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From chen...@apache.org
Subject svn commit: r1451742 - in /incubator/ctakes/trunk/ctakes-regression-test: ./ .settings/ desc/ desc/analysis_engine/ desc/collection_processing_engine/ src/ src/main/ src/main/java/ src/main/resources/ src/test/ src/test/java/ src/test/java/org/ src/tes...
Date Fri, 01 Mar 2013 22:29:40 GMT
Author: chenpei
Date: Fri Mar  1 22:29:38 2013
New Revision: 1451742

URL: http://svn.apache.org/r1451742
Log:
CTAKES-84 - Adding a Regression Test.
This is an initial pass.  The goal is to verify that upon changes: all the components still work as expected and that one did not break anything (including the bundled downstream modules).
The idea is to automate the testing that we used to do manually before each release including the optional components (as well as loading the different descriptor xml's and verifying the output xml).

Added:
    incubator/ctakes/trunk/ctakes-regression-test/
    incubator/ctakes/trunk/ctakes-regression-test/.classpath
    incubator/ctakes/trunk/ctakes-regression-test/.project
    incubator/ctakes/trunk/ctakes-regression-test/.settings/
    incubator/ctakes/trunk/ctakes-regression-test/.settings/org.eclipse.core.resources.prefs
    incubator/ctakes/trunk/ctakes-regression-test/.settings/org.eclipse.jdt.core.prefs
    incubator/ctakes/trunk/ctakes-regression-test/.settings/org.eclipse.m2e.core.prefs
    incubator/ctakes/trunk/ctakes-regression-test/desc/
    incubator/ctakes/trunk/ctakes-regression-test/desc/analysis_engine/
    incubator/ctakes/trunk/ctakes-regression-test/desc/analysis_engine/RegressionPipelineAggregateTest.xml
    incubator/ctakes/trunk/ctakes-regression-test/desc/collection_processing_engine/
    incubator/ctakes/trunk/ctakes-regression-test/desc/collection_processing_engine/RegressionPipelineCPETest.xml
    incubator/ctakes/trunk/ctakes-regression-test/pom.xml
    incubator/ctakes/trunk/ctakes-regression-test/src/
    incubator/ctakes/trunk/ctakes-regression-test/src/main/
    incubator/ctakes/trunk/ctakes-regression-test/src/main/java/
    incubator/ctakes/trunk/ctakes-regression-test/src/main/resources/
    incubator/ctakes/trunk/ctakes-regression-test/src/test/
    incubator/ctakes/trunk/ctakes-regression-test/src/test/java/
    incubator/ctakes/trunk/ctakes-regression-test/src/test/java/org/
    incubator/ctakes/trunk/ctakes-regression-test/src/test/java/org/apache/
    incubator/ctakes/trunk/ctakes-regression-test/src/test/java/org/apache/ctakes/
    incubator/ctakes/trunk/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/
    incubator/ctakes/trunk/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/
    incubator/ctakes/trunk/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java
    incubator/ctakes/trunk/ctakes-regression-test/src/test/resources/
    incubator/ctakes/trunk/ctakes-regression-test/target/
    incubator/ctakes/trunk/ctakes-regression-test/target/classes/
    incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/
    incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/MANIFEST.MF
    incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/maven/
    incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/maven/org.apache.ctakes/
    incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/maven/org.apache.ctakes/ctakes-regression-test/
    incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/maven/org.apache.ctakes/ctakes-regression-test/pom.properties
    incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/maven/org.apache.ctakes/ctakes-regression-test/pom.xml
    incubator/ctakes/trunk/ctakes-regression-test/target/test-classes/
    incubator/ctakes/trunk/ctakes-regression-test/target/test-classes/org/
    incubator/ctakes/trunk/ctakes-regression-test/target/test-classes/org/apache/
    incubator/ctakes/trunk/ctakes-regression-test/target/test-classes/org/apache/ctakes/
    incubator/ctakes/trunk/ctakes-regression-test/target/test-classes/org/apache/ctakes/regression/
    incubator/ctakes/trunk/ctakes-regression-test/target/test-classes/org/apache/ctakes/regression/test/
    incubator/ctakes/trunk/ctakes-regression-test/target/test-classes/org/apache/ctakes/regression/test/RegressionPipelineTest.class   (with props)
    incubator/ctakes/trunk/ctakes-regression-test/testdata/
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/cda/
    incubator/ctakes/trunk/ctakes-regression-test/testdata/expectedoutput/plaintext/
    incubator/ctakes/trunk/ctakes-regression-test/testdata/generatedoutput/
    incubator/ctakes/trunk/ctakes-regression-test/testdata/generatedoutput/cda/
    incubator/ctakes/trunk/ctakes-regression-test/testdata/generatedoutput/plaintext/
    incubator/ctakes/trunk/ctakes-regression-test/testdata/input/
    incubator/ctakes/trunk/ctakes-regression-test/testdata/input/cda/
    incubator/ctakes/trunk/ctakes-regression-test/testdata/input/cda/testpatient_cn_1.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/input/cda/testpatient_cn_2.xml
    incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/
    incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/SampleInputRadiologyNotes.txt
    incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc1_07543210_sample_current.txt
    incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc1_07543210_sample_past_smoker.txt
    incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc1_07543210_sample_unknown.txt
    incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc2_07543210_sample_current.txt
    incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc2_07543210_sample_past_smoker.txt
    incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/sample_note
    incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/sample_note_plaintext
    incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/testfakenote.txt
    incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/testpatient_plaintext_1.txt
    incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/testpatient_plaintext_2.txt
    incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/text1.txt

Added: incubator/ctakes/trunk/ctakes-regression-test/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/.classpath?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/.classpath (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/.classpath Fri Mar  1 22:29:38 2013
@@ -0,0 +1,31 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<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 excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<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: incubator/ctakes/trunk/ctakes-regression-test/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/.project?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/.project (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/.project Fri Mar  1 22:29:38 2013
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>ctakes-regression-test</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: incubator/ctakes/trunk/ctakes-regression-test/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/.settings/org.eclipse.core.resources.prefs?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/.settings/org.eclipse.core.resources.prefs (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/.settings/org.eclipse.core.resources.prefs Fri Mar  1 22:29:38 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

Added: incubator/ctakes/trunk/ctakes-regression-test/.settings/org.eclipse.jdt.core.prefs
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/.settings/org.eclipse.jdt.core.prefs?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/.settings/org.eclipse.jdt.core.prefs (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/.settings/org.eclipse.jdt.core.prefs Fri Mar  1 22:29:38 2013
@@ -0,0 +1,88 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.annotation.missingNonNullByDefaultAnnotation=ignore
+org.eclipse.jdt.core.compiler.annotation.nonnull=org.eclipse.jdt.annotation.NonNull
+org.eclipse.jdt.core.compiler.annotation.nonnullbydefault=org.eclipse.jdt.annotation.NonNullByDefault
+org.eclipse.jdt.core.compiler.annotation.nullable=org.eclipse.jdt.annotation.Nullable
+org.eclipse.jdt.core.compiler.annotation.nullanalysis=disabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.problem.annotationSuperInterface=warning
+org.eclipse.jdt.core.compiler.problem.autoboxing=ignore
+org.eclipse.jdt.core.compiler.problem.comparingIdentical=warning
+org.eclipse.jdt.core.compiler.problem.deadCode=warning
+org.eclipse.jdt.core.compiler.problem.deprecation=warning
+org.eclipse.jdt.core.compiler.problem.deprecationInDeprecatedCode=disabled
+org.eclipse.jdt.core.compiler.problem.deprecationWhenOverridingDeprecatedMethod=disabled
+org.eclipse.jdt.core.compiler.problem.discouragedReference=warning
+org.eclipse.jdt.core.compiler.problem.emptyStatement=warning
+org.eclipse.jdt.core.compiler.problem.explicitlyClosedAutoCloseable=warning
+org.eclipse.jdt.core.compiler.problem.fallthroughCase=ignore
+org.eclipse.jdt.core.compiler.problem.fatalOptionalError=disabled
+org.eclipse.jdt.core.compiler.problem.fieldHiding=warning
+org.eclipse.jdt.core.compiler.problem.finalParameterBound=warning
+org.eclipse.jdt.core.compiler.problem.finallyBlockNotCompletingNormally=warning
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.problem.hiddenCatchBlock=warning
+org.eclipse.jdt.core.compiler.problem.includeNullInfoFromAsserts=disabled
+org.eclipse.jdt.core.compiler.problem.incompatibleNonInheritedInterfaceMethod=warning
+org.eclipse.jdt.core.compiler.problem.incompleteEnumSwitch=warning
+org.eclipse.jdt.core.compiler.problem.indirectStaticAccess=warning
+org.eclipse.jdt.core.compiler.problem.localVariableHiding=warning
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+org.eclipse.jdt.core.compiler.problem.missingDefaultCase=ignore
+org.eclipse.jdt.core.compiler.problem.missingDeprecatedAnnotation=warning
+org.eclipse.jdt.core.compiler.problem.missingEnumCaseDespiteDefault=disabled
+org.eclipse.jdt.core.compiler.problem.missingHashCodeMethod=warning
+org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotation=warning
+org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotationForInterfaceMethodImplementation=disabled
+org.eclipse.jdt.core.compiler.problem.missingSerialVersion=warning
+org.eclipse.jdt.core.compiler.problem.missingSynchronizedOnInheritedMethod=warning
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+org.eclipse.jdt.core.compiler.problem.parameterAssignment=ignore
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+org.eclipse.jdt.core.compiler.problem.redundantSpecificationOfTypeArguments=warning
+org.eclipse.jdt.core.compiler.problem.redundantSuperinterface=warning
+org.eclipse.jdt.core.compiler.problem.reportMethodCanBePotentiallyStatic=ignore
+org.eclipse.jdt.core.compiler.problem.reportMethodCanBeStatic=warning
+org.eclipse.jdt.core.compiler.problem.specialParameterHidingField=disabled
+org.eclipse.jdt.core.compiler.problem.staticAccessReceiver=warning
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+org.eclipse.jdt.core.compiler.problem.typeParameterHiding=warning
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+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionExemptExceptionAndThrowable=enabled
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionIncludeDocCommentReference=enabled
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionWhenOverriding=disabled
+org.eclipse.jdt.core.compiler.problem.unusedImport=warning
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+org.eclipse.jdt.core.compiler.problem.unusedParameter=warning
+org.eclipse.jdt.core.compiler.problem.unusedParameterIncludeDocCommentReference=enabled
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+org.eclipse.jdt.core.compiler.problem.unusedPrivateMember=warning
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+org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning
+org.eclipse.jdt.core.compiler.source=1.6

Added: incubator/ctakes/trunk/ctakes-regression-test/.settings/org.eclipse.m2e.core.prefs
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/.settings/org.eclipse.m2e.core.prefs?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/.settings/org.eclipse.m2e.core.prefs (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/.settings/org.eclipse.m2e.core.prefs Fri Mar  1 22:29:38 2013
@@ -0,0 +1,4 @@
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

Added: incubator/ctakes/trunk/ctakes-regression-test/desc/analysis_engine/RegressionPipelineAggregateTest.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/desc/analysis_engine/RegressionPipelineAggregateTest.xml?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/desc/analysis_engine/RegressionPipelineAggregateTest.xml (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/desc/analysis_engine/RegressionPipelineAggregateTest.xml Fri Mar  1 22:29:38 2013
@@ -0,0 +1,204 @@
+<?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.
+
+-->
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+<primitive>false</primitive>
+<delegateAnalysisEngineSpecifiers>
+<delegateAnalysisEngine key="LookupWindowAnnotator">
+<import location="../../../ctakes-clinical-pipeline/desc/analysis_engine/LookupWindowAnnotator.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="SimpleSegmentAnnotator">
+<import location="../../../ctakes-clinical-pipeline/desc/analysis_engine/SimpleSegmentAnnotator.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="Chunker">
+<import location="../../../ctakes-chunker/desc/Chunker.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="ExtractionPrepAnnotator">
+<import location="../../../ctakes-clinical-pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="NegationAnnotator">
+<import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="SentenceDetectorAnnotator">
+<import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="TokenizerAnnotator">
+<import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="POSTagger">
+<import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="StatusAnnotator">
+<import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="AdjustNounPhraseToIncludeFollowingNP">
+<import location="../../../ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingNP.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="AdjustNounPhraseToIncludeFollowingPPNP">
+<import location="../../../ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingPPNP.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="LvgAnnotator">
+<import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
+<import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="DictionaryLookupAnnotator">
+<import location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotator.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="AssertionAnnotator">
+<import location="../../../ctakes-assertion/desc/AssertionMiniPipelineAnalysisEngine.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="DependencyParser">
+<import location="../../../ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserAE.xml"/>
+</delegateAnalysisEngine>
+</delegateAnalysisEngineSpecifiers>
+<analysisEngineMetaData>
+<name>AggregatePlaintextProcessor</name>
+<description>Runs the complete pipeline for annotating clinical documents in plain text format.  
+Includes adjusting NP chunks to include NP NP and NP PP NP.</description>
+<version></version>
+<vendor></vendor>
+<configurationParameters searchStrategy="language_fallback">
+<configurationParameter>
+<name>SegmentID</name>
+<description></description>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>false</mandatory>
+<overrides>
+<parameter>SimpleSegmentAnnotator/SegmentID</parameter>
+</overrides>
+</configurationParameter>
+<configurationParameter>
+<name>ChunkCreatorClass</name>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+<overrides>
+<parameter>Chunker/ChunkCreatorClass</parameter>
+</overrides>
+</configurationParameter>
+</configurationParameters>
+<configurationParameterSettings>
+<nameValuePair>
+<name>ChunkCreatorClass</name>
+<value>
+<string>org.apache.ctakes.chunker.ae.PhraseTypeChunkCreator</string>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+<flowConstraints>
+<fixedFlow>
+<node>SimpleSegmentAnnotator</node>
+<node>SentenceDetectorAnnotator</node>
+<node>TokenizerAnnotator</node>
+<node>LvgAnnotator</node>
+<node>ContextDependentTokenizerAnnotator</node>
+<node>POSTagger</node>
+<node>Chunker</node>
+<node>AdjustNounPhraseToIncludeFollowingNP</node>
+<node>AdjustNounPhraseToIncludeFollowingPPNP</node>
+<node>LookupWindowAnnotator</node>
+<node>DictionaryLookupAnnotator</node>
+<node>DependencyParser</node>
+<node>AssertionAnnotator</node>
+<!-- 
+	<node>StatusAnnotator</node>
+	<node>NegationAnnotator</node>
+ -->
+<node>ExtractionPrepAnnotator</node>
+</fixedFlow>
+</flowConstraints>
+<typePriorities>
+<name>Ordering</name>
+<description>For subiterator</description>
+<version>1.0</version>
+<priorityList>
+<type>org.apache.ctakes.typesystem.type.textspan.Segment</type>
+<type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+<type>org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+</priorityList>
+<priorityList>
+<type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+<type>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
+</priorityList>
+</typePriorities>
+<fsIndexCollection/>
+<capabilities>
+<capability>
+<inputs/>
+<outputs>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.NewlineToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.WordToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.VP</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.refsem.UmlsConcept</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.UCP</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.TimeAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.SymbolToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspanSegment</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.SBAR</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.RangeAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PunctuationToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.Property</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.Properties</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PRT</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PP</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.OntologyConcept</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.NumToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation</type>
+<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.lookup.type.LookupWindowAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.Lemma</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.LST</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.INTJ</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.FractionAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.structured.DocumentID</type>
+<type allAnnotatorFeatures="true">uima.tcas.DocumentAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.DateAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.CopySrcAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.CopyDestAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.ContractionToken</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.ContextAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.Chunk</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.CONJP</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+<type allAnnotatorFeatures="true">uima.cas.AnnotationBase</type>
+<type allAnnotatorFeatures="true">uima.tcas.Annotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.ADVP</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.ADJP</type>
+</outputs>
+<languagesSupported/>
+</capability>
+</capabilities>
+<operationalProperties>
+<modifiesCas>true</modifiesCas>
+<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+<outputsNewCASes>false</outputsNewCASes>
+</operationalProperties>
+</analysisEngineMetaData>
+<resourceManagerConfiguration/>
+</analysisEngineDescription>

Added: incubator/ctakes/trunk/ctakes-regression-test/desc/collection_processing_engine/RegressionPipelineCPETest.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/desc/collection_processing_engine/RegressionPipelineCPETest.xml?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/desc/collection_processing_engine/RegressionPipelineCPETest.xml (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/desc/collection_processing_engine/RegressionPipelineCPETest.xml Fri Mar  1 22:29:38 2013
@@ -0,0 +1,78 @@
+<?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.
+
+-->
+<cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<collectionReader>
+<collectionIterator>
+<descriptor>
+<import location="../../../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml"/>
+</descriptor>
+<configurationParameterSettings>
+<nameValuePair>
+<name>InputDirectory</name>
+<value>
+<string>testdata/input/plaintext</string>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+</collectionIterator>
+</collectionReader>
+<casProcessors casPoolSize="3" processingUnitThreadCount="1">
+<casProcessor deployment="integrated" name="RegressionPipelineAggregateTest">
+<descriptor>
+<import location="../analysis_engine/RegressionPipelineAggregateTest.xml"/>
+</descriptor>
+<deploymentParameters/>
+<errorHandling>
+<errorRateThreshold action="terminate" value="0/1000"/>
+<maxConsecutiveRestarts action="terminate" value="30"/>
+<timeout max="100000" default="-1"/>
+</errorHandling>
+<checkpoint batch="10000" time="1000ms"/>
+</casProcessor>
+<casProcessor deployment="integrated" name="Write CAS to XML file">
+<descriptor>
+<import location="../../../ctakes-core/desc/cas_consumer/FileWriterCasConsumer.xml"/>
+</descriptor>
+<deploymentParameters/>
+<errorHandling>
+<errorRateThreshold action="terminate" value="0/1000"/>
+<maxConsecutiveRestarts action="terminate" value="30"/>
+<timeout max="100000" default="-1"/>
+</errorHandling>
+<checkpoint batch="10000" time="1000ms"/>
+<configurationParameterSettings>
+<nameValuePair>
+<name>outputDir</name>
+<value>
+<string>testdata/generatedoutput/plaintext</string>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+</casProcessor>
+</casProcessors>
+<cpeConfig>
+<numToProcess>-1</numToProcess>
+<deployAs>immediate</deployAs>
+<checkpoint batch="0" time="300000"/>
+<timerImpl></timerImpl>
+</cpeConfig>
+</cpeDescription>

Added: incubator/ctakes/trunk/ctakes-regression-test/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/pom.xml?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/pom.xml (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/pom.xml Fri Mar  1 22:29:38 2013
@@ -0,0 +1,94 @@
+<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-incubating-SNAPSHOT</version>
+  </parent>
+  <artifactId>ctakes-regression-test</artifactId>
+  <name>ctakes-regression-test</name>
+  <description>ctakes-regression-test</description>
+  
+	<dependencies>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-type-system</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-utils</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>jdom</groupId>
+			<artifactId>jdom</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-context-tokenizer</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-dictionary-lookup</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-preprocessor</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-lvg</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-chunker</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-ne-contexts</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-pos-tagger</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-assertion</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-dependency-parser</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-clinical-pipeline</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-drug-ner</artifactId>
+		</dependency>		
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-smoking-status</artifactId>
+		</dependency>		
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-side-effect</artifactId>
+		</dependency>		
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-constituency-parser</artifactId>
+		</dependency>		
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-coreference</artifactId>
+		</dependency>				
+	</dependencies>  
+</project>
\ No newline at end of file

Added: incubator/ctakes/trunk/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java Fri Mar  1 22:29:38 2013
@@ -0,0 +1,92 @@
+/**
+ * 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.
+ */
+package org.apache.ctakes.regression.test;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Logger;
+import org.apache.uima.UIMAFramework;
+import org.apache.uima.collection.CollectionProcessingEngine;
+import org.apache.uima.collection.metadata.CpeDescription;
+import org.apache.uima.util.XMLInputSource;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+
+
+/**
+ * Runs a full pipeline and compares the xml output 
+ * to ensure all annotators work together in harmony.
+ * 
+ * The Apache cTAKES Release Manager should ensure that at a min
+ * this test passes before releasing.
+ * 
+ * If there are new modules, be sure to add the desc here.
+ * If there are changes, after it's been manually reviewed, 
+ * re-record the expected output and put them in output folder.
+ * 
+ * This also tests the UMLS annotator(s) so be sure to download
+ * the UMLS Resources per README and add the jvm params
+ * -Dctakes.umlsuser= -Dctakes.umlspw= parameters before running
+ *
+ */
+public class RegressionPipelineTest {
+
+	// LOG4J logger based on class name
+	private Logger logger = Logger.getLogger(getClass().getName());
+	private CollectionProcessingEngine mCPE;
+	private static final File dir = new File("testdata/generatedoutput");
+	private static final String CPEDESC = "desc/collection_processing_engine/RegressionPipelineCPETest.xml";
+	
+	@Test
+	public void test() throws Exception {
+		// create the pipeline
+		setUp();
+		
+		// Start Processing
+		logger.info("Running CPE");
+		mCPE.process();
+	}
+
+	@Before
+	public void setUp() throws Exception {
+
+		//Setup output dir
+	    Assert.assertTrue("Unable to create " + dir.getAbsolutePath(), dir.exists() || dir.mkdirs());
+	    
+		// parse CPE descriptor
+		logger.info("Parsing CPE Descriptor");
+		CpeDescription cpeDesc = UIMAFramework.getXMLParser()
+				.parseCpeDescription(new XMLInputSource(CPEDESC));
+		// instantiate CPE
+		logger.info("Instantiating CPE");
+		mCPE = UIMAFramework.produceCollectionProcessingEngine(cpeDesc);
+
+	}
+	
+	@Test
+	public void testCompareXMLOutput() throws IOException {
+		//TODO: need to implement here.
+	    //final File expected = new File("xyz.txt");
+	    //final File output = new File(dir, "xyz.txt");
+	    //Assert.assertEquals(FileUtils.readLines(expected), FileUtils.readLines(output));
+	}
+}

Added: incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/MANIFEST.MF
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/MANIFEST.MF?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/MANIFEST.MF (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/MANIFEST.MF Fri Mar  1 22:29:38 2013
@@ -0,0 +1,12 @@
+Manifest-Version: 1.0
+Implementation-Vendor: The Apache Software Foundation
+Implementation-Title: ctakes-regression-test
+Implementation-Version: 3.1.0-incubating-SNAPSHOT
+Implementation-Vendor-Id: org.apache.ctakes
+Specification-Vendor: The Apache Software Foundation
+Build-Jdk: 1.6.0_26
+Built-By: CH150124
+Created-By: Maven Integration for Eclipse
+Specification-Title: ctakes-regression-test
+Specification-Version: 3.1.0-incubating-SNAPSHOT
+

Added: incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/maven/org.apache.ctakes/ctakes-regression-test/pom.properties
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/maven/org.apache.ctakes/ctakes-regression-test/pom.properties?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/maven/org.apache.ctakes/ctakes-regression-test/pom.properties (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/maven/org.apache.ctakes/ctakes-regression-test/pom.properties Fri Mar  1 22:29:38 2013
@@ -0,0 +1,7 @@
+#Generated by Maven Integration for Eclipse
+#Fri Mar 01 17:22:04 EST 2013
+version=3.1.0-incubating-SNAPSHOT
+groupId=org.apache.ctakes
+m2e.projectName=ctakes-regression-test
+m2e.projectLocation=C\:\\Users\\CH150124\\workspaces\\apache-ctakes\\ctakes\\ctakes-regression-test
+artifactId=ctakes-regression-test

Added: incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/maven/org.apache.ctakes/ctakes-regression-test/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/maven/org.apache.ctakes/ctakes-regression-test/pom.xml?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/maven/org.apache.ctakes/ctakes-regression-test/pom.xml (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/target/classes/META-INF/maven/org.apache.ctakes/ctakes-regression-test/pom.xml Fri Mar  1 22:29:38 2013
@@ -0,0 +1,94 @@
+<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-incubating-SNAPSHOT</version>
+  </parent>
+  <artifactId>ctakes-regression-test</artifactId>
+  <name>ctakes-regression-test</name>
+  <description>ctakes-regression-test</description>
+  
+	<dependencies>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-type-system</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-utils</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>jdom</groupId>
+			<artifactId>jdom</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-context-tokenizer</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-dictionary-lookup</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-preprocessor</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-lvg</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-chunker</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-ne-contexts</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-pos-tagger</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-assertion</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-dependency-parser</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-clinical-pipeline</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-drug-ner</artifactId>
+		</dependency>		
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-smoking-status</artifactId>
+		</dependency>		
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-side-effect</artifactId>
+		</dependency>		
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-constituency-parser</artifactId>
+		</dependency>		
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-coreference</artifactId>
+		</dependency>				
+	</dependencies>  
+</project>
\ No newline at end of file

Added: incubator/ctakes/trunk/ctakes-regression-test/target/test-classes/org/apache/ctakes/regression/test/RegressionPipelineTest.class
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/target/test-classes/org/apache/ctakes/regression/test/RegressionPipelineTest.class?rev=1451742&view=auto
==============================================================================
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Added: incubator/ctakes/trunk/ctakes-regression-test/testdata/input/cda/testpatient_cn_1.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/testdata/input/cda/testpatient_cn_1.xml?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/testdata/input/cda/testpatient_cn_1.xml (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/testdata/input/cda/testpatient_cn_1.xml Fri Mar  1 22:29:38 2013
@@ -0,0 +1 @@
+<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE levelone SYSTEM "NotesIIST_RTF.DTD" [<!ENTITY deg '&#x00B0;'><!ENTITY sup2 '&#x00B2;'><!ENTITY micro '&#x00B5;'>]><levelone><clinical_document_header><id EX="###DOC_ID###" RT="2.16.840.1.113883.3.2.1.1"/><set_id EX="###SET_ID###" RT="2.16.840.1.113883.3.2.1.2"/><version_nbr V="###V_NBR###"/><document_type_cd V="687" S="2.16.840.1.113883.3.2.1.3" DN="Nutrition Consult"/><origination_dttm V="20030822T131513"/><confidentiality_cd V="0" S="2.16.840.1.113883.3.2.1.4"/><patient_encounter><practice_setting_cd V="4284" S="2.16.840.1.113883.3.2.1.7" DN="Nutr Clinic"/><encounter_tmr V="20030822"/><service_location><id EX="TBD" RT="2.16.840.1.113883.3.2.1.8"/></service_location><facility><organization><organization.nm V="MCR"/></organization></facility></patient_encounter><legal_authenticator><legal_authenticator.type_cd V="SPV"/><participation_tmr V=""/><signature_cd V="S"/><person><id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/><perso
 n_name><nm><GIV V="Julie"/><MID V="A"/><FAM V="Tester"/><PFX V=""/><SFX V="RD"/></nm><person_name.type_cd V="S"/></person_name></person></legal_authenticator><originator><originator.type_cd V="AUT"/><participation_tmr V="20030822T131513"/><person><id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/><person_name><nm><GIV V="Julie"/><MID V="A."/><FAM V="Tester"/><PFX V=""/><SFX V="RD"/></nm><person_name.type_cd V="L"/></person_name><telecom V="5-5555" USE="PG"/></person></originator><originating_organization><originating_organization.type_cd V="CST"/><organization><id EX="TBD" RT="2.16.840.1.113883.3.2.1.10"/><organization.nm V="Originating Organization - Coding TBD"/></organization></originating_organization><transcriptionist><transcriptionist.type_cd V="ENT"/><participation_tmr V="20030822T131513"/><person><id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/><person_name><nm><GIV V="Julie"/><MID V="A."/><FAM V="Tester"/></nm><person_name.type_cd V="L"/></person_name></person></tra
 nscriptionist><provider><provider.type_cd V="CON"/><participation_tmr V="20030822T131513"/><person><id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/><person_name><nm><GIV V="Julie"/><MID V="A."/><FAM V="Tester"/><PFX V=""/><SFX V="RD"/></nm><person_name.type_cd V="L"/></person_name><telecom V="5-5555" USE="PG"/></person></provider><patient><patient.type_cd V="PATSBJ"/><person><id EX="3-303-925" RT="2.16.840.1.113883.3.2.1.1"/><person_name><nm><GIV V="Terri"/><MID V="A."/><FAM V="Testing"/><PFX V="Judge"/><SFX V="Jr.,D.D.S."/></nm><person_name.type_cd V="L"/></person_name><addr><LIT V="100 Quality Control Avenue"/><CTY V="Rochester"/><STA V="MN"/><ZIP V="55905"/><CNT V="US"/></addr></person><is_known_by><id EX="TBD" RT="2.16.840.1.113883.3.2.2.1"/><is_known_to><id EX="TBD" RT="2.16.840.1.113883.3.2.1.10"/></is_known_to></is_known_by><birth_dttm V="19341123"/><administrative_gender_cd V="F" S="2.16.840.1.113883.3.2.2.2"/></patient><status_cd V="TBD" S="2.16.840.1.113883.3.2.1.
 16"/><cn1_admin_data><cn1_status_cd V="Fnl" S="2.16.840.1.113883.3.2.3.1"/><cn1_service_cd V="MNT" S="2.16.840.1.113883.3.2.3.2"/><cn1_event_cd V="CON" S="2.16.840.1.113883.3.2.3.3"/><cn1_document_id EX="000000000" RT="2.16.840.1.113883.3.2.3.4"/><cn1_revision_nbr V="1"/><cn1_site_cd V="RCH" S="2.16.840.1.113883.3.2.3.10"/></cn1_admin_data><document_title V="Document Service Name - Coding TBD" S="2.16.840.1.113883.3.2.1.17"/></clinical_document_header><body><section><caption><caption_cd V="20100" DN="Revision History" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Revision History</caption></section><section><caption><caption_cd V="20112" DN="I/R/P" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Impression / Report / Plan</caption><table><caption><caption_cd V="20003" DN="I/R/P" S="2.16.840.1.113883.3.1.21" SV="1.0"/></caption><tr><th>Problem</th><th>Plan</th></tr></table></section><section><caption><caption_cd V="20113" DN="Diagnoses" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Diagnosis</capti
 on><table><caption><caption_cd V="20003" DN="Diagnoses" S="2.16.840.1.113883.3.1.21" SV="1.0"/></caption><tr><th>Problem</th><th>Diagnosis</th></tr></table></section><section><caption><caption_cd V="20101" DN="Ref" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Referral Source</caption><paragraph><content>Dr. Nutritious</content></paragraph></section><section><caption><caption_cd V="20102" DN="CC" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Chief Complaint/Reason for Visit</caption><paragraph><content>Medical Nutrition Therapy for Hyperlipidemia</content></paragraph></section><section><caption><caption_cd V="20103" DN="HPI" S="2.16.840.1.113883.3.1.21" SV="1.0"/>History of Present Illness</caption><table><caption><caption_cd V="20003" DN="HPI" S="2.16.840.1.113883.3.1.21" SV="1.0"/></caption><tr><th>Problem</th><th>History</th></tr><tr><td/><td><paragraph><content>Referral from: Julie Tester, RD, LD, CNSD</content></paragraph></td></tr><tr><td/><td><paragraph><content>Phone contact: (555
 ) 555-1212</content></paragraph></td></tr><tr><td/><td><paragraph><content>Height: 144 cm   Current Weight: 45 kg   Date of current weight: 02-29-2001   Admit Weight:  53 kg   BMI: 18 kg/m2</content></paragraph></td></tr><tr><td/><td><paragraph><content>Diet: General</content></paragraph></td></tr><tr><td/><td><paragraph><content>Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity.</content></paragraph></td></tr><tr><td/><td><paragraph><content>Daily Protein needs: 40 grams,  assessed as 1.0 g/kg.</content></paragraph></td></tr><tr><td/><td><paragraph><content>Pt has been on a 3 day calorie count and has had an average intake of 1100 calories.  She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.  She agrees with the plan and has my number for further assessment. May want a Resting Metabolic Rate as well. She takes an aspirin a day for knee pain.</content></paragraph></td></tr></table><table><caption><caption_cd V="
 20004" DN="MC985" S="2.16.840.1.113883.3.1.21" SV="1.0"/></caption><tr><th><caption_cd V="30001" DN="PFH Date" S="2.16.840.1.113883.3.1.22" SV="1.0"/>PFH Date</th><th><caption_cd V="30002" DN="CVI Page#" S="2.16.840.1.113883.3.1.22" SV="1.0"/>CVI Page#</th><th><caption_cd V="30003" DN="CVI Date" S="2.16.840.1.113883.3.1.22" SV="1.0"/>CVI Date</th></tr><tr><td></td><td></td><td></td></tr></table></section><section><caption><caption_cd V="20107" DN="Med/Surg Hx" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Past Medical/Surgical History</caption></section><section><caption><caption_cd V="20105" DN="Allerg" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Allergies</caption></section><section><caption><caption_cd V="20108" DN="Soc Hist" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Social History</caption></section><section><caption><caption_cd V="20109" DN="Fam Hist" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Family History</caption></section><section><caption><caption_cd V="20104" DN="Meds" S="2.16.840.
 1.113883.3.1.21" SV="1.0"/>Current Medications</caption></section><section><caption><caption_cd V="20106" DN="Sys Rev" S="2.16.840.1.113883.3.1.21" SV="1.0"/>System Review</caption></section><section><caption><caption_cd V="20115" DN="Spec Instr" S=".16.840.1.113883.3.1.21" SV="1.0"/>Special Instructions</caption></section><section><caption><caption_cd V="20114" DN="Administrative" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Administrative</caption><table><caption><caption_cd V="20005" DN="Billing" S="2.16.840.1.113883.3.1.21" SV="1.0"/></caption><tr><th>Billing</th><th>Value</th></tr><tr><th><caption_cd V="30004" DN="Margin Code" S="2.16.840.1.113883.3.1.22" SV="1.0"/>Margin Code</th><td></td></tr><tr><th><caption_cd V="30005" DN="Total Time" S="2.16.840.1.113883.3.1.22" SV="1.0"/>Total Time</th><td></td></tr><tr><th><caption_cd V="30006" DN="Counseling Time" S="2.16.840.1.113883.3.1.22" SV="1.0"/>Counseling Time</th><td></td></tr></table></section></body></levelone>
\ No newline at end of file

Added: incubator/ctakes/trunk/ctakes-regression-test/testdata/input/cda/testpatient_cn_2.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/testdata/input/cda/testpatient_cn_2.xml?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/testdata/input/cda/testpatient_cn_2.xml (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/testdata/input/cda/testpatient_cn_2.xml Fri Mar  1 22:29:38 2013
@@ -0,0 +1 @@
+<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE levelone SYSTEM "NotesIIST_RTF.DTD" [<!ENTITY deg '&#x00B0;'><!ENTITY sup2 '&#x00B2;'><!ENTITY micro '&#x00B5;'>]><levelone><clinical_document_header><id EX="###DOC_ID###" RT="2.16.840.1.113883.3.2.1.1"/><set_id EX="###SET_ID###" RT="2.16.840.1.113883.3.2.1.2"/><version_nbr V="###V_NBR###"/><document_type_cd V="687" S="2.16.840.1.113883.3.2.1.3" DN="Nutrition Consult"/><origination_dttm V="20030822T131513"/><patient_encounter><practice_setting_cd V="4284" S="2.16.840.1.113883.3.2.1.7" DN="Nutr Clinic"/><encounter_tmr V="20030822"/><service_location><id EX="TBD" RT="2.16.840.1.113883.3.2.1.8"/></service_location><facility><organization><organization.nm V="MCR"/></organization></facility></patient_encounter><legal_authenticator><legal_authenticator.type_cd V="SPV"/><participation_tmr V=""/><signature_cd V="S"/><person><id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/><person_name><nm><GIV V="Julie"/><MID V="A"/><FAM V="Tester"/><
 PFX V=""/><SFX V="RD"/></nm><person_name.type_cd V="S"/></person_name></person></legal_authenticator><originator><originator.type_cd V="AUT"/><participation_tmr V="20030822T131513"/><person><id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/><person_name><nm><GIV V="Julie"/><MID V="A."/><FAM V="Tester"/><PFX V=""/><SFX V="RD"/></nm><person_name.type_cd V="L"/></person_name><telecom V="5-5555" USE="PG"/></person></originator><originating_organization><originating_organization.type_cd V="CST"/><organization><id EX="TBD" RT="2.16.840.1.113883.3.2.1.10"/><organization.nm V="Originating Organization - Coding TBD"/></organization></originating_organization><transcriptionist><transcriptionist.type_cd V="ENT"/><participation_tmr V="20030822T131513"/><person><id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/><person_name><nm><GIV V="Julie"/><MID V="A."/><FAM V="Tester"/></nm><person_name.type_cd V="L"/></person_name></person></transcriptionist><provider><provider.type_cd V="CON"/><parti
 cipation_tmr V="20030822T131513"/><person><id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/><person_name><nm><GIV V="Julie"/><MID V="A."/><FAM V="Tester"/><PFX V=""/><SFX V="RD"/></nm><person_name.type_cd V="L"/></person_name><telecom V="5-5555" USE="PG"/></person></provider><patient><patient.type_cd V="PATSBJ"/><person><id EX="3-303-925" RT="2.16.840.1.113883.3.2.1.1"/><person_name><nm><GIV V="Terri"/><MID V="A."/><FAM V="Testing"/><PFX V="Judge"/><SFX V="Jr.,D.D.S."/></nm><person_name.type_cd V="L"/></person_name><addr><LIT V="100 Quality Control Avenue"/><CTY V="Rochester"/><STA V="MN"/><ZIP V="55905"/><CNT V="US"/></addr></person><is_known_by><id EX="TBD" RT="2.16.840.1.113883.3.2.2.1"/><is_known_to><id EX="TBD" RT="2.16.840.1.113883.3.2.1.10"/></is_known_to></is_known_by><birth_dttm V="19341123"/><administrative_gender_cd V="F" S="2.16.840.1.113883.3.2.2.2"/></patient><status_cd V="TBD" S="2.16.840.1.113883.3.2.1.16"/><cn1_admin_data><cn1_status_cd V="Fnl" S="2.16.840.1
 .113883.3.2.3.1"/><cn1_service_cd V="MNT" S="2.16.840.1.113883.3.2.3.2"/><cn1_event_cd V="CON" S="2.16.840.1.113883.3.2.3.3"/><cn1_document_id EX="000000000" RT="2.16.840.1.113883.3.2.3.4"/><cn1_revision_nbr V="1"/><cn1_site_cd V="RCH" S="2.16.840.1.113883.3.2.3.10"/></cn1_admin_data><document_title V="Document Service Name - Coding TBD" S="2.16.840.1.113883.3.2.1.17"/></clinical_document_header><body><section><caption><caption_cd V="20100" DN="Revision History" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Revision History</caption></section><section><caption><caption_cd V="20112" DN="I/R/P" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Impression / Report / Plan</caption><table><caption><caption_cd V="20003" DN="I/R/P" S="2.16.840.1.113883.3.1.21" SV="1.0"/></caption><tr><th>Problem</th><th>Plan</th></tr></table></section><section><caption><caption_cd V="20113" DN="Diagnoses" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Diagnosis</caption><table><caption><caption_cd V="20003" DN="Diagnoses" S
 ="2.16.840.1.113883.3.1.21" SV="1.0"/></caption><tr><th>Problem</th><th>Diagnosis</th></tr></table></section><section><caption><caption_cd V="20101" DN="Ref" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Referral Source</caption><paragraph><content>Dr. Nutritious</content></paragraph></section><section><caption><caption_cd V="20102" DN="CC" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Chief Complaint/Reason for Visit</caption><paragraph><content>Medical Nutrition Therapy for Hyperlipidemia</content></paragraph></section><section><caption><caption_cd V="20103" DN="HPI" S="2.16.840.1.113883.3.1.21" SV="1.0"/>History of Present Illness</caption><table><caption><caption_cd V="20003" DN="HPI" S="2.16.840.1.113883.3.1.21" SV="1.0"/></caption><tr><th>Problem</th><th>History</th></tr><tr><td/><td><paragraph><content>Significant for her father, who died at 50 years from colon cancer.</content></paragraph></td></tr><tr><td/><td><paragraph><content>Phone contact: (555) 555-1212</content></paragraph
 ></td></tr><tr><td/><td><paragraph><content>Height: 144 cm   Current Weight: 45 kg</content></paragraph></td></tr><tr><td/><td><paragraph><content>Diet: General</content></paragraph></td></tr><tr><td/><td><paragraph><content>Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity.</content></paragraph></td></tr><tr><td/><td><paragraph><content>Daily Protein needs: 40 grams,  assessed as 1.0 g/kg.</content></paragraph></td></tr><tr><td/><td><paragraph><content>Colonoscopy. No pain or discomfort reported.</content></paragraph></td></tr></table></section></body></levelone>
\ No newline at end of file

Added: incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/SampleInputRadiologyNotes.txt
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/SampleInputRadiologyNotes.txt?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/SampleInputRadiologyNotes.txt (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/SampleInputRadiologyNotes.txt Fri Mar  1 22:29:38 2013
@@ -0,0 +1,7 @@
+CLINIC`rimsdate`rimstime`resultno`subtype`accesion`lastname`birth_dt`gender`status`secure`testcode`testdesc`doctor`COMMENTS
+54321`02/20/1999`13:21:00`14`GENRAD`987654-3`SMITH`04/03/1916`F`F`N`70955-RRIMS`CT ANGIO ABD W/WO CST ADD SECT`DAVIS, WILLIAM R`20Feb1999 1:21PM CT ABDOMEN w & PELVIS w Indications: ct abd/pel - hernia ventral nos;USE IV CON ORIGINAL REPORT - 10 Aug 2009 3:15PM ROMAYO CT abdomen and pelvis with IV contrast. Comparison with prior MR angiography dated 4-2-04. Again seen is a large ventral hernia containing multiple nonobstructed loops of small bowel and ascending colon. No evidence of vascular compromise within this hernial sac. PO changes of aortobifemoral graft with occluded right limb of the graft just below the bifurcation. Patent femoral crossover graft. Possible diffuse fatty infiltration of the liver. Severe atrophy of the left kidney. The left renal artery is not well delineated and may be occluded. Small scarring in the lower right kidney. Low-lying urinary bladder with a possible small cystocele. Sigmoid diverticulosis. Vascular calcifications. Degenerative changes o
 f the spine, symphysis pubis, and both SI and hip joints. Minimal atelectasis or fibrosis in the lung bases. Remainder of the study is unremarkable.. W. R. Davis MD 5-4321
+54321`02/20/1999`11:20:00`13`GENRAD`987654-4`SMITH`04/03/1916`F`F`N`07552-RRIMS`US Lower Extrem Art-Graft Cmpl`DAVIS, WILLIAM R`20Feb1999 11:20AM US Lower Extrem Art-Graft Cmpl ASO. Patent left femoral-popliteal  bypass. Diffuse tibial artery disease with posterior tibial occlusion. The anterior tibial is patent into the dorsalis pedis and the peroneal artery contributes to the plantar arch via a patent calcaneal branch. Right hypogastric artery stenosis. W. R. Davis MD 5-4321
+54321`02/20/2000`17:15:00`12`CT`876543-2`SMITH`04/03/1916`F`F`N`73200-RRIMS`CT EXT UPPER wo`DAVIS, WILLIAM R`20Feb2000 5:15PM Exam: CT RECONSTRUCTION 20Feb2000 3:17PM Exam: L CT EXT LOWER w Indications: le - L femur pain, r/o^osteomyelitis vs tumor ORIGINAL REPORT - 17 Apr 2006 2:31PM SMH CT left femur with IV contrast. No comparison exam. Along the mid left femoral diaphysis there is an aggressive, malignant appearing process involving the lateral cortex. Adjacent cortical scalloping is present. Codman's triangle's are seen at either end of the lesion consistent with aggressive periosteal reaction. The area of cortical scalloping measures 4.5 cm in length. There is some probable hazy mineral content within the peripheral lucent area suggesting that this is a malignant surface Osteogenic sarcoma. The other consideration is a periosteal Ewing's sarcoma. No associated soft tissue mass or fluid collections. Recommend further evaluation with MRI to evaluate for left femoral bone
  marrow involvement. Exam was discussed with Dr .W. R. Davis MD 5-4321
+12345`02/20/1999`13:21:00`14`GENRAD`987654-3`SMITH`04/03/1916`F`F`N`07075-RRIMS`Tibia Fibula 2vw AP/Lat`DAVIS, WILLIAM R`20Feb1999 1:21PM Exam: R Tibia Fibula 2vw AP/Lat Indications: Exposed tibia;R/O osteo;S/p BKA ORIGINAL REPORT - 02 Feb 1999 1:21PM ROMAYO Amputation through the proximal shafts of the right tibia and fibula. Ulceration of soft tissues distally. No radiographic evidence of osteomyelitis. The right popliteal artery is largely obscured by metallic artifact from a right TKA. No radiographic evidence of loosening. Extensive arterial calcification. Cast obscures detail. W. R. Davis MD 5-4321
+12345`02/20/1999`11:20:00`13`GENRAD`987654-4`SMITH`04/03/1916`F`F`N`07552-RRIMS`US Lower Extrem Art-Graft Cmpl`DAVIS, WILLIAM R`20Feb1999 11:20AM Exam: Both popliteal arteries are patent with normal flow. W. R. Davis MD 5-4321
+12345`02/20/2000`17:15:00`12`CT`876543-2`SMITH`04/03/1916`F`F`N`73200-RRIMS`CT EXT UPPER wo`DAVIS, WILLIAM R`20Feb2000 5:15PM Exam: CT RECONSTRUCTION 20Feb2000 3:17PM Exam: CT EXT UPPER W/O CONTRAST Indications: Indications: Left shoulder fracture 02/20/2001 3:55PM SMH (2B-3495) CT of the left shoulder including oblique sagittal and oblique coronal reformats demonstrates a slightly comminuted fracture of the surgical neck of the proximal left humerus with anterior and proximal displacement and posterior angulation of the distal fragment. The fracture extends proximally into the greater humeral tuberosity and, to a lesser degree, the inferior aspect of the lesser tuberosity. The articular surface of the humeral head is intact and glenohumeral alignment maintained. W. R. Davis MD 5-4321
\ No newline at end of file

Added: incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc1_07543210_sample_current.txt
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc1_07543210_sample_current.txt?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc1_07543210_sample_current.txt (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc1_07543210_sample_current.txt Fri Mar  1 22:29:38 2013
@@ -0,0 +1,2 @@
+Miss. CM is a energetic young woman who has had bouts with sleeplessness for the past year or so.  She said that her insomnia began with the death of her father who was killed in a train accident last year.
+Patient is 25 and claims she has smoked for the last five years or so. She used to smoke about half a pack a day, but for the last month she has been down to about 3-5 cigarettes a day. She is having trouble stopping altogether.
\ No newline at end of file

Added: incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc1_07543210_sample_past_smoker.txt
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc1_07543210_sample_past_smoker.txt?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc1_07543210_sample_past_smoker.txt (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc1_07543210_sample_past_smoker.txt Fri Mar  1 22:29:38 2013
@@ -0,0 +1,15 @@
+REVIEW OF SYSTEMS:
+General: Has gained about 10 lb in the past 4 yr, no fatigue
+Skin: No rashes or other changes
+Head: See present illness.
+Eyes: Reading glasses for 5 yr, last checked 1 yr ago. No double or blurry vision
+Ears: Hearing good. No tinnitus, vertigo, infections
+Nose, Sinuses: occasional mild cold. No hay fever, sinus trouble
+Mouth and Throat: Last to dentist 2 yr ago. Occasional canker sore
+Neck: No lumps, goiter, pain
+Breasts: No lumps, pain, discharge.
+Habits:
+Patient claims to have quit smoking about two years ago.
+FAMILY HISTORY
+- Mother died, 67, stroke; had varicose veins, headaches, hypertension
+- Father died, 43, train accident
\ No newline at end of file

Added: incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc1_07543210_sample_unknown.txt
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc1_07543210_sample_unknown.txt?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc1_07543210_sample_unknown.txt (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc1_07543210_sample_unknown.txt Fri Mar  1 22:29:38 2013
@@ -0,0 +1,105 @@
+Patient Centered Medicine 2
+Revised: 7/27/99
+DATA BASE: SAMPLE HISTORY
+IDENTIFYING DATA 
+CM is a 45-year-old, widowed, white saleswoman, born in the U.S.
+CHIEF COMPLAINT
+“Bad headaches”
+HISTORY OF PRESENT ILLNESS 
+Patient Perspective
+She thinks her headaches may be like those in the past. However, she now has high blood
+pressure and is concerned because her mother had high blood pressure and died of a
+stroke. She is also concerned that they make her irritable with her family.
+PAST MEDICAL HISTORY
+Significant Childhood Illnesses
+Only measles and chickenpox
+Immunizations
+Last tetanus 1998
+Flu vaccine last November
+Adult Illnesses/Hospitalizations
+- Kidney infection 1982 treated with ampicillin and developed a generalized rash.
+- Hypertension x 7 years, well controlled with home BPs normally 120-130/low 80s
+Patient Centered Medicine 2
+2 Revised: 7/27/99
+Psychiatric Illnesses/Hospitalizations
+None
+Operations
+Tonsillectomy, age 6,
+Appendectomy, age 13
+Injuries/Accidents
+1998 foot laceration, 4 stitches
+Obstetric History
+G3, P3, 3 living children. Menarche age 12. Last menses 2 weeks ago.
+Transfusions
+None
+CURRENT HEALTH STATUS
+Medications
+Aspirin for headaches
+Multivitamin 1 per day
+Hydrochlorothiazide 25 mg per day (x 7 years)
+No herbs or supplements
+Allergies/Drug Reactions
+Ampicillin causes rash
+Health Screening
+- Last pap smear 2000, normal.
+- Normal mammogram in 2000.
+- Does breast self-exams monthly
+- Cholesterol = 220 (in 2000)
+Diet, Sleep, Exercise
+- Diet – Low in calcium with little milk or cheese. She frequently eats mid-morning and
+evening snacks that are high in fat. She does follow a low salt diet.
+- Sleep – Generally good, average 7 hr
+- Exercise – “No time”
+Habits
+- Alcohol – Rare drink (wine) only, no history of abuse
+- Drugs – Never tried illegal drugs
+Alternative Therapies
+None
+Patient Centered Medicine 2
+PSYCHOSOCIAL HISTORY
+- 4 yr ago her husband died suddenly of heart attack, leaving little savings and no
+insurance.
+- Lives alone, recently moved to a small apartment to be near daughter
+- Cosmetic saleswoman for 15 years at Sears. Likes her job but feels stressed by demands
+from the new manager
+- Not sexually active since the death of her husband who was her only partner
+- Denies depression
+- Feels safe at work and home
+FAMILY HISTORY
+- Mother died, 67, stroke; had varicose veins, headaches, hypertension
+- Father died, 43, train accident
+- One brother, 56, has high blood pressure, otherwise well
+- One brother, 51, apparently well except for mild arthritis
+- Daughter, 23, “migraine headaches,” otherwise well
+- Son, 21, well
+- Son, 20, well
+REVIEW OF SYSTEMS:
+General: Has gained about 10 lb in the past 4 yr, no fatigue
+Skin: No rashes or other changes
+Head: See present illness.
+Eyes: Reading glasses for 5 yr, last checked 1 yr ago. No double or blurry vision
+Ears: Hearing good. No tinnitus, vertigo, infections
+Nose, Sinuses: occasional mild cold. No hay fever, sinus trouble
+Mouth and Throat: Last to dentist 2 yr ago. Occasional canker sore
+Neck: No lumps, goiter, pain
+Breasts: No lumps, pain, discharge.
+Respiratory: No cough, wheezing, shortness of breath, pneumonia, tuberculosis.
+Cardiac: No known heart disease. No orthopnea, chest pain, palpitations.
+Gastrointestinal: Appetite good; no reflux. Bowel movement about once daily though
+sometimes has hard stools for 2-3 d when especially tense; no diarrhea or
+bleeding. No pain, jaundice, gallbladder or liver trouble
+Urinary: No frequency, dysuria, hematuria or flank pain
+Genitoreproductive: Regular menstrual periods. No vaginal discharge or itch
+Musculoskeletal: Mild aching low back pain often after a long day’s work; no radiation
+down legs; used to do back exercises, but not now. No other joint pain
+Patient Centered Medicine 2
+Peripheral Vascular: Varicose veins appeared in both legs during first pregnancy. Has had
+swollen ankles after prolonged standing for 10 yr; no history of
+phlebitis or leg pain
+Neurological: No fainting, seizures, tremors, weakness, or tingling. Memory good
+Psychiatric: No anxiety or nervousness or depression
+Endocrine: No known thyroid trouble, temperature intolerance. Sweating average. No
+symptoms or history of diabetes
+Hematologic: No easy bleeding. No anemia
+Adapted from Bates’ Guide to Physical Examination and History Taking, Chapter 21, The Patient’s Record, pp. 722-
+726
\ No newline at end of file

Added: incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc2_07543210_sample_current.txt
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc2_07543210_sample_current.txt?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc2_07543210_sample_current.txt (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc2_07543210_sample_current.txt Fri Mar  1 22:29:38 2013
@@ -0,0 +1,119 @@
+Patient Centered Medicine 2
+Revised: 7/27/99
+DATA BASE: SAMPLE HISTORY
+IDENTIFYING DATA 
+CM is a 45-year-old, widowed, white saleswoman, born in the U.S.
+CHIEF COMPLAINT
+“Bad headaches”
+HISTORY OF PRESENT ILLNESS (HPI, Problem by problem)
+For about 3 months Mrs. M. has been increasingly troubled by headaches that are rightsided,
+usually throbbing, and can range from mild to moderately severe. Typically her
+headaches are rated at 4 over 10. She recently had a severe headache that she rated 8 over
+10 and missed work because of this headache. This was associated with nausea and
+vomiting. Headaches have increased in frequency and now average once a wk. The
+headaches usually last from 2 to 4 hours. However, the most recent headache, which was
+the most severe, lasted almost 8 hours. During a headache bright lights bother her and she
+just wants to lie down in a dark quiet room and fall asleep. Aspirin provides little relief.
+She has not noticed any association with food or drink. She has no other related symptoms,
+such as fever, dental pain, weakness, numbness or loss of vision. There is no history of head
+injury or trauma. She remembers having a similar kind of headache with nausea and
+vomiting that began at age 15, recurred through her mid-20s, then diminished to one every
+2 or 3 months and disappeared.
+Patient Perspective
+She thinks her headaches may be like those in the past. However, she now has high blood
+pressure and is concerned because her mother had high blood pressure and died of a
+stroke. She is also concerned that they make her irritable with her family.
+PAST MEDICAL HISTORY
+Significant Childhood Illnesses
+Only measles and chickenpox
+Immunizations
+Last tetanus 1998
+Flu vaccine last November
+Adult Illnesses/Hospitalizations
+- Kidney infection 1982 treated with ampicillin and developed a generalized rash.
+- Hypertension x 7 years, well controlled with home BPs normally 120-130/low 80s
+Patient Centered Medicine 2
+2 Revised: 7/27/99
+Psychiatric Illnesses/Hospitalizations
+None
+Operations
+Tonsillectomy, age 6,
+Appendectomy, age 13
+Injuries/Accidents
+1998 foot laceration, 4 stitches
+Obstetric History
+G3, P3, 3 living children. Menarche age 12. Last menses 2 weeks ago.
+Transfusions
+None
+CURRENT HEALTH STATUS
+Medications
+Aspirin for headaches
+Multivitamin 1 per day
+Hydrochlorothiazide 25 mg per day (x 7 years)
+No herbs or supplements
+Allergies/Drug Reactions
+Ampicillin causes rash
+Health Screening
+- Last pap smear 2000, normal.
+- Normal mammogram in 2000.
+- Does breast self-exams monthly
+- Cholesterol = 220 (in 2000)
+Diet, Sleep, Exercise
+- Diet – Low in calcium with little milk or cheese. She frequently eats mid-morning and
+evening snacks that are high in fat. She does follow a low salt diet.
+- Sleep – Generally good, average 7 hr
+- Exercise – “No time”
+Habits
+- Tobacco – 1 pack cigs per day from age 18
+- Alcohol – Rare drink (wine) only, no history of abuse
+- Drugs – Never tried illegal drugs
+Alternative Therapies
+None
+Patient Centered Medicine 2
+PSYCHOSOCIAL HISTORY
+- 4 yr ago her husband died suddenly of heart attack, leaving little savings and no
+insurance.
+- Lives alone, recently moved to a small apartment to be near daughter
+- Cosmetic saleswoman for 15 years at Sears. Likes her job but feels stressed by demands
+from the new manager
+- Not sexually active since the death of her husband who was her only partner
+- Denies depression
+- Feels safe at work and home
+FAMILY HISTORY
+- Mother died, 67, stroke; had varicose veins, headaches, hypertension
+- Father died, 43, train accident
+- One brother, 56, has high blood pressure, otherwise well
+- One brother, 51, apparently well except for mild arthritis
+- Daughter, 23, “migraine headaches,” otherwise well
+- Son, 21, well
+- Son, 20, well
+REVIEW OF SYSTEMS:
+General: Has gained about 10 lb in the past 4 yr, no fatigue
+Skin: No rashes or other changes
+Head: See present illness.
+Eyes: Reading glasses for 5 yr, last checked 1 yr ago. No double or blurry vision
+Ears: Hearing good. No tinnitus, vertigo, infections
+Nose, Sinuses: occasional mild cold. No hay fever, sinus trouble
+Mouth and Throat: Last to dentist 2 yr ago. Occasional canker sore
+Neck: No lumps, goiter, pain
+Breasts: No lumps, pain, discharge.
+Respiratory: No cough, wheezing, shortness of breath, pneumonia, tuberculosis.
+Cardiac: No known heart disease. No orthopnea, chest pain, palpitations.
+Gastrointestinal: Appetite good; no reflux. Bowel movement about once daily though
+sometimes has hard stools for 2-3 d when especially tense; no diarrhea or
+bleeding. No pain, jaundice, gallbladder or liver trouble
+Urinary: No frequency, dysuria, hematuria or flank pain
+Genitoreproductive: Regular menstrual periods. No vaginal discharge or itch
+Musculoskeletal: Mild aching low back pain often after a long day’s work; no radiation
+down legs; used to do back exercises, but not now. No other joint pain
+Patient Centered Medicine 2
+Peripheral Vascular: Varicose veins appeared in both legs during first pregnancy. Has had
+swollen ankles after prolonged standing for 10 yr; no history of
+phlebitis or leg pain
+Neurological: No fainting, seizures, tremors, weakness, or tingling. Memory good
+Psychiatric: No anxiety or nervousness or depression
+Endocrine: No known thyroid trouble, temperature intolerance. Sweating average. No
+symptoms or history of diabetes
+Hematologic: No easy bleeding. No anemia
+Adapted from Bates’ Guide to Physical Examination and History Taking, Chapter 21, The Patient’s Record, pp. 722-
+726
\ No newline at end of file

Added: incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc2_07543210_sample_past_smoker.txt
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc2_07543210_sample_past_smoker.txt?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc2_07543210_sample_past_smoker.txt (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/doc2_07543210_sample_past_smoker.txt Fri Mar  1 22:29:38 2013
@@ -0,0 +1,32 @@
+Patient Centered Medicine 2
+Revised: 2/7/10
+DATA BASE: SAMPLE HISTORY
+IDENTIFYING DATA 
+CM is a 45-year-old, widowed, white saleswoman, born in the U.S.
+CHIEF COMPLAINT
+“Insomnia”
+HISTORY OF PRESENT ILLNESS 
+She is also concerned that they make her irritable with her family.  She isn't sleeping well, since she quit smoking cigs.
+PAST MEDICAL HISTORY
+Significant Childhood Illnesses
+Only measles and chickenpox
+Immunizations
+Last tetanus 1998
+Flu vaccine last November
+Adult Illnesses/Hospitalizations
+- Kidney infection 1982 treated with ampicillin and developed a generalized rash.
+- Hypertension x 7 years, well controlled with home BPs normally 120-130/low 80s
+Patient Centered Medicine 2
+Psychiatric Illnesses/Hospitalizations
+None
+Operations
+Tonsillectomy, age 6,
+Appendectomy, age 13
+Habits
+tobacco : quit.
+Injuries/Accidents
+1998 foot laceration, 4 stitches
+Obstetric History
+G3, P3, 3 living children. Menarche age 12. Last menses 2 weeks ago.
+Transfusions
+None

Added: incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/sample_note
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/sample_note?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/sample_note (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/sample_note Fri Mar  1 22:29:38 2013
@@ -0,0 +1,7 @@
+IMPRESSION/REPORT/PLAN
+The patient has very typical history for claudication. Yet the patient does not have any significant bruit at the pelvic area, abdominal area.
+
+Aspirin 200-mg once-a-day.
+Ibuprofen increased from 200 mg to 300 mg p.o. twice a day.
+Aspirin 80 mg.
+acetaminophen discontinued.

Added: incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/sample_note_plaintext
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/sample_note_plaintext?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/sample_note_plaintext (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/sample_note_plaintext Fri Mar  1 22:29:38 2013
@@ -0,0 +1,2 @@
+S/P right knee arthroscopy.
+Knee x-ray.  Patient denies knee pain.

Added: incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/testfakenote.txt
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/testfakenote.txt?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/testfakenote.txt (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/testfakenote.txt Fri Mar  1 22:29:38 2013
@@ -0,0 +1,5 @@
+Mr. Johnson is presenting signs of a shark bite.  It occurred last week and has caused immense leg pain.  The pain was so severe that he had begun taking narcotics to relieve it.
+
+The patient also was concerned about a small lesion in his Broca's area and said the lesion was causing him to lettuce Wednesday baseball applesauce.
+
+After imaging which was inconclusive, the patient was released to go home and treat his pain himself.
\ No newline at end of file

Added: incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/testpatient_plaintext_1.txt
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/testpatient_plaintext_1.txt?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/testpatient_plaintext_1.txt (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/testpatient_plaintext_1.txt Fri Mar  1 22:29:38 2013
@@ -0,0 +1,12 @@
+
+Dr. Nutritious
+
+Medical Nutrition Therapy for Hyperlipidemia
+
+Referral from: Julie Tester, RD, LD, CNSD
+Phone contact: (555) 555-1212
+Height: 144 cm   Current Weight: 45 kg   Date of current weight: 02-29-2001   Admit Weight:  53 kg   BMI: 18 kg/m2
+Diet: General
+Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity.
+Daily Protein needs: 40 grams,  assessed as 1.0 g/kg.
+Pt has been on a 3-day calorie count and has had an average intake of 1100 calories.  She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.  She agrees with the plan and has my number for further assessment. May want a Resting Metabolic Rate as well. She takes an aspirin a day for knee pain.

Added: incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/testpatient_plaintext_2.txt
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/testpatient_plaintext_2.txt?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/testpatient_plaintext_2.txt (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/testpatient_plaintext_2.txt Fri Mar  1 22:29:38 2013
@@ -0,0 +1,12 @@
+
+Dr. Nutritious
+
+Medical Nutrition Therapy for Hyperlipidemia
+
+Significant for her father, who died at 50 years from colon cancer.
+Phone contact: (555) 555-1212
+Height: 144 cm   Current Weight: 45 kg
+Diet: General
+Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity.
+Daily Protein needs: 40 grams,  assessed as 1.0 g/kg.
+Colonoscopy. No pain or discomfort reported.

Added: incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/text1.txt
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/text1.txt?rev=1451742&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/text1.txt (added)
+++ incubator/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/text1.txt Fri Mar  1 22:29:38 2013
@@ -0,0 +1,4 @@
+
+The patient reported pain in her upper arm.
+No swelling.
+Aspirin 325 mg.



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