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From chen...@apache.org
Subject svn commit: r1412325 - in /incubator/ctakes/branches/ctakes-3.0.0-incubating: ./ ctakes-clinical-pipeline/ ctakes-dictionary-lookup/ ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/lookup/ ctakes-dictionary-lookup/src/main/reso...
Date Wed, 21 Nov 2012 22:01:40 GMT
Author: chenpei
Date: Wed Nov 21 22:01:37 2012
New Revision: 1412325

URL: http://svn.apache.org/viewvc?rev=1412325&view=rev
Log:
CTAKES-53 - move UMLS out of Apache distribution

Removed:
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/lookup/OrangeBook.zip
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/lookup/drug_index.zip
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/lookup/rxnorm_index/
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/lookup/snomed-like_codes_sample.zip
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/lookup/snomed-like_sample.zip
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/lookup/umls2011ab/
Modified:
    incubator/ctakes/branches/ctakes-3.0.0-incubating/NOTICE
    incubator/ctakes/branches/ctakes-3.0.0-incubating/README
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-clinical-pipeline/NOTICE
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-dictionary-lookup/pom.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-distribution/NOTICE

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/NOTICE
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/NOTICE?rev=1412325&r1=1412324&r2=1412325&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/NOTICE (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/NOTICE Wed Nov 21 22:01:37 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/branches/ctakes-3.0.0-incubating/README
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/README?rev=1412325&r1=1412324&r2=1412325&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/README (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/README Wed Nov 21 22:01:37 2012
@@ -19,7 +19,11 @@ 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://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/branches/ctakes-3.0.0-incubating/ctakes-clinical-pipeline/NOTICE
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-clinical-pipeline/NOTICE?rev=1412325&r1=1412324&r2=1412325&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-clinical-pipeline/NOTICE (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-clinical-pipeline/NOTICE Wed
Nov 21 22:01:37 2012
@@ -1,19 +1 @@
 
-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/

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-dictionary-lookup/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-dictionary-lookup/pom.xml?rev=1412325&r1=1412324&r2=1412325&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-dictionary-lookup/pom.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-dictionary-lookup/pom.xml Wed
Nov 21 22:01:37 2012
@@ -19,7 +19,7 @@
     under the License.
 
 -->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>ctakes-dictionary-lookup</artifactId>
 	<name>Apache cTAKES dictionary lookup</name>
@@ -53,5 +53,35 @@
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
 		</dependency>
+		
+			<!-- cTAKES Resources -->
+			<dependency>
+				<groupId>net.sourceforge.ctakesresources</groupId>
+				<artifactId>ctakes-resources-umls2011ab</artifactId>
+				<version>3.0.0</version>
+			</dependency>
 	</dependencies>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-dependency-plugin</artifactId>
+				<version>2.5.1</version>
+				<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/branches/ctakes-3.0.0-incubating/ctakes-distribution/NOTICE
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-distribution/NOTICE?rev=1412325&r1=1412324&r2=1412325&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-distribution/NOTICE (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-distribution/NOTICE Wed Nov 21
22:01:37 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).



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