incubator-ctakes-commits mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From chen...@apache.org
Subject svn commit: r1399458 - in /incubator/ctakes/trunk/ctakes-distribution/src/main: assembly/bin.xml bin/runctakesCPE.bat bin/runctakesCPE.sh bin/runctakesCVD.bat bin/runctakesCVD.sh
Date Wed, 17 Oct 2012 22:13:15 GMT
Author: chenpei
Date: Wed Oct 17 22:13:14 2012
New Revision: 1399458

URL: http://svn.apache.org/viewvc?rev=1399458&view=rev
Log:
https://issues.apache.org/jira/browse/CTAKES-83
- Also adding the system scoped libs to the distribution.
- Also adding the context tokenizer module
- Updated the startup scripts to auto detect the CTAKES_HOME directory.  (so it can work with
a double click or started with other directories).

Modified:
    incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/bin.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

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=1399458&r1=1399457&r2=1399458&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml (original)
+++ incubator/ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml Wed Oct 17 22:13:14
2012
@@ -15,6 +15,7 @@
 				<include>org.apache.ctakes:ctakes-chunker</include>
 				<include>org.apache.ctakes:ctakes-clinical-pipeline</include>
 				<include>org.apache.ctakes:ctakes-constituency-parser</include>
+				<include>org.apache.ctakes:ctakes-context-tokenizer</include>				
 				<include>org.apache.ctakes:ctakes-core</include>
 				<include>org.apache.ctakes:ctakes-coreference</include>
 				<include>org.apache.ctakes:ctakes-dependency-parser</include>
@@ -42,6 +43,48 @@
 	</dependencySets>
 
 	<fileSets>
+		<fileSet>
+			<!-- Temporary workaround: Adding in the system scoped libaries. Remove 
+				these once they are in Maven Central -->
+			<directory>../ctakes-core/lib</directory>
+			<outputDirectory>lib</outputDirectory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<includes>
+				<include>OpenAI_FSM.jar</include>
+				<include>FindStructAPI.jar</include>
+				<include>SQLWrapper.jar</include>
+			</includes>
+		</fileSet>
+		<fileSet>
+			<!-- Temporary workaround: Adding in the system scoped libaries. Remove 
+				these once they are in Maven Central -->
+			<directory>../ctakes-assertion/lib</directory>
+			<outputDirectory>lib</outputDirectory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<includes>
+				<include>med-facts-i2b2-1.2-SNAPSHOT.jar</include>
+				<include>med-facts-zoner-1.1.jar</include>
+				<include>jcarafe-core_2.9.1-0.9.8.3.RC4.jar</include>
+				<include>jcarafe-ext_2.9.1-0.9.8.3.RC4.jar</include>				
+			</includes>
+		</fileSet>
+		<fileSet>
+			<!-- Temporary workaround: Adding in the system scoped libaries. Remove 
+				these once they are in Maven Central -->
+			<directory>../ctakes-lvg/lib</directory>
+			<outputDirectory>lib</outputDirectory>
+			<filtered>true</filtered>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+			<includes>
+				<include>lvg2010dist.jar</include>				
+			</includes>
+		</fileSet>		
+
 
 		<fileSet>
 			<directory>../</directory>
@@ -97,7 +140,7 @@
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
 			<outputDirectory>desc/ctakes-chunker/desc</outputDirectory>
-		</fileSet>				
+		</fileSet>
 		<fileSet>
 			<directory>../ctakes-clinical-pipeline/desc</directory>
 			<filtered>true</filtered>
@@ -110,50 +153,51 @@
 			<filtered>true</filtered>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-constituency-paraser/desc</outputDirectory>
-		</fileSet>	
+			<outputDirectory>desc/ctakes-constituency-paraser/desc
+			</outputDirectory>
+		</fileSet>
 		<fileSet>
 			<directory>../ctakes-context-tokenizer/desc</directory>
 			<filtered>true</filtered>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
 			<outputDirectory>desc/ctakes-context-tokenizer/desc</outputDirectory>
-		</fileSet>	
+		</fileSet>
 		<fileSet>
 			<directory>../ctakes-core/desc</directory>
 			<filtered>true</filtered>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
 			<outputDirectory>desc/ctakes-core/desc</outputDirectory>
-		</fileSet>							
+		</fileSet>
 		<fileSet>
 			<directory>../ctakes-coreference/desc</directory>
 			<filtered>true</filtered>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
 			<outputDirectory>desc/ctakes-coreference/desc</outputDirectory>
-		</fileSet>						
+		</fileSet>
 		<fileSet>
 			<directory>../ctakes-dependency-parser/desc</directory>
 			<filtered>true</filtered>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
 			<outputDirectory>desc/ctakes-dependency-parser/desc</outputDirectory>
-		</fileSet>	
+		</fileSet>
 		<fileSet>
 			<directory>../ctakes-dictionary-lookup/desc</directory>
 			<filtered>true</filtered>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
 			<outputDirectory>desc/ctakes-dictionary-lookup/desc</outputDirectory>
-		</fileSet>	
+		</fileSet>
 		<fileSet>
 			<directory>../ctakes-drug-ner/desc</directory>
 			<filtered>true</filtered>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
 			<outputDirectory>desc/ctakes-drug-ner/desc</outputDirectory>
-		</fileSet>		
+		</fileSet>
 		<fileSet>
 			<directory>../ctakes-lvg/desc</directory>
 			<filtered>true</filtered>
@@ -167,42 +211,43 @@
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
 			<outputDirectory>desc/ctakes-ne-contexts/desc</outputDirectory>
-		</fileSet>			
+		</fileSet>
 		<fileSet>
 			<directory>../ctakes-pad-term-spotter/desc</directory>
 			<filtered>true</filtered>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
 			<outputDirectory>desc/ctakes-pad-term-spotter/desc</outputDirectory>
-		</fileSet>			
+		</fileSet>
 		<fileSet>
 			<directory>../ctakes-pos-tagger/desc</directory>
 			<filtered>true</filtered>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
 			<outputDirectory>desc/ctakes-pos-tagger/desc</outputDirectory>
-		</fileSet>	
+		</fileSet>
 		<fileSet>
 			<directory>../ctakes-preprocessor/desc</directory>
 			<filtered>true</filtered>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
 			<outputDirectory>desc/ctakes-preprocessor/desc</outputDirectory>
-		</fileSet>			
+		</fileSet>
 		<fileSet>
 			<directory>../ctakes-relation-extractor/desc</directory>
 			<filtered>true</filtered>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
-			<outputDirectory>desc/ctakes-relation-extractor/desc</outputDirectory>
-		</fileSet>		
+			<outputDirectory>desc/ctakes-relation-extractor/desc
+			</outputDirectory>
+		</fileSet>
 		<fileSet>
 			<directory>../ctakes-side-effect/desc</directory>
 			<filtered>true</filtered>
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
 			<outputDirectory>desc/ctakes-side-effect/desc</outputDirectory>
-		</fileSet>					
+		</fileSet>
 		<fileSet>
 			<directory>../ctakes-smoking-status/desc</directory>
 			<filtered>true</filtered>
@@ -216,6 +261,6 @@
 			<fileMode>644</fileMode>
 			<directoryMode>755</directoryMode>
 			<outputDirectory>desc/ctakes-type-system/desc</outputDirectory>
-		</fileSet>													
+		</fileSet>
 	</fileSets>
 </assembly>
\ No newline at end of file

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=1399458&r1=1399457&r2=1399458&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.bat (original)
+++ incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.bat Wed Oct 17 22:13:14
2012
@@ -1,21 +1,40 @@
-@REM
-@REM Licensed to the Apache Software Foundation (ASF) under one
-@REM or more contributor license agreements.  See the NOTICE file
-@REM distributed with this work for additional information
-@REM regarding copyright ownership.  The ASF licenses this file
-@REM to you under the Apache License, Version 2.0 (the
-@REM "License"); you may not use this file except in compliance
-@REM with the License.  You may obtain a copy of the License at
-@REM
-@REM   http://www.apache.org/licenses/LICENSE-2.0
-@REM
-@REM Unless required by applicable law or agreed to in writing,
-@REM software distributed under the License is distributed on an
-@REM "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-@REM KIND, either express or implied.  See the License for the
-@REM specific language governing permissions and limitations
-@REM under the License.
-@REM
-
-@REM Requires JAVA JDK 1.6+
-java -cp lib/;desc/ -Djava.util.logging.config.file=${UIMA_HOME}/Logger.properties -Xms512M
-Xmx1024M org.apache.uima.tools.cpm.CpmFrame
+@REM
+@REM Licensed to the Apache Software Foundation (ASF) under one
+@REM or more contributor license agreements.  See the NOTICE file
+@REM distributed with this work for additional information
+@REM regarding copyright ownership.  The ASF licenses this file
+@REM to you under the Apache License, Version 2.0 (the
+@REM "License"); you may not use this file except in compliance
+@REM with the License.  You may obtain a copy of the License at
+@REM
+@REM   http://www.apache.org/licenses/LICENSE-2.0
+@REM
+@REM Unless required by applicable law or agreed to in writing,
+@REM software distributed under the License is distributed on an
+@REM "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+@REM KIND, either express or implied.  See the License for the
+@REM specific language governing permissions and limitations
+@REM under the License.
+@REM
+
+@REM Requires JAVA JDK 1.6+
+
+@REM Guess CTAKES_HOME if not defined
+set CURRENT_DIR=%cd%
+if not "%CTAKES_HOME%" == "" goto gotHome
+set CTAKES_HOME=%CURRENT_DIR%
+if exist "%CTAKES_HOME%\bin\runctakesCPE.bat" goto okHome
+cd ..
+set CTAKES_HOME=%cd%
+
+:gotHome
+if exist "%CTAKES_HOME%\bin\runctakesCPE.bat" goto okHome
+echo The CTAKES_HOME environment variable is not defined correctly
+echo This environment variable is needed to run this program
+goto end
+
+:okHome
+cd %CTAKES_HOME%
+java -cp "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc" -Djava.util.logging.config.file=%UIMA_HOME%/Logger.properties
-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=1399458&r1=1399457&r2=1399458&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.sh (original)
+++ incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCPE.sh Wed Oct 17 22:13:14
2012
@@ -1,21 +1,38 @@
-#
-# Licensed to the Apache Software Foundation (ASF) under one
-# or more contributor license agreements.  See the NOTICE file
-# distributed with this work for additional information
-# regarding copyright ownership.  The ASF licenses this file
-# to you under the Apache License, Version 2.0 (the
-# "License"); you may not use this file except in compliance
-# with the License.  You may obtain a copy of the License at
-#
-#   http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing,
-# software distributed under the License is distributed on an
-# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-# KIND, either express or implied.  See the License for the
-# specific language governing permissions and limitations
-# under the License.
-#
-#
-# Requires JAVA JDK 1.6+
-java -cp lib/:desc/ -Djava.util.logging.config.file=${UIMA_HOME}/Logger.properties -Xms512M
-Xmx1024M org.apache.uima.tools.cpm.CpmFrame
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+#
+# Requires JAVA JDK 1.6+
+
+PRG="$0"
+while [ -h "$PRG" ]; do
+  ls=`ls -ld "$PRG"`
+  link=`expr "$ls" : '.*-> \(.*\)$'`
+  if expr "$link" : '/.*' > /dev/null; then
+    PRG="$link"
+  else
+    PRG=`dirname "$PRG"`/"$link"
+  fi
+done
+PRGDIR=`dirname "$PRG"`
+
+# Only set CTAKES_HOME if not already set
+[ -z "$CTAKES_HOME" ] && CTAKES_HOME=`cd "$PRGDIR/.." >/dev/null; pwd`
+
+cd $CTAKES_HOME
+java -cp $CTAKES_HOME/lib/*:$CTAKES_HOME/desc/ -Djava.util.logging.config.file=${UIMA_HOME}/Logger.properties
-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=1399458&r1=1399457&r2=1399458&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.bat (original)
+++ incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.bat Wed Oct 17 22:13:14
2012
@@ -18,4 +18,23 @@
 @REM
 
 @REM Requires JAVA JDK 1.6+
-java -cp lib/;desc/ -Djava.util.logging.config.file=${UIMA_HOME}/Logger.properties -Xms512M
-Xmx1024M org.apache.uima.tools.cvd.CVD
+
+@REM Guess CTAKES_HOME if not defined
+set CURRENT_DIR=%cd%
+if not "%CTAKES_HOME%" == "" goto gotHome
+set CTAKES_HOME=%CURRENT_DIR%
+if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto okHome
+cd ..
+set CTAKES_HOME=%cd%
+
+:gotHome
+if exist "%CTAKES_HOME%\bin\runctakesCVD.bat" goto okHome
+echo The CTAKES_HOME environment variable is not defined correctly
+echo This environment variable is needed to run this program
+goto end
+
+:okHome
+cd %CTAKES_HOME%
+java -cp "%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc" -Djava.util.logging.config.file=%UIMA_HOME%/Logger.properties
-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=1399458&r1=1399457&r2=1399458&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.sh (original)
+++ incubator/ctakes/trunk/ctakes-distribution/src/main/bin/runctakesCVD.sh Wed Oct 17 22:13:14
2012
@@ -18,4 +18,21 @@
 #
 #
 # Requires JAVA JDK 1.6+
-java -cp lib/:desc/ -Djava.util.logging.config.file=${UIMA_HOME}/Logger.properties -Xms512M
-Xmx1024M org.apache.uima.tools.cvd.CVD
+
+PRG="$0"
+while [ -h "$PRG" ]; do
+  ls=`ls -ld "$PRG"`
+  link=`expr "$ls" : '.*-> \(.*\)$'`
+  if expr "$link" : '/.*' > /dev/null; then
+    PRG="$link"
+  else
+    PRG=`dirname "$PRG"`/"$link"
+  fi
+done
+PRGDIR=`dirname "$PRG"`
+
+# Only set CTAKES_HOME if not already set
+[ -z "$CTAKES_HOME" ] && CTAKES_HOME=`cd "$PRGDIR/.." >/dev/null; pwd`
+
+cd $CTAKES_HOME
+java -cp $CTAKES_HOME/lib/*:$CTAKES_HOME/desc/ -Djava.util.logging.config.file=${UIMA_HOME}/Logger.properties
-Xms512M -Xmx1024M org.apache.uima.tools.cvd.CVD



Mime
View raw message