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From chen...@apache.org
Subject svn commit: r1602946 - in /ctakes/trunk: ctakes-chunker/desc/ ctakes-clinical-pipeline/desc/analysis_engine/auto/ ctakes-clinical-pipeline/desc/collection_processing_engine/assertion_training_steps/ ctakes-clinical-pipeline/src/main/java/org/apache/cta...
Date Mon, 16 Jun 2014 18:10:33 GMT
Author: chenpei
Date: Mon Jun 16 18:10:32 2014
New Revision: 1602946

URL: http://svn.apache.org/r1602946
Log:
CTAKES-301 - Create a cTAKES 3.2.0 Release
Applying ASF License Headers onto misc projects

Modified:
    ctakes/trunk/ctakes-chunker/desc/Chunker.xml
    ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/auto/defaultPipeline.xml
    ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/assertion_training_steps/process_gold_assertion_data.xml
    ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java
    ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java
    ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfCUIsGenerator.java
    ctakes/trunk/ctakes-constituency-parser/scripts/groovy/parser.groovy
    ctakes/trunk/ctakes-core-res/src/main/resources/log4j.xml
    ctakes/trunk/ctakes-core/desc/analysis_engine/SHARPKnowtatorXMLReader.xml
    ctakes/trunk/ctakes-core/desc/cas_consumer/__XmiWriterCasConsumer.xml
    ctakes/trunk/ctakes-core/desc/collection_reader/XmiCollectionReaderCtakes.xml
    ctakes/trunk/ctakes-core/scripts/groovy/cTAKES_clinical_pipeline.groovy
    ctakes/trunk/ctakes-core/scripts/groovy/run_cTAKES.groovy
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cpe/CmdLineCpeRunner.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XmiCollectionReaderCtakes.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SHARPKnowtatorXMLDefaults.java
    ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorTest.java
    ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java
    ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/AnnotationDepUtils.java
    ctakes/trunk/ctakes-dictionary-lookup-res/pom.xml
    ctakes/trunk/ctakes-dictionary-lookup-res/src/main/resources/org/apache/ctakes/dictionary/lookup/AssertionCuePhraseDictionaryLookupAnnotator.xml
    ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/AssertionCuePhraseDictionaryLookupAnnotator.xml
    ctakes/trunk/ctakes-drug-ner-res/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml
    ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml
    ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml
    ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml
    ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml
    ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml
    ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml
    ctakes/trunk/ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml
    ctakes/trunk/ctakes-lvg/src/main/test/org/apache/ctakes/lvg/test/TestLvgAnnotator.java
    ctakes/trunk/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
    ctakes/trunk/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystemDescription.xsl
    ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/struct/CounterMap.java
    ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/struct/CounterTreeMap.java
    ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/ApproximateMath.java
    ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/ApproximateSimilarity.java
    ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/SearchResult.java
    ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/TestCosineSimilarity.java
    ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/WikiIndex.java

Modified: ctakes/trunk/ctakes-chunker/desc/Chunker.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-chunker/desc/Chunker.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-chunker/desc/Chunker.xml (original)
+++ ctakes/trunk/ctakes-chunker/desc/Chunker.xml Mon Jun 16 18:10:32 2014
@@ -1,14 +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. -->
+<!--
+
+    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>

Modified: ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/auto/defaultPipeline.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/auto/defaultPipeline.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/auto/defaultPipeline.xml (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/auto/defaultPipeline.xml Mon Jun 16 18:10:32 2014
@@ -1,4 +1,24 @@
 <?xml version="1.0" encoding="UTF-8"?><analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<!--
+
+    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.
+
+-->
     <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
     <primitive>false</primitive>
     <delegateAnalysisEngineSpecifiers>

Modified: ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/assertion_training_steps/process_gold_assertion_data.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/assertion_training_steps/process_gold_assertion_data.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/assertion_training_steps/process_gold_assertion_data.xml (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/assertion_training_steps/process_gold_assertion_data.xml Mon Jun 16 18:10:32 2014
@@ -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.
+
+-->
 <cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
     <collectionReader>
         <collectionIterator>

Modified: ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.clinicalpipeline;
 
 import java.io.FileNotFoundException;

Modified: ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.clinicalpipeline.runtime;
 
 import java.io.File;

Modified: ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfCUIsGenerator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfCUIsGenerator.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfCUIsGenerator.java (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfCUIsGenerator.java Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.clinicalpipeline.runtime;
 
 import java.io.IOException;

Modified: ctakes/trunk/ctakes-constituency-parser/scripts/groovy/parser.groovy
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-constituency-parser/scripts/groovy/parser.groovy?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-constituency-parser/scripts/groovy/parser.groovy (original)
+++ ctakes/trunk/ctakes-constituency-parser/scripts/groovy/parser.groovy Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.
+ */
 #!/usr/bin/env groovy
 /**
 ** 	This assumes that you have installed Groovy and 

Modified: ctakes/trunk/ctakes-core-res/src/main/resources/log4j.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core-res/src/main/resources/log4j.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core-res/src/main/resources/log4j.xml (original)
+++ ctakes/trunk/ctakes-core-res/src/main/resources/log4j.xml Mon Jun 16 18:10:32 2014
@@ -1,4 +1,24 @@
 <?xml version="1.0" encoding="UTF-8" ?> <!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
+<!--
+
+    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.
+
+-->
 <log4j:configuration debug="true"
 	xmlns:log4j='http://jakarta.apache.org/log4j/'>
 	<appender name="consoleAppender" class="org.apache.log4j.ConsoleAppender">

Modified: ctakes/trunk/ctakes-core/desc/analysis_engine/SHARPKnowtatorXMLReader.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/desc/analysis_engine/SHARPKnowtatorXMLReader.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/desc/analysis_engine/SHARPKnowtatorXMLReader.xml (original)
+++ ctakes/trunk/ctakes-core/desc/analysis_engine/SHARPKnowtatorXMLReader.xml Mon Jun 16 18:10:32 2014
@@ -1,4 +1,24 @@
 <?xml version="1.0" encoding="UTF-8"?><taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<!--
+
+    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.
+
+-->
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
   <annotatorImplementationName>org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader</annotatorImplementationName>

Modified: ctakes/trunk/ctakes-core/desc/cas_consumer/__XmiWriterCasConsumer.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/desc/cas_consumer/__XmiWriterCasConsumer.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/desc/cas_consumer/__XmiWriterCasConsumer.xml (original)
+++ ctakes/trunk/ctakes-core/desc/cas_consumer/__XmiWriterCasConsumer.xml Mon Jun 16 18:10:32 2014
@@ -1,4 +1,24 @@
 <?xml version="1.0" encoding="UTF-8"?><casConsumerDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<!--
+
+    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.
+
+-->
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <implementationName>org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes</implementationName>
   <processingResourceMetaData>

Modified: ctakes/trunk/ctakes-core/desc/collection_reader/XmiCollectionReaderCtakes.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/desc/collection_reader/XmiCollectionReaderCtakes.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/desc/collection_reader/XmiCollectionReaderCtakes.xml (original)
+++ ctakes/trunk/ctakes-core/desc/collection_reader/XmiCollectionReaderCtakes.xml Mon Jun 16 18:10:32 2014
@@ -1,26 +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.
-	 ***************************************************************
-   -->
-   
+    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.
+
+-->
 <collectionReaderDescription  xmlns="http://uima.apache.org/resourceSpecifier">
     <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
     <implementationName>org.apache.ctakes.core.cr.XmiCollectionReaderCtakes</implementationName>

Modified: ctakes/trunk/ctakes-core/scripts/groovy/cTAKES_clinical_pipeline.groovy
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/scripts/groovy/cTAKES_clinical_pipeline.groovy?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/scripts/groovy/cTAKES_clinical_pipeline.groovy (original)
+++ ctakes/trunk/ctakes-core/scripts/groovy/cTAKES_clinical_pipeline.groovy Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.
+ */
 #!/usr/bin/env groovy
 
 /**

Modified: ctakes/trunk/ctakes-core/scripts/groovy/run_cTAKES.groovy
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/scripts/groovy/run_cTAKES.groovy?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/scripts/groovy/run_cTAKES.groovy (original)
+++ ctakes/trunk/ctakes-core/scripts/groovy/run_cTAKES.groovy Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.
+ */
 #!/usr/bin/env groovy
 
 /**

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.core.ae;
 
 

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.core.cc;
 
 /*

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cpe/CmdLineCpeRunner.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cpe/CmdLineCpeRunner.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cpe/CmdLineCpeRunner.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cpe/CmdLineCpeRunner.java Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.core.cpe;
 
 import org.apache.uima.UIMAFramework;

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XmiCollectionReaderCtakes.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XmiCollectionReaderCtakes.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XmiCollectionReaderCtakes.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XmiCollectionReaderCtakes.java Mon Jun 16 18:10:32 2014
@@ -1,4 +1,4 @@
-/*
+/**
  * 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
@@ -6,9 +6,9 @@
  * 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
@@ -16,7 +16,6 @@
  * specific language governing permissions and limitations
  * under the License.
  */
-
 package org.apache.ctakes.core.cr;
 
 import java.io.File;

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SHARPKnowtatorXMLDefaults.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SHARPKnowtatorXMLDefaults.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SHARPKnowtatorXMLDefaults.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/SHARPKnowtatorXMLDefaults.java Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.core.util;
 
 import org.apache.ctakes.typesystem.type.constants.CONST;

Modified: ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorTest.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorTest.java (original)
+++ ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorTest.java Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.core.ae;
 
 import static org.junit.Assert.assertEquals;

Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.coreference.cc;
 
 import java.io.File;

Modified: ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/AnnotationDepUtils.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/AnnotationDepUtils.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/AnnotationDepUtils.java (original)
+++ ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/AnnotationDepUtils.java Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.dependency.parser.util;
 
 import java.util.ArrayList;

Modified: ctakes/trunk/ctakes-dictionary-lookup-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-res/pom.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-res/pom.xml (original)
+++ ctakes/trunk/ctakes-dictionary-lookup-res/pom.xml Mon Jun 16 18:10:32 2014
@@ -70,6 +70,23 @@
 					</execution>
 				</executions>
 			</plugin>
+				<plugin>
+					<artifactId>maven-jar-plugin</artifactId>
+					<version>2.4</version>
+					<configuration>
+			          <includes>
+			          <!-- Dictionary lookup Resources that are unpacked
+			          automatically by maven
+			          	are not jar'd and included in the bin distro
+			          	by default please download them from SF if needed. 
+			           -->
+			            <include>**/*.class</include>
+			            <include>**/types/*.xml</include>			            
+			            <include>**/META-INF/**</include>
+			           
+			          </includes>
+	        		</configuration>
+				</plugin>	    	
 		</plugins>
 	</build>  
 </project>

Modified: ctakes/trunk/ctakes-dictionary-lookup-res/src/main/resources/org/apache/ctakes/dictionary/lookup/AssertionCuePhraseDictionaryLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-res/src/main/resources/org/apache/ctakes/dictionary/lookup/AssertionCuePhraseDictionaryLookupAnnotator.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-res/src/main/resources/org/apache/ctakes/dictionary/lookup/AssertionCuePhraseDictionaryLookupAnnotator.xml (original)
+++ ctakes/trunk/ctakes-dictionary-lookup-res/src/main/resources/org/apache/ctakes/dictionary/lookup/AssertionCuePhraseDictionaryLookupAnnotator.xml Mon Jun 16 18:10:32 2014
@@ -1,4 +1,24 @@
 <?xml version="1.0" encoding="UTF-8"?><taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<!--
+
+    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.
+
+-->
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
   <annotatorImplementationName>org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator</annotatorImplementationName>

Modified: ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/AssertionCuePhraseDictionaryLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/AssertionCuePhraseDictionaryLookupAnnotator.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/AssertionCuePhraseDictionaryLookupAnnotator.xml (original)
+++ ctakes/trunk/ctakes-dictionary-lookup/desc/analysis_engine/AssertionCuePhraseDictionaryLookupAnnotator.xml Mon Jun 16 18:10:32 2014
@@ -1,4 +1,24 @@
 <?xml version="1.0" encoding="UTF-8"?><taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<!--
+
+    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.
+
+-->
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
   <annotatorImplementationName>org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator</annotatorImplementationName>

Modified: ctakes/trunk/ctakes-drug-ner-res/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner-res/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner-res/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml (original)
+++ ctakes/trunk/ctakes-drug-ner-res/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml Mon Jun 16 18:10:32 2014
@@ -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>org.apache.ctakes.drugner.types.TypeSystem</name>
   <description/>

Modified: ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml (original)
+++ ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotator.xml Mon Jun 16 18:10:32 2014
@@ -1,4 +1,24 @@
 <?xml version="1.0" encoding="UTF-8"?><taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<!--
+
+    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.
+
+-->
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>
   <annotatorImplementationName>org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator</annotatorImplementationName>

Modified: ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml (original)
+++ ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml Mon Jun 16 18:10:32 2014
@@ -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>

Modified: ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml (original)
+++ ctakes/trunk/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml Mon Jun 16 18:10:32 2014
@@ -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.
+
+-->
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>

Modified: ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml (original)
+++ ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml Mon Jun 16 18:10:32 2014
@@ -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.
+
+-->
 <cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
     <collectionReader>
         <collectionIterator>

Modified: ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml (original)
+++ ctakes/trunk/ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml Mon Jun 16 18:10:32 2014
@@ -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.
+
+-->
 <cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
     <collectionReader>
         <collectionIterator>

Modified: ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml (original)
+++ ctakes/trunk/ctakes-drug-ner/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml Mon Jun 16 18:10:32 2014
@@ -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>org.apache.ctakes.drugner.types.TypeSystem</name>
   <description/>

Modified: ctakes/trunk/ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml (original)
+++ ctakes/trunk/ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml Mon Jun 16 18:10:32 2014
@@ -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.
+
+-->
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>

Modified: ctakes/trunk/ctakes-lvg/src/main/test/org/apache/ctakes/lvg/test/TestLvgAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-lvg/src/main/test/org/apache/ctakes/lvg/test/TestLvgAnnotator.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-lvg/src/main/test/org/apache/ctakes/lvg/test/TestLvgAnnotator.java (original)
+++ ctakes/trunk/ctakes-lvg/src/main/test/org/apache/ctakes/lvg/test/TestLvgAnnotator.java Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.lvg.test;
 
 import static org.junit.Assert.*;

Modified: ctakes/trunk/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
Binary files - no diff available.

Modified: ctakes/trunk/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystemDescription.xsl
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystemDescription.xsl?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
Binary files - no diff available.

Modified: ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/struct/CounterMap.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/struct/CounterMap.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/struct/CounterMap.java (original)
+++ ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/struct/CounterMap.java Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.utils.struct;
 
 import java.util.HashMap;

Modified: ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/struct/CounterTreeMap.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/struct/CounterTreeMap.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/struct/CounterTreeMap.java (original)
+++ ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/struct/CounterTreeMap.java Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.utils.struct;
 
 import java.util.Comparator;

Modified: ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/ApproximateMath.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/ApproximateMath.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/ApproximateMath.java (original)
+++ ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/ApproximateMath.java Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.utils.wiki;
 
 public class ApproximateMath {

Modified: ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/ApproximateSimilarity.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/ApproximateSimilarity.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/ApproximateSimilarity.java (original)
+++ ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/ApproximateSimilarity.java Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.utils.wiki;
 
 import org.apache.lucene.search.similarities.DefaultSimilarity;

Modified: ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/SearchResult.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/SearchResult.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/SearchResult.java (original)
+++ ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/SearchResult.java Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.utils.wiki;
 
 public class SearchResult {

Modified: ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/TestCosineSimilarity.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/TestCosineSimilarity.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/TestCosineSimilarity.java (original)
+++ ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/TestCosineSimilarity.java Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.utils.wiki;
 
 import java.io.IOException;

Modified: ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/WikiIndex.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/WikiIndex.java?rev=1602946&r1=1602945&r2=1602946&view=diff
==============================================================================
--- ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/WikiIndex.java (original)
+++ ctakes/trunk/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/WikiIndex.java Mon Jun 16 18:10:32 2014
@@ -1,3 +1,21 @@
+/**
+ * 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.utils.wiki;
 
 import java.io.File;



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