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From spmurph...@apache.org
Subject svn commit: r1418056 - in /incubator/ctakes/trunk/ctakes-drug-ner: ./ desc/analysis_engine/ desc/collection_processing_engine/ resources/launch/ src/main/java/org/apache/ctakes/drugner/ae/ src/main/resources/org/apache/ctakes/drugner/lookup/ src/main/r...
Date Thu, 06 Dec 2012 20:33:07 GMT
Author: spmurphy50
Date: Thu Dec  6 20:33:04 2012
New Revision: 1418056

URL: http://svn.apache.org/viewvc?rev=1418056&view=rev
Log:
Fix CTAKES-101

Added:
    incubator/ctakes/trunk/ctakes-drug-ner/resources/launch/CPE cTAKES (Drug NER).launch 
 (with props)
Modified:
    incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml
    incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
    incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml
    incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcessor.xml
    incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml
    incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugLookupWindowAnnotator.xml
    incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml
    incubator/ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml
    incubator/ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml
    incubator/ctakes/trunk/ctakes-drug-ner/pom.xml
    incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/CopyDrugAnnotator.java
    incubator/ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/lookup/LookupDesc_DrugNER.xml
    incubator/ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml

Modified: incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml?rev=1418056&r1=1418055&r2=1418056&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml
(original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml
Thu Dec  6 20:33:04 2012
@@ -40,7 +40,7 @@
           <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/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml?rev=1418056&r1=1418055&r2=1418056&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
(original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
Thu Dec  6 20:33:04 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/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml?rev=1418056&r1=1418055&r2=1418056&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml
(original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml
Thu Dec  6 20:33:04 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/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcessor.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcessor.xml?rev=1418056&r1=1418055&r2=1418056&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcessor.xml
(original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcessor.xml
Thu Dec  6 20:33:04 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/trunk/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml?rev=1418056&r1=1418055&r2=1418056&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml Thu
Dec  6 20:33:04 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/trunk/ctakes-drug-ner/desc/analysis_engine/DrugLookupWindowAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugLookupWindowAnnotator.xml?rev=1418056&r1=1418055&r2=1418056&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugLookupWindowAnnotator.xml
(original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugLookupWindowAnnotator.xml
Thu Dec  6 20:33:04 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/trunk/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml?rev=1418056&r1=1418055&r2=1418056&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/NegationDxAnnotator.xml Thu
Dec  6 20:33:04 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/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml?rev=1418056&r1=1418055&r2=1418056&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml
(original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml
Thu Dec  6 20:33:04 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/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml?rev=1418056&r1=1418055&r2=1418056&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml
(original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml
Thu Dec  6 20:33:04 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/trunk/ctakes-drug-ner/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/pom.xml?rev=1418056&r1=1418055&r2=1418056&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/pom.xml (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/pom.xml Thu Dec  6 20:33:04 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>

Added: incubator/ctakes/trunk/ctakes-drug-ner/resources/launch/CPE cTAKES (Drug NER).launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/resources/launch/CPE%20cTAKES%20%28Drug%20NER%29.launch?rev=1418056&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/resources/launch/CPE cTAKES (Drug NER).launch (added)
+++ incubator/ctakes/trunk/ctakes-drug-ner/resources/launch/CPE cTAKES (Drug NER).launch Thu
Dec  6 20:33:04 2012
@@ -0,0 +1,17 @@
+<?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-drug-ner"/>
+</listAttribute>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+<listEntry value="4"/>
+</listAttribute>
+<listAttribute key="org.eclipse.debug.ui.favoriteGroups">
+<listEntry value="org.eclipse.debug.ui.launchGroup.run"/>
+</listAttribute>
+<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-drug-ner"/>
+<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
+<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xms1024M -Xmx2048M"/>
+</launchConfiguration>

Propchange: incubator/ctakes/trunk/ctakes-drug-ner/resources/launch/CPE cTAKES (Drug NER).launch
------------------------------------------------------------------------------
    svn:mime-type = text/plain

Modified: incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/CopyDrugAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/CopyDrugAnnotator.java?rev=1418056&r1=1418055&r2=1418056&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/CopyDrugAnnotator.java
(original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/CopyDrugAnnotator.java
Thu Dec  6 20:33:04 2012
@@ -175,7 +175,7 @@ public class CopyDrugAnnotator extends J
 					Iterator lookupWindows = FSUtil.getAnnotationsInSpanIterator(jcas, org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation.type,
segment.getBegin(), segment.getEnd());
 					while (lookupWindows.hasNext()){
 						org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation lookup = (org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation)
lookupWindows.next();
-						edu.mayo.bmi.uima.lookup.type.DrugLookupWindowAnnotation drugLookup = new edu.mayo.bmi.uima.lookup.type.DrugLookupWindowAnnotation(jcas,
lookup.getBegin(), lookup.getEnd());
+						org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation drugLookup =
new org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation(jcas, lookup.getBegin(),
lookup.getEnd()); //Reorganized paths in 3.0 SPM
 						drugLookup.addToIndexes();
 					}
 				}

Modified: incubator/ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/lookup/LookupDesc_DrugNER.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/lookup/LookupDesc_DrugNER.xml?rev=1418056&r1=1418055&r2=1418056&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/lookup/LookupDesc_DrugNER.xml
(original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/lookup/LookupDesc_DrugNER.xml
Thu Dec  6 20:33:04 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/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml?rev=1418056&r1=1418055&r2=1418056&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml
(original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml
Thu Dec  6 20:33:04 2012
@@ -1,31 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!--
-
-    Licensed to the Apache Software Foundation (ASF) under one
-    or more contributor license agreements.  See the NOTICE file
-    distributed with this work for additional information
-    regarding copyright ownership.  The ASF licenses this file
-    to you under the Apache License, Version 2.0 (the
-    "License"); you may not use this file except in compliance
-    with the License.  You may obtain a copy of the License at
-
-      http://www.apache.org/licenses/LICENSE-2.0
-
-    Unless required by applicable law or agreed to in writing,
-    software distributed under the License is distributed on an
-    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-    KIND, either express or implied.  See the License for the
-    specific language governing permissions and limitations
-    under the License.
-
--->
 <typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <name>org.apache.ctakes.drugner.types.TypeSystem</name>
   <description/>
   <version>1.0</version>
   <vendor>Mayo Clinic</vendor>
-  <imports>
-  </imports>
   <types>
     <typeDescription>
       <name>org.apache.ctakes.drugner.type.FrequencyAnnotation</name>
@@ -327,7 +305,7 @@ 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>



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