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Posted to commits@ctakes.apache.org by ch...@apache.org on 2012/11/21 23:01:40 UTC
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...
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).