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From spmurph...@apache.org
Subject svn commit: r1423486 [2/2] - in /incubator/ctakes/branches/ctakes-3.0.0-incubating: ctakes-core/src/main/resources/org/apache/ctakes/core/analysis_engine/ ctakes-drug-ner/ ctakes-drug-ner/desc/analysis_engine/ ctakes-drug-ner/desc/cas_consumer/ ctakes-...
Date Tue, 18 Dec 2012 15:49:43 GMT
Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/pom.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/pom.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/pom.xml Tue
Dec 18 15:49:41 2012
@@ -58,6 +58,14 @@
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-chunker</artifactId>
+		</dependency>
+				<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-context-tokenizer</artifactId>
+		</dependency>	
 	</dependencies>
 	
 		<build>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml
(original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml
Tue Dec 18 15:49:41 2012
@@ -86,7 +86,7 @@ This param is optional.  If not specifie
     </configurationParameterSettings>
     <typeSystemDescription>
       <imports>
-        <import location="../type_system/SmokingProductionTypeSystem.xml"/>
+		<import name="org.apache.ctakes.smokingstatus.types.Typesystem"/>
       </imports>
     </typeSystemDescription>
     <capabilities>
@@ -128,7 +128,7 @@ This param is optional.  If not specifie
         <name>UimaDescriptorStep1</name>
         <description/>
         <fileResourceSpecifier>
-          <fileUrl>file:analysis_engine/ProductionPostSentenceAggregate_step1.xml</fileUrl>
+          <fileUrl>file:org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml</fileUrl>
         </fileResourceSpecifier>
         <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
       </externalResource>
@@ -136,7 +136,7 @@ This param is optional.  If not specifie
         <name>UimaDescriptorStep2</name>
         <description/>
         <fileResourceSpecifier>
-          <fileUrl>file:analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml</fileUrl>
+          <fileUrl>file:org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml</fileUrl>
         </fileResourceSpecifier>
         <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
       </externalResource>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.xml
(original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.xml
Tue Dec 18 15:49:41 2012
@@ -1,106 +1,86 @@
 <?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.
-
--->
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
-<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
-<primitive>true</primitive>
-<annotatorImplementationName>org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator</annotatorImplementationName>
-<analysisEngineMetaData>
-<name>KuRuleBasedClassifierAnnotator</name>
-<description>Known vs Unknow classifier using smoking related keywords</description>
-<version></version>
-<vendor></vendor>
-<configurationParameters>
-<configurationParameter>
-<name>CaseSensitive</name>
-<type>Boolean</type>
-<multiValued>false</multiValued>
-<mandatory>true</mandatory>
-</configurationParameter>
-<configurationParameter>
-<name>classAttribute</name>
-<type>String</type>
-<multiValued>false</multiValued>
-<mandatory>true</mandatory>
-</configurationParameter>
-<configurationParameter>
-<name>SmokingWordsFile</name>
-<description>smoking related keywords to identify "known" class</description>
-<type>String</type>
-<multiValued>false</multiValued>
-<mandatory>true</mandatory>
-</configurationParameter>
-<configurationParameter>
-<name>UnknownWordsFile</name>
-<description>If this word/phrase appears, treat the sentence as UNKNOWN</description>
-<type>String</type>
-<multiValued>false</multiValued>
-<mandatory>true</mandatory>
-</configurationParameter>
-</configurationParameters>
-<configurationParameterSettings>
-<nameValuePair>
-<name>SmokingWordsFile</name>
-<value>
-<string>ss/data/KU/keywords.txt</string>
-</value>
-</nameValuePair>
-<nameValuePair>
-<name>classAttribute</name>
-<value>
-<string>smoking_status</string>
-</value>
-</nameValuePair>
-<nameValuePair>
-<name>CaseSensitive</name>
-<value>
-<boolean>false</boolean>
-</value>
-</nameValuePair>
-<nameValuePair>
-<name>UnknownWordsFile</name>
-<value>
-<string>ss/data/KU/unknown_words.txt</string>
-</value>
-</nameValuePair>
-</configurationParameterSettings>
-<typeSystemDescription>
-<imports>
-<import location="../type_system/SmokingProductionTypeSystem.xml"/>
-</imports>
-</typeSystemDescription>
-<typePriorities/>
-<fsIndexCollection/>
-<capabilities>
-<capability>
-<inputs/>
-<outputs/>
-<languagesSupported/>
-</capability>
-</capabilities>
-<operationalProperties>
-<modifiesCas>true</modifiesCas>
-<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
-<outputsNewCASes>false</outputsNewCASes>
-</operationalProperties>
-</analysisEngineMetaData>
-<resourceManagerConfiguration/>
+  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+  <primitive>true</primitive>
+  <annotatorImplementationName>org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator</annotatorImplementationName>
+  <analysisEngineMetaData>
+    <name>KuRuleBasedClassifierAnnotator</name>
+    <description>Known vs Unknow classifier using smoking related keywords</description>
+    <version/>
+    <vendor/>
+    <configurationParameters>
+      <configurationParameter>
+        <name>CaseSensitive</name>
+        <type>Boolean</type>
+        <multiValued>false</multiValued>
+        <mandatory>true</mandatory>
+      </configurationParameter>
+      <configurationParameter>
+        <name>classAttribute</name>
+        <type>String</type>
+        <multiValued>false</multiValued>
+        <mandatory>true</mandatory>
+      </configurationParameter>
+      <configurationParameter>
+        <name>SmokingWordsFile</name>
+        <description>smoking related keywords to identify "known" class</description>
+        <type>String</type>
+        <multiValued>false</multiValued>
+        <mandatory>true</mandatory>
+      </configurationParameter>
+      <configurationParameter>
+        <name>UnknownWordsFile</name>
+        <description>If this word/phrase appears, treat the sentence as UNKNOWN</description>
+        <type>String</type>
+        <multiValued>false</multiValued>
+        <mandatory>true</mandatory>
+      </configurationParameter>
+    </configurationParameters>
+    <configurationParameterSettings>
+      <nameValuePair>
+        <name>SmokingWordsFile</name>
+        <value>
+          <string>org/apache/ctakes/smokingstatus/data/KU/keywords.txt</string>
+        </value>
+      </nameValuePair>
+      <nameValuePair>
+        <name>classAttribute</name>
+        <value>
+          <string>smoking_status</string>
+        </value>
+      </nameValuePair>
+      <nameValuePair>
+        <name>CaseSensitive</name>
+        <value>
+          <boolean>false</boolean>
+        </value>
+      </nameValuePair>
+      <nameValuePair>
+        <name>UnknownWordsFile</name>
+        <value>
+          <string>org/apache/ctakes/smokingstatus/data/KU/unknown_words.txt</string>
+        </value>
+      </nameValuePair>
+    </configurationParameterSettings>
+    <typeSystemDescription>
+      <imports>
+        <import name="org.apache.ctakes.smokingstatus.types.Typesystem"/>
+      </imports>
+    </typeSystemDescription>
+    <typePriorities/>
+    <fsIndexCollection/>
+    <capabilities>
+      <capability>
+        <inputs/>
+        <outputs/>
+        <languagesSupported/>
+      </capability>
+    </capabilities>
+    <operationalProperties>
+      <modifiesCas>true</modifiesCas>
+      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+      <outputsNewCASes>false</outputsNewCASes>
+    </operationalProperties>
+  </analysisEngineMetaData>
+  <resourceManagerConfiguration/>
 </taeDescription>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/NonsmokerDictionaryLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/NonsmokerDictionaryLookupAnnotator.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/NonsmokerDictionaryLookupAnnotator.xml
(original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/NonsmokerDictionaryLookupAnnotator.xml
Tue Dec 18 15:49:41 2012
@@ -32,7 +32,7 @@
 <configurationParameterSettings/>
 <typeSystemDescription>
 <imports>
-<import location="../type_system/SmokingProductionTypeSystem.xml"/>
+        <import name="org.apache.ctakes.smokingstatus.types.Typesystem"/>
 </imports>
 </typeSystemDescription>
 <typePriorities/>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/PcsClassifierAnnotator_libsvm.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/PcsClassifierAnnotator_libsvm.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/PcsClassifierAnnotator_libsvm.xml
(original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/PcsClassifierAnnotator_libsvm.xml
Tue Dec 18 15:49:41 2012
@@ -46,7 +46,7 @@
 </configurationParameterSettings>
 <typeSystemDescription>
 <imports>
-<import location="../type_system/SmokingProductionTypeSystem.xml"/>
+        <import name="org.apache.ctakes.smokingstatus.types.Typesystem"/>
 </imports>
 </typeSystemDescription>
 <typePriorities/>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml
(original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml
Tue Dec 18 15:49:41 2012
@@ -32,7 +32,7 @@
 <configurationParameterSettings/>
 <typeSystemDescription>
 <imports>
-<import location="../type_system/SmokingProductionTypeSystem.xml"/>
+        <import name="org.apache.ctakes.smokingstatus.types.Typesystem"/>
 </imports>
 </typeSystemDescription>
 <capabilities>

Added: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/launch/UIMA
CAS Visual Debugger (Smoking Status).launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/launch/UIMA%20CAS%20Visual%20Debugger%20%28Smoking%20Status%29.launch?rev=1423486&view=auto
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/launch/UIMA CAS
Visual Debugger (Smoking Status).launch (added)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/launch/UIMA CAS
Visual Debugger (Smoking Status).launch Tue Dec 18 15:49:41 2012
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
+<listEntry value="/ctakes-smoking-status"/>
+</listAttribute>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+<listEntry value="4"/>
+</listAttribute>
+<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.m2e.launchconfig.classpathProvider"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.cvd.CVD"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-smoking-status"/>
+<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
+</launchConfiguration>

Propchange: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/launch/UIMA
CAS Visual Debugger (Smoking Status).launch
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/launch/UIMA_CPE_GUI--Smokin_Status.launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/launch/UIMA_CPE_GUI--Smokin_Status.launch?rev=1423486&view=auto
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/launch/UIMA_CPE_GUI--Smokin_Status.launch
(added)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/launch/UIMA_CPE_GUI--Smokin_Status.launch
Tue Dec 18 15:49:41 2012
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
+<listEntry value="/ctakes-smoking-status"/>
+</listAttribute>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+<listEntry value="4"/>
+</listAttribute>
+<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
+<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.m2e.launchconfig.classpathProvider"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.cpm.CpmFrame"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-smoking-status"/>
+<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
+<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xms500M -Xmx500M"/>
+</launchConfiguration>

Propchange: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/launch/UIMA_CPE_GUI--Smokin_Status.launch
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/data/SmokingStatusLookupConfig.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/data/SmokingStatusLookupConfig.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/data/SmokingStatusLookupConfig.xml
(original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/data/SmokingStatusLookupConfig.xml
Tue Dec 18 15:49:41 2012
@@ -44,7 +44,7 @@
 			<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl">
 				<properties/>
 			</lookupInitializer>
-			<lookupConsumer className="org.apache.ctakes.dictionary.lookup.ae.SmokerNamedEntityLookupConsumerImpl">
+			<lookupConsumer className="org.apache.ctakes.smokingstatus.lookup.ae.SmokerNamedEntityLookupConsumerImpl">
 				<properties>
 					<property key="codingScheme" value="NONE"/>
 					<property key="codeMetaField" value="0"/>
@@ -56,7 +56,7 @@
 			<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl">
 				<properties/>
 			</lookupInitializer>
-			<lookupConsumer className="org.apache.ctakes.dictionary.lookup.ae.NonSmokerNamedEntityLookupConsumerImpl">
+			<lookupConsumer className="org.apache.ctakes.smokingstatus.lookup.ae.NonSmokerNamedEntityLookupConsumerImpl">
 				<properties>
 					<property key="codingScheme" value="NONE"/>
 					<property key="codeMetaField" value="0"/>



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