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From vjapa...@apache.org
Subject svn commit: r1551254 [1/26] - in /ctakes/branches/ytex: ctakes-ytex-res/ ctakes-ytex-res/.settings/ ctakes-ytex-res/src/ ctakes-ytex-res/src/main/ ctakes-ytex-res/src/main/resources/ ctakes-ytex-res/src/main/resources/org/ ctakes-ytex-res/src/main/reso...
Date Mon, 16 Dec 2013 16:30:40 GMT
Author: vjapache
Date: Mon Dec 16 16:30:30 2013
New Revision: 1551254

URL: http://svn.apache.org/r1551254
Log:
ytex initial check-in

Added:
    ctakes/branches/ytex/ctakes-ytex/
    ctakes/branches/ytex/ctakes-ytex-res/
    ctakes/branches/ytex/ctakes-ytex-res/.classpath
    ctakes/branches/ytex/ctakes-ytex-res/.project
    ctakes/branches/ytex/ctakes-ytex-res/.settings/
    ctakes/branches/ytex/ctakes-ytex-res/.settings/org.eclipse.core.resources.prefs
    ctakes/branches/ytex/ctakes-ytex-res/.settings/org.eclipse.jdt.core.prefs
    ctakes/branches/ytex/ctakes-ytex-res/.settings/org.eclipse.m2e.core.prefs
    ctakes/branches/ytex/ctakes-ytex-res/LICENSE
    ctakes/branches/ytex/ctakes-ytex-res/pom.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/ehcache.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/jdl/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/jdl/xdl.xsd
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-datasource.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel-sim.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel.hbm.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/dictionary/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/dictionary/lookup/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_SNOMED.template.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_stem_SNOMED.template.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernel/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernel/ehcache.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernel/model/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernel/model/ClassifierEvaluation.hbm.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernel/model/KernelEvaluation.hbm.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/negex/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/negex/negex_triggers.txt
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/negex/negex_triggers_orig.txt
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/simSvcBeanRefContext.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/tools/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/tools/docanalyzer/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/tools/docanalyzer/icon.gif   (with props)
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/tools/docanalyzer/icon.psd   (with props)
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/tools/docanalyzer/logo.gif   (with props)
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/tools/docanalyzer/logo.psd   (with props)
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-dao.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-mapper.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima.hbm.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/Document.hbm.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/NamedEntityRegex.hbm.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/model/SegmentRegex.hbm.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/umls/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/umls/model/
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/umls/model/FWord.hbm.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/umls/model/UMLS.hbm.template.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex-default.properties
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex-umls.properties
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mssql.example
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mysql.example
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.orcl.example
    ctakes/branches/ytex/ctakes-ytex-res/src/test/
    ctakes/branches/ytex/ctakes-ytex-res/src/test/resources/
    ctakes/branches/ytex/ctakes-ytex-res/src/test/resources/org/
    ctakes/branches/ytex/ctakes-ytex-res/src/test/resources/org/apache/
    ctakes/branches/ytex/ctakes-ytex-res/src/test/resources/org/apache/ctakes/
    ctakes/branches/ytex/ctakes-ytex-res/src/test/resources/org/apache/ctakes/ytex/
    ctakes/branches/ytex/ctakes-ytex-res/src/test/resources/org/apache/ctakes/ytex/dictionary/
    ctakes/branches/ytex/ctakes-ytex-res/src/test/resources/org/apache/ctakes/ytex/dictionary/lookup/
    ctakes/branches/ytex/ctakes-ytex-uima/
    ctakes/branches/ytex/ctakes-ytex-uima/.classpath
    ctakes/branches/ytex/ctakes-ytex-uima/.project
    ctakes/branches/ytex/ctakes-ytex-uima/.settings/
    ctakes/branches/ytex/ctakes-ytex-uima/.settings/org.eclipse.core.resources.prefs
    ctakes/branches/ytex/ctakes-ytex-uima/.settings/org.eclipse.jdt.core.prefs
    ctakes/branches/ytex/ctakes-ytex-uima/.settings/org.eclipse.m2e.core.prefs
    ctakes/branches/ytex/ctakes-ytex-uima/LICENSE
    ctakes/branches/ytex/ctakes-ytex-uima/conceptGraph/
    ctakes/branches/ytex/ctakes-ytex-uima/conceptGraph/test.gz   (with props)
    ctakes/branches/ytex/ctakes-ytex-uima/conceptGraph/test.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DBConsumer.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DateAnnotator.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotator.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotatorOld.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DrugAggregatePlaintextProcessor.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/DrugNerDictionaryLookupAnnotator.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/MetaMapToCTakesAnnotator.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/NamedEntityRegexAnnotator.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/NegexAnnotator.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SenseDisambiguatorAnnotator.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SentenceDetectorAnnotator.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipeline.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipelineNoDBConsumer.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/collection_reader/
    ctakes/branches/ytex/ctakes-ytex-uima/desc/collection_reader/DBCollectionReader.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/
    ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/Coref-resolver_CPE.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/DrugNER_PlainText_CPE.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/FileSystemCollectionReader.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext_ctakes.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/cpe/test_plaintext_metamap.xml
    ctakes/branches/ytex/ctakes-ytex-uima/pom.xml
    ctakes/branches/ytex/ctakes-ytex-uima/src/
    ctakes/branches/ytex/ctakes-ytex-uima/src/main/
    ctakes/branches/ytex/ctakes-ytex-uima/src/main/java/
    ctakes/branches/ytex/ctakes-ytex-uima/src/main/java/org/
    ctakes/branches/ytex/ctakes-ytex-uima/src/main/java/org/apache/
    ctakes/branches/ytex/ctakes-ytex-uima/src/main/java/org/apache/ctakes/
    ctakes/branches/ytex/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/
    ctakes/branches/ytex/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/
    ctakes/branches/ytex/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java
    ctakes/branches/ytex/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/DBPing.java
    ctakes/branches/ytex/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/ExportCAS.java
    ctakes/branches/ytex/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/RunCPE.java
    ctakes/branches/ytex/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/SetupAuiFirstWord.java
    ctakes/branches/ytex/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/docanalyzer/
    ctakes/branches/ytex/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/docanalyzer/DBAnnotationViewerDialog.java
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/java/
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/java/org/
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/java/org/apache/
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/java/org/apache/ctakes/
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    ctakes/branches/ytex/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/DBCollectionReaderTest.java
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DBConsumerTest.java
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotatorTest.java
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DictionaryLookupAnnotatorTest.java
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/NamedEntityRegexTest.java
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SegmentRegexTest.java
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SentenceDetectorTest.java
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/resources/
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/resources/org/
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/resources/org/apache/
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/resources/org/apache/ctakes/
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/resources/org/apache/ctakes/ytex/
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/resources/org/apache/ctakes/ytex/dictionary/
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/resources/org/apache/ctakes/ytex/dictionary/lookup/
    ctakes/branches/ytex/ctakes-ytex/.classpath
    ctakes/branches/ytex/ctakes-ytex/.project
    ctakes/branches/ytex/ctakes-ytex/.settings/
    ctakes/branches/ytex/ctakes-ytex/.settings/org.eclipse.core.resources.prefs
    ctakes/branches/ytex/ctakes-ytex/.settings/org.eclipse.jdt.core.prefs
    ctakes/branches/ytex/ctakes-ytex/.settings/org.eclipse.m2e.core.prefs
    ctakes/branches/ytex/ctakes-ytex/LICENSE
    ctakes/branches/ytex/ctakes-ytex/README
    ctakes/branches/ytex/ctakes-ytex/pom.xml
    ctakes/branches/ytex/ctakes-ytex/scripts/
    ctakes/branches/ytex/ctakes-ytex/scripts/build-classpath.xml
    ctakes/branches/ytex/ctakes-ytex/scripts/build-setup.xml
    ctakes/branches/ytex/ctakes-ytex/scripts/data/
    ctakes/branches/ytex/ctakes-ytex/scripts/data/build.xml
    ctakes/branches/ytex/ctakes-ytex/scripts/data/conn.xml.template
    ctakes/branches/ytex/ctakes-ytex/scripts/data/examples/
    ctakes/branches/ytex/ctakes-ytex/scripts/data/examples/fracture_demo.txt
    ctakes/branches/ytex/ctakes-ytex/scripts/data/examples/fracture_demo.xml
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/kernel/
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/kernel/create_tables.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/kernel/drop_tables.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/kernel/ic_copy.template.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/kernel/ic_create.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/uima/
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/uima/create_document.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/uima/create_reference.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/uima/create_view.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/uima/drop_document.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/uima/drop_reference.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/uima/drop_view.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/uima/fracture_demo.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/umls/
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/umls/create_indices.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/umls/create_tables.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/umls/create_view.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/umls/drop_tables.sql
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    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/umls/insert_view.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/
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    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/esld/abs/create_abstraction.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/esld/abs/create_sp.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/esld/abs/drop_abstraction.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/esld/create_document.sql
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    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/esld/postprocessing/classifyDocs.bat
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_ascites.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_livermass.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_radiology.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_varices.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/esld/postprocessing/create_view.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/esld/postprocessing/delete_analysis_batch.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/esld/postprocessing/insert_radiology_review.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/esld/postprocessing/link_documents.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/esld/postprocessing/mark_duplicates.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/esld/postprocessing/runPostProcessing.bat
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/esld/postprocessing/runScriptOnAnalysisBatch.bat
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/esld/postprocessing/score_report.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/esld/postprocessing/score_report_all.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/kernel/
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/kernel/create_tables.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/kernel/drop_tables.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/uima/
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/uima/create_document.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/uima/create_reference.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/uima/create_view.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/uima/drop_document.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/uima/drop_reference.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/uima/drop_view.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/uima/fracture_demo.sql
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/umls/
    ctakes/branches/ytex/ctakes-ytex/scripts/data/mssql/umls/create_indices.sql
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--- ctakes/branches/ytex/ctakes-ytex-res/.settings/org.eclipse.m2e.core.prefs (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/.settings/org.eclipse.m2e.core.prefs Mon Dec 16 16:30:30 2013
@@ -0,0 +1,4 @@
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

Added: ctakes/branches/ytex/ctakes-ytex-res/LICENSE
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/LICENSE?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/LICENSE (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/LICENSE Mon Dec 16 16:30:30 2013
@@ -0,0 +1,202 @@
+
+                                 Apache License
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+
+   Unless required by applicable law or agreed to in writing, software
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Added: ctakes/branches/ytex/ctakes-ytex-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/pom.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/pom.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/pom.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,32 @@
+<?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.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <parent>
+    <groupId>org.apache.ctakes</groupId>
+    <artifactId>ctakes</artifactId>
+    <version>3.2.0-SNAPSHOT</version>
+  </parent>
+  <artifactId>ctakes-ytex-res</artifactId>
+  <name>Apache cTAKES Resources ctakes-ytex-res</name>
+  <description>Resources Project for yex</description>
+</project>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/ehcache.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/ehcache.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/ehcache.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/ehcache.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- comment the jdbcDictionaryCache in to enable dictionary lookup caching. 
+	This might improve dictionary lookup performance, but can lead to OutOfMemory 
+	errors (even though ehCache should limit the size to 50M) -->
+<ehcache maxBytesLocalHeap="50M"  updateCheck="false">
+	<defaultCache eternal="false" timeToIdleSeconds="120"
+		timeToLiveSeconds="120" overflowToDisk="false"
+		memoryStoreEvictionPolicy="LRU" />
+
+	<!-- <cache name="jdbcDictionaryCache" maxElementsInMemory="10000" overflowToDisk="false" 
+		memoryStoreEvictionPolicy="LRU" /> -->
+</ehcache>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/jdl/xdl.xsd
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/jdl/xdl.xsd?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/jdl/xdl.xsd (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/jdl/xdl.xsd Mon Dec 16 16:30:30 2013
@@ -0,0 +1,110 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<xs:schema elementFormDefault="qualified" xmlns:xs="http://www.w3.org/2001/XMLSchema">
+  <xs:complexType name="jdbcType">
+    <xs:sequence>
+      <xs:element minOccurs="0" name="driver" type="xs:token" />
+      <xs:element minOccurs="0" name="url" type="xs:token" />
+      <xs:element minOccurs="0" name="username" type="xs:token" />
+      <xs:element minOccurs="0" name="password" type="xs:token" />
+    </xs:sequence>
+  </xs:complexType>
+  <xs:complexType name="connType">
+    <xs:choice>
+      <xs:element name="jdbc" type="jdbcType" />
+    </xs:choice>
+  </xs:complexType>
+  <xs:simpleType name="sqlCallType">
+    <xs:restriction base="xs:normalizedString" />
+  </xs:simpleType>
+  <xs:simpleType name="sqlNameType">
+    <xs:restriction base="xs:token">
+      <xs:maxLength value="256" />
+      <xs:pattern value="[a-zA-Z\[\]]{1}([\[\]\.a-zA-Z0-9_#$])*" />
+    </xs:restriction>
+  </xs:simpleType>
+  <xs:simpleType name="xpathExpressionType">
+    <xs:restriction base="xs:token">
+    </xs:restriction>
+  </xs:simpleType>
+  <xs:complexType name="columnCsvLoadType">
+    <xs:choice minOccurs="0">
+      <xs:element name="constant" type="xs:string" />
+      <xs:element name="seq" type="xs:nonNegativeInteger" />
+    </xs:choice>
+    <xs:attribute name="name" type="sqlNameType" use="required" />
+    <xs:attribute name="skip" type="xs:boolean" />
+    <xs:attribute name="format" type="xs:string" />
+    <xs:attribute name="pattern" type="xs:string" />
+  </xs:complexType>
+  <xs:complexType name="csvLoadType">
+    <xs:sequence>
+      <xs:element maxOccurs="unbounded" name="column">
+        <xs:complexType>
+          <xs:complexContent mixed="false">
+            <xs:extension base="columnCsvLoadType" />
+          </xs:complexContent>
+        </xs:complexType>
+      </xs:element>
+    </xs:sequence>
+    <xs:attribute name="table" type="sqlNameType" use="required" />
+    <xs:attribute name="commit" type="xs:positiveInteger" />
+    <xs:attribute name="skip" type="xs:positiveInteger" />
+    <xs:attribute default="," name="delimiter">
+      <xs:simpleType>
+        <xs:restriction base="xs:string">
+          <xs:length value="1" />
+        </xs:restriction>
+      </xs:simpleType>
+    </xs:attribute>
+    <xs:attribute default="&quot;" name="encapsulator">
+      <xs:simpleType>
+        <xs:restriction base="xs:token">
+          <xs:length value="1" />
+        </xs:restriction>
+      </xs:simpleType>
+    </xs:attribute>
+  </xs:complexType>
+  <xs:complexType name="columnXmlLoadType">
+    <xs:choice>
+      <xs:element name="constant" type="xs:string" />
+      <xs:element name="seq" type="xs:nonNegativeInteger" />
+      <xs:element name="xpath" type="xpathExpressionType" />
+      <xs:element name="xleaf" type="xpathExpressionType" />
+    </xs:choice>
+    <xs:attribute name="name" type="sqlNameType" use="required" />
+  </xs:complexType>
+  <xs:complexType name="xmlLoadType">
+    <xs:sequence>
+      <xs:element minOccurs="0" default="/" name="xroot" type="xpathExpressionType" />
+      <xs:element maxOccurs="unbounded" name="column">
+        <xs:complexType>
+          <xs:complexContent mixed="false">
+            <xs:extension base="columnXmlLoadType" />
+          </xs:complexContent>
+        </xs:complexType>
+      </xs:element>
+    </xs:sequence>
+    <xs:attribute name="table" type="sqlNameType" use="required" />
+    <xs:attribute name="commit" type="xs:positiveInteger" />
+  </xs:complexType>
+  <xs:complexType name="loadType">
+    <xs:choice>
+      <xs:element name="csv">
+        <xs:complexType>
+          <xs:complexContent mixed="false">
+            <xs:extension base="csvLoadType" />
+          </xs:complexContent>
+        </xs:complexType>
+      </xs:element>
+      <xs:element name="xml">
+        <xs:complexType>
+          <xs:complexContent mixed="false">
+            <xs:extension base="xmlLoadType" />
+          </xs:complexContent>
+        </xs:complexType>
+      </xs:element>
+    </xs:choice>
+  </xs:complexType>
+  <xs:element name="conn" type="connType" />
+  <xs:element name="load" type="loadType" />
+</xs:schema>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-datasource.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-datasource.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-datasource.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-datasource.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,91 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:aop="http://www.springframework.org/schema/aop"
+	xmlns:tx="http://www.springframework.org/schema/tx"
+	xsi:schemaLocation="
+http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
+http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx-2.5.xsd
+http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop-2.5.xsd">
+	<bean
+		class="org.springframework.beans.factory.config.PropertyPlaceholderConfigurer">
+		<property name="locations">
+			<list>
+				<value>classpath:org/apache/ctakes/ytex/ytex-default.properties
+				</value>
+				<value>classpath:org/apache/ctakes/ytex/ytex.properties</value>
+				<value>classpath:org/apache/ctakes/ytex/ytex-umls.properties</value>
+			</list>
+		</property>
+		<property name="systemPropertiesModeName">
+			<value>SYSTEM_PROPERTIES_MODE_OVERRIDE</value>
+		</property>
+	</bean>
+	<bean id="ytexProperties"
+		class="org.springframework.beans.factory.config.PropertiesFactoryBean">
+		<property name="location" value="classpath:org/apache/ctakes/ytex/ytex.properties" />
+	</bean>
+	<bean id="hibernateProperties"
+		class="org.springframework.beans.factory.config.PropertiesFactoryBean">
+		<property name="properties">
+			<props>
+				<prop key="hibernate.dialect">${hibernate.dialect}</prop>
+				<!-- <prop key="hibernate.show_sql">true</prop> -->
+				<prop key="hibernate.default_schema">${db.schema}</prop>
+				<prop key="hibernate.cache.region.factory_class">org.hibernate.cache.ehcache.EhCacheRegionFactory
+				</prop>
+				<prop key="hibernate.cache.use_query_cache">true</prop>
+				<!-- to enable batch inserts -->
+				<prop key="hibernate.jdbc.batch_size">${hibernate.jdbc.batch_size}</prop>
+				<prop key="hibernate.order_inserts">${hibernate.order_inserts}</prop>
+				<prop key="hibernate.order_updates">${hibernate.order_updates}</prop>
+				<prop key="hibernate.cache.provider_configuration_file_resource_path">/org/apache/ctakes/ytex/kernel/ehcache.xml</prop>
+				<!-- <prop key="hibernate.connection.isolation">1</prop> -->
+			</props>
+		</property>
+	</bean>
+	<bean id="dataSource" class="org.apache.commons.dbcp.BasicDataSource"
+		destroy-method="close">
+		<property name="driverClassName" value="${db.driver}" />
+		<property name="url" value="${db.url}" />
+		<property name="username" value="${db.username}" />
+		<property name="password" value="${db.password}" />
+		<!-- <property name="defaultTransactionIsolation" value="1" /> -->
+	</bean>
+	<!-- the transactional advice (what 'happens'; see the <aop:advisor/> bean 
+		below) we use read uncommitted because when we annotate documents in parallel, 
+		we read and write to the document table. However, the txs don't interfere 
+		with eachother - they don't touch the same rows - so there is no need to 
+		serialize the transactions. serializing the transactions will actually cause 
+		deadlocks -->
+	<!-- we have to use the old-fashioned transaction aspect configuration because 
+		no variable substitution in tx:method element <tx:advice id="txAdvice" transaction-manager="transactionManager"> 
+		<tx:attributes> <tx:method name="*" propagation="REQUIRED" isolation="${db.isolationLevel}" 
+		/> </tx:attributes> </tx:advice> -->
+	<bean id="txAdvice"
+		class="org.springframework.transaction.interceptor.TransactionInterceptor">
+		<property name="transactionManager" ref="transactionManager" />
+		<property name="transactionAttributes">
+			<props>
+				<prop key="*">PROPAGATION_REQUIRED,ISOLATION_${db.isolationLevel}
+				</prop>
+			</props>
+		</property>
+	</bean>
+	<bean id="txTemplate"
+		class="org.springframework.transaction.support.TransactionTemplate">
+		<property name="transactionManager" ref="transactionManager" />
+		<property name="propagationBehaviorName" value="PROPAGATION_REQUIRED" />
+		<property name="isolationLevelName" value="ISOLATION_${db.isolationLevel}" />
+	</bean>
+	<bean id="txTemplateNew"
+		class="org.springframework.transaction.support.TransactionTemplate">
+		<property name="transactionManager" ref="transactionManager" />
+		<property name="propagationBehaviorName" value="PROPAGATION_REQUIRES_NEW" />
+		<property name="isolationLevelName" value="ISOLATION_${db.isolationLevel}" />
+	</bean>
+
+	<bean id="transactionManager"
+		class="org.springframework.orm.hibernate4.HibernateTransactionManager">
+		<property name="sessionFactory" ref="sessionFactory" />
+	</bean>
+</beans>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel-sim.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel-sim.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel-sim.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel-sim.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,48 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:aop="http://www.springframework.org/schema/aop"
+	xmlns:tx="http://www.springframework.org/schema/tx"
+	xsi:schemaLocation="
+http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
+http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx-2.5.xsd
+http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop-2.5.xsd">
+	<bean id="conceptSimilarityService" class="org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl"
+		init-method="init">
+		<property name="transactionManager" ref="transactionManager" />
+		<property name="conceptDao" ref="conceptDao" />
+		<property name="classifierEvaluationDao" ref="classifierEvaluationDao" />
+		<property name="cacheManager" ref="cacheManager" />
+		<property name="pageRankService" ref="pageRankService" />
+		<property name="corpusName" value="${ytex.corpusName}" />
+		<property name="conceptGraphName" value="${ytex.conceptGraphName}" />
+		<property name="conceptSetName" value="${ytex.conceptSetName}" />
+		<property name="preload" value="${ytex.conceptPreload}" />
+	</bean>
+	<bean id="abstractConceptKernel" class="org.apache.ctakes.ytex.kernel.evaluator.ConceptKernel"
+		abstract="true" init-method="init">
+		<property name="conceptSimilarityService" ref="conceptSimilarityService" />
+		<property name="cacheManager" ref="cacheManager" />
+	</bean>
+	<bean id="abstractLinKernel" class="org.apache.ctakes.ytex.kernel.evaluator.LinKernel"
+		abstract="true">
+		<property name="conceptSimilarityService" ref="conceptSimilarityService" />
+		<property name="cacheManager" ref="cacheManager" />
+	</bean>
+	<bean id="abstractSemanticSimKernel" class="org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel"
+		abstract="true">
+		<property name="conceptSimilarityService" ref="conceptSimilarityService" />
+		<property name="cacheManager" ref="cacheManager" />
+	</bean>
+	<bean id="mainSuiSemanticTypeKernel" class="org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel"
+		init-method="init">
+		<property name="conceptSimilarityService" ref="conceptSimilarityService" />
+	</bean>
+	<bean id="tuiSemanticTypeKernel" class="org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel"
+		init-method="init">
+		<property name="mode" value="TUI" />
+		<property name="conceptSimilarityService" ref="conceptSimilarityService" />
+	</bean>
+	<bean id="wordSenseDisambiguator" class="org.apache.ctakes.ytex.kernel.wsd.WordSenseDisambiguatorImpl">
+		<property name="conceptSimilarityService" ref="conceptSimilarityService" />
+	</bean>
+</beans>
\ No newline at end of file

Added: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel.hbm.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel.hbm.xml?rev=1551254&view=auto
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel.hbm.xml (added)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel.hbm.xml Mon Dec 16 16:30:30 2013
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:aop="http://www.springframework.org/schema/aop"
+	xmlns:tx="http://www.springframework.org/schema/tx"
+	xsi:schemaLocation="
+http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
+http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx-2.5.xsd
+http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop-2.5.xsd">
+	<bean id="sessionFactory"
+		class="org.springframework.orm.hibernate4.LocalSessionFactoryBean">
+		<property name="dataSource" ref="dataSource" />
+		<property name="mappingResources">
+			<list>
+				<value>org/apache/ctakes/ytex/kernel/model/KernelEvaluation.hbm.xml</value>
+				<value>org/apache/ctakes/ytex/kernel/model/ClassifierEvaluation.hbm.xml</value>
+				<value>org/apache/ctakes/ytex/umls/model/FWord.hbm.xml</value>
+				<value>org/apache/ctakes/ytex/umls/model/UMLS.hbm.xml</value>
+			</list>
+		</property>
+		<property name="hibernateProperties" ref="hibernateProperties" />
+	</bean>
+</beans>
\ No newline at end of file



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