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Posted to commits@ctakes.apache.org by ch...@apache.org on 2012/11/27 18:37:19 UTC
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...
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>