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Posted to commits@ctakes.apache.org by ch...@apache.org on 2013/04/02 19:44:41 UTC
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...
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