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From spmurph...@apache.org
Subject svn commit: r1423486 [1/2] - in /incubator/ctakes/branches/ctakes-3.0.0-incubating: ctakes-core/src/main/resources/org/apache/ctakes/core/analysis_engine/ ctakes-drug-ner/ ctakes-drug-ner/desc/analysis_engine/ ctakes-drug-ner/desc/cas_consumer/ ctakes-...
Date Tue, 18 Dec 2012 15:49:43 GMT
Author: spmurphy50
Date: Tue Dec 18 15:49:41 2012
New Revision: 1423486

URL: http://svn.apache.org/viewvc?rev=1423486&view=rev
Log:
cTAKES 101

Added:
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-core/src/main/resources/org/apache/ctakes/core/analysis_engine/
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-core/src/main/resources/org/apache/ctakes/core/analysis_engine/SentenceDetectorAnnotator.xml   (with props)
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-core/src/main/resources/org/apache/ctakes/core/analysis_engine/TokenizerAnnotator.xml   (with props)
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-ne-contexts/src/main/resources/
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-ne-contexts/src/main/resources/org/
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-ne-contexts/src/main/resources/org/apache/
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-ne-contexts/src/main/resources/org/apache/ctakes/
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-ne-contexts/src/main/resources/org/apache/ctakes/necontexts/
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-ne-contexts/src/main/resources/org/apache/ctakes/necontexts/desc/
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-ne-contexts/src/main/resources/org/apache/ctakes/necontexts/desc/NegationAnnotator.xml   (with props)
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/launch/UIMA_CPE_GUI--PAD_term_spotter.launch   (with props)
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/launch/UIMA CAS Visual Debugger (Smoking Status).launch   (with props)
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/launch/UIMA_CPE_GUI--Smokin_Status.launch   (with props)
Modified:
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcessor.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugLookupWindowAnnotator.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/cas_consumer/DrugNERCasConsumer.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/pom.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/lookup/LookupDesc_DrugNER.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/cas_consumer/PADOffsetsRecordConsumer.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/collection_processing_engine/Radiology_sample.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/launch/UIMA CAS Visual Debugger (PAD Term Spotter).launch
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/pom.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/NonsmokerDictionaryLookupAnnotator.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/PcsClassifierAnnotator_libsvm.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/desc/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml
    incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-smoking-status/src/main/resources/org/apache/ctakes/smokingstatus/data/SmokingStatusLookupConfig.xml

Added: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-core/src/main/resources/org/apache/ctakes/core/analysis_engine/SentenceDetectorAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-core/src/main/resources/org/apache/ctakes/core/analysis_engine/SentenceDetectorAnnotator.xml?rev=1423486&view=auto
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-core/src/main/resources/org/apache/ctakes/core/analysis_engine/SentenceDetectorAnnotator.xml (added)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-core/src/main/resources/org/apache/ctakes/core/analysis_engine/SentenceDetectorAnnotator.xml Tue Dec 18 15:49:41 2012
@@ -0,0 +1,93 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+<primitive>true</primitive>
+<annotatorImplementationName>org.apache.ctakes.core.ae.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>
+</configurationParameters>
+<configurationParameterSettings>
+<nameValuePair>
+<name>SegmentsToSkip</name>
+<value>
+<array/>
+</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>
+<externalResourceDependencies>
+<externalResourceDependency>
+<key>MaxentModel</key>
+<description></description>
+<interfaceName>org.apache.ctakes.core.resource.MaxentModelResource</interfaceName>
+<optional>false</optional>
+</externalResourceDependency>
+</externalResourceDependencies>
+<resourceManagerConfiguration>
+<externalResources>
+<externalResource>
+<name>MaxentModelFile</name>
+<description></description>
+<fileResourceSpecifier>
+<fileUrl>file:org/apache/ctakes/core/sentdetect/sdmed.mod</fileUrl>
+</fileResourceSpecifier>
+<implementationName>org.apache.ctakes.core.resource.SuffixMaxentModelResourceImpl</implementationName>
+</externalResource>
+</externalResources>
+<externalResourceBindings>
+<externalResourceBinding>
+<key>MaxentModel</key>
+<resourceName>MaxentModelFile</resourceName>
+</externalResourceBinding>
+</externalResourceBindings>
+</resourceManagerConfiguration>
+</taeDescription>

Propchange: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-core/src/main/resources/org/apache/ctakes/core/analysis_engine/SentenceDetectorAnnotator.xml
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Added: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-core/src/main/resources/org/apache/ctakes/core/analysis_engine/TokenizerAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-core/src/main/resources/org/apache/ctakes/core/analysis_engine/TokenizerAnnotator.xml?rev=1423486&view=auto
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-core/src/main/resources/org/apache/ctakes/core/analysis_engine/TokenizerAnnotator.xml (added)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-core/src/main/resources/org/apache/ctakes/core/analysis_engine/TokenizerAnnotator.xml Tue Dec 18 15:49:41 2012
@@ -0,0 +1,76 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+    KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+
+-->
+<taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+<primitive>true</primitive>
+<annotatorImplementationName>org.apache.ctakes.core.ae.TokenizerAnnotatorPTB</annotatorImplementationName>
+<analysisEngineMetaData>
+<name>TokenizerAnnotatorPTB</name>
+<description>Discovers tokens in the given text, following Penn TreeBank tokenization rules.  These tokens consist of words, punctuation, etc...</description>
+<version>2.3</version>
+<vendor>Mayo Clinic</vendor>
+<configurationParameters>
+<configurationParameter>
+<name>SegmentsToSkip</name>
+<description>Segments to skip.</description>
+<type>String</type>
+<multiValued>true</multiValued>
+<mandatory>false</mandatory>
+</configurationParameter>
+</configurationParameters>
+<configurationParameterSettings>
+<nameValuePair>
+<name>SegmentsToSkip</name>
+<value>
+<array/>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+<typeSystemDescription>
+<imports>
+<import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
+</imports>
+</typeSystemDescription>
+<typePriorities/>
+<fsIndexCollection/>
+<capabilities>
+<capability>
+<inputs>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Segment</type>
+</inputs>
+<outputs>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+</outputs>
+<languagesSupported/>
+</capability>
+</capabilities>
+<operationalProperties>
+<modifiesCas>true</modifiesCas>
+<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+<outputsNewCASes>false</outputsNewCASes>
+</operationalProperties>
+</analysisEngineMetaData>
+<externalResourceDependencies>
+</externalResourceDependencies>
+<resourceManagerConfiguration>
+</resourceManagerConfiguration>
+</taeDescription>

Propchange: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-core/src/main/resources/org/apache/ctakes/core/analysis_engine/TokenizerAnnotator.xml
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml Tue Dec 18 15:49:41 2012
@@ -1,129 +1,108 @@
-<?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>1.0</version>
-    <vendor>Mayo</vendor>
-    <configurationParameters/>
-    <configurationParameterSettings/>
-    <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">edu.mayo.bmi.uima.lookup.type.NamedEntity</type>
-        </outputs>
-        <languagesSupported/>
-      </capability>
-    </capabilities>
-    <operationalProperties>
-      <modifiesCas>true</modifiesCas>
-      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
-      <outputsNewCASes>false</outputsNewCASes>
-    </operationalProperties>
-  </analysisEngineMetaData>
-  <externalResourceDependencies>
-    <externalResourceDependency>
-      <key>LookupDescriptor</key>
-      <description/>
-      <interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
-      <optional>false</optional>
-    </externalResourceDependency>
-    <externalResourceDependency>
-      <key>RxnormIndexReader</key>
-      <description/>
-      <interfaceName>org.apache.ctakes.core.resource.LuceneIndexReaderResource</interfaceName>
-      <optional>false</optional>
-    </externalResourceDependency>
-  </externalResourceDependencies>
-  <resourceManagerConfiguration>
-    <externalResources>
-      <externalResource>
-        <name>LookupDescriptorFile</name>
-        <description/>
-        <fileResourceSpecifier>
-          <fileUrl>file:org/apache/ctakes/drugner/lookup/LookupDesc_DrugNER.xml</fileUrl>
-        </fileResourceSpecifier>
-        <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
-      </externalResource>
-      <externalResource>
-        <name>RxnormIndex</name>
-        <description/>
-        <configurableDataResourceSpecifier>
-          <url/>
-          <resourceMetaData>
-            <name/>
-            <configurationParameters>
-              <configurationParameter>
-                <name>UseMemoryIndex</name>
-                <type>Boolean</type>
-                <multiValued>false</multiValued>
-                <mandatory>true</mandatory>
-              </configurationParameter>
-              <configurationParameter>
-                <name>IndexDirectory</name>
-                <type>String</type>
-                <multiValued>false</multiValued>
-                <mandatory>true</mandatory>
-              </configurationParameter>
-            </configurationParameters>
-            <configurationParameterSettings>
-              <nameValuePair>
-                <name>UseMemoryIndex</name>
-                <value>
-                  <boolean>true</boolean>
-                </value>
-              </nameValuePair>
-              <nameValuePair>
-                <name>IndexDirectory</name>
-                <value>
-                  <string>org/apache/ctakes/drugner/lookup/drug_index</string>
-                </value>
-              </nameValuePair>
-            </configurationParameterSettings>
-          </resourceMetaData>
-        </configurableDataResourceSpecifier>
-        <implementationName>org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl</implementationName>
-      </externalResource>
-    </externalResources>
-    <externalResourceBindings>
-      <externalResourceBinding>
-        <key>LookupDescriptor</key>
-        <resourceName>LookupDescriptorFile</resourceName>
-      </externalResourceBinding>
-      <externalResourceBinding>
-        <key>RxnormIndexReader</key>
-        <resourceName>RxnormIndex</resourceName>
-      </externalResourceBinding>
-    </externalResourceBindings>
-  </resourceManagerConfiguration>
-</taeDescription>
+<?xml version="1.0" encoding="UTF-8"?><taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+  <primitive>true</primitive>
+  <annotatorImplementationName>org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator</annotatorImplementationName>
+  <analysisEngineMetaData>
+    <name>DictionaryLookupAnnotator</name>
+    <description/>
+    <version>1.0</version>
+    <vendor>Mayo</vendor>
+    <configurationParameters/>
+    <configurationParameterSettings/>
+    <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.lookup.type.NamedEntity</type>
+        </outputs>
+        <languagesSupported/>
+      </capability>
+    </capabilities>
+    <operationalProperties>
+      <modifiesCas>true</modifiesCas>
+      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+      <outputsNewCASes>false</outputsNewCASes>
+    </operationalProperties>
+  </analysisEngineMetaData>
+  <externalResourceDependencies>
+    <externalResourceDependency>
+      <key>LookupDescriptor</key>
+      <description/>
+      <interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
+      <optional>false</optional>
+    </externalResourceDependency>
+    <externalResourceDependency>
+      <key>RxnormIndexReader</key>
+      <description/>
+      <interfaceName>org.apache.ctakes.core.resource.LuceneIndexReaderResource</interfaceName>
+      <optional>false</optional>
+    </externalResourceDependency>
+  </externalResourceDependencies>
+  <resourceManagerConfiguration>
+    <externalResources>
+      <externalResource>
+        <name>LookupDescriptorFile</name>
+        <description/>
+        <fileResourceSpecifier>
+          <fileUrl>file:org/apache/ctakes/drugner/lookup/LookupDesc_DrugNER.xml</fileUrl>
+        </fileResourceSpecifier>
+        <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
+      </externalResource>
+      <externalResource>
+        <name>RxnormIndex</name>
+        <description/>
+        <configurableDataResourceSpecifier>
+          <url/>
+          <resourceMetaData>
+            <name/>
+            <configurationParameters>
+              <configurationParameter>
+                <name>UseMemoryIndex</name>
+                <type>Boolean</type>
+                <multiValued>false</multiValued>
+                <mandatory>true</mandatory>
+              </configurationParameter>
+              <configurationParameter>
+                <name>IndexDirectory</name>
+                <type>String</type>
+                <multiValued>false</multiValued>
+                <mandatory>true</mandatory>
+              </configurationParameter>
+            </configurationParameters>
+            <configurationParameterSettings>
+              <nameValuePair>
+                <name>UseMemoryIndex</name>
+                <value>
+                  <boolean>true</boolean>
+                </value>
+              </nameValuePair>
+              <nameValuePair>
+                <name>IndexDirectory</name>
+                <value>
+                  <string>org/apache/ctakes/dictionary/lookup/drug_index</string>
+                </value>
+              </nameValuePair>
+            </configurationParameterSettings>
+          </resourceMetaData>
+        </configurableDataResourceSpecifier>
+        <implementationName>org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl</implementationName>
+      </externalResource>
+    </externalResources>
+    <externalResourceBindings>
+      <externalResourceBinding>
+        <key>LookupDescriptor</key>
+        <resourceName>LookupDescriptorFile</resourceName>
+      </externalResourceBinding>
+      <externalResourceBinding>
+        <key>RxnormIndexReader</key>
+        <resourceName>RxnormIndex</resourceName>
+      </externalResourceBinding>
+    </externalResourceBindings>
+  </resourceManagerConfiguration>
+</taeDescription>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml Tue Dec 18 15:49:41 2012
@@ -112,7 +112,7 @@
           <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation</type>
         </inputs>
         <outputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.lookup.type.NamedEntity</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.lookup.type.NamedEntity</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml Tue Dec 18 15:49:41 2012
@@ -1,142 +1,122 @@
-<?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="DrugMentionAnnotator">
-      <import location="DrugMentionAnnotator.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="Chunker">
-      <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="TokenizerAnnotator">
-      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
-      <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="StatusAnnotator">
-      <import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.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="DictionaryLookupAnnotator">
-      <import location="DictionaryLookupAnnotator.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="DrugLookupWindowAnnotator">
-      <import location="DrugLookupWindowAnnotator.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="SimpleSegmentAnnotator">
-      <import location="../../../ctakes-core/desc/analysis_engine/SimpleSegmentAnnotator.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="LvgAnnotator">
-      <import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="POSTagger">
-      <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
-    </delegateAnalysisEngine>
-  </delegateAnalysisEngineSpecifiers>
-  <analysisEngineMetaData>
-    <name>AggregatePlaintextProcessor</name>
-    <description>Runs the complete pipeline for annotating clinical documents in plain text format.</description>
-    <version/>
-    <vendor/>
-    <configurationParameters searchStrategy="language_fallback">
-      <configurationParameter>
-        <name>SegmentID</name>
-        <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>edu.mayo.bmi.uima.chunker.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>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>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/>
-        <languagesSupported/>
-      </capability>
-    </capabilities>
-    <operationalProperties>
-      <modifiesCas>true</modifiesCas>
-      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
-      <outputsNewCASes>false</outputsNewCASes>
-    </operationalProperties>
-  </analysisEngineMetaData>
-  <resourceManagerConfiguration/>
-</analysisEngineDescription>
+<?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 location="DrugMentionAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="Chunker">
+      <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="TokenizerAnnotator">
+      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
+      <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="StatusAnnotator">
+      <import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.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="DictionaryLookupAnnotator">
+      <import location="DictionaryLookupAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="DrugLookupWindowAnnotator">
+      <import location="DrugLookupWindowAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="SimpleSegmentAnnotator">
+      <import location="../../../ctakes-core/desc/analysis_engine/SimpleSegmentAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="LvgAnnotator">
+      <import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="POSTagger">
+      <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
+    </delegateAnalysisEngine>
+  </delegateAnalysisEngineSpecifiers>
+  <analysisEngineMetaData>
+    <name>AggregatePlaintextProcessor</name>
+    <description>Runs the complete pipeline for annotating clinical documents in plain text format.</description>
+    <version/>
+    <vendor/>
+    <configurationParameters searchStrategy="language_fallback">
+      <configurationParameter>
+        <name>SegmentID</name>
+        <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>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>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/>
+        <languagesSupported/>
+      </capability>
+    </capabilities>
+    <operationalProperties>
+      <modifiesCas>true</modifiesCas>
+      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+      <outputsNewCASes>false</outputsNewCASes>
+    </operationalProperties>
+  </analysisEngineMetaData>
+  <resourceManagerConfiguration/>
+</analysisEngineDescription>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcessor.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcessor.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcessor.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcessor.xml Tue Dec 18 15:49:41 2012
@@ -90,7 +90,7 @@
       <nameValuePair>
         <name>ChunkCreatorClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.chunker.PhraseTypeChunkCreator</string>
+          <string>org.apache.ctakes.chunker.ae.PhraseTypeChunkCreator</string>
         </value>
       </nameValuePair>
     </configurationParameterSettings>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml Tue Dec 18 15:49:41 2012
@@ -1,24 +1,4 @@
 <?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>
@@ -67,7 +47,7 @@
       <nameValuePair>
         <name>destDrugObjClass</name>
         <value>
-          <string>edu.mayo.bmi.uima.lookup.type.DrugLookupWindowAnnotation</string>
+          <string>org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation</string>
         </value>
       </nameValuePair>
       <nameValuePair>
@@ -93,16 +73,16 @@
     </configurationParameterSettings>
     <typeSystemDescription>
       <imports>
-        <import location="../type_system/NERTypeSystem.xml"/>
+        <import name="org.apache.ctakes.drugner.types.Typesystem"/>
       </imports>
       <types>
         <typeDescription>
-          <name>edu.mayo.bmi.uima.common.types.CopySrcAnnotation</name>
+          <name>org.apache.ctakes.common.types.CopySrcAnnotation</name>
           <description>Used for testing CopyAnnotator.</description>
           <supertypeName>uima.tcas.Annotation</supertypeName>
         </typeDescription>
         <typeDescription>
-          <name>edu.mayo.bmi.uima.common.types.CopyDestAnnotation</name>
+          <name>org.apache.ctakes.common.types.CopyDestAnnotation</name>
           <description>Used for testing CopyAnnotator.</description>
           <supertypeName>uima.tcas.Annotation</supertypeName>
         </typeDescription>
@@ -118,7 +98,7 @@
         </inputs>
         <outputs>
           <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.lookup.type.DrugLookupWindowAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugLookupWindowAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugLookupWindowAnnotator.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugLookupWindowAnnotator.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/DrugLookupWindowAnnotator.xml Tue Dec 18 15:49:41 2012
@@ -52,7 +52,7 @@
     <capabilities>
       <capability>
         <inputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.cdt.types.ProblemListAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.cdt.types.ProblemListAnnotation</type>
           <type allAnnotatorFeatures="true">uima.tt.PNPAnnotation</type>
           <type allAnnotatorFeatures="true">uima.tt.NPSAnnotation</type>
           <type allAnnotatorFeatures="true">uima.tt.NPPAnnotation</type>
@@ -60,11 +60,11 @@
           <type allAnnotatorFeatures="true">uima.tt.NPAnnotation</type>
           <type allAnnotatorFeatures="true">uima.tt.CNPAnnotation</type>
           <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Segment</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.chunker.type.NP</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.chunker.type.NP</type>
         </inputs>
         <outputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.lookup.types.LookupWindowAnnotation</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.lookup.type.DrugLookupWindowAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml Tue Dec 18 15:49:41 2012
@@ -22,7 +22,7 @@
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
 <primitive>true</primitive>
-<annotatorImplementationName>edu.mayo.bmi.uima.ctx.ae.ContextAnnotator</annotatorImplementationName>
+<annotatorImplementationName>org.apache.ctakes.ctx.ae.ContextAnnotator</annotatorImplementationName>
 <analysisEngineMetaData>
 <name>NegationAnnotator</name>
 <description>Changes in 1.1:
@@ -121,11 +121,11 @@
 <capabilities>
 <capability>
 <inputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.common.types.NamedEntityAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.common.types.NamedEntityAnnotation</type>
 <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
 </inputs>
 <outputs>
-<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.ctx.types.ContextAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.ctx.types.ContextAnnotation</type>
 </outputs>
 <languagesSupported/>
 </capability>
@@ -139,7 +139,7 @@
 <externalResourceDependency>
 <key>BoundaryData</key>
 <description>the file resource handle that will be used in the annotator</description>
-<interfaceName>edu.mayo.bmi.uima.common.resource.FileResource</interfaceName>
+<interfaceName>org.apache.ctakes.common.resource.FileResource</interfaceName>
 <optional>false</optional>
 </externalResourceDependency>
 </externalResourceDependencies>
@@ -151,7 +151,7 @@
 <fileResourceSpecifier>
 <fileUrl>file:org/apache/ctakes/drugner/cni/negation/boundaryData.txt</fileUrl>
 </fileResourceSpecifier>
-<implementationName>edu.mayo.bmi.uima.common.resource.FileResourceImpl</implementationName>
+<implementationName>org.apache.ctakes.common.resource.FileResourceImpl</implementationName>
 </externalResource>
 </externalResources>
 <externalResourceBindings>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/cas_consumer/DrugNERCasConsumer.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/cas_consumer/DrugNERCasConsumer.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/cas_consumer/DrugNERCasConsumer.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/cas_consumer/DrugNERCasConsumer.xml Tue Dec 18 15:49:41 2012
@@ -85,10 +85,6 @@
       </nameValuePair>
     </configurationParameterSettings>
     <typeSystemDescription>
-      <imports>
-        <import location="../type_system/NERTypeSystem.xml"/>
-        <import location="../../../ctakes-clinical-pipeline/desc/CDAToTextTypeSystem.xml"/>
-      </imports>
     </typeSystemDescription>
     <typePriorities/>
     <fsIndexCollection/>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml Tue Dec 18 15:49:41 2012
@@ -1,78 +1,58 @@
-<?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>/path_to_your_workspace/ctakes-drug-ner/data</string>
-</value>
-</nameValuePair>
-</configurationParameterSettings>
-</collectionIterator>
-</collectionReader>
-<casProcessors casPoolSize="3" processingUnitThreadCount="1">
-<casProcessor deployment="integrated" name="AggregateTAE">
-<descriptor>
-<import location="../analysis_engine/DrugAggregateCDAProcessor.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="XCAS Writer CAS Consumer">
-<descriptor>
-<import location="../../../ctakes-core/desc/cas_consumer/XCasWriterCasConsumer.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>OutputDirectory</name>
-<value>
-<string>data</string>
-</value>
-</nameValuePair>
-</configurationParameterSettings>
-</casProcessor>
-</casProcessors>
-<cpeConfig>
-<numToProcess>-1</numToProcess>
-<deployAs>immediate</deployAs>
-<checkpoint batch="0" time="300000ms"/>
-<timerImpl></timerImpl>
-</cpeConfig>
-</cpeDescription>
+<?xml version="1.0" encoding="UTF-8"?>
+<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>data</string>
+                    </value>
+                </nameValuePair>
+            </configurationParameterSettings>
+        </collectionIterator>
+    </collectionReader>
+    <casProcessors casPoolSize="3" processingUnitThreadCount="1">
+        <casProcessor deployment="integrated" name="AggregateTAE">
+            <descriptor>
+                <import location="../analysis_engine/DrugAggregateCDAProcessor.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>data/output</string>
+                    </value>
+                </nameValuePair>
+            </configurationParameterSettings>
+        </casProcessor>
+    </casProcessors>
+    <cpeConfig>
+        <numToProcess>-1</numToProcess>
+        <deployAs>immediate</deployAs>
+        <checkpoint batch="0" time="300000ms"/>
+        <timerImpl/>
+    </cpeConfig>
+</cpeDescription>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml Tue Dec 18 15:49:41 2012
@@ -1,24 +1,4 @@
 <?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>
@@ -48,9 +28,9 @@
             </errorHandling>
             <checkpoint batch="10000" time="1000ms"/>
         </casProcessor>
-        <casProcessor deployment="integrated" name="XCAS Writer CAS Consumer">
+        <casProcessor deployment="integrated" name="Write CAS to XML file">
             <descriptor>
-                <import location="../../../ctakes-core/desc/cas_consumer/XCasWriterCasConsumer.xml"/>
+                <import location="../../../ctakes-core/desc/cas_consumer/FileWriterCasConsumer.xml"/>
             </descriptor>
             <deploymentParameters/>
             <errorHandling>
@@ -61,7 +41,7 @@
             <checkpoint batch="10000" time="1000ms"/>
             <configurationParameterSettings>
                 <nameValuePair>
-                    <name>OutputDirectory</name>
+                    <name>outputDir</name>
                     <value>
                         <string>data/output</string>
                     </value>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/pom.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/pom.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/pom.xml Tue Dec 18 15:49:41 2012
@@ -85,6 +85,14 @@
 			<scope>system</scope>
 			<systemPath>${project.basedir}/../ctakes-core/lib/OpenAI_FSM.jar</systemPath>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-chunker</artifactId>
+		</dependency>
+				<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-lvg</artifactId>
+		</dependency>
 	</dependencies>
 	
 	<build>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/lookup/LookupDesc_DrugNER.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/lookup/LookupDesc_DrugNER.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/lookup/LookupDesc_DrugNER.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/lookup/LookupDesc_DrugNER.xml Tue Dec 18 15:49:41 2012
@@ -132,7 +132,7 @@
 				<properties>
 					<property key="textMetaFields" value="preferred_designation|other_designation"/>
 					<property key="maxPermutationLevel" value="3"/>
-					<property key="windowAnnotations" value="edu.mayo.bmi.uima.lookup.type.DrugLookupWindowAnnotation"/>
+					<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation"/>
 					<property key="exclusionTags" value="CC,CD,DT,EX,LS,MD,PDT,POS,PP,PP$,PRP,PRP$,RP,TO,WDT,WP,WPS,WRB"/> <!-- ohnlp ID# 3378705 -->
 				</properties>
 			</lookupInitializer>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml Tue Dec 18 15:49:41 2012
@@ -327,7 +327,7 @@ Strongly encouraged to use bold text</de
       </features>
     </typeDescription>
     <typeDescription>
-      <name>edu.mayo.bmi.uima.lookup.type.DrugLookupWindowAnnotation</name>
+      <name>org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation</name>
       <description>Similar to LookupWindowAnnotation however, these annotations are restricted to the segments/sections specified in the parameter - sectionOverrideSet - in DrugCNP2LookupWindow</description>
       <supertypeName>uima.tcas.Annotation</supertypeName>
     </typeDescription>

Added: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-ne-contexts/src/main/resources/org/apache/ctakes/necontexts/desc/NegationAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-ne-contexts/src/main/resources/org/apache/ctakes/necontexts/desc/NegationAnnotator.xml?rev=1423486&view=auto
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-ne-contexts/src/main/resources/org/apache/ctakes/necontexts/desc/NegationAnnotator.xml (added)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-ne-contexts/src/main/resources/org/apache/ctakes/necontexts/desc/NegationAnnotator.xml Tue Dec 18 15:49:41 2012
@@ -0,0 +1,160 @@
+<?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.necontexts.ContextAnnotator</annotatorImplementationName>
+<analysisEngineMetaData>
+<name>NegationAnnotator</name>
+<configurationParameters>
+<configurationParameter>
+<name>MaxLeftScopeSize</name>
+<description></description>
+<type>Integer</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+<configurationParameter>
+<name>MaxRightScopeSize</name>
+<description></description>
+<type>Integer</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+<configurationParameter>
+<name>ScopeOrder</name>
+<description></description>
+<type>String</type>
+<multiValued>true</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+<configurationParameter>
+<name>ContextAnalyzerClass</name>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+<configurationParameter>
+<name>ContextHitConsumerClass</name>
+<description></description>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+<configurationParameter>
+<name>WindowAnnotationClass</name>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+<configurationParameter>
+<name>FocusAnnotationClass</name>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+<configurationParameter>
+<name>ContextAnnotationClass</name>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+</configurationParameters>
+<configurationParameterSettings>
+<nameValuePair>
+<name>MaxLeftScopeSize</name>
+<value>
+<integer>7</integer>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>MaxRightScopeSize</name>
+<value>
+<integer>7</integer>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>ScopeOrder</name>
+<value>
+<array>
+<string>LEFT</string>
+<string>RIGHT</string>
+</array>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>ContextHitConsumerClass</name>
+<value>
+<string>org.apache.ctakes.necontexts.negation.NegationContextHitConsumer</string>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>WindowAnnotationClass</name>
+<value>
+<string>org.apache.ctakes.typesystem.type.textspan.Sentence</string>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>FocusAnnotationClass</name>
+<value>
+<string>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</string>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>ContextAnnotationClass</name>
+<value>
+<string>org.apache.ctakes.typesystem.type.syntax.BaseToken</string>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>ContextAnalyzerClass</name>
+<value>
+<string>org.apache.ctakes.necontexts.negation.NegationContextAnalyzer</string>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+<typeSystemDescription>
+<imports>
+</imports>
+</typeSystemDescription>
+<typePriorities/>
+<fsIndexCollection/>
+<capabilities>
+<capability>
+<inputs>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+</inputs>
+<outputs>
+<type allAnnotatorFeatures="true">org.apache.ctakes.necontexts.type.ContextAnnotation</type>
+</outputs>
+<languagesSupported/>
+</capability>
+</capabilities>
+<operationalProperties>
+<modifiesCas>true</modifiesCas>
+<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+<outputsNewCASes>false</outputsNewCASes>
+</operationalProperties>
+</analysisEngineMetaData>
+<resourceManagerConfiguration/>
+</taeDescription>

Propchange: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-ne-contexts/src/main/resources/org/apache/ctakes/necontexts/desc/NegationAnnotator.xml
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml Tue Dec 18 15:49:41 2012
@@ -32,7 +32,7 @@
 <configurationParameterSettings/>
 <typeSystemDescription>
 <imports>
-<import location="../type_system/PADSiteAndTerm.xml"/>
+<import name="org.apache.ctakes.padtermspotter.types.Typesystem"/>
 </imports>
 </typeSystemDescription>
 <typePriorities/>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml Tue Dec 18 15:49:41 2012
@@ -1,118 +1,98 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!--
-
-    Licensed to the Apache Software Foundation (ASF) under one
-    or more contributor license agreements.  See the NOTICE file
-    distributed with this work for additional information
-    regarding copyright ownership.  The ASF licenses this file
-    to you under the Apache License, Version 2.0 (the
-    "License"); you may not use this file except in compliance
-    with the License.  You may obtain a copy of the License at
-
-      http://www.apache.org/licenses/LICENSE-2.0
-
-    Unless required by applicable law or agreed to in writing,
-    software distributed under the License is distributed on an
-    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-    KIND, either express or implied.  See the License for the
-    specific language governing permissions and limitations
-    under the License.
-
--->
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
-<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
-<primitive>false</primitive>
-<delegateAnalysisEngineSpecifiers>
-<delegateAnalysisEngine key="PAD_Hit">
-<import location="PAD_Hit.xml"/>
-</delegateAnalysisEngine>
-<delegateAnalysisEngine key="DxStatusAnnotator">
-<import location="DxStatusAnnotator.xml"/>
-</delegateAnalysisEngine>
-<delegateAnalysisEngine key="SimpleSegmentAnnotator">
-<import location="../../../ctakes-core/desc/analysis_engine/SimpleSegmentAnnotator.xml"/>
-</delegateAnalysisEngine>
-<delegateAnalysisEngine key="SubSectionBoundaryAnnotator">
-<import location="SubSectionBoundaryAnnotator.xml"/>
-</delegateAnalysisEngine>
-<delegateAnalysisEngine key="Chunker">
-<import location="../../../ctakes-chunker/desc/Chunker.xml"/>
-</delegateAnalysisEngine>
-<delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
-<import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.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="NegationDxAnnotator">
-<import location="NegationDxAnnotator.xml"/>
-</delegateAnalysisEngine>
-<delegateAnalysisEngine key="POSTagger">
-<import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
-</delegateAnalysisEngine>
-<delegateAnalysisEngine key="Radiology_DictionaryLookupCSVAnnotator">
-<import location="Radiology_DictionaryLookupCSVAnnotator.xml"/>
-</delegateAnalysisEngine>
-</delegateAnalysisEngineSpecifiers>
-<analysisEngineMetaData>
-<name>PAD_term_spotter</name>
-<description>Term spotter for Peripheral Artery Disease (PAD) </description>
-<version>1.0</version>
-<vendor>Mayo Clinic</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>
-</configurationParameters>
-<configurationParameterSettings>
-<nameValuePair>
-<name>ChunkCreatorClass</name>
-<value>
-<string>edu.mayo.bmi.uima.chunker.PhraseTypeChunkCreator</string>
-</value>
-</nameValuePair>
-</configurationParameterSettings>
-<flowConstraints>
-<fixedFlow>
-<node>SimpleSegmentAnnotator</node>
-<node>TokenizerAnnotator</node>
-<node>SentenceDetectorAnnotator</node>
-<node>SubSectionBoundaryAnnotator</node>
-<node>ContextDependentTokenizerAnnotator</node>
-<node>POSTagger</node>
-<node>Chunker</node>
-<node>Radiology_DictionaryLookupCSVAnnotator</node>
-<node>NegationAnnotator</node>
-<node>PAD_Hit</node>
-<node>DxStatusAnnotator</node>
-<node>NegationDxAnnotator</node>
-</fixedFlow>
-</flowConstraints>
-<fsIndexCollection/>
-<capabilities>
-<capability>
-<inputs/>
-<outputs/>
-<languagesSupported/>
-</capability>
-</capabilities>
-<operationalProperties>
-<modifiesCas>true</modifiesCas>
-<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
-<outputsNewCASes>false</outputsNewCASes>
-</operationalProperties>
-</analysisEngineMetaData>
-<resourceManagerConfiguration/>
+  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+  <primitive>false</primitive>
+  <delegateAnalysisEngineSpecifiers>
+    <delegateAnalysisEngine key="SubSectionBoundaryAnnotator">
+      <import location="SubSectionBoundaryAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="Chunker">
+      <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="TokenizerAnnotator">
+      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
+      <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="NegationDxAnnotator">
+      <import location="NegationDxAnnotator.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="Radiology_DictionaryLookupCSVAnnotator">
+      <import location="Radiology_DictionaryLookupCSVAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="PAD_Hit">
+      <import location="PAD_Hit.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="DxStatusAnnotator">
+      <import location="DxStatusAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="SimpleSegmentAnnotator">
+      <import location="../../../ctakes-core/desc/analysis_engine/SimpleSegmentAnnotator.xml"/>
+    </delegateAnalysisEngine>
+    <delegateAnalysisEngine key="POSTagger">
+      <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
+    </delegateAnalysisEngine>
+  </delegateAnalysisEngineSpecifiers>
+  <analysisEngineMetaData>
+    <name>PAD_term_spotter</name>
+    <description>Term spotter for Peripheral Artery Disease (PAD)</description>
+    <version>1.0</version>
+    <vendor>Mayo Clinic</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>
+    </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>SubSectionBoundaryAnnotator</node>
+        <node>ContextDependentTokenizerAnnotator</node>
+        <node>POSTagger</node>
+        <node>Chunker</node>
+        <node>Radiology_DictionaryLookupCSVAnnotator</node>
+        <node>NegationAnnotator</node>
+        <node>PAD_Hit</node>
+        <node>DxStatusAnnotator</node>
+        <node>NegationDxAnnotator</node>
+      </fixedFlow>
+    </flowConstraints>
+    <fsIndexCollection/>
+    <capabilities>
+      <capability>
+        <inputs/>
+        <outputs/>
+        <languagesSupported/>
+      </capability>
+    </capabilities>
+    <operationalProperties>
+      <modifiesCas>true</modifiesCas>
+      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+      <outputsNewCASes>false</outputsNewCASes>
+    </operationalProperties>
+  </analysisEngineMetaData>
+  <resourceManagerConfiguration/>
 </taeDescription>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/cas_consumer/PADOffsetsRecordConsumer.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/cas_consumer/PADOffsetsRecordConsumer.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/cas_consumer/PADOffsetsRecordConsumer.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/cas_consumer/PADOffsetsRecordConsumer.xml Tue Dec 18 15:49:41 2012
@@ -56,9 +56,6 @@
 </nameValuePair>
 </configurationParameterSettings>
 <typeSystemDescription>
-<imports>
-<import location="../type_system/PADSiteAndTerm.xml"/>
-</imports>
 </typeSystemDescription>
 <capabilities/>
 <operationalProperties>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/collection_processing_engine/Radiology_sample.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/collection_processing_engine/Radiology_sample.xml?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/collection_processing_engine/Radiology_sample.xml (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/desc/collection_processing_engine/Radiology_sample.xml Tue Dec 18 15:49:41 2012
@@ -1,108 +1,88 @@
 <?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="../collection_reader/RadiologyRecordsCollectionReader.xml"/>
-</descriptor>
-<configurationParameterSettings>
-<nameValuePair>
-<name>InputFileName</name>
-<value>
-<string>{inst-root-dir}/PAD term spotter/data/SampleInputRadiologyNotes.txt</string>
-</value>
-</nameValuePair>
-<nameValuePair>
-<name>CommentString</name>
-<value>
-<string>CLINIC</string>
-</value>
-</nameValuePair>
-<nameValuePair>
-<name>IdDelimeter</name>
-<value>
-<string>`</string>
-</value>
-</nameValuePair>
-<nameValuePair>
-<name>ColumnCount</name>
-<value>
-<integer>15</integer>
-</value>
-</nameValuePair>
-<nameValuePair>
-<name>FilterExamTypes</name>
-<value>
-<string>{inst-root-dir}/PAD term spotter/resources/lookup/radiology/examsForPAD.csv</string>
-</value>
-</nameValuePair>
-<nameValuePair>
-<name>FilterExamColumnNumber</name>
-<value>
-<integer>11</integer>
-</value>
-</nameValuePair>
-</configurationParameterSettings>
-</collectionIterator>
-</collectionReader>
-<casProcessors casPoolSize="3" processingUnitThreadCount="1">
-<casProcessor deployment="integrated" name="PAD_term_spotter">
-<descriptor>
-<import location="../analysis_engine/Radiology_TermSpotterAnnotatorTAE.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="PADOffSetRecord">
-<descriptor>
-<import location="../cas_consumer/PADOffsetsRecordConsumer.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>outputFileName</name>
-<value>
-<string>{inst-root-dir}/PAD term spotter/output/Sample_PAD_record_level.txt</string>
-</value>
-</nameValuePair>
-</configurationParameterSettings>
-</casProcessor>
-</casProcessors>
-<cpeConfig>
-<numToProcess>-1</numToProcess>
-<deployAs>immediate</deployAs>
-<checkpoint batch="0" time="300000ms"/>
-<timerImpl></timerImpl>
-</cpeConfig>
+    <collectionReader>
+        <collectionIterator>
+            <descriptor>
+                <import location="../collection_reader/RadiologyRecordsCollectionReader.xml"/>
+            </descriptor>
+            <configurationParameterSettings>
+                <nameValuePair>
+                    <name>InputFileName</name>
+                    <value>
+                        <string>data/SampleInputRadiologyNotes.txt</string>
+                    </value>
+                </nameValuePair>
+                <nameValuePair>
+                    <name>CommentString</name>
+                    <value>
+                        <string>CLINIC</string>
+                    </value>
+                </nameValuePair>
+                <nameValuePair>
+                    <name>IdDelimeter</name>
+                    <value>
+                        <string>`</string>
+                    </value>
+                </nameValuePair>
+                <nameValuePair>
+                    <name>ColumnCount</name>
+                    <value>
+                        <integer>15</integer>
+                    </value>
+                </nameValuePair>
+                <nameValuePair>
+                    <name>FilterExamTypes</name>
+                    <value>
+                        <string>src/main/resources/org/apache/ctakes/padtermspotter/lookup/radiology/examsForPAD.csv</string>
+                    </value>
+                </nameValuePair>
+                <nameValuePair>
+                    <name>FilterExamColumnNumber</name>
+                    <value>
+                        <integer>11</integer>
+                    </value>
+                </nameValuePair>
+            </configurationParameterSettings>
+        </collectionIterator>
+    </collectionReader>
+    <casProcessors casPoolSize="3" processingUnitThreadCount="1">
+        <casProcessor deployment="integrated" name="PAD_term_spotter">
+            <descriptor>
+                <import location="../analysis_engine/Radiology_TermSpotterAnnotatorTAE.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="PADOffSetRecord">
+            <descriptor>
+                <import location="../cas_consumer/PADOffsetsRecordConsumer.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>outputFileName</name>
+                    <value>
+                        <string>output\PAD_output.txt</string>
+                    </value>
+                </nameValuePair>
+            </configurationParameterSettings>
+        </casProcessor>
+    </casProcessors>
+    <cpeConfig>
+        <numToProcess>-1</numToProcess>
+        <deployAs>immediate</deployAs>
+        <checkpoint batch="0" time="300000ms"/>
+        <timerImpl/>
+    </cpeConfig>
 </cpeDescription>

Modified: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/launch/UIMA CAS Visual Debugger (PAD Term Spotter).launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/launch/UIMA%20CAS%20Visual%20Debugger%20%28PAD%20Term%20Spotter%29.launch?rev=1423486&r1=1423485&r2=1423486&view=diff
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/launch/UIMA CAS Visual Debugger (PAD Term Spotter).launch (original)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/launch/UIMA CAS Visual Debugger (PAD Term Spotter).launch Tue Dec 18 15:49:41 2012
@@ -10,9 +10,9 @@
 <stringAttribute key="org.eclipse.debug.ui.target_debug_perspective" value="perspective_default"/>
 <stringAttribute key="org.eclipse.debug.ui.target_run_perspective" value="perspective_default"/>
 <stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.m2e.launchconfig.classpathProvider"/>
-<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="com.ibm.uima.annot_view.Gladis"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.cvd.CVD"/>
 <stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-pad-term-spotter"/>
 <stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
 <stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="&quot;-Djava.util.logging.config.file=${env_var:UIMA_HOME}/Logger.properties&quot;  -Xms700M -Xmx700M"/>
-<stringAttribute key="org.eclipse.jdt.launching.WORKING_DIRECTORY" value="${workspace_loc:core}"/>
+<stringAttribute key="org.eclipse.jdt.launching.WORKING_DIRECTORY" value="${workspace_loc:ctakes-core}"/>
 </launchConfiguration>

Added: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/launch/UIMA_CPE_GUI--PAD_term_spotter.launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/launch/UIMA_CPE_GUI--PAD_term_spotter.launch?rev=1423486&view=auto
==============================================================================
--- incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/launch/UIMA_CPE_GUI--PAD_term_spotter.launch (added)
+++ incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/launch/UIMA_CPE_GUI--PAD_term_spotter.launch Tue Dec 18 15:49:41 2012
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
+<listEntry value="/ctakes-pad-term-spotter"/>
+</listAttribute>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+<listEntry value="4"/>
+</listAttribute>
+<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
+<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.m2e.launchconfig.classpathProvider"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.cpm.CpmFrame"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-pad-term-spotter"/>
+<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
+<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xms500M -Xmx500M"/>
+</launchConfiguration>

Propchange: incubator/ctakes/branches/ctakes-3.0.0-incubating/ctakes-pad-term-spotter/launch/UIMA_CPE_GUI--PAD_term_spotter.launch
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