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From chen...@apache.org
Subject svn commit: r1402304 - in /incubator/ctakes/trunk: ./ ctakes-distribution/src/main/assembly/ ctakes-distribution/src/main/bin/
Date Thu, 25 Oct 2012 19:51:45 GMT
Author: chenpei
Date: Thu Oct 25 19:51:44 2012
New Revision: 1402304

URL: http://svn.apache.org/viewvc?rev=1402304&view=rev
Log:
CTAKES-89 - During assembly copy the resources from src/main/resources to a resources directory
which could then be added to the classpath during runtime scripts. exclude them in the jars
for now since things like lucene can't read them from a jar anyway.  This is a non issue for
eclipse ide development since maven automatically copies them to target and is in the classpath
anyway.

Modified:
    incubator/ctakes/trunk/README
    incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml
    incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/src.xml
    incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.bat
    incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.sh
    incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.bat
    incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.sh
    incubator/ctakes/trunk/pom.xml

Modified: incubator/ctakes/trunk/README
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/README?rev=1402304&r1=1402303&r2=1402304&view=diff
==============================================================================
--- incubator/ctakes/trunk/README (original)
+++ incubator/ctakes/trunk/README Thu Oct 25 19:51:44 2012
@@ -1,5 +1,18 @@
 
-Javadocs are found within the docs directory.
+Apache cTAKES
+===============================
+Detail documentation could found on:
+http://incubator.apache.org/ctakes
 
-Other documentation is found online at
-https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/OHNLP_Documentation_and_Downloads
+Requirements
+-----------
+Java 1.6 is required to run cTAKES
+Maven 3.0.0 is required for building it
+
+Running the default pipeline in the UIMA CAS Visual Debugger
+or Collection Processing Engine
+-----------
+Run bin/runctakesCVD/CPE.sh.bat
+Load AE (analysis engine)
+Select desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor
+Enter note and run analysis engine.
\ No newline at end of file

Modified: incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml?rev=1402304&r1=1402303&r2=1402304&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml (original)
+++ incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml Thu Oct 25 19:51:44
2012
@@ -24,7 +24,7 @@
     xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2
http://maven.apache.org/xsd/assembly-1.1.2.xsd">
 	<id>bin</id>
 	<formats>
-		<format>tar.gz</format>
+		<format>tar.gz</format> 
 		<format>zip</format>
 	</formats>
 
@@ -161,120 +161,138 @@
 		<!-- Copy all of the XML Descriptors. Temp Preserving this structure so 
 			that the relative paths still work. -->
 		<fileSet>
-			<directory>../ctakes-assertion/desc</directory>
+			<directory>../</directory>
+			<outputDirectory>desc</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-assertion/desc</outputDirectory>
+		      <includes>
+		        <include>*/desc/**</include>
+		      </includes>			
 		</fileSet>
+		
 		<fileSet>
-			<directory>../ctakes-chunker/desc</directory>
+		    <directory>../ctakes-assertion/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-chunker/desc</outputDirectory>
-		</fileSet>
+    	</fileSet>
 		<fileSet>
-			<directory>../ctakes-clinical-pipeline/desc</directory>
+		    <directory>../ctakes-chunker/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-clinical-pipeline/desc</outputDirectory>
-		</fileSet>
+    	</fileSet>
 		<fileSet>
-			<directory>../ctakes-constituency-paraser/desc</directory>
+		    <directory>../ctakes-clinical-pipeline/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-constituency-paraser/desc
-			</outputDirectory>
-		</fileSet>
+    	</fileSet>    	
 		<fileSet>
-			<directory>../ctakes-context-tokenizer/desc</directory>
+		    <directory>../ctakes-constituency-parser/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-context-tokenizer/desc</outputDirectory>
-		</fileSet>
+    	</fileSet>    	
 		<fileSet>
-			<directory>../ctakes-core/desc</directory>
+		    <directory>../ctakes-context-tokenizer/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-core/desc</outputDirectory>
-		</fileSet>
+    	</fileSet>    	
 		<fileSet>
-			<directory>../ctakes-coreference/desc</directory>
+		    <directory>../ctakes-core/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-coreference/desc</outputDirectory>
-		</fileSet>
+			<excludes><exclude>log4j.xml</exclude></excludes>
+    	</fileSet>
 		<fileSet>
-			<directory>../ctakes-dependency-parser/desc</directory>
+		    <directory>../ctakes-coreference/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-dependency-parser/desc</outputDirectory>
-		</fileSet>
+    	</fileSet>    	   
 		<fileSet>
-			<directory>../ctakes-dictionary-lookup/desc</directory>
+		    <directory>../ctakes-dependency-parser/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-dictionary-lookup/desc</outputDirectory>
-		</fileSet>
+    	</fileSet>    	
 		<fileSet>
-			<directory>../ctakes-drug-ner/desc</directory>
+		    <directory>../ctakes-dictionary-lookup/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-drug-ner/desc</outputDirectory>
-		</fileSet>
+    	</fileSet>    	 	
 		<fileSet>
-			<directory>../ctakes-lvg/desc</directory>
+		    <directory>../ctakes-drug-ner/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-lvg/desc</outputDirectory>
-		</fileSet>
+    	</fileSet>    	
 		<fileSet>
-			<directory>../ctakes-ne-contexts/desc</directory>
+		    <directory>../ctakes-lvg/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-ne-contexts/desc</outputDirectory>
-		</fileSet>
+    	</fileSet>    	
 		<fileSet>
-			<directory>../ctakes-pad-term-spotter/desc</directory>
+		    <directory>../ctakes-ne-contexts/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-pad-term-spotter/desc</outputDirectory>
-		</fileSet>
+    	</fileSet>    	
 		<fileSet>
-			<directory>../ctakes-pos-tagger/desc</directory>
+		    <directory>../ctakes-pad-term-spotter/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-pos-tagger/desc</outputDirectory>
-		</fileSet>
+    	</fileSet>    	
 		<fileSet>
-			<directory>../ctakes-preprocessor/desc</directory>
+		    <directory>../ctakes-pos-tagger/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-preprocessor/desc</outputDirectory>
-		</fileSet>
+    	</fileSet>    
 		<fileSet>
-			<directory>../ctakes-relation-extractor/desc</directory>
+		    <directory>../ctakes-preprocessor/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-relation-extractor/desc
-			</outputDirectory>
-		</fileSet>
+    	</fileSet>    	
 		<fileSet>
-			<directory>../ctakes-side-effect/desc</directory>
+		    <directory>../ctakes-relation-extractor/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-side-effect/desc</outputDirectory>
-		</fileSet>
+    	</fileSet>  
 		<fileSet>
-			<directory>../ctakes-smoking-status/desc</directory>
+		    <directory>../ctakes-side-effect/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-smoking-status/desc</outputDirectory>
-		</fileSet>
+    	</fileSet>    	  		
 		<fileSet>
-			<directory>../ctakes-type-system/desc</directory>
+		    <directory>../ctakes-smoking-status/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-type-system/desc</outputDirectory>
-		</fileSet>
+    	</fileSet>
+    	<!-- Type System types should already be in the jar -->
+    	<!-- 
+		<fileSet>
+		    <directory>../ctakes-type-system/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+    	</fileSet>   
+    	--> 	
+		<fileSet>
+		    <directory>../ctakes-utils/src/main/resources</directory>
+		    <outputDirectory>resources</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+    	</fileSet>    	    	
 	</fileSets>
 </assembly>
\ No newline at end of file

Modified: incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/src.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/src.xml?rev=1402304&r1=1402303&r2=1402304&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/src.xml (original)
+++ incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/src.xml Thu Oct 25 19:51:44
2012
@@ -38,6 +38,7 @@
         <exclude>**/.*/**</exclude>
         <exclude>**/pom.xml.releaseBackup</exclude>
         <exclude>**/release.properties</exclude>
+        <exclude>ctakes-temporal/**</exclude>
       </excludes>
     </fileSet>
   </fileSets>

Modified: incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.bat
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.bat?rev=1402304&r1=1402303&r2=1402304&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.bat (original)
+++ incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.bat Thu Oct 25 19:51:44
2012
@@ -35,6 +35,6 @@ goto end
 
 :okHome
 cd %CTAKES_HOME%
-java -cp "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/*" -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml
-Xms512M -Xmx1024M org.apache.uima.tools.cpm.CpmFrame
+java -cp "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/" -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml
-Xms512M -Xmx1024M org.apache.uima.tools.cpm.CpmFrame
 
 :end
\ No newline at end of file

Modified: incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.sh
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.sh?rev=1402304&r1=1402303&r2=1402304&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.sh (original)
+++ incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.sh Thu Oct 25 19:51:44
2012
@@ -35,4 +35,4 @@ PRGDIR=`dirname "$PRG"`
 [ -z "$CTAKES_HOME" ] && CTAKES_HOME=`cd "$PRGDIR/.." >/dev/null; pwd`
 
 cd $CTAKES_HOME
-java -cp $CTAKES_HOME/lib/*:$CTAKES_HOME/desc/ -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml
-Xms512M -Xmx1024M org.apache.uima.tools.cpm.CpmFrame
+java -cp $CTAKES_HOME/lib/*:$CTAKES_HOME/desc/:$CTAKES_HOME/resources/ -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml
-Xms512M -Xmx1024M org.apache.uima.tools.cpm.CpmFrame

Modified: incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.bat
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.bat?rev=1402304&r1=1402303&r2=1402304&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.bat (original)
+++ incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.bat Thu Oct 25 19:51:44
2012
@@ -35,6 +35,6 @@ goto end
 
 :okHome
 cd %CTAKES_HOME%
-java -cp "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc" -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml
-Xms512M -Xmx1024M org.apache.uima.tools.cvd.CVD
+java -cp "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/" -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml
-Xms512M -Xmx1024M org.apache.uima.tools.cvd.CVD
 
 :end
\ No newline at end of file

Modified: incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.sh
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.sh?rev=1402304&r1=1402303&r2=1402304&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.sh (original)
+++ incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.sh Thu Oct 25 19:51:44
2012
@@ -33,4 +33,4 @@ PRGDIR=`dirname "$PRG"`
 [ -z "$CTAKES_HOME" ] && CTAKES_HOME=`cd "$PRGDIR/.." >/dev/null; pwd`
 
 cd $CTAKES_HOME
-java -cp $CTAKES_HOME/lib/*:$CTAKES_HOME/desc/ -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml
-Xms512M -Xmx1024M org.apache.uima.tools.cvd.CVD
+java -cp $CTAKES_HOME/lib/*:$CTAKES_HOME/desc/:$CTAKES_HOME/resources/ -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml
-Xms512M -Xmx1024M org.apache.uima.tools.cvd.CVD

Modified: incubator/ctakes/trunk/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/pom.xml?rev=1402304&r1=1402303&r2=1402304&view=diff
==============================================================================
--- incubator/ctakes/trunk/pom.xml (original)
+++ incubator/ctakes/trunk/pom.xml Thu Oct 25 19:51:44 2012
@@ -470,6 +470,15 @@
 				<plugin>
 					<artifactId>maven-jar-plugin</artifactId>
 					<version>2.4</version>
+					<configuration>
+			          <includes>
+			          <!-- Resources will be copied by the assembly
+			          No need for it to be inside the jar -->
+			            <include>**/*.class</include>
+			            <include>**/types/*.xml</include>			            
+			            <include>**/META-INF/**</include>
+			          </includes>
+	        		</configuration>
 				</plugin>
 				<plugin>
 					<artifactId>maven-javadoc-plugin</artifactId>



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