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From chen...@apache.org
Subject svn commit: r1414280 - in /incubator/ctakes/trunk: ./ ctakes-dictionary-lookup/ ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/lookup/rxnorm_index/ ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/looku...
Date Tue, 27 Nov 2012 17:37:19 GMT
Author: chenpei
Date: Tue Nov 27 17:37:18 2012
New Revision: 1414280

URL: http://svn.apache.org/viewvc?rev=1414280&view=rev
Log:
CTAKES-53 - move UMLS out of Apache distribution
Making the same changes from 3.0.0
Deleting rxnorm_index and umls2011ab from the src.  Updating the pom's to pull it in from
maven central instead.

Removed:
    incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/lookup/rxnorm_index/
    incubator/ctakes/trunk/ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/lookup/umls2011ab/
Modified:
    incubator/ctakes/trunk/NOTICE
    incubator/ctakes/trunk/README
    incubator/ctakes/trunk/ctakes-dictionary-lookup/pom.xml
    incubator/ctakes/trunk/ctakes-distribution/NOTICE
    incubator/ctakes/trunk/pom.xml

Modified: incubator/ctakes/trunk/NOTICE
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/NOTICE?rev=1414280&r1=1414279&r2=1414280&view=diff
==============================================================================
--- incubator/ctakes/trunk/NOTICE (original)
+++ incubator/ctakes/trunk/NOTICE Tue Nov 27 17:37:18 2012
@@ -24,23 +24,4 @@ Portions of cTAKES were originally devel
 The MITRE corporation. 
 Copyright (c) 2012 The MITRE Corporation.
 
-Some material in the UMLS Metathesaurus is from copyrighted sources of
-the respective copyright holders. Users of the UMLS Metathesaurus are 
-solely responsible for compliance with any copyright, patent or 
-trademark restrictions and are referred to the copyright, patent or 
-trademark notices appearing in the original sources, all of which are 
-hereby incorporated by reference.
-
-This material includes SNOMED Clinical Terms� (SNOMED CT�) which is 
-used by permission of the International Health Terminology Standards 
-Development Organisation (IHTSDO). All rights reserved. SNOMED CT�, 
-was originally created by The College of American Pathologists. 
-"SNOMED" and "SNOMED CT" are registered trademarks of the IHTSDO.
-
-cTAKES includes the following vocabularies from the UMLS Metathesaurus:
- - SNOMED CT
- - NCI Thesaurus http://ncit.nci.nih.gov/
- - Medical Subject Headings http://www.nlm.nih.gov/mesh/
- - RxNorm http://www.nlm.nih.gov/research/umls/rxnorm/
- 
 Please see the NOTICE file within each PEAR file for the other notices.

Modified: incubator/ctakes/trunk/README
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/README?rev=1414280&r1=1414279&r2=1414280&view=diff
==============================================================================
--- incubator/ctakes/trunk/README (original)
+++ incubator/ctakes/trunk/README Tue Nov 27 17:37:18 2012
@@ -19,7 +19,12 @@ Enter note and run analysis engine.
 
 Notes
 -----------
-If you plan to use the UMLS Resources, set/export env variables
+If you plan to use the UMLS Resources,
+Download and unpack the umls resources and add them to the resources directory
+from http://search.maven.org/remotecontent?filepath=net/sourceforge/ctakesresources/ctakes-resources-distribution/3.1.0/ctakes-resources-distribution-3.1.0-bin.zip
+http://sourceforge.net/projects/ctakesresources/files/
+
+Also set/export env variables
 export ctakes.umlsuser=[username], ctakes.umlspw=[password]
 or add the system properties to the java args
 -Dctakes.umlsuser=[username] -Dctakes.umlspw=[password]
\ No newline at end of file

Modified: incubator/ctakes/trunk/ctakes-dictionary-lookup/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/pom.xml?rev=1414280&r1=1414279&r2=1414280&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/pom.xml (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/pom.xml Tue Nov 27 17:37:18 2012
@@ -65,5 +65,33 @@
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
 		</dependency>
+
+		<!-- cTAKES Resources -->
+		<dependency>
+			<groupId>net.sourceforge.ctakesresources</groupId>
+			<artifactId>ctakes-resources-umls2011ab</artifactId>
+			<version>3.1.0</version>
+		</dependency>
 	</dependencies>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-dependency-plugin</artifactId>
+				<executions>
+					<execution>
+						<id>unpack-dependencies</id>
+						<phase>process-resources</phase>
+						<goals>
+							<goal>unpack-dependencies</goal>
+						</goals>
+						<configuration>
+							<includeArtifactIds>ctakes-resources-umls2011ab</includeArtifactIds>
+							<outputDirectory>${project.build.directory}/classes</outputDirectory>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
+		</plugins>
+	</build>
 </project>

Modified: incubator/ctakes/trunk/ctakes-distribution/NOTICE
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-distribution/NOTICE?rev=1414280&r1=1414279&r2=1414280&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/NOTICE (original)
+++ incubator/ctakes/trunk/ctakes-distribution/NOTICE Tue Nov 27 17:37:18 2012
@@ -20,24 +20,6 @@ University of Colorado and are licensed 
 Foundation under the "Software Grant License Agreement".
 Copyright (c) 2012 University of Colorado.
 
-Some material in the UMLS Metathesaurus is from copyrighted sources of
-the respective copyright holders. Users of the UMLS Metathesaurus are 
-solely responsible for compliance with any copyright, patent or 
-trademark restrictions and are referred to the copyright, patent or 
-trademark notices appearing in the original sources, all of which are 
-hereby incorporated by reference.
-This material includes SNOMED Clinical Terms� (SNOMED CT�) which is 
-used by permission of the International Health Terminology Standards 
-Development Organisation (IHTSDO). All rights reserved. SNOMED CT�, 
-was originally created by The College of American Pathologists. 
-"SNOMED" and "SNOMED CT" are registered trademarks of the IHTSDO.
-cTAKES includes the following vocabularies from the UMLS Metathesaurus:
- - SNOMED CT
- - NCI Thesaurus http://ncit.nci.nih.gov/
- - Medical Subject Headings http://www.nlm.nih.gov/mesh/
- - RxNorm http://www.nlm.nih.gov/research/umls/rxnorm/
-Please see the NOTICE file within each PEAR file for the other notices.
-
 This product contains hsqldb developed by the HSQL Development Group 
 (http://hsqldb.org), licensed based on the
 BSD license (see LICENSE file).

Modified: incubator/ctakes/trunk/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/pom.xml?rev=1414280&r1=1414279&r2=1414280&view=diff
==============================================================================
--- incubator/ctakes/trunk/pom.xml (original)
+++ incubator/ctakes/trunk/pom.xml Tue Nov 27 17:37:18 2012
@@ -521,6 +521,10 @@
 					<version>2.5</version>
 				</plugin>
 				<plugin>
+					<artifactId>maven-dependency-plugin</artifactId>
+					<version>2.6</version>
+				</plugin>				
+				<plugin>
 					<artifactId>maven-site-plugin</artifactId>
 					<version>3.1</version>
 				</plugin>
@@ -584,18 +588,37 @@
 						<numUnapprovedLicenses>0</numUnapprovedLicenses>								
 					</configuration>
 				</plugin>
-				<!--
-				Ignore the Maven remote resources plugin in Eclipse. We don't use it from Eclipse,
-				and it causes a warning if m2e is not configured to ignore it as below.
-				-->
 				<plugin>
 					<groupId>org.eclipse.m2e</groupId>
 					<artifactId>lifecycle-mapping</artifactId>
-					<version>1.0.0</version>
+					<version>1.0</version>
 					<configuration>
 						<lifecycleMappingMetadata>
 							<pluginExecutions>
 								<pluginExecution>
+								<!-- 
+								This is needed to execute/unpack resources in m2e eclipse ide
+								Currently used in the ctakes-dictionary-lookup project  
+								-->
+									<pluginExecutionFilter>
+										<groupId>org.apache.maven.plugins</groupId>
+										<artifactId>maven-dependency-plugin</artifactId>
+										<versionRange>[2.6,)</versionRange>
+										<goals>
+											<goal>unpack-dependencies</goal>
+										</goals>
+									</pluginExecutionFilter>
+									<action>
+										<execute>
+											<runOnIncremental>true</runOnIncremental>
+										</execute>
+									</action>
+								</pluginExecution>
+								<pluginExecution>
+								<!--
+								Ignore the Maven remote resources plugin in Eclipse. We don't use it from Eclipse,
+								and it causes a warning if m2e is not configured to ignore it as below.
+								-->								
 									<pluginExecutionFilter>
 										<groupId>org.apache.maven.plugins</groupId>
 										<artifactId>maven-remote-resources-plugin</artifactId>
@@ -607,7 +630,7 @@
 									<action>
 										<ignore />
 									</action>
-								</pluginExecution>
+								</pluginExecution>																
 							</pluginExecutions>
 						</lifecycleMappingMetadata>
 					</configuration>



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