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From chen...@apache.org
Subject svn commit: r1390134 [2/2] - in /incubator/ctakes/trunk: ./ ctakes-assertion/ ctakes-assertion/desc/ ctakes-assertion/lib/ ctakes-assertion/metadata/ ctakes-assertion/src/main/java/edu/mayo/bmi/attributes/ ctakes-assertion/src/main/java/edu/mayo/bmi/ui...
Date Tue, 25 Sep 2012 21:06:20 GMT
Modified: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/ConstraintConstructorFindContainedBy.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/ConstraintConstructorFindContainedBy.java?rev=1390134&r1=1389906&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/ConstraintConstructorFindContainedBy.java
(original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/ConstraintConstructorFindContainedBy.java
Tue Sep 25 21:06:18 2012
@@ -1,26 +1,22 @@
-/*
- * Copyright: (c) 2012   The MITRE Corporation. All rights reserved.
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
  *
- * Except as contained in the copyright notice above, or as used to identify 
- * MITRE  as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * http://www.apache.org/licenses/LICENSE-2.0 
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and 
- * limitations under the License. 
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
  */
-
-package org.mitre.medfacts.i2b2.api.ctakes;
+package org.apache.ctakes.assertion.medfacts.i2b2.api;
 
 import org.apache.uima.cas.ConstraintFactory;
 import org.apache.uima.cas.FSIntConstraint;

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

Modified: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/SingleDocumentProcessorCtakes.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/SingleDocumentProcessorCtakes.java?rev=1390134&r1=1389906&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/SingleDocumentProcessorCtakes.java
(original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/SingleDocumentProcessorCtakes.java
Tue Sep 25 21:06:18 2012
@@ -1,26 +1,22 @@
-/*
- * Copyright: (c) 2012   The MITRE Corporation. All rights reserved.
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
  *
- * Except as contained in the copyright notice above, or as used to identify 
- * MITRE  as the author of this software, the trade names, trademarks, service
- * marks, or product names of the copyright holder shall not be used in
- * advertising, promotion or otherwise in connection with this software without
- * prior written authorization of the copyright holder.
- * 
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- * http://www.apache.org/licenses/LICENSE-2.0 
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and 
- * limitations under the License. 
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
  */
-
-package org.mitre.medfacts.i2b2.api.ctakes;
+package org.apache.ctakes.assertion.medfacts.i2b2.api;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -47,14 +43,14 @@ import org.mitre.medfacts.zoner.Characte
 import org.mitre.medfacts.zoner.LineAndTokenPosition;
 import org.mitre.medfacts.zoner.LineTokenToCharacterOffsetConverter;
 
-import edu.mayo.bmi.uima.core.type.syntax.BaseToken;
-import edu.mayo.bmi.uima.core.type.syntax.PunctuationToken;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence;
-import edu.mayo.bmi.uima.core.type.textspan.Sentence_Type;
-import edu.mayo.bmi.uima.core.type.syntax.WordToken;
-import edu.mayo.bmi.uima.core.type.syntax.NumToken;
-import edu.mayo.bmi.uima.core.type.syntax.NewlineToken;
-import edu.mayo.bmi.uima.core.type.syntax.SymbolToken;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.PunctuationToken;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.ctakes.typesystem.type.textspan.Sentence_Type;
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.syntax.NumToken;
+import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
+import org.apache.ctakes.typesystem.type.syntax.SymbolToken;
 
 public class SingleDocumentProcessorCtakes extends SingleDocumentProcessor
 {

Modified: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Assertion.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Assertion.java?rev=1390134&r1=1389906&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Assertion.java
(original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Assertion.java
Tue Sep 25 21:06:18 2012
@@ -1,7 +1,25 @@
+/**
+ * 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.
+ */
 
 
 /* First created by JCasGen Mon May 23 12:04:33 EDT 2011 */
-package org.mitre.medfacts.types;
+package org.apache.ctakes.assertion.medfacts.types;
 
 import org.apache.uima.jcas.JCas; 
 import org.apache.uima.jcas.JCasRegistry;

Modified: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Assertion_Type.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Assertion_Type.java?rev=1390134&r1=1389906&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Assertion_Type.java
(original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Assertion_Type.java
Tue Sep 25 21:06:18 2012
@@ -1,6 +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.
+ */
 
 /* First created by JCasGen Mon May 23 12:04:34 EDT 2011 */
-package org.mitre.medfacts.types;
+package org.apache.ctakes.assertion.medfacts.types;
 
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.JCasRegistry;

Modified: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Concept.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Concept.java?rev=1390134&r1=1389906&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Concept.java
(original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Concept.java
Tue Sep 25 21:06:18 2012
@@ -1,7 +1,25 @@
+/**
+ * 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.
+ */
 
 
 /* First created by JCasGen Mon May 23 12:04:34 EDT 2011 */
-package org.mitre.medfacts.types;
+package org.apache.ctakes.assertion.medfacts.types;
 
 import org.apache.uima.jcas.JCas; 
 import org.apache.uima.jcas.JCasRegistry;

Modified: incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Concept_Type.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Concept_Type.java?rev=1390134&r1=1389906&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Concept_Type.java
(original)
+++ incubator/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/types/Concept_Type.java
Tue Sep 25 21:06:18 2012
@@ -1,6 +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.
+ */
 
 /* First created by JCasGen Mon May 23 12:04:34 EDT 2011 */
-package org.mitre.medfacts.types;
+package org.apache.ctakes.assertion.medfacts.types;
 
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.JCasRegistry;

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml?rev=1390134&r1=1390133&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/pom.xml Tue Sep 25 21:06:18 2012
@@ -60,6 +60,14 @@
 			<groupId>org.apache.ctakes</groupId>
 			<artifactId>ctakes-pos-tagger</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-assertion</artifactId>
+		</dependency>	
+		<dependency>
+			<groupId>org.apache.ctakes</groupId>
+			<artifactId>ctakes-dependency-parser</artifactId>
+		</dependency>			
 	</dependencies>
 	
 </project>

Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/resources/launch/UIMA_CVD--clinical_documents_pipeline.launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/resources/launch/UIMA_CVD--clinical_documents_pipeline.launch?rev=1390134&r1=1390133&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/resources/launch/UIMA_CVD--clinical_documents_pipeline.launch
(original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/resources/launch/UIMA_CVD--clinical_documents_pipeline.launch
Tue Sep 25 21:06:18 2012
@@ -1,15 +1,41 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/ctakes-clinical-pipeline"/>
-</listAttribute>
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
-<listEntry value="4"/>
-</listAttribute>
-<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
-<stringAttribute key="org.eclipse.debug.ui.target_debug_perspective" value="perspective_default"/>
-<stringAttribute key="org.eclipse.debug.ui.target_run_perspective" value="perspective_default"/>
-<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.annot_view.Gladis"/>
-<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-clinical-pipeline"/>
-<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="&quot;-Djava.util.logging.config.file=${env_var:UIMA_HOME}/Logger.properties&quot;
 -Xms500M -Xmx1g"/>
-</launchConfiguration>
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
+<listEntry value="/ctakes-clinical-pipeline"/>
+</listAttribute>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+<listEntry value="4"/>
+</listAttribute>
+<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
+<stringAttribute key="org.eclipse.debug.ui.target_debug_perspective" value="perspective_default"/>
+<stringAttribute key="org.eclipse.debug.ui.target_run_perspective" value="perspective_default"/>
+<listAttribute key="org.eclipse.jdt.launching.CLASSPATH">
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
containerPath=&quot;org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6&quot;
path=&quot;1&quot; type=&quot;4&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
path=&quot;3&quot; projectName=&quot;ctakes-clinical-pipeline&quot; type=&quot;1&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
containerPath=&quot;org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER&quot; path=&quot;3&quot;
type=&quot;4&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
internalArchive=&quot;/ctakes-dependency-parser/resources&quot; path=&quot;3&quot;
type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
internalArchive=&quot;/ctakes-assertion/resources&quot; path=&quot;3&quot;
type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
internalArchive=&quot;/ctakes-chunker/resources&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
internalArchive=&quot;/ctakes-clinical-pipeline/resources&quot; path=&quot;3&quot;
type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
internalArchive=&quot;/ctakes-constituency-parser/resources&quot; path=&quot;3&quot;
type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
internalArchive=&quot;/ctakes-context-tokenizer/resources&quot; path=&quot;3&quot;
type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
internalArchive=&quot;/ctakes-core/resources&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
internalArchive=&quot;/ctakes-coreference/resources&quot; path=&quot;3&quot;
type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
internalArchive=&quot;/ctakes-dictionary-lookup/resources&quot; path=&quot;3&quot;
type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
internalArchive=&quot;/ctakes-drug-ner/resources&quot; path=&quot;3&quot;
type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
internalArchive=&quot;/ctakes-lvg/resources&quot; path=&quot;3&quot; type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
internalArchive=&quot;/ctakes-ne-contexts/resources&quot; path=&quot;3&quot;
type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
internalArchive=&quot;/ctakes-pad-term-spotter/resources&quot; path=&quot;3&quot;
type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
internalArchive=&quot;/ctakes-pos-tagger/resources&quot; path=&quot;3&quot;
type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
internalArchive=&quot;/ctakes-preprocessor/resources&quot; path=&quot;3&quot;
type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
internalArchive=&quot;/ctakes-relation-extractor/resources&quot; path=&quot;3&quot;
type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
internalArchive=&quot;/ctakes-side-effect/resources&quot; path=&quot;3&quot;
type=&quot;2&quot;/&gt;&#13;&#10;"/>
+<listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;
standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry
internalArchive=&quot;/ctakes-smoking-status/resources&quot; path=&quot;3&quot;
type=&quot;2&quot;/&gt;&#13;&#10;"/>
+</listAttribute>
+<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.m2e.launchconfig.classpathProvider"/>
+<booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="false"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.annot_view.Gladis"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-clinical-pipeline"/>
+<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
+<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="&quot;-Djava.util.logging.config.file=${env_var:UIMA_HOME}/Logger.properties&quot;
 -Xms500M -Xmx1g"/>
+</launchConfiguration>

Modified: incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyUtility.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyUtility.java?rev=1390134&r1=1390133&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyUtility.java
(original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyUtility.java
Tue Sep 25 21:06:18 2012
@@ -38,7 +38,7 @@ import org.apache.ctakes.typesystem.type
  */
 public abstract class DependencyUtility {
 
-	public static Logger logger = Logger.getLogger("edu.mayo.bmi.nlp.parser.util.DependencyUtility");
+	public static Logger logger = Logger.getLogger("org.apache.ctakes.dependency.parser.util.DependencyUtility");
 
 	public static void addToIndexes( JCas jcas, ArrayList<ConllDependencyNode> nodes )
{
 		for (int i=0; i<nodes.size(); i++) {

Modified: incubator/ctakes/trunk/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/pom.xml?rev=1390134&r1=1390133&r2=1390134&view=diff
==============================================================================
--- incubator/ctakes/trunk/pom.xml (original)
+++ incubator/ctakes/trunk/pom.xml Tue Sep 25 21:06:18 2012
@@ -45,7 +45,7 @@
 		<module>ctakes-relation-extractor</module>
 		<module>ctakes-clinical-pipeline</module>
 		<module>ctakes-pad-term-spotter</module>
-		<module>ctakes-assertion</module>		
+		<module>ctakes-assertion</module>
 	</modules>
 	<dependencyManagement>
 		<dependencies>
@@ -110,7 +110,7 @@
 					ctakes-assertion
 				</artifactId>
 				<version>${ctakes.version}</version>
-			</dependency>			
+			</dependency>
 			<dependency>
 				<groupId>org.apache.ctakes</groupId>
 				<artifactId>
@@ -149,6 +149,13 @@
 			<dependency>
 				<groupId>org.apache.ctakes</groupId>
 				<artifactId>
+					ctakes-dependency-parser
+				</artifactId>
+				<version>${ctakes.version}</version>
+			</dependency>
+			<dependency>
+				<groupId>org.apache.ctakes</groupId>
+				<artifactId>
 					ctakes-relation-extractor
 				</artifactId>
 				<version>${ctakes.version}</version>
@@ -264,6 +271,11 @@
 				<version>2.4</version>
 			</dependency>
 			<dependency>
+				<groupId>commons-cli</groupId>
+				<artifactId>commons-cli</artifactId>
+				<version>1.2</version>
+			</dependency>
+			<dependency>
 				<groupId>commons-logging</groupId>
 				<artifactId>commons-logging</artifactId>
 				<version>1.1.1</version>



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