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From chen...@apache.org
Subject svn commit: r1388092 [3/22] - in /incubator/ctakes/trunk: ./ ctakes-chunker/ ctakes-chunker/desc/ ctakes-chunker/scripts/groovy/data/chunk/ ctakes-chunker/scripts/java/data/chunk/ ctakes-chunker/scripts/java/data/chunk/genia/ ctakes-chunker/src/main/ja...
Date Thu, 20 Sep 2012 16:07:33 GMT
Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/SectionSegmentAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/SectionSegmentAnnotator.xml?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/SectionSegmentAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/SectionSegmentAnnotator.xml Thu Sep 20 16:07:04 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.
+
+-->
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <primitive>true</primitive>

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/SimpleSegmentAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/SimpleSegmentAnnotator.xml?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/SimpleSegmentAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/SimpleSegmentAnnotator.xml Thu Sep 20 16:07:04 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.
+
+-->
 <taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
 <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
 <primitive>true</primitive>

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test1.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test1.xml?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test1.xml (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test1.xml Thu Sep 20 16:07:04 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.
+
+-->
 <cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
 <collectionReader>
 <collectionIterator>

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_cda.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_cda.xml?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_cda.xml (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_cda.xml Thu Sep 20 16:07:04 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.
+
+-->
 <cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
     <collectionReader>
         <collectionIterator>

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_plaintext.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_plaintext.xml?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_plaintext.xml (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_plaintext.xml Thu Sep 20 16:07:04 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.
+
+-->
 <cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
     <collectionReader>
         <collectionIterator>

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCPE.bat
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCPE.bat?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCPE.bat (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCPE.bat Thu Sep 20 16:07:04 2012
@@ -1,2 +1,21 @@
+@REM
+@REM Licensed to the Apache Software Foundation (ASF) under one
+@REM or more contributor license agreements.  See the NOTICE file
+@REM distributed with this work for additional information
+@REM regarding copyright ownership.  The ASF licenses this file
+@REM to you under the Apache License, Version 2.0 (the
+@REM "License"); you may not use this file except in compliance
+@REM with the License.  You may obtain a copy of the License at
+@REM
+@REM   http://www.apache.org/licenses/LICENSE-2.0
+@REM
+@REM Unless required by applicable law or agreed to in writing,
+@REM software distributed under the License is distributed on an
+@REM "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+@REM KIND, either express or implied.  See the License for the
+@REM specific language governing permissions and limitations
+@REM under the License.
+@REM
+
 java  -Xms1024M -Xmx2048M -cp resources;cTAKESdesc;cTAKES.jar edu.mayo.bmi.ctakes.main.cTAKESCPEGUI
 

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCPE.sh
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCPE.sh?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCPE.sh (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCPE.sh Thu Sep 20 16:07:04 2012
@@ -1,2 +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.
+#
+
 java  -Xms1024M -Xmx2048M  -cp resources:cTAKESdesc:cTAKES.jar edu.mayo.bmi.ctakes.main.cTAKESCPEGUI
 

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCVD.bat
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCVD.bat?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCVD.bat (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCVD.bat Thu Sep 20 16:07:04 2012
@@ -1,2 +1,21 @@
+@REM
+@REM Licensed to the Apache Software Foundation (ASF) under one
+@REM or more contributor license agreements.  See the NOTICE file
+@REM distributed with this work for additional information
+@REM regarding copyright ownership.  The ASF licenses this file
+@REM to you under the Apache License, Version 2.0 (the
+@REM "License"); you may not use this file except in compliance
+@REM with the License.  You may obtain a copy of the License at
+@REM
+@REM   http://www.apache.org/licenses/LICENSE-2.0
+@REM
+@REM Unless required by applicable law or agreed to in writing,
+@REM software distributed under the License is distributed on an
+@REM "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+@REM KIND, either express or implied.  See the License for the
+@REM specific language governing permissions and limitations
+@REM under the License.
+@REM
+
 java -Xms1024M -Xmx2048M  -cp resources;cTAKESdesc;cTAKES.jar edu.mayo.bmi.ctakes.main.cTAKESCVDGUI
 

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCVD.sh
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCVD.sh?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCVD.sh (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/runctakesCVD.sh Thu Sep 20 16:07:04 2012
@@ -1,2 +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.
+#
+
 java  -Xms1024M -Xmx2048M  -cp resources:cTAKESdesc:cTAKES.jar edu.mayo.bmi.ctakes.main.cTAKESCVDGUI
 

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/edu/mayo/bmi/ctakes/main/cTAKESCPEGUI.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/edu/mayo/bmi/ctakes/main/cTAKESCPEGUI.java?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/edu/mayo/bmi/ctakes/main/cTAKESCPEGUI.java (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/edu/mayo/bmi/ctakes/main/cTAKESCPEGUI.java Thu Sep 20 16:07:04 2012
@@ -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 edu.mayo.bmi.ctakes.main;
 
  

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/edu/mayo/bmi/ctakes/main/cTAKESCVDGUI.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/edu/mayo/bmi/ctakes/main/cTAKESCVDGUI.java?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/edu/mayo/bmi/ctakes/main/cTAKESCVDGUI.java (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/edu/mayo/bmi/ctakes/main/cTAKESCVDGUI.java Thu Sep 20 16:07:04 2012
@@ -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 edu.mayo.bmi.ctakes.main;
 
 import java.io.File;

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/edu/mayo/bmi/uima/cni/ae/ExtractionPrepAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/edu/mayo/bmi/uima/cni/ae/ExtractionPrepAnnotator.java?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/edu/mayo/bmi/uima/cni/ae/ExtractionPrepAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/edu/mayo/bmi/uima/cni/ae/ExtractionPrepAnnotator.java Thu Sep 20 16:07:04 2012
@@ -1,26 +1,21 @@
-/*
- * Copyright: (c) 2009   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. 
- */
+/**
+ * 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 edu.mayo.bmi.uima.cni.ae;
 
 import java.util.HashSet;

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/test/data/output/NotesIIST_RTF.DTD
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/test/data/output/NotesIIST_RTF.DTD?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/test/data/output/NotesIIST_RTF.DTD (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/test/data/output/NotesIIST_RTF.DTD Thu Sep 20 16:07:04 2012
@@ -1,4 +1,24 @@
 <!--
+
+    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.
+
+-->
+<!--
 *==================================================================================*
 *   File name: NotesIIST_RTF.dtd                                                   *
 *==================================================================================*

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/test/data/output/testpatient_cn_1.xml.included.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/test/data/output/testpatient_cn_1.xml.included.xml?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/test/data/output/testpatient_cn_1.xml.included.xml (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/test/data/output/testpatient_cn_1.xml.included.xml Thu Sep 20 16:07:04 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.
+
+-->
 <CAS version="2">
     <uima.cas.Sofa _indexed="0" _id="6" sofaNum="1" sofaID="_InitialView" mimeType="text" sofaString="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;?&gt;&lt;!DOCTYPE levelone SYSTEM &quot;NotesIIST_RTF.DTD&quot; [&lt;!ENTITY deg '&amp;#x00B0;'&gt;&lt;!ENTITY sup2 '&amp;#x00B2;'&gt;&lt;!ENTITY micro '&amp;#x00B5;'&gt;]&gt;&lt;levelone&gt;&lt;clinical_document_header&gt;&lt;id EX=&quot;###DOC_ID###&quot; RT=&quot;2.16.840.1.113883.3.2.1.1&quot;/&gt;&lt;set_id EX=&quot;###SET_ID###&quot; RT=&quot;2.16.840.1.113883.3.2.1.2&quot;/&gt;&lt;version_nbr V=&quot;###V_NBR###&quot;/&gt;&lt;document_type_cd V=&quot;687&quot; S=&quot;2.16.840.1.113883.3.2.1.3&quot; DN=&quot;Nutrition Consult&quot;/&gt;&lt;origination_dttm V=&quot;20030822T131513&quot;/&gt;&lt;confidentiality_cd V=&quot;0&quot; S=&quot;2.16.840.1.113883.3.2.1.4&quot;/&gt;&lt;patient_encounter&gt;&lt;practice_setting_cd V=&quot;4284&quot; S=&quot;2.16.840.1.113883.3.2.1.7&quot; DN=&quot;Nutr Clinic&quot;/&gt;&l
 t;encounter_tmr V=&quot;20030822&quot;/&gt;&lt;service_location&gt;&lt;id EX=&quot;TBD&quot; RT=&quot;2.16.840.1.113883.3.2.1.8&quot;/&gt;&lt;/service_location&gt;&lt;facility&gt;&lt;organization&gt;&lt;organization.nm V=&quot;MCR&quot;/&gt;&lt;/organization&gt;&lt;/facility&gt;&lt;/patient_encounter&gt;&lt;legal_authenticator&gt;&lt;legal_authenticator.type_cd V=&quot;SPV&quot;/&gt;&lt;participation_tmr V=&quot;&quot;/&gt;&lt;signature_cd V=&quot;S&quot;/&gt;&lt;person&gt;&lt;id EX=&quot;99999999&quot; RT=&quot;2.16.840.1.113883.3.2.1.9&quot;/&gt;&lt;person_name&gt;&lt;nm&gt;&lt;GIV V=&quot;Julie&quot;/&gt;&lt;MID V=&quot;A&quot;/&gt;&lt;FAM V=&quot;Tester&quot;/&gt;&lt;PFX V=&quot;&quot;/&gt;&lt;SFX V=&quot;RD&quot;/&gt;&lt;/nm&gt;&lt;person_name.type_cd V=&quot;S&quot;/&gt;&lt;/person_name&gt;&lt;/person&gt;&lt;/legal_authenticator&gt;&lt;originator&gt;&lt;originator.type_cd V=&quot;AUT&quot;/&gt;&lt;participation_tmr V=&quot;20030822T131513&quot;/&gt;&lt;person&gt;&lt;id
  EX=&quot;99999999&quot; RT=&quot;2.16.840.1.113883.3.2.1.9&quot;/&gt;&lt;person_name&gt;&lt;nm&gt;&lt;GIV V=&quot;Julie&quot;/&gt;&lt;MID V=&quot;A.&quot;/&gt;&lt;FAM V=&quot;Tester&quot;/&gt;&lt;PFX V=&quot;&quot;/&gt;&lt;SFX V=&quot;RD&quot;/&gt;&lt;/nm&gt;&lt;person_name.type_cd V=&quot;L&quot;/&gt;&lt;/person_name&gt;&lt;telecom V=&quot;5-5555&quot; USE=&quot;PG&quot;/&gt;&lt;/person&gt;&lt;/originator&gt;&lt;originating_organization&gt;&lt;originating_organization.type_cd V=&quot;CST&quot;/&gt;&lt;organization&gt;&lt;id EX=&quot;TBD&quot; RT=&quot;2.16.840.1.113883.3.2.1.10&quot;/&gt;&lt;organization.nm V=&quot;Originating Organization - Coding TBD&quot;/&gt;&lt;/organization&gt;&lt;/originating_organization&gt;&lt;transcriptionist&gt;&lt;transcriptionist.type_cd V=&quot;ENT&quot;/&gt;&lt;participation_tmr V=&quot;20030822T131513&quot;/&gt;&lt;person&gt;&lt;id EX=&quot;99999999&quot; RT=&quot;2.16.840.1.113883.3.2.1.9&quot;/&gt;&lt;person_name&gt;&lt;nm&gt;&lt;GIV V=&q
 uot;Julie&quot;/&gt;&lt;MID V=&quot;A.&quot;/&gt;&lt;FAM V=&quot;Tester&quot;/&gt;&lt;/nm&gt;&lt;person_name.type_cd V=&quot;L&quot;/&gt;&lt;/person_name&gt;&lt;/person&gt;&lt;/transcriptionist&gt;&lt;provider&gt;&lt;provider.type_cd V=&quot;CON&quot;/&gt;&lt;participation_tmr V=&quot;20030822T131513&quot;/&gt;&lt;person&gt;&lt;id EX=&quot;99999999&quot; RT=&quot;2.16.840.1.113883.3.2.1.9&quot;/&gt;&lt;person_name&gt;&lt;nm&gt;&lt;GIV V=&quot;Julie&quot;/&gt;&lt;MID V=&quot;A.&quot;/&gt;&lt;FAM V=&quot;Tester&quot;/&gt;&lt;PFX V=&quot;&quot;/&gt;&lt;SFX V=&quot;RD&quot;/&gt;&lt;/nm&gt;&lt;person_name.type_cd V=&quot;L&quot;/&gt;&lt;/person_name&gt;&lt;telecom V=&quot;5-5555&quot; USE=&quot;PG&quot;/&gt;&lt;/person&gt;&lt;/provider&gt;&lt;patient&gt;&lt;patient.type_cd V=&quot;PATSBJ&quot;/&gt;&lt;person&gt;&lt;id EX=&quot;3-303-925&quot; RT=&quot;2.16.840.1.113883.3.2.1.1&quot;/&gt;&lt;person_name&gt;&lt;nm&gt;&lt;GIV V=&quot;Terri&quot;/&gt;&lt;MID V=&quot;A.&quot;/&gt;&lt;
 FAM V=&quot;Testing&quot;/&gt;&lt;PFX V=&quot;Judge&quot;/&gt;&lt;SFX V=&quot;Jr.,D.D.S.&quot;/&gt;&lt;/nm&gt;&lt;person_name.type_cd V=&quot;L&quot;/&gt;&lt;/person_name&gt;&lt;addr&gt;&lt;LIT V=&quot;100 Quality Control Avenue&quot;/&gt;&lt;CTY V=&quot;Rochester&quot;/&gt;&lt;STA V=&quot;MN&quot;/&gt;&lt;ZIP V=&quot;55905&quot;/&gt;&lt;CNT V=&quot;US&quot;/&gt;&lt;/addr&gt;&lt;/person&gt;&lt;is_known_by&gt;&lt;id EX=&quot;TBD&quot; RT=&quot;2.16.840.1.113883.3.2.2.1&quot;/&gt;&lt;is_known_to&gt;&lt;id EX=&quot;TBD&quot; RT=&quot;2.16.840.1.113883.3.2.1.10&quot;/&gt;&lt;/is_known_to&gt;&lt;/is_known_by&gt;&lt;birth_dttm V=&quot;19341123&quot;/&gt;&lt;administrative_gender_cd V=&quot;F&quot; S=&quot;2.16.840.1.113883.3.2.2.2&quot;/&gt;&lt;/patient&gt;&lt;status_cd V=&quot;TBD&quot; S=&quot;2.16.840.1.113883.3.2.1.16&quot;/&gt;&lt;cn1_admin_data&gt;&lt;cn1_status_cd V=&quot;Fnl&quot; S=&quot;2.16.840.1.113883.3.2.3.1&quot;/&gt;&lt;cn1_service_cd V=&quot;MNT&quot; S=&quot;2.16
 .840.1.113883.3.2.3.2&quot;/&gt;&lt;cn1_event_cd V=&quot;CON&quot; S=&quot;2.16.840.1.113883.3.2.3.3&quot;/&gt;&lt;cn1_document_id EX=&quot;000000000&quot; RT=&quot;2.16.840.1.113883.3.2.3.4&quot;/&gt;&lt;cn1_revision_nbr V=&quot;1&quot;/&gt;&lt;cn1_site_cd V=&quot;RCH&quot; S=&quot;2.16.840.1.113883.3.2.3.10&quot;/&gt;&lt;/cn1_admin_data&gt;&lt;document_title V=&quot;Document Service Name - Coding TBD&quot; S=&quot;2.16.840.1.113883.3.2.1.17&quot;/&gt;&lt;/clinical_document_header&gt;&lt;body&gt;&lt;section&gt;&lt;caption&gt;&lt;caption_cd V=&quot;20100&quot; DN=&quot;Revision History&quot; S=&quot;2.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;Revision History&lt;/caption&gt;&lt;/section&gt;&lt;section&gt;&lt;caption&gt;&lt;caption_cd V=&quot;20112&quot; DN=&quot;I/R/P&quot; S=&quot;2.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;Impression / Report / Plan&lt;/caption&gt;&lt;table&gt;&lt;caption&gt;&lt;caption_cd V=&quot;20003&quot; DN=&quot;I/R/P&quot; S=&quo
 t;2.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;&lt;/caption&gt;&lt;tr&gt;&lt;th&gt;Problem&lt;/th&gt;&lt;th&gt;Plan&lt;/th&gt;&lt;/tr&gt;&lt;/table&gt;&lt;/section&gt;&lt;section&gt;&lt;caption&gt;&lt;caption_cd V=&quot;20113&quot; DN=&quot;Diagnoses&quot; S=&quot;2.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;Diagnosis&lt;/caption&gt;&lt;table&gt;&lt;caption&gt;&lt;caption_cd V=&quot;20003&quot; DN=&quot;Diagnoses&quot; S=&quot;2.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;&lt;/caption&gt;&lt;tr&gt;&lt;th&gt;Problem&lt;/th&gt;&lt;th&gt;Diagnosis&lt;/th&gt;&lt;/tr&gt;&lt;/table&gt;&lt;/section&gt;&lt;section&gt;&lt;caption&gt;&lt;caption_cd V=&quot;20101&quot; DN=&quot;Ref&quot; S=&quot;2.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;Referral Source&lt;/caption&gt;&lt;paragraph&gt;&lt;content&gt;Dr. Nutritious&lt;/content&gt;&lt;/paragraph&gt;&lt;/section&gt;&lt;section&gt;&lt;caption&gt;&lt;caption_cd V=&quot;20102&quot; DN=&quot;CC&quot; S=&qu
 ot;2.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;Chief Complaint/Reason for Visit&lt;/caption&gt;&lt;paragraph&gt;&lt;content&gt;Medical Nutrition Therapy for Hyperlipidemia&lt;/content&gt;&lt;/paragraph&gt;&lt;/section&gt;&lt;section&gt;&lt;caption&gt;&lt;caption_cd V=&quot;20103&quot; DN=&quot;HPI&quot; S=&quot;2.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;History of Present Illness&lt;/caption&gt;&lt;table&gt;&lt;caption&gt;&lt;caption_cd V=&quot;20003&quot; DN=&quot;HPI&quot; S=&quot;2.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;&lt;/caption&gt;&lt;tr&gt;&lt;th&gt;Problem&lt;/th&gt;&lt;th&gt;History&lt;/th&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td/&gt;&lt;td&gt;&lt;paragraph&gt;&lt;content&gt;Referral from: Julie Tester, RD, LD, CNSD&lt;/content&gt;&lt;/paragraph&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td/&gt;&lt;td&gt;&lt;paragraph&gt;&lt;content&gt;Phone contact: (555) 555-1212&lt;/content&gt;&lt;/paragraph&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td/&gt;&lt;
 td&gt;&lt;paragraph&gt;&lt;content&gt;Height: 144 cm   Current Weight: 45 kg   Date of current weight: 02-29-2001   Admit Weight:  53 kg   BMI: 18 kg/m2&lt;/content&gt;&lt;/paragraph&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td/&gt;&lt;td&gt;&lt;paragraph&gt;&lt;content&gt;Diet: General&lt;/content&gt;&lt;/paragraph&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td/&gt;&lt;td&gt;&lt;paragraph&gt;&lt;content&gt;Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity.&lt;/content&gt;&lt;/paragraph&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td/&gt;&lt;td&gt;&lt;paragraph&gt;&lt;content&gt;Daily Protein needs: 40 grams,  assessed as 1.0 g/kg.&lt;/content&gt;&lt;/paragraph&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td/&gt;&lt;td&gt;&lt;paragraph&gt;&lt;content&gt;Pt has been on a 3 day calorie count and has had an average intake of 1100 calories.  She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.  She agrees with the plan and has my number 
 for further assessment. May want a Resting Metabolic Rate as well. She takes an aspirin a day for knee pain.&lt;/content&gt;&lt;/paragraph&gt;&lt;/td&gt;&lt;/tr&gt;&lt;/table&gt;&lt;table&gt;&lt;caption&gt;&lt;caption_cd V=&quot;20004&quot; DN=&quot;MC985&quot; S=&quot;2.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;&lt;/caption&gt;&lt;tr&gt;&lt;th&gt;&lt;caption_cd V=&quot;30001&quot; DN=&quot;PFH Date&quot; S=&quot;2.16.840.1.113883.3.1.22&quot; SV=&quot;1.0&quot;/&gt;PFH Date&lt;/th&gt;&lt;th&gt;&lt;caption_cd V=&quot;30002&quot; DN=&quot;CVI Page#&quot; S=&quot;2.16.840.1.113883.3.1.22&quot; SV=&quot;1.0&quot;/&gt;CVI Page#&lt;/th&gt;&lt;th&gt;&lt;caption_cd V=&quot;30003&quot; DN=&quot;CVI Date&quot; S=&quot;2.16.840.1.113883.3.1.22&quot; SV=&quot;1.0&quot;/&gt;CVI Date&lt;/th&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;/tr&gt;&lt;/table&gt;&lt;/section&gt;&lt;section&gt;&lt;caption&gt;&lt;caption_cd V=&quot;20107&quo
 t; DN=&quot;Med/Surg Hx&quot; S=&quot;2.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;Past Medical/Surgical History&lt;/caption&gt;&lt;/section&gt;&lt;section&gt;&lt;caption&gt;&lt;caption_cd V=&quot;20105&quot; DN=&quot;Allerg&quot; S=&quot;2.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;Allergies&lt;/caption&gt;&lt;/section&gt;&lt;section&gt;&lt;caption&gt;&lt;caption_cd V=&quot;20108&quot; DN=&quot;Soc Hist&quot; S=&quot;2.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;Social History&lt;/caption&gt;&lt;/section&gt;&lt;section&gt;&lt;caption&gt;&lt;caption_cd V=&quot;20109&quot; DN=&quot;Fam Hist&quot; S=&quot;2.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;Family History&lt;/caption&gt;&lt;/section&gt;&lt;section&gt;&lt;caption&gt;&lt;caption_cd V=&quot;20104&quot; DN=&quot;Meds&quot; S=&quot;2.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;Current Medications&lt;/caption&gt;&lt;/section&gt;&lt;section&gt;&lt;caption&gt;&lt;caption_cd V=&quot;2
 0106&quot; DN=&quot;Sys Rev&quot; S=&quot;2.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;System Review&lt;/caption&gt;&lt;/section&gt;&lt;section&gt;&lt;caption&gt;&lt;caption_cd V=&quot;20115&quot; DN=&quot;Spec Instr&quot; S=&quot;.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;Special Instructions&lt;/caption&gt;&lt;/section&gt;&lt;section&gt;&lt;caption&gt;&lt;caption_cd V=&quot;20114&quot; DN=&quot;Administrative&quot; S=&quot;2.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;Administrative&lt;/caption&gt;&lt;table&gt;&lt;caption&gt;&lt;caption_cd V=&quot;20005&quot; DN=&quot;Billing&quot; S=&quot;2.16.840.1.113883.3.1.21&quot; SV=&quot;1.0&quot;/&gt;&lt;/caption&gt;&lt;tr&gt;&lt;th&gt;Billing&lt;/th&gt;&lt;th&gt;Value&lt;/th&gt;&lt;/tr&gt;&lt;tr&gt;&lt;th&gt;&lt;caption_cd V=&quot;30004&quot; DN=&quot;Margin Code&quot; S=&quot;2.16.840.1.113883.3.1.22&quot; SV=&quot;1.0&quot;/&gt;Margin Code&lt;/th&gt;&lt;td&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;th&gt;
 &lt;caption_cd V=&quot;30005&quot; DN=&quot;Total Time&quot; S=&quot;2.16.840.1.113883.3.1.22&quot; SV=&quot;1.0&quot;/&gt;Total Time&lt;/th&gt;&lt;td&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;th&gt;&lt;caption_cd V=&quot;30006&quot; DN=&quot;Counseling Time&quot; S=&quot;2.16.840.1.113883.3.1.22&quot; SV=&quot;1.0&quot;/&gt;Counseling Time&lt;/th&gt;&lt;td&gt;&lt;/td&gt;&lt;/tr&gt;&lt;/table&gt;&lt;/section&gt;&lt;/body&gt;&lt;/levelone&gt;"/>
     <uima.cas.Sofa _indexed="0" _id="18" sofaNum="2" sofaID="plaintext" mimeType="text" sofaString="[start section id=&quot;20101&quot;]&#10;&#10;Dr. Nutritious&#10;&#10;[end section id=&quot;20101&quot;]&#10;&#10;[start section id=&quot;20102&quot;]&#10;&#10;Medical Nutrition Therapy for Hyperlipidemia&#10;&#10;[end section id=&quot;20102&quot;]&#10;&#10;[start section id=&quot;20103&quot;]&#10;&#10;Referral from: Julie Tester, RD, LD, CNSD&#10;Phone contact: (555) 555-1212&#10;Height: 144 cm   Current Weight: 45 kg   Date of current weight: 02-29-2001   Admit Weight:  53 kg   BMI: 18 kg/m2&#10;Diet: General&#10;Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity.&#10;Daily Protein needs: 40 grams,  assessed as 1.0 g/kg.&#10;Pt has been on a 3-day calorie count and has had an average intake of 1100 calories.  She was instructed to drink 2-3 cans of liquid supplement to help promote weight gain.  She agrees with the plan and has my number for furthe
 r assessment. May want a Resting Metabolic Rate as well. She takes an aspirin a day for knee pain.&#10;&#10;[end section id=&quot;20103&quot;]&#10;&#10;"/>

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/test/data/testpatient_cn_1.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/test/data/testpatient_cn_1.xml?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/test/data/testpatient_cn_1.xml (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/test/data/testpatient_cn_1.xml Thu Sep 20 16:07:04 2012
@@ -1 +1,20 @@
-<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE levelone SYSTEM "NotesIIST_RTF.DTD" [<!ENTITY deg '&#x00B0;'><!ENTITY sup2 '&#x00B2;'><!ENTITY micro '&#x00B5;'>]><levelone><clinical_document_header><id EX="###DOC_ID###" RT="2.16.840.1.113883.3.2.1.1"/><set_id EX="###SET_ID###" RT="2.16.840.1.113883.3.2.1.2"/><version_nbr V="###V_NBR###"/><document_type_cd V="687" S="2.16.840.1.113883.3.2.1.3" DN="Nutrition Consult"/><origination_dttm V="20030822T131513"/><confidentiality_cd V="0" S="2.16.840.1.113883.3.2.1.4"/><patient_encounter><practice_setting_cd V="4284" S="2.16.840.1.113883.3.2.1.7" DN="Nutr Clinic"/><encounter_tmr V="20030822"/><service_location><id EX="TBD" RT="2.16.840.1.113883.3.2.1.8"/></service_location><facility><organization><organization.nm V="MCR"/></organization></facility></patient_encounter><legal_authenticator><legal_authenticator.type_cd V="SPV"/><participation_tmr V=""/><signature_cd V="S"/><person><id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/><perso
 n_name><nm><GIV V="Julie"/><MID V="A"/><FAM V="Tester"/><PFX V=""/><SFX V="RD"/></nm><person_name.type_cd V="S"/></person_name></person></legal_authenticator><originator><originator.type_cd V="AUT"/><participation_tmr V="20030822T131513"/><person><id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/><person_name><nm><GIV V="Julie"/><MID V="A."/><FAM V="Tester"/><PFX V=""/><SFX V="RD"/></nm><person_name.type_cd V="L"/></person_name><telecom V="5-5555" USE="PG"/></person></originator><originating_organization><originating_organization.type_cd V="CST"/><organization><id EX="TBD" RT="2.16.840.1.113883.3.2.1.10"/><organization.nm V="Originating Organization - Coding TBD"/></organization></originating_organization><transcriptionist><transcriptionist.type_cd V="ENT"/><participation_tmr V="20030822T131513"/><person><id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/><person_name><nm><GIV V="Julie"/><MID V="A."/><FAM V="Tester"/></nm><person_name.type_cd V="L"/></person_name></person></tra
 nscriptionist><provider><provider.type_cd V="CON"/><participation_tmr V="20030822T131513"/><person><id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/><person_name><nm><GIV V="Julie"/><MID V="A."/><FAM V="Tester"/><PFX V=""/><SFX V="RD"/></nm><person_name.type_cd V="L"/></person_name><telecom V="5-5555" USE="PG"/></person></provider><patient><patient.type_cd V="PATSBJ"/><person><id EX="3-303-925" RT="2.16.840.1.113883.3.2.1.1"/><person_name><nm><GIV V="Terri"/><MID V="A."/><FAM V="Testing"/><PFX V="Judge"/><SFX V="Jr.,D.D.S."/></nm><person_name.type_cd V="L"/></person_name><addr><LIT V="100 Quality Control Avenue"/><CTY V="Rochester"/><STA V="MN"/><ZIP V="55905"/><CNT V="US"/></addr></person><is_known_by><id EX="TBD" RT="2.16.840.1.113883.3.2.2.1"/><is_known_to><id EX="TBD" RT="2.16.840.1.113883.3.2.1.10"/></is_known_to></is_known_by><birth_dttm V="19341123"/><administrative_gender_cd V="F" S="2.16.840.1.113883.3.2.2.2"/></patient><status_cd V="TBD" S="2.16.840.1.113883.3.2.1.
 16"/><cn1_admin_data><cn1_status_cd V="Fnl" S="2.16.840.1.113883.3.2.3.1"/><cn1_service_cd V="MNT" S="2.16.840.1.113883.3.2.3.2"/><cn1_event_cd V="CON" S="2.16.840.1.113883.3.2.3.3"/><cn1_document_id EX="000000000" RT="2.16.840.1.113883.3.2.3.4"/><cn1_revision_nbr V="1"/><cn1_site_cd V="RCH" S="2.16.840.1.113883.3.2.3.10"/></cn1_admin_data><document_title V="Document Service Name - Coding TBD" S="2.16.840.1.113883.3.2.1.17"/></clinical_document_header><body><section><caption><caption_cd V="20100" DN="Revision History" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Revision History</caption></section><section><caption><caption_cd V="20112" DN="I/R/P" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Impression / Report / Plan</caption><table><caption><caption_cd V="20003" DN="I/R/P" S="2.16.840.1.113883.3.1.21" SV="1.0"/></caption><tr><th>Problem</th><th>Plan</th></tr></table></section><section><caption><caption_cd V="20113" DN="Diagnoses" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Diagnosis</capti
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\ No newline at end of file
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+
+    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.
+
+-->

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/test/data/testpatient_cn_2.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/test/data/testpatient_cn_2.xml?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/test/data/testpatient_cn_2.xml (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/test/data/testpatient_cn_2.xml Thu Sep 20 16:07:04 2012
@@ -1 +1,20 @@
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 cipation_tmr V="20030822T131513"/><person><id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/><person_name><nm><GIV V="Julie"/><MID V="A."/><FAM V="Tester"/><PFX V=""/><SFX V="RD"/></nm><person_name.type_cd V="L"/></person_name><telecom V="5-5555" USE="PG"/></person></provider><patient><patient.type_cd V="PATSBJ"/><person><id EX="3-303-925" RT="2.16.840.1.113883.3.2.1.1"/><person_name><nm><GIV V="Terri"/><MID V="A."/><FAM V="Testing"/><PFX V="Judge"/><SFX V="Jr.,D.D.S."/></nm><person_name.type_cd V="L"/></person_name><addr><LIT V="100 Quality Control Avenue"/><CTY V="Rochester"/><STA V="MN"/><ZIP V="55905"/><CNT V="US"/></addr></person><is_known_by><id EX="TBD" RT="2.16.840.1.113883.3.2.2.1"/><is_known_to><id EX="TBD" RT="2.16.840.1.113883.3.2.1.10"/></is_known_to></is_known_by><birth_dttm V="19341123"/><administrative_gender_cd V="F" S="2.16.840.1.113883.3.2.2.2"/></patient><status_cd V="TBD" S="2.16.840.1.113883.3.2.1.16"/><cn1_admin_data><cn1_status_cd V="Fnl" S="2.16.840.1
 .113883.3.2.3.1"/><cn1_service_cd V="MNT" S="2.16.840.1.113883.3.2.3.2"/><cn1_event_cd V="CON" S="2.16.840.1.113883.3.2.3.3"/><cn1_document_id EX="000000000" RT="2.16.840.1.113883.3.2.3.4"/><cn1_revision_nbr V="1"/><cn1_site_cd V="RCH" S="2.16.840.1.113883.3.2.3.10"/></cn1_admin_data><document_title V="Document Service Name - Coding TBD" S="2.16.840.1.113883.3.2.1.17"/></clinical_document_header><body><section><caption><caption_cd V="20100" DN="Revision History" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Revision History</caption></section><section><caption><caption_cd V="20112" DN="I/R/P" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Impression / Report / Plan</caption><table><caption><caption_cd V="20003" DN="I/R/P" S="2.16.840.1.113883.3.1.21" SV="1.0"/></caption><tr><th>Problem</th><th>Plan</th></tr></table></section><section><caption><caption_cd V="20113" DN="Diagnoses" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Diagnosis</caption><table><caption><caption_cd V="20003" DN="Diagnoses" S
 ="2.16.840.1.113883.3.1.21" SV="1.0"/></caption><tr><th>Problem</th><th>Diagnosis</th></tr></table></section><section><caption><caption_cd V="20101" DN="Ref" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Referral Source</caption><paragraph><content>Dr. Nutritious</content></paragraph></section><section><caption><caption_cd V="20102" DN="CC" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Chief Complaint/Reason for Visit</caption><paragraph><content>Medical Nutrition Therapy for Hyperlipidemia</content></paragraph></section><section><caption><caption_cd V="20103" DN="HPI" S="2.16.840.1.113883.3.1.21" SV="1.0"/>History of Present Illness</caption><table><caption><caption_cd V="20003" DN="HPI" S="2.16.840.1.113883.3.1.21" SV="1.0"/></caption><tr><th>Problem</th><th>History</th></tr><tr><td/><td><paragraph><content>Significant for her father, who died at 50 years from colon cancer.</content></paragraph></td></tr><tr><td/><td><paragraph><content>Phone contact: (555) 555-1212</content></paragraph
 ></td></tr><tr><td/><td><paragraph><content>Height: 144 cm   Current Weight: 45 kg</content></paragraph></td></tr><tr><td/><td><paragraph><content>Diet: General</content></paragraph></td></tr><tr><td/><td><paragraph><content>Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity.</content></paragraph></td></tr><tr><td/><td><paragraph><content>Daily Protein needs: 40 grams,  assessed as 1.0 g/kg.</content></paragraph></td></tr><tr><td/><td><paragraph><content>Colonoscopy. No pain or discomfort reported.</content></paragraph></td></tr></table></section></body></levelone>
\ No newline at end of file
+<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE levelone SYSTEM "NotesIIST_RTF.DTD" [<!ENTITY deg '&#x00B0;'><!ENTITY sup2 '&#x00B2;'><!ENTITY micro '&#x00B5;'>]><levelone><clinical_document_header><id EX="###DOC_ID###" RT="2.16.840.1.113883.3.2.1.1"/><set_id EX="###SET_ID###" RT="2.16.840.1.113883.3.2.1.2"/><version_nbr V="###V_NBR###"/><document_type_cd V="687" S="2.16.840.1.113883.3.2.1.3" DN="Nutrition Consult"/><origination_dttm V="20030822T131513"/><patient_encounter><practice_setting_cd V="4284" S="2.16.840.1.113883.3.2.1.7" DN="Nutr Clinic"/><encounter_tmr V="20030822"/><service_location><id EX="TBD" RT="2.16.840.1.113883.3.2.1.8"/></service_location><facility><organization><organization.nm V="MCR"/></organization></facility></patient_encounter><legal_authenticator><legal_authenticator.type_cd V="SPV"/><participation_tmr V=""/><signature_cd V="S"/><person><id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/><person_name><nm><GIV V="Julie"/><MID V="A"/><FAM V="Tester"/><
 PFX V=""/><SFX V="RD"/></nm><person_name.type_cd V="S"/></person_name></person></legal_authenticator><originator><originator.type_cd V="AUT"/><participation_tmr V="20030822T131513"/><person><id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/><person_name><nm><GIV V="Julie"/><MID V="A."/><FAM V="Tester"/><PFX V=""/><SFX V="RD"/></nm><person_name.type_cd V="L"/></person_name><telecom V="5-5555" USE="PG"/></person></originator><originating_organization><originating_organization.type_cd V="CST"/><organization><id EX="TBD" RT="2.16.840.1.113883.3.2.1.10"/><organization.nm V="Originating Organization - Coding TBD"/></organization></originating_organization><transcriptionist><transcriptionist.type_cd V="ENT"/><participation_tmr V="20030822T131513"/><person><id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/><person_name><nm><GIV V="Julie"/><MID V="A."/><FAM V="Tester"/></nm><person_name.type_cd V="L"/></person_name></person></transcriptionist><provider><provider.type_cd V="CON"/><parti
 cipation_tmr V="20030822T131513"/><person><id EX="99999999" RT="2.16.840.1.113883.3.2.1.9"/><person_name><nm><GIV V="Julie"/><MID V="A."/><FAM V="Tester"/><PFX V=""/><SFX V="RD"/></nm><person_name.type_cd V="L"/></person_name><telecom V="5-5555" USE="PG"/></person></provider><patient><patient.type_cd V="PATSBJ"/><person><id EX="3-303-925" RT="2.16.840.1.113883.3.2.1.1"/><person_name><nm><GIV V="Terri"/><MID V="A."/><FAM V="Testing"/><PFX V="Judge"/><SFX V="Jr.,D.D.S."/></nm><person_name.type_cd V="L"/></person_name><addr><LIT V="100 Quality Control Avenue"/><CTY V="Rochester"/><STA V="MN"/><ZIP V="55905"/><CNT V="US"/></addr></person><is_known_by><id EX="TBD" RT="2.16.840.1.113883.3.2.2.1"/><is_known_to><id EX="TBD" RT="2.16.840.1.113883.3.2.1.10"/></is_known_to></is_known_by><birth_dttm V="19341123"/><administrative_gender_cd V="F" S="2.16.840.1.113883.3.2.2.2"/></patient><status_cd V="TBD" S="2.16.840.1.113883.3.2.1.16"/><cn1_admin_data><cn1_status_cd V="Fnl" S="2.16.840.1
 .113883.3.2.3.1"/><cn1_service_cd V="MNT" S="2.16.840.1.113883.3.2.3.2"/><cn1_event_cd V="CON" S="2.16.840.1.113883.3.2.3.3"/><cn1_document_id EX="000000000" RT="2.16.840.1.113883.3.2.3.4"/><cn1_revision_nbr V="1"/><cn1_site_cd V="RCH" S="2.16.840.1.113883.3.2.3.10"/></cn1_admin_data><document_title V="Document Service Name - Coding TBD" S="2.16.840.1.113883.3.2.1.17"/></clinical_document_header><body><section><caption><caption_cd V="20100" DN="Revision History" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Revision History</caption></section><section><caption><caption_cd V="20112" DN="I/R/P" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Impression / Report / Plan</caption><table><caption><caption_cd V="20003" DN="I/R/P" S="2.16.840.1.113883.3.1.21" SV="1.0"/></caption><tr><th>Problem</th><th>Plan</th></tr></table></section><section><caption><caption_cd V="20113" DN="Diagnoses" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Diagnosis</caption><table><caption><caption_cd V="20003" DN="Diagnoses" S
 ="2.16.840.1.113883.3.1.21" SV="1.0"/></caption><tr><th>Problem</th><th>Diagnosis</th></tr></table></section><section><caption><caption_cd V="20101" DN="Ref" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Referral Source</caption><paragraph><content>Dr. Nutritious</content></paragraph></section><section><caption><caption_cd V="20102" DN="CC" S="2.16.840.1.113883.3.1.21" SV="1.0"/>Chief Complaint/Reason for Visit</caption><paragraph><content>Medical Nutrition Therapy for Hyperlipidemia</content></paragraph></section><section><caption><caption_cd V="20103" DN="HPI" S="2.16.840.1.113883.3.1.21" SV="1.0"/>History of Present Illness</caption><table><caption><caption_cd V="20003" DN="HPI" S="2.16.840.1.113883.3.1.21" SV="1.0"/></caption><tr><th>Problem</th><th>History</th></tr><tr><td/><td><paragraph><content>Significant for her father, who died at 50 years from colon cancer.</content></paragraph></td></tr><tr><td/><td><paragraph><content>Phone contact: (555) 555-1212</content></paragraph
 ></td></tr><tr><td/><td><paragraph><content>Height: 144 cm   Current Weight: 45 kg</content></paragraph></td></tr><tr><td/><td><paragraph><content>Diet: General</content></paragraph></td></tr><tr><td/><td><paragraph><content>Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for activity.</content></paragraph></td></tr><tr><td/><td><paragraph><content>Daily Protein needs: 40 grams,  assessed as 1.0 g/kg.</content></paragraph></td></tr><tr><td/><td><paragraph><content>Colonoscopy. No pain or discomfort reported.</content></paragraph></td></tr></table></section></body></levelone><!--
+
+    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.
+
+-->

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/.classpath
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/.classpath?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/.classpath (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/.classpath Thu Sep 20 16:07:04 2012
@@ -1,28 +1,9 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/UIMA"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/cTakes"/>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<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 kind="con" path="org.eclipse.jdt.USER_LIBRARY/cTakes"/>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/data/test/output/testfakenote.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/data/test/output/testfakenote.xml?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/data/test/output/testfakenote.xml (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/data/test/output/testfakenote.xml Thu Sep 20 16:07:04 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.
+
+-->
 <CAS version="2">
     <uima.cas.Sofa _indexed="0" _id="6" sofaNum="1" sofaID="_InitialView" mimeType="text" sofaString="Mr. Johnson is presenting signs of a shark bite.  It occurred last week and has caused immense leg pain.  The pain was so severe that he had begun taking narcotics to relieve it.&#10;&#10;The patient also was concerned about a small lesion in his Broca's area and said the lesion was causing him to lettuce Wednesday baseball applesauce.&#10;&#10;After imaging which was inconclusive, the patient was released to go home and treat his pain himself.&#10;&#10;"/>
     <uima.tcas.DocumentAnnotation _indexed="1" _id="1" _ref_sofa="6" begin="0" end="434" language="en"/>

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/desc/ConstituencyParserAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/desc/ConstituencyParserAnnotator.xml?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/desc/ConstituencyParserAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/desc/ConstituencyParserAnnotator.xml Thu Sep 20 16:07:04 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>true</primitive>

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/desc/analysis_engine/AggregateParsingProcessor.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/desc/analysis_engine/AggregateParsingProcessor.xml?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/desc/analysis_engine/AggregateParsingProcessor.xml (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/desc/analysis_engine/AggregateParsingProcessor.xml Thu Sep 20 16:07:04 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>

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/desc/analysis_engine/ParserEvaluatorAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/desc/analysis_engine/ParserEvaluatorAnnotator.xml?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/desc/analysis_engine/ParserEvaluatorAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/desc/analysis_engine/ParserEvaluatorAnnotator.xml Thu Sep 20 16:07:04 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>true</primitive>

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/desc/cas_consumer/ParseTreeWriterConsumer.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/desc/cas_consumer/ParseTreeWriterConsumer.xml?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/desc/cas_consumer/ParseTreeWriterConsumer.xml (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/desc/cas_consumer/ParseTreeWriterConsumer.xml Thu Sep 20 16:07:04 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.
+
+-->
 <casConsumerDescription xmlns="http://uima.apache.org/resourceSpecifier">
   <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
   <implementationName>org.chboston.cnlp.ctakes.parser.uima.co.ParserTreeWriterConsumer</implementationName>

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/desc/collection_processing_engine/ParsingCPE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/desc/collection_processing_engine/ParsingCPE.xml?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/desc/collection_processing_engine/ParsingCPE.xml (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/desc/collection_processing_engine/ParsingCPE.xml Thu Sep 20 16:07:04 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.
+
+-->
 <cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
     <collectionReader>
         <collectionIterator>

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/desc/types/LabeledTree.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/desc/types/LabeledTree.xml?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/desc/types/LabeledTree.xml (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/desc/types/LabeledTree.xml Thu Sep 20 16:07:04 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>LabeledTree</name>
   <description/>

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/metadata/install.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/metadata/install.xml?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/metadata/install.xml (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/metadata/install.xml Thu Sep 20 16:07:04 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>

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/MaxentParserWrapper.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/MaxentParserWrapper.java?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/MaxentParserWrapper.java (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/MaxentParserWrapper.java Thu Sep 20 16:07:04 2012
@@ -1,4 +1,21 @@
-/*    Copyright 2011 Children's Hospital Boston
+/**
+ * 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 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

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/ParserWrapper.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/ParserWrapper.java?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/ParserWrapper.java (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/ParserWrapper.java Thu Sep 20 16:07:04 2012
@@ -1,4 +1,21 @@
-/*    Copyright 2011 Children's Hospital Boston
+/**
+ * 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 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

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/treekernel/TreeExtractor.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/treekernel/TreeExtractor.java?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/treekernel/TreeExtractor.java (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/treekernel/TreeExtractor.java Thu Sep 20 16:07:04 2012
@@ -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.chboston.cnlp.ctakes.parser.treekernel;
 
 import java.util.ArrayList;

Modified: incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/treekernel/TreeKernel.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/treekernel/TreeKernel.java?rev=1388092&r1=1388091&r2=1388092&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/treekernel/TreeKernel.java (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/src/main/java/org/chboston/cnlp/ctakes/parser/treekernel/TreeKernel.java Thu Sep 20 16:07:04 2012
@@ -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.chboston.cnlp.ctakes.parser.treekernel;
 
 import opennlp.tools.parser.Parse;



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