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From chen...@apache.org
Subject svn commit: r1588552 [40/42] - in /ctakes/sandbox/ctakes-web-client: ./ .settings/ WebContent/ WebContent/META-INF/ WebContent/WEB-INF/ WebContent/WEB-INF/lib/ src/ src/main/ src/main/java/ src/main/java/org/ src/main/java/org/apache/ src/main/java/org...
Date Fri, 18 Apr 2014 19:48:35 GMT
Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SentenceAdjuster.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SentenceAdjuster.xml?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SentenceAdjuster.xml (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SentenceAdjuster.xml Fri Apr 18 19:47:21 2014
@@ -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>

Propchange: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SentenceAdjuster.xml
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    svn:mime-type = text/plain

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml Fri Apr 18 19:47:21 2014
@@ -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>

Propchange: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/keywords.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/keywords.txt?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/keywords.txt (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/keywords.txt Fri Apr 18 19:47:21 2014
@@ -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

Propchange: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/keywords.txt
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/unknown_words.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/unknown_words.txt?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/unknown_words.txt (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/unknown_words.txt Fri Apr 18 19:47:21 2014
@@ -0,0 +1,2 @@
+smoke detector
+tobacco distributor
\ No newline at end of file

Propchange: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/KU/unknown_words.txt
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/keywords_PCS.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/keywords_PCS.txt?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/keywords_PCS.txt (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/keywords_PCS.txt Fri Apr 18 19:47:21 2014
@@ -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

Propchange: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/keywords_PCS.txt
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    svn:mime-type = text/plain

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/pcs_libsvm-2.91.model
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/pcs_libsvm-2.91.model?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/pcs_libsvm-2.91.model (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/pcs_libsvm-2.91.model Fri Apr 18 19:47:21 2014
@@ -0,0 +1,129 @@
+svm_type c_svc
+kernel_type polynomial
+degree 1
+gamma 1.0
+coef0 1.0
+nr_class 3
+total_sv 118
+rho 0.9179349680682859 -0.7178582819575792 -1.0744536101383289
+label 2 1 3
+nr_sv 56 53 9
+SV
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+-1.0 -1.0 1:0.0 2:1.0 3:0.0 4:0.0 5:0.0 6:1.0 7:0.0 8:0.0 9:0.0 10:0.0 11:0.0 12:0.0 13:1.0 14:0.0 15:0.0 16:0.0 17:0.0 18:0.0 19:0.0 20:0.0 21:0.0 22:0.0 23:0.0 24:0.0 25:0.0 26:0.0 27:0.0 28:0.0 29:0.0 30:0.0 31:0.0 32:0.0 33:0.0 34:0.0 35:0.0 36:0.0 37:1.0 38:0.0 39:0.0 40:0.0 41:0.0 42:0.0 43:0.0 44:0.0 45:0.0 46:0.0 47:0.0 48:0.0 49:0.0 50:0.0 51:0.0 52:0.0 53:0.0 54:0.0 55:0.0 56:0.0 57:0.0 58:0.0 59:0.0 60:0.0 61:0.0 62:0.0 63:0.0 64:0.0 65:0.0 66:0.0 67:0.0 68:0.0 69:0.0 70:0.0 71:0.0 72:0.0 73:0.0 74:0.0 75:0.0 76:0.0 77:0.0 78:0.0 79:0.0 80:0.0 81:0.0 82:0.0 

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/stopwords_PCS.txt
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/stopwords_PCS.txt?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/stopwords_PCS.txt (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/stopwords_PCS.txt Fri Apr 18 19:47:21 2014
@@ -0,0 +1,3 @@
+a
+an
+the

Propchange: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/stopwords_PCS.txt
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    svn:mime-type = text/plain

Added: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/SmokingStatusLookupConfig.xml
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/SmokingStatusLookupConfig.xml?rev=1588552&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/SmokingStatusLookupConfig.xml (added)
+++ ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/SmokingStatusLookupConfig.xml Fri Apr 18 19:47:21 2014
@@ -0,0 +1,67 @@
+<?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.
+
+-->
+<lookupSpecification>
+	<!--  Defines what Gazetteers will be used in terms of implementation specifics and metaField configuration. -->
+	<dictionaries>
+		<dictionary id="GAZ_SMOKING_STATUS" externalResourceKey="SmokerDictionary" caseSensitive="false">
+			<implementation>
+				<csvImpl delimiter="|" indexedFieldNames="0"/>
+			</implementation>
+			<lookupField fieldName="0"/>
+			<metaFields/>
+		</dictionary>
+		<dictionary id="GAZ_NONSMOKING_STATUS" externalResourceKey="NonSmokerDictionary" caseSensitive="false">
+			<implementation>
+				<csvImpl delimiter="|" indexedFieldNames="0"/>
+			</implementation>
+			<lookupField fieldName="0"/>
+			<metaFields/>
+		</dictionary>
+	</dictionaries>
+	<!-- Binds together the components necessary to perform the complete lookup logic start to end. -->
+	<lookupBindings>
+		<lookupBinding>
+			<dictionaryRef idRef="GAZ_SMOKING_STATUS"/>
+			<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl">
+				<properties/>
+			</lookupInitializer>
+			<lookupConsumer className="org.apache.ctakes.smokingstatus.lookup.ae.SmokerNamedEntityLookupConsumerImpl">
+				<properties>
+					<property key="codingScheme" value="NONE"/>
+					<property key="codeMetaField" value="0"/>
+				</properties>
+			</lookupConsumer>
+		</lookupBinding>
+		<lookupBinding>
+			<dictionaryRef idRef="GAZ_NONSMOKING_STATUS"/>
+			<lookupInitializer className="org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl">
+				<properties/>
+			</lookupInitializer>
+			<lookupConsumer className="org.apache.ctakes.smokingstatus.lookup.ae.NonSmokerNamedEntityLookupConsumerImpl">
+				<properties>
+					<property key="codingScheme" value="NONE"/>
+					<property key="codeMetaField" value="0"/>
+				</properties>
+			</lookupConsumer>
+		</lookupBinding>
+	</lookupBindings>
+</lookupSpecification>
\ No newline at end of file

Propchange: ctakes/sandbox/ctakes-web-client/src/main/resources/org/apache/ctakes/smokingstatus/data/SmokingStatusLookupConfig.xml
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