		<version>3.1.0-SNAPSHOT</version>
 	</parent>
-	
 	<dependencies>
-		<dependency>
+	     <dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-coreference-res</artifactId>
-		</dependency>	    
+		</dependency>		    
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-type-system</artifactId>

Modified: ctakes/trunk/ctakes-dependency-parser/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dependency-parser/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dependency-parser/pom.xml (original)
+++ ctakes/trunk/ctakes-dependency-parser/pom.xml Wed May  8 19:02:55 2013
@@ -29,10 +29,10 @@
 		<version>3.1.0-SNAPSHOT</version>
 	</parent>
 	<dependencies>
-		<dependency>
+	     <dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-dependency-parser-res</artifactId>
-		</dependency>	    
+		</dependency>		        
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-type-system</artifactId>

Modified: ctakes/trunk/ctakes-dictionary-lookup/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup/pom.xml (original)
+++ ctakes/trunk/ctakes-dictionary-lookup/pom.xml Wed May  8 19:02:55 2013
@@ -28,16 +28,16 @@
 		<artifactId>ctakes</artifactId>
 		<version>3.1.0-SNAPSHOT</version>
 	</parent>
-	<dependencies>
+		<dependencies>
+	     <dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-dictionary-lookup-res</artifactId>
+		</dependency>		    
 		<dependency>
 			<groupId>hsqldb</groupId>
 			<artifactId>hsqldb</artifactId>
 			<version>1.8.0.10</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-dictionary-lookup-res</artifactId>
-		</dependency>			
+		</dependency>	
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-type-system</artifactId>

Modified: ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml (original)
+++ ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml Wed May  8 19:02:55 2013
@@ -159,12 +159,36 @@
 			<directoryMode>755</directoryMode>
     	</fileSet>
 		<fileSet>
+		    <directory>../ctakes-assertion-res/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+    	</fileSet>    
+		<fileSet>
+		    <directory>../ctakes-assertion-zoner/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+    	</fileSet>
+		<fileSet>
+		    <directory>../ctakes-assertion-zoner-res/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+    	</fileSet>      		
+		<fileSet>
 		    <directory>../ctakes-chunker/src/main/resources</directory>
 		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
     	</fileSet>
 		<fileSet>
+		    <directory>../ctakes-chunker-res/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+    	</fileSet>    	
+		<fileSet>
 		    <directory>../ctakes-clinical-pipeline/src/main/resources</directory>
 		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
@@ -175,7 +199,13 @@
 		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-    	</fileSet>    	
+    	</fileSet>   
+		<fileSet>
+		    <directory>../ctakes-constituency-parser-res/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+    	</fileSet>     	 	
 		<fileSet>
 		    <directory>../ctakes-context-tokenizer/src/main/resources</directory>
 		    <outputDirectory>resources</outputDirectory>
@@ -190,23 +220,48 @@
 			<excludes><exclude>log4j.xml</exclude></excludes>
     	</fileSet>
 		<fileSet>
+		    <directory>../ctakes-core-res/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<excludes><exclude>log4j.xml</exclude></excludes>
+    	</fileSet>    	
+		<fileSet>
 		    <directory>../ctakes-coreference/src/main/resources</directory>
 		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-    	</fileSet>    	   
+    	</fileSet>
+		<fileSet>
+		    <directory>../ctakes-coreference-res/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+    	</fileSet>      	    	   
 		<fileSet>
 		    <directory>../ctakes-dependency-parser/src/main/resources</directory>
 		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-    	</fileSet>    	
+    	</fileSet>   
+		<fileSet>
+		    <directory>../ctakes-dependency-parser-res/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+    	</fileSet>      	 	
 		<fileSet>
 		    <directory>../ctakes-dictionary-lookup/src/main/resources</directory>
 		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-    	</fileSet>    	 	
+    	</fileSet>    	 
+		<fileSet>
+		    <directory>../ctakes-dictionary-lookup-res/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+    	</fileSet>      		
 		<fileSet>
 		    <directory>../ctakes-drug-ner/src/main/resources</directory>
 		    <outputDirectory>resources</outputDirectory>
@@ -214,17 +269,35 @@
 			<directoryMode>755</directoryMode>
     	</fileSet>    	
 		<fileSet>
+		    <directory>../ctakes-drug-ner-res/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+    	</fileSet>        	
+		<fileSet>
 		    <directory>../ctakes-lvg/src/main/resources</directory>
 		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-    	</fileSet>    	
+    	</fileSet>    
+		<fileSet>
+		    <directory>../ctakes-lvg-res/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+    	</fileSet>     		
 		<fileSet>
 		    <directory>../ctakes-ne-contexts/src/main/resources</directory>
 		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-    	</fileSet>    	
+    	</fileSet>   
+		<fileSet>
+		    <directory>../ctakes-ne-contexts-res/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+    	</fileSet>      	 	
 		<fileSet>
 		    <directory>../ctakes-pad-term-spotter/src/main/resources</directory>
 		    <outputDirectory>resources</outputDirectory>
@@ -232,11 +305,23 @@
 			<directoryMode>755</directoryMode>
     	</fileSet>    	
 		<fileSet>
+		    <directory>../ctakes-pad-term-spotter-res/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+    	</fileSet>       	
+		<fileSet>
 		    <directory>../ctakes-pos-tagger/src/main/resources</directory>
 		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-    	</fileSet>    
+    	</fileSet>   
+		<fileSet>
+		    <directory>../ctakes-pos-tagger-res/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+    	</fileSet>        	 
 		<fileSet>
 		    <directory>../ctakes-preprocessor/src/main/resources</directory>
 		    <outputDirectory>resources</outputDirectory>
@@ -250,17 +335,35 @@
 			<directoryMode>755</directoryMode>
     	</fileSet>  
 		<fileSet>
+		    <directory>../ctakes-relation-extractor-res/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+    	</fileSet>    	
+		<fileSet>
 		    <directory>../ctakes-side-effect/src/main/resources</directory>
 		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-    	</fileSet>    	  		
+    	</fileSet>    	
+		<fileSet>
+		    <directory>../ctakes-side-effect-res/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+    	</fileSet>       	  		
 		<fileSet>
 		    <directory>../ctakes-smoking-status/src/main/resources</directory>
 		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
     	</fileSet>
+		<fileSet>
+		    <directory>../ctakes-smoking-status-res/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+    	</fileSet>    	
     	<!-- Type System types should already be in the jar -->
     	<!-- 
 		<fileSet>

Modified: ctakes/trunk/ctakes-drug-ner-res/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner-res/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner-res/.classpath (original)
+++ ctakes/trunk/ctakes-drug-ner-res/.classpath Wed May  8 19:02:55 2013
@@ -11,12 +11,6 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
 	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
 		<attributes>
 			<attribute name="optional" value="true"/>

Modified: ctakes/trunk/ctakes-drug-ner-res/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner-res/.settings/org.eclipse.core.resources.prefs?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner-res/.settings/org.eclipse.core.resources.prefs (original)
+++ ctakes/trunk/ctakes-drug-ner-res/.settings/org.eclipse.core.resources.prefs Wed May  8 19:02:55 2013
@@ -2,5 +2,4 @@ eclipse.preferences.version=1
 encoding//src/main/java=UTF-8
 encoding//src/main/resources=UTF-8
 encoding//src/test/java=UTF-8
-encoding//target/generated-sources/jcasgen=UTF-8
 encoding/<project>=UTF-8

Modified: ctakes/trunk/ctakes-drug-ner-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner-res/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner-res/pom.xml (original)
+++ ctakes/trunk/ctakes-drug-ner-res/pom.xml Wed May  8 19:02:55 2013
@@ -13,16 +13,5 @@
 		<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-type-system</artifactId>
 	 </dependency>
-  </dependencies>  
-    	<build>
-		<plugins>
-			<plugin>
-				<groupId>org.cleartk</groupId>
-				<artifactId>jcasgen-maven-plugin</artifactId>
-				<configuration>
-					<typeSystem>src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml</typeSystem>
-				</configuration>
-			</plugin>
-		</plugins>
-	</build>
+  </dependencies>
 </project>
\ No newline at end of file

Modified: ctakes/trunk/ctakes-drug-ner/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner/.classpath (original)
+++ ctakes/trunk/ctakes-drug-ner/.classpath Wed May  8 19:02:55 2013
@@ -1,27 +1,37 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

Modified: ctakes/trunk/ctakes-drug-ner/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner/pom.xml (original)
+++ ctakes/trunk/ctakes-drug-ner/pom.xml Wed May  8 19:02:55 2013
@@ -28,12 +28,11 @@
 		<artifactId>ctakes</artifactId>
 		<version>3.1.0-SNAPSHOT</version>
 	</parent>
-	
 	<dependencies>
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-drug-ner-res</artifactId>
-		</dependency>	    
+		</dependency>	      
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-type-system</artifactId>
@@ -95,4 +94,15 @@
 			<artifactId>ctakes-lvg</artifactId>
 		</dependency>
 	</dependencies>
+    <build>
+		<plugins>
+			<plugin>
+				<groupId>org.cleartk</groupId>
+				<artifactId>jcasgen-maven-plugin</artifactId>
+				<configuration>
+					<typeSystem>src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml</typeSystem>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>	
 </project>

Added: ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml?rev=1480409&view=auto
==============================================================================
--- ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml (added)
+++ ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml Wed May  8 19:02:55 2013
@@ -0,0 +1,313 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <name>org.apache.ctakes.drugner.types.TypeSystem</name>
+  <description/>
+  <version>1.0</version>
+  <vendor>Mayo Clinic</vendor>
+  <types>
+    <typeDescription>
+      <name>org.apache.ctakes.drugner.type.FrequencyAnnotation</name>
+      <description>The frequency determination for the Drug NER profile.</description>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.drugner.type.DurationAnnotation</name>
+      <description>The duration determination for the Drug NER profile.</description>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.drugner.type.RouteAnnotation</name>
+      <description>The route determination for the Drug NER profile.</description>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+      <features>
+        <featureDescription>
+          <name>intakeMethod</name>
+          <description>Means by which the drug was taken.</description>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+      </features>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.drugner.type.SuffixStrengthAnnotation</name>
+      <description>The suffix portion of dosage strength determination for the Drug NER profile.</description>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.drugner.type.FractionStrengthAnnotation</name>
+      <description>The fraction portion of dosages strength determination for the Drug NER profile.</description>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.drugner.type.RangeStrengthAnnotation</name>
+      <description>The range portion of dosages stength determination for the Drug NER profile.</description>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.drugner.type.DecimalStrengthAnnotation</name>
+      <description>The decimal portion of dosages stength determination for the Drug NER profile.</description>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation</name>
+      <description>The change status of dosages determination for the Drug NER profile.</description>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+      <features>
+        <featureDescription>
+          <name>changeStatus</name>
+          <description>Indicates the drug change status of 'stop', 'start', 'increase', 'decrease', or 'noChange'.</description>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+      </features>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.drugner.type.DosagesAnnotation</name>
+      <description>The dosage determination for the Drug NER profile.</description>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.drugner.type.StrengthAnnotation</name>
+      <description>Holds the value representing the unit of the drug dosage.</description>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.drugner.type.StrengthUnitAnnotation</name>
+      <description/>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.drugner.type.FrequencyUnitAnnotation</name>
+      <description>The value represents the unit portion of the drug frequency.</description>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+      <features>
+        <featureDescription>
+          <name>period</name>
+          <description>The periodic unit used, e.g day, month, hour, etc.</description>
+          <rangeTypeName>uima.cas.Float</rangeTypeName>
+        </featureDescription>
+      </features>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.drugner.type.FormAnnotation</name>
+      <description>The value represents the form portion of the drug mention.</description>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.drugner.type.SubSectionAnnotation</name>
+      <description/>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+      <features>
+        <featureDescription>
+          <name>subSectionBodyBegin</name>
+          <description>Sub-section body begin offset.</description>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>subSectionBodyEnd</name>
+          <description>Sub-section body end offset.</description>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>status</name>
+          <description>Status of 'possible', 'history of', or 'family history of'.</description>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>subSectionHeaderBegin</name>
+          <description>Begin offset of subSection header</description>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>subSectionHeaderEnd</name>
+          <description>Ending offset of subsection header</description>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>parentSectionId</name>
+          <description>The section in which the subsection was found.</description>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+      </features>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.drugner.type.DrugMentionAnnotation</name>
+      <description/>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+      <features>
+        <featureDescription>
+          <name>status</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>confidence</name>
+          <description>The confidence of the annotation.</description>
+          <rangeTypeName>uima.cas.Float</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>frequency</name>
+          <description>Frequency refers to how often the patient needs to take the drug. Frequency is divided into frequency number and frequency unit. E.g. twice daily</description>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>frequencyBegin</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>frequencyEnd</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>duration</name>
+          <description>Duration refers to for how long the patient is expected to take the drug. E.g. 'for 2 weeks' 
+Strongly encouraged to use bold text</description>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>durationBegin</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>durationEnd</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>route</name>
+          <description>Medication route refers to the way that a drug is introduced into the body. E.g oral 
+Strongly encouraged to use bold text</description>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>routeBegin</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>routeEnd</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>drugChangeStatus</name>
+          <description>Status refers to the whether the medication is currently being taken or not.</description>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>dosage</name>
+          <description>Dosage refers to how many of each drug the patient is taking. E.g. 5 mg</description>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>dosageBegin</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>dosageEnd</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>strength</name>
+          <description/>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>strengthBegin</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>strengthEnd</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>strengthUnit</name>
+          <description/>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>suBegin</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>suEnd</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>form</name>
+          <description>Form refers to the physical appearance of the drug. E.g. cream</description>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>formBegin</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>formEnd</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>frequencyUnit</name>
+          <description/>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>fuBegin</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>fuEnd</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>startDate</name>
+          <description/>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>reason</name>
+          <description/>
+          <rangeTypeName>uima.cas.FSArray</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>changeStatusBegin</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+        <featureDescription>
+          <name>changeStatusEnd</name>
+          <description/>
+          <rangeTypeName>uima.cas.Integer</rangeTypeName>
+        </featureDescription>
+      </features>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.drugner.type.ChunkAnnotation</name>
+      <description/>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+      <features>
+        <featureDescription>
+          <name>sentenceID</name>
+          <description/>
+          <rangeTypeName>uima.cas.String</rangeTypeName>
+        </featureDescription>
+      </features>
+    </typeDescription>
+    <typeDescription>
+      <name>org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation</name>
+      <description>Similar to LookupWindowAnnotation however, these annotations are restricted to the segments/sections specified in the parameter - sectionOverrideSet - in DrugCNP2LookupWindow</description>
+      <supertypeName>uima.tcas.Annotation</supertypeName>
+    </typeDescription>
+  </types>
+</typeSystemDescription>

Modified: ctakes/trunk/ctakes-lvg/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-lvg/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-lvg/pom.xml (original)
+++ ctakes/trunk/ctakes-lvg/pom.xml Wed May  8 19:02:55 2013
@@ -29,7 +29,7 @@
 		<artifactId>ctakes</artifactId>
 		<version>3.1.0-SNAPSHOT</version>
 	</parent>
-	<dependencies>
+	<dependencies>  
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-lvg-res</artifactId>

Modified: ctakes/trunk/ctakes-ne-contexts/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ne-contexts/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ne-contexts/pom.xml (original)
+++ ctakes/trunk/ctakes-ne-contexts/pom.xml Wed May  8 19:02:55 2013
@@ -32,7 +32,7 @@
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-ne-contexts-res</artifactId>
-		</dependency>	    
+		</dependency>	      
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-type-system</artifactId>

Modified: ctakes/trunk/ctakes-pad-term-spotter-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pad-term-spotter-res/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-pad-term-spotter-res/pom.xml (original)
+++ ctakes/trunk/ctakes-pad-term-spotter-res/pom.xml Wed May  8 19:02:55 2013
@@ -34,16 +34,5 @@
 		<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-type-system</artifactId>
 	 </dependency>
-  </dependencies>    
-		<build>
-		<plugins>
-			<plugin>
-				<groupId>org.cleartk</groupId>
-				<artifactId>jcasgen-maven-plugin</artifactId>
-				<configuration>
-					<typeSystem>src/main/resources/org/apache/ctakes/padtermspotter/types/TypeSystem.xml</typeSystem>
-				</configuration>
-			</plugin>
-		</plugins>
-	</build>  
+  </dependencies>
 </project>
\ No newline at end of file

Modified: ctakes/trunk/ctakes-pad-term-spotter/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pad-term-spotter/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-pad-term-spotter/.classpath (original)
+++ ctakes/trunk/ctakes-pad-term-spotter/.classpath Wed May  8 19:02:55 2013
@@ -1,27 +1,38 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

Modified: ctakes/trunk/ctakes-pad-term-spotter/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pad-term-spotter/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-pad-term-spotter/pom.xml (original)
+++ ctakes/trunk/ctakes-pad-term-spotter/pom.xml Wed May  8 19:02:55 2013
@@ -33,7 +33,7 @@
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-pad-term-spotter-res</artifactId>
-		</dependency>	    
+		</dependency>	      
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-type-system</artifactId>
@@ -71,4 +71,15 @@
 			<artifactId>ctakes-context-tokenizer</artifactId>
 		</dependency>	
 	</dependencies>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.cleartk</groupId>
+				<artifactId>jcasgen-maven-plugin</artifactId>
+				<configuration>
+					<typeSystem>src/main/resources/org/apache/ctakes/padtermspotter/types/TypeSystem.xml</typeSystem>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>  	
 </project>

Added: ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/types/TypeSystem.xml?rev=1480409&view=auto
==============================================================================
--- ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/types/TypeSystem.xml (added)
+++ ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/types/TypeSystem.xml Wed May  8 19:02:55 2013
@@ -0,0 +1,158 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    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.
+
+-->
+<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
+	<name>org.apache.ctakes.padtermspotter.types.TypeSystem</name>
+	<description>Represents Term and Location entities required for PAD
+		project.</description>
+	<version>1.0</version>
+	<vendor>Mayo</vendor>
+	<imports>
+		<import name="org.apache.ctakes.typesystem.types.TypeSystem" />
+	</imports>
+	<types>
+		<typeDescription>
+			<name>org.apache.ctakes.padtermspotter.type.PADTerm</name>
+			<description />
+			<supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
+			</supertypeName>
+			<features>
+				<featureDescription>
+					<name>hitDictionaryValue</name>
+					<description>Value from the Dictionary that was successfully looked
+						up</description>
+					<rangeTypeName>uima.cas.String</rangeTypeName>
+				</featureDescription>
+				<featureDescription>
+					<name>isStandAlone</name>
+					<description>Identifies weather this term needs another dictionary
+						hit to be considered as a valid hit. Currently this is being used
+						for Unstable Angina which requires "Term" and "Location" to be
+						present in the text to be considered as a valid hit.
+
+						Valid values are 0 and 1. Where, 0 is false (not standalone) and 1 is
+						true (is standalone)
+					</description>
+					<rangeTypeName>uima.cas.Integer</rangeTypeName>
+				</featureDescription>
+				<featureDescription>
+					<name>relatedTokens</name>
+					<description>identifies the token that this PADTerm spans
+					</description>
+					<rangeTypeName>uima.cas.FSArray</rangeTypeName>
+				</featureDescription>
+			</features>
+		</typeDescription>
+		<typeDescription>
+			<name>org.apache.ctakes.padtermspotter.type.PADLocation</name>
+			<description />
+			<supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
+			</supertypeName>
+			<features>
+				<featureDescription>
+					<name>hitDictionaryValue</name>
+					<description>Value from the Dictionary that was successfully looked
+						up</description>
+					<rangeTypeName>uima.cas.String</rangeTypeName>
+				</featureDescription>
+				<featureDescription>
+					<name>isStandAlone</name>
+					<description>Identifies weather this term needs another dictionary
+						hit to be considered as a valid hit. Currently this is being used
+						for Unstable Angina which requires "Term" and "Location" to be
+						present in the text to be considered as a valid hit.
+
+						Valid values are 0 and 1. Where, 0 is false (not standalone) and 1 is
+						true (is standalone)
+					</description>
+					<rangeTypeName>uima.cas.Integer</rangeTypeName>
+				</featureDescription>
+				<featureDescription>
+					<name>relatedTokens</name>
+					<description>identifies the token that this PADTerm spans
+					</description>
+					<rangeTypeName>uima.cas.FSArray</rangeTypeName>
+				</featureDescription>
+			</features>
+		</typeDescription>
+		<typeDescription>
+			<name>org.apache.ctakes.padtermspotter.type.PADHit</name>
+			<description>Would represent one of the following
+				Term (in the case of a stand alone term)
+				Term + Location
+				Location + term
+			</description>
+			<supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
+			</supertypeName>
+			<features>
+				<featureDescription>
+					<name>uaTerm</name>
+					<description />
+					<rangeTypeName>org.apache.ctakes.padtermspotter.type.PADTerm
+					</rangeTypeName>
+				</featureDescription>
+				<featureDescription>
+					<name>uaLocation</name>
+					<description />
+					<rangeTypeName>org.apache.ctakes.padtermspotter.type.PADLocation
+					</rangeTypeName>
+				</featureDescription>
+			</features>
+		</typeDescription>
+		<typeDescription>
+			<name>org.apache.ctakes.padtermspotter.type.SubSection</name>
+			<description></description>
+			<supertypeName>uima.tcas.Annotation</supertypeName>
+			<features>
+				<featureDescription>
+					<name>parentSectionId</name>
+					<description></description>
+					<rangeTypeName>uima.cas.String</rangeTypeName>
+				</featureDescription>
+				<featureDescription>
+					<name>subSectionBodyBegin</name>
+					<description></description>
+					<rangeTypeName>uima.cas.Integer</rangeTypeName>
+				</featureDescription>
+				<featureDescription>
+					<name>subSectionBodyEnd</name>
+					<description></description>
+					<rangeTypeName>uima.cas.Integer</rangeTypeName>
+				</featureDescription>
+				<featureDescription>
+					<name>status</name>
+					<description></description>
+					<rangeTypeName>uima.cas.Integer</rangeTypeName>
+				</featureDescription>
+				<featureDescription>
+					<name>subSectionHeaderBegin</name>
+					<description></description>
+					<rangeTypeName>uima.cas.Integer</rangeTypeName>
+				</featureDescription>
+				<featureDescription>
+					<name>subSectionHeaderEnd</name>
+					<description></description>
+					<rangeTypeName>uima.cas.Integer</rangeTypeName>
+				</featureDescription>
+			</features>
+		</typeDescription>
+	</types>
+</typeSystemDescription>

Modified: ctakes/trunk/ctakes-pos-tagger/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pos-tagger/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-pos-tagger/pom.xml (original)
+++ ctakes/trunk/ctakes-pos-tagger/pom.xml Wed May  8 19:02:55 2013
@@ -28,7 +28,7 @@
 		<artifactId>ctakes</artifactId>
 		<version>3.1.0-SNAPSHOT</version>
 	</parent>
-	<dependencies>
+	<dependencies> 
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-pos-tagger-res</artifactId>

Modified: ctakes/trunk/ctakes-side-effect-res/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-side-effect-res/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-side-effect-res/.classpath (original)
+++ ctakes/trunk/ctakes-side-effect-res/.classpath Wed May  8 19:02:55 2013
@@ -11,12 +11,6 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
 	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
 		<attributes>
 			<attribute name="optional" value="true"/>

Modified: ctakes/trunk/ctakes-side-effect-res/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-side-effect-res/.settings/org.eclipse.core.resources.prefs?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-side-effect-res/.settings/org.eclipse.core.resources.prefs (original)
+++ ctakes/trunk/ctakes-side-effect-res/.settings/org.eclipse.core.resources.prefs Wed May  8 19:02:55 2013
@@ -2,5 +2,4 @@ eclipse.preferences.version=1
 encoding//src/main/java=UTF-8
 encoding//src/main/resources=UTF-8
 encoding//src/test/java=UTF-8
-encoding//target/generated-sources/jcasgen=UTF-8
 encoding/<project>=UTF-8

Modified: ctakes/trunk/ctakes-side-effect-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-side-effect-res/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-side-effect-res/pom.xml (original)
+++ ctakes/trunk/ctakes-side-effect-res/pom.xml Wed May  8 19:02:55 2013
@@ -34,16 +34,5 @@
 		<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-type-system</artifactId>
 	 </dependency>
-  </dependencies>  
-	<build>
-		<plugins>
-			<plugin>
-				<groupId>org.cleartk</groupId>
-				<artifactId>jcasgen-maven-plugin</artifactId>
-				<configuration>
-					<typeSystem>src/main/resources/org/apache/ctakes/sideeffect/types/TypeSystem.xml</typeSystem>
-				</configuration>
-			</plugin>
-		</plugins>
-	</build>  
+  </dependencies> 
 </project>
\ No newline at end of file



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