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From chen...@apache.org
Subject 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/
Date Mon, 15 Oct 2012 20:37:08 GMT
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



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