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Posted to commits@ctakes.apache.org by ch...@apache.org on 2012/10/15 22:37:08 UTC
svn commit: r1398497 - in /incubator/ctakes/trunk/ctakes-clinical-pipeline:
pom.xml runctakesCPE.bat runctakesCPE.sh runctakesCVD.bat runctakesCVD.sh
src/main/java/org/apache/ctakes/clinicalpipeline/main/
Author: chenpei
Date: Mon Oct 15 20:37:08 2012
New Revision: 1398497
URL: http://svn.apache.org/viewvc?rev=1398497&view=rev
Log:
https://issues.apache.org/jira/browse/CTAKES-81
- Delete cTAKESCVDGUI.java and cTAKESCPEGUI.java; they look like a copy and paste of org.apache.uima.tools.cvd.CVD, org.apache.uima.tools.cpm.CpmFrame. Just launch the UIMA classes; I couldn't see a need to have our own copies; if we really need to customize it, I would suggest extended UIMA and override any special functionality. Otherwise, we'll end up maintaining these ourselves which is not ideal.
- Add profiles the pom.xml to allow launch CVD, CPE from mvn using Maven to dynamically resolve all of the required dependencies. (We won't have to maintain yet another set of scripts that contain dependencies or require some uber-jar.)
- Update the existing runctakesCPE.sh, etc to use "mvn exec:exec -PrunCPE" instead.
Removed:
incubator/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/main/
Modified:
incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml
incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCPE.bat
incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCPE.sh
incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCVD.bat
incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCVD.sh
Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml?rev=1398497&r1=1398496&r2=1398497&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml Mon Oct 15 20:37:08 2012
@@ -9,7 +9,7 @@
<version>3.0.0-SNAPSHOT</version>
<relativePath>..</relativePath>
</parent>
-
+
<dependencies>
<dependency>
@@ -63,11 +63,149 @@
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-assertion</artifactId>
- </dependency>
+ </dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dependency-parser</artifactId>
- </dependency>
+ </dependency>
</dependencies>
-
+ <profiles>
+ <profile>
+ <id>runCPE</id>
+ <activation>
+ <property>
+ <name>runCPE</name>
+ </property>
+ </activation>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>exec-maven-plugin</artifactId>
+ <version>1.2.1</version>
+ <configuration>
+ <includeProjectDependencies>true</includeProjectDependencies>
+ <includePluginDependencies>true</includePluginDependencies>
+ <executableDependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-clinical-pipeline</artifactId>
+ </executableDependency>
+ <executions>
+ <execution>
+ <goals>
+ <goal>exec</goal>
+ </goals>
+ <configuration></configuration>
+ </execution>
+ </executions>
+ <executable>java</executable>
+ <longClasspath>false</longClasspath>
+ <arguments>
+ <argument>-Djava.util.logging.config.file=${UIMA_HOME}/Logger.properties</argument>
+ <argument>-Xms512M</argument>
+ <argument>-Xmx1024M</argument>
+ <argument>-classpath</argument>
+ <classpath />
+ <argument>org.apache.uima.tools.cpm.CpmFrame</argument>
+ </arguments>
+ </configuration>
+ <dependencies>
+ <!-- System lib dependencies is causing a world of pain. Remove these
+ when they're uploaded to Maven Central -->
+ <dependency>
+ <groupId>net.sourceforge.openai</groupId>
+ <artifactId>fsm</artifactId>
+ <version>0.1a</version>
+ <scope>system</scope>
+ <systemPath>${project.basedir}/../ctakes-core/lib/OpenAI_FSM.jar</systemPath>
+ </dependency>
+ <dependency>
+ <groupId>findstruct</groupId>
+ <artifactId>findstruct</artifactId>
+ <version>0.0.1</version>
+ <scope>system</scope>
+ <systemPath>${project.basedir}/../ctakes-core/lib/FindStructAPI.jar</systemPath>
+ </dependency>
+ <dependency>
+ <groupId>sqlWrapper</groupId>
+ <artifactId>sqlWrapper</artifactId>
+ <version>0.0.1</version>
+ <scope>system</scope>
+ <systemPath>${project.basedir}/../ctakes-core/lib/SQLWrapper.jar</systemPath>
+ </dependency>
+ </dependencies>
+ </plugin>
+ </plugins>
+ </build>
+ </profile>
+ <profile>
+ <id>runCVD</id>
+ <activation>
+ <property>
+ <name>runCVD</name>
+ </property>
+ </activation>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>exec-maven-plugin</artifactId>
+ <version>1.2.1</version>
+ <configuration>
+ <includeProjectDependencies>true</includeProjectDependencies>
+ <includePluginDependencies>true</includePluginDependencies>
+ <executableDependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-clinical-pipeline</artifactId>
+ </executableDependency>
+ <executions>
+ <execution>
+ <goals>
+ <goal>exec</goal>
+ </goals>
+ <configuration></configuration>
+ </execution>
+ </executions>
+ <executable>java</executable>
+ <longClasspath>false</longClasspath>
+ <arguments>
+ <argument>-Djava.util.logging.config.file=${UIMA_HOME}/Logger.properties</argument>
+ <argument>-Xms512M</argument>
+ <argument>-Xmx1024M</argument>
+ <argument>-classpath</argument>
+ <classpath />
+ <argument>org.apache.uima.tools.cvd.CVD</argument>
+ </arguments>
+ </configuration>
+ <dependencies>
+ <!-- System lib dependencies is causing a world of pain. Remove these
+ when they're uploaded to Maven Central -->
+ <dependency>
+ <groupId>net.sourceforge.openai</groupId>
+ <artifactId>fsm</artifactId>
+ <version>0.1a</version>
+ <scope>system</scope>
+ <systemPath>${project.basedir}/../ctakes-core/lib/OpenAI_FSM.jar</systemPath>
+ </dependency>
+ <dependency>
+ <groupId>findstruct</groupId>
+ <artifactId>findstruct</artifactId>
+ <version>0.0.1</version>
+ <scope>system</scope>
+ <systemPath>${project.basedir}/../ctakes-core/lib/FindStructAPI.jar</systemPath>
+ </dependency>
+ <dependency>
+ <groupId>sqlWrapper</groupId>
+ <artifactId>sqlWrapper</artifactId>
+ <version>0.0.1</version>
+ <scope>system</scope>
+ <systemPath>${project.basedir}/../ctakes-core/lib/SQLWrapper.jar</systemPath>
+ </dependency>
+ </dependencies>
+ </plugin>
+ </plugins>
+ </build>
+ </profile>
+ </profiles>
+
</project>
Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCPE.bat
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCPE.bat?rev=1398497&r1=1398496&r2=1398497&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCPE.bat (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCPE.bat Mon Oct 15 20:37:08 2012
@@ -17,5 +17,5 @@
@REM under the License.
@REM
-java -Xms1024M -Xmx2048M -cp resources;cTAKESdesc;cTAKES.jar org.apache.ctakes.clinicalpipeline.main.cTAKESCPEGUI
-
+@REM Requires JAVA JDK 1.6+, Maven 2 installed
+mvn exec:exec -PrunCPE
Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCPE.sh
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCPE.sh?rev=1398497&r1=1398496&r2=1398497&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCPE.sh (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCPE.sh Mon Oct 15 20:37:08 2012
@@ -16,6 +16,6 @@
# specific language governing permissions and limitations
# under the License.
#
-
-java -Xms1024M -Xmx2048M -cp resources:cTAKESdesc:cTAKES.jar org.apache.ctakes.clinicalpipeline.main.cTAKESCPEGUI
-
+#
+# Requires JAVA JDK 1.6+, Maven 2 installed
+mvn exec:exec -PrunCPE
Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCVD.bat
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCVD.bat?rev=1398497&r1=1398496&r2=1398497&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCVD.bat (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCVD.bat Mon Oct 15 20:37:08 2012
@@ -17,5 +17,5 @@
@REM under the License.
@REM
-java -Xms1024M -Xmx2048M -cp resources;cTAKESdesc;cTAKES.jar org.apache.ctakes.clinicalpipeline.main.cTAKESCVDGUI
-
+@REM Requires JAVA JDK 1.6+, Maven 2 installed
+mvn exec:exec -PrunCVD
Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCVD.sh
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCVD.sh?rev=1398497&r1=1398496&r2=1398497&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCVD.sh (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCVD.sh Mon Oct 15 20:37:08 2012
@@ -16,6 +16,6 @@
# specific language governing permissions and limitations
# under the License.
#
-
-java -Xms1024M -Xmx2048M -cp resources:cTAKESdesc:cTAKES.jar org.apache.ctakes.clinicalpipeline.main.cTAKESCVDGUI
-
+#
+# Requires JAVA JDK 1.6+, Maven 2 installed
+mvn exec:exec -PrunCVD