You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@ctakes.apache.org by ch...@apache.org on 2013/05/08 21:02:56 UTC
svn commit: r1480409 [1/2] - in /ctakes/trunk: ctakes-assertion-res/
ctakes-assertion-res/.settings/
ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/types/
ctakes-assertion-zoner-res/ ctakes-assertion-zoner-res/.settings/
ctakes-ass...
Author: chenpei
Date: Wed May 8 19:02:55 2013
New Revision: 1480409
URL: http://svn.apache.org/r1480409
Log:
CTAKES-183 - Move the resources/models from src/main/resources to their own projects {project}-res
1) The various TypeSystem.xml files doesn't/shouldn't need to be in the resource/models projects. I think that was an oversight on my part last time.
2) I noticed that some of the projects have drivers or main classes which I assume a lot of folks are able to and plan to run pipelines directly from individual projects. If this is true, then I think it is actually easier to leave it as is and default to have the corresponding -res dependency in the pom.xml. Since it's maven controlled now, an external app can always add <exclude ctakes-drug-ner-res/>. This is just based on observation-- otherwise, each project will need to think about *-res during runtime if it's not in the pom.xml
Added:
ctakes/trunk/ctakes-assertion-zoner/src/main/resources/
ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/
ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/
ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/
ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/
ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/
ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/
ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml
ctakes/trunk/ctakes-assertion/src/main/resources/
ctakes/trunk/ctakes-assertion/src/main/resources/org/
ctakes/trunk/ctakes-assertion/src/main/resources/org/apache/
ctakes/trunk/ctakes-assertion/src/main/resources/org/apache/ctakes/
ctakes/trunk/ctakes-assertion/src/main/resources/org/apache/ctakes/assertion/
ctakes/trunk/ctakes-assertion/src/main/resources/org/apache/ctakes/assertion/types/
ctakes/trunk/ctakes-assertion/src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml
ctakes/trunk/ctakes-constituency-parser/src/main/resources/
ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/
ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/
ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/ctakes/
ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/
ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/
ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/types/
ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml
ctakes/trunk/ctakes-drug-ner/src/main/resources/
ctakes/trunk/ctakes-drug-ner/src/main/resources/org/
ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/
ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/
ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/
ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/
ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml
ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/
ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/
ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/
ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/
ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/
ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/types/
ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/types/TypeSystem.xml
ctakes/trunk/ctakes-side-effect/src/main/resources/
ctakes/trunk/ctakes-side-effect/src/main/resources/org/
ctakes/trunk/ctakes-side-effect/src/main/resources/org/apache/
ctakes/trunk/ctakes-side-effect/src/main/resources/org/apache/ctakes/
ctakes/trunk/ctakes-side-effect/src/main/resources/org/apache/ctakes/sideeffect/
ctakes/trunk/ctakes-side-effect/src/main/resources/org/apache/ctakes/sideeffect/types/
ctakes/trunk/ctakes-side-effect/src/main/resources/org/apache/ctakes/sideeffect/types/TypeSystem.xml
ctakes/trunk/ctakes-smoking-status/src/main/resources/
ctakes/trunk/ctakes-smoking-status/src/main/resources/org/
ctakes/trunk/ctakes-smoking-status/src/main/resources/org/apache/
ctakes/trunk/ctakes-smoking-status/src/main/resources/org/apache/ctakes/
ctakes/trunk/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/
ctakes/trunk/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/
ctakes/trunk/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml
Removed:
ctakes/trunk/ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/types/
ctakes/trunk/ctakes-assertion-zoner-res/src/main/resources/org/apache/
ctakes/trunk/ctakes-assertion-zoner/pom.xml.backup01
ctakes/trunk/ctakes-constituency-parser-res/src/main/resources/org/apache/ctakes/constituency/parser/types/
ctakes/trunk/ctakes-pad-term-spotter-res/src/main/resources/org/apache/ctakes/padtermspotter/types/
ctakes/trunk/ctakes-side-effect-res/src/main/resources/org/apache/ctakes/sideeffect/types/
ctakes/trunk/ctakes-side-effect/src/main/java/edu/mayo/
ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/types/
Modified:
ctakes/trunk/ctakes-assertion-res/.classpath
ctakes/trunk/ctakes-assertion-res/.settings/org.eclipse.core.resources.prefs
ctakes/trunk/ctakes-assertion-res/pom.xml
ctakes/trunk/ctakes-assertion-zoner-res/.classpath
ctakes/trunk/ctakes-assertion-zoner-res/.settings/org.eclipse.core.resources.prefs
ctakes/trunk/ctakes-assertion-zoner-res/pom.xml
ctakes/trunk/ctakes-assertion-zoner/.classpath
ctakes/trunk/ctakes-assertion-zoner/pom.xml
ctakes/trunk/ctakes-assertion/.classpath
ctakes/trunk/ctakes-assertion/pom.xml
ctakes/trunk/ctakes-chunker/pom.xml
ctakes/trunk/ctakes-constituency-parser-res/.classpath
ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.core.resources.prefs
ctakes/trunk/ctakes-constituency-parser-res/pom.xml
ctakes/trunk/ctakes-constituency-parser/.classpath
ctakes/trunk/ctakes-constituency-parser/pom.xml
ctakes/trunk/ctakes-core/pom.xml
ctakes/trunk/ctakes-coreference/pom.xml
ctakes/trunk/ctakes-dependency-parser/pom.xml
ctakes/trunk/ctakes-dictionary-lookup/pom.xml
ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml
ctakes/trunk/ctakes-drug-ner-res/.classpath
ctakes/trunk/ctakes-drug-ner-res/.settings/org.eclipse.core.resources.prefs
ctakes/trunk/ctakes-drug-ner-res/pom.xml
ctakes/trunk/ctakes-drug-ner/.classpath
ctakes/trunk/ctakes-drug-ner/pom.xml
ctakes/trunk/ctakes-lvg/pom.xml
ctakes/trunk/ctakes-ne-contexts/pom.xml
ctakes/trunk/ctakes-pad-term-spotter-res/pom.xml
ctakes/trunk/ctakes-pad-term-spotter/.classpath
ctakes/trunk/ctakes-pad-term-spotter/pom.xml
ctakes/trunk/ctakes-pos-tagger/pom.xml
ctakes/trunk/ctakes-side-effect-res/.classpath
ctakes/trunk/ctakes-side-effect-res/.settings/org.eclipse.core.resources.prefs
ctakes/trunk/ctakes-side-effect-res/pom.xml
ctakes/trunk/ctakes-side-effect/.classpath
ctakes/trunk/ctakes-side-effect/pom.xml
ctakes/trunk/ctakes-smoking-status-res/.classpath
ctakes/trunk/ctakes-smoking-status-res/.settings/org.eclipse.core.resources.prefs
ctakes/trunk/ctakes-smoking-status-res/pom.xml
ctakes/trunk/ctakes-smoking-status/.classpath
ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml
ctakes/trunk/ctakes-smoking-status/pom.xml
ctakes/trunk/ctakes-temporal/.classpath
Modified: ctakes/trunk/ctakes-assertion-res/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-res/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-res/.classpath (original)
+++ ctakes/trunk/ctakes-assertion-res/.classpath Wed May 8 19:02:55 2013
@@ -17,12 +17,6 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
- <classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
<attributes>
<attribute name="maven.pomderived" value="true"/>
Modified: ctakes/trunk/ctakes-assertion-res/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-res/.settings/org.eclipse.core.resources.prefs?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-res/.settings/org.eclipse.core.resources.prefs (original)
+++ ctakes/trunk/ctakes-assertion-res/.settings/org.eclipse.core.resources.prefs Wed May 8 19:02:55 2013
@@ -2,5 +2,4 @@ eclipse.preferences.version=1
encoding//src/main/java=UTF-8
encoding//src/main/resources=UTF-8
encoding//src/test/java=UTF-8
-encoding//target/generated-sources/jcasgen=UTF-8
encoding/<project>=UTF-8
Modified: ctakes/trunk/ctakes-assertion-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-res/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-res/pom.xml (original)
+++ ctakes/trunk/ctakes-assertion-res/pom.xml Wed May 8 19:02:55 2013
@@ -33,17 +33,6 @@
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-type-system</artifactId>
- </dependency>
+ </dependency>
</dependencies>
- <build>
- <plugins>
- <plugin>
- <groupId>org.cleartk</groupId>
- <artifactId>jcasgen-maven-plugin</artifactId>
- <configuration>
- <typeSystem>src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml</typeSystem>
- </configuration>
- </plugin>
- </plugins>
- </build>
</project>
\ No newline at end of file
Modified: ctakes/trunk/ctakes-assertion-zoner-res/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner-res/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner-res/.classpath (original)
+++ ctakes/trunk/ctakes-assertion-zoner-res/.classpath Wed May 8 19:02:55 2013
@@ -11,12 +11,6 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
- <classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
<classpathentry kind="src" output="target/test-classes" path="src/test/java">
<attributes>
<attribute name="optional" value="true"/>
Modified: ctakes/trunk/ctakes-assertion-zoner-res/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner-res/.settings/org.eclipse.core.resources.prefs?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner-res/.settings/org.eclipse.core.resources.prefs (original)
+++ ctakes/trunk/ctakes-assertion-zoner-res/.settings/org.eclipse.core.resources.prefs Wed May 8 19:02:55 2013
@@ -2,5 +2,4 @@ eclipse.preferences.version=1
encoding//src/main/java=UTF-8
encoding//src/main/resources=UTF-8
encoding//src/test/java=UTF-8
-encoding//target/generated-sources/jcasgen=UTF-8
encoding/<project>=UTF-8
Modified: ctakes/trunk/ctakes-assertion-zoner-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner-res/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner-res/pom.xml (original)
+++ ctakes/trunk/ctakes-assertion-zoner-res/pom.xml Wed May 8 19:02:55 2013
@@ -33,17 +33,6 @@
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-type-system</artifactId>
- </dependency>
- </dependencies>
- <build>
- <plugins>
- <plugin>
- <groupId>org.cleartk</groupId>
- <artifactId>jcasgen-maven-plugin</artifactId>
- <configuration>
- <typeSystem>src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml</typeSystem>
- </configuration>
- </plugin>
- </plugins>
- </build>
+ </dependency>
+ </dependencies>
</project>
\ No newline at end of file
Modified: ctakes/trunk/ctakes-assertion-zoner/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner/.classpath (original)
+++ ctakes/trunk/ctakes-assertion-zoner/.classpath Wed May 8 19:02:55 2013
@@ -1,26 +1,37 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" output="target/classes" path="src/main/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="src" output="target/test-classes" path="src/test/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/classes" path="src/main/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/test-classes" path="src/test/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
Modified: ctakes/trunk/ctakes-assertion-zoner/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner/pom.xml (original)
+++ ctakes/trunk/ctakes-assertion-zoner/pom.xml Wed May 8 19:02:55 2013
@@ -29,10 +29,10 @@
<version>3.1.0-SNAPSHOT</version>
</parent>
<dependencies>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-assertion-zoner-res</artifactId>
- </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-assertion-zoner-res</artifactId>
+ </dependency>
<dependency>
<groupId>net.sf.mastif</groupId>
<artifactId>mastif-zoner</artifactId>
@@ -50,7 +50,16 @@
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-core</artifactId>
</dependency>
-
</dependencies>
-
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.cleartk</groupId>
+ <artifactId>jcasgen-maven-plugin</artifactId>
+ <configuration>
+ <typeSystem>src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml</typeSystem>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
</project>
Added: ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml?rev=1480409&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml (added)
+++ ctakes/trunk/ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml Wed May 8 19:02:55 2013
@@ -0,0 +1,66 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ 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.
+
+-->
+<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
+ <name>org.apache.ctakes.assertion.types.TypeSystem</name>
+ <description/>
+ <version>1.0</version>
+ <vendor/>
+ <types>
+ <typeDescription>
+ <name>org.apache.ctakes.assertion.zoner.types.Heading</name>
+ <description>a section heading</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>label</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.assertion.zoner.types.Zone</name>
+ <description>A document Zone, including its heading</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>label</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.assertion.zoner.types.Subzone</name>
+ <description/>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>label</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ </types>
+</typeSystemDescription>
+
Modified: ctakes/trunk/ctakes-assertion/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/.classpath (original)
+++ ctakes/trunk/ctakes-assertion/.classpath Wed May 8 19:02:55 2013
@@ -1,27 +1,38 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" output="target/classes" path="src/main/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
- <classpathentry kind="src" output="target/test-classes" path="src/test/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" output="target/classes" path="src/main/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
+ <classpathentry kind="src" output="target/test-classes" path="src/test/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
Modified: ctakes/trunk/ctakes-assertion/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/pom.xml (original)
+++ ctakes/trunk/ctakes-assertion/pom.xml Wed May 8 19:02:55 2013
@@ -238,4 +238,15 @@
<artifactId>ctakes-chunker</artifactId>
</dependency>
</dependencies>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.cleartk</groupId>
+ <artifactId>jcasgen-maven-plugin</artifactId>
+ <configuration>
+ <typeSystem>src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml</typeSystem>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
</project>
Added: ctakes/trunk/ctakes-assertion/src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml?rev=1480409&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml (added)
+++ ctakes/trunk/ctakes-assertion/src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml Wed May 8 19:02:55 2013
@@ -0,0 +1,73 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ 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.
+
+-->
+<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
+ <name>org.apache.ctakes.assertion.types.TypeSystem</name>
+ <description/>
+ <version>1.0</version>
+ <vendor/>
+ <types>
+ <typeDescription>
+ <name>org.apache.ctakes.assertion.medfacts.types.Concept</name>
+ <description/>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>conceptType</name>
+ <description>the concept type -- one of problem, treatment, or test</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>conceptText</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>externalId</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>originalEntityExternalId</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.assertion.medfacts.types.Assertion</name>
+ <description/>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>assertionType</name>
+ <description>assertion type -- one of present, absent, possible, conditional, hypothetical, or assocated_with_someone_else</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>associatedConcept</name>
+ <description/>
+ <rangeTypeName>org.apache.ctakes.assertion.medfacts.types.Concept</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ </types>
+</typeSystemDescription>
Modified: ctakes/trunk/ctakes-chunker/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-chunker/pom.xml (original)
+++ ctakes/trunk/ctakes-chunker/pom.xml Wed May 8 19:02:55 2013
@@ -29,10 +29,10 @@
<version>3.1.0-SNAPSHOT</version>
</parent>
<dependencies>
- <dependency>
+ <dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-chunker-res</artifactId>
- </dependency>
+ </dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-type-system</artifactId>
Modified: ctakes/trunk/ctakes-constituency-parser-res/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser-res/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser-res/.classpath (original)
+++ ctakes/trunk/ctakes-constituency-parser-res/.classpath Wed May 8 19:02:55 2013
@@ -17,12 +17,6 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
- <classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
<attributes>
<attribute name="maven.pomderived" value="true"/>
Modified: ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.core.resources.prefs?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.core.resources.prefs (original)
+++ ctakes/trunk/ctakes-constituency-parser-res/.settings/org.eclipse.core.resources.prefs Wed May 8 19:02:55 2013
@@ -2,5 +2,4 @@ eclipse.preferences.version=1
encoding//src/main/java=UTF-8
encoding//src/main/resources=UTF-8
encoding//src/test/java=UTF-8
-encoding//target/generated-sources/jcasgen=UTF-8
encoding/<project>=UTF-8
Modified: ctakes/trunk/ctakes-constituency-parser-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser-res/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser-res/pom.xml (original)
+++ ctakes/trunk/ctakes-constituency-parser-res/pom.xml Wed May 8 19:02:55 2013
@@ -33,17 +33,7 @@
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-type-system</artifactId>
- </dependency>
+ </dependency>
</dependencies>
- <build>
- <plugins>
- <plugin>
- <groupId>org.cleartk</groupId>
- <artifactId>jcasgen-maven-plugin</artifactId>
- <configuration>
- <typeSystem>src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml</typeSystem>
- </configuration>
- </plugin>
- </plugins>
- </build>
+
</project>
\ No newline at end of file
Modified: ctakes/trunk/ctakes-constituency-parser/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser/.classpath (original)
+++ ctakes/trunk/ctakes-constituency-parser/.classpath Wed May 8 19:02:55 2013
@@ -1,28 +1,37 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" output="target/classes" path="src/main/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/cTakes"/>
- <classpathentry kind="src" output="target/test-classes" path="src/test/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" output="target/classes" path="src/main/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/test-classes" path="src/test/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
Modified: ctakes/trunk/ctakes-constituency-parser/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser/pom.xml (original)
+++ ctakes/trunk/ctakes-constituency-parser/pom.xml Wed May 8 19:02:55 2013
@@ -28,11 +28,11 @@
<artifactId>ctakes</artifactId>
<version>3.1.0-SNAPSHOT</version>
</parent>
- <dependencies>
+ <dependencies>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-constituency-parser-res</artifactId>
- </dependency>
+ </dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-type-system</artifactId>
@@ -62,4 +62,15 @@
<artifactId>junit</artifactId>
</dependency>
</dependencies>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.cleartk</groupId>
+ <artifactId>jcasgen-maven-plugin</artifactId>
+ <configuration>
+ <typeSystem>src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml</typeSystem>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
</project>
Added: ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml?rev=1480409&view=auto
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml (added)
+++ ctakes/trunk/ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml Wed May 8 19:02:55 2013
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ 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.
+
+-->
+<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
+ <name>org.apache.ctakes.constituency.parser.types.LabeledTree</name>
+ <description/>
+ <version>1.0</version>
+ <vendor/>
+ <types>
+ <typeDescription>
+ <name>org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree</name>
+ <description/>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>label</name>
+ <description/>
+ <rangeTypeName>uima.cas.Boolean</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>tree</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ </types>
+</typeSystemDescription>
Modified: ctakes/trunk/ctakes-core/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/pom.xml (original)
+++ ctakes/trunk/ctakes-core/pom.xml Wed May 8 19:02:55 2013
@@ -28,13 +28,12 @@
<artifactId>ctakes</artifactId>
<version>3.1.0-SNAPSHOT</version>
</parent>
-
<dependencies>
- <dependency>
+ <dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-core-res</artifactId>
- </dependency>
- <dependency>
+ </dependency>
+ <dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-type-system</artifactId>
</dependency>
Modified: ctakes/trunk/ctakes-coreference/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/pom.xml (original)
+++ ctakes/trunk/ctakes-coreference/pom.xml Wed May 8 19:02:55 2013
@@ -28,12 +28,11 @@
<artifactId>ctakes</artifactId>
<version>3.1.0-SNAPSHOT</version>
</parent>
-
<dependencies>
- <dependency>
+ <dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-coreference-res</artifactId>
- </dependency>
+ </dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-type-system</artifactId>
Modified: ctakes/trunk/ctakes-dependency-parser/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dependency-parser/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dependency-parser/pom.xml (original)
+++ ctakes/trunk/ctakes-dependency-parser/pom.xml Wed May 8 19:02:55 2013
@@ -29,10 +29,10 @@
<version>3.1.0-SNAPSHOT</version>
</parent>
<dependencies>
- <dependency>
+ <dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-dependency-parser-res</artifactId>
- </dependency>
+ </dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-type-system</artifactId>
Modified: ctakes/trunk/ctakes-dictionary-lookup/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup/pom.xml (original)
+++ ctakes/trunk/ctakes-dictionary-lookup/pom.xml Wed May 8 19:02:55 2013
@@ -28,16 +28,16 @@
<artifactId>ctakes</artifactId>
<version>3.1.0-SNAPSHOT</version>
</parent>
- <dependencies>
+ <dependencies>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-dictionary-lookup-res</artifactId>
+ </dependency>
<dependency>
<groupId>hsqldb</groupId>
<artifactId>hsqldb</artifactId>
<version>1.8.0.10</version>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-dictionary-lookup-res</artifactId>
- </dependency>
+ </dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-type-system</artifactId>
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=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml (original)
+++ ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml Wed May 8 19:02:55 2013
@@ -159,12 +159,36 @@
<directoryMode>755</directoryMode>
</fileSet>
<fileSet>
+ <directory>../ctakes-assertion-res/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ </fileSet>
+ <fileSet>
+ <directory>../ctakes-assertion-zoner/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ </fileSet>
+ <fileSet>
+ <directory>../ctakes-assertion-zoner-res/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ </fileSet>
+ <fileSet>
<directory>../ctakes-chunker/src/main/resources</directory>
<outputDirectory>resources</outputDirectory>
<fileMode>644</fileMode>
<directoryMode>755</directoryMode>
</fileSet>
<fileSet>
+ <directory>../ctakes-chunker-res/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ </fileSet>
+ <fileSet>
<directory>../ctakes-clinical-pipeline/src/main/resources</directory>
<outputDirectory>resources</outputDirectory>
<fileMode>644</fileMode>
@@ -175,7 +199,13 @@
<outputDirectory>resources</outputDirectory>
<fileMode>644</fileMode>
<directoryMode>755</directoryMode>
- </fileSet>
+ </fileSet>
+ <fileSet>
+ <directory>../ctakes-constituency-parser-res/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ </fileSet>
<fileSet>
<directory>../ctakes-context-tokenizer/src/main/resources</directory>
<outputDirectory>resources</outputDirectory>
@@ -190,23 +220,48 @@
<excludes><exclude>log4j.xml</exclude></excludes>
</fileSet>
<fileSet>
+ <directory>../ctakes-core-res/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ <excludes><exclude>log4j.xml</exclude></excludes>
+ </fileSet>
+ <fileSet>
<directory>../ctakes-coreference/src/main/resources</directory>
<outputDirectory>resources</outputDirectory>
<fileMode>644</fileMode>
<directoryMode>755</directoryMode>
- </fileSet>
+ </fileSet>
+ <fileSet>
+ <directory>../ctakes-coreference-res/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ </fileSet>
<fileSet>
<directory>../ctakes-dependency-parser/src/main/resources</directory>
<outputDirectory>resources</outputDirectory>
<fileMode>644</fileMode>
<directoryMode>755</directoryMode>
- </fileSet>
+ </fileSet>
+ <fileSet>
+ <directory>../ctakes-dependency-parser-res/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ </fileSet>
<fileSet>
<directory>../ctakes-dictionary-lookup/src/main/resources</directory>
<outputDirectory>resources</outputDirectory>
<fileMode>644</fileMode>
<directoryMode>755</directoryMode>
- </fileSet>
+ </fileSet>
+ <fileSet>
+ <directory>../ctakes-dictionary-lookup-res/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ </fileSet>
<fileSet>
<directory>../ctakes-drug-ner/src/main/resources</directory>
<outputDirectory>resources</outputDirectory>
@@ -214,17 +269,35 @@
<directoryMode>755</directoryMode>
</fileSet>
<fileSet>
+ <directory>../ctakes-drug-ner-res/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ </fileSet>
+ <fileSet>
<directory>../ctakes-lvg/src/main/resources</directory>
<outputDirectory>resources</outputDirectory>
<fileMode>644</fileMode>
<directoryMode>755</directoryMode>
- </fileSet>
+ </fileSet>
+ <fileSet>
+ <directory>../ctakes-lvg-res/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ </fileSet>
<fileSet>
<directory>../ctakes-ne-contexts/src/main/resources</directory>
<outputDirectory>resources</outputDirectory>
<fileMode>644</fileMode>
<directoryMode>755</directoryMode>
- </fileSet>
+ </fileSet>
+ <fileSet>
+ <directory>../ctakes-ne-contexts-res/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ </fileSet>
<fileSet>
<directory>../ctakes-pad-term-spotter/src/main/resources</directory>
<outputDirectory>resources</outputDirectory>
@@ -232,11 +305,23 @@
<directoryMode>755</directoryMode>
</fileSet>
<fileSet>
+ <directory>../ctakes-pad-term-spotter-res/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ </fileSet>
+ <fileSet>
<directory>../ctakes-pos-tagger/src/main/resources</directory>
<outputDirectory>resources</outputDirectory>
<fileMode>644</fileMode>
<directoryMode>755</directoryMode>
- </fileSet>
+ </fileSet>
+ <fileSet>
+ <directory>../ctakes-pos-tagger-res/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ </fileSet>
<fileSet>
<directory>../ctakes-preprocessor/src/main/resources</directory>
<outputDirectory>resources</outputDirectory>
@@ -250,17 +335,35 @@
<directoryMode>755</directoryMode>
</fileSet>
<fileSet>
+ <directory>../ctakes-relation-extractor-res/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ </fileSet>
+ <fileSet>
<directory>../ctakes-side-effect/src/main/resources</directory>
<outputDirectory>resources</outputDirectory>
<fileMode>644</fileMode>
<directoryMode>755</directoryMode>
- </fileSet>
+ </fileSet>
+ <fileSet>
+ <directory>../ctakes-side-effect-res/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ </fileSet>
<fileSet>
<directory>../ctakes-smoking-status/src/main/resources</directory>
<outputDirectory>resources</outputDirectory>
<fileMode>644</fileMode>
<directoryMode>755</directoryMode>
</fileSet>
+ <fileSet>
+ <directory>../ctakes-smoking-status-res/src/main/resources</directory>
+ <outputDirectory>resources</outputDirectory>
+ <fileMode>644</fileMode>
+ <directoryMode>755</directoryMode>
+ </fileSet>
<!-- Type System types should already be in the jar -->
<!--
<fileSet>
Modified: ctakes/trunk/ctakes-drug-ner-res/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner-res/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner-res/.classpath (original)
+++ ctakes/trunk/ctakes-drug-ner-res/.classpath Wed May 8 19:02:55 2013
@@ -11,12 +11,6 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
- <classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
<classpathentry kind="src" output="target/test-classes" path="src/test/java">
<attributes>
<attribute name="optional" value="true"/>
Modified: ctakes/trunk/ctakes-drug-ner-res/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner-res/.settings/org.eclipse.core.resources.prefs?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner-res/.settings/org.eclipse.core.resources.prefs (original)
+++ ctakes/trunk/ctakes-drug-ner-res/.settings/org.eclipse.core.resources.prefs Wed May 8 19:02:55 2013
@@ -2,5 +2,4 @@ eclipse.preferences.version=1
encoding//src/main/java=UTF-8
encoding//src/main/resources=UTF-8
encoding//src/test/java=UTF-8
-encoding//target/generated-sources/jcasgen=UTF-8
encoding/<project>=UTF-8
Modified: ctakes/trunk/ctakes-drug-ner-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner-res/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner-res/pom.xml (original)
+++ ctakes/trunk/ctakes-drug-ner-res/pom.xml Wed May 8 19:02:55 2013
@@ -13,16 +13,5 @@
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-type-system</artifactId>
</dependency>
- </dependencies>
- <build>
- <plugins>
- <plugin>
- <groupId>org.cleartk</groupId>
- <artifactId>jcasgen-maven-plugin</artifactId>
- <configuration>
- <typeSystem>src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml</typeSystem>
- </configuration>
- </plugin>
- </plugins>
- </build>
+ </dependencies>
</project>
\ No newline at end of file
Modified: ctakes/trunk/ctakes-drug-ner/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner/.classpath (original)
+++ ctakes/trunk/ctakes-drug-ner/.classpath Wed May 8 19:02:55 2013
@@ -1,27 +1,37 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" output="target/classes" path="src/main/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
- <classpathentry kind="src" output="target/test-classes" path="src/test/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/classes" path="src/main/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/test-classes" path="src/test/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
Modified: ctakes/trunk/ctakes-drug-ner/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner/pom.xml (original)
+++ ctakes/trunk/ctakes-drug-ner/pom.xml Wed May 8 19:02:55 2013
@@ -28,12 +28,11 @@
<artifactId>ctakes</artifactId>
<version>3.1.0-SNAPSHOT</version>
</parent>
-
<dependencies>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-drug-ner-res</artifactId>
- </dependency>
+ </dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-type-system</artifactId>
@@ -95,4 +94,15 @@
<artifactId>ctakes-lvg</artifactId>
</dependency>
</dependencies>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.cleartk</groupId>
+ <artifactId>jcasgen-maven-plugin</artifactId>
+ <configuration>
+ <typeSystem>src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml</typeSystem>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
</project>
Added: ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml?rev=1480409&view=auto
==============================================================================
--- ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml (added)
+++ ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml Wed May 8 19:02:55 2013
@@ -0,0 +1,313 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
+ <name>org.apache.ctakes.drugner.types.TypeSystem</name>
+ <description/>
+ <version>1.0</version>
+ <vendor>Mayo Clinic</vendor>
+ <types>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.FrequencyAnnotation</name>
+ <description>The frequency determination for the Drug NER profile.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.DurationAnnotation</name>
+ <description>The duration determination for the Drug NER profile.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.RouteAnnotation</name>
+ <description>The route determination for the Drug NER profile.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>intakeMethod</name>
+ <description>Means by which the drug was taken.</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.SuffixStrengthAnnotation</name>
+ <description>The suffix portion of dosage strength determination for the Drug NER profile.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.FractionStrengthAnnotation</name>
+ <description>The fraction portion of dosages strength determination for the Drug NER profile.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.RangeStrengthAnnotation</name>
+ <description>The range portion of dosages stength determination for the Drug NER profile.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.DecimalStrengthAnnotation</name>
+ <description>The decimal portion of dosages stength determination for the Drug NER profile.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation</name>
+ <description>The change status of dosages determination for the Drug NER profile.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>changeStatus</name>
+ <description>Indicates the drug change status of 'stop', 'start', 'increase', 'decrease', or 'noChange'.</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.DosagesAnnotation</name>
+ <description>The dosage determination for the Drug NER profile.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.StrengthAnnotation</name>
+ <description>Holds the value representing the unit of the drug dosage.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.StrengthUnitAnnotation</name>
+ <description/>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.FrequencyUnitAnnotation</name>
+ <description>The value represents the unit portion of the drug frequency.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>period</name>
+ <description>The periodic unit used, e.g day, month, hour, etc.</description>
+ <rangeTypeName>uima.cas.Float</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.FormAnnotation</name>
+ <description>The value represents the form portion of the drug mention.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.SubSectionAnnotation</name>
+ <description/>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>subSectionBodyBegin</name>
+ <description>Sub-section body begin offset.</description>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>subSectionBodyEnd</name>
+ <description>Sub-section body end offset.</description>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>status</name>
+ <description>Status of 'possible', 'history of', or 'family history of'.</description>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>subSectionHeaderBegin</name>
+ <description>Begin offset of subSection header</description>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>subSectionHeaderEnd</name>
+ <description>Ending offset of subsection header</description>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>parentSectionId</name>
+ <description>The section in which the subsection was found.</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.DrugMentionAnnotation</name>
+ <description/>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>status</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>confidence</name>
+ <description>The confidence of the annotation.</description>
+ <rangeTypeName>uima.cas.Float</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>frequency</name>
+ <description>Frequency refers to how often the patient needs to take the drug. Frequency is divided into frequency number and frequency unit. E.g. twice daily</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>frequencyBegin</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>frequencyEnd</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>duration</name>
+ <description>Duration refers to for how long the patient is expected to take the drug. E.g. 'for 2 weeks'
+Strongly encouraged to use bold text</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>durationBegin</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>durationEnd</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>route</name>
+ <description>Medication route refers to the way that a drug is introduced into the body. E.g oral
+Strongly encouraged to use bold text</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>routeBegin</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>routeEnd</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>drugChangeStatus</name>
+ <description>Status refers to the whether the medication is currently being taken or not.</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>dosage</name>
+ <description>Dosage refers to how many of each drug the patient is taking. E.g. 5 mg</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>dosageBegin</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>dosageEnd</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>strength</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>strengthBegin</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>strengthEnd</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>strengthUnit</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>suBegin</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>suEnd</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>form</name>
+ <description>Form refers to the physical appearance of the drug. E.g. cream</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>formBegin</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>formEnd</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>frequencyUnit</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>fuBegin</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>fuEnd</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>startDate</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>reason</name>
+ <description/>
+ <rangeTypeName>uima.cas.FSArray</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>changeStatusBegin</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>changeStatusEnd</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.ChunkAnnotation</name>
+ <description/>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>sentenceID</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation</name>
+ <description>Similar to LookupWindowAnnotation however, these annotations are restricted to the segments/sections specified in the parameter - sectionOverrideSet - in DrugCNP2LookupWindow</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ </types>
+</typeSystemDescription>
Modified: ctakes/trunk/ctakes-lvg/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-lvg/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-lvg/pom.xml (original)
+++ ctakes/trunk/ctakes-lvg/pom.xml Wed May 8 19:02:55 2013
@@ -29,7 +29,7 @@
<artifactId>ctakes</artifactId>
<version>3.1.0-SNAPSHOT</version>
</parent>
- <dependencies>
+ <dependencies>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-lvg-res</artifactId>
Modified: ctakes/trunk/ctakes-ne-contexts/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ne-contexts/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ne-contexts/pom.xml (original)
+++ ctakes/trunk/ctakes-ne-contexts/pom.xml Wed May 8 19:02:55 2013
@@ -32,7 +32,7 @@
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-ne-contexts-res</artifactId>
- </dependency>
+ </dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-type-system</artifactId>
Modified: ctakes/trunk/ctakes-pad-term-spotter-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pad-term-spotter-res/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-pad-term-spotter-res/pom.xml (original)
+++ ctakes/trunk/ctakes-pad-term-spotter-res/pom.xml Wed May 8 19:02:55 2013
@@ -34,16 +34,5 @@
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-type-system</artifactId>
</dependency>
- </dependencies>
- <build>
- <plugins>
- <plugin>
- <groupId>org.cleartk</groupId>
- <artifactId>jcasgen-maven-plugin</artifactId>
- <configuration>
- <typeSystem>src/main/resources/org/apache/ctakes/padtermspotter/types/TypeSystem.xml</typeSystem>
- </configuration>
- </plugin>
- </plugins>
- </build>
+ </dependencies>
</project>
\ No newline at end of file
Modified: ctakes/trunk/ctakes-pad-term-spotter/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pad-term-spotter/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-pad-term-spotter/.classpath (original)
+++ ctakes/trunk/ctakes-pad-term-spotter/.classpath Wed May 8 19:02:55 2013
@@ -1,27 +1,38 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" output="target/classes" path="src/main/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
- <classpathentry kind="src" output="target/test-classes" path="src/test/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" output="target/classes" path="src/main/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
+ <classpathentry kind="src" output="target/test-classes" path="src/test/java">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
+ <attributes>
+ <attribute name="optional" value="true"/>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+ <attributes>
+ <attribute name="maven.pomderived" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
Modified: ctakes/trunk/ctakes-pad-term-spotter/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pad-term-spotter/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-pad-term-spotter/pom.xml (original)
+++ ctakes/trunk/ctakes-pad-term-spotter/pom.xml Wed May 8 19:02:55 2013
@@ -33,7 +33,7 @@
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-pad-term-spotter-res</artifactId>
- </dependency>
+ </dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-type-system</artifactId>
@@ -71,4 +71,15 @@
<artifactId>ctakes-context-tokenizer</artifactId>
</dependency>
</dependencies>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.cleartk</groupId>
+ <artifactId>jcasgen-maven-plugin</artifactId>
+ <configuration>
+ <typeSystem>src/main/resources/org/apache/ctakes/padtermspotter/types/TypeSystem.xml</typeSystem>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
</project>
Added: ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/types/TypeSystem.xml?rev=1480409&view=auto
==============================================================================
--- ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/types/TypeSystem.xml (added)
+++ ctakes/trunk/ctakes-pad-term-spotter/src/main/resources/org/apache/ctakes/padtermspotter/types/TypeSystem.xml Wed May 8 19:02:55 2013
@@ -0,0 +1,158 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ 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.
+
+-->
+<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
+ <name>org.apache.ctakes.padtermspotter.types.TypeSystem</name>
+ <description>Represents Term and Location entities required for PAD
+ project.</description>
+ <version>1.0</version>
+ <vendor>Mayo</vendor>
+ <imports>
+ <import name="org.apache.ctakes.typesystem.types.TypeSystem" />
+ </imports>
+ <types>
+ <typeDescription>
+ <name>org.apache.ctakes.padtermspotter.type.PADTerm</name>
+ <description />
+ <supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
+ </supertypeName>
+ <features>
+ <featureDescription>
+ <name>hitDictionaryValue</name>
+ <description>Value from the Dictionary that was successfully looked
+ up</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>isStandAlone</name>
+ <description>Identifies weather this term needs another dictionary
+ hit to be considered as a valid hit. Currently this is being used
+ for Unstable Angina which requires "Term" and "Location" to be
+ present in the text to be considered as a valid hit.
+
+ Valid values are 0 and 1. Where, 0 is false (not standalone) and 1 is
+ true (is standalone)
+ </description>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>relatedTokens</name>
+ <description>identifies the token that this PADTerm spans
+ </description>
+ <rangeTypeName>uima.cas.FSArray</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.padtermspotter.type.PADLocation</name>
+ <description />
+ <supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
+ </supertypeName>
+ <features>
+ <featureDescription>
+ <name>hitDictionaryValue</name>
+ <description>Value from the Dictionary that was successfully looked
+ up</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>isStandAlone</name>
+ <description>Identifies weather this term needs another dictionary
+ hit to be considered as a valid hit. Currently this is being used
+ for Unstable Angina which requires "Term" and "Location" to be
+ present in the text to be considered as a valid hit.
+
+ Valid values are 0 and 1. Where, 0 is false (not standalone) and 1 is
+ true (is standalone)
+ </description>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>relatedTokens</name>
+ <description>identifies the token that this PADTerm spans
+ </description>
+ <rangeTypeName>uima.cas.FSArray</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.padtermspotter.type.PADHit</name>
+ <description>Would represent one of the following
+ Term (in the case of a stand alone term)
+ Term + Location
+ Location + term
+ </description>
+ <supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
+ </supertypeName>
+ <features>
+ <featureDescription>
+ <name>uaTerm</name>
+ <description />
+ <rangeTypeName>org.apache.ctakes.padtermspotter.type.PADTerm
+ </rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>uaLocation</name>
+ <description />
+ <rangeTypeName>org.apache.ctakes.padtermspotter.type.PADLocation
+ </rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.padtermspotter.type.SubSection</name>
+ <description></description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>parentSectionId</name>
+ <description></description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>subSectionBodyBegin</name>
+ <description></description>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>subSectionBodyEnd</name>
+ <description></description>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>status</name>
+ <description></description>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>subSectionHeaderBegin</name>
+ <description></description>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>subSectionHeaderEnd</name>
+ <description></description>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ </types>
+</typeSystemDescription>
Modified: ctakes/trunk/ctakes-pos-tagger/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-pos-tagger/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-pos-tagger/pom.xml (original)
+++ ctakes/trunk/ctakes-pos-tagger/pom.xml Wed May 8 19:02:55 2013
@@ -28,7 +28,7 @@
<artifactId>ctakes</artifactId>
<version>3.1.0-SNAPSHOT</version>
</parent>
- <dependencies>
+ <dependencies>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-pos-tagger-res</artifactId>
Modified: ctakes/trunk/ctakes-side-effect-res/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-side-effect-res/.classpath?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-side-effect-res/.classpath (original)
+++ ctakes/trunk/ctakes-side-effect-res/.classpath Wed May 8 19:02:55 2013
@@ -11,12 +11,6 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
- <classpathentry kind="src" output="target/classes" path="target/generated-sources/jcasgen">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
<classpathentry kind="src" output="target/test-classes" path="src/test/java">
<attributes>
<attribute name="optional" value="true"/>
Modified: ctakes/trunk/ctakes-side-effect-res/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-side-effect-res/.settings/org.eclipse.core.resources.prefs?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-side-effect-res/.settings/org.eclipse.core.resources.prefs (original)
+++ ctakes/trunk/ctakes-side-effect-res/.settings/org.eclipse.core.resources.prefs Wed May 8 19:02:55 2013
@@ -2,5 +2,4 @@ eclipse.preferences.version=1
encoding//src/main/java=UTF-8
encoding//src/main/resources=UTF-8
encoding//src/test/java=UTF-8
-encoding//target/generated-sources/jcasgen=UTF-8
encoding/<project>=UTF-8
Modified: ctakes/trunk/ctakes-side-effect-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-side-effect-res/pom.xml?rev=1480409&r1=1480408&r2=1480409&view=diff
==============================================================================
--- ctakes/trunk/ctakes-side-effect-res/pom.xml (original)
+++ ctakes/trunk/ctakes-side-effect-res/pom.xml Wed May 8 19:02:55 2013
@@ -34,16 +34,5 @@
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-type-system</artifactId>
</dependency>
- </dependencies>
- <build>
- <plugins>
- <plugin>
- <groupId>org.cleartk</groupId>
- <artifactId>jcasgen-maven-plugin</artifactId>
- <configuration>
- <typeSystem>src/main/resources/org/apache/ctakes/sideeffect/types/TypeSystem.xml</typeSystem>
- </configuration>
- </plugin>
- </plugins>
- </build>
+ </dependencies>
</project>
\ No newline at end of file