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From vjapa...@apache.org
Subject svn commit: r1551254 [4/26] - in /ctakes/branches/ytex: ctakes-ytex-res/ ctakes-ytex-res/.settings/ ctakes-ytex-res/src/ ctakes-ytex-res/src/main/ ctakes-ytex-res/src/main/resources/ ctakes-ytex-res/src/main/resources/org/ ctakes-ytex-res/src/main/reso...
Date Mon, 16 Dec 2013 16:30:40 GMT
Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DateAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DateAnnotator.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DateAnnotator.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DateAnnotator.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+  <primitive>true</primitive>
+  <annotatorImplementationName>org.apache.ctakes.ytex.uima.annotators.DateAnnotator</annotatorImplementationName>
+  <analysisEngineMetaData>
+    <name>DateAnnotator</name>
+    <description/>
+    <version>1.0</version>
+    <vendor/>
+    <configurationParameters/>
+    <configurationParameterSettings/>
+    <typeSystemDescription>
+      <imports>
+        <import name="org.apache.ctakes.ytex.uima.TypeSystem"/>
+      </imports>
+    </typeSystemDescription>
+    <typePriorities/>
+    <fsIndexCollection/>
+    <capabilities>
+      <capability>
+        <inputs/>
+        <outputs/>
+        <languagesSupported/>
+      </capability>
+    </capabilities>
+    <operationalProperties>
+      <modifiesCas>true</modifiesCas>
+      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+      <outputsNewCASes>false</outputsNewCASes>
+    </operationalProperties>
+  </analysisEngineMetaData>
+  <resourceManagerConfiguration/>
+</analysisEngineDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotator.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotator.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotator.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,146 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Licensed to the Apache Software Foundation (ASF) under one or more contributor 
+	license agreements. See the NOTICE file distributed with this work for additional 
+	information regarding copyright ownership. The ASF licenses this file to 
+	you under the Apache License, Version 2.0 (the "License"); you may not use 
+	this file except in compliance with the License. You may obtain a copy of 
+	the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required 
+	by applicable law or agreed to in writing, software distributed under the 
+	License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS 
+	OF ANY KIND, either express or implied. See the License for the specific 
+	language governing permissions and limitations under the License. -->
+<taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+	<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+	<primitive>true</primitive>
+	<annotatorImplementationName>org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator
+	</annotatorImplementationName>
+	<analysisEngineMetaData>
+		<name>DictionaryLookupAnnotator</name>
+		<description />
+		<version />
+		<vendor />
+		<configurationParameters>
+			<configurationParameter>
+				<name>maxListSize</name>
+				<description>Specifies the maximum number of items to be returned
+					from an lucene query.
+				</description>
+				<type>Integer</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+			</configurationParameter>
+		</configurationParameters>
+		<configurationParameterSettings>
+			<nameValuePair>
+				<name>maxListSize</name>
+				<value>
+					<integer>2147483647</integer>
+				</value>
+			</nameValuePair>
+		</configurationParameterSettings>
+		<typeSystemDescription>
+			<imports>
+			</imports>
+		</typeSystemDescription>
+		<typePriorities />
+		<fsIndexCollection />
+		<capabilities>
+			<capability>
+				<inputs>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation
+					</type>
+				</inputs>
+				<outputs>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
+					</type>
+				</outputs>
+				<languagesSupported />
+			</capability>
+		</capabilities>
+		<operationalProperties>
+			<modifiesCas>true</modifiesCas>
+			<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+			<outputsNewCASes>false</outputsNewCASes>
+		</operationalProperties>
+	</analysisEngineMetaData>
+	<externalResourceDependencies>
+		<externalResourceDependency>
+			<key>DbConnection</key>
+			<description />
+			<interfaceName>org.apache.ctakes.core.resource.JdbcConnectionResource
+			</interfaceName>
+			<optional>false</optional>
+		</externalResourceDependency>
+		<externalResourceDependency>
+			<key>LookupDescriptor</key>
+			<description />
+			<interfaceName>org.apache.ctakes.core.resource.FileResource
+			</interfaceName>
+			<optional>false</optional>
+		</externalResourceDependency>
+	</externalResourceDependencies>
+	<resourceManagerConfiguration>
+		<externalResources>
+			<externalResource>
+				<name>LookupDescriptorFile</name>
+				<description />
+				<fileResourceSpecifier>
+					<fileUrl>file:org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_SNOMED.xml
+					</fileUrl>
+				</fileResourceSpecifier>
+				<implementationName>org.apache.ctakes.core.resource.FileResourceImpl
+				</implementationName>
+			</externalResource>
+			<externalResource>
+				<name>DbConnectionResrc</name>
+				<description />
+				<configurableDataResourceSpecifier>
+					<url />
+					<resourceMetaData>
+						<name />
+						<configurationParameters>
+							<configurationParameter>
+								<name>DriverClassName</name>
+								<type>String</type>
+								<multiValued>false</multiValued>
+								<mandatory>false</mandatory>
+							</configurationParameter>
+							<configurationParameter>
+								<name>URL</name>
+								<type>String</type>
+								<multiValued>false</multiValued>
+								<mandatory>false</mandatory>
+							</configurationParameter>
+							<configurationParameter>
+								<name>Username</name>
+								<type>String</type>
+								<multiValued>false</multiValued>
+								<mandatory>false</mandatory>
+							</configurationParameter>
+							<configurationParameter>
+								<name>Password</name>
+								<type>String</type>
+								<multiValued>false</multiValued>
+								<mandatory>false</mandatory>
+							</configurationParameter>
+						</configurationParameters>
+					</resourceMetaData>
+				</configurableDataResourceSpecifier>
+				<implementationName>org.apache.ctakes.ytex.uima.resource.InitableJdbcConnectionResourceImpl
+				</implementationName>
+			</externalResource>
+		</externalResources>
+		<externalResourceBindings>
+			<externalResourceBinding>
+				<key>LookupDescriptor</key>
+				<resourceName>LookupDescriptorFile</resourceName>
+			</externalResourceBinding>
+			<externalResourceBinding>
+				<key>DbConnection</key>
+				<resourceName>DbConnectionResrc</resourceName>
+			</externalResourceBinding>
+		</externalResourceBindings>
+	</resourceManagerConfiguration>
+</taeDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotatorOld.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotatorOld.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotatorOld.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotatorOld.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,140 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+	<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+	<primitive>true</primitive>
+	<annotatorImplementationName>edu.mayo.bmi.uima.lookup.ae.DictionaryLookupAnnotator
+	</annotatorImplementationName>
+	<analysisEngineMetaData>
+		<name>DictionaryLookupAnnotator</name>
+		<description />
+		<version />
+		<vendor />
+		<configurationParameters>
+			<configurationParameter>
+				<name>maxListSize</name>
+				<description>Specifies the maximum number of items to be returned
+					from an lucene query.</description>
+				<type>Integer</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+			</configurationParameter>
+		</configurationParameters>
+		<configurationParameterSettings>
+			<nameValuePair>
+				<name>maxListSize</name>
+				<value>
+					<integer>2147483647</integer>
+				</value>
+			</nameValuePair>
+		</configurationParameterSettings>
+		<typeSystemDescription>
+			<imports>
+				<import name="org.apache.ctakes.ytex.types.TypeSystem" />
+			</imports>
+		</typeSystemDescription>
+		<typePriorities />
+		<fsIndexCollection />
+		<capabilities>
+			<capability>
+				<inputs>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken
+
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Sentence
+					</type>
+				</inputs>
+				<outputs>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.MedicationEventMention
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.EntityMention
+					</type>
+				</outputs>
+				<languagesSupported />
+			</capability>
+		</capabilities>
+		<operationalProperties>
+			<modifiesCas>true</modifiesCas>
+			<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+			<outputsNewCASes>false</outputsNewCASes>
+		</operationalProperties>
+	</analysisEngineMetaData>
+	<externalResourceDependencies>
+		<externalResourceDependency>
+			<key>LookupDescriptor</key>
+			<description />
+			<interfaceName>edu.mayo.bmi.uima.core.resource.FileResource
+			</interfaceName>
+			<optional>false</optional>
+		</externalResourceDependency>
+		<externalResourceDependency>
+			<key>DbConnection</key>
+			<description />
+			<interfaceName>edu.mayo.bmi.uima.core.resource.JdbcConnectionResource
+			</interfaceName>
+			<optional>false</optional>
+		</externalResourceDependency>
+	</externalResourceDependencies>
+	<resourceManagerConfiguration>
+		<externalResources>
+			<externalResource>
+				<name>LookupDescriptorFile</name>
+				<description />
+				<fileResourceSpecifier>
+					<fileUrl>ytex/uima/annotators/LookupDesc_SNOMED.xml</fileUrl>
+				</fileResourceSpecifier>
+				<implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl
+				</implementationName>
+			</externalResource>
+			<externalResource>
+				<name>DbConnectionResrc</name>
+				<description />
+				<configurableDataResourceSpecifier>
+					<url />
+					<resourceMetaData>
+						<name />
+						<configurationParameters>
+							<configurationParameter>
+								<name>DriverClassName</name>
+								<type>String</type>
+								<multiValued>false</multiValued>
+								<mandatory>false</mandatory>
+							</configurationParameter>
+							<configurationParameter>
+								<name>URL</name>
+								<type>String</type>
+								<multiValued>false</multiValued>
+								<mandatory>false</mandatory>
+							</configurationParameter>
+							<configurationParameter>
+								<name>Username</name>
+								<type>String</type>
+								<multiValued>false</multiValued>
+								<mandatory>false</mandatory>
+							</configurationParameter>
+							<configurationParameter>
+								<name>Password</name>
+								<type>String</type>
+								<multiValued>false</multiValued>
+								<mandatory>false</mandatory>
+							</configurationParameter>
+						</configurationParameters>
+					</resourceMetaData>
+				</configurableDataResourceSpecifier>
+				<implementationName>ytex.uima.resource.InitableJdbcConnectionResourceImpl
+				</implementationName>
+			</externalResource>
+		</externalResources>
+		<externalResourceBindings>
+			<externalResourceBinding>
+				<key>LookupDescriptor</key>
+				<resourceName>LookupDescriptorFile</resourceName>
+			</externalResourceBinding>
+			<externalResourceBinding>
+				<key>DbConnection</key>
+				<resourceName>DbConnectionResrc</resourceName>
+			</externalResourceBinding>
+		</externalResourceBindings>
+	</resourceManagerConfiguration>
+</taeDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,149 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+  <primitive>false</primitive>
+  <delegateAnalysisEngineSpecifiers>
+    <delegateAnalysisEngine key="DrugMentionAnnotator">
+      <import name="drugnerdesc.analysis_engine.DrugMentionAnnotator"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="Chunker">
+      <import name="chunkerdesc.analysis_engine.Chunker"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="TokenizerAnnotator">
+      <import name="coredesc.analysis_engine.TokenizerAnnotator"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
+      <import name="cdtdesc.analysis_engine.ContextDependentTokenizerAnnotator"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="StatusAnnotator">
+      <import name="necontextdesc.analysis_engine.StatusAnnotator"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="NegationAnnotator">
+      <import name="ytex.uima.annotators.NegexAnnotator"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="SegmentRegexAnnotator">
+      <import name="ytex.uima.annotators.SegmentRegexAnnotator"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="SentenceDetectorAnnotator">
+      <import name="ytex.uima.annotators.SentenceDetectorAnnotator"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="DictionaryLookupAnnotator">
+      <import name="ytex.drugnerdesc.analysis_engine.DictionaryLookupAnnotator"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="DrugLookupWindowAnnotator">
+      <import name="drugnerdesc.analysis_engine.DrugLookupWindowAnnotator"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="POSTagger">
+      <import name="posdesc.analysis_engine.POSTagger"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="LvgAnnotator">
+      <import name="lvgdesc.analysis_engine.LvgAnnotator"/>
+    </delegateAnalysisEngine>
+  </delegateAnalysisEngineSpecifiers>
+  <analysisEngineMetaData>
+    <name>DrugAggregatePlaintextProcessor</name>
+    <description>adaptation of cTAKES DrugAggregatePlaintextProcessor</description>
+    <version/>
+    <vendor/>
+    <configurationParameters searchStrategy="language_fallback">
+      <configurationParameter>
+        <name>ChunkCreatorClass</name>
+        <type>String</type>
+        <multiValued>false</multiValued>
+        <mandatory>true</mandatory>
+        <overrides>
+          <parameter>Chunker/ChunkCreatorClass</parameter>
+        </overrides>
+      </configurationParameter>
+      <configurationParameter>
+        <name>medicationRelatedSection</name>
+        <description>Section ids that need to be considered when generating
+					the DrugMentionAnnotation</description>
+        <type>String</type>
+        <multiValued>true</multiValued>
+        <mandatory>false</mandatory>
+        <overrides>
+          <parameter>DrugMentionAnnotator/medicationRelatedSection</parameter>
+        </overrides>
+      </configurationParameter>
+    </configurationParameters>
+    <configurationParameterSettings>
+      <nameValuePair>
+        <name>ChunkCreatorClass</name>
+        <value>
+          <string>edu.mayo.bmi.uima.chunker.PhraseTypeChunkCreator</string>
+        </value>
+      </nameValuePair>
+      <nameValuePair>
+        <name>medicationRelatedSection</name>
+        <value>
+          <array>
+            <string>SIMPLE_SEGMENT</string>
+            <string>DEFAULT</string>
+            <string>CLINICAL_HISTORY</string>
+          </array>
+        </value>
+      </nameValuePair>
+    </configurationParameterSettings>
+    <flowConstraints>
+      <fixedFlow>
+        <node>SegmentRegexAnnotator</node>
+        <node>SentenceDetectorAnnotator</node>
+        <node>TokenizerAnnotator</node>
+        <node>LvgAnnotator</node>
+        <node>ContextDependentTokenizerAnnotator</node>
+        <node>POSTagger</node>
+        <node>Chunker</node>
+        <node>DrugLookupWindowAnnotator</node>
+        <node>DictionaryLookupAnnotator</node>
+        <node>DrugMentionAnnotator</node>
+        <node>StatusAnnotator</node>
+        <node>NegationAnnotator</node>
+      </fixedFlow>
+    </flowConstraints>
+    <typePriorities>
+      <name>Ordering</name>
+      <description>For subiterator</description>
+      <version>1.0</version>
+      <priorityList>
+        <type>edu.mayo.bmi.uima.core.type.textspan.Segment</type>
+        <type>edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
+        <type>edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+      </priorityList>
+      <priorityList>
+        <type>edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
+        <type>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation</type>
+      </priorityList>
+    </typePriorities>
+    <fsIndexCollection/>
+    <capabilities>
+      <capability>
+        <inputs/>
+        <outputs/>
+        <languagesSupported/>
+      </capability>
+    </capabilities>
+    <operationalProperties>
+      <modifiesCas>true</modifiesCas>
+      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+      <outputsNewCASes>false</outputsNewCASes>
+    </operationalProperties>
+  </analysisEngineMetaData>
+  <resourceManagerConfiguration>
+    <externalResources>
+      <externalResource>
+        <name>LookupDesc_RXNORM</name>
+        <description/>
+        <fileResourceSpecifier>
+          <fileUrl>ytex/drugnerdesc/analysis_engine/LookupDesc_RXNORM.xml</fileUrl>
+        </fileResourceSpecifier>
+      </externalResource>
+    </externalResources>
+    <externalResourceBindings>
+      <externalResourceBinding>
+        <key>DictionaryLookupAnnotator/LookupDescriptor</key>
+        <resourceName>LookupDesc_RXNORM</resourceName>
+      </externalResourceBinding>
+    </externalResourceBindings>
+  </resourceManagerConfiguration>
+</analysisEngineDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DrugNerDictionaryLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DrugNerDictionaryLookupAnnotator.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DrugNerDictionaryLookupAnnotator.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DrugNerDictionaryLookupAnnotator.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,140 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+	<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+	<primitive>true</primitive>
+	<annotatorImplementationName>edu.mayo.bmi.uima.lookup.ae.DictionaryLookupAnnotator
+	</annotatorImplementationName>
+	<analysisEngineMetaData>
+		<name>DictionaryLookupAnnotator</name>
+		<description />
+		<version />
+		<vendor />
+		<configurationParameters>
+			<configurationParameter>
+				<name>maxListSize</name>
+				<description>Specifies the maximum number of items to be returned
+					from an lucene query.</description>
+				<type>Integer</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+			</configurationParameter>
+		</configurationParameters>
+		<configurationParameterSettings>
+			<nameValuePair>
+				<name>maxListSize</name>
+				<value>
+					<integer>2147483647</integer>
+				</value>
+			</nameValuePair>
+		</configurationParameterSettings>
+		<typeSystemDescription>
+			<imports>
+				<import name="ytex.uima.YTEXTypes" />
+			</imports>
+		</typeSystemDescription>
+		<typePriorities />
+		<fsIndexCollection />
+		<capabilities>
+			<capability>
+				<inputs>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken
+					
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.LookupWindowAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Sentence
+					</type>
+				</inputs>
+				<outputs>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.MedicationEventMention
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.EntityMention
+					</type>
+				</outputs>
+				<languagesSupported />
+			</capability>
+		</capabilities>
+		<operationalProperties>
+			<modifiesCas>true</modifiesCas>
+			<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+			<outputsNewCASes>false</outputsNewCASes>
+		</operationalProperties>
+	</analysisEngineMetaData>
+	<externalResourceDependencies>
+		<externalResourceDependency>
+			<key>LookupDescriptor</key>
+			<description />
+			<interfaceName>edu.mayo.bmi.uima.core.resource.FileResource
+			</interfaceName>
+			<optional>false</optional>
+		</externalResourceDependency>
+		<externalResourceDependency>
+			<key>DbConnection</key>
+			<description />
+			<interfaceName>edu.mayo.bmi.uima.core.resource.JdbcConnectionResource
+			</interfaceName>
+			<optional>false</optional>
+		</externalResourceDependency>
+	</externalResourceDependencies>
+	<resourceManagerConfiguration>
+		<externalResources>
+			<externalResource>
+				<name>LookupDescriptorFile</name>
+				<description />
+				<fileResourceSpecifier>
+					<fileUrl>ytex/drugnerdesc/analysis_engine/LookupDesc_RXNORM.xml</fileUrl>
+				</fileResourceSpecifier>
+				<implementationName>edu.mayo.bmi.uima.core.resource.FileResourceImpl
+				</implementationName>
+			</externalResource>
+			<externalResource>
+				<name>DbConnectionResrc</name>
+				<description />
+				<configurableDataResourceSpecifier>
+					<url />
+					<resourceMetaData>
+						<name />
+						<configurationParameters>
+							<configurationParameter>
+								<name>DriverClassName</name>
+								<type>String</type>
+								<multiValued>false</multiValued>
+								<mandatory>false</mandatory>
+							</configurationParameter>
+							<configurationParameter>
+								<name>URL</name>
+								<type>String</type>
+								<multiValued>false</multiValued>
+								<mandatory>false</mandatory>
+							</configurationParameter>
+							<configurationParameter>
+								<name>Username</name>
+								<type>String</type>
+								<multiValued>false</multiValued>
+								<mandatory>false</mandatory>
+							</configurationParameter>
+							<configurationParameter>
+								<name>Password</name>
+								<type>String</type>
+								<multiValued>false</multiValued>
+								<mandatory>false</mandatory>
+							</configurationParameter>
+						</configurationParameters>
+					</resourceMetaData>
+				</configurableDataResourceSpecifier>
+				<implementationName>ytex.uima.resource.InitableJdbcConnectionResourceImpl
+				</implementationName>
+			</externalResource>
+		</externalResources>
+		<externalResourceBindings>
+			<externalResourceBinding>
+				<key>LookupDescriptor</key>
+				<resourceName>LookupDescriptorFile</resourceName>
+			</externalResourceBinding>
+			<externalResourceBinding>
+				<key>DbConnection</key>
+				<resourceName>DbConnectionResrc</resourceName>
+			</externalResourceBinding>
+		</externalResourceBindings>
+	</resourceManagerConfiguration>
+</taeDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/MetaMapToCTakesAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/MetaMapToCTakesAnnotator.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/MetaMapToCTakesAnnotator.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/MetaMapToCTakesAnnotator.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,59 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+	<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+	<primitive>true</primitive>
+	<annotatorImplementationName>ytex.uima.annotators.MetaMapToCTakesAnnotator
+	</annotatorImplementationName>
+	<analysisEngineMetaData>
+		<name>MetaMapToCTakesAnnotator</name>
+		<description />
+		<version>1.0</version>
+		<vendor />
+		<configurationParameters>
+			<configurationParameter>
+				<name>checkMedications</name>
+				<type>Boolean</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+			</configurationParameter>
+		</configurationParameters>
+		<configurationParameterSettings>
+			<nameValuePair>
+				<name>checkMedications</name>
+				<value>
+					<boolean>false</boolean>
+				</value>
+			</nameValuePair>
+		</configurationParameterSettings>
+		<typeSystemDescription>
+			<imports>
+				<import name="ytex.uima.YTEXTypes" />
+				<import name="MetaMapApiTypeSystem" />
+			</imports>
+		</typeSystemDescription>
+		<typePriorities />
+		<fsIndexCollection />
+		<capabilities>
+			<capability>
+				<inputs>
+					<type allAnnotatorFeatures="true">org.metamap.uima.ts.Candidate
+					</type>
+				</inputs>
+				<outputs>
+					<type>edu.mayo.bmi.uima.core.type.textsem.EntityMention</type>
+					<type>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation
+					</type>
+					<type>edu.mayo.bmi.uima.core.type.textsem.MedicationEventMention
+					</type>
+				</outputs>
+				<languagesSupported />
+			</capability>
+		</capabilities>
+		<operationalProperties>
+			<modifiesCas>true</modifiesCas>
+			<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+			<outputsNewCASes>false</outputsNewCASes>
+		</operationalProperties>
+	</analysisEngineMetaData>
+	<resourceManagerConfiguration />
+</analysisEngineDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/NamedEntityRegexAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/NamedEntityRegexAnnotator.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/NamedEntityRegexAnnotator.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/NamedEntityRegexAnnotator.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+  <primitive>true</primitive>
+  <annotatorImplementationName>ytex.uima.annotators.NamedEntityRegexAnnotator</annotatorImplementationName>
+  <analysisEngineMetaData>
+    <name>NamedEntityRegexAnnotator</name>
+    <description/>
+    <version>1.0</version>
+    <vendor/>
+    <configurationParameters/>
+    <configurationParameterSettings/>
+    <typeSystemDescription>
+      <imports>
+        <import name="ytex.uima.YTEXTypes"/>
+      </imports>
+    </typeSystemDescription>
+    <typePriorities/>
+    <fsIndexCollection/>
+    <capabilities>
+      <capability>
+        <inputs/>
+        <outputs/>
+        <languagesSupported/>
+      </capability>
+    </capabilities>
+    <operationalProperties>
+      <modifiesCas>true</modifiesCas>
+      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+      <outputsNewCASes>false</outputsNewCASes>
+    </operationalProperties>
+  </analysisEngineMetaData>
+  <resourceManagerConfiguration/>
+</analysisEngineDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/NegexAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/NegexAnnotator.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/NegexAnnotator.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/NegexAnnotator.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,60 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+  <primitive>true</primitive>
+  <annotatorImplementationName>ytex.uima.annotators.NegexAnnotator</annotatorImplementationName>
+  <analysisEngineMetaData>
+    <name>NegexAnnotator</name>
+    <description>NegexAnnotator based on the original negex java code.</description>
+    <version>1.0</version>
+    <vendor/>
+    <configurationParameters>
+      <configurationParameter>
+        <name>negatePossibilities</name>
+        <type>Boolean</type>
+        <multiValued>false</multiValued>
+        <mandatory>false</mandatory>
+      </configurationParameter>
+      <configurationParameter>
+        <name>targetTypeName</name>
+        <type>String</type>
+        <multiValued>false</multiValued>
+        <mandatory>false</mandatory>
+      </configurationParameter>
+    </configurationParameters>
+    <configurationParameterSettings>
+      <nameValuePair>
+        <name>negatePossibilities</name>
+        <value>
+          <boolean>true</boolean>
+        </value>
+      </nameValuePair>
+      <nameValuePair>
+        <name>targetTypeName</name>
+        <value>
+          <string>ytex.uima.types.WordToken</string>
+        </value>
+      </nameValuePair>
+    </configurationParameterSettings>
+    <typeSystemDescription>
+      <imports>
+        <import name="ytex.uima.YTEXTypes"/>
+      </imports>
+    </typeSystemDescription>
+    <typePriorities/>
+    <fsIndexCollection/>
+    <capabilities>
+      <capability>
+        <inputs/>
+        <outputs/>
+        <languagesSupported/>
+      </capability>
+    </capabilities>
+    <operationalProperties>
+      <modifiesCas>true</modifiesCas>
+      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+      <outputsNewCASes>false</outputsNewCASes>
+    </operationalProperties>
+  </analysisEngineMetaData>
+  <resourceManagerConfiguration/>
+</analysisEngineDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,35 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+	<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+	<primitive>true</primitive>
+	<annotatorImplementationName>org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
+	</annotatorImplementationName>
+	<analysisEngineMetaData>
+		<name>SegmentAnnotator</name>
+		<description />
+		<version>1.0</version>
+		<vendor />
+		<configurationParameters />
+		<configurationParameterSettings />
+		<typeSystemDescription>
+			<imports>
+				<import name="org.apache.ctakes.ytex.types.TypeSystem" />
+			</imports>
+		</typeSystemDescription>
+		<typePriorities />
+		<fsIndexCollection />
+		<capabilities>
+			<capability>
+				<inputs />
+				<outputs />
+				<languagesSupported />
+			</capability>
+		</capabilities>
+		<operationalProperties>
+			<modifiesCas>true</modifiesCas>
+			<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+			<outputsNewCASes>false</outputsNewCASes>
+		</operationalProperties>
+	</analysisEngineMetaData>
+	<resourceManagerConfiguration />
+</analysisEngineDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SenseDisambiguatorAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SenseDisambiguatorAnnotator.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SenseDisambiguatorAnnotator.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SenseDisambiguatorAnnotator.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,51 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+	<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+	<primitive>true</primitive>
+	<annotatorImplementationName>ytex.uima.annotators.SenseDisambiguatorAnnotator
+	</annotatorImplementationName>
+	<analysisEngineMetaData>
+		<name>SenseDisambiguatorAnnotator</name>
+		<description />
+		<version>1.0</version>
+		<vendor />
+		<configurationParameters>
+			<configurationParameter>
+				<name>metric</name>
+				<type>String</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+			</configurationParameter>
+			<configurationParameter>
+				<name>windowSize</name>
+				<type>Integer</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+			</configurationParameter>
+		</configurationParameters>
+		<configurationParameterSettings />
+		<typeSystemDescription>
+			<imports>
+				<import name="ytex.uima.YTEXTypes" />
+			</imports>
+		</typeSystemDescription>
+		<typePriorities />
+		<fsIndexCollection />
+		<capabilities>
+			<capability>
+				<inputs>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.NamedEntity
+					</type>
+				</inputs>
+				<outputs />
+				<languagesSupported />
+			</capability>
+		</capabilities>
+		<operationalProperties>
+			<modifiesCas>true</modifiesCas>
+			<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+			<outputsNewCASes>false</outputsNewCASes>
+		</operationalProperties>
+	</analysisEngineMetaData>
+	<resourceManagerConfiguration />
+</analysisEngineDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SentenceDetectorAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SentenceDetectorAnnotator.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SentenceDetectorAnnotator.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SentenceDetectorAnnotator.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,80 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+<primitive>true</primitive>
+<annotatorImplementationName>org.apache.ctakes.ytex.uima.annotators.SentenceDetector</annotatorImplementationName>
+<analysisEngineMetaData>
+<name>Sentence Detector annotator</name>
+<description>Discovers sentence boundaries.</description>
+<version>2.1</version>
+<vendor>Mayo Clinic</vendor>
+<configurationParameters>
+<configurationParameter>
+<name>SegmentsToSkip</name>
+<type>String</type>
+<multiValued>true</multiValued>
+<mandatory>false</mandatory>
+</configurationParameter>
+<configurationParameter>
+<name>SentenceModelFile</name>
+<description>The file that contains the MaxEnt model used by the Sentence Dectector</description>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+</configurationParameters>
+<configurationParameterSettings>
+<nameValuePair>
+<name>SegmentsToSkip</name>
+<value>
+<array/>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>SentenceModelFile</name>
+<value>
+<string>org/apache/ctakes/core/sentdetect/sd-med-model.zip</string>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+<typeSystemDescription/>
+<typePriorities/>
+<fsIndexCollection/>
+<capabilities>
+<capability>
+<inputs>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+</inputs>
+<outputs>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+</outputs>
+<languagesSupported/>
+</capability>
+</capabilities>
+<operationalProperties>
+<modifiesCas>true</modifiesCas>
+<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+<outputsNewCASes>false</outputsNewCASes>
+</operationalProperties>
+</analysisEngineMetaData>
+</taeDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipeline.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipeline.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipeline.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipeline.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,148 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+	<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+	<primitive>false</primitive>
+	<delegateAnalysisEngineSpecifiers>
+		<delegateAnalysisEngine key="AggregatePlaintextUMLSProcessor">
+	      <import location="./AggregatePlaintextUMLSProcessor.xml"/>
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="DBConsumer">
+	      <import location="./DBConsumer.xml"/>
+		</delegateAnalysisEngine>
+	</delegateAnalysisEngineSpecifiers>
+	<analysisEngineMetaData>
+		<name>YTEXPipeline</name>
+		<description>ctakes AggregatePlaintextUMLSProcessor with following
+			changes: Replaced cTAKES NegationAnnotator with YTEX NegexAnnotator,
+			replaced cTAKES SimpleSegment with YTEX SegmentRegexAnnotator.
+			Reconfigured DictionaryLookup to use YTEX dictionary.
+			Added
+			DateAnnotator, SenseDisambiguatorAnnotator,
+			NamedEntityRegexAnnotator, DBConsumer
+		</description>
+		<version />
+		<vendor />
+		<configurationParameters searchStrategy="language_fallback">
+			<configurationParameter>
+				<name>analysisBatch</name>
+				<type>String</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+				<overrides>
+					<parameter>DBConsumer/analysisBatch</parameter>
+				</overrides>
+			</configurationParameter>
+			<configurationParameter>
+				<name>storeDocText</name>
+				<type>Boolean</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+				<overrides>
+					<parameter>DBConsumer/storeDocText</parameter>
+				</overrides>
+			</configurationParameter>
+			<configurationParameter>
+				<name>storeCAS</name>
+				<type>Boolean</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+				<overrides>
+					<parameter>DBConsumer/storeCAS</parameter>
+				</overrides>
+			</configurationParameter>
+			<configurationParameter>
+				<name>typesToIgnore</name>
+				<description>uima types (fully qualified class names) that should
+					not be saved in the database.
+				</description>
+				<type>String</type>
+				<multiValued>true</multiValued>
+				<mandatory>false</mandatory>
+				<overrides>
+					<parameter>DBConsumer/typesToIgnore</parameter>
+				</overrides>
+			</configurationParameter>
+			<configurationParameter>
+				<name>insertAnnotationContainmentLinks</name>
+				<description>should containment links be added
+				</description>
+				<type>Boolean</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+				<overrides>
+					<parameter>DBConsumer/insertAnnotationContainmentLinks</parameter>
+				</overrides>
+			</configurationParameter>
+		</configurationParameters>
+		<configurationParameterSettings>
+			<nameValuePair>
+				<name>xmiOutputDirectory</name>
+				<value>
+					<string />
+				</value>
+			</nameValuePair>
+			<nameValuePair>
+				<name>analysisBatch</name>
+				<value>
+					<string>test</string>
+				</value>
+			</nameValuePair>
+			<nameValuePair>
+				<name>storeDocText</name>
+				<value>
+					<boolean>true</boolean>
+				</value>
+			</nameValuePair>
+			<nameValuePair>
+				<name>storeCAS</name>
+				<value>
+					<boolean>true</boolean>
+				</value>
+			</nameValuePair>
+			<nameValuePair>
+				<name>insertAnnotationContainmentLinks</name>
+				<value>
+					<boolean>true</boolean>
+				</value>
+			</nameValuePair>
+			<nameValuePair>
+				<name>typesToIgnore</name>
+				<value>
+					<array>
+						<string>org.apache.ctakes.typesystem.type.syntax.ContractionToken</string>
+						<string>org.apache.ctakes.typesystem.type.syntax.NewlineToken</string>
+						<string>org.apache.ctakes.typesystem.type.syntax.PunctuationToken
+						</string>
+						<string>org.apache.ctakes.typesystem.type.syntax.SymbolToken</string>
+						<string>org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation
+						</string>
+						<string>org.apache.ctakes.typesystem.type.textsem.DateAnnotation</string>
+						<string>org.apache.ctakes.typesystem.type.textsem.FractionAnnotation
+						</string>
+						<string>org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation
+						</string>
+						<string>org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation
+						</string>
+						<string>org.apache.ctakes.typesystem.type.textsem.RangeAnnotation
+						</string>
+						<string>org.apache.ctakes.typesystem.type.textsem.TimeAnnotation</string>
+						<string>org.apache.ctakes.typesystem.type.syntax.NP</string>
+						<string>org.apache.ctakes.typesystem.type.syntax.VP</string>
+					</array>
+				</value>
+			</nameValuePair>
+		</configurationParameterSettings>
+		<flowConstraints>
+			<fixedFlow>
+				<node>AggregatePlaintextUMLSProcessor</node>
+				<node>DBConsumer</node>
+			</fixedFlow>
+		</flowConstraints>
+		<operationalProperties>
+			<modifiesCas>true</modifiesCas>
+			<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+			<outputsNewCASes>false</outputsNewCASes>
+		</operationalProperties>
+	</analysisEngineMetaData>
+	<resourceManagerConfiguration />
+</analysisEngineDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipelineNoDBConsumer.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipelineNoDBConsumer.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipelineNoDBConsumer.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipelineNoDBConsumer.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,343 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+	<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+	<primitive>false</primitive>
+	<delegateAnalysisEngineSpecifiers>
+		<delegateAnalysisEngine key="TokenizerAnnotator">
+			<import name="coredesc.analysis_engine.TokenizerAnnotator" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
+			<import name="cdtdesc.analysis_engine.ContextDependentTokenizerAnnotator" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="StatusAnnotator">
+			<import name="necontextdesc.analysis_engine.StatusAnnotator" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="NegationAnnotator">
+			<import name="ytex.uima.annotators.NegexAnnotator" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="SegmentRegexAnnotator">
+			<import name="ytex.uima.annotators.SegmentRegexAnnotator" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="SentenceDetectorAnnotator">
+			<import name="ytex.uima.annotators.SentenceDetectorAnnotator" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="SenseDisambiguatorAnnotator">
+			<import name="ytex.uima.annotators.SenseDisambiguatorAnnotator" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="AdjustNounPhraseToIncludeFollowingNP">
+			<import
+				name="chunkerdesc.analysis_engine.AdjustNounPhraseToIncludeFollowingNP" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="AdjustNounPhraseToIncludeFollowingPPNP">
+			<import
+				name="chunkerdesc.analysis_engine.AdjustNounPhraseToIncludeFollowingPPNP" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="POSTagger">
+			<import name="posdesc.analysis_engine.POSTagger" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="Chunker">
+			<import name="chunkerdesc.analysis_engine.Chunker" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="DateAnnotator">
+			<import name="ytex.uima.annotators.DateAnnotator" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="ExtractionPrepAnnotator">
+			<import name="cdpdesc.analysis_engine.ExtractionPrepAnnotator" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="LookupWindowAnnotator">
+			<import name="cdpdesc.analysis_engine.LookupWindowAnnotator" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="NamedEntityRegexAnnotator">
+			<import name="ytex.uima.annotators.NamedEntityRegexAnnotator" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="DictionaryLookupAnnotator">
+			<import name="ytex.uima.annotators.DictionaryLookupAnnotator" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="LvgAnnotator">
+			<import name="lvgdesc.analysis_engine.LvgAnnotator" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="DBConsumer">
+			<import name="ytex.uima.annotators.DBConsumer" />
+		</delegateAnalysisEngine>
+	</delegateAnalysisEngineSpecifiers>
+	<analysisEngineMetaData>
+		<name>YTEXPipeline</name>
+		<description>ctakes AggregatePlaintextUMLSProcessor with following
+			changes: Replaced cTAKES NegationAnnotator with YTEX NegexAnnotator,
+			replaced cTAKES SimpleSegment with YTEX SegmentRegexAnnotator.
+			Reconfigured DictionaryLookup to use YTEX dictionary.
+			Added
+			DateAnnotator, SenseDisambiguatorAnnotator,
+			NamedEntityRegexAnnotator, DBConsumer
+		</description>
+		<version />
+		<vendor />
+		<configurationParameters searchStrategy="language_fallback">
+			<configurationParameter>
+				<name>ChunkCreatorClass</name>
+				<type>String</type>
+				<multiValued>false</multiValued>
+				<mandatory>true</mandatory>
+				<overrides>
+					<parameter>Chunker/ChunkCreatorClass</parameter>
+				</overrides>
+			</configurationParameter>
+			<configurationParameter>
+				<name>xmiOutputDirectory</name>
+				<type>String</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+				<overrides>
+					<parameter>DBConsumer/xmiOutputDirectory</parameter>
+				</overrides>
+			</configurationParameter>
+			<configurationParameter>
+				<name>analysisBatch</name>
+				<type>String</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+				<overrides>
+					<parameter>DBConsumer/analysisBatch</parameter>
+				</overrides>
+			</configurationParameter>
+			<configurationParameter>
+				<name>storeDocText</name>
+				<type>Boolean</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+				<overrides>
+					<parameter>DBConsumer/storeDocText</parameter>
+				</overrides>
+			</configurationParameter>
+			<configurationParameter>
+				<name>storeCAS</name>
+				<type>Boolean</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+				<overrides>
+					<parameter>DBConsumer/storeCAS</parameter>
+				</overrides>
+			</configurationParameter>
+			<configurationParameter>
+				<name>typesToIgnore</name>
+				<description>uima types (fully qualified class names) that should
+					not be saved in the database.
+				</description>
+				<type>String</type>
+				<multiValued>true</multiValued>
+				<mandatory>false</mandatory>
+				<overrides>
+					<parameter>DBConsumer/typesToIgnore</parameter>
+				</overrides>
+			</configurationParameter>
+			<configurationParameter>
+				<name>insertAnnotationContainmentLinks</name>
+				<description>should containment links be added
+				</description>
+				<type>Boolean</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+				<overrides>
+					<parameter>DBConsumer/insertAnnotationContainmentLinks</parameter>
+				</overrides>
+			</configurationParameter>
+		</configurationParameters>
+		<configurationParameterSettings>
+			<nameValuePair>
+				<name>ChunkCreatorClass</name>
+				<value>
+					<string>edu.mayo.bmi.uima.chunker.PhraseTypeChunkCreator</string>
+				</value>
+			</nameValuePair>
+			<nameValuePair>
+				<name>xmiOutputDirectory</name>
+				<value>
+					<string />
+				</value>
+			</nameValuePair>
+			<nameValuePair>
+				<name>analysisBatch</name>
+				<value>
+					<string>test</string>
+				</value>
+			</nameValuePair>
+			<nameValuePair>
+				<name>storeDocText</name>
+				<value>
+					<boolean>true</boolean>
+				</value>
+			</nameValuePair>
+			<nameValuePair>
+				<name>storeCAS</name>
+				<value>
+					<boolean>true</boolean>
+				</value>
+			</nameValuePair>
+			<nameValuePair>
+				<name>insertAnnotationContainmentLinks</name>
+				<value>
+					<boolean>true</boolean>
+				</value>
+			</nameValuePair>
+			<nameValuePair>
+				<name>typesToIgnore</name>
+				<value>
+					<array>
+						<string>edu.mayo.bmi.uima.core.type.ContractionToken</string>
+						<string>edu.mayo.bmi.uima.core.type.syntax.NewlineToken</string>
+						<string>edu.mayo.bmi.uima.core.type.syntax.PunctuationToken
+						</string>
+						<string>edu.mayo.bmi.uima.core.type.syntax.SymbolToken</string>
+						<string>edu.mayo.bmi.uima.cdt.type.textsem.RomanNumeralAnnotation
+						</string>
+						<string>edu.mayo.bmi.uima.cdt.type.textsem.DateAnnotation</string>
+						<string>edu.mayo.bmi.uima.cdt.type.textsem.FractionAnnotation
+						</string>
+						<string>edu.mayo.bmi.uima.cdt.type.textsem.MeasurementAnnotation
+						</string>
+						<string>edu.mayo.bmi.uima.cdt.type.textsem.PersonTitleAnnotation
+						</string>
+						<string>edu.mayo.bmi.uima.cdt.type.textsem.RangeAnnotation
+						</string>
+						<string>edu.mayo.bmi.uima.cdt.type.textsem.TimeAnnotation</string>
+						<string>edu.mayo.bmi.uima.core.type.syntax.NP</string>
+						<string>edu.mayo.bmi.uima.core.type.syntax.VP</string>
+					</array>
+				</value>
+			</nameValuePair>
+		</configurationParameterSettings>
+		<flowConstraints>
+			<fixedFlow>
+				<node>SegmentRegexAnnotator</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>NamedEntityRegexAnnotator</node>
+				<node>SenseDisambiguatorAnnotator</node>
+				<node>StatusAnnotator</node>
+				<node>NegationAnnotator</node>
+				<node>DateAnnotator</node>
+				<node>ExtractionPrepAnnotator</node>
+			</fixedFlow>
+		</flowConstraints>
+		<typePriorities>
+			<name>Ordering</name>
+			<description>For subiterator</description>
+			<version>1.0</version>
+			<priorityList>
+				<type>edu.mayo.bmi.uima.core.type.textspan.Segment</type>
+				<type>edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
+				<type>edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+			</priorityList>
+			<priorityList>
+				<type>edu.mayo.bmi.uima.core.type.textspan.Sentence</type>
+				<type>edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation
+				</type>
+			</priorityList>
+		</typePriorities>
+		<fsIndexCollection />
+		<capabilities>
+			<capability>
+				<inputs />
+				<outputs>
+
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.NewlineToken
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.WordToken
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.VP
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.refsem.UmlsConcept
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.UCP
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.TimeAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.SymbolToken
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspan.Sentence
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textspanSegment
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.SBAR
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.RomanNumeralAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.RangeAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.PunctuationToken
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.Property
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.Properties
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.PersonTitleAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.PRT
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.PP
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.OntologyConcept
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.NumToken
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.MeasurementAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.lookup.type.LookupWindowAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.Lemma
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.LST
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.INTJ
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.FractionAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.structured.DocumentID
+					</type>
+					<type allAnnotatorFeatures="true">uima.tcas.DocumentAnnotation</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.DateAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.CopySrcAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.CopyDestAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.ContractionToken
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.ContextAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.Chunk
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.CONJP
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken
+					</type>
+					<type allAnnotatorFeatures="true">uima.cas.AnnotationBase</type>
+					<type allAnnotatorFeatures="true">uima.tcas.Annotation</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.ADVP
+					</type>
+					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.ADJP
+					</type>
+				</outputs>
+				<languagesSupported />
+			</capability>
+		</capabilities>
+		<operationalProperties>
+			<modifiesCas>true</modifiesCas>
+			<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+			<outputsNewCASes>false</outputsNewCASes>
+		</operationalProperties>
+	</analysisEngineMetaData>
+	<resourceManagerConfiguration />
+</analysisEngineDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/collection_reader/DBCollectionReader.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/collection_reader/DBCollectionReader.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/collection_reader/DBCollectionReader.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/collection_reader/DBCollectionReader.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,92 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<collectionReaderDescription xmlns="http://uima.apache.org/resourceSpecifier">
+	<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+	<implementationName>org.apache.ctakes.ytex.uima.DBCollectionReader
+	</implementationName>
+	<processingResourceMetaData>
+		<name>DBcollectionReader</name>
+		<description />
+		<version>1.0</version>
+		<vendor />
+		<configurationParameters>
+			<configurationParameter>
+				<name>queryGetDocumentKeys</name>
+				<type>String</type>
+				<multiValued>false</multiValued>
+				<mandatory>true</mandatory>
+			</configurationParameter>
+			<configurationParameter>
+				<name>queryGetDocument</name>
+				<type>String</type>
+				<multiValued>false</multiValued>
+				<mandatory>true</mandatory>
+			</configurationParameter>
+			<configurationParameter>
+				<name>dbDriver</name>
+				<description>Fully qualified class name of jdbc driver to use to
+					retrieve documents. If null, will use db.driver from
+					ytex.properties
+				</description>
+				<type>String</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+			</configurationParameter>
+			<configurationParameter>
+				<name>dbURL</name>
+				<description>optional jdbc url to retrieve documents. If not
+					specified, will use default ytex jdbc url. Only use this if your
+					documents reside on a different database from the ytex database. If
+					needed, specify the username and password in the url.
+				</description>
+				<type>String</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+			</configurationParameter>
+			<configurationParameter>
+				<name>keyNameToLowerCase</name>
+				<description>convert key names to lower case, defaults to true
+				</description>
+				<type>Boolean</type>
+				<multiValued>false</multiValued>
+				<mandatory>false</mandatory>
+			</configurationParameter>
+		</configurationParameters>
+		<configurationParameterSettings>
+			<nameValuePair>
+				<name>queryGetDocumentKeys</name>
+				<value>
+					<string>select 
+					</string>
+				</value>
+			</nameValuePair>
+			<nameValuePair>
+				<name>queryGetDocument</name>
+				<value>
+					<string>select doc_text from esld.dummy_document where site_id =
+						:site_id and uid = :uid and document_type_id = :document_type_id
+					</string>
+				</value>
+			</nameValuePair>
+		</configurationParameterSettings>
+		<typeSystemDescription>
+			<imports>
+				<import name="org.apache.ctakes.ytex.types.TypeSystem" />
+			</imports>
+		</typeSystemDescription>
+		<typePriorities />
+		<fsIndexCollection />
+		<capabilities>
+			<capability>
+				<inputs />
+				<outputs />
+				<languagesSupported />
+			</capability>
+		</capabilities>
+		<operationalProperties>
+			<modifiesCas>true</modifiesCas>
+			<multipleDeploymentAllowed>false</multipleDeploymentAllowed>
+			<outputsNewCASes>true</outputsNewCASes>
+		</operationalProperties>
+	</processingResourceMetaData>
+	<resourceManagerConfiguration />
+</collectionReaderDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/Coref-resolver_CPE.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/Coref-resolver_CPE.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/Coref-resolver_CPE.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/Coref-resolver_CPE.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,70 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+	<collectionReader>
+		<collectionIterator>
+			<descriptor>
+				<import
+					name="coredesc.collection_reader.FilesInDirectoryCollectionReader" />
+			</descriptor>
+			<configurationParameterSettings>
+				<nameValuePair>
+					<name>InputDirectory</name>
+					<value>
+						<string>examples/pubmed/abstracts</string>
+					</value>
+				</nameValuePair>
+			</configurationParameterSettings>
+		</collectionIterator>
+	</collectionReader>
+	<casProcessors casPoolSize="3" processingUnitThreadCount="1">
+		<casProcessor deployment="integrated" name="CorefPlaintextProcessor">
+			<descriptor>
+				<import name="ytex.corefdesc.analysis_engine.CorefProcessor" />
+			</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="YTEX DBConsumer">
+			<descriptor>
+				<import name="ytex.uima.annotators.DBConsumer" />
+			</descriptor>
+			<checkpoint batch="10000" time="1000ms" />
+			<configurationParameterSettings>
+				<nameValuePair>
+					<name>typesToIgnore</name>
+					<value>
+						<array>
+							<string>edu.mayo.bmi.uima.core.type.ContractionToken</string>
+							<string>edu.mayo.bmi.uima.core.type.NewlineToken</string>
+							<string>edu.mayo.bmi.uima.core.type.PunctuationToken</string>
+							<string>edu.mayo.bmi.uima.core.type.SymbolToken</string>
+							<string>edu.mayo.bmi.uima.cdt.type.RomanNumeralAnnotation
+							</string>
+							<string>edu.mayo.bmi.uima.cdt.type.DateAnnotation</string>
+							<string>edu.mayo.bmi.uima.cdt.type.FractionAnnotation</string>
+							<string>edu.mayo.bmi.uima.cdt.type.MeasurementAnnotation</string>
+							<string>edu.mayo.bmi.uima.cdt.type.PersonTitleAnnotation</string>
+							<string>edu.mayo.bmi.uima.cdt.type.RangeAnnotation</string>
+							<string>edu.mayo.bmi.uima.cdt.type.TimeAnnotation</string>
+							<!-- <string>edu.mayo.bmi.uima.chunker.type.NP</string> -->
+							<string>edu.mayo.bmi.uima.chunker.type.VP</string>
+						</array>
+					</value>
+				</nameValuePair>
+			</configurationParameterSettings>
+
+		</casProcessor>
+	</casProcessors>
+	<cpeConfig>
+		<numToProcess>-1</numToProcess>
+		<deployAs>immediate</deployAs>
+		<checkpoint batch="0" time="300000" />
+		<timerImpl />
+	</cpeConfig>
+</cpeDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/DrugNER_PlainText_CPE.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/DrugNER_PlainText_CPE.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/DrugNER_PlainText_CPE.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/DrugNER_PlainText_CPE.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+	<collectionReader>
+		<collectionIterator>
+			<descriptor>
+				<import
+					name="coredesc.collection_reader.FilesInDirectoryCollectionReader" />
+			</descriptor>
+			<configurationParameterSettings>
+				<nameValuePair>
+					<name>InputDirectory</name>
+					<value>
+						<string>examples/drugnertest</string>
+					</value>
+				</nameValuePair>
+			</configurationParameterSettings>
+		</collectionIterator>
+	</collectionReader>
+	<casProcessors casPoolSize="3" processingUnitThreadCount="1">
+		<casProcessor deployment="integrated" name="AggregatePlaintextProcessor">
+			<descriptor>
+				<import
+					name="ytex.drugnerdesc.analysis_engine.DrugAggregatePlaintextProcessor" />
+			</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="YTEX DBConsumer">
+			<descriptor>
+				<import name="ytex.uima.annotators.DBConsumer" />
+			</descriptor>
+			<checkpoint batch="10000" time="1000ms" />
+		</casProcessor>
+	</casProcessors>
+	<cpeConfig>
+		<numToProcess>-1</numToProcess>
+		<deployAs>immediate</deployAs>
+		<checkpoint batch="0" time="300000ms" />
+		<timerImpl />
+	</cpeConfig>
+</cpeDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/FileSystemCollectionReader.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/FileSystemCollectionReader.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/FileSystemCollectionReader.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/FileSystemCollectionReader.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,80 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<!--
+Copied from uima examples, modified to use the 
+org.apache.uima.tools.components.FileSystemCollectionReader
+A simple collection reader that reads text files from a directory in the
+filesystem.  The Java class for this collection reader is in uima_core.jar. 
+-->
+<collectionReaderDescription  xmlns="http://uima.apache.org/resourceSpecifier">
+    <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+    <implementationName>org.apache.uima.tools.components.FileSystemCollectionReader</implementationName>
+    <processingResourceMetaData>
+        <name>File System Collection Reader</name>
+        <description>Reads files from the filesystem.  This CollectionReader may be used
+          with or without a CAS Initializer.  If a CAS Initializer is supplied, it will
+          be passed an InputStream to the file and must populate the CAS from that
+          InputStream.  If no CAS Initializer is supplied, this CollectionReader will
+          read the file itself and set treat the entire contents of the file as the
+          document to be inserted into the CAS.</description>
+        <version>1.0</version>
+        <vendor>The Apache Software Foundation</vendor>
+        <configurationParameters>
+            <configurationParameter>
+                <name>InputDirectory</name>
+                <description>Directory containing input files</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>true</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>Encoding</name>
+                <description>Character encoding for the documents.  If not specified,
+                   the default system encoding will be used.  Note that this parameter
+                   only applies if there is no CAS Initializer provided; otherwise,
+                   it is the CAS Initializer's responsibility to deal with character
+                   encoding issues. </description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+            <configurationParameter>
+                <name>Language</name>
+                <description>ISO language code for the documents</description>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>false</mandatory>
+            </configurationParameter>
+        </configurationParameters>
+		<configurationParameterSettings>
+		    <nameValuePair>
+		        <name>InputDirectory</name>
+		        <value>
+		            <string>C:\java\apache-uima/examples/data</string>
+		        </value>
+		    </nameValuePair>
+		</configurationParameterSettings>
+
+        <!-- Type System of CASes returned by this Collection Reader -->
+
+        <typeSystemDescription>
+          <imports>
+            <import name="org.apache.uima.examples.SourceDocumentInformation"/>
+          </imports>
+        </typeSystemDescription>
+
+        <capabilities>
+          	<capability>
+          		<inputs/>
+          		<outputs>
+          			<type allAnnotatorFeatures="true">org.apache.uima.examples.SourceDocumentInformation</type>
+          		</outputs>
+          	</capability>
+        </capabilities>
+		<operationalProperties>
+			<modifiesCas>true</modifiesCas>
+			<multipleDeploymentAllowed>false</multipleDeploymentAllowed>
+			<outputsNewCASes>true</outputsNewCASes>
+		</operationalProperties>		
+    </processingResourceMetaData>
+</collectionReaderDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+	<collectionReader>
+		<collectionIterator>
+			<descriptor>
+				<import
+					name="coredesc.collection_reader.FilesInDirectoryCollectionReader" />
+			</descriptor>
+			<configurationParameterSettings>
+				<nameValuePair>
+					<name>InputDirectory</name>
+					<value>
+						<string>examples/pubmed/abstracts</string>
+					</value>
+				</nameValuePair>
+			</configurationParameterSettings>
+		</collectionIterator>
+	</collectionReader>
+	<casProcessors casPoolSize="3" processingUnitThreadCount="1">
+		<casProcessor deployment="integrated" name="AggregatePlaintextUMLSProcessor">
+			<descriptor>
+				<import name="ytex.cdpdesc.analysis_engine.AggregatePlaintextUMLSProcessor" />
+			</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="YTEX DBConsumer">
+			<descriptor>
+				<import name="ytex.uima.annotators.DBConsumer" />
+			</descriptor>
+			<checkpoint batch="10000" time="1000ms" />
+		</casProcessor>
+	</casProcessors>
+	<cpeConfig>
+		<numToProcess>-1</numToProcess>
+		<deployAs>immediate</deployAs>
+		<checkpoint batch="0" time="300000" />
+		<timerImpl />
+	</cpeConfig>
+</cpeDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext_ctakes.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext_ctakes.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext_ctakes.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext_ctakes.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+	<collectionReader>
+		<collectionIterator>
+			<descriptor>
+				<import
+					name="coredesc.collection_reader.FilesInDirectoryCollectionReader" />
+			</descriptor>
+			<configurationParameterSettings>
+				<nameValuePair>
+					<name>InputDirectory</name>
+					<value>
+						<string>examples/pubmed/abstracts</string>
+					</value>
+				</nameValuePair>
+			</configurationParameterSettings>
+		</collectionIterator>
+	</collectionReader>
+	<casProcessors casPoolSize="3" processingUnitThreadCount="1">
+		<casProcessor deployment="integrated" name="AggregatePlaintextUMLSProcessor">
+			<descriptor>
+				<import name="cdpdesc.analysis_engine.AggregatePlaintextUMLSProcessorCTakes" />
+			</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="YTEX DBConsumer">
+			<descriptor>
+				<import name="ytex.uima.annotators.DBConsumer" />
+			</descriptor>
+			<checkpoint batch="10000" time="1000ms" />
+		</casProcessor>
+	</casProcessors>
+	<cpeConfig>
+		<numToProcess>-1</numToProcess>
+		<deployAs>immediate</deployAs>
+		<checkpoint batch="0" time="300000" />
+		<timerImpl />
+	</cpeConfig>
+</cpeDescription>

Added: ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext_metamap.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext_metamap.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext_metamap.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext_metamap.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,68 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+	<collectionReader>
+		<collectionIterator>
+			<descriptor>
+				<import
+					name="coredesc.collection_reader.FilesInDirectoryCollectionReader" />
+			</descriptor>
+			<configurationParameterSettings>
+				<nameValuePair>
+					<name>InputDirectory</name>
+					<value>
+						<string>examples/pubmed/abstracts</string>
+					</value>
+				</nameValuePair>
+			</configurationParameterSettings>
+		</collectionIterator>
+	</collectionReader>
+	<casProcessors casPoolSize="3" processingUnitThreadCount="1">
+		<casProcessor deployment="integrated" name="MetaMapApiAE">
+			<descriptor>
+				<import name="MetaMapApiAE" />
+			</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="YTEX MetaMapSenseDisambiguatorAnnotator">
+			<descriptor>
+				<import name="ytex.uima.annotators.MetaMapSenseDisambiguatorAnnotator" />
+			</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="YTEX DBConsumer">
+			<descriptor>
+				<import name="ytex.uima.annotators.DBConsumer" />
+			</descriptor>
+			<checkpoint batch="10000" time="1000ms" />
+			<configurationParameterSettings>
+                <nameValuePair>
+                    <name>insertAnnotationContainmentLinks</name>
+                    <value>
+                        <boolean>false</boolean>
+                    </value>
+                </nameValuePair>				
+			</configurationParameterSettings>
+		</casProcessor>
+	</casProcessors>
+	<cpeConfig>
+		<numToProcess>-1</numToProcess>
+		<deployAs>immediate</deployAs>
+		<checkpoint batch="0" time="300000" />
+		<timerImpl />
+	</cpeConfig>
+</cpeDescription>



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