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From seanfi...@apache.org
Subject svn commit: r1800177 - in /ctakes/trunk: ctakes-assertion-zoner/ ctakes-assertion/ ctakes-chunker/ ctakes-clinical-pipeline/ ctakes-constituency-parser/ ctakes-context-tokenizer/ ctakes-core/ ctakes-coreference/ ctakes-dependency-parser/ ctakes-diction...
Date Wed, 28 Jun 2017 14:47:27 GMT
Author: seanfinan
Date: Wed Jun 28 14:47:27 2017
New Revision: 1800177

URL: http://svn.apache.org/viewvc?rev=1800177&view=rev
Log:
CTAKES-443 : stop rebuilding the type system for every module
CTAKES-448 : dependency tree is a mess

Modified:
    ctakes/trunk/ctakes-assertion-zoner/pom.xml
    ctakes/trunk/ctakes-assertion/pom.xml
    ctakes/trunk/ctakes-chunker/pom.xml
    ctakes/trunk/ctakes-clinical-pipeline/pom.xml
    ctakes/trunk/ctakes-constituency-parser/pom.xml
    ctakes/trunk/ctakes-context-tokenizer/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-drug-ner/pom.xml
    ctakes/trunk/ctakes-gui/pom.xml
    ctakes/trunk/ctakes-lvg/pom.xml
    ctakes/trunk/ctakes-ne-contexts/pom.xml
    ctakes/trunk/ctakes-pos-tagger/pom.xml
    ctakes/trunk/ctakes-regression-test/pom.xml
    ctakes/trunk/ctakes-relation-extractor/pom.xml
    ctakes/trunk/ctakes-side-effect/pom.xml
    ctakes/trunk/ctakes-smoking-status/pom.xml
    ctakes/trunk/ctakes-template-filler/pom.xml
    ctakes/trunk/ctakes-temporal/pom.xml
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CompareFeatureStructures.java
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintInconsistentAnnotations.java
    ctakes/trunk/ctakes-type-system/pom.xml
    ctakes/trunk/ctakes-utils/pom.xml
    ctakes/trunk/ctakes-ytex-uima/pom.xml
    ctakes/trunk/ctakes-ytex/pom.xml

Modified: ctakes/trunk/ctakes-assertion-zoner/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner/pom.xml (original)
+++ ctakes/trunk/ctakes-assertion-zoner/pom.xml Wed Jun 28 14:47:27 2017
@@ -38,23 +38,26 @@
 			<artifactId>mastif-zoner</artifactId>
 			<version>1.4</version>
 		</dependency>
-		<dependency>
-      <groupId>org.apache.uima</groupId>
-      <artifactId>uimaj-core</artifactId>
-		</dependency>
+        <!--  uimaj core is added by core (via utils).  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.uima</groupId>-->
+        <!--<artifactId>uimaj-core</artifactId>-->
+        <!--</dependency>-->
 		<!-- we excluded spring-context uimafit transitive dependency in the parent pom, include it here -->
-		<dependency>
-				<groupId>org.springframework</groupId>
-				<artifactId>spring-context</artifactId>
-		</dependency>
+        <!--  Spring context is added by core (via type system).  -->
+        <!--<dependency>-->
+        <!--<groupId>org.springframework</groupId>-->
+        <!--<artifactId>spring-context</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
       <groupId>org.apache.ctakes</groupId>
       <artifactId>ctakes-core</artifactId>
     </dependency>
-		<dependency>
-			<groupId>org.apache.uima</groupId>
-			<artifactId>uimafit-core</artifactId>
-		</dependency>
+        <!--  uimafit core is added by core (via type system).  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.uima</groupId>-->
+        <!--<artifactId>uimafit-core</artifactId>-->
+        <!--</dependency>-->
 	</dependencies>
 	<build>
 		<plugins>
@@ -67,9 +70,10 @@
 				      <goals><goal>generate</goal></goals>
 				      <configuration>
 				        <typeSystemIncludes>
-				          <typeSystemInclude>src/main/resources/org/apache/ctakes/**/types/TypeSystem.xml</typeSystemInclude>				          
+                            <typeSystemInclude>src/main/resources/org/apache/ctakes/**/types/TypeSystem.xml
+                            </typeSystemInclude>
 				        </typeSystemIncludes>
-				        <limitToProject>false</limitToProject>
+                          <limitToProject>true</limitToProject>
 				      </configuration>
 				    </execution>
 				    </executions>

Modified: ctakes/trunk/ctakes-assertion/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/pom.xml (original)
+++ ctakes/trunk/ctakes-assertion/pom.xml Wed Jun 28 14:47:27 2017
@@ -32,19 +32,21 @@
 	<dependency>
 		<groupId>org.apache.ctakes</groupId>
 		<artifactId>ctakes-assertion-res</artifactId>
-	</dependency>	    
-	<dependency>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes-core</artifactId>
 	</dependency>
+        <!--  Core added by Constituency parser, context tokenizer, chunker and dependency parser (via pos tagger).  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-core</artifactId>-->
+        <!--</dependency>-->
     <dependency>
       <groupId>org.apache.ctakes</groupId>
       <artifactId>ctakes-constituency-parser</artifactId>
     </dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-pos-tagger</artifactId>
-		</dependency>
+        <!--  pos tagger added by Dependency parser and Chunker.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-pos-tagger</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-dependency-parser</artifactId>
@@ -60,27 +62,22 @@
 		<dependency>
 			<groupId>org.cleartk</groupId>
 			<artifactId>cleartk-eval</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>
+        <!--  args4j added by dependency parser.  -->
+        <!--<dependency>-->
+        <!--<groupId>args4j</groupId>-->
+        <!--<artifactId>args4j</artifactId>-->
+        <!--</dependency>-->
+        <!--  commons-lang added by dependency parser.  -->
+        <!--<dependency>-->
+        <!--<groupId>commons-lang</groupId>-->
+        <!--<artifactId>commons-lang</artifactId>-->
+        <!--</dependency>-->
+        <!--  commons-lang added by dependency parser.  -->
+        <!--<dependency>-->
+        <!--<groupId>commons-logging</groupId>-->
+        <!--<artifactId>commons-logging</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>commons-cli</groupId>
 			<artifactId>commons-cli</artifactId>
@@ -89,23 +86,21 @@
 			<groupId>com.carrotsearch</groupId>
 			<artifactId>hppc</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.opennlp</groupId>
-			<artifactId>opennlp-tools</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.opennlp</groupId>
-			<artifactId>opennlp-maxent</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.lucene</groupId>
-			<artifactId>lucene-core</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>tw.edu.ntu.csie</groupId>
-			<artifactId>libsvm</artifactId>
-		</dependency>
-
+        <!--  lucene core added by dependency parser.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.lucene</groupId>-->
+        <!--<artifactId>lucene-core</artifactId>-->
+        <!--</dependency>-->
+		<dependency>
+            <groupId>org.apache.uima</groupId>
+            <artifactId>uimaj-document-annotation</artifactId>
+            <version>2.9.0</version>
+		</dependency>
+        <!--  libsvm added by type system.  -->
+        <!--<dependency>-->
+        <!--<groupId>tw.edu.ntu.csie</groupId>-->
+        <!--<artifactId>libsvm</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>org.springframework</groupId>
 			<artifactId>spring-core</artifactId>
@@ -132,11 +127,11 @@
 			<artifactId>sbinary_2.9.0</artifactId>
 			<version>0.4.0</version>
 		</dependency>
-
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-lvg</artifactId>
-		</dependency>
+        <!--  LVG added by dependency parser.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-lvg</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-context-tokenizer</artifactId>
@@ -145,10 +140,12 @@
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-chunker</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-relation-extractor</artifactId>
-		</dependency>
+        <!--  assertion does not depend upon ctakes-relation-extractor.  It uses relation types in:
+         JudgeAttributeInstances and MiPACQKnowtatorXMLReader -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-relation-extractor</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>org.cleartk</groupId>
 			<artifactId>cleartk-ml-liblinear</artifactId>
@@ -165,9 +162,10 @@
 				      <goals><goal>generate</goal></goals>
 				      <configuration>
 				        <typeSystemIncludes>
-				          <typeSystemInclude>src/main/resources/org/apache/ctakes/**/types/TypeSystem.xml</typeSystemInclude>				          
+                            <typeSystemInclude>src/main/resources/org/apache/ctakes/**/types/TypeSystem.xml
+                            </typeSystemInclude>
 				        </typeSystemIncludes>
-				        <limitToProject>false</limitToProject>
+                          <limitToProject>true</limitToProject>
 				      </configuration>
 				    </execution>
 				    </executions>

Modified: ctakes/trunk/ctakes-chunker/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-chunker/pom.xml (original)
+++ ctakes/trunk/ctakes-chunker/pom.xml Wed Jun 28 14:47:27 2017
@@ -32,38 +32,45 @@
       	<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-chunker-res</artifactId>
-		</dependency>		      
-		<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>
+        <!--  type system is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-type-system</artifactId>-->
+        <!--</dependency>-->
+        <!--  core is added by pos tagger.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-core</artifactId>-->
+        <!--</dependency>-->
+        <!--  utils is added by core.  -->
+        <!--<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>log4j</groupId>
-			<artifactId>log4j</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.opennlp</groupId>
-			<artifactId>opennlp-tools</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.opennlp</groupId>
-			<artifactId>opennlp-maxent</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-		</dependency>
+        <!--  log4j is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>log4j</groupId>-->
+        <!--<artifactId>log4j</artifactId>-->
+        <!--</dependency>-->
+        <!--  opennlp tools is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.opennlp</groupId>-->
+        <!--<artifactId>opennlp-tools</artifactId>-->
+        <!--</dependency>-->
+        <!--  opennlp maxent is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.opennlp</groupId>-->
+        <!--<artifactId>opennlp-maxent</artifactId>-->
+        <!--</dependency>-->
+        <!--  junit is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>junit</groupId>-->
+        <!--<artifactId>junit</artifactId>-->
+        <!--</dependency>-->
 	</dependencies>
 </project>

Modified: ctakes/trunk/ctakes-clinical-pipeline/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/pom.xml (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/pom.xml Wed Jun 28 14:47:27 2017
@@ -18,77 +18,63 @@
 		<artifactId>ctakes</artifactId>
 		<version>4.0.1-SNAPSHOT</version>
 	</parent>
-
-
 	<dependencies>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-core</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-utils</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-context-tokenizer</artifactId>
-		</dependency>
+        <!--  lookup contains core  -->
+        <dependency>
+            <groupId>org.apache.ctakes</groupId>
+            <artifactId>ctakes-dictionary-lookup-fast</artifactId>
+        </dependency>
+        <!--  Context Tokenizer added by Assertion.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-context-tokenizer</artifactId>-->
+        <!--</dependency>-->
+        <!--  Preprocessor not used by default pipeline.  -->
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-preprocessor</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-lvg</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-chunker</artifactId>
-		</dependency>
+        <!--  LVG not used by default pipeline.  -->
+        <!--  LVG added by Assertion.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-lvg</artifactId>-->
+        <!--</dependency>-->
+        <!--  Chunker added by Assertion.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-chunker</artifactId>-->
+        <!--</dependency>-->
+        <!--  NE contexts not used by default pipeline, can switch out for assertion.  -->
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-ne-contexts</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-pos-tagger</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-drug-ner</artifactId>
-		</dependency>		
+        <!--  POS Tagger added by Assertion (via dependency parser) and by Chunker.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-pos-tagger</artifactId>-->
+        <!--</dependency>-->
+        <!--  Drug NER not used by default pipeline.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-drug-ner</artifactId>-->
+        <!--</dependency>		-->
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-assertion</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-dependency-parser</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-ytex</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-ytex-res</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-ytex-uima</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-dictionary-lookup-fast</artifactId>
-		</dependency>
-        <dependency>
-            <groupId>org.apache.ctakes</groupId>
-            <artifactId>ctakes-constituency-parser</artifactId>
-        </dependency>
-        <dependency>
-          <groupId>org.apache.ctakes</groupId>
-        	<artifactId>ctakes-coreference</artifactId>
-        </dependency>
+        <!--  Dependency parser added by Assertion.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-dependency-parser</artifactId>-->
+        <!--</dependency>-->
+        <!--  ytex should depend upon ctakes-clinical-pipeline , not the other way around.  -->
+        <!--  Constituency parser added by Assertion.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-constituency-parser</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-clinical-pipeline-res</artifactId>

Modified: ctakes/trunk/ctakes-constituency-parser/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser/pom.xml (original)
+++ ctakes/trunk/ctakes-constituency-parser/pom.xml Wed Jun 28 14:47:27 2017
@@ -35,32 +35,12 @@
 		</dependency>	 	    
 		<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.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>
 	<build>
 		<plugins>
@@ -73,9 +53,10 @@
 				      <goals><goal>generate</goal></goals>
 				      <configuration>
 				        <typeSystemIncludes>
-				          <typeSystemInclude>src/main/resources/org/apache/ctakes/**/types/LabeledTree.xml</typeSystemInclude>				          
+                            <typeSystemInclude>src/main/resources/org/apache/ctakes/**/types/LabeledTree.xml
+                            </typeSystemInclude>
 				        </typeSystemIncludes>
-				        <limitToProject>false</limitToProject>
+                          <limitToProject>true</limitToProject>
 				      </configuration>
 				    </execution>
 				    </executions>

Modified: ctakes/trunk/ctakes-context-tokenizer/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-context-tokenizer/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-context-tokenizer/pom.xml (original)
+++ ctakes/trunk/ctakes-context-tokenizer/pom.xml Wed Jun 28 14:47:27 2017
@@ -29,26 +29,30 @@
 		<version>4.0.1-SNAPSHOT</version>
 	</parent>
 	<dependencies>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-type-system</artifactId>
-		</dependency>
+        <!--  type system is added by core.  -->
+        <!--<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>
+        <!--  utils is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-utils</artifactId>-->
+        <!--</dependency>-->
+        <!--  log4j is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>log4j</groupId>-->
+        <!--<artifactId>log4j</artifactId>-->
+        <!--</dependency>-->
+        <!--  junit is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>junit</groupId>-->
+        <!--<artifactId>junit</artifactId>-->
+        <!--<scope>test</scope>-->
+        <!--</dependency>-->
 	</dependencies>
 </project>

Modified: ctakes/trunk/ctakes-core/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/pom.xml (original)
+++ ctakes/trunk/ctakes-core/pom.xml Wed Jun 28 14:47:27 2017
@@ -37,19 +37,21 @@
 			<groupId>xerces</groupId>
 			<artifactId>xercesImpl</artifactId>
 		</dependency>
-  		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-type-system</artifactId>
-		</dependency>
+        <!--  type system is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-type-system</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-utils</artifactId>
 		</dependency>
 		<!-- we excluded spring-context uimafit transitive dependency in the parent pom, include it here -->
-		<dependency>
-				<groupId>org.springframework</groupId>
-				<artifactId>spring-context</artifactId>
-		</dependency>		
+        <!--  spring context is added by type system.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.springframework</groupId>-->
+        <!--<artifactId>spring-context</artifactId>-->
+        <!--</dependency>		-->
 		<dependency>
 			<!-- needed for uimafit, but excluded in parent pom -->
 			<groupId>commons-io</groupId>
@@ -68,14 +70,16 @@
 			<groupId>org.cleartk</groupId>
 			<artifactId>cleartk-util</artifactId>
 		</dependency>
+        <!--  TODO Get rid of guava  -->
 		<dependency>
 			<groupId>com.google.guava</groupId>
 			<artifactId>guava</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>log4j</groupId>
-			<artifactId>log4j</artifactId>
-		</dependency>
+        <!--  log4j is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>log4j</groupId>-->
+        <!--<artifactId>log4j</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>org.apache.opennlp</groupId>
 			<artifactId>opennlp-tools</artifactId>
@@ -84,15 +88,16 @@
 			<groupId>org.apache.opennlp</groupId>
 			<artifactId>opennlp-maxent</artifactId>
 		</dependency>
-      <!--  Todo : is lucene necessary at this level?  -->
-		<dependency>
-			<groupId>org.apache.lucene</groupId>
-			<artifactId>lucene-core</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-		</dependency>
+        <!--  lucene core is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.lucene</groupId>-->
+        <!--<artifactId>lucene-core</artifactId>-->
+        <!--</dependency>-->
+        <!--  junit is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>junit</groupId>-->
+        <!--<artifactId>junit</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>edu.mit.findstruct</groupId>
 			<artifactId>findstructapi</artifactId>
@@ -114,10 +119,11 @@
          <groupId>com.lexicalscope.jewelcli</groupId>
          <artifactId>jewelcli</artifactId>
       </dependency>
-      <dependency>
-         <groupId>org.apache.uima</groupId>
-		<artifactId>uimafit-core</artifactId>
-         </dependency>
+        <!--  uimafit core is added by type system.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.uima</groupId>-->
+        <!--<artifactId>uimafit-core</artifactId>-->
+        <!--</dependency>-->
       <dependency>
          <groupId>org.cleartk</groupId>
          <artifactId>cleartk-ml</artifactId>

Modified: ctakes/trunk/ctakes-coreference/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/pom.xml (original)
+++ ctakes/trunk/ctakes-coreference/pom.xml Wed Jun 28 14:47:27 2017
@@ -32,47 +32,9 @@
 	     <dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-coreference-res</artifactId>
-		</dependency>		    
-		<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>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-relation-extractor</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-assertion</artifactId>
 		</dependency>
+        <!--  ctakes-temporal contains relation-extractor. relation-extractor contains clinical-pipeline.
+        Those three contain everything else needed.  -->
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-temporal</artifactId>
@@ -80,22 +42,25 @@
 	</dependencies>
 	<build>
 		<plugins>
-				<plugin>
-				  <groupId>org.apache.uima</groupId>
-				  <artifactId>jcasgen-maven-plugin</artifactId>
-				  <version>2.9.0</version>				  
-				  <executions>
-				    <execution>
-				      <goals><goal>generate</goal></goals>
-				      <configuration>
-				        <typeSystemIncludes>
-				          <typeSystemInclude>src/main/resources/org/apache/ctakes/**/types/TypeSystem.xml</typeSystemInclude>				          
-				        </typeSystemIncludes>
-				        <limitToProject>false</limitToProject>
-				      </configuration>
-				    </execution>
-				    </executions>
-				</plugin>
-		</plugins>				
- 	</build>
+            <plugin>
+                <groupId>org.apache.uima</groupId>
+                <artifactId>jcasgen-maven-plugin</artifactId>
+                <version>2.9.0</version>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>generate</goal>
+                        </goals>
+                        <configuration>
+                            <typeSystemIncludes>
+                                <typeSystemInclude>src/main/resources/org/apache/ctakes/coreference/types/*.xml
+                                </typeSystemInclude>
+                            </typeSystemIncludes>
+                            <limitToProject>true</limitToProject>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
 </project>

Modified: ctakes/trunk/ctakes-dependency-parser/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dependency-parser/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dependency-parser/pom.xml (original)
+++ ctakes/trunk/ctakes-dependency-parser/pom.xml Wed Jun 28 14:47:27 2017
@@ -32,15 +32,17 @@
 	     <dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-dependency-parser-res</artifactId>
-		</dependency>		        
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-type-system</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-core</artifactId>
 		</dependency>
+        <!--  type system is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-type-system</artifactId>-->
+        <!--</dependency>-->
+        <!--  core is added by pos tagger and lvg.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-core</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-lvg</artifactId>
@@ -49,39 +51,46 @@
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-pos-tagger</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-utils</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>com.googlecode.clearnlp</groupId>
-			<artifactId>clearnlp</artifactId>
-		</dependency>
+        <!--  utils is added by pos tagger (via core).  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-utils</artifactId>-->
+        <!--</dependency>-->
+        <!--  clearnlp is added by pos tagger.  -->
+        <!--<dependency>-->
+        <!--<groupId>com.googlecode.clearnlp</groupId>-->
+        <!--<artifactId>clearnlp</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>args4j</groupId>
 			<artifactId>args4j</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.cleartk</groupId>
-			<artifactId>cleartk-util</artifactId>
-		</dependency>
+        <!--  junit is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>junit</groupId>-->
+        <!--<artifactId>junit</artifactId>-->
+        <!--</dependency>-->
+        <!--  cleartk util is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.cleartk</groupId>-->
+        <!--<artifactId>cleartk-util</artifactId>-->
+        <!--</dependency>-->
 		<!-- we excluded spring-context uimafit transitive dependency in the parent pom, include it here -->
-		<dependency>
-				<groupId>org.springframework</groupId>
-				<artifactId>spring-context</artifactId>
-		</dependency>		
+        <!--  spring context is added by type system.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.springframework</groupId>-->
+        <!--<artifactId>spring-context</artifactId>-->
+        <!--</dependency>		-->
+        <!--  TODO where is hppc actually used?  -->
 		<dependency>
 			<groupId>com.carrotsearch</groupId>
 			<artifactId>hppc</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>commons-io</groupId>
-			<artifactId>commons-io</artifactId>
-		</dependency>
+        <!--  commons-io is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>commons-io</groupId>-->
+        <!--<artifactId>commons-io</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>commons-lang</groupId>
 			<artifactId>commons-lang</artifactId>
@@ -90,10 +99,11 @@
 			<groupId>commons-logging</groupId>
 			<artifactId>commons-logging</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.uima</groupId>
-			<artifactId>uimafit-core</artifactId>
-		</dependency>
+        <!--  uimafit core is added by type system.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.uima</groupId>-->
+        <!--<artifactId>uimafit-core</artifactId>-->
+        <!--</dependency>-->
 	</dependencies>
 	<description>This wraps the ClearNLP dependency parser and semantic role labeler into a UIMA friendly annotator</description>
 </project>

Modified: ctakes/trunk/ctakes-dictionary-lookup/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup/pom.xml (original)
+++ ctakes/trunk/ctakes-dictionary-lookup/pom.xml Wed Jun 28 14:47:27 2017
@@ -38,41 +38,49 @@
 			<artifactId>hsqldb</artifactId>
          <version>2.3.4</version>
       </dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-type-system</artifactId>
-		</dependency>
+            <!--  type system is added by utils via core.  -->
+            <!--<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>log4j</groupId>
-			<artifactId>log4j</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.lucene</groupId>
-			<artifactId>lucene-core</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.lucene</groupId>
-			<artifactId>lucene-queries</artifactId>
-		</dependency>		
-		<dependency>
-			<groupId>org.apache.lucene</groupId>
-			<artifactId>lucene-queryparser</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.lucene</groupId>
-			<artifactId>lucene-analyzers-common</artifactId>
-		</dependency>				
-		<dependency>
-			<groupId>jdom</groupId>
-			<artifactId>jdom</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-		</dependency>
+            <!--  log4j is added by utils.  -->
+            <!--<dependency>-->
+            <!--<groupId>log4j</groupId>-->
+            <!--<artifactId>log4j</artifactId>-->
+            <!--</dependency>-->
+            <!--  lucene core is added by utils.  -->
+            <!--<dependency>-->
+            <!--<groupId>org.apache.lucene</groupId>-->
+            <!--<artifactId>lucene-core</artifactId>-->
+            <!--</dependency>-->
+            <!--  lucene queries is added by utils.  -->
+            <!--<dependency>-->
+            <!--<groupId>org.apache.lucene</groupId>-->
+            <!--<artifactId>lucene-queries</artifactId>-->
+            <!--</dependency>		-->
+            <!--  lucene queryparser is added by utils.  -->
+            <!--<dependency>-->
+            <!--<groupId>org.apache.lucene</groupId>-->
+            <!--<artifactId>lucene-queryparser</artifactId>-->
+            <!--</dependency>-->
+            <!--  lucene analyzers common is added by utils.  -->
+            <!--<dependency>-->
+            <!--<groupId>org.apache.lucene</groupId>-->
+            <!--<artifactId>lucene-analyzers-common</artifactId>-->
+            <!--</dependency>				-->
+            <!--  jdom is added by core.  -->
+            <!--<dependency>-->
+            <!--<groupId>jdom</groupId>-->
+            <!--<artifactId>jdom</artifactId>-->
+            <!--</dependency>-->
+            <!--  junit is added by utils.  -->
+            <!--<dependency>-->
+            <!--<groupId>junit</groupId>-->
+            <!--<artifactId>junit</artifactId>-->
+            <!--</dependency>-->
 	</dependencies>
 </project>

Modified: ctakes/trunk/ctakes-drug-ner/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner/pom.xml (original)
+++ ctakes/trunk/ctakes-drug-ner/pom.xml Wed Jun 28 14:47:27 2017
@@ -32,19 +32,22 @@
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-drug-ner-res</artifactId>
-		</dependency>	      
-		<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>
+        <!--  type system is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-type-system</artifactId>-->
+        <!--</dependency>-->
+        <!--  core is added by lookup, lvg, etc.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-core</artifactId>-->
+        <!--</dependency>-->
+        <!--  utils is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-utils</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-dictionary-lookup</artifactId>
@@ -57,34 +60,41 @@
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-ne-contexts</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>log4j</groupId>
-			<artifactId>log4j</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.opennlp</groupId>
-			<artifactId>opennlp-tools</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>jdom</groupId>
-			<artifactId>jdom</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>tw.edu.ntu.csie</groupId>
-			<artifactId>libsvm</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.lucene</groupId>
-			<artifactId>lucene-core</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>net.sourceforge.openai</groupId>
-			<artifactId>openaifsm</artifactId>
-		</dependency>	
+        <!--  log4j is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>log4j</groupId>-->
+        <!--<artifactId>log4j</artifactId>-->
+        <!--</dependency>-->
+        <!--  opennlp tools is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.opennlp</groupId>-->
+        <!--<artifactId>opennlp-tools</artifactId>-->
+        <!--</dependency>-->
+        <!--  jdom is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>jdom</groupId>-->
+        <!--<artifactId>jdom</artifactId>-->
+        <!--</dependency>-->
+        <!--  junit is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>junit</groupId>-->
+        <!--<artifactId>junit</artifactId>-->
+        <!--</dependency>-->
+        <!--  libsvm is added by type system.  -->
+        <!--<dependency>-->
+        <!--<groupId>tw.edu.ntu.csie</groupId>-->
+        <!--<artifactId>libsvm</artifactId>-->
+        <!--</dependency>-->
+        <!--  lucene core is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.lucene</groupId>-->
+        <!--<artifactId>lucene-core</artifactId>-->
+        <!--</dependency>-->
+        <!--  openaifsm is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>net.sourceforge.openai</groupId>-->
+        <!--<artifactId>openaifsm</artifactId>-->
+        <!--</dependency>	-->
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-chunker</artifactId>
@@ -107,7 +117,7 @@
 				        <typeSystemIncludes>
 				          <typeSystemInclude>src/main/resources/org/apache/ctakes/**/types/TypeSystem.xml</typeSystemInclude>				          
 				        </typeSystemIncludes>
-				        <limitToProject>false</limitToProject>
+                          <limitToProject>true</limitToProject>
 				      </configuration>
 				    </execution>
 				    </executions>

Modified: ctakes/trunk/ctakes-gui/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-gui/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-gui/pom.xml (original)
+++ ctakes/trunk/ctakes-gui/pom.xml Wed Jun 28 14:47:27 2017
@@ -28,14 +28,6 @@
          <version>2.3.4</version>
       </dependency>
       <dependency>
-         <groupId>log4j</groupId>
-         <artifactId>log4j</artifactId>
-      </dependency>
-      <dependency>
-         <groupId>junit</groupId>
-         <artifactId>junit</artifactId>
-      </dependency>
-      <dependency>
          <groupId>io.github.lukehutch</groupId>
          <artifactId>fast-classpath-scanner</artifactId>
          <version>2.0.18</version>

Modified: ctakes/trunk/ctakes-lvg/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-lvg/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-lvg/pom.xml (original)
+++ ctakes/trunk/ctakes-lvg/pom.xml Wed Jun 28 14:47:27 2017
@@ -33,28 +33,32 @@
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-lvg-res</artifactId>
-		</dependency>	    
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-type-system</artifactId>
 		</dependency>
+        <!--  type system is added by utils.  -->
+        <!--<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>
+        <!--  utils is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-utils</artifactId>-->
+        <!--</dependency>-->
+        <!--  log4j is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>log4j</groupId>-->
+        <!--<artifactId>log4j</artifactId>-->
+        <!--</dependency>-->
+        <!--  junit is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>junit</groupId>-->
+        <!--<artifactId>junit</artifactId>-->
+        <!--<scope>test</scope>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>gov.nih.nlm.nls.lvg</groupId>
 			<artifactId>lvgdist</artifactId>

Modified: ctakes/trunk/ctakes-ne-contexts/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ne-contexts/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ne-contexts/pom.xml (original)
+++ ctakes/trunk/ctakes-ne-contexts/pom.xml Wed Jun 28 14:47:27 2017
@@ -35,27 +35,11 @@
 		</dependency>	      
 		<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.uima</groupId>
 			<artifactId>uimaj-document-annotation</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>log4j</groupId>
-			<artifactId>log4j</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-		</dependency>
 	</dependencies>
 </project>

Modified: ctakes/trunk/ctakes-pos-tagger/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pos-tagger/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-pos-tagger/pom.xml (original)
+++ ctakes/trunk/ctakes-pos-tagger/pom.xml Wed Jun 28 14:47:27 2017
@@ -32,42 +32,49 @@
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-pos-tagger-res</artifactId>
-		</dependency>	    
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-type-system</artifactId>
 		</dependency>
+        <!--  type system is added by utils.  -->
+        <!--<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>org.apache.opennlp</groupId>
-			<artifactId>opennlp-tools</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.opennlp</groupId>
-			<artifactId>opennlp-maxent</artifactId>
-		</dependency>
+        <!--  utils is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-utils</artifactId>-->
+        <!--</dependency>-->
+        <!--  log4j is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>log4j</groupId>-->
+        <!--<artifactId>log4j</artifactId>-->
+        <!--</dependency>-->
+        <!--  opennlp tools is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.opennlp</groupId>-->
+        <!--<artifactId>opennlp-tools</artifactId>-->
+        <!--</dependency>-->
+        <!--  opennlp maxent is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.opennlp</groupId>-->
+        <!--<artifactId>opennlp-maxent</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>com.googlecode.clearnlp</groupId>
 			<artifactId>clearnlp</artifactId>
-		</dependency>		
-		<dependency>
-			<groupId>jdom</groupId>
-			<artifactId>jdom</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
 		</dependency>
+        <!--  jdom is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>jdom</groupId>-->
+        <!--<artifactId>jdom</artifactId>-->
+        <!--</dependency>-->
+        <!--  junit is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>junit</groupId>-->
+        <!--<artifactId>junit</artifactId>-->
+        <!--</dependency>-->
 	</dependencies>
 </project>

Modified: ctakes/trunk/ctakes-regression-test/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-regression-test/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-regression-test/pom.xml (original)
+++ ctakes/trunk/ctakes-regression-test/pom.xml Wed Jun 28 14:47:27 2017
@@ -10,68 +10,83 @@
   <description>Apache cTAKES Regression-test</description>
   
 	<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>jdom</groupId>
-			<artifactId>jdom</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-context-tokenizer</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-preprocessor</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-lvg</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-chunker</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-ne-contexts</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-pos-tagger</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-assertion</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-dependency-parser</artifactId>
-		</dependency>
+        <!--  type system is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-type-system</artifactId>-->
+        <!--</dependency>-->
+        <!--  core is added by everybody.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-core</artifactId>-->
+        <!--</dependency>-->
+        <!--  utils is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-utils</artifactId>-->
+        <!--</dependency>-->
+        <!--  jdom is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>jdom</groupId>-->
+        <!--<artifactId>jdom</artifactId>-->
+        <!--</dependency>-->
+        <!--  junit is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>junit</groupId>-->
+        <!--<artifactId>junit</artifactId>-->
+        <!--</dependency>-->
+        <!--  context tokenizer is added by assertion.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-context-tokenizer</artifactId>-->
+        <!--</dependency>-->
+        <!--  pre-processor is added by clinical pipeline.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-preprocessor</artifactId>-->
+        <!--</dependency>-->
+        <!--  lvg is added by dependency parser.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-lvg</artifactId>-->
+        <!--</dependency>-->
+        <!--  chunker is added by assertion.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-chunker</artifactId>-->
+        <!--</dependency>-->
+        <!--  ne contexts is added by clinical pipeline.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-ne-contexts</artifactId>-->
+        <!--</dependency>-->
+        <!--  pos tagger is added by chunker.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-pos-tagger</artifactId>-->
+        <!--</dependency>-->
+        <!--  assertion is added by clinical pipeline.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-assertion</artifactId>-->
+        <!--</dependency>-->
+        <!--  dependency parser is added by assertion.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-dependency-parser</artifactId>-->
+        <!--</dependency>-->
 		<!--  If clinical-pipeline is a dependency then everything in clinical-pipeline should be removed.
 				This makes maintenance much easier wrt upgraded versions and removed/unused modules (e.g. old lookup).-->
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-clinical-pipeline</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-drug-ner</artifactId>
-		</dependency>		
+        <!--  clinical pipeline is added by relation extractor.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-clinical-pipeline</artifactId>-->
+        <!--</dependency>-->
+        <!--  drug-ner is added by smoking status, side effect.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-drug-ner</artifactId>-->
+        <!--</dependency>		-->
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-smoking-status</artifactId>
@@ -79,11 +94,12 @@
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-side-effect</artifactId>
-		</dependency>		
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-constituency-parser</artifactId>
-		</dependency>		
+        </dependency>
+        <!--  constituency parser is added by assertion.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-constituency-parser</artifactId>-->
+        <!--</dependency>		-->
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-coreference</artifactId>

Modified: ctakes/trunk/ctakes-relation-extractor/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/pom.xml (original)
+++ ctakes/trunk/ctakes-relation-extractor/pom.xml Wed Jun 28 14:47:27 2017
@@ -32,137 +32,75 @@
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-relation-extractor-res</artifactId>
-		</dependency>	    
-		<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-eval</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>com.lexicalscope.jewelcli</groupId>
-			<artifactId>jewelcli</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-tools</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.opennlp</groupId>
-			<artifactId>opennlp-maxent</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>
-        
+        <!--  Clinical Pipeline contains ctakes modules that are needed.  -->
 		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
+			<groupId>org.apache.ctakes</groupId>
+            <artifactId>ctakes-clinical-pipeline</artifactId>
 		</dependency>
-	<dependency>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes-context-tokenizer</artifactId>
-	</dependency>
-	<dependency>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes-constituency-parser</artifactId>
-	</dependency>
-	<dependency>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes-ne-contexts</artifactId>
-	</dependency>
-	<dependency>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes-chunker</artifactId>
-	</dependency>
-	<dependency>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes-dependency-parser</artifactId>
-	</dependency>
+        <!--  ctakes-core contains cleartk-ml, -util -->
+        <!--  cleartk-eval is added by assertion.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.cleartk</groupId>-->
+        <!--<artifactId>cleartk-eval</artifactId>-->
+        <!--</dependency>-->
+        <!--  cleartk-ml-libsvm is added by assertion.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.cleartk</groupId>-->
+        <!--<artifactId>cleartk-ml-libsvm</artifactId>-->
+        <!--</dependency>-->
+        <!--  cleartk-ml-opennlp-maxent is added by assertion.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.cleartk</groupId>-->
+        <!--<artifactId>cleartk-ml-opennlp-maxent</artifactId>-->
+        <!--</dependency>-->
+        <!--  commons-lang is added by dependency parser.  -->
+        <!--<dependency>-->
+        <!--<groupId>commons-lang</groupId>-->
+        <!--<artifactId>commons-lang</artifactId>-->
+        <!--</dependency>-->
+        <!--  commons-logging is added by dependency parser.  -->
+        <!--<dependency>-->
+        <!--<groupId>commons-logging</groupId>-->
+        <!--<artifactId>commons-logging</artifactId>-->
+        <!--</dependency>-->
+        <!--  guave is added by core unfortunately.  -->
+        <!--<dependency>-->
+        <!--<groupId>com.google.guava</groupId>-->
+        <!--<artifactId>guava</artifactId>-->
+        <!--</dependency>-->
+        <!--  hppc is added by dependency parser.  -->
+        <!--<dependency>-->
+        <!--<groupId>com.carrotsearch</groupId>-->
+        <!--<artifactId>hppc</artifactId>-->
+        <!--</dependency>-->
+        <!--  ctakes-core contains opennlp-utils, -maxent, jdom  -->
+        <!--  lucene core is added by utils.  -->
+        <!--  lucene-core is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.lucene</groupId>-->
+        <!--<artifactId>lucene-core</artifactId>-->
+        <!--</dependency>-->
+        <!--  libsvm is added by relation extractor.  -->
+        <!--<dependency>-->
+        <!--<groupId>tw.edu.ntu.csie</groupId>-->
+        <!--<artifactId>libsvm</artifactId>-->
+        <!--</dependency>-->
+        <!--  spring core is added by assertion.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.springframework</groupId>-->
+        <!--<artifactId>spring-core</artifactId>-->
+        <!--</dependency>-->
 	<dependency>
 		<groupId>edu.mit</groupId>
 		<artifactId>jwi</artifactId>
 		<version>2.2.3</version>
 	</dependency>
-	<dependency>
-		<groupId>org.apache.uima</groupId>
-		<artifactId>uimafit-core</artifactId>
-	</dependency>
-	<dependency>
-		<groupId>org.cleartk</groupId>
-		<artifactId>cleartk-ml-liblinear</artifactId>
-	</dependency>
+        <!--  ctakes-core contains uimafit-core  -->
+        <!--  cleartk-ml-liblinear is added by assertion  -->
+        <!--<dependency>-->
+        <!--<groupId>org.cleartk</groupId>-->
+        <!--<artifactId>cleartk-ml-liblinear</artifactId>-->
+        <!--</dependency>-->
 	</dependencies>
 </project>

Modified: ctakes/trunk/ctakes-side-effect/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-side-effect/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-side-effect/pom.xml (original)
+++ ctakes/trunk/ctakes-side-effect/pom.xml Wed Jun 28 14:47:27 2017
@@ -33,15 +33,17 @@
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-side-effect-res</artifactId>
-		</dependency>	    
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-type-system</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-core</artifactId>
 		</dependency>
+        <!--  type system is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-type-system</artifactId>-->
+        <!--</dependency>-->
+        <!--  core is added by everything.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-core</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-dictionary-lookup</artifactId>
@@ -50,30 +52,36 @@
 			<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>
-		<dependency>
-            <groupId>org.apache.lucene</groupId>
-            <artifactId>lucene-core</artifactId>
-        </dependency>
-       	<dependency>
-            <groupId>tw.edu.ntu.csie</groupId>
-            <artifactId>libsvm</artifactId>
-		</dependency>		
+        <!--  utils is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-utils</artifactId>-->
+        <!--</dependency>-->
+        <!--  log4j is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>log4j</groupId>-->
+        <!--<artifactId>log4j</artifactId>-->
+        <!--</dependency>-->
+        <!--  jdom is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>jdom</groupId>-->
+        <!--<artifactId>jdom</artifactId>-->
+        <!--</dependency>-->
+        <!--  junit is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>junit</groupId>-->
+        <!--<artifactId>junit</artifactId>-->
+        <!--</dependency>-->
+        <!--  lucene core is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.lucene</groupId>-->
+        <!--<artifactId>lucene-core</artifactId>-->
+        <!--</dependency>-->
+        <!--  libsvm is added by type system.  -->
+        <!--<dependency>-->
+        <!--<groupId>tw.edu.ntu.csie</groupId>-->
+        <!--<artifactId>libsvm</artifactId>-->
+        <!--</dependency>		-->
 	</dependencies>
 	<build>
 		<plugins>
@@ -86,9 +94,10 @@
 				      <goals><goal>generate</goal></goals>
 				      <configuration>
 				        <typeSystemIncludes>
-				          <typeSystemInclude>src/main/resources/org/apache/ctakes/**/types/TypeSystem.xml</typeSystemInclude>				          
+                            <typeSystemInclude>src/main/resources/org/apache/ctakes/**/types/TypeSystem.xml
+                            </typeSystemInclude>
 				        </typeSystemIncludes>
-				        <limitToProject>false</limitToProject>
+                          <limitToProject>true</limitToProject>
 				      </configuration>
 				    </execution>
 				    </executions>

Modified: ctakes/trunk/ctakes-smoking-status/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-smoking-status/pom.xml (original)
+++ ctakes/trunk/ctakes-smoking-status/pom.xml Wed Jun 28 14:47:27 2017
@@ -33,15 +33,17 @@
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-smoking-status-res</artifactId>
-		</dependency>	    
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-type-system</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-core</artifactId>
 		</dependency>
+        <!--  type system is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-type-system</artifactId>-->
+        <!--</dependency>-->
+        <!--  core is added by everything.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-core</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-dictionary-lookup</artifactId>
@@ -50,30 +52,36 @@
 			<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>
-		<dependency>
-            <groupId>org.apache.lucene</groupId>
-            <artifactId>lucene-core</artifactId>
-        </dependency>
-       	<dependency>
-            <groupId>tw.edu.ntu.csie</groupId>
-            <artifactId>libsvm</artifactId>
-		</dependency>
+        <!--  utils is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-utils</artifactId>-->
+        <!--</dependency>-->
+        <!--  log4j is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>log4j</groupId>-->
+        <!--<artifactId>log4j</artifactId>-->
+        <!--</dependency>-->
+        <!--  jdom is added by core.  -->
+        <!--<dependency>-->
+        <!--<groupId>jdom</groupId>-->
+        <!--<artifactId>jdom</artifactId>-->
+        <!--</dependency>-->
+        <!--  junit is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>junit</groupId>-->
+        <!--<artifactId>junit</artifactId>-->
+        <!--</dependency>-->
+        <!--  lucene core is added by utils.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.lucene</groupId>-->
+        <!--<artifactId>lucene-core</artifactId>-->
+        <!--</dependency>-->
+        <!--  libsvm is added by type system.  -->
+        <!--<dependency>-->
+        <!--<groupId>tw.edu.ntu.csie</groupId>-->
+        <!--<artifactId>libsvm</artifactId>-->
+        <!--</dependency>-->
 	</dependencies>	
 	<build>
 		<plugins>
@@ -88,7 +96,7 @@
 				        <typeSystemIncludes>
 				          <typeSystemInclude>src/main/resources/org/apache/ctakes/**/types/TypeSystem.xml</typeSystemInclude>				          
 				        </typeSystemIncludes>
-				        <limitToProject>false</limitToProject>
+                          <limitToProject>true</limitToProject>
 				      </configuration>
 				    </execution>
 				    </executions>

Modified: ctakes/trunk/ctakes-template-filler/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-template-filler/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-template-filler/pom.xml (original)
+++ ctakes/trunk/ctakes-template-filler/pom.xml Wed Jun 28 14:47:27 2017
@@ -30,55 +30,64 @@
 		<version>4.0.1-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>
+        <!--  type system is added by utils  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-type-system</artifactId>-->
+        <!--</dependency>-->
+        <!--  core is added by everything.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-core</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-drug-ner</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-drug-ner-res</artifactId>
-		</dependency>
+        <!--  Oh come on ... drug ner and drug ner res?  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-drug-ner-res</artifactId>-->
+        <!--</dependency>-->
 		<!--  If clinical-pipeline is a dependency then everything in clinical-pipeline should be removed.
 				This makes maintenance much easier wrt upgraded versions and removed/unused modules (e.g. old lookup).-->
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-clinical-pipeline</artifactId>
-		</dependency>
+        <!--  clinical pipeline is added by realtion extractor.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-clinical-pipeline</artifactId>-->
+        <!--</dependency>-->
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-relation-extractor</artifactId>
-		</dependency>	    
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-relation-extractor-res</artifactId>
-		</dependency>	    
-	<dependency>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes-chunker</artifactId>
-	</dependency>
-	<dependency>
-		<groupId>org.apache.ctakes</groupId>
-		<artifactId>ctakes-dictionary-lookup</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>
+        <!--  Oh come on ... relation extractor and relation extractor res?  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-relation-extractor-res</artifactId>-->
+        <!--</dependency>-->
+        <!--  chunkeris added by assertion.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-chunker</artifactId>-->
+        <!--</dependency>-->
+        <!--  We really need to get rid of dictionary lookup.  -->
+        <!--  dictionary lookup is in drug ner.  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.ctakes</groupId>-->
+        <!--<artifactId>ctakes-dictionary-lookup</artifactId>-->
+        <!--</dependency>-->
+        <!--  Honestly, I am just tired of writing from where these things come.  -->
+        <!--<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: ctakes/trunk/ctakes-temporal/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/pom.xml (original)
+++ ctakes/trunk/ctakes-temporal/pom.xml Wed Jun 28 14:47:27 2017
@@ -34,70 +34,13 @@
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-temporal-res</artifactId>
-		</dependency>	    
-		<dependency>
-			<groupId>org.jdom</groupId>
-			<artifactId>jdom2</artifactId>
-		</dependency>
-        <dependency>
-            <groupId>com.lexicalscope.jewelcli</groupId>
-            <artifactId>jewelcli</artifactId>
         </dependency>
-		<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-context-tokenizer</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-pos-tagger</artifactId>
-		</dependency>
-		<!--  If chunker is a dependency then everything in chunker should be removed.  core, type-system, pos-tagger ...
-				This makes maintenance much easier wrt upgraded versions and removed/unused modules (e.g. old lookup).-->
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-chunker</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-dictionary-lookup-fast</artifactId>
-		</dependency>
-			<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-lvg</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.ctakes</groupId>
-			<artifactId>ctakes-dependency-parser</artifactId>
-		</dependency>
+        <!--  Relation extractor uses clinical-pipeline.  No need to redeclare all those dependencies.  -->
 		<dependency>
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-relation-extractor</artifactId>
 		</dependency>
     <dependency>
-      <groupId>org.apache.ctakes</groupId>
-      <artifactId>ctakes-constituency-parser</artifactId>
-    </dependency>
-    <dependency>
-      <groupId>org.cleartk</groupId>
-      <artifactId>cleartk-util</artifactId>
-    </dependency>
-    <dependency>
-      <groupId>org.cleartk</groupId>
-      <artifactId>cleartk-ml</artifactId>
-    </dependency>
-    <dependency>
-      <groupId>org.cleartk</groupId>
-      <artifactId>cleartk-eval</artifactId>
-    </dependency>
-    <dependency>
       <groupId>org.cleartk</groupId>
       <artifactId>cleartk-timeml</artifactId>
     </dependency>
@@ -107,10 +50,6 @@
 		</dependency>
 		<dependency>
 			<groupId>org.cleartk</groupId>
-			<artifactId>cleartk-ml-libsvm</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.cleartk</groupId>
 			<artifactId>cleartk-ml-tksvmlight</artifactId>
 		</dependency>
 		<dependency>

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CompareFeatureStructures.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CompareFeatureStructures.java?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CompareFeatureStructures.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CompareFeatureStructures.java Wed Jun 28 14:47:27 2017
@@ -18,42 +18,35 @@
  */
 package org.apache.ctakes.temporal.data.analysis;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Set;
-
-import javax.annotation.Nullable;
-
+import com.google.common.base.Function;
+import com.google.common.base.Objects;
+import com.google.common.collect.*;
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+import difflib.Chunk;
+import difflib.Delta;
+import difflib.Patch;
+import difflib.myers.Equalizer;
+import difflib.myers.MyersDiff;
 import org.apache.uima.cas.CASException;
 import org.apache.uima.cas.Feature;
 import org.apache.uima.cas.FeatureStructure;
 import org.apache.uima.cas.Type;
 import org.apache.uima.cas.impl.XmiCasDeserializer;
+import org.apache.uima.fit.factory.JCasFactory;
+import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FSArray;
 import org.apache.uima.jcas.cas.NonEmptyFSList;
 import org.apache.uima.jcas.tcas.Annotation;
-import org.apache.uima.fit.factory.JCasFactory;
-import org.apache.uima.fit.util.JCasUtil;
 
-import com.google.common.base.Function;
-import com.google.common.base.Objects;
-import com.google.common.collect.ArrayListMultimap;
-import com.google.common.collect.Iterators;
-import com.google.common.collect.ListMultimap;
-import com.google.common.collect.Lists;
-import com.google.common.collect.Ordering;
-import com.google.common.collect.Sets;
-import com.lexicalscope.jewel.cli.CliFactory;
-import com.lexicalscope.jewel.cli.Option;
+import java.io.File;
+import java.io.FileInputStream;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
 
-import difflib.Chunk;
-import difflib.Delta;
-import difflib.Patch;
-import difflib.myers.Equalizer;
-import difflib.myers.MyersDiff;
+//import javax.annotation.Nullable;
 
 public class CompareFeatureStructures {
   static interface Options {
@@ -226,7 +219,10 @@ public class CompareFeatureStructures {
       Ordering.natural().<Comparable<?>> lexicographical().onResultOf(
           new Function<FeatureStructure, Iterable<Comparable<?>>>() {
             @Override
-            public Iterable<Comparable<?>> apply(@Nullable FeatureStructure input) {
+            //  All of guava just for two @Nullable?  temporal has about 100 you be outdated errors and warnings.
+            // findbugs is the least of worries.
+//            public Iterable<Comparable<?>> apply(@Nullable FeatureStructure input) {
+            public Iterable<Comparable<?>> apply( FeatureStructure input ) {
               List<Integer> offsets = Lists.newArrayList();
               this.findOffsets(input, offsets);
               List<Comparable<?>> result =

Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintInconsistentAnnotations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintInconsistentAnnotations.java?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintInconsistentAnnotations.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintInconsistentAnnotations.java Wed Jun 28 14:47:27 2017
@@ -18,14 +18,10 @@
  */
 package org.apache.ctakes.temporal.data.analysis;
 
-import java.io.File;
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Set;
-
-import javax.annotation.Nullable;
-
+import com.google.common.base.Function;
+import com.google.common.collect.*;
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
 import org.apache.ctakes.temporal.eval.CommandLine;
 import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMIReader;
 import org.apache.ctakes.temporal.eval.THYMEData;
@@ -42,14 +38,13 @@ import org.cleartk.util.ViewUriUtil;
 import org.cleartk.util.ae.UriToDocumentTextAnnotator;
 import org.cleartk.util.cr.UriCollectionReader;
 
-import com.google.common.base.Function;
-import com.google.common.collect.HashMultimap;
-import com.google.common.collect.Lists;
-import com.google.common.collect.Multimap;
-import com.google.common.collect.Ordering;
-import com.google.common.collect.Sets;
-import com.lexicalscope.jewel.cli.CliFactory;
-import com.lexicalscope.jewel.cli.Option;
+import java.io.File;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+
+//import javax.annotation.Nullable;
 
 public class PrintInconsistentAnnotations {
   static interface Options {
@@ -164,7 +159,10 @@ public class PrintInconsistentAnnotation
           Ordering<EventMention> byBegin =
               Ordering.natural().onResultOf(new Function<EventMention, Integer>() {
                 @Override
-                public Integer apply(@Nullable EventMention event) {
+                // all of guava for two @Nullable ?  temporal has about 100 you be outdated errors and warnings.
+                // findbugs is the least of worries.
+//                public Integer apply(@Nullable EventMention event) {
+                public Integer apply( EventMention event ) {
                   return event.getBegin();
                 }
               });

Modified: ctakes/trunk/ctakes-type-system/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-type-system/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-type-system/pom.xml (original)
+++ ctakes/trunk/ctakes-type-system/pom.xml Wed Jun 28 14:47:27 2017
@@ -64,9 +64,10 @@
 				      <goals><goal>generate</goal></goals>
 				      <configuration>
 				        <typeSystemIncludes>
-				          <typeSystemInclude>src/main/resources/org/apache/ctakes/**/types/TypeSystem.xml</typeSystemInclude>				          
+                            <typeSystemInclude>src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
+                            </typeSystemInclude>
 				        </typeSystemIncludes>
-				        <limitToProject>false</limitToProject>
+                          <limitToProject>true</limitToProject>
 				      </configuration>
 				    </execution>
 				    </executions>

Modified: ctakes/trunk/ctakes-utils/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-utils/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-utils/pom.xml (original)
+++ ctakes/trunk/ctakes-utils/pom.xml Wed Jun 28 14:47:27 2017
@@ -58,9 +58,10 @@
 			<groupId>org.apache.lucene</groupId>
 			<artifactId>lucene-analyzers-common</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.uima</groupId>
-			<artifactId>uimaj-core</artifactId>
-		</dependency>
+        <!--  uimaj-core is added by type system  -->
+        <!--<dependency>-->
+        <!--<groupId>org.apache.uima</groupId>-->
+        <!--<artifactId>uimaj-core</artifactId>-->
+        <!--</dependency>-->
 	</dependencies>
 </project>

Modified: ctakes/trunk/ctakes-ytex-uima/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/pom.xml (original)
+++ ctakes/trunk/ctakes-ytex-uima/pom.xml Wed Jun 28 14:47:27 2017
@@ -125,7 +125,7 @@
 				        <typeSystemIncludes>
 				          <typeSystemInclude>src/main/resources/org/apache/ctakes/**/types/TypeSystem.xml</typeSystemInclude>				          
 				        </typeSystemIncludes>
-				        <limitToProject>false</limitToProject>
+						  <limitToProject>true</limitToProject>
 				      </configuration>
 				    </execution>
 				    </executions>

Modified: ctakes/trunk/ctakes-ytex/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/pom.xml?rev=1800177&r1=1800176&r2=1800177&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/pom.xml (original)
+++ ctakes/trunk/ctakes-ytex/pom.xml Wed Jun 28 14:47:27 2017
@@ -101,11 +101,6 @@
 			<version>${ctakes.version}</version>
 		</dependency>
 		<dependency>
-			<groupId>org.hsqldb</groupId>
-			<artifactId>hsqldb</artifactId>
-			<version>2.3.4</version>
-		</dependency>
-		<dependency>
 			<groupId>commons-lang</groupId>
 			<artifactId>commons-lang</artifactId>
 		</dependency>
@@ -134,19 +129,11 @@
 			<version>3.5.0</version>
 		</dependency>
 		<dependency>
-			<groupId>log4j</groupId>
-			<artifactId>log4j</artifactId>
-		</dependency>
-		<dependency>
 			<groupId>org.slf4j</groupId>
 			<artifactId>slf4j-log4j12</artifactId>
 			<version>1.6.1</version>
 		</dependency>
 		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-		</dependency>
-		<dependency>
 			<groupId>org.springframework</groupId>
 			<artifactId>spring-core</artifactId>
 		</dependency>
@@ -207,6 +194,11 @@
 			<artifactId>ant</artifactId>
 			<version>1.9.2</version>
 		</dependency>
+		<!--  ytex should depend upon ctakes-clinical-pipeline , not the other way around.  -->
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-clinical-pipeline</artifactId>
+		</dependency>
 	</dependencies>
 	<build>
 		<extensions>



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