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From chen...@apache.org
Subject svn commit: r1463641 [41/42] - 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/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/pcs_libsvm-2.91.model
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/pcs_libsvm-2.91.model?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/pcs_libsvm-2.91.model (added)
+++ ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/pcs_libsvm-2.91.model Tue Apr  2 17:41:30 2013
@@ -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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Added: ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/stopwords_PCS.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/stopwords_PCS.txt?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/stopwords_PCS.txt (added)
+++ ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/PCS/stopwords_PCS.txt Tue Apr  2 17:41:30 2013
@@ -0,0 +1,3 @@
+a
+an
+the

Added: ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/SmokingStatusLookupConfig.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/SmokingStatusLookupConfig.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/SmokingStatusLookupConfig.xml (added)
+++ ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/SmokingStatusLookupConfig.xml Tue Apr  2 17:41:30 2013
@@ -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

Added: ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/context/boundaryData.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/context/boundaryData.txt?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/context/boundaryData.txt (added)
+++ ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/context/boundaryData.txt Tue Apr  2 17:41:30 2013
@@ -0,0 +1,22 @@
+but
+however
+nevertheless
+notwithstanding
+though
+although
+if
+when
+how
+what
+which
+while
+since
+then
+i
+he
+she
+they
+we
+;
+.
+)
\ No newline at end of file

Added: ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/context/negationContradictionWords.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/context/negationContradictionWords.txt?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/context/negationContradictionWords.txt (added)
+++ ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/context/negationContradictionWords.txt Tue Apr  2 17:41:30 2013
@@ -0,0 +1,8 @@
+quit
+quits
+stop
+stops
+stopped
+discontinue
+discontinues
+discontinued
\ No newline at end of file

Added: ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/nonsmoker.dictionary
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/nonsmoker.dictionary?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/nonsmoker.dictionary (added)
+++ ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/nonsmoker.dictionary Tue Apr  2 17:41:30 2013
@@ -0,0 +1,4 @@
+non-smoker
+nonsmoker
+non-smoking
+nonsmoking

Added: ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/smoker.dictionary
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/smoker.dictionary?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/smoker.dictionary (added)
+++ ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/data/smoker.dictionary Tue Apr  2 17:41:30 2013
@@ -0,0 +1,15 @@
+smoke
+smokes
+smoked
+smoking
+smoker
+tobacco
+tobaccos
+tob
+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/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml (added)
+++ ctakes/trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml Tue Apr  2 17:41:30 2013
@@ -0,0 +1,190 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
+	<name>org.apache.ctakes.smokingstatus.types.TypeSystem</name>
+	<description />
+	<version>1.0</version>
+	<vendor />
+	<imports>
+		<import name="org.apache.ctakes.typesystem.types.TypeSystem" />
+	</imports>
+	<types>
+		<typeDescription>
+			<name>org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence</name>
+			<description>Represents a single sentence from an I2B2 record.
+			</description>
+			<supertypeName>uima.tcas.Annotation</supertypeName>
+			<features>
+				<featureDescription>
+					<name>recordID</name>
+					<description>ID of record that this sentence belongs to.
+					</description>
+					<rangeTypeName>uima.cas.String</rangeTypeName>
+				</featureDescription>
+				<featureDescription>
+					<name>classification</name>
+					<description>Smoking status classification for the given sentence.
+					</description>
+					<rangeTypeName>uima.cas.String</rangeTypeName>
+				</featureDescription>
+				<featureDescription>
+					<name>recordTextBegin</name>
+					<description>Begin offset of the sentence relative to the entire
+						record text.
+					</description>
+					<rangeTypeName>uima.cas.Integer</rangeTypeName>
+				</featureDescription>
+				<featureDescription>
+					<name>recordTextEnd</name>
+					<description>End offset of the sentence relative to the entire
+						record text.
+					</description>
+					<rangeTypeName>uima.cas.Integer</rangeTypeName>
+				</featureDescription>
+			</features>
+		</typeDescription>
+		<typeDescription>
+			<name>org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation
+			</name>
+			<description />
+			<supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
+			</supertypeName>
+		</typeDescription>
+		<typeDescription>
+			<name>org.apache.ctakes.smokingstatus.type.NonSmokerNamedEntityAnnotation
+			</name>
+			<description />
+			<supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
+			</supertypeName>
+		</typeDescription>
+		<typeDescription>
+			<name>org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification
+			</name>
+			<description>Represents classification related to the document
+			</description>
+			<supertypeName>uima.tcas.Annotation</supertypeName>
+			<features>
+				<featureDescription>
+					<name>classification</name>
+					<description>represents the document level classification that
+						RecordResolutionAnnotator assigns
+					</description>
+					<rangeTypeName>uima.cas.String</rangeTypeName>
+				</featureDescription>
+				<featureDescription>
+					<name>recordID</name>
+					<description>Represents the document record id</description>
+					<rangeTypeName>uima.cas.String</rangeTypeName>
+				</featureDescription>
+			</features>
+		</typeDescription>
+		<typeDescription>
+			<name>org.apache.ctakes.smokingstatus.type.UnknownSmokerNamedEntityAnnotation
+			</name>
+			<description />
+			<supertypeName>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
+			</supertypeName>
+		</typeDescription>
+		<typeDescription>
+			<name>org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue
+			</name>
+			<description>Corresponds to the ARFF numeric attributes.
+			</description>
+			<supertypeName>org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue
+			</supertypeName>
+			<features>
+				<featureDescription>
+					<name>numericValue</name>
+					<description></description>
+					<rangeTypeName>uima.cas.String</rangeTypeName>
+				</featureDescription>
+			</features>
+		</typeDescription>
+		<typeDescription>
+			<name>org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue
+			</name>
+			<description></description>
+			<supertypeName>uima.tcas.Annotation</supertypeName>
+			<features>
+				<featureDescription>
+					<name>attributeName</name>
+					<description></description>
+					<rangeTypeName>uima.cas.String</rangeTypeName>
+				</featureDescription>
+			</features>
+		</typeDescription>
+		<typeDescription>
+			<name>org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue
+			</name>
+			<description></description>
+			<supertypeName>org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue
+			</supertypeName>
+			<features>
+				<featureDescription>
+					<name>nominalValue</name>
+					<description></description>
+					<rangeTypeName>uima.cas.String</rangeTypeName>
+				</featureDescription>
+			</features>
+		</typeDescription>
+		<typeDescription>
+			<name>org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue
+			</name>
+			<description></description>
+			<supertypeName>org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue
+			</supertypeName>
+			<features>
+				<featureDescription>
+					<name>attributeStringValue</name>
+					<description></description>
+					<rangeTypeName>uima.cas.String</rangeTypeName>
+				</featureDescription>
+			</features>
+		</typeDescription>
+		<typeDescription>
+			<name>org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue
+			</name>
+			<description></description>
+			<supertypeName>org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue
+			</supertypeName>
+			<features>
+				<featureDescription>
+					<name>dateValue</name>
+					<description></description>
+					<rangeTypeName>uima.cas.String</rangeTypeName>
+				</featureDescription>
+			</features>
+		</typeDescription>
+		<typeDescription>
+			<name>org.apache.ctakes.smokingstatus.type.libsvm.DocumentID</name>
+			<description></description>
+			<supertypeName>uima.tcas.Annotation</supertypeName>
+			<features>
+				<featureDescription>
+					<name>documentID</name>
+					<description></description>
+					<rangeTypeName>uima.cas.String</rangeTypeName>
+				</featureDescription>
+			</features>
+		</typeDescription>
+	</types>
+</typeSystemDescription>

Added: ctakes/trunk/ctakes-temporal-res/.classpath
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal-res/.classpath?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal-res/.classpath (added)
+++ ctakes/trunk/ctakes-temporal-res/.classpath Tue Apr  2 17:41:30 2013
@@ -0,0 +1,31 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

Added: ctakes/trunk/ctakes-temporal-res/.project
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal-res/.project?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal-res/.project (added)
+++ ctakes/trunk/ctakes-temporal-res/.project Tue Apr  2 17:41:30 2013
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>ctakes-temporal-res</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+</projectDescription>

Added: ctakes/trunk/ctakes-temporal-res/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal-res/.settings/org.eclipse.core.resources.prefs?rev=1463641&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal-res/.settings/org.eclipse.core.resources.prefs (added)
+++ ctakes/trunk/ctakes-temporal-res/.settings/org.eclipse.core.resources.prefs Tue Apr  2 17:41:30 2013
@@ -0,0 +1,5 @@
+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding//src/main/resources=UTF-8
+encoding//src/test/java=UTF-8
+encoding/<project>=UTF-8



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