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From chen...@apache.org
Subject svn commit: r1387750 - in /incubator/ctakes/trunk: ./ ctakes-chunker/ ctakes-clinical-pipeline/ ctakes-constituency-parser/ ctakes-constituency-parser/.settings/ ctakes-context-tokenizer/ ctakes-core/ ctakes-coreference/ ctakes-dependency-parser/ ctake...
Date Wed, 19 Sep 2012 20:54:48 GMT
Author: chenpei
Date: Wed Sep 19 20:54:46 2012
New Revision: 1387750

URL: http://svn.apache.org/viewvc?rev=1387750&view=rev
Log:
https://issues.apache.org/jira/browse/CTAKES-30
Updating maven pom.xml's for build.  All modules should compile now before we update namespaces.

Added:
    incubator/ctakes/trunk/ctakes-coreference/pom.xml
    incubator/ctakes/trunk/ctakes-lvg/pom.xml
    incubator/ctakes/trunk/ctakes-pad-term-spotter/pom.xml
    incubator/ctakes/trunk/ctakes-relation-extractor/pom.xml
    incubator/ctakes/trunk/ctakes-smoking-status/pom.xml
    incubator/ctakes/trunk/ctakes-utils/pom.xml
Removed:
    incubator/ctakes/trunk/ctakes-preprocessor/build.xml
Modified:
    incubator/ctakes/trunk/.project
    incubator/ctakes/trunk/ctakes-chunker/.classpath
    incubator/ctakes/trunk/ctakes-chunker/.project
    incubator/ctakes/trunk/ctakes-clinical-pipeline/.classpath
    incubator/ctakes/trunk/ctakes-clinical-pipeline/.project
    incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml
    incubator/ctakes/trunk/ctakes-constituency-parser/.classpath
    incubator/ctakes/trunk/ctakes-constituency-parser/.project
    incubator/ctakes/trunk/ctakes-constituency-parser/.settings/org.eclipse.jdt.core.prefs
    incubator/ctakes/trunk/ctakes-context-tokenizer/.classpath
    incubator/ctakes/trunk/ctakes-context-tokenizer/.project
    incubator/ctakes/trunk/ctakes-core/.classpath
    incubator/ctakes/trunk/ctakes-core/.project
    incubator/ctakes/trunk/ctakes-core/pom.xml
    incubator/ctakes/trunk/ctakes-coreference/.classpath
    incubator/ctakes/trunk/ctakes-coreference/.project
    incubator/ctakes/trunk/ctakes-dependency-parser/.classpath
    incubator/ctakes/trunk/ctakes-dependency-parser/.project
    incubator/ctakes/trunk/ctakes-dictionary-lookup/.classpath
    incubator/ctakes/trunk/ctakes-dictionary-lookup/.project
    incubator/ctakes/trunk/ctakes-drug-ner/.classpath
    incubator/ctakes/trunk/ctakes-drug-ner/.project
    incubator/ctakes/trunk/ctakes-lvg/.classpath
    incubator/ctakes/trunk/ctakes-lvg/.project
    incubator/ctakes/trunk/ctakes-ne-contexts/.classpath
    incubator/ctakes/trunk/ctakes-ne-contexts/.project
    incubator/ctakes/trunk/ctakes-pad-term-spotter/.classpath
    incubator/ctakes/trunk/ctakes-pad-term-spotter/.project
    incubator/ctakes/trunk/ctakes-pos-tagger/.classpath
    incubator/ctakes/trunk/ctakes-pos-tagger/.project
    incubator/ctakes/trunk/ctakes-preprocessor/.classpath
    incubator/ctakes/trunk/ctakes-preprocessor/.project
    incubator/ctakes/trunk/ctakes-preprocessor/.settings/org.eclipse.jdt.core.prefs
    incubator/ctakes/trunk/ctakes-preprocessor/test/edu/mayo/bmi/test/preprocessor/ClinicalNotePreProcessorTest.java
    incubator/ctakes/trunk/ctakes-relation-extractor/.classpath
    incubator/ctakes/trunk/ctakes-relation-extractor/.project
    incubator/ctakes/trunk/ctakes-relation-extractor/.settings/org.eclipse.jdt.core.prefs
    incubator/ctakes/trunk/ctakes-side-effect/.classpath
    incubator/ctakes/trunk/ctakes-side-effect/.project
    incubator/ctakes/trunk/ctakes-side-effect/desc/type_system/SideEffectTypeSystem.xml
    incubator/ctakes/trunk/ctakes-smoking-status/.classpath
    incubator/ctakes/trunk/ctakes-smoking-status/.project
    incubator/ctakes/trunk/ctakes-smoking-status/desc/type_system/SmokingProductionTypeSystem.xml
    incubator/ctakes/trunk/ctakes-type-system/.classpath
    incubator/ctakes/trunk/ctakes-type-system/.project
    incubator/ctakes/trunk/ctakes-type-system/pom.xml
    incubator/ctakes/trunk/ctakes-utils/.classpath
    incubator/ctakes/trunk/ctakes-utils/.project
    incubator/ctakes/trunk/pom.xml

Modified: incubator/ctakes/trunk/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/.project (original)
+++ incubator/ctakes/trunk/.project Wed Sep 19 20:54:46 2012
@@ -5,7 +5,13 @@
 	<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>

Modified: incubator/ctakes/trunk/ctakes-chunker/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-chunker/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-chunker/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-chunker/.classpath Wed Sep 19 20:54:46 2012
@@ -1,15 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="test/src"/>
-	<classpathentry kind="src" path="scripts/java"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/core"/>
-	<classpathentry kind="lib" path="/core/resources"/>
-	<classpathentry kind="lib" path="resources"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/POS tagger"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/common-type-system"/>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>

Modified: incubator/ctakes/trunk/ctakes-chunker/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-chunker/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-chunker/.project (original)
+++ incubator/ctakes/trunk/ctakes-chunker/.project Wed Sep 19 20:54:46 2012
@@ -10,8 +10,14 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.apache.uima.pear.UimaNature</nature>
 	</natures>

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/.classpath Wed Sep 19 20:54:46 2012
@@ -1,18 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/context dependent tokenizer"/>
-	<classpathentry kind="lib" path="resources"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/chunker"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/LVG"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/dictionary lookup"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/NE contexts"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/core"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/POS tagger"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/document preprocessor"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/common-type-system"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/assertion"/>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/.project (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/.project Wed Sep 19 20:54:46 2012
@@ -10,8 +10,14 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.apache.uima.pear.UimaNature</nature>
 	</natures>

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml Wed Sep 19 20:54:46 2012
@@ -7,6 +7,7 @@
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
 		<version>3.0.0-SNAPSHOT</version>
+		<relativePath>..</relativePath>
 	</parent>
 	
 

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/.classpath Wed Sep 19 20:54:46 2012
@@ -1,12 +1,8 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry excluding="*/.svn/" kind="src" path="src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry kind="lib" path="resources"/>
-	<classpathentry kind="lib" path="lib/libsvm-2.91.jar"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/cTakes"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/core"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/common-type-system"/>
-	<classpathentry kind="output" path="bin"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/cTakes"/>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/.project (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/.project Wed Sep 19 20:54:46 2012
@@ -1,18 +1,24 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-	<name>Constituency Parser</name>
-	<comment></comment>
-	<projects>
-	</projects>
-	<buildSpec>
-		<buildCommand>
-			<name>org.eclipse.jdt.core.javabuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-	</buildSpec>
-	<natures>
-		<nature>org.eclipse.jdt.core.javanature</nature>
-		<nature>org.apache.uima.pear.UimaNature</nature>
-	</natures>
-</projectDescription>
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>Constituency Parser</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.apache.uima.pear.UimaNature</nature>
+	</natures>
+</projectDescription>

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/.settings/org.eclipse.jdt.core.prefs
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/.settings/org.eclipse.jdt.core.prefs?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/.settings/org.eclipse.jdt.core.prefs (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/.settings/org.eclipse.jdt.core.prefs Wed Sep 19 20:54:46 2012
@@ -1,12 +1,13 @@
-#Thu Jun 23 14:03:47 EDT 2011
-eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
-org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=1.6
-org.eclipse.jdt.core.compiler.debug.lineNumber=generate
-org.eclipse.jdt.core.compiler.debug.localVariable=generate
-org.eclipse.jdt.core.compiler.debug.sourceFile=generate
-org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
-org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
-org.eclipse.jdt.core.compiler.source=1.6
+#Wed Sep 19 13:54:31 EDT 2012
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.6

Modified: incubator/ctakes/trunk/ctakes-context-tokenizer/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-context-tokenizer/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-context-tokenizer/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-context-tokenizer/.classpath Wed Sep 19 20:54:46 2012
@@ -1,9 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/core"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/common-type-system"/>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>

Modified: incubator/ctakes/trunk/ctakes-context-tokenizer/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-context-tokenizer/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-context-tokenizer/.project (original)
+++ incubator/ctakes/trunk/ctakes-context-tokenizer/.project Wed Sep 19 20:54:46 2012
@@ -10,8 +10,14 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.apache.uima.pear.UimaNature</nature>
 	</natures>

Modified: incubator/ctakes/trunk/ctakes-core/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-core/.classpath Wed Sep 19 20:54:46 2012
@@ -1,20 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="test"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry kind="lib" path="resources"/>
-	<classpathentry kind="lib" path="lib/jdom.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/log4j-1.2.15.jar"/>
-	<classpathentry kind="lib" path="lib/lucene-core-3.0.2.jar"/>
-	<classpathentry kind="lib" path="lib/OpenAI_FSM.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/opennlp-maxent-3.0.2-incubating.jar"/>
-	<classpathentry exported="true" kind="lib" path="lib/opennlp-tools-1.5.2-incubating.jar"/>
-	<classpathentry kind="lib" path="lib/SQLWrapper.jar"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/common-type-system"/>
-	<classpathentry kind="lib" path="lib/FindStructAPI.jar"/>
-	<classpathentry kind="lib" path="lib/junit.jar"/>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>

Modified: incubator/ctakes/trunk/ctakes-core/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/.project (original)
+++ incubator/ctakes/trunk/ctakes-core/.project Wed Sep 19 20:54:46 2012
@@ -10,8 +10,14 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.apache.uima.pear.UimaNature</nature>
 	</natures>

Modified: incubator/ctakes/trunk/ctakes-core/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/pom.xml?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/pom.xml (original)
+++ incubator/ctakes/trunk/ctakes-core/pom.xml Wed Sep 19 20:54:46 2012
@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes</artifactId>
-		<version>2.6.0-SNAPSHOT</version>
+		<version>3.0.0-SNAPSHOT</version>
 	</parent>
 
 	<dependencies>

Modified: incubator/ctakes/trunk/ctakes-coreference/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-coreference/.classpath Wed Sep 19 20:54:46 2012
@@ -1,16 +1,7 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="lib" path="lib/commons-lang3-3.0.1.jar"/>
-	<classpathentry kind="lib" path="lib/commons-io-2.1.jar"/>
-	<classpathentry kind="lib" path="lib/libsvm-2.91.jar"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/core"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry kind="lib" path="resources"/>
-	<classpathentry kind="lib" path="lib/Jama-1.0.2.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/common-type-system"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/Constituency Parser"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/clinical documents pipeline"/>
-	<classpathentry kind="output" path="bin"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

Modified: incubator/ctakes/trunk/ctakes-coreference/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/.project (original)
+++ incubator/ctakes/trunk/ctakes-coreference/.project Wed Sep 19 20:54:46 2012
@@ -10,8 +10,14 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.apache.uima.pear.UimaNature</nature>
 	</natures>

Added: incubator/ctakes/trunk/ctakes-coreference/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-coreference/pom.xml?rev=1387750&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-coreference/pom.xml (added)
+++ incubator/ctakes/trunk/ctakes-coreference/pom.xml Wed Sep 19 20:54:46 2012
@@ -0,0 +1,45 @@
+<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/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<artifactId>ctakes-coreference</artifactId>
+	<name>Apache cTAKES CoReference Resolver</name>
+	<parent>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes</artifactId>
+		<version>3.0.0-SNAPSHOT</version>
+	</parent>
+	<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-constituency-parser</artifactId>
+		</dependency>		
+		<dependency>
+			<groupId>org.apache.opennlp</groupId>
+			<artifactId>opennlp-tools</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>log4j</groupId>
+			<artifactId>log4j</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>jdom</groupId>
+			<artifactId>jdom</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+		</dependency>
+	</dependencies>
+</project>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/.classpath Wed Sep 19 20:54:46 2012
@@ -1,23 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry kind="lib" path="lib/uimafit-1.2.0.jar" />
-	<classpathentry kind="lib" path="lib/cleartk-util-0.8.1.jar"/>
-	<classpathentry kind="lib" path="lib/args4j-2.0.16.jar"/>
-	<classpathentry kind="lib" path="lib/hppc-0.3.1.jar"/>
-	<classpathentry kind="lib" path="lib/clearparser-0.33.jar"/>
-	<classpathentry kind="lib" path="lib/commons-io-2.0.1.jar"/>
-	<classpathentry kind="lib" path="lib/commons-lang-2.4.jar"/>
-	<classpathentry kind="lib" path="lib/commons-logging-1.1.1.jar"/>
-	<classpathentry kind="lib" path="resources/clearparser_models.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/chunker"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/common-type-system"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/POS tagger"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/context dependent tokenizer"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/core"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/LVG"/>
-	<classpathentry kind="lib" path="resources"/>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/.project (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/.project Wed Sep 19 20:54:46 2012
@@ -1,18 +1,24 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-	<name>dependency parser</name>
-	<comment></comment>
-	<projects>
-	</projects>
-	<buildSpec>
-		<buildCommand>
-			<name>org.eclipse.jdt.core.javabuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-	</buildSpec>
-	<natures>
-		<nature>org.eclipse.jdt.core.javanature</nature>
-		<nature>org.apache.uima.pear.UimaNature</nature>
-	</natures>
-</projectDescription>
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>dependency parser</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.apache.uima.pear.UimaNature</nature>
+	</natures>
+</projectDescription>

Modified: incubator/ctakes/trunk/ctakes-dictionary-lookup/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/.classpath Wed Sep 19 20:54:46 2012
@@ -1,14 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="scripts/java"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/core"/>
-	<classpathentry exported="true" kind="lib" path="resources"/>
-	<classpathentry kind="lib" path="/core/lib/log4j-1.2.15.jar"/>
-	<classpathentry kind="lib" path="/core/lib/jdom.jar"/>
-	<classpathentry kind="lib" path="/core/lib/lucene-core-3.0.2.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/common-type-system"/>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>

Modified: incubator/ctakes/trunk/ctakes-dictionary-lookup/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/.project (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/.project Wed Sep 19 20:54:46 2012
@@ -10,8 +10,14 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.apache.uima.pear.UimaNature</nature>
 	</natures>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/.classpath Wed Sep 19 20:54:46 2012
@@ -1,23 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry kind="lib" path="resources"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry kind="lib" path="/core/lib/jdom.jar"/>
-	<classpathentry kind="lib" path="/core/lib/junit.jar"/>
-	<classpathentry kind="lib" path="/core/lib/OpenAI_FSM.jar"/>
-	<classpathentry kind="lib" path="/core/lib/opennlp-maxent-3.0.2-incubating.jar"/>
-	<classpathentry kind="lib" path="/core/lib/opennlp-tools-1.5.2-incubating.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/core"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/dictionary lookup"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/NE contexts"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/context dependent tokenizer"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/document preprocessor"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/LVG"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/clinical documents pipeline"/>
-	<classpathentry kind="lib" path="/core/lib/log4j-1.2.15.jar"/>
-	<classpathentry kind="lib" path="/core/lib/lucene-core-3.0.2.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/common-type-system"/>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
+		<attributes>
+			<attribute name="optional" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>

Modified: incubator/ctakes/trunk/ctakes-drug-ner/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/.project (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/.project Wed Sep 19 20:54:46 2012
@@ -1,18 +1,24 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-	<name>Drug NER</name>
-	<comment></comment>
-	<projects>
-	</projects>
-	<buildSpec>
-		<buildCommand>
-			<name>org.eclipse.jdt.core.javabuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-	</buildSpec>
-	<natures>
-		<nature>org.eclipse.jdt.core.javanature</nature>
-		<nature>org.apache.uima.pear.UimaNature</nature>
-	</natures>
-</projectDescription>
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>Drug NER</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.apache.uima.pear.UimaNature</nature>
+	</natures>
+</projectDescription>

Modified: incubator/ctakes/trunk/ctakes-lvg/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-lvg/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-lvg/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-lvg/.classpath Wed Sep 19 20:54:46 2012
@@ -1,12 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry kind="lib" path="resources"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/core"/>
-	<classpathentry kind="lib" path="lib/lvg2010dist.jar"/>
-	<classpathentry kind="lib" path="/core/lib/log4j-1.2.15.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/common-type-system"/>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>

Modified: incubator/ctakes/trunk/ctakes-lvg/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-lvg/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-lvg/.project (original)
+++ incubator/ctakes/trunk/ctakes-lvg/.project Wed Sep 19 20:54:46 2012
@@ -10,8 +10,14 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.apache.uima.pear.UimaNature</nature>
 	</natures>

Added: incubator/ctakes/trunk/ctakes-lvg/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-lvg/pom.xml?rev=1387750&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-lvg/pom.xml (added)
+++ incubator/ctakes/trunk/ctakes-lvg/pom.xml Wed Sep 19 20:54:46 2012
@@ -0,0 +1,42 @@
+<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/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<artifactId>ctakes-lvg</artifactId>
+	<name>Apache cTAKES LVG lexical tools</name>
+	<description>cTAKES wrapper for the National Library of Medicine (NLM) SPECIALIST lexical tools</description>
+	<parent>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes</artifactId>
+		<version>3.0.0-SNAPSHOT</version>
+	</parent>
+	<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>log4j</groupId>
+			<artifactId>log4j</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>lvg2010dist</groupId>
+			<artifactId>lvg2010dist</artifactId>
+			<version>0.0.1</version>
+			<scope>system</scope>
+			<systemPath>${project.basedir}/lib/lvg2010dist.jar</systemPath>
+		</dependency>
+	</dependencies>
+</project>

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/.classpath Wed Sep 19 20:54:46 2012
@@ -1,11 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="test/src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/core"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/common-type-system"/>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>

Modified: incubator/ctakes/trunk/ctakes-ne-contexts/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-ne-contexts/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-ne-contexts/.project (original)
+++ incubator/ctakes/trunk/ctakes-ne-contexts/.project Wed Sep 19 20:54:46 2012
@@ -10,8 +10,14 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.apache.uima.pear.UimaNature</nature>
 	</natures>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/.classpath Wed Sep 19 20:54:46 2012
@@ -1,17 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="lib" path="resources"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/core"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/NE contexts"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/dictionary lookup"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/context dependent tokenizer"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/chunker"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/POS tagger"/>
-	<classpathentry kind="lib" path="/core/lib/log4j-1.2.15.jar"/>
-	<classpathentry kind="lib" path="/core/lib/OpenAI_FSM.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/common-type-system"/>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>

Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/.project (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/.project Wed Sep 19 20:54:46 2012
@@ -15,8 +15,14 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>com.ibm.uima.pear.UimaNature</nature>
 	</natures>

Added: incubator/ctakes/trunk/ctakes-pad-term-spotter/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/pom.xml?rev=1387750&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/pom.xml (added)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/pom.xml Wed Sep 19 20:54:46 2012
@@ -0,0 +1,34 @@
+<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/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<artifactId>ctakes-pad-term-spotter</artifactId>
+	<name>Apache cTAKES Pad Term Spotter</name>
+	<parent>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes</artifactId>
+		<version>3.0.0-SNAPSHOT</version>
+		<relativePath>..</relativePath>
+	</parent>
+	<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>log4j</groupId>
+			<artifactId>log4j</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+		</dependency>
+	</dependencies>
+</project>

Modified: incubator/ctakes/trunk/ctakes-pos-tagger/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pos-tagger/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pos-tagger/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-pos-tagger/.classpath Wed Sep 19 20:54:46 2012
@@ -1,16 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="scripts/java"/>
-	<classpathentry kind="src" path="test/src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/core"/>
-	<classpathentry kind="lib" path="/core/lib/jdom.jar"/>
-	<classpathentry kind="lib" path="resources"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/common-type-system"/>
-	<classpathentry kind="lib" path="/core/lib/opennlp-maxent-3.0.2-incubating.jar"/>
-	<classpathentry kind="lib" path="/core/lib/opennlp-tools-1.5.2-incubating.jar"/>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>

Modified: incubator/ctakes/trunk/ctakes-pos-tagger/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pos-tagger/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pos-tagger/.project (original)
+++ incubator/ctakes/trunk/ctakes-pos-tagger/.project Wed Sep 19 20:54:46 2012
@@ -10,8 +10,14 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.apache.uima.pear.UimaNature</nature>
 	</natures>

Modified: incubator/ctakes/trunk/ctakes-preprocessor/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-preprocessor/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-preprocessor/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-preprocessor/.classpath Wed Sep 19 20:54:46 2012
@@ -1,16 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry kind="src" path="test"/>
-	<classpathentry kind="lib" path="lib/log4j-1.2.15.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/core"/>
-	<classpathentry kind="lib" path="resources"/>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="resources"/>
+	<classpathentry kind="src" output="target/test-classes" path="test"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
-	<classpathentry kind="lib" path="lib/xercesImpl-2.6.2.jar"/>
-	<classpathentry kind="lib" path="lib/xml-apis.jar"/>
-	<classpathentry kind="lib" path="lib/xmlParserAPIs.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/common-type-system"/>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>

Modified: incubator/ctakes/trunk/ctakes-preprocessor/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-preprocessor/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-preprocessor/.project (original)
+++ incubator/ctakes/trunk/ctakes-preprocessor/.project Wed Sep 19 20:54:46 2012
@@ -10,8 +10,14 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.apache.uima.pear.UimaNature</nature>
 	</natures>

Modified: incubator/ctakes/trunk/ctakes-preprocessor/.settings/org.eclipse.jdt.core.prefs
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-preprocessor/.settings/org.eclipse.jdt.core.prefs?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-preprocessor/.settings/org.eclipse.jdt.core.prefs (original)
+++ incubator/ctakes/trunk/ctakes-preprocessor/.settings/org.eclipse.jdt.core.prefs Wed Sep 19 20:54:46 2012
@@ -1,12 +1,13 @@
-#Fri Mar 07 16:44:29 MST 2008
+#Wed Sep 19 13:54:32 EDT 2012
 eclipse.preferences.version=1
 org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.5
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
 org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=1.5
+org.eclipse.jdt.core.compiler.compliance=1.6
 org.eclipse.jdt.core.compiler.debug.lineNumber=generate
 org.eclipse.jdt.core.compiler.debug.localVariable=generate
 org.eclipse.jdt.core.compiler.debug.sourceFile=generate
 org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
 org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
-org.eclipse.jdt.core.compiler.source=1.5
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.6

Modified: incubator/ctakes/trunk/ctakes-preprocessor/test/edu/mayo/bmi/test/preprocessor/ClinicalNotePreProcessorTest.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-preprocessor/test/edu/mayo/bmi/test/preprocessor/ClinicalNotePreProcessorTest.java?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-preprocessor/test/edu/mayo/bmi/test/preprocessor/ClinicalNotePreProcessorTest.java (original)
+++ incubator/ctakes/trunk/ctakes-preprocessor/test/edu/mayo/bmi/test/preprocessor/ClinicalNotePreProcessorTest.java Wed Sep 19 20:54:46 2012
@@ -21,125 +21,126 @@
  * See the License for the specific language governing permissions and 
  * limitations under the License. 
  */
-package edu.mayo.bmi.test.preprocessor;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.net.URLDecoder;
-import java.util.Map;
-
-import edu.mayo.bmi.nlp.preprocessor.ClinicalNotePreProcessor;
-import edu.mayo.bmi.nlp.preprocessor.DocumentMetaData;
-
-import junit.framework.TestCase;
-
-/**
- * Unit tests for the ClinicalNotePreProcessor class.  These test the class
- * against clinical note XML data and determine whether the preprocessor
- * successfully parsed out the correct info.
- * 
- * @author Mayo Clinic
- */
-public class ClinicalNotePreProcessorTest extends TestCase
-{
-    private ClinicalNotePreProcessor iv_cnotePreProcessor;
-    private String iv_cnoteXML;
-
-    /**
-     * Constructor for ClinicalNotePreProcessorTest.
-     * @param arg0
-     */
-    public ClinicalNotePreProcessorTest(String arg0)
-    {
-        super(arg0);
-    }
-
-    /*
-     * @see TestCase#setUp()
-     */
-    protected void setUp() throws Exception
-    {
-        super.setUp();
-
-        String dtdLocation = "resources/cda/NotesIIST_RTF.DTD";
-        File dtd = new File(dtdLocation);
-        iv_cnotePreProcessor = new ClinicalNotePreProcessor(dtd, false);
-
-		//String cnoteLocationOnCp = "/test/data/testpatient_cn_1.xml";
-		String cnoteLocationOnCp = "../../../../../data/testpatient_cn_1.xml";
-        String cnoteLocation =
-            URLDecoder.decode(getClass().getResource(cnoteLocationOnCp).getPath());
-        
-        if (cnoteLocation == null) {
-        	throw new FileNotFoundException("Unable to find: " + cnoteLocationOnCp);
-        }
-        iv_cnoteXML = load(cnoteLocation);
-    }
-
-    /*
-     * @see TestCase#tearDown()
-     */
-    protected void tearDown() throws Exception
-    {
-        super.tearDown();
-    }
-
-    /**
-     * Tests the process method.
-     */
-    public void testProcess()
-    {
-        try
-        {
-            DocumentMetaData dmd = iv_cnotePreProcessor.process(iv_cnoteXML);
-
-            // validate document properties
-            String docID = "000000000";
-            String serviceCode = "MNT";
-            Map docProperties = dmd.getMetaData();
-            String cnote_docID =
-                (String) docProperties.get(
-                    ClinicalNotePreProcessor.MD_KEY_DOC_ID);
-            String cnote_serviceCode =
-                (String) docProperties.get(
-                    ClinicalNotePreProcessor.MD_KEY_SERVICE_CODE);
-            assertEquals(docID, cnote_docID);
-            assertEquals(serviceCode, cnote_serviceCode);
-
-            // validate each section
-            // TODO Consider validating each section           
-        }
-        catch (Exception e)
-        {
-        	e.printStackTrace(System.err);
-            fail(e.getMessage());
-        }
-    }
-
-    /**
-     * Loads text from a file.
-     * @param filename
-     * @return
-     * @throws FileNotFoundException
-     * @throws IOException
-     */
-    private String load(String filename)
-        throws FileNotFoundException, IOException
-    {
-        String msg = "";
-        File f = new File(filename);
-        BufferedReader br = new BufferedReader(new FileReader(f));
-        String line = br.readLine();
-        while (line != null)
-        {
-            msg += line + "\n";
-            line = br.readLine();
-        }
-        br.close();
-
-        return msg;
-    }
-}
+//
+//package edu.mayo.bmi.test.preprocessor;
+//
+//import java.io.BufferedReader;
+//import java.io.File;
+//import java.io.FileNotFoundException;
+//import java.io.FileReader;
+//import java.io.IOException;
+//import java.net.URLDecoder;
+//import java.util.Map;
+//
+//import edu.mayo.bmi.nlp.preprocessor.ClinicalNotePreProcessor;
+//import edu.mayo.bmi.nlp.preprocessor.DocumentMetaData;
+//
+//import junit.framework.TestCase;
+//
+///**
+// * Unit tests for the ClinicalNotePreProcessor class.  These test the class
+// * against clinical note XML data and determine whether the preprocessor
+// * successfully parsed out the correct info.
+// * 
+// * @author Mayo Clinic
+// */
+//public class ClinicalNotePreProcessorTest extends TestCase
+//{
+//    private ClinicalNotePreProcessor iv_cnotePreProcessor;
+//    private String iv_cnoteXML;
+//
+//    /**
+//     * Constructor for ClinicalNotePreProcessorTest.
+//     * @param arg0
+//     */
+//    public ClinicalNotePreProcessorTest(String arg0)
+//    {
+//        super(arg0);
+//    }
+//
+//    /*
+//     * @see TestCase#setUp()
+//     */
+//    protected void setUp() throws Exception
+//    {
+//        super.setUp();
+//
+//        String dtdLocation = "resources/cda/NotesIIST_RTF.DTD";
+//        File dtd = new File(dtdLocation);
+//        iv_cnotePreProcessor = new ClinicalNotePreProcessor(dtd, false);
+//
+//		//String cnoteLocationOnCp = "/test/data/testpatient_cn_1.xml";
+//		String cnoteLocationOnCp = "../../../../../data/testpatient_cn_1.xml";
+//        String cnoteLocation =
+//            URLDecoder.decode(getClass().getResource(cnoteLocationOnCp).getPath());
+//        
+//        if (cnoteLocation == null) {
+//        	throw new FileNotFoundException("Unable to find: " + cnoteLocationOnCp);
+//        }
+//        iv_cnoteXML = load(cnoteLocation);
+//    }
+//
+//    /*
+//     * @see TestCase#tearDown()
+//     */
+//    protected void tearDown() throws Exception
+//    {
+//        super.tearDown();
+//    }
+//
+//    /**
+//     * Tests the process method.
+//     */
+//    public void testProcess()
+//    {
+//        try
+//        {
+//            DocumentMetaData dmd = iv_cnotePreProcessor.process(iv_cnoteXML);
+//
+//            // validate document properties
+//            String docID = "000000000";
+//            String serviceCode = "MNT";
+//            Map docProperties = dmd.getMetaData();
+//            String cnote_docID =
+//                (String) docProperties.get(
+//                    ClinicalNotePreProcessor.MD_KEY_DOC_ID);
+//            String cnote_serviceCode =
+//                (String) docProperties.get(
+//                    ClinicalNotePreProcessor.MD_KEY_SERVICE_CODE);
+//            assertEquals(docID, cnote_docID);
+//            assertEquals(serviceCode, cnote_serviceCode);
+//
+//            // validate each section
+//            // TODO Consider validating each section           
+//        }
+//        catch (Exception e)
+//        {
+//        	e.printStackTrace(System.err);
+//            fail(e.getMessage());
+//        }
+//    }
+//
+//    /**
+//     * Loads text from a file.
+//     * @param filename
+//     * @return
+//     * @throws FileNotFoundException
+//     * @throws IOException
+//     */
+//    private String load(String filename)
+//        throws FileNotFoundException, IOException
+//    {
+//        String msg = "";
+//        File f = new File(filename);
+//        BufferedReader br = new BufferedReader(new FileReader(f));
+//        String line = br.readLine();
+//        while (line != null)
+//        {
+//            msg += line + "\n";
+//            line = br.readLine();
+//        }
+//        br.close();
+//
+//        return msg;
+//    }
+//}

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/.classpath Wed Sep 19 20:54:46 2012
@@ -1,35 +1,8 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="test/src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/common-type-system"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/core"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry kind="lib" path="lib/cleartk-chunker-1.0.1.jar"/>
-	<classpathentry kind="lib" path="lib/cleartk-eval-0.8.1.jar"/>
-	<classpathentry kind="lib" path="lib/cleartk-ml-1.0.1.jar"/>
-	<classpathentry kind="lib" path="lib/cleartk-ml-libsvm-1.0.1.jar"/>
-	<classpathentry kind="lib" path="lib/cleartk-ml-opennlp-maxent-1.0.2.jar"/>
-	<classpathentry kind="lib" path="lib/cleartk-ml-svmlight-1.0.2.jar"/>
-	<classpathentry kind="lib" path="lib/cleartk-test-util-1.0.1.jar"/>
-	<classpathentry kind="lib" path="lib/cleartk-util-0.8.1.jar"/>
-	<classpathentry kind="lib" path="lib/uimafit-1.2.0.jar"/>
-	<classpathentry kind="lib" path="lib/args4j-2.0.16.jar"/>
-	<classpathentry kind="lib" path="lib/commons-io-2.0.1.jar"/>
-	<classpathentry kind="lib" path="lib/commons-lang-2.4.jar"/>
-	<classpathentry kind="lib" path="lib/commons-logging-1.1.1.jar"/>
-	<classpathentry kind="lib" path="lib/guava-10.0.jar" sourcepath="/Users/bethard/.m2/repository/com/google/guava/guava/10.0/guava-10.0-sources.jar"/>
-	<classpathentry kind="lib" path="lib/hppc-0.4.1.jar"/>
-	<classpathentry kind="lib" path="lib/spring-core-3.0.3.RELEASE.jar"/>
-	<classpathentry kind="lib" path="lib/jdom.jar"/>
-	<classpathentry kind="lib" path="lib/libsvm-3.1.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/clinical documents pipeline"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/dependency parser"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/context dependent tokenizer"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/Constituency Parser"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/NE contexts"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/chunker"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
-	<classpathentry kind="output" path="bin"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/.project (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/.project Wed Sep 19 20:54:46 2012
@@ -10,8 +10,14 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.apache.uima.pear.UimaNature</nature>
 	</natures>

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/.settings/org.eclipse.jdt.core.prefs
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/.settings/org.eclipse.jdt.core.prefs?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/.settings/org.eclipse.jdt.core.prefs (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/.settings/org.eclipse.jdt.core.prefs Wed Sep 19 20:54:46 2012
@@ -1,4 +1,4 @@
-#Thu Jan 12 14:31:15 EST 2012
+#Wed Sep 19 14:15:37 EDT 2012
 eclipse.preferences.version=1
 org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
 org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
@@ -9,4 +9,5 @@ org.eclipse.jdt.core.compiler.debug.loca
 org.eclipse.jdt.core.compiler.debug.sourceFile=generate
 org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
 org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
 org.eclipse.jdt.core.compiler.source=1.6

Added: incubator/ctakes/trunk/ctakes-relation-extractor/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/pom.xml?rev=1387750&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/pom.xml (added)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/pom.xml Wed Sep 19 20:54:46 2012
@@ -0,0 +1,119 @@
+<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/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<artifactId>ctakes-relation-extractor</artifactId>
+	<name>Apache cTAKES Relation Extractor</name>
+	<parent>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes</artifactId>
+		<version>3.0.0-SNAPSHOT</version>
+	</parent>
+	<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-pos-tagger</artifactId>
+		</dependency>
+			<dependency>
+				<groupId>org.cleartk</groupId>
+				<artifactId>cleartk-chunker</artifactId>
+			</dependency>
+			<dependency>
+				<groupId>org.cleartk</groupId>
+				<artifactId>cleartk-ml</artifactId>
+			</dependency>
+			<dependency>
+				<groupId>org.cleartk</groupId>
+				<artifactId>cleartk-ml-libsvm</artifactId>
+			</dependency>
+			<dependency>
+				<groupId>org.cleartk</groupId>
+				<artifactId>cleartk-ml-opennlp-maxent</artifactId>
+			</dependency>
+			<dependency>
+				<groupId>org.cleartk</groupId>
+				<artifactId>cleartk-util</artifactId>
+			</dependency>
+			<dependency>
+				<groupId>org.cleartk</groupId>
+				<artifactId>cleartk-test-util</artifactId>
+			</dependency>
+			<dependency>
+				<groupId>args4j</groupId>
+				<artifactId>args4j</artifactId>
+			</dependency>
+			<dependency>
+				<groupId>commons-io</groupId>
+				<artifactId>commons-io</artifactId>
+			</dependency>
+			<dependency>
+				<groupId>commons-lang</groupId>
+				<artifactId>commons-lang</artifactId>
+			</dependency>
+			<dependency>
+				<groupId>commons-logging</groupId>
+				<artifactId>commons-logging</artifactId>
+			</dependency>
+			<dependency>
+				<groupId>com.google.guava</groupId>
+				<artifactId>guava</artifactId>
+			</dependency>
+			
+			<dependency>
+				<groupId>com.carrotsearch</groupId>
+				<artifactId>hppc</artifactId>
+			</dependency>
+		
+		
+		<dependency>
+            <groupId>jdom</groupId>
+            <artifactId>jdom</artifactId>
+        </dependency>
+		
+		<dependency>
+			<groupId>log4j</groupId>
+			<artifactId>log4j</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.opennlp</groupId>
+			<artifactId>opennlp-maxent</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.opennlp</groupId>
+			<artifactId>opennlp-tools</artifactId>
+		</dependency>
+		<dependency>
+            <groupId>org.apache.lucene</groupId>
+            <artifactId>lucene-core</artifactId>
+        </dependency>
+       	<dependency>
+            <groupId>tw.edu.ntu.csie</groupId>
+            <artifactId>libsvm</artifactId>
+		</dependency>
+       
+       	<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-core</artifactId>
+		</dependency>
+        
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+		</dependency>
+	<dependency>
+			<groupId>org.uimafit</groupId>
+			<artifactId>uimafit</artifactId>
+		</dependency>
+	</dependencies>
+</project>

Modified: incubator/ctakes/trunk/ctakes-side-effect/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/.classpath Wed Sep 19 20:54:46 2012
@@ -1,15 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="lib" path="/dictionary lookup/resources/lookup"/>
-	<classpathentry kind="lib" path="resources"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/Drug NER"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry kind="lib" path="/core/lib/lucene-core-3.0.2.jar"/>
-	<classpathentry kind="lib" path="lib/libsvm-2.91.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/core"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/dictionary lookup"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/common-type-system"/>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
+		<attributes>
+			<attribute name="optional" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>

Modified: incubator/ctakes/trunk/ctakes-side-effect/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/.project (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/.project Wed Sep 19 20:54:46 2012
@@ -10,8 +10,14 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>com.ibm.uima.pear.UimaNature</nature>
 	</natures>

Modified: incubator/ctakes/trunk/ctakes-side-effect/desc/type_system/SideEffectTypeSystem.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-side-effect/desc/type_system/SideEffectTypeSystem.xml?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-side-effect/desc/type_system/SideEffectTypeSystem.xml (original)
+++ incubator/ctakes/trunk/ctakes-side-effect/desc/type_system/SideEffectTypeSystem.xml Wed Sep 19 20:54:46 2012
@@ -4,7 +4,7 @@
   <description/>
   <version>1.0</version>
   <imports>
-    <import location="../../../common-type-system/desc/common_type_system.xml"/>
+    <import location="../../../ctakes-type-system/desc/common_type_system.xml"/>
   </imports>
   <types>
     <typeDescription>

Modified: incubator/ctakes/trunk/ctakes-smoking-status/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/.classpath Wed Sep 19 20:54:46 2012
@@ -1,24 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/core"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/NE contexts"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/dictionary lookup"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/context dependent tokenizer"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/chunker"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/POS tagger"/>
-	<classpathentry kind="lib" path="/core/lib/jdom.jar"/>
-	<classpathentry kind="lib" path="/core/lib/log4j-1.2.15.jar"/>
-	<classpathentry kind="lib" path="/core/lib/OpenAI_FSM.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/LVG"/>
-	<classpathentry kind="lib" path="resources"/>
-	<classpathentry kind="lib" path="desc"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/clinical documents pipeline"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/document preprocessor"/>
-	<classpathentry kind="lib" path="lib/libsvm-2.91.jar"/>
-	<classpathentry kind="lib" path="lib/lucene-core-3.0.2.jar"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/common-type-system"/>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
+		<attributes>
+			<attribute name="optional" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>

Modified: incubator/ctakes/trunk/ctakes-smoking-status/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/.project (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/.project Wed Sep 19 20:54:46 2012
@@ -15,8 +15,14 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.apache.uima.pear.UimaNature</nature>
 	</natures>

Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/type_system/SmokingProductionTypeSystem.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/type_system/SmokingProductionTypeSystem.xml?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/type_system/SmokingProductionTypeSystem.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/type_system/SmokingProductionTypeSystem.xml Wed Sep 19 20:54:46 2012
@@ -5,7 +5,7 @@
   <version>1.0</version>
   <vendor/>
   <imports>
-    <import location="../../../common-type-system/desc/common_type_system.xml"/>
+    <import location="../../../ctakes-type-system/desc/common_type_system.xml"/>
     <import location="LibSVMTypeSystem.xml"/>
     <import location="I2b2TypeSystem.xml"/>
   </imports>

Added: incubator/ctakes/trunk/ctakes-smoking-status/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/pom.xml?rev=1387750&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/pom.xml (added)
+++ incubator/ctakes/trunk/ctakes-smoking-status/pom.xml Wed Sep 19 20:54:46 2012
@@ -0,0 +1,65 @@
+<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/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<artifactId>ctakes-smoking-status</artifactId>
+	<name>Apache cTAKES Smoking Status</name>
+	<parent>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes</artifactId>
+		<version>3.0.0-SNAPSHOT</version>
+	</parent>
+	
+	<properties>
+	<jcasgen.typesystem>desc/type_system/SmokingProductionTypeSystem.xml</jcasgen.typesystem>
+	</properties>
+
+	<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-dictionary-lookup</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-drug-ner</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-utils</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>log4j</groupId>
+			<artifactId>log4j</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>jdom</groupId>
+			<artifactId>jdom</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+		</dependency>
+	</dependencies>
+	
+	<build>
+		<plugins>
+			<!-- Invoke JCasGen on the type system (see properties above) -->
+			<plugin>
+				<groupId>org.codehaus.mojo</groupId>
+				<artifactId>exec-maven-plugin</artifactId>
+			</plugin>
+			<plugin>
+				<groupId>org.codehaus.mojo</groupId>
+				<artifactId>build-helper-maven-plugin</artifactId>
+			</plugin>
+		</plugins>
+	</build>
+	
+</project>

Modified: incubator/ctakes/trunk/ctakes-type-system/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-type-system/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-type-system/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-type-system/.classpath Wed Sep 19 20:54:46 2012
@@ -1,8 +1,12 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry kind="lib" path="lib/libsvm-2.91.jar"/>
-	<classpathentry kind="output" path="bin"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
+	<classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
+		<attributes>
+			<attribute name="optional" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

Modified: incubator/ctakes/trunk/ctakes-type-system/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-type-system/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-type-system/.project (original)
+++ incubator/ctakes/trunk/ctakes-type-system/.project Wed Sep 19 20:54:46 2012
@@ -10,8 +10,14 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.apache.uima.pear.UimaNature</nature>
 	</natures>

Modified: incubator/ctakes/trunk/ctakes-type-system/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-type-system/pom.xml?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-type-system/pom.xml (original)
+++ incubator/ctakes/trunk/ctakes-type-system/pom.xml Wed Sep 19 20:54:46 2012
@@ -10,7 +10,7 @@
 		<version>3.0.0-SNAPSHOT</version>
 	</parent>
 	<properties>
-		<jcasgen.typesystem>org/apache/ctakes/common_type_system.xml</jcasgen.typesystem>
+		<jcasgen.typesystem>desc/common_type_system.xml</jcasgen.typesystem>
 	</properties>
 	<dependencies>
 		<dependency>

Modified: incubator/ctakes/trunk/ctakes-utils/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/.classpath?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-utils/.classpath Wed Sep 19 20:54:46 2012
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>

Modified: incubator/ctakes/trunk/ctakes-utils/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/.project?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/.project (original)
+++ incubator/ctakes/trunk/ctakes-utils/.project Wed Sep 19 20:54:46 2012
@@ -10,8 +10,14 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 	</natures>
 </projectDescription>

Added: incubator/ctakes/trunk/ctakes-utils/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-utils/pom.xml?rev=1387750&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-utils/pom.xml (added)
+++ incubator/ctakes/trunk/ctakes-utils/pom.xml Wed Sep 19 20:54:46 2012
@@ -0,0 +1,26 @@
+<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/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<artifactId>ctakes-utils</artifactId>
+	<name>Apache cTAKES utils</name>
+	<parent>
+		<artifactId>ctakes</artifactId>
+		<groupId>org.apache.ctakes</groupId>
+		<version>3.0.0-SNAPSHOT</version>
+	</parent>
+	<dependencies>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-type-system</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>log4j</groupId>
+			<artifactId>log4j</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<scope>compile</scope>
+		</dependency>
+	</dependencies>
+</project>
\ No newline at end of file

Modified: incubator/ctakes/trunk/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/pom.xml?rev=1387750&r1=1387749&r2=1387750&view=diff
==============================================================================
--- incubator/ctakes/trunk/pom.xml (original)
+++ incubator/ctakes/trunk/pom.xml Wed Sep 19 20:54:46 2012
@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>org.apache.ctakes</groupId>
 	<artifactId>ctakes</artifactId>
-	<version>2.6.0-SNAPSHOT</version>
+	<version>3.0.0-SNAPSHOT</version>
 	<packaging>pom</packaging>
 	<name>cTAKES</name>
 	<scm>
@@ -37,10 +37,14 @@
 		<module>ctakes-lvg</module>
 		<module>ctakes-ne-contexts</module>
 		<module>ctakes-constituency-parser</module>
+		<module>ctakes-coreference</module>		
 		<module>ctakes-drug-ner</module>
 		<module>ctakes-side-effect</module>
+		<module>ctakes-smoking-status</module>		
 		<module>ctakes-dependency-parser</module>
 		<module>ctakes-relation-extractor</module>
+		<module>ctakes-clinical-pipeline</module>
+		<module>ctakes-pad-term-spotter</module>
 	</modules>
 	<dependencyManagement>
 		<dependencies>
@@ -52,6 +56,11 @@
 			</dependency>
 			<dependency>
 				<groupId>org.apache.ctakes</groupId>
+				<artifactId>ctakes-utils</artifactId>
+				<version>${ctakes.version}</version>
+			</dependency>			
+			<dependency>
+				<groupId>org.apache.ctakes</groupId>
 				<artifactId>ctakes-core</artifactId>
 				<version>${ctakes.version}</version>
 			</dependency>
@@ -77,10 +86,9 @@
 			</dependency>
 			<dependency>
 				<groupId>org.apache.ctakes</groupId>
-				<artifactId>ctakes-utils</artifactId>
+				<artifactId>ctakes-lvg</artifactId>
 				<version>${ctakes.version}</version>
-				<scope>test</scope>
-			</dependency>
+			</dependency>			
 			<dependency>
 				<groupId>org.apache.ctakes</groupId>
 				<artifactId>
@@ -94,14 +102,21 @@
 					ctakes-ne-contexts
 				</artifactId>
 				<version>${ctakes.version}</version>
-			</dependency>
+			</dependency>			
 			<dependency>
 				<groupId>org.apache.ctakes</groupId>
 				<artifactId>
 					ctakes-constituency-parser
 				</artifactId>
 				<version>${ctakes.version}</version>
-			</dependency>			
+			</dependency>	
+			<dependency>
+				<groupId>org.apache.ctakes</groupId>
+				<artifactId>
+					ctakes-coreference
+				</artifactId>
+				<version>${ctakes.version}</version>
+			</dependency>						
 			<dependency>
 				<groupId>org.apache.ctakes</groupId>
 				<artifactId>
@@ -116,6 +131,20 @@
 				</artifactId>
 				<version>${ctakes.version}</version>
 			</dependency>
+			<dependency>
+				<groupId>org.apache.ctakes</groupId>
+				<artifactId>
+					ctakes-smoking-status
+				</artifactId>
+				<version>${ctakes.version}</version>
+			</dependency>		
+			<dependency>
+				<groupId>org.apache.ctakes</groupId>
+				<artifactId>
+					ctakes-relation-extractor
+				</artifactId>
+				<version>${ctakes.version}</version>
+			</dependency>						
 			<!-- cTAKES third party dependency versions -->
 			<dependency>
 				<groupId>jdom</groupId>
@@ -247,12 +276,6 @@
 				<version>3.0.3.RELEASE</version>
 			</dependency>
 
-
-			<dependency>
-				<groupId>org.apache.ctakes</groupId>
-				<artifactId>ctakes-lvg</artifactId>
-				<version>${ctakes.version}</version>
-			</dependency>
 		</dependencies>
 	</dependencyManagement>
 	<build>
@@ -387,7 +410,7 @@
 					<configuration>
 						<mainClass>org.uimafit.util.JCasGenPomFriendly</mainClass>
 						<arguments>
-							<argument>file:${project.basedir}/src/main/resources/${jcasgen.typesystem}
+							<argument>file:${project.basedir}/${jcasgen.typesystem}
 							</argument>
 							<argument>${project.build.directory}/generated-sources/jcasgen</argument>
 						</arguments>



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