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Posted to commits@ctakes.apache.org by se...@apache.org on 2016/10/23 20:48:38 UTC
svn commit: r1766319 - in /ctakes/trunk/ctakes-distribution: pom.xml
src/main/assembly/bin.xml src/main/bin/runClinicalPipeline.bat
src/main/bin/runClinicalPipeline.sh
Author: seanfinan
Date: Sun Oct 23 20:48:37 2016
New Revision: 1766319
URL: http://svn.apache.org/viewvc?rev=1766319&view=rev
Log:
Add ctakes-examples
Copy resources
check for $JAVA_HOME
Modified:
ctakes/trunk/ctakes-distribution/pom.xml
ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml
ctakes/trunk/ctakes-distribution/src/main/bin/runClinicalPipeline.bat
ctakes/trunk/ctakes-distribution/src/main/bin/runClinicalPipeline.sh
Modified: ctakes/trunk/ctakes-distribution/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-distribution/pom.xml?rev=1766319&r1=1766318&r2=1766319&view=diff
==============================================================================
--- ctakes/trunk/ctakes-distribution/pom.xml (original)
+++ ctakes/trunk/ctakes-distribution/pom.xml Sun Oct 23 20:48:37 2016
@@ -56,6 +56,10 @@
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dictionary-lookup-fast</artifactId>
</dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-examples</artifactId>
+ </dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-preprocessor</artifactId>
@@ -133,7 +137,7 @@
<artifactId>ctakes-ytex-web</artifactId>
<version>${project.version}</version>
<classifier>classes</classifier>
- </dependency>
+ </dependency>
</dependencies>
<build>
Modified: ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml?rev=1766319&r1=1766318&r2=1766319&view=diff
==============================================================================
--- ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml (original)
+++ ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml Sun Oct 23 20:48:37 2016
@@ -60,6 +60,7 @@
<include>org.apache.ctakes:ctakes-ytex</include>
<include>org.apache.ctakes:ctakes-ytex-uima</include>
<include>org.apache.ctakes:ctakes-ytex-web</include>
+ <include>org.apache.ctakes:ctakes-examples</include>
</includes>
<excludes>
@@ -99,6 +100,18 @@
</includes>
</fileSet>
<!-- The Type System needs to exist outside the lib/*.jar file. Otherwise it cannot be used with the CVD. -->
+ <fileSet>
+ <directory>../ctakes-clinical-pipeline-res/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ </fileSet>
+ <fileSet>
+ <directory>../ctakes-ne-contexts-res/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ </fileSet>
<fileSet>
<directory>../ctakes-examples-res/src/main/resources</directory>
<outputDirectory>resources</outputDirectory>
@@ -155,7 +168,23 @@
<outputDirectory>resources</outputDirectory>
<fileMode>644</fileMode>
<directoryMode>755</directoryMode>
- </fileSet>
+ </fileSet>
+ <fileSet>
+ <directory>../ctakes-core-res/src/main/resources/org/apache/ctakes/core/pipeline</directory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ <includes>
+ <include>DefaultTokenizerPipeline.piper</include>
+ </includes>
+ <outputDirectory>resources/org/apache/ctakes/core/pipeline</outputDirectory>
+ </fileSet>
+ <!-- Copy user resources -->
+ <fileSet>
+ <directory>../resources</directory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ <outputDirectory>resources</outputDirectory>
+ </fileSet>
<fileSet>
<directory>../</directory>
<outputDirectory></outputDirectory>
@@ -169,7 +198,6 @@
<fileSet>
<directory>.</directory>
<outputDirectory></outputDirectory>
-
<fileMode>644</fileMode>
<directoryMode>755</directoryMode>
<includes>
@@ -201,7 +229,6 @@
<directoryMode>755</directoryMode>
<outputDirectory>config</outputDirectory>
</fileSet>
-
<!-- Copy a default log4j config that could be overridden during runtime -->
<fileSet>
<directory>../ctakes-core-res/src/main/resources</directory>
Modified: ctakes/trunk/ctakes-distribution/src/main/bin/runClinicalPipeline.bat
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-distribution/src/main/bin/runClinicalPipeline.bat?rev=1766319&r1=1766318&r2=1766319&view=diff
==============================================================================
--- ctakes/trunk/ctakes-distribution/src/main/bin/runClinicalPipeline.bat (original)
+++ ctakes/trunk/ctakes-distribution/src/main/bin/runClinicalPipeline.bat Sun Oct 23 20:48:37 2016
@@ -42,7 +42,15 @@ goto end
:okHome
@set PATH=%PATH%;%CTAKES_HOME%\lib\auth\x64
+@REM use JAVA_HOME if set
+if exist "%JAVA_HOME%\bin\java.exe" set PATH=%JAVA_HOME%\bin;%PATH%
+
cd %CTAKES_HOME%
-java -cp "%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/;%CTAKES_HOME%/lib/*" -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml -Xms512M -Xmx3g org.apache.ctakes.core.pipeline.PiperFileRunner -p org/apache/ctakes/clinical/pipeline/DefaultClinicalPipeline.piper %*
+set CLASS_PATH=%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/;%CTAKES_HOME%/lib/*
+set LOG4J_PARM=-Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml
+set PIPE_RUNNER=org.apache.ctakes.core.pipeline.PiperFileRunner
+set FAST_PIPER=resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
+java -cp "%CLASS_PATH%" %LOG4J_PARM% -Xms512M -Xmx3g %PIPE_RUNNER% -p %FAST_PIPER% %*
cd %CURRENT_DIR%
-:end
\ No newline at end of file
+
+:end
Modified: ctakes/trunk/ctakes-distribution/src/main/bin/runClinicalPipeline.sh
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-distribution/src/main/bin/runClinicalPipeline.sh?rev=1766319&r1=1766318&r2=1766319&view=diff
==============================================================================
--- ctakes/trunk/ctakes-distribution/src/main/bin/runClinicalPipeline.sh (original)
+++ ctakes/trunk/ctakes-distribution/src/main/bin/runClinicalPipeline.sh Sun Oct 23 20:48:37 2016
@@ -42,4 +42,4 @@ PRGDIR=`dirname "$PRG"`
[ -z "$CTAKES_HOME" ] && CTAKES_HOME=`cd "$PRGDIR/.." >/dev/null; pwd`
cd $CTAKES_HOME
-java -cp $CTAKES_HOME/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/* -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g org.apache.ctakes.core.pipeline.PiperFileRunner -p org/apache/ctakes/clinical/pipeline/DefaultClinicalPipeline.piper "$@"
+java -cp $CTAKES_HOME/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/* -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g org.apache.ctakes.core.pipeline.PiperFileRunner -p org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper "$@"