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From chen...@apache.org
Subject svn commit: r1463641 [40/42] - in /ctakes/trunk: ctakes-assertion-res/ ctakes-assertion-res/.settings/ ctakes-assertion-res/src/ ctakes-assertion-res/src/main/ ctakes-assertion-res/src/main/resources/ ctakes-assertion-res/src/main/resources/org/ ctakes...
Date Tue, 02 Apr 2013 17:44:41 GMT
Added: ctakes/trunk/ctakes-smoking-status-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/pom.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/pom.xml (added)
+++ ctakes/trunk/ctakes-smoking-status-res/pom.xml Tue Apr  2 17:41:30 2013
@@ -0,0 +1,49 @@
+<?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.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <parent>
+    <groupId>org.apache.ctakes</groupId>
+    <artifactId>ctakes</artifactId>
+    <version>3.1.0-SNAPSHOT</version>
+  </parent>
+  <artifactId>ctakes-smoking-status-res</artifactId>
+  <name>Apache cTAKES Resources smoking-status</name>
+  <description>Resources Project for ctakes-smoking-status</description>
+  <dependencies>
+     <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/smokingstatus/types/TypeSystem.xml</typeSystem>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>  
+</project>
\ No newline at end of file

Added: ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ArtificialSentenceAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ArtificialSentenceAnnotator.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ArtificialSentenceAnnotator.xml
(added)
+++ ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ArtificialSentenceAnnotator.xml
Tue Apr  2 17:41:30 2013
@@ -0,0 +1,94 @@
+<?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.core.ae.CopyAnnotator</annotatorImplementationName>
+<analysisEngineMetaData>
+<name>ArtificialSentenceAnnotator</name>
+<description>Artificially creates a new SentenceAnnotation object by treating the entire
document as a sentence.  The offset values from the DocumentAnnotation object are transferred
over to the new SentenceAnnotation object.</description>
+<version></version>
+<vendor>Mayo</vendor>
+<configurationParameters>
+<configurationParameter>
+<name>srcObjClass</name>
+<description>Source JCas object class.  This must be an object that already exists
in the JCas.</description>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+<configurationParameter>
+<name>destObjClass</name>
+<description>Destination JCas object class.  A new JCas object will be created.</description>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+<configurationParameter>
+<name>dataBindMap</name>
+<description>Binds data from source to destination.  Format for each entry is the getter
method name of the source to the setter method name of the destination.  e.g. getMyValue|setMyValue</description>
+<type>String</type>
+<multiValued>true</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+</configurationParameters>
+<configurationParameterSettings>
+<nameValuePair>
+<name>srcObjClass</name>
+<value>
+<string>org.apache.uima.jcas.tcas.DocumentAnnotation</string>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>destObjClass</name>
+<value>
+<string>org.apache.ctakes.typesystem.type.textspan.Sentence</string>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>dataBindMap</name>
+<value>
+<array>
+<string>getBegin|setBegin</string>
+<string>getEnd|setEnd</string>
+</array>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+<typeSystemDescription/>
+<typePriorities/>
+<fsIndexCollection/>
+<capabilities>
+<capability>
+<inputs/>
+<outputs/>
+<languagesSupported/>
+</capability>
+</capabilities>
+<operationalProperties>
+<modifiesCas>true</modifiesCas>
+<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+<outputsNewCASes>false</outputsNewCASes>
+</operationalProperties>
+</analysisEngineMetaData>
+<resourceManagerConfiguration/>
+</taeDescription>

Added: ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/KuRuleBasedClassifierAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/KuRuleBasedClassifierAnnotator.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/KuRuleBasedClassifierAnnotator.xml
(added)
+++ ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/KuRuleBasedClassifierAnnotator.xml
Tue Apr  2 17:41:30 2013
@@ -0,0 +1,86 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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/>
+    <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>

Added: ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/PcsClassifierAnnotator_libsvm.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/PcsClassifierAnnotator_libsvm.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/PcsClassifierAnnotator_libsvm.xml
(added)
+++ ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/PcsClassifierAnnotator_libsvm.xml
Tue Apr  2 17:41:30 2013
@@ -0,0 +1,136 @@
+<?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.PcsClassifierAnnotator_libsvm</annotatorImplementationName>
+<analysisEngineMetaData>
+<name>PcsClassifierAnnotator_libsvm</name>
+<description>PCS classifier using libsvm. This annotator plays the same role as PcsBOWFeatureAnnotator.xml,
PcsClassifierAnnotator.xml, and BOWFeatureRemovalAnnotator.xml, which use Weka.</description>
+<version></version>
+<vendor></vendor>
+<configurationParameters>
+<configurationParameter>
+<name>CaseSensitive</name>
+<type>Boolean</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+</configurationParameters>
+<configurationParameterSettings>
+<nameValuePair>
+<name>CaseSensitive</name>
+<value>
+<boolean>false</boolean>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+<typeSystemDescription>
+<imports>
+        <import name="org.apache.ctakes.smokingstatus.types.TypeSystem"/>
+</imports>
+</typeSystemDescription>
+<typePriorities/>
+<fsIndexCollection/>
+<capabilities>
+<capability>
+<inputs>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+</inputs>
+<outputs>
+<type allAnnotatorFeatures="true">org.apache.ctakes.smokingstatus.type.libsvms.StringAttributeValue</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.smokingstatus.type.libsvms.NumericAttributeValue</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.smokingstatus.type.libsvms.DateAttributeValue</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.smokingstatus.type.libsvms.AttributeValue</type>
+</outputs>
+<languagesSupported/>
+</capability>
+</capabilities>
+<operationalProperties>
+<modifiesCas>true</modifiesCas>
+<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+<outputsNewCASes>false</outputsNewCASes>
+</operationalProperties>
+</analysisEngineMetaData>
+<externalResourceDependencies>
+<externalResourceDependency>
+<key>PathOfModel</key>
+<description></description>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
+<optional>false</optional>
+</externalResourceDependency>
+<externalResourceDependency>
+<key>StopWordsFile</key>
+<description></description>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
+<optional>false</optional>
+</externalResourceDependency>
+<externalResourceDependency>
+<key>PCSKeyWordFile</key>
+<description/>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
+<optional>false</optional>
+</externalResourceDependency>
+</externalResourceDependencies>
+<resourceManagerConfiguration>
+<externalResources>
+<externalResource>
+<name>PathOfModelResc</name>
+<description></description>
+<fileResourceSpecifier>
+<fileUrl>file:org/apache/ctakes/smokingstatus/data/PCS/pcs_libsvm-2.91.model</fileUrl>
+</fileResourceSpecifier>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
+</externalResource>
+<externalResource>
+<name>PCSKeyWordFileResc</name>
+<description/>
+<fileResourceSpecifier>
+<fileUrl>file:org/apache/ctakes/smokingstatus/data/PCS/keywords_PCS.txt</fileUrl>
+</fileResourceSpecifier>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
+</externalResource>
+<externalResource>
+<name>StopWordsFileResc</name>
+<description></description>
+<fileResourceSpecifier>
+<fileUrl>file:org/apache/ctakes/smokingstatus/data/PCS/stopwords_PCS.txt</fileUrl>
+</fileResourceSpecifier>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
+</externalResource>
+</externalResources>
+<externalResourceBindings>
+<externalResourceBinding>
+<key>PathOfModel</key>
+<resourceName>PathOfModelResc</resourceName>
+</externalResourceBinding>
+<externalResourceBinding>
+<key>StopWordsFile</key>
+<resourceName>StopWordsFileResc</resourceName>
+</externalResourceBinding>
+<externalResourceBinding>
+<key>PCSKeyWordFile</key>
+<resourceName>PCSKeyWordFileResc</resourceName>
+</externalResourceBinding>
+</externalResourceBindings>
+</resourceManagerConfiguration>
+</taeDescription>

Added: ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml
(added)
+++ ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml
Tue Apr  2 17:41:30 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.
+
+-->
+<taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+  <primitive>false</primitive>
+  <delegateAnalysisEngineSpecifiers>
+    <delegateAnalysisEngine key="TokenizerAnnotator">
+      <import name="org.apache.ctakes.core.analysis_engine.TokenizerAnnotator"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="KuRuleBasedClassifierAnnotator">
+      <import location="KuRuleBasedClassifierAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="SentenceDetectAnnotator">
+      <import name="org.apache.ctakes.core.analysis_engine.SentenceDetectorAnnotator"/>
+    </delegateAnalysisEngine>
+  </delegateAnalysisEngineSpecifiers>
+  <analysisEngineMetaData>
+    <name>ProductionPostSentenceAggregate_step1</name>
+    <description>Aggregate TAE used to run the Smoking Status pipeline.  This should
be followed by the RecordResolutionCasConsumer.</description>
+    <version/>
+    <vendor/>
+    <configurationParameters searchStrategy="language_fallback"/>
+    <configurationParameterSettings/>
+    <flowConstraints>
+      <fixedFlow>
+        <node>SentenceDetectAnnotator</node>
+        <node>TokenizerAnnotator</node>
+        <node>KuRuleBasedClassifierAnnotator</node>
+      </fixedFlow>
+    </flowConstraints>
+    <typePriorities/>
+    <fsIndexCollection/>
+    <capabilities>
+      <capability>
+        <inputs/>
+        <outputs/>
+        <languagesSupported/>
+      </capability>
+    </capabilities>
+    <operationalProperties>
+      <modifiesCas>true</modifiesCas>
+      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+      <outputsNewCASes>false</outputsNewCASes>
+    </operationalProperties>
+  </analysisEngineMetaData>
+  <resourceManagerConfiguration/>
+</taeDescription>

Added: ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml
(added)
+++ ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml
Tue Apr  2 17:41:30 2013
@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="UTF-8"?><taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+  <primitive>false</primitive>
+  <delegateAnalysisEngineSpecifiers>
+    <delegateAnalysisEngine key="NegationAnnotator">
+      <import name="org.apache.ctakes.necontexts.desc.NegationAnnotator"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="SentenceAdjuster">
+      <import location="SentenceAdjuster.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="SmokingStatusDictionaryLookupAnnotator">
+      <import location="SmokingStatusDictionaryLookupAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="PcsClassifierAnnotator_libsvm">
+      <import location="PcsClassifierAnnotator_libsvm.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="ArtificialSentenceAnnotator">
+      <import location="ArtificialSentenceAnnotator.xml"/>
+    </delegateAnalysisEngine>
+  </delegateAnalysisEngineSpecifiers>
+  <analysisEngineMetaData>
+    <name>Smoking Status AE</name>
+    <description>Aggregate AE used to run the Smoking Status pipeline.  This should
be followed by the RecordResolutionCasConsumer.</description>
+    <version/>
+    <vendor/>
+    <configurationParameters searchStrategy="language_fallback"/>
+    <configurationParameterSettings/>
+    <flowConstraints>
+      <fixedFlow>
+        <node>PcsClassifierAnnotator_libsvm</node>
+        <node>ArtificialSentenceAnnotator</node>
+        <node>SentenceAdjuster</node>
+        <node>SmokingStatusDictionaryLookupAnnotator</node>
+        <node>NegationAnnotator</node>
+      </fixedFlow>
+    </flowConstraints>
+    <fsIndexCollection/>
+    <capabilities>
+      <capability>
+        <inputs/>
+        <outputs/>
+        <languagesSupported/>
+      </capability>
+    </capabilities>
+    <operationalProperties>
+      <modifiesCas>true</modifiesCas>
+      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+      <outputsNewCASes>false</outputsNewCASes>
+    </operationalProperties>
+  </analysisEngineMetaData>
+  <resourceManagerConfiguration/>
+</taeDescription>

Added: ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SentenceAdjuster.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SentenceAdjuster.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SentenceAdjuster.xml
(added)
+++ ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SentenceAdjuster.xml
Tue Apr  2 17:41:30 2013
@@ -0,0 +1,111 @@
+<?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.watson.ibm.com/resourceSpecifier">
+  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+  <primitive>true</primitive>
+  <annotatorImplementationName>org.apache.ctakes.smokingstatus.ae.SentenceAdjuster</annotatorImplementationName>
+  <analysisEngineMetaData>
+    <name>Sentence Adjuster</name>
+    <description>This annotator expands sentence annotations of type "Tobacco: none"
to allow the correct negation  recognition of the relevant NEs.</description>
+    <version>1.0</version>
+    <vendor>Mayo Clinic</vendor>
+    <configurationParameters>
+      <configurationParameter>
+        <name>UseSegments</name>
+        <description>Flag whether to use segments or full doc text.</description>
+        <type>Boolean</type>
+        <multiValued>false</multiValued>
+        <mandatory>false</mandatory>
+      </configurationParameter>
+      <configurationParameter>
+        <name>SegmentsToSkip</name>
+        <description>Segments to skip.</description>
+        <type>String</type>
+        <multiValued>true</multiValued>
+        <mandatory>false</mandatory>
+      </configurationParameter>
+      <configurationParameter>
+        <name>WordsToIgnore</name>
+        <description>Set of words that PostModifier should ignore (act as if the word
was not there) when looking for a pattern match.</description>
+        <type>String</type>
+        <multiValued>true</multiValued>
+        <mandatory>false</mandatory>
+      </configurationParameter>
+      <configurationParameter>
+        <name>WordsInPattern</name>
+        <type>String</type>
+        <multiValued>true</multiValued>
+        <mandatory>true</mandatory>
+      </configurationParameter>
+    </configurationParameters>
+    <configurationParameterSettings>
+      <nameValuePair>
+        <name>UseSegments</name>
+        <value>
+          <boolean>false</boolean>
+        </value>
+      </nameValuePair>
+      <nameValuePair>
+        <name>SegmentsToSkip</name>
+        <value>
+          <array>
+            <string/>
+          </array>
+        </value>
+      </nameValuePair>
+      <nameValuePair>
+        <name>WordsToIgnore</name>
+        <value>
+          <array/>
+        </value>
+      </nameValuePair>
+      <nameValuePair>
+        <name>WordsInPattern</name>
+        <value>
+          <array>
+            <string>no</string>
+            <string>none</string>
+            <string>never</string>
+            <string>quit</string>
+            <string>smoked</string>
+            <string>:</string>
+          </array>
+        </value>
+      </nameValuePair>
+    </configurationParameterSettings>
+    <typeSystemDescription/>
+    <typePriorities/>
+    <fsIndexCollection/>
+    <capabilities>
+      <capability>
+        <inputs/>
+        <outputs/>
+        <languagesSupported/>
+      </capability>
+    </capabilities>
+    <operationalProperties>
+      <modifiesCas>true</modifiesCas>
+      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+    </operationalProperties>
+  </analysisEngineMetaData>
+  <resourceManagerConfiguration/>
+</taeDescription>

Added: ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml
(added)
+++ ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml
Tue Apr  2 17:41:30 2013
@@ -0,0 +1,118 @@
+<?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.dictionary.lookup.ae.DictionaryLookupAnnotator</annotatorImplementationName>
+<analysisEngineMetaData>
+<name>DictionaryLookupAnnotator</name>
+<description>Performs dictionary lookup and stores the hits as NamedEntityAnnotation
objects. </description>
+<version></version>
+<vendor></vendor>
+<configurationParameters/>
+<configurationParameterSettings/>
+<typeSystemDescription>
+<imports>
+        <import name="org.apache.ctakes.smokingstatus.types.TypeSystem"/>
+</imports>
+</typeSystemDescription>
+<capabilities>
+<capability>
+<inputs>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+</inputs>
+<outputs>
+<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.lookup.type.NamedEntity</type>
+</outputs>
+<languagesSupported/>
+</capability>
+</capabilities>
+<operationalProperties>
+<modifiesCas>true</modifiesCas>
+<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+<outputsNewCASes>false</outputsNewCASes>
+</operationalProperties>
+</analysisEngineMetaData>
+<externalResourceDependencies>
+<externalResourceDependency>
+<key>LookupDescriptor</key>
+<description></description>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
+<optional>false</optional>
+</externalResourceDependency>
+<externalResourceDependency>
+<key>SmokerDictionary</key>
+<description></description>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
+<optional>false</optional>
+</externalResourceDependency>
+<externalResourceDependency>
+<key>NonSmokerDictionary</key>
+<description></description>
+<interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
+<optional>false</optional>
+</externalResourceDependency>
+</externalResourceDependencies>
+<resourceManagerConfiguration>
+<externalResources>
+<externalResource>
+<name>LookupDescriptorFile</name>
+<description></description>
+<fileResourceSpecifier>
+<fileUrl>file:org/apache/ctakes/smokingstatus/data/SmokingStatusLookupConfig.xml</fileUrl>
+</fileResourceSpecifier>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
+</externalResource>
+<externalResource>
+<name>DictionaryFileSmoker</name>
+<description></description>
+<fileResourceSpecifier>
+<fileUrl>file:org/apache/ctakes/smokingstatus/data/smoker.dictionary</fileUrl>
+</fileResourceSpecifier>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
+</externalResource>
+<externalResource>
+<name>DictionaryFileNonSmoker</name>
+<description></description>
+<fileResourceSpecifier>
+<fileUrl>file:org/apache/ctakes/smokingstatus/data/nonsmoker.dictionary</fileUrl>
+</fileResourceSpecifier>
+<implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
+</externalResource>
+</externalResources>
+<externalResourceBindings>
+<externalResourceBinding>
+<key>LookupDescriptor</key>
+<resourceName>LookupDescriptorFile</resourceName>
+</externalResourceBinding>
+<externalResourceBinding>
+<key>SmokerDictionary</key>
+<resourceName>DictionaryFileSmoker</resourceName>
+</externalResourceBinding>
+<externalResourceBinding>
+<key>NonSmokerDictionary</key>
+<resourceName>DictionaryFileNonSmoker</resourceName>
+</externalResourceBinding>
+</externalResourceBindings>
+</resourceManagerConfiguration>
+</taeDescription>

Added: ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/keywords.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/keywords.txt?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/keywords.txt
(added)
+++ ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/keywords.txt
Tue Apr  2 17:41:30 2013
@@ -0,0 +1,21 @@
+smoker
+smoking
+smoke
+smokes
+smoked
+ex-smoker
+exsmoker
+non-smoker
+nonsmoker
+non-smoking
+nonsmoking
+tob
+tobacco
+tobaccos
+nicotine
+cigar
+cigars
+cig
+cigs
+cigarette
+cigarettes
\ No newline at end of file

Added: ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/unknown_words.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/unknown_words.txt?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/unknown_words.txt
(added)
+++ ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/unknown_words.txt
Tue Apr  2 17:41:30 2013
@@ -0,0 +1,2 @@
+smoke detector
+tobacco distributor
\ No newline at end of file

Added: ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/keywords_PCS.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/keywords_PCS.txt?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/keywords_PCS.txt
(added)
+++ ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/keywords_PCS.txt
Tue Apr  2 17:41:30 2013
@@ -0,0 +1,81 @@
+tried
+history_of
+will
+ago
+quitting
+smoking
+nicotine_patch
+smoked
+continued_to
+previous
+has_discontinued
+previously
+prior
+ex-smoker
+encouraged
+years
+has_quit
+month
+stops
+day
+refraining
+former
+past
+zyban
+days_ago
+to_stop
+remote
+discussed
+quit
+stop
+tobacco
+refrain
+currently
+years_ago
+smokes
+discontinued
+history
+exsmoker
+days
+smoker
+when
+months
+smoking_history
+yrs_ago
+used_to
+stopped
+continues_to
+nicotine
+discontinues
+yrs
+discontinuing
+was_smoker
+distant
+week
+is_smoker
+to_discontinue
+to_refrain
+discontinue
+refrained
+current
+wellbutrin
+still
+refrains
+while
+stopping
+has_stopped
+weeks_ago
+was
+use_to
+smoking_sensation
+quits
+year
+to_quit
+smoking_cessation
+continue_to
+weeks
+year_ago
+counselled
+is
+smoke
+months_ago



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