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From chen...@apache.org
Subject svn commit: r1390134 [1/2] - in /incubator/ctakes/trunk: ./ ctakes-assertion/ ctakes-assertion/desc/ ctakes-assertion/lib/ ctakes-assertion/metadata/ ctakes-assertion/src/main/java/edu/mayo/bmi/attributes/ ctakes-assertion/src/main/java/edu/mayo/bmi/ui...
Date Tue, 25 Sep 2012 21:06:20 GMT
Author: chenpei
Date: Tue Sep 25 21:06:18 2012
New Revision: 1390134

URL: http://svn.apache.org/viewvc?rev=1390134&view=rev
Log:
assertion module was not in trunk before... Adding to trunk applying the same namespace changes.
adding the dependencies to the pom.xml and pull it off maven central instead of local /lib where possible.

Added:
    incubator/ctakes/trunk/ctakes-assertion/pom.xml
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java
      - copied, changed from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/edu/mayo/bmi/uima/attributes/GenericAttributeAnalysisEngine.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/SubjectAttributeAnalysisEngine.java
      - copied, changed from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/edu/mayo/bmi/uima/attributes/SubjectAttributeAnalysisEngine.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/generic/
      - copied from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/edu/mayo/bmi/attributes/generic/
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/
      - copied from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/edu/mayo/bmi/attributes/subject/
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java
      - copied, changed from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/AssertionAnalysisEngine.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/CasIndexer.java
      - copied, changed from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/CasIndexer.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptConverterAnalysisEngine.java
      - copied, changed from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/ConceptConverterAnalysisEngine.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptLookup.java
      - copied, changed from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/ConceptLookup.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConvertXMIAssertionsToi2b2Format.java
      - copied, changed from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/ConvertXMIAssertionsToi2b2Format.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/Converti2b2AnnotationsToCTAKES.java
      - copied, changed from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/Converti2b2AnnotationsToCTAKES.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/
      - copied from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/cleartk/
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/
      - copied from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/i2b2/api/ctakes/
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/
      - copied from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/types/
Removed:
    incubator/ctakes/trunk/ctakes-assertion/lib/cleartk-eval-0.8.1.jar
    incubator/ctakes/trunk/ctakes-assertion/lib/cleartk-examples-0.6.0.jar
    incubator/ctakes/trunk/ctakes-assertion/lib/cleartk-ml-1.0.1.jar
    incubator/ctakes/trunk/ctakes-assertion/lib/cleartk-ml-opennlp-maxent-1.0.2.jar
    incubator/ctakes/trunk/ctakes-assertion/lib/cleartk-test-util-1.0.1.jar
    incubator/ctakes/trunk/ctakes-assertion/lib/cleartk-type-system-1.0.0.jar
    incubator/ctakes/trunk/ctakes-assertion/lib/cleartk-util-0.8.1.jar
    incubator/ctakes/trunk/ctakes-assertion/lib/commons-cli-1.2.jar
    incubator/ctakes/trunk/ctakes-assertion/lib/commons-lang-2.6.jar
    incubator/ctakes/trunk/ctakes-assertion/lib/jackson-core-asl-1.5.0.jar
    incubator/ctakes/trunk/ctakes-assertion/lib/jackson-mapper-asl-1.5.0.jar
    incubator/ctakes/trunk/ctakes-assertion/lib/opennlp-maxent-3.0.2-incubating.jar
    incubator/ctakes/trunk/ctakes-assertion/lib/sbinary_2.9.0-0.4.0.jar
    incubator/ctakes/trunk/ctakes-assertion/lib/scala-library-2.9.0.jar
    incubator/ctakes/trunk/ctakes-assertion/lib/uimafit-1.2.0.jar
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/edu/mayo/bmi/attributes/
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/edu/mayo/bmi/uima/attributes/
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/i2b2/api/
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/types/
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/
Modified:
    incubator/ctakes/trunk/ctakes-assertion/.classpath
    incubator/ctakes/trunk/ctakes-assertion/.project
    incubator/ctakes/trunk/ctakes-assertion/desc/AssertionMiniPipelineAnalysisEngine.xml
    incubator/ctakes/trunk/ctakes-assertion/desc/GenericAttributeAnalysisEngine.xml
    incubator/ctakes/trunk/ctakes-assertion/desc/SubjectAttributeAnalysisEngine.xml
    incubator/ctakes/trunk/ctakes-assertion/desc/assertionAnalysisEngine.xml
    incubator/ctakes/trunk/ctakes-assertion/desc/conceptConverterAnalysisEngine.xml
    incubator/ctakes/trunk/ctakes-assertion/desc/medfactsTypeSystem.xml
    incubator/ctakes/trunk/ctakes-assertion/metadata/install.xml
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/generic/GenericAttributeClassifier.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/CharacterOffsetToLineTokenConverterCtakesImpl.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/ConstraintConstructor.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/ConstraintConstructorFindContainedBy.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/ConstraintConstructorFindContainedWithin.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/SingleDocumentProcessorCtakes.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Assertion.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Assertion_Type.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Concept.java
    incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Concept_Type.java
    incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml
    incubator/ctakes/trunk/ctakes-clinical-pipeline/resources/launch/UIMA_CVD--clinical_documents_pipeline.launch
    incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyUtility.java
    incubator/ctakes/trunk/pom.xml

Modified: incubator/ctakes/trunk/ctakes-assertion/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/.classpath?rev=1390134&r1=1390133&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-assertion/.classpath Tue Sep 25 21:06:18 2012
@@ -1,30 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="conf"/>
-	<classpathentry kind="src" path="resources"/>
-	<classpathentry kind="lib" path="lib/commons-cli-1.2.jar"/>
-	<classpathentry kind="lib" path="lib/commons-lang-2.6.jar"/>
-	<classpathentry kind="lib" path="lib/jackson-core-asl-1.5.0.jar"/>
-	<classpathentry kind="lib" path="lib/jackson-mapper-asl-1.5.0.jar"/>
-	<classpathentry kind="lib" path="lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar"/>
-	<classpathentry kind="lib" path="lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar"/>
-	<classpathentry kind="lib" path="lib/med-facts-i2b2-1.2-SNAPSHOT.jar"/>
-	<classpathentry kind="lib" path="lib/med-facts-zoner-1.1.jar"/>
-	<classpathentry kind="lib" path="lib/sbinary_2.9.0-0.4.0.jar"/>
-	<classpathentry kind="lib" path="lib/scala-library-2.9.0.jar"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/common-type-system"/>
+	<classpathentry kind="src" output="target/classes" path="src/main/java"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/dependency parser"/>
-	<classpathentry kind="lib" path="/core/lib/log4j-1.2.15.jar"/>
-	<classpathentry kind="lib" path="/core/lib/uimafit-1.2.0.jar"/>
-	<classpathentry kind="lib" path="lib/cleartk-eval-0.8.1.jar"/>
-	<classpathentry kind="lib" path="lib/cleartk-examples-0.6.0.jar"/>
-	<classpathentry kind="lib" path="lib/cleartk-ml-1.0.1.jar"/>
-	<classpathentry kind="lib" path="lib/cleartk-ml-opennlp-maxent-1.0.2.jar"/>
-	<classpathentry kind="lib" path="lib/cleartk-test-util-1.0.1.jar"/>
-	<classpathentry kind="lib" path="lib/cleartk-type-system-1.0.0.jar"/>
-	<classpathentry kind="lib" path="lib/cleartk-util-0.8.1.jar"/>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>

Modified: incubator/ctakes/trunk/ctakes-assertion/.project
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/.project?rev=1390134&r1=1390133&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/.project (original)
+++ incubator/ctakes/trunk/ctakes-assertion/.project Tue Sep 25 21:06:18 2012
@@ -1,17 +1,23 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-	<name>assertion</name>
-	<comment></comment>
-	<projects>
-	</projects>
-	<buildSpec>
-		<buildCommand>
-			<name>org.eclipse.jdt.core.javabuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-	</buildSpec>
-	<natures>
-		<nature>org.eclipse.jdt.core.javanature</nature>
-	</natures>
-</projectDescription>
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>ctakes-assertion</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>

Modified: incubator/ctakes/trunk/ctakes-assertion/desc/AssertionMiniPipelineAnalysisEngine.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/desc/AssertionMiniPipelineAnalysisEngine.xml?rev=1390134&r1=1390133&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/desc/AssertionMiniPipelineAnalysisEngine.xml (original)
+++ incubator/ctakes/trunk/ctakes-assertion/desc/AssertionMiniPipelineAnalysisEngine.xml Tue Sep 25 21:06:18 2012
@@ -1,4 +1,24 @@
 <?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>
@@ -35,13 +55,13 @@
     <capabilities>
       <capability>
         <inputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.refsem.UmlsConcept</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.refsem.OntologyConcept</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.EntityMention</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.refsem.UmlsConcept</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.refsem.OntologyConcept</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.EntityMention</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
         </inputs>
         <outputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.EntityMention</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.EntityMention</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/trunk/ctakes-assertion/desc/GenericAttributeAnalysisEngine.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/desc/GenericAttributeAnalysisEngine.xml?rev=1390134&r1=1390133&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/desc/GenericAttributeAnalysisEngine.xml (original)
+++ incubator/ctakes/trunk/ctakes-assertion/desc/GenericAttributeAnalysisEngine.xml Tue Sep 25 21:06:18 2012
@@ -1,8 +1,28 @@
 <?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>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.attributes.GenericAttributeAnalysisEngine</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.assertion.attributes.GenericAttributeAnalysisEngine</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>GenericAttributeAnalysisEngine</name>
     <description>Assigns the generic of each IdentifiedAnnotation in the text.   Requires dependency parses upstream.</description>
@@ -12,7 +32,7 @@
     <configurationParameterSettings/>
     <typeSystemDescription>
       <imports>
-        <import location="../../common-type-system/desc/common_type_system.xml"/>
+        <import location="../../ctakes-type-system/desc/common_type_system.xml"/>
       </imports>
     </typeSystemDescription>
     <typePriorities/>
@@ -20,11 +40,11 @@
     <capabilities>
       <capability>
         <inputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.EntityMention</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.EntityMention</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
         </inputs>
         <outputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.EntityMention</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.EntityMention</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/trunk/ctakes-assertion/desc/SubjectAttributeAnalysisEngine.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/desc/SubjectAttributeAnalysisEngine.xml?rev=1390134&r1=1390133&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/desc/SubjectAttributeAnalysisEngine.xml (original)
+++ incubator/ctakes/trunk/ctakes-assertion/desc/SubjectAttributeAnalysisEngine.xml Tue Sep 25 21:06:18 2012
@@ -1,8 +1,28 @@
 <?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>true</primitive>
-  <annotatorImplementationName>edu.mayo.bmi.uima.attributes.SubjectAttributeAnalysisEngine</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.assertion.attributes.SubjectAttributeAnalysisEngine</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>SubjectAttributeAnalysisEngine</name>
     <description>Assigns the subject of each IdentifiedAnnotation in the text.   Requires dependency parses and semantic role labels upstream.  It is also preferable to find the generic attribute before finding subject.</description>
@@ -12,7 +32,7 @@
     <configurationParameterSettings/>
     <typeSystemDescription>
       <imports>
-        <import location="../../common-type-system/desc/common_type_system.xml"/>
+        <import location="../../ctakes-type-system/desc/common_type_system.xml"/>
       </imports>
     </typeSystemDescription>
     <typePriorities/>
@@ -20,11 +40,11 @@
     <capabilities>
       <capability>
         <inputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.EntityMention</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.EntityMention</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
         </inputs>
         <outputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.EntityMention</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.EntityMention</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/trunk/ctakes-assertion/desc/assertionAnalysisEngine.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/desc/assertionAnalysisEngine.xml?rev=1390134&r1=1390133&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/desc/assertionAnalysisEngine.xml (original)
+++ incubator/ctakes/trunk/ctakes-assertion/desc/assertionAnalysisEngine.xml Tue Sep 25 21:06:18 2012
@@ -1,8 +1,28 @@
 <?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>true</primitive>
-  <annotatorImplementationName>org.mitre.medfacts.uima.assertion.AssertionAnalysisEngine</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>assertionAnalysisEngine</name>
     <description/>
@@ -13,7 +33,7 @@
     <typeSystemDescription>
       <imports>
         <import location="medfactsTypeSystem.xml"/>
-        <import location="../../common-type-system/desc/common_type_system.xml"/>
+        <import location="../../ctakes-type-system/desc/common_type_system.xml"/>
       </imports>
     </typeSystemDescription>
     <typePriorities/>
@@ -21,12 +41,12 @@
     <capabilities>
       <capability>
         <inputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.EntityMention</type>
-          <type allAnnotatorFeatures="true">org.mitre.medfacts.types.Concept</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.EntityMention</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.assertion.medfacts.types.Concept</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
         </inputs>
         <outputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.EntityMention</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.EntityMention</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/trunk/ctakes-assertion/desc/conceptConverterAnalysisEngine.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/desc/conceptConverterAnalysisEngine.xml?rev=1390134&r1=1390133&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/desc/conceptConverterAnalysisEngine.xml (original)
+++ incubator/ctakes/trunk/ctakes-assertion/desc/conceptConverterAnalysisEngine.xml Tue Sep 25 21:06:18 2012
@@ -1,8 +1,28 @@
 <?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>true</primitive>
-  <annotatorImplementationName>org.mitre.medfacts.uima.assertion.ConceptConverterAnalysisEngine</annotatorImplementationName>
+  <annotatorImplementationName>org.apache.ctakes.assertion.medfacts.ConceptConverterAnalysisEngine</annotatorImplementationName>
   <analysisEngineMetaData>
     <name>conceptConverterAnalysisEngine</name>
     <description/>
@@ -13,7 +33,7 @@
     <typeSystemDescription>
       <imports>
         <import location="medfactsTypeSystem.xml"/>
-        <import location="../../common-type-system/desc/common_type_system.xml"/>
+        <import location="../../ctakes-type-system/desc/common_type_system.xml"/>
       </imports>
     </typeSystemDescription>
     <typePriorities/>
@@ -21,13 +41,13 @@
     <capabilities>
       <capability>
         <inputs>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.refsem.UmlsConcept</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.refsem.OntologyConcept</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.textsem.EntityMention</type>
-          <type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.syntax.BaseToken</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.refsem.UmlsConcept</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.refsem.OntologyConcept</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.EntityMention</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
         </inputs>
         <outputs>
-          <type allAnnotatorFeatures="true">org.mitre.medfacts.types.Concept</type>
+          <type allAnnotatorFeatures="true">org.apache.ctakes.assertion.medfacts.types.Concept</type>
         </outputs>
         <languagesSupported/>
       </capability>

Modified: incubator/ctakes/trunk/ctakes-assertion/desc/medfactsTypeSystem.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/desc/medfactsTypeSystem.xml?rev=1390134&r1=1390133&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/desc/medfactsTypeSystem.xml (original)
+++ incubator/ctakes/trunk/ctakes-assertion/desc/medfactsTypeSystem.xml Tue Sep 25 21:06:18 2012
@@ -1,4 +1,24 @@
 <?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>medfactsTypeSystem</name>
   <description/>
@@ -6,7 +26,7 @@
   <vendor/>
   <types>
     <typeDescription>
-      <name>org.mitre.medfacts.types.Concept</name>
+      <name>org.apache.ctakes.assertion.medfacts.types.Concept</name>
       <description/>
       <supertypeName>uima.tcas.Annotation</supertypeName>
       <features>
@@ -33,7 +53,7 @@
       </features>
     </typeDescription>
     <typeDescription>
-      <name>org.mitre.medfacts.types.Assertion</name>
+      <name>org.apache.ctakes.assertion.medfacts.types.Assertion</name>
       <description/>
       <supertypeName>uima.tcas.Annotation</supertypeName>
       <features>
@@ -45,7 +65,7 @@
         <featureDescription>
           <name>associatedConcept</name>
           <description/>
-          <rangeTypeName>org.mitre.medfacts.types.Concept</rangeTypeName>
+          <rangeTypeName>org.apache.ctakes.assertion.medfacts.types.Concept</rangeTypeName>
         </featureDescription>
       </features>
     </typeDescription>

Modified: incubator/ctakes/trunk/ctakes-assertion/metadata/install.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/metadata/install.xml?rev=1390134&r1=1390133&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/metadata/install.xml (original)
+++ incubator/ctakes/trunk/ctakes-assertion/metadata/install.xml Tue Sep 25 21:06:18 2012
@@ -1,4 +1,24 @@
 <?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.
+
+-->
 <COMPONENT_INSTALLATION_DESCRIPTOR>
 	<OS>
 		<NAME>Windows and Linux</NAME>

Added: incubator/ctakes/trunk/ctakes-assertion/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/pom.xml?rev=1390134&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/pom.xml (added)
+++ incubator/ctakes/trunk/ctakes-assertion/pom.xml Tue Sep 25 21:06:18 2012
@@ -0,0 +1,182 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<artifactId>ctakes-assertion</artifactId>
+	<name>Apache cTAKES Assertion</name>
+	<parent>
+		<groupId>org.apache.ctakes</groupId>
+		<artifactId>ctakes</artifactId>
+		<version>3.0.0-SNAPSHOT</version>
+	</parent>
+	<properties>
+		<jcasgen.typesystem>desc/medfactsTypeSystem.xml</jcasgen.typesystem>
+	</properties>
+	<dependencies>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-type-system</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-utils</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-pos-tagger</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-dependency-parser</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.cleartk</groupId>
+			<artifactId>cleartk-chunker</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.cleartk</groupId>
+			<artifactId>cleartk-ml</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.cleartk</groupId>
+			<artifactId>cleartk-ml-libsvm</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.cleartk</groupId>
+			<artifactId>cleartk-ml-opennlp-maxent</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.cleartk</groupId>
+			<artifactId>cleartk-util</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.cleartk</groupId>
+			<artifactId>cleartk-test-util</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>args4j</groupId>
+			<artifactId>args4j</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>commons-io</groupId>
+			<artifactId>commons-io</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>commons-lang</groupId>
+			<artifactId>commons-lang</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>commons-logging</groupId>
+			<artifactId>commons-logging</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.google.guava</groupId>
+			<artifactId>guava</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>commons-cli</groupId>
+			<artifactId>commons-cli</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.carrotsearch</groupId>
+			<artifactId>hppc</artifactId>
+		</dependency>
+
+
+		<dependency>
+			<groupId>jdom</groupId>
+			<artifactId>jdom</artifactId>
+		</dependency>
+
+		<dependency>
+			<groupId>log4j</groupId>
+			<artifactId>log4j</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.opennlp</groupId>
+			<artifactId>opennlp-maxent</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.opennlp</groupId>
+			<artifactId>opennlp-tools</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.lucene</groupId>
+			<artifactId>lucene-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>tw.edu.ntu.csie</groupId>
+			<artifactId>libsvm</artifactId>
+		</dependency>
+
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-core</artifactId>
+		</dependency>
+
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.uimafit</groupId>
+			<artifactId>uimafit</artifactId>
+		</dependency>
+
+		<dependency>
+			<groupId>org.codehaus.jackson</groupId>
+			<artifactId>jackson-core-asl</artifactId>
+			<version>1.5.0</version>
+		</dependency>
+		<dependency>
+			<groupId>org.codehaus.jackson</groupId>
+			<artifactId>jackson-mapper-asl</artifactId>
+			<version>1.5.0</version>
+		</dependency>
+
+		<dependency>
+			<groupId>org.scala-lang</groupId>
+			<artifactId>scala-library</artifactId>
+			<version>2.9.0</version>
+		</dependency>
+		<dependency>
+			<groupId>org.scala-tools.sbinary</groupId>
+			<artifactId>sbinary_2.9.0</artifactId>
+			<version>0.4.0</version>
+		</dependency>
+
+		<!-- Dependencies that still need to be uploaded to Maven Central; when 
+			done, the dependency versions should be moved into the parent pom -->
+		<dependency>
+			<groupId>org.mitre.medfacts</groupId>
+			<artifactId>medfacts-i2b2</artifactId>
+			<version>1.2</version>
+			<scope>system</scope>
+			<systemPath>${project.basedir}/lib/med-facts-i2b2-1.2-SNAPSHOT.jar</systemPath>
+		</dependency>
+		<dependency>
+			<groupId>org.mitre.medfacts</groupId>
+			<artifactId>medfacts-zoner</artifactId>
+			<version>1.1</version>
+			<scope>system</scope>
+			<systemPath>${project.basedir}/lib/med-facts-zoner-1.1.jar</systemPath>
+		</dependency>
+		<dependency>
+			<groupId>org.mitre.jcarafe.core</groupId>
+			<artifactId>jcarafe.core</artifactId>
+			<version>2.9.1</version>
+			<scope>system</scope>
+			<systemPath>${project.basedir}/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar</systemPath>
+		</dependency>
+		<dependency>
+			<groupId>org.mitre.jcarafe.ext</groupId>
+			<artifactId>jcarafe.ext</artifactId>
+			<version>2.9.1</version>
+			<scope>system</scope>
+			<systemPath>${project.basedir}/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar</systemPath>
+		</dependency>
+	</dependencies>
+</project>

Copied: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java (from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/edu/mayo/bmi/uima/attributes/GenericAttributeAnalysisEngine.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java?p2=incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java&p1=incubator/ctakes/trunk/ctakes-assertion/src/main/java/edu/mayo/bmi/uima/attributes/GenericAttributeAnalysisEngine.java&r1=1389906&r2=1390134&rev=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/edu/mayo/bmi/uima/attributes/GenericAttributeAnalysisEngine.java (original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java Tue Sep 25 21:06:18 2012
@@ -1,27 +1,22 @@
-/*
- * Copyright: (c) 2012   Mayo Foundation for Medical Education and 
- * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
- * triple-shield Mayo logo are trademarks and service marks of MFMER.
- *
- * Except as contained in the copyright notice above, or as used to identify 
- * MFMER as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * http://www.apache.org/licenses/LICENSE-2.0 
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and 
- * limitations under the License. 
- */
-package edu.mayo.bmi.uima.attributes;
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.ctakes.assertion.attributes;
 
 import org.apache.log4j.Logger;
 import org.apache.uima.UimaContext;
@@ -31,8 +26,8 @@ import org.apache.uima.resource.Resource
 import org.uimafit.component.JCasAnnotator_ImplBase;
 import org.uimafit.util.JCasUtil;
 
-import edu.mayo.bmi.attributes.generic.GenericAttributeClassifier;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 /**
  * <br>

Copied: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/SubjectAttributeAnalysisEngine.java (from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/edu/mayo/bmi/uima/attributes/SubjectAttributeAnalysisEngine.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/SubjectAttributeAnalysisEngine.java?p2=incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/SubjectAttributeAnalysisEngine.java&p1=incubator/ctakes/trunk/ctakes-assertion/src/main/java/edu/mayo/bmi/uima/attributes/SubjectAttributeAnalysisEngine.java&r1=1389906&r2=1390134&rev=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/edu/mayo/bmi/uima/attributes/SubjectAttributeAnalysisEngine.java (original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/SubjectAttributeAnalysisEngine.java Tue Sep 25 21:06:18 2012
@@ -1,27 +1,22 @@
-/*
- * Copyright: (c) 2012   Mayo Foundation for Medical Education and 
- * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
- * triple-shield Mayo logo are trademarks and service marks of MFMER.
- *
- * Except as contained in the copyright notice above, or as used to identify 
- * MFMER as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * http://www.apache.org/licenses/LICENSE-2.0 
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and 
- * limitations under the License. 
- */
-package edu.mayo.bmi.uima.attributes;
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.ctakes.assertion.attributes;
 
 import org.apache.log4j.Logger;
 import org.apache.uima.UimaContext;
@@ -31,8 +26,8 @@ import org.apache.uima.resource.Resource
 import org.uimafit.component.JCasAnnotator_ImplBase;
 import org.uimafit.util.JCasUtil;
 
-import edu.mayo.bmi.attributes.subject.SubjectAttributeClassifier;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 /**
  * <br>

Modified: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/generic/GenericAttributeClassifier.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/generic/GenericAttributeClassifier.java?rev=1390134&r1=1389906&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/generic/GenericAttributeClassifier.java (original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/generic/GenericAttributeClassifier.java Tue Sep 25 21:06:18 2012
@@ -1,27 +1,22 @@
-/*
- * Copyright: (c) 2012   Mayo Foundation for Medical Education and 
- * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
- * triple-shield Mayo logo are trademarks and service marks of MFMER.
+/**
+ * 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
  *
- * Except as contained in the copyright notice above, or as used to identify 
- * MFMER as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed 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. 
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
  */
-package edu.mayo.bmi.attributes.generic;
+package org.apache.ctakes.assertion.attributes.generic;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -37,15 +32,15 @@ import org.apache.uima.jcas.tcas.Annotat
 import org.uimafit.util.JCasUtil;
 import org.xml.sax.SAXException;
 
-import edu.mayo.bmi.nlp.parser.util.DependencyUtility;
-import edu.mayo.bmi.uima.core.type.constants.CONST;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.syntax.Chunk;
-import edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode;
-import edu.mayo.bmi.uima.core.type.textsem.EntityMention;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
-import edu.mayo.bmi.uima.core.type.textsem.SemanticArgument;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.dependency.parser.util.DependencyUtility;
+import org.apache.ctakes.typesystem.type.constants.CONST;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.Chunk;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.SemanticArgument;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 
 /**

Modified: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java?rev=1390134&r1=1389906&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java (original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java Tue Sep 25 21:06:18 2012
@@ -1,27 +1,22 @@
-/*
- * Copyright: (c) 2012   Mayo Foundation for Medical Education and 
- * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
- * triple-shield Mayo logo are trademarks and service marks of MFMER.
+/**
+ * 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
  *
- * Except as contained in the copyright notice above, or as used to identify 
- * MFMER as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed 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. 
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
  */
-package edu.mayo.bmi.attributes.subject;
+package org.apache.ctakes.assertion.attributes.subject;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -38,18 +33,18 @@ import org.apache.uima.jcas.tcas.Annotat
 import org.uimafit.util.JCasUtil;
 import org.xml.sax.SAXException;
 
-import edu.mayo.bmi.nlp.parser.util.DependencyPath;
-import edu.mayo.bmi.nlp.parser.util.DependencyUtility;
-import edu.mayo.bmi.uima.core.type.constants.CONST;
-import edu.mayo.bmi.uima.core.type.relation.Relation;
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.syntax.ConllDependencyNode;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
-import edu.mayo.bmi.uima.core.type.textsem.Predicate;
-import edu.mayo.bmi.uima.core.type.textsem.SemanticArgument;
-import edu.mayo.bmi.uima.core.type.textsem.SemanticRoleRelation;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.dependency.parser.util.DependencyPath;
+import org.apache.ctakes.dependency.parser.util.DependencyUtility;
+import org.apache.ctakes.typesystem.type.constants.CONST;
+import org.apache.ctakes.typesystem.type.relation.Relation;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.Predicate;
+import org.apache.ctakes.typesystem.type.textsem.SemanticArgument;
+import org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 
 /**

Copied: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java (from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/AssertionAnalysisEngine.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java?p2=incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java&p1=incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/AssertionAnalysisEngine.java&r1=1389906&r2=1390134&rev=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/AssertionAnalysisEngine.java (original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java Tue Sep 25 21:06:18 2012
@@ -1,26 +1,22 @@
-/*
- * Copyright: (c) 2012   The MITRE Corporation. All rights reserved.
+/**
+ * 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
  *
- * Except as contained in the copyright notice above, or as used to identify 
- * MITRE  as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed 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. 
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
  */
-
-package org.mitre.medfacts.uima.assertion;
+package org.apache.ctakes.assertion.medfacts;
 
 import java.io.File;
 import java.io.PrintWriter;
@@ -51,20 +47,21 @@ import org.mitre.medfacts.i2b2.annotatio
 import org.mitre.medfacts.i2b2.api.ApiConcept;
 import org.mitre.medfacts.i2b2.api.AssertionDecoderConfiguration;
 import org.mitre.medfacts.i2b2.api.SingleDocumentProcessor;
-import org.mitre.medfacts.i2b2.api.ctakes.CharacterOffsetToLineTokenConverterCtakesImpl;
-import org.mitre.medfacts.i2b2.api.ctakes.SingleDocumentProcessorCtakes;
 import org.mitre.medfacts.i2b2.cli.BatchRunner;
 import org.mitre.medfacts.i2b2.util.StringHandling;
-import org.mitre.medfacts.types.Assertion;
-import org.mitre.medfacts.types.Concept;
-import org.mitre.medfacts.types.Concept_Type;
 import org.mitre.medfacts.zoner.CharacterOffsetToLineTokenConverter;
 import org.mitre.medfacts.zoner.LineTokenToCharacterOffsetConverter;
 
-import edu.mayo.bmi.attributes.generic.GenericAttributeClassifier;
-import edu.mayo.bmi.attributes.subject.SubjectAttributeClassifier;
-import edu.mayo.bmi.uima.core.type.constants.CONST;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+
+import org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier;
+import org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier;
+import org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl;
+import org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes;
+import org.apache.ctakes.assertion.medfacts.types.Assertion;
+import org.apache.ctakes.assertion.medfacts.types.Concept;
+import org.apache.ctakes.assertion.medfacts.types.Concept_Type;
+import org.apache.ctakes.typesystem.type.constants.CONST;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 public class AssertionAnalysisEngine extends JCasAnnotator_ImplBase
 {

Copied: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/CasIndexer.java (from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/CasIndexer.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/CasIndexer.java?p2=incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/CasIndexer.java&p1=incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/CasIndexer.java&r1=1389906&r2=1390134&rev=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/CasIndexer.java (original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/CasIndexer.java Tue Sep 25 21:06:18 2012
@@ -1,26 +1,22 @@
-/*
- * Copyright: (c) 2012   The MITRE Corporation. All rights reserved.
+/**
+ * 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
  *
- * Except as contained in the copyright notice above, or as used to identify 
- * MITRE  as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed 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. 
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
  */
-
-package org.mitre.medfacts.uima.assertion;
+package org.apache.ctakes.assertion.medfacts;
 
 import java.io.PrintWriter;
 import java.io.StringWriter;
@@ -36,7 +32,7 @@ import org.apache.uima.cas.text.Annotati
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 
-import edu.mayo.bmi.uima.core.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
 
 public class CasIndexer<T extends Annotation>
 {

Copied: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptConverterAnalysisEngine.java (from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/ConceptConverterAnalysisEngine.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptConverterAnalysisEngine.java?p2=incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptConverterAnalysisEngine.java&p1=incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/ConceptConverterAnalysisEngine.java&r1=1389906&r2=1390134&rev=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/ConceptConverterAnalysisEngine.java (original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptConverterAnalysisEngine.java Tue Sep 25 21:06:18 2012
@@ -1,26 +1,22 @@
-/*
- * Copyright: (c) 2012   The MITRE Corporation. All rights reserved.
+/**
+ * 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
  *
- * Except as contained in the copyright notice above, or as used to identify 
- * MITRE  as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed 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. 
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
  */
-
-package org.mitre.medfacts.uima.assertion;
+package org.apache.ctakes.assertion.medfacts;
 
 import java.io.File;
 import java.util.ArrayList;
@@ -51,16 +47,16 @@ import org.mitre.medfacts.i2b2.api.Asser
 import org.mitre.medfacts.i2b2.api.SingleDocumentProcessor;
 import org.mitre.medfacts.i2b2.cli.BatchRunner;
 import org.mitre.medfacts.i2b2.util.StringHandling;
-import org.mitre.medfacts.types.Assertion;
-import org.mitre.medfacts.types.Concept;
-import org.mitre.medfacts.types.Concept_Type;
 import org.mitre.medfacts.zoner.LineTokenToCharacterOffsetConverter;
 
-import edu.mayo.bmi.uima.core.type.refsem.OntologyConcept;
-import edu.mayo.bmi.uima.core.type.refsem.UmlsConcept;
-import edu.mayo.bmi.uima.core.type.textsem.EntityMention;
-import edu.mayo.bmi.uima.core.type.textsem.EventMention;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.assertion.medfacts.types.Assertion;
+import org.apache.ctakes.assertion.medfacts.types.Concept;
+import org.apache.ctakes.assertion.medfacts.types.Concept_Type;
+import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
+import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 
 public class ConceptConverterAnalysisEngine extends JCasAnnotator_ImplBase
 {

Copied: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptLookup.java (from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/ConceptLookup.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptLookup.java?p2=incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptLookup.java&p1=incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/ConceptLookup.java&r1=1389906&r2=1390134&rev=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/ConceptLookup.java (original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptLookup.java Tue Sep 25 21:06:18 2012
@@ -1,26 +1,22 @@
-/*
- * Copyright: (c) 2012   The MITRE Corporation. All rights reserved.
+/**
+ * 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
  *
- * Except as contained in the copyright notice above, or as used to identify 
- * MITRE  as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed 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. 
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
  */
-
-package org.mitre.medfacts.uima.assertion;
+package org.apache.ctakes.assertion.medfacts;
 
 import java.util.Arrays;
 import java.util.HashSet;
@@ -30,8 +26,8 @@ import org.apache.uima.cas.FeatureStruct
 import org.apache.uima.jcas.cas.FSArray;
 import org.mitre.medfacts.i2b2.annotation.ConceptType;
 
-import edu.mayo.bmi.uima.core.type.refsem.OntologyConcept;
-import edu.mayo.bmi.uima.core.type.refsem.UmlsConcept;
+import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
+import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
 
 public class ConceptLookup
 {

Copied: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConvertXMIAssertionsToi2b2Format.java (from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/ConvertXMIAssertionsToi2b2Format.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConvertXMIAssertionsToi2b2Format.java?p2=incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConvertXMIAssertionsToi2b2Format.java&p1=incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/ConvertXMIAssertionsToi2b2Format.java&r1=1389906&r2=1390134&rev=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/ConvertXMIAssertionsToi2b2Format.java (original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConvertXMIAssertionsToi2b2Format.java Tue Sep 25 21:06:18 2012
@@ -1,31 +1,29 @@
-/*
- * Copyright: (c) 2012   The MITRE Corporation. All rights reserved.
+/**
+ * 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
  *
- * Except as contained in the copyright notice above, or as used to identify 
- * MITRE  as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed 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. 
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
  */
-
-package org.mitre.medfacts.uima.assertion;
+package org.apache.ctakes.assertion.medfacts;
 
 import org.mitre.medfacts.zoner.CharacterOffsetToLineTokenConverter;
 import org.mitre.medfacts.zoner.CharacterOffsetToLineTokenConverterDefaultImpl;
 import java.io.File;
 import java.io.FileInputStream;
+
+import org.apache.ctakes.assertion.medfacts.types.Assertion;
 import org.apache.uima.cas.impl.XmiCasDeserializer;
 import org.xml.sax.SAXException;
 import org.apache.uima.collection.CollectionException;
@@ -43,7 +41,6 @@ import org.apache.uima.jcas.cas.Sofa; 
 import org.apache.uima.resource.metadata.TypeSystemDescription;
 import org.apache.uima.util.InvalidXMLException;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.mitre.medfacts.types.Assertion;
 import org.apache.uima.cas.text.AnnotationIndex;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.mitre.medfacts.zoner.LineAndTokenPosition;

Copied: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/Converti2b2AnnotationsToCTAKES.java (from r1389906, incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/Converti2b2AnnotationsToCTAKES.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/Converti2b2AnnotationsToCTAKES.java?p2=incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/Converti2b2AnnotationsToCTAKES.java&p1=incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/Converti2b2AnnotationsToCTAKES.java&r1=1389906&r2=1390134&rev=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/mitre/medfacts/uima/assertion/Converti2b2AnnotationsToCTAKES.java (original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/Converti2b2AnnotationsToCTAKES.java Tue Sep 25 21:06:18 2012
@@ -1,26 +1,22 @@
-/*
- * Copyright: (c) 2012   The MITRE Corporation. All rights reserved.
+/**
+ * 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
  *
- * Except as contained in the copyright notice above, or as used to identify 
- * MITRE  as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed 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. 
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
  */
-
-package org.mitre.medfacts.uima.assertion;
+package org.apache.ctakes.assertion.medfacts;
 
 import org.mitre.medfacts.zoner.CharacterOffsetToLineTokenConverter;
 import org.mitre.medfacts.zoner.CharacterOffsetToLineTokenConverterDefaultImpl;
@@ -43,7 +39,6 @@ import org.apache.uima.jcas.cas.Sofa; 
 import org.apache.uima.resource.metadata.TypeSystemDescription;
 import org.apache.uima.util.InvalidXMLException;
 import org.apache.uima.resource.ResourceInitializationException;
-import org.mitre.medfacts.types.Assertion;
 import org.mitre.medfacts.i2b2.annotation.Annotation;
 import org.apache.uima.cas.text.AnnotationIndex;
 //import org.apache.uima.jcas.tcas.Annotation;
@@ -56,13 +51,15 @@ import org.mitre.medfacts.i2b2.util.Stri
 import org.mitre.medfacts.zoner.LineTokenToCharacterOffsetConverter;
 import org.mitre.medfacts.i2b2.processors.AssertionFileProcessor;
 import java.util.List;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
+
+import org.apache.ctakes.assertion.medfacts.types.Assertion;
+import org.apache.ctakes.assertion.medfacts.types.Concept;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
 import org.apache.uima.jcas.JCas;
 import java.io.FileOutputStream;
 import org.apache.uima.cas.impl.XmiCasSerializer;
 import org.apache.uima.util.XMLSerializer;
-import org.mitre.medfacts.types.Concept;
 
 
 

Modified: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java?rev=1390134&r1=1389906&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java (original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java Tue Sep 25 21:06:18 2012
@@ -1,4 +1,22 @@
-package org.mitre.medfacts.uima.assertion.cleartk;
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.ctakes.assertion.medfacts.cleartk;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -28,10 +46,10 @@ import org.cleartk.classifier.feature.pr
 import org.cleartk.type.test.Token;
 import org.uimafit.util.JCasUtil;
 
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.textsem.EntityMention;
-import edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 public class AssertionCleartkAnalysisEngine extends
     CleartkSequenceAnnotator<String>

Modified: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/CharacterOffsetToLineTokenConverterCtakesImpl.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/CharacterOffsetToLineTokenConverterCtakesImpl.java?rev=1390134&r1=1389906&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/CharacterOffsetToLineTokenConverterCtakesImpl.java (original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/CharacterOffsetToLineTokenConverterCtakesImpl.java Tue Sep 25 21:06:18 2012
@@ -1,26 +1,22 @@
-/*
- * Copyright: (c) 2012   The MITRE Corporation. All rights reserved.
+/**
+ * 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
  *
- * Except as contained in the copyright notice above, or as used to identify 
- * MITRE  as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed 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. 
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
  */
-
-package org.mitre.medfacts.i2b2.api.ctakes;
+package org.apache.ctakes.assertion.medfacts.i2b2.api;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -37,8 +33,8 @@ import org.mitre.medfacts.i2b2.api.ApiCo
 import org.mitre.medfacts.zoner.CharacterOffsetToLineTokenConverter;
 import org.mitre.medfacts.zoner.LineAndTokenPosition;
 
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
 
 public class CharacterOffsetToLineTokenConverterCtakesImpl implements CharacterOffsetToLineTokenConverter
 {

Modified: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/ConstraintConstructor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/ConstraintConstructor.java?rev=1390134&r1=1389906&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/ConstraintConstructor.java (original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/ConstraintConstructor.java Tue Sep 25 21:06:18 2012
@@ -1,26 +1,22 @@
-/*
- * Copyright: (c) 2012   The MITRE Corporation. All rights reserved.
+/**
+ * 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
  *
- * Except as contained in the copyright notice above, or as used to identify 
- * MITRE  as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed 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. 
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
  */
-
-package org.mitre.medfacts.i2b2.api.ctakes;
+package org.apache.ctakes.assertion.medfacts.i2b2.api;
 
 import org.apache.uima.cas.ConstraintFactory;
 import org.apache.uima.cas.FSIntConstraint;



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